This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 92 arm-level results and 20 clinical features across 4651 patients, 515 significant findings detected with Q value < 0.25.
-
Amp Peak 1(1p34.2) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'TUMOR.STAGE'.
-
Amp Peak 2(1p22.3) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'TUMOR.STAGE'.
-
Amp Peak 3(1q21.3) cnv correlated to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.
-
Amp Peak 4(1q32.1) cnv correlated to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'NEOPLASM.DISEASESTAGE'.
-
Amp Peak 5(1q44) cnv correlated to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'PATHOLOGY.N'.
-
Amp Peak 6(2p15) cnv correlated to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Amp Peak 7(2q31.2) cnv correlated to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Amp Peak 8(3q26.2) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'KARNOFSKY.PERFORMANCE.SCORE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'NUMBERPACKYEARSSMOKED'.
-
Amp Peak 9(4p16.3) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'NEOPLASM.DISEASESTAGE'.
-
Amp Peak 10(4q12) cnv correlated to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'PATHOLOGY.T'.
-
Amp Peak 11(5p15.33) cnv correlated to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'KARNOFSKY.PERFORMANCE.SCORE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Amp Peak 12(5q35.3) cnv correlated to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Amp Peak 13(6p22.3) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGICSPREAD(M)', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Amp Peak 14(6p21.1) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Amp Peak 15(6q21) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', and 'HISTOLOGICAL.TYPE'.
-
Amp Peak 16(7p11.2) cnv correlated to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Amp Peak 17(7q21.2) cnv correlated to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Amp Peak 18(7q36.3) cnv correlated to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Amp Peak 19(8p11.23) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Amp Peak 20(8p11.21) cnv correlated to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Amp Peak 21(8q24.21) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'KARNOFSKY.PERFORMANCE.SCORE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Amp Peak 22(9p13.3) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'PATHOLOGY.T'.
-
Amp Peak 23(10p15.1) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'TOBACCOSMOKINGHISTORYINDICATOR'.
-
Amp Peak 24(10q22.2) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.
-
Amp Peak 25(11q13.3) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Amp Peak 26(12p13.33) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Amp Peak 27(12p12.1) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Amp Peak 28(12q14.1) cnv correlated to 'Time to Death', 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.
-
Amp Peak 29(12q15) cnv correlated to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Amp Peak 30(13q34) cnv correlated to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'PATHOLOGICSPREAD(M)', 'TUMOR.STAGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', 'TOBACCOSMOKINGHISTORYINDICATOR', and 'NEOPLASM.DISEASESTAGE'.
-
Amp Peak 31(14q13.3) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Amp Peak 32(15q26.3) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Amp Peak 33(17q12) cnv correlated to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'PATHOLOGICSPREAD(M)'.
-
Amp Peak 34(17q25.3) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Amp Peak 35(18q11.2) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'PATHOLOGY.T'.
-
Amp Peak 36(19p13.2) cnv correlated to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Amp Peak 37(19p13.12) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Amp Peak 38(19q12) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'TUMOR.STAGE'.
-
Amp Peak 39(20q11.21) cnv correlated to 'Time to Death', 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Amp Peak 40(20q13.2) cnv correlated to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Amp Peak 41(Xq28) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
-
Del Peak 1(1p36.23) cnv correlated to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.
-
Del Peak 2(1p36.11) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'TUMOR.STAGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', 'TOBACCOSMOKINGHISTORYINDICATOR', 'NUMBER.OF.LYMPH.NODES', and 'NEOPLASM.DISEASESTAGE'.
-
Del Peak 3(1p13.2) cnv correlated to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'RADIATIONS.RADIATION.REGIMENINDICATION', 'TOBACCOSMOKINGHISTORYINDICATOR', and 'NUMBER.OF.LYMPH.NODES'.
-
Del Peak 4(2q22.1) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'TUMOR.STAGE'.
-
Del Peak 5(2q37.3) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'TOBACCOSMOKINGHISTORYINDICATOR'.
-
Del Peak 6(3p25.3) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'TOBACCOSMOKINGHISTORYINDICATOR'.
-
Del Peak 7(3p14.2) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'KARNOFSKY.PERFORMANCE.SCORE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'TOBACCOSMOKINGHISTORYINDICATOR'.
-
Del Peak 8(4p16.3) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Del Peak 9(4q22.1) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Del Peak 10(4q34.3) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Del Peak 11(5q11.2) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'KARNOFSKY.PERFORMANCE.SCORE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', 'NUMBERPACKYEARSSMOKED', 'TOBACCOSMOKINGHISTORYINDICATOR', and 'NEOPLASM.DISEASESTAGE'.
-
Del Peak 12(5q21.3) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'KARNOFSKY.PERFORMANCE.SCORE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'PATHOLOGICSPREAD(M)', 'RADIATIONS.RADIATION.REGIMENINDICATION', 'TOBACCOSMOKINGHISTORYINDICATOR', and 'NEOPLASM.DISEASESTAGE'.
-
Del Peak 13(6p25.3) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', and 'HISTOLOGICAL.TYPE'.
-
Del Peak 14(6q22.31) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.
-
Del Peak 15(6q26) cnv correlated to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.
-
Del Peak 16(7p22.3) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'TUMOR.STAGE'.
-
Del Peak 17(7q36.1) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'PATHOLOGICSPREAD(M)'.
-
Del Peak 18(8p23.2) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'KARNOFSKY.PERFORMANCE.SCORE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Del Peak 19(8p21.2) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'KARNOFSKY.PERFORMANCE.SCORE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Del Peak 20(9p23) cnv correlated to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', and 'PATHOLOGY.T'.
-
Del Peak 21(9p21.3) cnv correlated to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Del Peak 22(9q21.11) cnv correlated to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Del Peak 23(9q34.13) cnv correlated to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Del Peak 24(9q34.3) cnv correlated to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Del Peak 25(10p15.3) cnv correlated to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Del Peak 26(10q23.31) cnv correlated to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'YEAROFTOBACCOSMOKINGONSET'.
-
Del Peak 27(10q26.3) cnv correlated to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Del Peak 28(11p15.5) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
-
Del Peak 29(11q22.3) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
-
Del Peak 30(11q25) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
-
Del Peak 31(12p13.1) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', and 'HISTOLOGICAL.TYPE'.
-
Del Peak 32(12q23.1) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.
-
Del Peak 33(12q24.33) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'TUMOR.STAGE'.
-
Del Peak 34(13q11) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', 'TUMOR.STAGE', and 'TOBACCOSMOKINGHISTORYINDICATOR'.
-
Del Peak 35(13q14.2) cnv correlated to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.
-
Del Peak 36(14q24.1) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
-
Del Peak 37(15q11.2) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Del Peak 38(15q15.1) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Del Peak 39(16p13.3) cnv correlated to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'TUMOR.STAGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'NEOPLASM.DISEASESTAGE'.
-
Del Peak 40(16q23.1) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Del Peak 41(17p12) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'KARNOFSKY.PERFORMANCE.SCORE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Del Peak 42(17q11.2) cnv correlated to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Del Peak 43(18q21.2) cnv correlated to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'PATHOLOGICSPREAD(M)', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Del Peak 44(18q23) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'PATHOLOGICSPREAD(M)', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Del Peak 45(19p13.3) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Del Peak 46(19q13.32) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'TUMOR.STAGE'.
-
Del Peak 47(19q13.43) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'TUMOR.STAGE'.
-
Del Peak 48(20p12.1) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Del Peak 49(21q11.2) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
Del Peak 50(22q13.32) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'COMPLETENESS.OF.RESECTION'.
-
Del Peak 51(Xp21.1) cnv correlated to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 92 arm-level results and 20 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 515 significant findings detected.
Clinical Features |
Time to Death |
AGE |
PRIMARY SITE OF DISEASE |
GENDER |
KARNOFSKY PERFORMANCE SCORE |
HISTOLOGICAL TYPE |
PATHOLOGY T |
PATHOLOGY N |
PATHOLOGICSPREAD(M) |
TUMOR STAGE |
RADIATIONS RADIATION REGIMENINDICATION |
NUMBERPACKYEARSSMOKED | TOBACCOSMOKINGHISTORYINDICATOR | YEAROFTOBACCOSMOKINGONSET |
DISTANT METASTASIS |
LYMPH NODE METASTASIS |
COMPLETENESS OF RESECTION |
NUMBER OF LYMPH NODES |
TUMOR STAGECODE |
NEOPLASM DISEASESTAGE |
||
nCNV (%) | nWild-Type | logrank test | t-test | Chi-square test | Fisher's exact test | t-test | Chi-square test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | t-test | Chi-square test | t-test | Fisher's exact test | Chi-square test | Fisher's exact test | t-test | t-test | Chi-square test | |
Amp Peak 30(13q34) | 0 (0%) | 3687 |
0.676 (1.00) |
5.94e-06 (0.00794) |
3.58e-172 (6.15e-169) |
0.115 (1.00) |
0.192 (1.00) |
3.68e-134 (6.26e-131) |
5.87e-27 (9.03e-24) |
5.81e-08 (8.09e-05) |
3.46e-05 (0.0444) |
9.81e-11 (1.42e-07) |
2.15e-15 (3.19e-12) |
0.257 (1.00) |
9.51e-08 (0.000132) |
0.167 (1.00) |
0.332 (1.00) |
0.00635 (1.00) |
0.00176 (1.00) |
0.607 (1.00) |
2.86e-06 (0.00384) |
|
Del Peak 11(5q11 2) | 0 (0%) | 3247 |
0.705 (1.00) |
0.0591 (1.00) |
5.24e-169 (8.99e-166) |
0.643 (1.00) |
8.31e-05 (0.105) |
1.1e-150 (1.87e-147) |
3.14e-17 (4.71e-14) |
2.66e-05 (0.0344) |
0.00177 (1.00) |
4.37e-06 (0.00584) |
9.91e-14 (1.46e-10) |
6.24e-06 (0.00833) |
5.67e-05 (0.0722) |
0.36 (1.00) |
0.156 (1.00) |
0.0205 (1.00) |
0.21 (1.00) |
0.0757 (1.00) |
2.6e-05 (0.0337) |
|
Amp Peak 39(20q11 21) | 0 (0%) | 2477 |
0.00019 (0.235) |
1.91e-15 (2.84e-12) |
4.96e-100 (8.23e-97) |
8.43e-05 (0.106) |
0.0832 (1.00) |
3.74e-112 (6.27e-109) |
1.33e-23 (2.03e-20) |
1.18e-05 (0.0156) |
0.0021 (1.00) |
7.69e-10 (1.1e-06) |
1.76e-05 (0.0231) |
0.00618 (1.00) |
0.0196 (1.00) |
0.107 (1.00) |
0.688 (1.00) |
0.666 (1.00) |
0.00129 (1.00) |
0.422 (1.00) |
0.00646 (1.00) |
|
Del Peak 12(5q21 3) | 0 (0%) | 3230 |
0.705 (1.00) |
0.00789 (1.00) |
8.65e-176 (1.49e-172) |
0.869 (1.00) |
1.8e-05 (0.0235) |
8.17e-150 (1.39e-146) |
3.33e-16 (4.96e-13) |
1.5e-05 (0.0197) |
4.4e-05 (0.0561) |
0.000538 (0.642) |
1.72e-14 (2.55e-11) |
0.00048 (0.578) |
3.54e-05 (0.0454) |
0.0707 (1.00) |
0.2 (1.00) |
0.121 (1.00) |
0.642 (1.00) |
0.661 (1.00) |
9.36e-06 (0.0124) |
|
Amp Peak 8(3q26 2) | 0 (0%) | 2786 |
0.0442 (1.00) |
0.0195 (1.00) |
2.48e-239 (4.29e-236) |
0.321 (1.00) |
3.29e-05 (0.0424) |
7.01e-241 (1.22e-237) |
2.63e-22 (4.01e-19) |
4.82e-10 (6.89e-07) |
0.00212 (1.00) |
1.14e-23 (1.75e-20) |
1.41e-13 (2.07e-10) |
2.49e-05 (0.0323) |
0.016 (1.00) |
0.419 (1.00) |
0.361 (1.00) |
0.427 (1.00) |
0.0158 (1.00) |
0.0142 (1.00) |
0.000305 (0.373) |
|
Amp Peak 21(8q24 21) | 0 (0%) | 2221 |
0.00193 (1.00) |
0.656 (1.00) |
1.94e-213 (3.35e-210) |
2.5e-08 (3.5e-05) |
1.3e-05 (0.0171) |
2.05e-129 (3.48e-126) |
2.1e-26 (3.23e-23) |
4.03e-11 (5.84e-08) |
0.00837 (1.00) |
6.46e-19 (9.75e-16) |
4.46e-22 (6.79e-19) |
0.987 (1.00) |
0.0379 (1.00) |
0.285 (1.00) |
0.115 (1.00) |
0.00829 (1.00) |
0.0912 (1.00) |
0.0329 (1.00) |
0.0631 (1.00) |
|
Del Peak 7(3p14 2) | 0 (0%) | 2885 |
0.137 (1.00) |
0.674 (1.00) |
2.82e-247 (4.9e-244) |
3.08e-34 (4.82e-31) |
2.12e-05 (0.0276) |
1.54e-199 (2.66e-196) |
8.81e-20 (1.33e-16) |
0.0712 (1.00) |
0.119 (1.00) |
3.07e-17 (4.6e-14) |
4.04e-20 (6.11e-17) |
0.000361 (0.437) |
2.41e-17 (3.62e-14) |
0.802 (1.00) |
0.427 (1.00) |
0.941 (1.00) |
0.0116 (1.00) |
0.0399 (1.00) |
0.657 (1.00) |
|
Del Peak 41(17p12) | 0 (0%) | 2547 |
0.0465 (1.00) |
0.315 (1.00) |
1.07e-240 (1.85e-237) |
1.18e-26 (1.81e-23) |
2.8e-05 (0.0362) |
1e-188 (1.72e-185) |
1.09e-12 (1.6e-09) |
1.42e-07 (0.000197) |
0.00213 (1.00) |
9.6e-31 (1.49e-27) |
1.53e-27 (2.36e-24) |
0.209 (1.00) |
0.559 (1.00) |
0.734 (1.00) |
0.961 (1.00) |
0.0216 (1.00) |
0.255 (1.00) |
0.011 (1.00) |
0.11 (1.00) |
|
Del Peak 43(18q21 2) | 0 (0%) | 2838 |
0.273 (1.00) |
1.98e-06 (0.00267) |
2.16e-160 (3.7e-157) |
0.0396 (1.00) |
0.00615 (1.00) |
3.7e-112 (6.21e-109) |
1.41e-23 (2.15e-20) |
2.41e-10 (3.46e-07) |
8.73e-07 (0.00119) |
3.65e-17 (5.47e-14) |
6.39e-27 (9.84e-24) |
0.11 (1.00) |
0.216 (1.00) |
0.0197 (1.00) |
0.182 (1.00) |
0.0699 (1.00) |
0.00168 (1.00) |
0.0054 (1.00) |
0.124 (1.00) |
|
Amp Peak 3(1q21 3) | 0 (0%) | 2591 |
1.44e-06 (0.00195) |
0.00644 (1.00) |
5.02e-206 (8.67e-203) |
1.59e-35 (2.49e-32) |
0.0281 (1.00) |
5.21e-127 (8.83e-124) |
1.17e-14 (1.74e-11) |
0.00195 (1.00) |
4.31e-05 (0.0551) |
3.44e-07 (0.000473) |
0.019 (1.00) |
0.736 (1.00) |
0.00255 (1.00) |
0.797 (1.00) |
0.652 (1.00) |
0.469 (1.00) |
0.393 (1.00) |
0.025 (1.00) |
0.18 (1.00) |
|
Amp Peak 11(5p15 33) | 0 (0%) | 2938 |
0.115 (1.00) |
1.62e-05 (0.0212) |
2.24e-160 (3.83e-157) |
0.063 (1.00) |
0.000192 (0.237) |
1.59e-116 (2.68e-113) |
1.28e-19 (1.93e-16) |
0.202 (1.00) |
0.00756 (1.00) |
5.66e-05 (0.072) |
9.11e-16 (1.36e-12) |
0.357 (1.00) |
0.000648 (0.771) |
0.883 (1.00) |
0.607 (1.00) |
0.0282 (1.00) |
0.812 (1.00) |
0.342 (1.00) |
0.0343 (1.00) |
|
Amp Peak 12(5q35 3) | 0 (0%) | 3697 |
9.9e-06 (0.0131) |
0.515 (1.00) |
1.49e-155 (2.55e-152) |
0.624 (1.00) |
0.287 (1.00) |
5.88e-130 (9.97e-127) |
1.77e-17 (2.66e-14) |
6.66e-05 (0.0846) |
0.000659 (0.784) |
9.07e-07 (0.00123) |
8.09e-08 (0.000112) |
0.323 (1.00) |
0.749 (1.00) |
0.686 (1.00) |
0.0912 (1.00) |
0.471 (1.00) |
0.0622 (1.00) |
0.636 (1.00) |
0.0548 (1.00) |
|
Amp Peak 16(7p11 2) | 0 (0%) | 2594 |
0 (0) |
0.000519 (0.623) |
4.82e-156 (8.23e-153) |
4.27e-32 (6.65e-29) |
0.334 (1.00) |
1.33e-52 (2.13e-49) |
2.1e-09 (2.99e-06) |
4.56e-07 (0.000623) |
0.00263 (1.00) |
0.0511 (1.00) |
7.18e-13 (1.05e-09) |
0.859 (1.00) |
0.223 (1.00) |
0.0699 (1.00) |
0.192 (1.00) |
0.635 (1.00) |
0.0415 (1.00) |
0.0694 (1.00) |
0.00244 (1.00) |
|
Amp Peak 23(10p15 1) | 0 (0%) | 3713 |
0.0144 (1.00) |
0.401 (1.00) |
8.14e-107 (1.36e-103) |
1.03e-21 (1.56e-18) |
0.42 (1.00) |
2.93e-70 (4.76e-67) |
3.06e-06 (0.00411) |
0.428 (1.00) |
0.315 (1.00) |
5.14e-16 (7.65e-13) |
8.77e-07 (0.00119) |
0.454 (1.00) |
7.11e-07 (0.000971) |
0.139 (1.00) |
0.221 (1.00) |
0.775 (1.00) |
0.000869 (1.00) |
0.686 (1.00) |
0.0385 (1.00) |
|
Amp Peak 25(11q13 3) | 0 (0%) | 3501 |
0.0311 (1.00) |
0.201 (1.00) |
2.29e-120 (3.88e-117) |
0.000162 (0.201) |
0.167 (1.00) |
1.72e-67 (2.79e-64) |
3.36e-09 (4.78e-06) |
3.55e-06 (0.00476) |
0.0522 (1.00) |
2.61e-07 (0.00036) |
1.38e-05 (0.0181) |
0.112 (1.00) |
0.0467 (1.00) |
0.054 (1.00) |
0.96 (1.00) |
0.278 (1.00) |
0.314 (1.00) |
0.041 (1.00) |
0.746 (1.00) |
|
Amp Peak 40(20q13 2) | 0 (0%) | 2395 |
0.0817 (1.00) |
2.73e-08 (3.82e-05) |
3.02e-111 (5.05e-108) |
0.378 (1.00) |
0.674 (1.00) |
2.81e-119 (4.73e-116) |
1.02e-23 (1.55e-20) |
0.000324 (0.395) |
0.000166 (0.206) |
3.26e-13 (4.78e-10) |
6.37e-06 (0.00847) |
0.764 (1.00) |
0.00544 (1.00) |
0.849 (1.00) |
0.0773 (1.00) |
0.506 (1.00) |
0.00354 (1.00) |
0.988 (1.00) |
0.206 (1.00) |
|
Del Peak 2(1p36 11) | 0 (0%) | 3276 |
0.0382 (1.00) |
0.00417 (1.00) |
2.35e-75 (3.84e-72) |
0.0197 (1.00) |
0.0171 (1.00) |
1.16e-45 (1.84e-42) |
0.00424 (1.00) |
0.00895 (1.00) |
0.0279 (1.00) |
1.02e-05 (0.0135) |
2.95e-10 (4.23e-07) |
0.00739 (1.00) |
0.000119 (0.148) |
0.567 (1.00) |
0.567 (1.00) |
0.00793 (1.00) |
0.00605 (1.00) |
4.02e-05 (0.0515) |
5.18e-05 (0.066) |
|
Del Peak 6(3p25 3) | 0 (0%) | 3021 |
0.88 (1.00) |
0.0653 (1.00) |
0 (0) |
1.72e-36 (2.71e-33) |
0.000337 (0.41) |
5.86e-225 (1.01e-221) |
2.3e-21 (3.49e-18) |
0.208 (1.00) |
0.00147 (1.00) |
1.54e-14 (2.28e-11) |
2.46e-27 (3.79e-24) |
0.00196 (1.00) |
8.43e-18 (1.27e-14) |
0.262 (1.00) |
0.112 (1.00) |
0.943 (1.00) |
0.156 (1.00) |
0.0172 (1.00) |
0.392 (1.00) |
|
Del Peak 18(8p23 2) | 0 (0%) | 2583 |
0.0305 (1.00) |
0.000318 (0.388) |
4.6e-129 (7.79e-126) |
0.0276 (1.00) |
7.36e-05 (0.0931) |
9.65e-91 (1.59e-87) |
3.31e-05 (0.0427) |
5.54e-09 (7.85e-06) |
0.567 (1.00) |
2.21e-08 (3.09e-05) |
3.83e-21 (5.81e-18) |
0.00323 (1.00) |
0.0876 (1.00) |
0.719 (1.00) |
0.668 (1.00) |
0.0501 (1.00) |
0.0585 (1.00) |
0.00246 (1.00) |
0.968 (1.00) |
|
Del Peak 19(8p21 2) | 0 (0%) | 2565 |
0.027 (1.00) |
0.000822 (0.964) |
5.87e-133 (9.97e-130) |
8.03e-05 (0.101) |
1.51e-05 (0.0199) |
5.32e-94 (8.78e-91) |
0.00206 (1.00) |
6.31e-09 (8.92e-06) |
0.247 (1.00) |
2.83e-11 (4.1e-08) |
6.66e-22 (1.01e-18) |
0.104 (1.00) |
0.135 (1.00) |
0.915 (1.00) |
0.72 (1.00) |
0.111 (1.00) |
0.221 (1.00) |
0.00127 (1.00) |
0.67 (1.00) |
|
Del Peak 37(15q11 2) | 0 (0%) | 3152 |
0.0866 (1.00) |
0.00102 (1.00) |
7.95e-75 (1.3e-71) |
3.56e-05 (0.0456) |
0.0563 (1.00) |
3.04e-80 (4.98e-77) |
7.04e-07 (0.000961) |
7.75e-07 (0.00106) |
0.00411 (1.00) |
3.67e-10 (5.26e-07) |
1.66e-06 (0.00224) |
0.893 (1.00) |
0.558 (1.00) |
0.128 (1.00) |
0.261 (1.00) |
0.599 (1.00) |
0.391 (1.00) |
0.0828 (1.00) |
0.14 (1.00) |
|
Del Peak 38(15q15 1) | 0 (0%) | 3027 |
0.0244 (1.00) |
0.00282 (1.00) |
4.09e-92 (6.73e-89) |
1.95e-07 (0.00027) |
0.111 (1.00) |
2.29e-101 (3.81e-98) |
4.02e-07 (0.000551) |
9.24e-07 (0.00125) |
0.00487 (1.00) |
1.31e-16 (1.96e-13) |
2.13e-05 (0.0278) |
0.872 (1.00) |
0.355 (1.00) |
0.423 (1.00) |
0.864 (1.00) |
0.652 (1.00) |
0.777 (1.00) |
0.179 (1.00) |
0.607 (1.00) |
|
Del Peak 44(18q23) | 0 (0%) | 2778 |
0.35 (1.00) |
0.000251 (0.308) |
4.93e-163 (8.44e-160) |
0.0674 (1.00) |
0.0104 (1.00) |
2.15e-116 (3.62e-113) |
1.9e-22 (2.9e-19) |
6.46e-10 (9.22e-07) |
6.05e-05 (0.0769) |
2.49e-19 (3.76e-16) |
1.11e-25 (1.7e-22) |
0.186 (1.00) |
0.0327 (1.00) |
0.00732 (1.00) |
0.126 (1.00) |
0.028 (1.00) |
0.00719 (1.00) |
0.00118 (1.00) |
0.218 (1.00) |
|
Del Peak 45(19p13 3) | 0 (0%) | 3088 |
0.0975 (1.00) |
0.789 (1.00) |
6.56e-269 (1.14e-265) |
1.22e-22 (1.86e-19) |
0.0867 (1.00) |
2.22e-237 (3.84e-234) |
7.92e-17 (1.18e-13) |
4.24e-06 (0.00568) |
0.000366 (0.442) |
8.26e-44 (1.31e-40) |
7.2e-19 (1.08e-15) |
0.339 (1.00) |
0.253 (1.00) |
0.0439 (1.00) |
0.379 (1.00) |
0.432 (1.00) |
0.00272 (1.00) |
0.113 (1.00) |
0.52 (1.00) |
|
Amp Peak 4(1q32 1) | 0 (0%) | 2602 |
1.78e-05 (0.0233) |
0.0877 (1.00) |
6.43e-187 (1.11e-183) |
4.15e-28 (6.41e-25) |
0.00457 (1.00) |
1.42e-104 (2.37e-101) |
1.12e-15 (1.67e-12) |
0.00216 (1.00) |
0.000735 (0.866) |
0.0143 (1.00) |
0.701 (1.00) |
0.257 (1.00) |
0.00427 (1.00) |
0.0477 (1.00) |
0.413 (1.00) |
0.0829 (1.00) |
0.375 (1.00) |
0.0199 (1.00) |
9.71e-06 (0.0129) |
|
Amp Peak 5(1q44) | 0 (0%) | 2698 |
1.25e-06 (0.00169) |
0.189 (1.00) |
4.2e-184 (7.22e-181) |
4.53e-31 (7.04e-28) |
0.014 (1.00) |
3.46e-96 (5.73e-93) |
7.27e-14 (1.07e-10) |
4.85e-05 (0.0618) |
0.00045 (0.542) |
0.000332 (0.403) |
0.0274 (1.00) |
0.477 (1.00) |
0.00328 (1.00) |
0.337 (1.00) |
0.577 (1.00) |
0.0319 (1.00) |
0.712 (1.00) |
0.0534 (1.00) |
0.000607 (0.723) |
|
Amp Peak 9(4p16 3) | 0 (0%) | 4112 |
0.0205 (1.00) |
0.841 (1.00) |
2.63e-44 (4.16e-41) |
6.16e-05 (0.0783) |
0.284 (1.00) |
9.73e-47 (1.55e-43) |
1.38e-07 (0.000191) |
0.896 (1.00) |
0.034 (1.00) |
1.93e-08 (2.71e-05) |
0.107 (1.00) |
0.535 (1.00) |
0.791 (1.00) |
0.177 (1.00) |
0.0562 (1.00) |
0.118 (1.00) |
0.00199 (1.00) |
0.656 (1.00) |
7.36e-05 (0.0931) |
|
Amp Peak 13(6p22 3) | 0 (0%) | 3586 |
0.0243 (1.00) |
0.102 (1.00) |
1.74e-115 (2.92e-112) |
6.53e-11 (9.45e-08) |
0.437 (1.00) |
2.66e-91 (4.38e-88) |
0.000905 (1.00) |
0.0228 (1.00) |
0.00017 (0.21) |
3.21e-13 (4.72e-10) |
1.61e-10 (2.33e-07) |
0.585 (1.00) |
0.00274 (1.00) |
0.182 (1.00) |
0.204 (1.00) |
0.172 (1.00) |
0.0494 (1.00) |
0.0631 (1.00) |
0.0205 (1.00) |
|
Amp Peak 18(7q36 3) | 0 (0%) | 2783 |
0 (0) |
0.96 (1.00) |
4.4e-158 (7.52e-155) |
2.93e-13 (4.31e-10) |
0.033 (1.00) |
3.21e-53 (5.16e-50) |
0.00161 (1.00) |
0.0162 (1.00) |
0.000717 (0.848) |
1.84e-06 (0.00249) |
4.66e-08 (6.49e-05) |
0.688 (1.00) |
0.00505 (1.00) |
0.509 (1.00) |
0.729 (1.00) |
0.993 (1.00) |
0.162 (1.00) |
0.829 (1.00) |
0.0291 (1.00) |
|
Amp Peak 20(8p11 21) | 0 (0%) | 3246 |
0.000308 (0.376) |
7.12e-06 (0.00946) |
7.88e-77 (1.29e-73) |
0.0108 (1.00) |
0.0025 (1.00) |
1.1e-45 (1.74e-42) |
1.34e-11 (1.95e-08) |
0.277 (1.00) |
0.00459 (1.00) |
2.88e-05 (0.0373) |
2.27e-08 (3.18e-05) |
0.568 (1.00) |
0.076 (1.00) |
0.049 (1.00) |
0.7 (1.00) |
0.67 (1.00) |
0.0373 (1.00) |
0.536 (1.00) |
0.45 (1.00) |
|
Del Peak 3(1p13 2) | 0 (0%) | 3673 |
0.0714 (1.00) |
2.26e-05 (0.0294) |
1.18e-68 (1.92e-65) |
0.101 (1.00) |
0.00293 (1.00) |
3.6e-38 (5.67e-35) |
0.114 (1.00) |
0.00211 (1.00) |
0.273 (1.00) |
0.551 (1.00) |
1.14e-11 (1.66e-08) |
0.0174 (1.00) |
8.76e-05 (0.11) |
0.976 (1.00) |
0.522 (1.00) |
0.00448 (1.00) |
0.0165 (1.00) |
0.000101 (0.127) |
0.00125 (1.00) |
|
Del Peak 8(4p16 3) | 0 (0%) | 3291 |
0.144 (1.00) |
0.167 (1.00) |
3.49e-53 (5.59e-50) |
0.0274 (1.00) |
0.00067 (0.795) |
6.2e-60 (1e-56) |
9.16e-07 (0.00124) |
0.000126 (0.157) |
0.202 (1.00) |
0.000177 (0.219) |
0.000184 (0.227) |
0.0159 (1.00) |
0.0013 (1.00) |
0.644 (1.00) |
0.793 (1.00) |
0.704 (1.00) |
0.242 (1.00) |
0.00534 (1.00) |
0.314 (1.00) |
|
Del Peak 21(9p21 3) | 0 (0%) | 2719 |
0 (0) |
0.0163 (1.00) |
5.76e-162 (9.86e-159) |
2.67e-22 (4.06e-19) |
0.0181 (1.00) |
3.34e-109 (5.58e-106) |
2.4e-16 (3.58e-13) |
0.0613 (1.00) |
0.141 (1.00) |
0.203 (1.00) |
8.2e-07 (0.00112) |
0.0218 (1.00) |
0.147 (1.00) |
0.000529 (0.634) |
0.161 (1.00) |
0.000571 (0.681) |
0.824 (1.00) |
0.0247 (1.00) |
0.000212 (0.261) |
|
Del Peak 22(9q21 11) | 0 (0%) | 3305 |
0.198 (1.00) |
3.24e-07 (0.000446) |
4.8e-86 (7.88e-83) |
0.0811 (1.00) |
0.0317 (1.00) |
4.54e-71 (7.37e-68) |
1.48e-09 (2.11e-06) |
0.0144 (1.00) |
0.006 (1.00) |
2.63e-09 (3.75e-06) |
9.63e-14 (1.42e-10) |
0.0642 (1.00) |
0.192 (1.00) |
0.0593 (1.00) |
0.0678 (1.00) |
0.272 (1.00) |
0.232 (1.00) |
0.231 (1.00) |
0.0858 (1.00) |
|
Del Peak 23(9q34 13) | 0 (0%) | 3277 |
0.577 (1.00) |
7.74e-05 (0.0977) |
7.47e-104 (1.24e-100) |
0.000957 (1.00) |
0.228 (1.00) |
1.92e-84 (3.16e-81) |
1.73e-08 (2.44e-05) |
0.0208 (1.00) |
0.013 (1.00) |
2.46e-13 (3.62e-10) |
1.9e-14 (2.81e-11) |
0.0181 (1.00) |
0.13 (1.00) |
0.00379 (1.00) |
0.887 (1.00) |
0.0384 (1.00) |
0.612 (1.00) |
0.714 (1.00) |
0.243 (1.00) |
|
Del Peak 24(9q34 3) | 0 (0%) | 3275 |
0.639 (1.00) |
0.000148 (0.184) |
8.36e-98 (1.39e-94) |
0.000759 (0.893) |
0.142 (1.00) |
9.53e-81 (1.56e-77) |
9.21e-09 (1.3e-05) |
0.0013 (1.00) |
0.0156 (1.00) |
2.71e-12 (3.95e-09) |
7.05e-14 (1.04e-10) |
0.028 (1.00) |
0.253 (1.00) |
0.00443 (1.00) |
0.947 (1.00) |
0.0583 (1.00) |
0.358 (1.00) |
0.408 (1.00) |
0.266 (1.00) |
|
Del Peak 25(10p15 3) | 0 (0%) | 3409 |
0 (0) |
0.999 (1.00) |
4.91e-243 (8.52e-240) |
1.84e-25 (2.82e-22) |
0.0806 (1.00) |
2.64e-48 (4.22e-45) |
4.26e-07 (0.000583) |
0.00118 (1.00) |
0.587 (1.00) |
0.129 (1.00) |
1.22e-34 (1.91e-31) |
0.119 (1.00) |
0.0077 (1.00) |
0.0481 (1.00) |
0.435 (1.00) |
0.776 (1.00) |
0.755 (1.00) |
0.0162 (1.00) |
0.599 (1.00) |
|
Del Peak 26(10q23 31) | 0 (0%) | 3001 |
0 (0) |
0.488 (1.00) |
5.8e-192 (9.99e-189) |
2.92e-11 (4.23e-08) |
0.235 (1.00) |
2.27e-44 (3.59e-41) |
0.0549 (1.00) |
0.0961 (1.00) |
0.407 (1.00) |
0.00646 (1.00) |
2.29e-29 (3.55e-26) |
0.0626 (1.00) |
0.129 (1.00) |
7.23e-05 (0.0916) |
0.406 (1.00) |
0.13 (1.00) |
0.179 (1.00) |
0.46 (1.00) |
0.0204 (1.00) |
|
Del Peak 30(11q25) | 0 (0%) | 3383 |
0.826 (1.00) |
0.122 (1.00) |
4.75e-90 (7.81e-87) |
0.000114 (0.143) |
0.0102 (1.00) |
1.71e-62 (2.76e-59) |
9.7e-11 (1.4e-07) |
3.1e-09 (4.4e-06) |
0.215 (1.00) |
2.59e-05 (0.0336) |
0.368 (1.00) |
0.168 (1.00) |
0.26 (1.00) |
0.33 (1.00) |
0.481 (1.00) |
0.354 (1.00) |
0.595 (1.00) |
0.00433 (1.00) |
0.0511 (1.00) |
|
Del Peak 32(12q23 1) | 0 (0%) | 3943 |
0.953 (1.00) |
0.233 (1.00) |
4.66e-53 (7.48e-50) |
1.3e-08 (1.83e-05) |
0.619 (1.00) |
2.77e-55 (4.45e-52) |
3.72e-05 (0.0476) |
0.0668 (1.00) |
1.39e-05 (0.0183) |
1.58e-06 (0.00214) |
0.00116 (1.00) |
0.294 (1.00) |
0.845 (1.00) |
0.471 (1.00) |
0.962 (1.00) |
0.412 (1.00) |
0.486 (1.00) |
0.245 (1.00) |
0.151 (1.00) |
|
Del Peak 34(13q11) | 0 (0%) | 3055 |
0.000303 (0.37) |
0.78 (1.00) |
9.08e-157 (1.55e-153) |
0.2 (1.00) |
0.000368 (0.444) |
2.19e-151 (3.74e-148) |
1.89e-28 (2.93e-25) |
0.00442 (1.00) |
7.09e-06 (0.00943) |
9.02e-08 (0.000125) |
0.198 (1.00) |
0.00324 (1.00) |
1.62e-06 (0.00218) |
0.468 (1.00) |
0.938 (1.00) |
0.918 (1.00) |
0.268 (1.00) |
0.243 (1.00) |
0.472 (1.00) |
|
Del Peak 35(13q14 2) | 0 (0%) | 2877 |
5.46e-06 (0.00729) |
0.0302 (1.00) |
1.57e-163 (2.68e-160) |
0.0134 (1.00) |
0.00113 (1.00) |
7.05e-156 (1.2e-152) |
2.06e-27 (3.18e-24) |
0.00341 (1.00) |
2.6e-05 (0.0337) |
1.27e-08 (1.79e-05) |
0.969 (1.00) |
0.0136 (1.00) |
0.000718 (0.848) |
0.914 (1.00) |
0.903 (1.00) |
0.465 (1.00) |
0.27 (1.00) |
0.544 (1.00) |
0.853 (1.00) |
|
Del Peak 39(16p13 3) | 0 (0%) | 3888 |
3.06e-05 (0.0394) |
0.00642 (1.00) |
3.17e-130 (5.37e-127) |
0.0121 (1.00) |
0.109 (1.00) |
1.02e-100 (1.7e-97) |
0.000741 (0.872) |
0.253 (1.00) |
0.161 (1.00) |
8.54e-13 (1.25e-09) |
3.38e-09 (4.8e-06) |
0.484 (1.00) |
0.00476 (1.00) |
0.312 (1.00) |
0.0011 (1.00) |
0.445 (1.00) |
0.379 (1.00) |
0.173 (1.00) |
7.08e-09 (1e-05) |
|
Del Peak 40(16q23 1) | 0 (0%) | 2998 |
0.0046 (1.00) |
0.37 (1.00) |
2.05e-249 (3.56e-246) |
5.49e-72 (8.94e-69) |
0.216 (1.00) |
8.25e-194 (1.42e-190) |
4.44e-10 (6.35e-07) |
0.0426 (1.00) |
0.051 (1.00) |
3.97e-34 (6.2e-31) |
9.07e-05 (0.114) |
0.241 (1.00) |
0.0153 (1.00) |
0.259 (1.00) |
0.0515 (1.00) |
0.256 (1.00) |
0.000591 (0.705) |
0.764 (1.00) |
0.000216 (0.266) |
|
Del Peak 42(17q11 2) | 0 (0%) | 3504 |
0.803 (1.00) |
1.14e-05 (0.015) |
1.98e-263 (3.45e-260) |
1.06e-51 (1.7e-48) |
0.237 (1.00) |
9.39e-235 (1.62e-231) |
0.00178 (1.00) |
0.696 (1.00) |
0.237 (1.00) |
6.83e-59 (1.1e-55) |
3.35e-09 (4.76e-06) |
0.0662 (1.00) |
0.059 (1.00) |
0.514 (1.00) |
0.113 (1.00) |
0.859 (1.00) |
0.00172 (1.00) |
0.285 (1.00) |
0.0168 (1.00) |
|
Del Peak 50(22q13 32) | 0 (0%) | 2835 |
0.000205 (0.253) |
0.308 (1.00) |
1.85e-172 (3.17e-169) |
4.14e-26 (6.35e-23) |
0.128 (1.00) |
8.76e-187 (1.51e-183) |
7.66e-05 (0.0968) |
0.00384 (1.00) |
0.00223 (1.00) |
2.75e-45 (4.37e-42) |
0.0418 (1.00) |
0.0863 (1.00) |
0.0907 (1.00) |
0.0148 (1.00) |
0.834 (1.00) |
0.0978 (1.00) |
0.000108 (0.135) |
0.309 (1.00) |
0.587 (1.00) |
|
Amp Peak 1(1p34 2) | 0 (0%) | 3821 |
0.0251 (1.00) |
0.677 (1.00) |
4.52e-119 (7.61e-116) |
5.11e-13 (7.48e-10) |
0.17 (1.00) |
1.04e-111 (1.74e-108) |
6.36e-06 (0.00847) |
0.805 (1.00) |
0.00193 (1.00) |
2.25e-17 (3.37e-14) |
0.0126 (1.00) |
0.759 (1.00) |
0.145 (1.00) |
0.566 (1.00) |
0.13 (1.00) |
0.257 (1.00) |
0.0158 (1.00) |
0.942 (1.00) |
0.000712 (0.843) |
|
Amp Peak 2(1p22 3) | 0 (0%) | 3856 |
0.701 (1.00) |
0.677 (1.00) |
2.34e-45 (3.7e-42) |
4.85e-11 (7.02e-08) |
0.283 (1.00) |
6.93e-41 (1.09e-37) |
8.67e-05 (0.109) |
0.224 (1.00) |
0.0509 (1.00) |
3.46e-05 (0.0444) |
0.839 (1.00) |
0.575 (1.00) |
0.0109 (1.00) |
0.272 (1.00) |
0.426 (1.00) |
0.765 (1.00) |
0.0688 (1.00) |
0.647 (1.00) |
0.189 (1.00) |
|
Amp Peak 6(2p15) | 0 (0%) | 3570 |
0.929 (1.00) |
1.25e-06 (0.00169) |
4.91e-75 (8.02e-72) |
0.886 (1.00) |
0.000219 (0.269) |
2.14e-49 (3.41e-46) |
0.000663 (0.786) |
0.0182 (1.00) |
0.0819 (1.00) |
4.26e-05 (0.0545) |
4.72e-13 (6.92e-10) |
0.594 (1.00) |
0.00722 (1.00) |
0.754 (1.00) |
0.193 (1.00) |
0.0667 (1.00) |
0.486 (1.00) |
0.0256 (1.00) |
0.00081 (0.951) |
|
Amp Peak 7(2q31 2) | 0 (0%) | 3724 |
0.215 (1.00) |
3.58e-06 (0.0048) |
5.68e-77 (9.3e-74) |
0.253 (1.00) |
0.197 (1.00) |
6.05e-36 (9.48e-33) |
0.00656 (1.00) |
0.0537 (1.00) |
0.0986 (1.00) |
2.17e-05 (0.0283) |
3.68e-13 (5.39e-10) |
0.295 (1.00) |
0.000382 (0.461) |
0.407 (1.00) |
0.613 (1.00) |
0.805 (1.00) |
0.441 (1.00) |
0.0039 (1.00) |
0.853 (1.00) |
|
Amp Peak 14(6p21 1) | 0 (0%) | 3657 |
0.0149 (1.00) |
0.00145 (1.00) |
8.63e-74 (1.41e-70) |
2.33e-05 (0.0303) |
0.0929 (1.00) |
1.64e-59 (2.64e-56) |
0.00212 (1.00) |
0.00612 (1.00) |
0.000879 (1.00) |
1.23e-07 (0.00017) |
2.11e-07 (0.000292) |
0.222 (1.00) |
0.393 (1.00) |
0.127 (1.00) |
1 (1.00) |
0.5 (1.00) |
0.385 (1.00) |
0.203 (1.00) |
0.407 (1.00) |
|
Amp Peak 17(7q21 2) | 0 (0%) | 2728 |
0 (0) |
0.101 (1.00) |
3.72e-139 (6.32e-136) |
8.63e-28 (1.33e-24) |
0.925 (1.00) |
4.86e-38 (7.65e-35) |
0.00142 (1.00) |
0.000338 (0.411) |
0.00463 (1.00) |
0.104 (1.00) |
5.62e-12 (8.2e-09) |
0.0358 (1.00) |
0.00316 (1.00) |
0.765 (1.00) |
0.413 (1.00) |
0.903 (1.00) |
0.0677 (1.00) |
0.0297 (1.00) |
0.0251 (1.00) |
|
Amp Peak 26(12p13 33) | 0 (0%) | 3292 |
0.134 (1.00) |
0.00342 (1.00) |
1.48e-73 (2.41e-70) |
0.815 (1.00) |
0.00123 (1.00) |
7.83e-52 (1.25e-48) |
9.81e-06 (0.013) |
0.56 (1.00) |
0.123 (1.00) |
1.28e-08 (1.8e-05) |
7.44e-13 (1.09e-09) |
0.283 (1.00) |
0.391 (1.00) |
0.773 (1.00) |
0.816 (1.00) |
0.138 (1.00) |
0.734 (1.00) |
0.334 (1.00) |
0.0513 (1.00) |
|
Amp Peak 27(12p12 1) | 0 (0%) | 3329 |
0.0199 (1.00) |
0.000341 (0.414) |
7.8e-71 (1.27e-67) |
0.946 (1.00) |
0.0023 (1.00) |
2.71e-47 (4.32e-44) |
1.78e-05 (0.0233) |
0.887 (1.00) |
0.123 (1.00) |
5.86e-08 (8.15e-05) |
1.86e-10 (2.67e-07) |
0.194 (1.00) |
0.161 (1.00) |
0.92 (1.00) |
0.41 (1.00) |
0.31 (1.00) |
0.925 (1.00) |
0.238 (1.00) |
0.0175 (1.00) |
|
Amp Peak 28(12q14 1) | 0 (0%) | 3554 |
7.95e-05 (0.1) |
0.00011 (0.138) |
5.75e-23 (8.78e-20) |
0.0991 (1.00) |
0.168 (1.00) |
1.56e-17 (2.35e-14) |
0.0513 (1.00) |
0.239 (1.00) |
0.514 (1.00) |
9.74e-05 (0.122) |
0.00692 (1.00) |
0.743 (1.00) |
0.147 (1.00) |
0.0463 (1.00) |
0.818 (1.00) |
0.102 (1.00) |
0.755 (1.00) |
0.822 (1.00) |
0.036 (1.00) |
|
Amp Peak 31(14q13 3) | 0 (0%) | 3888 |
0.523 (1.00) |
0.478 (1.00) |
3.33e-93 (5.5e-90) |
0.774 (1.00) |
0.0149 (1.00) |
1.21e-71 (1.97e-68) |
1.82e-11 (2.65e-08) |
0.0104 (1.00) |
4.45e-08 (6.21e-05) |
0.798 (1.00) |
2.98e-07 (0.000409) |
0.335 (1.00) |
0.00427 (1.00) |
0.0453 (1.00) |
0.877 (1.00) |
0.42 (1.00) |
0.124 (1.00) |
0.038 (1.00) |
0.0061 (1.00) |
|
Amp Peak 33(17q12) | 0 (0%) | 3648 |
0.612 (1.00) |
4.28e-05 (0.0547) |
1.47e-88 (2.42e-85) |
0.018 (1.00) |
0.0638 (1.00) |
3.07e-71 (4.99e-68) |
1.44e-06 (0.00195) |
0.000784 (0.922) |
2.21e-06 (0.00297) |
0.00293 (1.00) |
0.00097 (1.00) |
0.332 (1.00) |
0.166 (1.00) |
0.475 (1.00) |
0.73 (1.00) |
0.0764 (1.00) |
0.148 (1.00) |
0.0894 (1.00) |
0.209 (1.00) |
|
Amp Peak 34(17q25 3) | 0 (0%) | 3319 |
0.633 (1.00) |
0.0557 (1.00) |
8.39e-95 (1.39e-91) |
0.00716 (1.00) |
0.016 (1.00) |
1.85e-74 (3.01e-71) |
1.94e-07 (0.000268) |
0.000322 (0.393) |
5.94e-09 (8.41e-06) |
0.0571 (1.00) |
3.76e-07 (0.000516) |
0.34 (1.00) |
0.046 (1.00) |
0.0201 (1.00) |
0.445 (1.00) |
0.502 (1.00) |
0.257 (1.00) |
0.806 (1.00) |
0.157 (1.00) |
|
Amp Peak 36(19p13 2) | 0 (0%) | 3794 |
1.09e-09 (1.55e-06) |
0.123 (1.00) |
2.35e-71 (3.82e-68) |
0.00851 (1.00) |
0.998 (1.00) |
1.17e-30 (1.82e-27) |
0.000492 (0.591) |
0.00114 (1.00) |
0.393 (1.00) |
7.78e-09 (1.1e-05) |
3.08e-11 (4.47e-08) |
0.705 (1.00) |
0.194 (1.00) |
0.516 (1.00) |
0.574 (1.00) |
0.975 (1.00) |
0.538 (1.00) |
0.245 (1.00) |
0.771 (1.00) |
|
Amp Peak 41(Xq28) | 0 (0%) | 3672 |
0.939 (1.00) |
0.864 (1.00) |
2.19e-57 (3.53e-54) |
0.0154 (1.00) |
0.0443 (1.00) |
4.22e-30 (6.55e-27) |
2.67e-08 (3.74e-05) |
8.82e-05 (0.111) |
0.0388 (1.00) |
2.91e-07 (4e-04) |
0.00103 (1.00) |
0.975 (1.00) |
0.401 (1.00) |
0.617 (1.00) |
0.111 (1.00) |
0.525 (1.00) |
0.187 (1.00) |
0.32 (1.00) |
0.0328 (1.00) |
|
Del Peak 9(4q22 1) | 0 (0%) | 3174 |
0.397 (1.00) |
0.0174 (1.00) |
1.3e-123 (2.19e-120) |
0.00292 (1.00) |
0.00493 (1.00) |
3.96e-108 (6.62e-105) |
3.4e-08 (4.75e-05) |
0.0105 (1.00) |
0.16 (1.00) |
8.59e-22 (1.31e-18) |
1.72e-14 (2.55e-11) |
0.0226 (1.00) |
0.0098 (1.00) |
0.0671 (1.00) |
0.799 (1.00) |
0.148 (1.00) |
0.213 (1.00) |
0.00127 (1.00) |
0.321 (1.00) |
|
Del Peak 10(4q34 3) | 0 (0%) | 2971 |
0.0166 (1.00) |
0.0343 (1.00) |
2.74e-125 (4.63e-122) |
0.0124 (1.00) |
0.00238 (1.00) |
1.47e-119 (2.48e-116) |
5.9e-09 (8.35e-06) |
0.0128 (1.00) |
0.445 (1.00) |
8.71e-16 (1.3e-12) |
7.92e-11 (1.14e-07) |
0.00226 (1.00) |
0.00843 (1.00) |
0.863 (1.00) |
0.586 (1.00) |
0.148 (1.00) |
0.558 (1.00) |
0.0155 (1.00) |
0.256 (1.00) |
|
Del Peak 16(7p22 3) | 0 (0%) | 4131 |
0.431 (1.00) |
0.00177 (1.00) |
1.33e-144 (2.26e-141) |
4.91e-27 (7.57e-24) |
0.258 (1.00) |
8.12e-126 (1.37e-122) |
3.04e-07 (0.000418) |
0.512 (1.00) |
0.0718 (1.00) |
2.28e-28 (3.53e-25) |
0.00105 (1.00) |
0.092 (1.00) |
0.65 (1.00) |
0.659 (1.00) |
1 (1.00) |
0.737 (1.00) |
0.17 (1.00) |
0.159 (1.00) |
0.00798 (1.00) |
|
Del Peak 20(9p23) | 0 (0%) | 2997 |
0 (0) |
0.0133 (1.00) |
3.56e-93 (5.87e-90) |
1.64e-10 (2.36e-07) |
0.0593 (1.00) |
2.59e-84 (4.25e-81) |
1.05e-09 (1.49e-06) |
0.0709 (1.00) |
0.14 (1.00) |
0.0111 (1.00) |
0.402 (1.00) |
0.0515 (1.00) |
0.208 (1.00) |
0.115 (1.00) |
0.572 (1.00) |
0.00579 (1.00) |
0.713 (1.00) |
0.00768 (1.00) |
0.00663 (1.00) |
|
Del Peak 27(10q26 3) | 0 (0%) | 3082 |
0 (0) |
0.413 (1.00) |
6.56e-206 (1.13e-202) |
1.1e-12 (1.61e-09) |
0.515 (1.00) |
3.27e-38 (5.16e-35) |
0.101 (1.00) |
0.297 (1.00) |
0.802 (1.00) |
0.156 (1.00) |
1.05e-33 (1.64e-30) |
0.113 (1.00) |
0.0376 (1.00) |
0.0249 (1.00) |
0.371 (1.00) |
0.258 (1.00) |
0.519 (1.00) |
0.144 (1.00) |
0.0223 (1.00) |
|
Del Peak 28(11p15 5) | 0 (0%) | 3347 |
0.00713 (1.00) |
0.69 (1.00) |
6.24e-116 (1.05e-112) |
0.000255 (0.313) |
0.00987 (1.00) |
2.96e-119 (4.98e-116) |
3.58e-10 (5.13e-07) |
0.000168 (0.209) |
0.0233 (1.00) |
1.79e-16 (2.68e-13) |
0.00289 (1.00) |
0.0396 (1.00) |
0.000346 (0.419) |
0.722 (1.00) |
0.353 (1.00) |
0.503 (1.00) |
0.292 (1.00) |
0.000365 (0.441) |
0.0892 (1.00) |
|
Del Peak 29(11q22 3) | 0 (0%) | 3399 |
0.849 (1.00) |
0.653 (1.00) |
2.27e-95 (3.76e-92) |
0.000537 (0.641) |
0.0216 (1.00) |
6e-56 (9.66e-53) |
4.74e-09 (6.72e-06) |
3.12e-08 (4.36e-05) |
0.556 (1.00) |
2.74e-05 (0.0355) |
0.464 (1.00) |
0.262 (1.00) |
0.285 (1.00) |
0.232 (1.00) |
0.518 (1.00) |
0.502 (1.00) |
0.919 (1.00) |
0.0175 (1.00) |
0.271 (1.00) |
|
Del Peak 33(12q24 33) | 0 (0%) | 3878 |
0.0715 (1.00) |
0.415 (1.00) |
2.68e-59 (4.32e-56) |
1.54e-08 (2.17e-05) |
0.15 (1.00) |
1.4e-61 (2.27e-58) |
9.64e-06 (0.0128) |
0.041 (1.00) |
0.0227 (1.00) |
2.17e-08 (3.05e-05) |
0.0158 (1.00) |
0.891 (1.00) |
0.656 (1.00) |
0.184 (1.00) |
0.649 (1.00) |
0.833 (1.00) |
0.193 (1.00) |
0.178 (1.00) |
0.684 (1.00) |
|
Del Peak 36(14q24 1) | 0 (0%) | 3161 |
0.00121 (1.00) |
0.783 (1.00) |
1.3e-49 (2.08e-46) |
0.72 (1.00) |
0.962 (1.00) |
2.93e-51 (4.69e-48) |
2.02e-05 (0.0263) |
3.01e-05 (0.0388) |
0.00278 (1.00) |
2.81e-08 (3.92e-05) |
0.000364 (0.44) |
0.784 (1.00) |
0.061 (1.00) |
0.794 (1.00) |
0.564 (1.00) |
0.237 (1.00) |
0.422 (1.00) |
0.66 (1.00) |
0.458 (1.00) |
|
Del Peak 46(19q13 32) | 0 (0%) | 3653 |
0.00461 (1.00) |
0.38 (1.00) |
5.86e-114 (9.84e-111) |
1.1e-07 (0.000152) |
0.755 (1.00) |
6.78e-107 (1.13e-103) |
6.59e-06 (0.00877) |
0.0486 (1.00) |
0.0131 (1.00) |
2.14e-20 (3.24e-17) |
0.0199 (1.00) |
0.676 (1.00) |
0.0939 (1.00) |
0.0476 (1.00) |
0.429 (1.00) |
0.38 (1.00) |
0.00539 (1.00) |
0.089 (1.00) |
0.132 (1.00) |
|
Del Peak 47(19q13 43) | 0 (0%) | 3737 |
0.0061 (1.00) |
0.755 (1.00) |
7.62e-104 (1.27e-100) |
2e-06 (0.00269) |
0.956 (1.00) |
8.06e-97 (1.34e-93) |
3.89e-06 (0.00521) |
0.0158 (1.00) |
0.0212 (1.00) |
2.97e-17 (4.45e-14) |
0.027 (1.00) |
0.138 (1.00) |
0.0812 (1.00) |
0.0821 (1.00) |
0.535 (1.00) |
0.952 (1.00) |
0.00146 (1.00) |
0.0455 (1.00) |
0.292 (1.00) |
|
Del Peak 49(21q11 2) | 0 (0%) | 3526 |
0.206 (1.00) |
0.00111 (1.00) |
1.48e-67 (2.4e-64) |
0.0105 (1.00) |
0.00551 (1.00) |
6.88e-46 (1.09e-42) |
8.93e-06 (0.0119) |
8.8e-05 (0.11) |
0.0389 (1.00) |
0.0602 (1.00) |
1.78e-11 (2.59e-08) |
0.038 (1.00) |
0.00204 (1.00) |
0.674 (1.00) |
0.724 (1.00) |
0.352 (1.00) |
0.405 (1.00) |
0.139 (1.00) |
0.0264 (1.00) |
|
Amp Peak 10(4q12) | 0 (0%) | 4044 |
8.29e-05 (0.104) |
0.151 (1.00) |
5.03e-36 (7.9e-33) |
0.136 (1.00) |
0.429 (1.00) |
3.41e-33 (5.31e-30) |
3.79e-10 (5.43e-07) |
0.058 (1.00) |
0.2 (1.00) |
0.0774 (1.00) |
0.308 (1.00) |
0.874 (1.00) |
0.103 (1.00) |
0.0378 (1.00) |
0.267 (1.00) |
0.142 (1.00) |
0.403 (1.00) |
0.414 (1.00) |
0.00193 (1.00) |
|
Amp Peak 19(8p11 23) | 0 (0%) | 3419 |
0.00942 (1.00) |
0.00246 (1.00) |
3.4e-66 (5.5e-63) |
0.491 (1.00) |
0.000484 (0.582) |
1.65e-37 (2.59e-34) |
7.37e-09 (1.04e-05) |
0.263 (1.00) |
0.000713 (0.843) |
0.00932 (1.00) |
0.000163 (0.202) |
0.206 (1.00) |
0.0215 (1.00) |
0.182 (1.00) |
0.414 (1.00) |
0.0963 (1.00) |
0.563 (1.00) |
0.0947 (1.00) |
0.241 (1.00) |
|
Amp Peak 24(10q22 2) | 0 (0%) | 4026 |
0.00707 (1.00) |
0.839 (1.00) |
3e-77 (4.91e-74) |
3.16e-20 (4.78e-17) |
0.497 (1.00) |
4.23e-46 (6.73e-43) |
0.000835 (0.977) |
0.0842 (1.00) |
0.631 (1.00) |
2.76e-10 (3.97e-07) |
0.00296 (1.00) |
0.451 (1.00) |
0.173 (1.00) |
0.124 (1.00) |
0.611 (1.00) |
0.524 (1.00) |
0.0778 (1.00) |
0.0524 (1.00) |
0.315 (1.00) |
|
Amp Peak 29(12q15) | 0 (0%) | 3539 |
0.0148 (1.00) |
3.48e-05 (0.0446) |
1.88e-32 (2.93e-29) |
0.134 (1.00) |
0.0513 (1.00) |
9.77e-22 (1.48e-18) |
0.00452 (1.00) |
0.189 (1.00) |
0.203 (1.00) |
0.00811 (1.00) |
9.9e-07 (0.00134) |
0.886 (1.00) |
0.251 (1.00) |
0.396 (1.00) |
0.497 (1.00) |
0.0983 (1.00) |
0.786 (1.00) |
0.479 (1.00) |
0.0727 (1.00) |
|
Amp Peak 32(15q26 3) | 0 (0%) | 3957 |
0.45 (1.00) |
0.325 (1.00) |
1.14e-50 (1.82e-47) |
0.0497 (1.00) |
0.00465 (1.00) |
3.88e-47 (6.17e-44) |
1.68e-10 (2.42e-07) |
0.0147 (1.00) |
0.207 (1.00) |
0.00973 (1.00) |
2.33e-07 (0.000322) |
0.559 (1.00) |
0.00128 (1.00) |
0.665 (1.00) |
0.0573 (1.00) |
0.975 (1.00) |
0.04 (1.00) |
0.986 (1.00) |
0.929 (1.00) |
|
Amp Peak 37(19p13 12) | 0 (0%) | 3580 |
0.00107 (1.00) |
0.679 (1.00) |
3.26e-105 (5.44e-102) |
0.000345 (0.418) |
0.422 (1.00) |
3.65e-107 (6.1e-104) |
0.000327 (0.398) |
0.00401 (1.00) |
0.329 (1.00) |
8.9e-29 (1.38e-25) |
9.43e-05 (0.118) |
0.326 (1.00) |
0.262 (1.00) |
0.936 (1.00) |
0.319 (1.00) |
0.656 (1.00) |
0.0327 (1.00) |
0.256 (1.00) |
0.874 (1.00) |
|
Amp Peak 38(19q12) | 0 (0%) | 3327 |
0.000215 (0.265) |
0.00751 (1.00) |
7.8e-78 (1.28e-74) |
0.189 (1.00) |
0.194 (1.00) |
7.99e-96 (1.32e-92) |
3.69e-06 (0.00494) |
0.00731 (1.00) |
0.105 (1.00) |
7.63e-17 (1.14e-13) |
0.498 (1.00) |
0.0795 (1.00) |
0.000728 (0.858) |
0.267 (1.00) |
0.757 (1.00) |
0.279 (1.00) |
0.112 (1.00) |
0.473 (1.00) |
0.0105 (1.00) |
|
Del Peak 4(2q22 1) | 0 (0%) | 3959 |
0.142 (1.00) |
0.812 (1.00) |
1.6e-44 (2.53e-41) |
0.000535 (0.64) |
0.0411 (1.00) |
1.03e-36 (1.62e-33) |
1.24e-05 (0.0163) |
0.00168 (1.00) |
0.307 (1.00) |
1.08e-05 (0.0142) |
0.024 (1.00) |
0.312 (1.00) |
0.0472 (1.00) |
0.143 (1.00) |
0.224 (1.00) |
0.475 (1.00) |
0.0973 (1.00) |
0.792 (1.00) |
0.282 (1.00) |
|
Del Peak 15(6q26) | 0 (0%) | 3167 |
0.0462 (1.00) |
6.33e-06 (0.00844) |
2.31e-104 (3.85e-101) |
0.00267 (1.00) |
0.572 (1.00) |
3.37e-104 (5.61e-101) |
0.00127 (1.00) |
0.676 (1.00) |
0.172 (1.00) |
1.02e-13 (1.5e-10) |
0.00159 (1.00) |
0.0781 (1.00) |
0.0649 (1.00) |
0.128 (1.00) |
0.798 (1.00) |
0.404 (1.00) |
0.405 (1.00) |
0.258 (1.00) |
0.173 (1.00) |
|
Del Peak 17(7q36 1) | 0 (0%) | 4112 |
0.599 (1.00) |
0.235 (1.00) |
9.82e-56 (1.58e-52) |
0.00322 (1.00) |
0.00142 (1.00) |
1.46e-49 (2.32e-46) |
7.27e-11 (1.05e-07) |
0.0471 (1.00) |
0.000181 (0.224) |
0.189 (1.00) |
0.21 (1.00) |
0.0945 (1.00) |
0.854 (1.00) |
0.386 (1.00) |
0.213 (1.00) |
0.798 (1.00) |
0.249 (1.00) |
0.443 (1.00) |
0.428 (1.00) |
|
Del Peak 51(Xp21 1) | 0 (0%) | 3441 |
1.5e-05 (0.0197) |
0.205 (1.00) |
1.34e-113 (2.25e-110) |
0.0201 (1.00) |
0.152 (1.00) |
6.27e-103 (1.04e-99) |
0.0101 (1.00) |
0.00924 (1.00) |
0.353 (1.00) |
1.1e-18 (1.65e-15) |
0.00199 (1.00) |
0.342 (1.00) |
0.384 (1.00) |
0.59 (1.00) |
0.818 (1.00) |
0.459 (1.00) |
0.0515 (1.00) |
0.193 (1.00) |
0.119 (1.00) |
|
Amp Peak 15(6q21) | 0 (0%) | 4068 |
0.204 (1.00) |
0.0576 (1.00) |
6.27e-28 (9.69e-25) |
4.19e-07 (0.000573) |
0.638 (1.00) |
1.03e-26 (1.58e-23) |
0.00022 (0.27) |
0.183 (1.00) |
0.158 (1.00) |
0.000271 (0.332) |
0.0569 (1.00) |
0.639 (1.00) |
0.967 (1.00) |
0.596 (1.00) |
0.685 (1.00) |
0.55 (1.00) |
0.0192 (1.00) |
0.823 (1.00) |
0.0664 (1.00) |
|
Amp Peak 22(9p13 3) | 0 (0%) | 3868 |
0.759 (1.00) |
0.431 (1.00) |
2.06e-34 (3.22e-31) |
0.417 (1.00) |
0.274 (1.00) |
2.44e-31 (3.8e-28) |
4.21e-07 (0.000576) |
0.00328 (1.00) |
0.36 (1.00) |
0.000534 (0.639) |
0.54 (1.00) |
0.344 (1.00) |
0.701 (1.00) |
0.684 (1.00) |
0.674 (1.00) |
0.781 (1.00) |
0.0605 (1.00) |
0.0325 (1.00) |
0.02 (1.00) |
|
Amp Peak 35(18q11 2) | 0 (0%) | 3945 |
0.984 (1.00) |
0.00669 (1.00) |
1.36e-38 (2.14e-35) |
0.175 (1.00) |
0.00219 (1.00) |
5.07e-47 (8.08e-44) |
6.41e-12 (9.33e-09) |
0.0434 (1.00) |
0.00107 (1.00) |
0.0244 (1.00) |
0.151 (1.00) |
0.0469 (1.00) |
0.392 (1.00) |
0.877 (1.00) |
1 (1.00) |
0.0987 (1.00) |
0.434 (1.00) |
0.62 (1.00) |
0.545 (1.00) |
|
Del Peak 5(2q37 3) | 0 (0%) | 3727 |
0.454 (1.00) |
0.0985 (1.00) |
3.31e-67 (5.35e-64) |
0.00136 (1.00) |
0.279 (1.00) |
2.82e-45 (4.46e-42) |
0.00366 (1.00) |
0.0697 (1.00) |
0.00102 (1.00) |
0.000815 (0.956) |
0.00546 (1.00) |
0.0376 (1.00) |
2.28e-06 (0.00307) |
0.0507 (1.00) |
0.414 (1.00) |
0.187 (1.00) |
0.674 (1.00) |
0.754 (1.00) |
0.0152 (1.00) |
|
Del Peak 13(6p25 3) | 0 (0%) | 3859 |
0.0267 (1.00) |
0.796 (1.00) |
3.78e-16 (5.63e-13) |
7.04e-05 (0.0893) |
0.0194 (1.00) |
1.05e-13 (1.55e-10) |
0.321 (1.00) |
0.655 (1.00) |
0.766 (1.00) |
0.219 (1.00) |
0.127 (1.00) |
0.632 (1.00) |
0.327 (1.00) |
0.131 (1.00) |
0.891 (1.00) |
0.32 (1.00) |
0.0546 (1.00) |
0.764 (1.00) |
0.603 (1.00) |
|
Del Peak 14(6q22 31) | 0 (0%) | 3285 |
0.00334 (1.00) |
0.000533 (0.639) |
3.9e-93 (6.44e-90) |
0.0569 (1.00) |
0.171 (1.00) |
1.53e-94 (2.52e-91) |
0.00105 (1.00) |
0.804 (1.00) |
0.171 (1.00) |
3.81e-10 (5.45e-07) |
0.00124 (1.00) |
0.0397 (1.00) |
0.148 (1.00) |
0.0146 (1.00) |
0.252 (1.00) |
0.258 (1.00) |
0.159 (1.00) |
0.0783 (1.00) |
0.0522 (1.00) |
|
Del Peak 31(12p13 1) | 0 (0%) | 4036 |
0.268 (1.00) |
0.236 (1.00) |
5.87e-21 (8.9e-18) |
2.28e-07 (0.000315) |
0.926 (1.00) |
2.52e-36 (3.96e-33) |
0.401 (1.00) |
0.263 (1.00) |
0.000269 (0.329) |
0.0428 (1.00) |
0.499 (1.00) |
0.0571 (1.00) |
0.443 (1.00) |
0.0227 (1.00) |
0.26 (1.00) |
0.651 (1.00) |
0.2 (1.00) |
0.55 (1.00) |
0.633 (1.00) |
|
Del Peak 48(20p12 1) | 0 (0%) | 4125 |
0.333 (1.00) |
0.48 (1.00) |
5.06e-36 (7.93e-33) |
0.25 (1.00) |
0.833 (1.00) |
3.04e-28 (4.7e-25) |
0.000662 (0.786) |
0.000911 (1.00) |
0.0274 (1.00) |
0.00576 (1.00) |
2.98e-05 (0.0385) |
0.225 (1.00) |
0.616 (1.00) |
0.0215 (1.00) |
0.864 (1.00) |
0.947 (1.00) |
0.234 (1.00) |
0.581 (1.00) |
0.303 (1.00) |
|
Del Peak 1(1p36 23) | 0 (0%) | 3302 |
0.812 (1.00) |
0.101 (1.00) |
8.82e-39 (1.39e-35) |
0.503 (1.00) |
0.231 (1.00) |
3.35e-32 (5.22e-29) |
0.0118 (1.00) |
0.0108 (1.00) |
0.0434 (1.00) |
0.00307 (1.00) |
0.207 (1.00) |
0.0354 (1.00) |
0.00703 (1.00) |
0.24 (1.00) |
0.689 (1.00) |
0.0369 (1.00) |
0.142 (1.00) |
0.000722 (0.851) |
0.000694 (0.822) |
P value = 4.52e-119 (Chi-square test), Q value = 7.6e-116
Table S1. Gene #1: 'Amp Peak 1(1p34.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 1(1P34.2) CNV | 40 | 77 | 124 | 22 | 52 | 46 | 16 | 163 | 1 | 276 | 1 | 7 |
AMP PEAK 1(1P34.2) WILD-TYPE | 91 | 467 | 733 | 390 | 402 | 275 | 477 | 551 | 1 | 272 | 1 | 152 |
Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1p34.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D1V3.png)
P value = 5.11e-13 (Fisher's exact test), Q value = 7.5e-10
Table S2. Gene #1: 'Amp Peak 1(1p34.2)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
AMP PEAK 1(1P34.2) CNV | 609 | 216 |
AMP PEAK 1(1P34.2) WILD-TYPE | 2315 | 1501 |
Figure S2. Get High-res Image Gene #1: 'Amp Peak 1(1p34.2)' versus Clinical Feature #4: 'GENDER'
![](D1V4.png)
P value = 1.04e-111 (Chi-square test), Q value = 1.7e-108
Table S3. Gene #1: 'Amp Peak 1(1p34.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 1(1P34.2) CNV | 20 | 2 | 14 | 46 | 22 | 0 | 16 | 4 | 15 | 73 | 3 | 1 | 5 | 0 | 1 | 0 | 6 | 0 | 0 | 1 | 1 | 52 | 0 | 5 | 1 | 0 | 13 | 1 | 5 | 2 | 278 | 33 | 0 | 2 |
AMP PEAK 1(1P34.2) WILD-TYPE | 336 | 52 | 337 | 275 | 82 | 12 | 477 | 7 | 64 | 170 | 4 | 3 | 12 | 2 | 2 | 2 | 12 | 1 | 1 | 0 | 2 | 263 | 5 | 13 | 3 | 3 | 36 | 9 | 138 | 11 | 274 | 52 | 1 | 18 |
Figure S3. Get High-res Image Gene #1: 'Amp Peak 1(1p34.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D1V6.png)
P value = 6.36e-06 (Fisher's exact test), Q value = 0.0085
Table S4. Gene #1: 'Amp Peak 1(1p34.2)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
AMP PEAK 1(1P34.2) CNV | 43 | 97 | 50 | 29 |
AMP PEAK 1(1P34.2) WILD-TYPE | 405 | 514 | 638 | 179 |
Figure S4. Get High-res Image Gene #1: 'Amp Peak 1(1p34.2)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D1V7.png)
P value = 2.25e-17 (Fisher's exact test), Q value = 3.4e-14
Table S5. Gene #1: 'Amp Peak 1(1p34.2)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
AMP PEAK 1(1P34.2) CNV | 94 | 60 | 256 | 81 |
AMP PEAK 1(1P34.2) WILD-TYPE | 591 | 427 | 620 | 339 |
Figure S5. Get High-res Image Gene #1: 'Amp Peak 1(1p34.2)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D1V10.png)
P value = 2.34e-45 (Chi-square test), Q value = 3.7e-42
Table S6. Gene #2: 'Amp Peak 2(1p22.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 2(1P22.3) CNV | 39 | 74 | 188 | 19 | 76 | 38 | 18 | 163 | 1 | 163 | 0 | 11 |
AMP PEAK 2(1P22.3) WILD-TYPE | 92 | 470 | 669 | 393 | 378 | 283 | 475 | 551 | 1 | 385 | 2 | 148 |
Figure S6. Get High-res Image Gene #2: 'Amp Peak 2(1p22.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D2V3.png)
P value = 4.85e-11 (Fisher's exact test), Q value = 7e-08
Table S7. Gene #2: 'Amp Peak 2(1p22.3)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
AMP PEAK 2(1P22.3) CNV | 578 | 212 |
AMP PEAK 2(1P22.3) WILD-TYPE | 2346 | 1505 |
Figure S7. Get High-res Image Gene #2: 'Amp Peak 2(1p22.3)' versus Clinical Feature #4: 'GENDER'
![](D2V4.png)
P value = 6.93e-41 (Chi-square test), Q value = 1.1e-37
Table S8. Gene #2: 'Amp Peak 2(1p22.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 2(1P22.3) CNV | 17 | 2 | 47 | 38 | 30 | 2 | 18 | 4 | 19 | 65 | 2 | 0 | 8 | 0 | 2 | 0 | 3 | 1 | 0 | 0 | 2 | 56 | 3 | 4 | 1 | 0 | 11 | 1 | 9 | 2 | 164 | 25 | 0 | 2 |
AMP PEAK 2(1P22.3) WILD-TYPE | 339 | 52 | 304 | 283 | 74 | 10 | 475 | 7 | 60 | 178 | 5 | 4 | 9 | 2 | 1 | 2 | 15 | 0 | 1 | 1 | 1 | 259 | 2 | 14 | 3 | 3 | 38 | 9 | 134 | 11 | 388 | 60 | 1 | 18 |
Figure S8. Get High-res Image Gene #2: 'Amp Peak 2(1p22.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D2V6.png)
P value = 8.67e-05 (Fisher's exact test), Q value = 0.11
Table S9. Gene #2: 'Amp Peak 2(1p22.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
AMP PEAK 2(1P22.3) CNV | 41 | 93 | 53 | 28 |
AMP PEAK 2(1P22.3) WILD-TYPE | 407 | 518 | 635 | 180 |
Figure S9. Get High-res Image Gene #2: 'Amp Peak 2(1p22.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D2V7.png)
P value = 3.46e-05 (Fisher's exact test), Q value = 0.044
Table S10. Gene #2: 'Amp Peak 2(1p22.3)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
AMP PEAK 2(1P22.3) CNV | 83 | 57 | 173 | 61 |
AMP PEAK 2(1P22.3) WILD-TYPE | 602 | 430 | 703 | 359 |
Figure S10. Get High-res Image Gene #2: 'Amp Peak 2(1p22.3)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D2V10.png)
P value = 1.44e-06 (logrank test), Q value = 0.002
Table S11. Gene #3: 'Amp Peak 3(1q21.3)' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4) |
AMP PEAK 3(1Q21.3) CNV | 1950 | 562 | 0.0 - 224.0 (14.9) |
AMP PEAK 3(1Q21.3) WILD-TYPE | 2420 | 844 | 0.0 - 210.9 (14.1) |
Figure S11. Get High-res Image Gene #3: 'Amp Peak 3(1q21.3)' versus Clinical Feature #1: 'Time to Death'
![](D3V1.png)
P value = 5.02e-206 (Chi-square test), Q value = 8.7e-203
Table S12. Gene #3: 'Amp Peak 3(1q21.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 3(1Q21.3) CNV | 68 | 92 | 616 | 79 | 200 | 87 | 60 | 458 | 0 | 344 | 2 | 45 |
AMP PEAK 3(1Q21.3) WILD-TYPE | 63 | 452 | 241 | 333 | 254 | 234 | 433 | 256 | 2 | 204 | 0 | 114 |
Figure S12. Get High-res Image Gene #3: 'Amp Peak 3(1q21.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D3V3.png)
P value = 1.59e-35 (Fisher's exact test), Q value = 2.5e-32
Table S13. Gene #3: 'Amp Peak 3(1q21.3)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
AMP PEAK 3(1Q21.3) CNV | 1496 | 558 |
AMP PEAK 3(1Q21.3) WILD-TYPE | 1428 | 1159 |
Figure S13. Get High-res Image Gene #3: 'Amp Peak 3(1q21.3)' versus Clinical Feature #4: 'GENDER'
![](D3V4.png)
P value = 5.21e-127 (Chi-square test), Q value = 8.8e-124
Table S14. Gene #3: 'Amp Peak 3(1q21.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 3(1Q21.3) CNV | 72 | 7 | 137 | 87 | 82 | 11 | 60 | 10 | 61 | 174 | 6 | 0 | 14 | 2 | 2 | 1 | 13 | 1 | 0 | 1 | 2 | 168 | 4 | 8 | 3 | 0 | 22 | 8 | 41 | 3 | 346 | 55 | 0 | 2 |
AMP PEAK 3(1Q21.3) WILD-TYPE | 284 | 47 | 214 | 234 | 22 | 1 | 433 | 1 | 18 | 69 | 1 | 4 | 3 | 0 | 1 | 1 | 5 | 0 | 1 | 0 | 1 | 147 | 1 | 10 | 1 | 3 | 27 | 2 | 102 | 10 | 206 | 30 | 1 | 18 |
Figure S14. Get High-res Image Gene #3: 'Amp Peak 3(1q21.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D3V6.png)
P value = 1.17e-14 (Fisher's exact test), Q value = 1.7e-11
Table S15. Gene #3: 'Amp Peak 3(1q21.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
AMP PEAK 3(1Q21.3) CNV | 124 | 276 | 170 | 74 |
AMP PEAK 3(1Q21.3) WILD-TYPE | 324 | 335 | 518 | 134 |
Figure S15. Get High-res Image Gene #3: 'Amp Peak 3(1q21.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D3V7.png)
P value = 4.31e-05 (Chi-square test), Q value = 0.055
Table S16. Gene #3: 'Amp Peak 3(1q21.3)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 1398 | 167 | 9 | 1 | 148 |
AMP PEAK 3(1Q21.3) CNV | 447 | 47 | 3 | 0 | 76 |
AMP PEAK 3(1Q21.3) WILD-TYPE | 951 | 120 | 6 | 1 | 72 |
Figure S16. Get High-res Image Gene #3: 'Amp Peak 3(1q21.3)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'
![](D3V9.png)
P value = 3.44e-07 (Fisher's exact test), Q value = 0.00047
Table S17. Gene #3: 'Amp Peak 3(1q21.3)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
AMP PEAK 3(1Q21.3) CNV | 247 | 167 | 414 | 151 |
AMP PEAK 3(1Q21.3) WILD-TYPE | 438 | 320 | 462 | 269 |
Figure S17. Get High-res Image Gene #3: 'Amp Peak 3(1q21.3)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D3V10.png)
P value = 1.78e-05 (logrank test), Q value = 0.023
Table S18. Gene #4: 'Amp Peak 4(1q32.1)' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4) |
AMP PEAK 4(1Q32.1) CNV | 1936 | 556 | 0.0 - 223.4 (14.6) |
AMP PEAK 4(1Q32.1) WILD-TYPE | 2434 | 850 | 0.0 - 224.0 (14.3) |
Figure S18. Get High-res Image Gene #4: 'Amp Peak 4(1q32.1)' versus Clinical Feature #1: 'Time to Death'
![](D4V1.png)
P value = 6.43e-187 (Chi-square test), Q value = 1.1e-183
Table S19. Gene #4: 'Amp Peak 4(1q32.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 4(1Q32.1) CNV | 45 | 148 | 659 | 86 | 190 | 87 | 58 | 448 | 0 | 270 | 2 | 47 |
AMP PEAK 4(1Q32.1) WILD-TYPE | 86 | 396 | 198 | 326 | 264 | 234 | 435 | 266 | 2 | 278 | 0 | 112 |
Figure S19. Get High-res Image Gene #4: 'Amp Peak 4(1q32.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D4V3.png)
P value = 4.15e-28 (Fisher's exact test), Q value = 6.4e-25
Table S20. Gene #4: 'Amp Peak 4(1q32.1)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
AMP PEAK 4(1Q32.1) CNV | 1465 | 577 |
AMP PEAK 4(1Q32.1) WILD-TYPE | 1459 | 1140 |
Figure S20. Get High-res Image Gene #4: 'Amp Peak 4(1q32.1)' versus Clinical Feature #4: 'GENDER'
![](D4V4.png)
P value = 1.42e-104 (Chi-square test), Q value = 2.4e-101
Table S21. Gene #4: 'Amp Peak 4(1q32.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 4(1Q32.1) CNV | 79 | 7 | 146 | 87 | 86 | 11 | 58 | 10 | 56 | 173 | 6 | 0 | 14 | 2 | 2 | 0 | 13 | 1 | 0 | 1 | 3 | 164 | 4 | 6 | 2 | 1 | 9 | 7 | 42 | 4 | 272 | 38 | 0 | 4 |
AMP PEAK 4(1Q32.1) WILD-TYPE | 277 | 47 | 205 | 234 | 18 | 1 | 435 | 1 | 23 | 70 | 1 | 4 | 3 | 0 | 1 | 2 | 5 | 0 | 1 | 0 | 0 | 151 | 1 | 12 | 2 | 2 | 40 | 3 | 101 | 9 | 280 | 47 | 1 | 16 |
Figure S21. Get High-res Image Gene #4: 'Amp Peak 4(1q32.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D4V6.png)
P value = 1.12e-15 (Fisher's exact test), Q value = 1.7e-12
Table S22. Gene #4: 'Amp Peak 4(1q32.1)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
AMP PEAK 4(1Q32.1) CNV | 121 | 278 | 169 | 75 |
AMP PEAK 4(1Q32.1) WILD-TYPE | 327 | 333 | 519 | 133 |
Figure S22. Get High-res Image Gene #4: 'Amp Peak 4(1q32.1)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D4V7.png)
P value = 9.71e-06 (Chi-square test), Q value = 0.013
Table S23. Gene #4: 'Amp Peak 4(1q32.1)' versus Clinical Feature #20: 'NEOPLASM.DISEASESTAGE'
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 71 | 45 | 2 | 34 | 246 | 165 | 29 | 107 | 22 | 36 | 35 | 12 |
AMP PEAK 4(1Q32.1) CNV | 45 | 28 | 2 | 15 | 191 | 129 | 14 | 82 | 18 | 30 | 20 | 10 |
AMP PEAK 4(1Q32.1) WILD-TYPE | 26 | 17 | 0 | 19 | 55 | 36 | 15 | 25 | 4 | 6 | 15 | 2 |
Figure S23. Get High-res Image Gene #4: 'Amp Peak 4(1q32.1)' versus Clinical Feature #20: 'NEOPLASM.DISEASESTAGE'
![](D4V20.png)
P value = 1.25e-06 (logrank test), Q value = 0.0017
Table S24. Gene #5: 'Amp Peak 5(1q44)' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4) |
AMP PEAK 5(1Q44) CNV | 1848 | 528 | 0.0 - 223.4 (15.1) |
AMP PEAK 5(1Q44) WILD-TYPE | 2522 | 878 | 0.0 - 224.0 (14.0) |
Figure S24. Get High-res Image Gene #5: 'Amp Peak 5(1q44)' versus Clinical Feature #1: 'Time to Death'
![](D5V1.png)
P value = 4.2e-184 (Chi-square test), Q value = 7.2e-181
Table S25. Gene #5: 'Amp Peak 5(1q44)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 5(1Q44) CNV | 50 | 93 | 620 | 85 | 184 | 94 | 55 | 431 | 2 | 283 | 2 | 46 |
AMP PEAK 5(1Q44) WILD-TYPE | 81 | 451 | 237 | 327 | 270 | 227 | 438 | 283 | 0 | 265 | 0 | 113 |
Figure S25. Get High-res Image Gene #5: 'Amp Peak 5(1q44)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D5V3.png)
P value = 4.53e-31 (Fisher's exact test), Q value = 7e-28
Table S26. Gene #5: 'Amp Peak 5(1q44)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
AMP PEAK 5(1Q44) CNV | 1413 | 533 |
AMP PEAK 5(1Q44) WILD-TYPE | 1511 | 1184 |
Figure S26. Get High-res Image Gene #5: 'Amp Peak 5(1q44)' versus Clinical Feature #4: 'GENDER'
![](D5V4.png)
P value = 3.46e-96 (Chi-square test), Q value = 5.7e-93
Table S27. Gene #5: 'Amp Peak 5(1q44)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 5(1Q44) CNV | 76 | 9 | 141 | 94 | 84 | 11 | 55 | 10 | 51 | 164 | 6 | 1 | 13 | 2 | 2 | 0 | 12 | 1 | 0 | 1 | 3 | 162 | 4 | 5 | 2 | 1 | 13 | 6 | 41 | 4 | 287 | 38 | 0 | 3 |
AMP PEAK 5(1Q44) WILD-TYPE | 280 | 45 | 210 | 227 | 20 | 1 | 438 | 1 | 28 | 79 | 1 | 3 | 4 | 0 | 1 | 2 | 6 | 0 | 1 | 0 | 0 | 153 | 1 | 13 | 2 | 2 | 36 | 4 | 102 | 9 | 265 | 47 | 1 | 17 |
Figure S27. Get High-res Image Gene #5: 'Amp Peak 5(1q44)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D5V6.png)
P value = 7.27e-14 (Fisher's exact test), Q value = 1.1e-10
Table S28. Gene #5: 'Amp Peak 5(1q44)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
AMP PEAK 5(1Q44) CNV | 117 | 263 | 167 | 81 |
AMP PEAK 5(1Q44) WILD-TYPE | 331 | 348 | 521 | 127 |
Figure S28. Get High-res Image Gene #5: 'Amp Peak 5(1q44)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D5V7.png)
P value = 4.85e-05 (Fisher's exact test), Q value = 0.062
Table S29. Gene #5: 'Amp Peak 5(1q44)' versus Clinical Feature #8: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 1036 | 343 | 279 | 11 |
AMP PEAK 5(1Q44) CNV | 318 | 149 | 110 | 5 |
AMP PEAK 5(1Q44) WILD-TYPE | 718 | 194 | 169 | 6 |
Figure S29. Get High-res Image Gene #5: 'Amp Peak 5(1q44)' versus Clinical Feature #8: 'PATHOLOGY.N'
![](D5V8.png)
P value = 1.25e-06 (t-test), Q value = 0.0017
Table S30. Gene #6: 'Amp Peak 6(2p15)' versus Clinical Feature #2: 'AGE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 4585 | 61.9 (12.6) |
AMP PEAK 6(2P15) CNV | 1058 | 63.5 (11.7) |
AMP PEAK 6(2P15) WILD-TYPE | 3527 | 61.4 (12.8) |
Figure S30. Get High-res Image Gene #6: 'Amp Peak 6(2p15)' versus Clinical Feature #2: 'AGE'
![](D6V2.png)
P value = 4.91e-75 (Chi-square test), Q value = 8e-72
Table S31. Gene #6: 'Amp Peak 6(2p15)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 6(2P15) CNV | 49 | 30 | 149 | 73 | 85 | 71 | 69 | 296 | 0 | 218 | 0 | 36 |
AMP PEAK 6(2P15) WILD-TYPE | 82 | 514 | 708 | 339 | 369 | 250 | 424 | 418 | 2 | 330 | 2 | 123 |
Figure S31. Get High-res Image Gene #6: 'Amp Peak 6(2p15)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D6V3.png)
P value = 2.14e-49 (Chi-square test), Q value = 3.4e-46
Table S32. Gene #6: 'Amp Peak 6(2p15)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 6(2P15) CNV | 67 | 6 | 44 | 71 | 22 | 0 | 69 | 3 | 27 | 77 | 6 | 0 | 3 | 2 | 1 | 0 | 4 | 1 | 0 | 0 | 1 | 169 | 0 | 5 | 2 | 0 | 20 | 1 | 36 | 0 | 218 | 36 | 0 | 2 |
AMP PEAK 6(2P15) WILD-TYPE | 289 | 48 | 307 | 250 | 82 | 12 | 424 | 8 | 52 | 166 | 1 | 4 | 14 | 0 | 2 | 2 | 14 | 0 | 1 | 1 | 2 | 146 | 5 | 13 | 2 | 3 | 29 | 9 | 107 | 13 | 334 | 49 | 1 | 18 |
Figure S32. Get High-res Image Gene #6: 'Amp Peak 6(2p15)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D6V6.png)
P value = 4.26e-05 (Fisher's exact test), Q value = 0.054
Table S33. Gene #6: 'Amp Peak 6(2p15)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
AMP PEAK 6(2P15) CNV | 169 | 141 | 302 | 103 |
AMP PEAK 6(2P15) WILD-TYPE | 516 | 346 | 574 | 317 |
Figure S33. Get High-res Image Gene #6: 'Amp Peak 6(2p15)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D6V10.png)
P value = 4.72e-13 (Fisher's exact test), Q value = 6.9e-10
Table S34. Gene #6: 'Amp Peak 6(2p15)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
AMP PEAK 6(2P15) CNV | 117 | 964 |
AMP PEAK 6(2P15) WILD-TYPE | 718 | 2852 |
Figure S34. Get High-res Image Gene #6: 'Amp Peak 6(2p15)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D6V11.png)
P value = 3.58e-06 (t-test), Q value = 0.0048
Table S35. Gene #7: 'Amp Peak 7(2q31.2)' versus Clinical Feature #2: 'AGE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 4585 | 61.9 (12.6) |
AMP PEAK 7(2Q31.2) CNV | 906 | 63.5 (11.6) |
AMP PEAK 7(2Q31.2) WILD-TYPE | 3679 | 61.5 (12.8) |
Figure S35. Get High-res Image Gene #7: 'Amp Peak 7(2q31.2)' versus Clinical Feature #2: 'AGE'
![](D7V2.png)
P value = 5.68e-77 (Chi-square test), Q value = 9.3e-74
Table S36. Gene #7: 'Amp Peak 7(2q31.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 7(2Q31.2) CNV | 20 | 28 | 82 | 70 | 75 | 68 | 75 | 233 | 0 | 230 | 1 | 40 |
AMP PEAK 7(2Q31.2) WILD-TYPE | 111 | 516 | 775 | 342 | 379 | 253 | 418 | 481 | 2 | 318 | 1 | 119 |
Figure S36. Get High-res Image Gene #7: 'Amp Peak 7(2q31.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D7V3.png)
P value = 6.05e-36 (Chi-square test), Q value = 9.5e-33
Table S37. Gene #7: 'Amp Peak 7(2q31.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 7(2Q31.2) CNV | 64 | 6 | 36 | 68 | 13 | 0 | 75 | 3 | 32 | 73 | 4 | 0 | 4 | 0 | 1 | 0 | 5 | 1 | 0 | 1 | 1 | 106 | 0 | 3 | 2 | 0 | 8 | 0 | 40 | 0 | 231 | 36 | 0 | 1 |
AMP PEAK 7(2Q31.2) WILD-TYPE | 292 | 48 | 315 | 253 | 91 | 12 | 418 | 8 | 47 | 170 | 3 | 4 | 13 | 2 | 2 | 2 | 13 | 0 | 1 | 0 | 2 | 209 | 5 | 15 | 2 | 3 | 41 | 10 | 103 | 13 | 321 | 49 | 1 | 19 |
Figure S37. Get High-res Image Gene #7: 'Amp Peak 7(2q31.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D7V6.png)
P value = 2.17e-05 (Fisher's exact test), Q value = 0.028
Table S38. Gene #7: 'Amp Peak 7(2q31.2)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
AMP PEAK 7(2Q31.2) CNV | 161 | 121 | 287 | 94 |
AMP PEAK 7(2Q31.2) WILD-TYPE | 524 | 366 | 589 | 326 |
Figure S38. Get High-res Image Gene #7: 'Amp Peak 7(2q31.2)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D7V10.png)
P value = 3.68e-13 (Fisher's exact test), Q value = 5.4e-10
Table S39. Gene #7: 'Amp Peak 7(2q31.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
AMP PEAK 7(2Q31.2) CNV | 94 | 833 |
AMP PEAK 7(2Q31.2) WILD-TYPE | 741 | 2983 |
Figure S39. Get High-res Image Gene #7: 'Amp Peak 7(2q31.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D7V11.png)
P value = 2.48e-239 (Chi-square test), Q value = 4.3e-236
Table S40. Gene #8: 'Amp Peak 8(3q26.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 8(3Q26.2) CNV | 76 | 79 | 274 | 65 | 126 | 238 | 78 | 428 | 1 | 453 | 2 | 37 |
AMP PEAK 8(3Q26.2) WILD-TYPE | 55 | 465 | 583 | 347 | 328 | 83 | 415 | 286 | 1 | 95 | 0 | 122 |
Figure S40. Get High-res Image Gene #8: 'Amp Peak 8(3q26.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D8V3.png)
P value = 3.29e-05 (t-test), Q value = 0.042
Table S41. Gene #8: 'Amp Peak 8(3q26.2)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 641 | 73.6 (23.9) |
AMP PEAK 8(3Q26.2) CNV | 214 | 67.2 (30.4) |
AMP PEAK 8(3Q26.2) WILD-TYPE | 427 | 76.8 (19.2) |
Figure S41. Get High-res Image Gene #8: 'Amp Peak 8(3q26.2)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'
![](D8V5.png)
P value = 7.01e-241 (Chi-square test), Q value = 1.2e-237
Table S42. Gene #8: 'Amp Peak 8(3q26.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 8(3Q26.2) CNV | 59 | 6 | 57 | 238 | 43 | 0 | 78 | 4 | 31 | 83 | 7 | 1 | 5 | 1 | 1 | 0 | 4 | 1 | 0 | 1 | 1 | 288 | 1 | 6 | 0 | 0 | 28 | 3 | 36 | 1 | 456 | 63 | 0 | 3 |
AMP PEAK 8(3Q26.2) WILD-TYPE | 297 | 48 | 294 | 83 | 61 | 12 | 415 | 7 | 48 | 160 | 0 | 3 | 12 | 1 | 2 | 2 | 14 | 0 | 1 | 0 | 2 | 27 | 4 | 12 | 4 | 3 | 21 | 7 | 107 | 12 | 96 | 22 | 1 | 17 |
Figure S42. Get High-res Image Gene #8: 'Amp Peak 8(3q26.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D8V6.png)
P value = 2.63e-22 (Fisher's exact test), Q value = 4e-19
Table S43. Gene #8: 'Amp Peak 8(3q26.2)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
AMP PEAK 8(3Q26.2) CNV | 147 | 321 | 202 | 116 |
AMP PEAK 8(3Q26.2) WILD-TYPE | 301 | 290 | 486 | 92 |
Figure S43. Get High-res Image Gene #8: 'Amp Peak 8(3q26.2)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D8V7.png)
P value = 4.82e-10 (Fisher's exact test), Q value = 6.9e-07
Table S44. Gene #8: 'Amp Peak 8(3q26.2)' versus Clinical Feature #8: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 1036 | 343 | 279 | 11 |
AMP PEAK 8(3Q26.2) CNV | 399 | 179 | 146 | 11 |
AMP PEAK 8(3Q26.2) WILD-TYPE | 637 | 164 | 133 | 0 |
Figure S44. Get High-res Image Gene #8: 'Amp Peak 8(3q26.2)' versus Clinical Feature #8: 'PATHOLOGY.N'
![](D8V8.png)
P value = 1.14e-23 (Fisher's exact test), Q value = 1.8e-20
Table S45. Gene #8: 'Amp Peak 8(3q26.2)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
AMP PEAK 8(3Q26.2) CNV | 256 | 197 | 527 | 245 |
AMP PEAK 8(3Q26.2) WILD-TYPE | 429 | 290 | 349 | 175 |
Figure S45. Get High-res Image Gene #8: 'Amp Peak 8(3q26.2)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D8V10.png)
P value = 1.41e-13 (Fisher's exact test), Q value = 2.1e-10
Table S46. Gene #8: 'Amp Peak 8(3q26.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
AMP PEAK 8(3Q26.2) CNV | 241 | 1624 |
AMP PEAK 8(3Q26.2) WILD-TYPE | 594 | 2192 |
Figure S46. Get High-res Image Gene #8: 'Amp Peak 8(3q26.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D8V11.png)
P value = 2.49e-05 (t-test), Q value = 0.032
Table S47. Gene #8: 'Amp Peak 8(3q26.2)' versus Clinical Feature #12: 'NUMBERPACKYEARSSMOKED'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 804 | 46.7 (32.6) |
AMP PEAK 8(3Q26.2) CNV | 524 | 50.0 (34.8) |
AMP PEAK 8(3Q26.2) WILD-TYPE | 280 | 40.5 (27.2) |
Figure S47. Get High-res Image Gene #8: 'Amp Peak 8(3q26.2)' versus Clinical Feature #12: 'NUMBERPACKYEARSSMOKED'
![](D8V12.png)
P value = 2.63e-44 (Chi-square test), Q value = 4.2e-41
Table S48. Gene #9: 'Amp Peak 9(4p16.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 9(4P16.3) CNV | 27 | 45 | 93 | 12 | 42 | 38 | 13 | 104 | 0 | 150 | 1 | 10 |
AMP PEAK 9(4P16.3) WILD-TYPE | 104 | 499 | 764 | 400 | 412 | 283 | 480 | 610 | 2 | 398 | 1 | 149 |
Figure S48. Get High-res Image Gene #9: 'Amp Peak 9(4p16.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D9V3.png)
P value = 6.16e-05 (Fisher's exact test), Q value = 0.078
Table S49. Gene #9: 'Amp Peak 9(4p16.3)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
AMP PEAK 9(4P16.3) CNV | 379 | 156 |
AMP PEAK 9(4P16.3) WILD-TYPE | 2545 | 1561 |
Figure S49. Get High-res Image Gene #9: 'Amp Peak 9(4p16.3)' versus Clinical Feature #4: 'GENDER'
![](D9V4.png)
P value = 9.73e-47 (Chi-square test), Q value = 1.5e-43
Table S50. Gene #9: 'Amp Peak 9(4p16.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 9(4P16.3) CNV | 12 | 0 | 12 | 38 | 13 | 0 | 13 | 2 | 10 | 52 | 3 | 0 | 3 | 0 | 1 | 0 | 2 | 0 | 0 | 0 | 0 | 30 | 0 | 1 | 1 | 0 | 13 | 1 | 10 | 0 | 151 | 29 | 0 | 3 |
AMP PEAK 9(4P16.3) WILD-TYPE | 344 | 54 | 339 | 283 | 91 | 12 | 480 | 9 | 69 | 191 | 4 | 4 | 14 | 2 | 2 | 2 | 16 | 1 | 1 | 1 | 3 | 285 | 5 | 17 | 3 | 3 | 36 | 9 | 133 | 13 | 401 | 56 | 1 | 17 |
Figure S50. Get High-res Image Gene #9: 'Amp Peak 9(4p16.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D9V6.png)
P value = 1.38e-07 (Fisher's exact test), Q value = 0.00019
Table S51. Gene #9: 'Amp Peak 9(4p16.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
AMP PEAK 9(4P16.3) CNV | 18 | 76 | 36 | 21 |
AMP PEAK 9(4P16.3) WILD-TYPE | 430 | 535 | 652 | 187 |
Figure S51. Get High-res Image Gene #9: 'Amp Peak 9(4p16.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D9V7.png)
P value = 1.93e-08 (Fisher's exact test), Q value = 2.7e-05
Table S52. Gene #9: 'Amp Peak 9(4p16.3)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
AMP PEAK 9(4P16.3) CNV | 56 | 40 | 152 | 51 |
AMP PEAK 9(4P16.3) WILD-TYPE | 629 | 447 | 724 | 369 |
Figure S52. Get High-res Image Gene #9: 'Amp Peak 9(4p16.3)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D9V10.png)
P value = 7.36e-05 (Chi-square test), Q value = 0.093
Table S53. Gene #9: 'Amp Peak 9(4p16.3)' versus Clinical Feature #20: 'NEOPLASM.DISEASESTAGE'
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 71 | 45 | 2 | 34 | 246 | 165 | 29 | 107 | 22 | 36 | 35 | 12 |
AMP PEAK 9(4P16.3) CNV | 6 | 2 | 1 | 10 | 25 | 15 | 4 | 9 | 8 | 8 | 4 | 0 |
AMP PEAK 9(4P16.3) WILD-TYPE | 65 | 43 | 1 | 24 | 221 | 150 | 25 | 98 | 14 | 28 | 31 | 12 |
Figure S53. Get High-res Image Gene #9: 'Amp Peak 9(4p16.3)' versus Clinical Feature #20: 'NEOPLASM.DISEASESTAGE'
![](D9V20.png)
P value = 8.29e-05 (logrank test), Q value = 0.1
Table S54. Gene #10: 'Amp Peak 10(4q12)' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4) |
AMP PEAK 10(4Q12) CNV | 576 | 220 | 0.1 - 224.0 (13.0) |
AMP PEAK 10(4Q12) WILD-TYPE | 3794 | 1186 | 0.0 - 223.4 (14.8) |
Figure S54. Get High-res Image Gene #10: 'Amp Peak 10(4q12)' versus Clinical Feature #1: 'Time to Death'
![](D10V1.png)
P value = 5.03e-36 (Chi-square test), Q value = 7.9e-33
Table S55. Gene #10: 'Amp Peak 10(4q12)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 10(4Q12) CNV | 15 | 101 | 117 | 18 | 19 | 52 | 12 | 149 | 1 | 108 | 1 | 11 |
AMP PEAK 10(4Q12) WILD-TYPE | 116 | 443 | 740 | 394 | 435 | 269 | 481 | 565 | 1 | 440 | 1 | 148 |
Figure S55. Get High-res Image Gene #10: 'Amp Peak 10(4q12)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D10V3.png)
P value = 3.41e-33 (Chi-square test), Q value = 5.3e-30
Table S56. Gene #10: 'Amp Peak 10(4q12)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 10(4Q12) CNV | 17 | 1 | 6 | 52 | 21 | 0 | 12 | 4 | 11 | 50 | 3 | 0 | 4 | 1 | 1 | 0 | 1 | 0 | 0 | 0 | 1 | 73 | 0 | 1 | 0 | 0 | 6 | 1 | 11 | 0 | 110 | 12 | 0 | 8 |
AMP PEAK 10(4Q12) WILD-TYPE | 339 | 53 | 345 | 269 | 83 | 12 | 481 | 7 | 68 | 193 | 4 | 4 | 13 | 1 | 2 | 2 | 17 | 1 | 1 | 1 | 2 | 242 | 5 | 17 | 4 | 3 | 43 | 9 | 132 | 13 | 442 | 73 | 1 | 12 |
Figure S56. Get High-res Image Gene #10: 'Amp Peak 10(4q12)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D10V6.png)
P value = 3.79e-10 (Fisher's exact test), Q value = 5.4e-07
Table S57. Gene #10: 'Amp Peak 10(4q12)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
AMP PEAK 10(4Q12) CNV | 30 | 104 | 48 | 33 |
AMP PEAK 10(4Q12) WILD-TYPE | 418 | 507 | 640 | 175 |
Figure S57. Get High-res Image Gene #10: 'Amp Peak 10(4q12)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D10V7.png)
P value = 1.62e-05 (t-test), Q value = 0.021
Table S58. Gene #11: 'Amp Peak 11(5p15.33)' versus Clinical Feature #2: 'AGE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 4585 | 61.9 (12.6) |
AMP PEAK 11(5P15.33) CNV | 1676 | 62.9 (11.8) |
AMP PEAK 11(5P15.33) WILD-TYPE | 2909 | 61.3 (13.0) |
Figure S58. Get High-res Image Gene #11: 'Amp Peak 11(5p15.33)' versus Clinical Feature #2: 'AGE'
![](D11V2.png)
P value = 2.24e-160 (Chi-square test), Q value = 3.8e-157
Table S59. Gene #11: 'Amp Peak 11(5p15.33)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 11(5P15.33) CNV | 61 | 54 | 308 | 78 | 67 | 145 | 158 | 509 | 1 | 289 | 2 | 37 |
AMP PEAK 11(5P15.33) WILD-TYPE | 70 | 490 | 549 | 334 | 387 | 176 | 335 | 205 | 1 | 259 | 0 | 122 |
Figure S59. Get High-res Image Gene #11: 'Amp Peak 11(5p15.33)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D11V3.png)
P value = 0.000192 (t-test), Q value = 0.24
Table S60. Gene #11: 'Amp Peak 11(5p15.33)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 641 | 73.6 (23.9) |
AMP PEAK 11(5P15.33) CNV | 173 | 66.1 (33.6) |
AMP PEAK 11(5P15.33) WILD-TYPE | 468 | 76.3 (18.5) |
Figure S60. Get High-res Image Gene #11: 'Amp Peak 11(5p15.33)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'
![](D11V5.png)
P value = 1.59e-116 (Chi-square test), Q value = 2.7e-113
Table S61. Gene #11: 'Amp Peak 11(5p15.33)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 11(5P15.33) CNV | 69 | 9 | 24 | 145 | 38 | 5 | 158 | 8 | 45 | 166 | 5 | 1 | 13 | 2 | 2 | 0 | 12 | 1 | 0 | 1 | 3 | 249 | 0 | 3 | 1 | 0 | 15 | 3 | 36 | 1 | 292 | 40 | 1 | 2 |
AMP PEAK 11(5P15.33) WILD-TYPE | 287 | 45 | 327 | 176 | 66 | 7 | 335 | 3 | 34 | 77 | 2 | 3 | 4 | 0 | 1 | 2 | 6 | 0 | 1 | 0 | 0 | 66 | 5 | 15 | 3 | 3 | 34 | 7 | 107 | 12 | 260 | 45 | 0 | 18 |
Figure S61. Get High-res Image Gene #11: 'Amp Peak 11(5p15.33)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D11V6.png)
P value = 1.28e-19 (Fisher's exact test), Q value = 1.9e-16
Table S62. Gene #11: 'Amp Peak 11(5p15.33)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
AMP PEAK 11(5P15.33) CNV | 196 | 344 | 208 | 87 |
AMP PEAK 11(5P15.33) WILD-TYPE | 252 | 267 | 480 | 121 |
Figure S62. Get High-res Image Gene #11: 'Amp Peak 11(5p15.33)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D11V7.png)
P value = 5.66e-05 (Fisher's exact test), Q value = 0.072
Table S63. Gene #11: 'Amp Peak 11(5p15.33)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
AMP PEAK 11(5P15.33) CNV | 328 | 185 | 429 | 167 |
AMP PEAK 11(5P15.33) WILD-TYPE | 357 | 302 | 447 | 253 |
Figure S63. Get High-res Image Gene #11: 'Amp Peak 11(5p15.33)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D11V10.png)
P value = 9.11e-16 (Fisher's exact test), Q value = 1.4e-12
Table S64. Gene #11: 'Amp Peak 11(5p15.33)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
AMP PEAK 11(5P15.33) CNV | 208 | 1505 |
AMP PEAK 11(5P15.33) WILD-TYPE | 627 | 2311 |
Figure S64. Get High-res Image Gene #11: 'Amp Peak 11(5p15.33)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D11V11.png)
P value = 9.9e-06 (logrank test), Q value = 0.013
Table S65. Gene #12: 'Amp Peak 12(5q35.3)' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4) |
AMP PEAK 12(5Q35.3) CNV | 908 | 268 | 0.0 - 224.0 (19.6) |
AMP PEAK 12(5Q35.3) WILD-TYPE | 3462 | 1138 | 0.0 - 223.4 (13.3) |
Figure S65. Get High-res Image Gene #12: 'Amp Peak 12(5q35.3)' versus Clinical Feature #1: 'Time to Death'
![](D12V1.png)
P value = 1.49e-155 (Chi-square test), Q value = 2.5e-152
Table S66. Gene #12: 'Amp Peak 12(5q35.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 12(5Q35.3) CNV | 11 | 48 | 220 | 37 | 38 | 20 | 311 | 108 | 0 | 136 | 0 | 22 |
AMP PEAK 12(5Q35.3) WILD-TYPE | 120 | 496 | 637 | 375 | 416 | 301 | 182 | 606 | 2 | 412 | 2 | 137 |
Figure S66. Get High-res Image Gene #12: 'Amp Peak 12(5q35.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D12V3.png)
P value = 5.88e-130 (Chi-square test), Q value = 1e-126
Table S67. Gene #12: 'Amp Peak 12(5q35.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 12(5Q35.3) CNV | 33 | 4 | 15 | 20 | 25 | 5 | 311 | 4 | 15 | 54 | 1 | 1 | 5 | 1 | 0 | 0 | 4 | 0 | 0 | 0 | 0 | 22 | 0 | 3 | 1 | 0 | 4 | 2 | 21 | 1 | 136 | 20 | 1 | 2 |
AMP PEAK 12(5Q35.3) WILD-TYPE | 323 | 50 | 336 | 301 | 79 | 7 | 182 | 7 | 64 | 189 | 6 | 3 | 12 | 1 | 3 | 2 | 14 | 1 | 1 | 1 | 3 | 293 | 5 | 15 | 3 | 3 | 45 | 8 | 122 | 12 | 416 | 65 | 0 | 18 |
Figure S67. Get High-res Image Gene #12: 'Amp Peak 12(5q35.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D12V6.png)
P value = 1.77e-17 (Fisher's exact test), Q value = 2.7e-14
Table S68. Gene #12: 'Amp Peak 12(5q35.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
AMP PEAK 12(5Q35.3) CNV | 172 | 112 | 168 | 22 |
AMP PEAK 12(5Q35.3) WILD-TYPE | 276 | 499 | 520 | 186 |
Figure S68. Get High-res Image Gene #12: 'Amp Peak 12(5q35.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D12V7.png)
P value = 6.66e-05 (Fisher's exact test), Q value = 0.085
Table S69. Gene #12: 'Amp Peak 12(5q35.3)' versus Clinical Feature #8: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 1036 | 343 | 279 | 11 |
AMP PEAK 12(5Q35.3) CNV | 227 | 47 | 36 | 4 |
AMP PEAK 12(5Q35.3) WILD-TYPE | 809 | 296 | 243 | 7 |
Figure S69. Get High-res Image Gene #12: 'Amp Peak 12(5q35.3)' versus Clinical Feature #8: 'PATHOLOGY.N'
![](D12V8.png)
P value = 9.07e-07 (Fisher's exact test), Q value = 0.0012
Table S70. Gene #12: 'Amp Peak 12(5q35.3)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
AMP PEAK 12(5Q35.3) CNV | 196 | 77 | 235 | 96 |
AMP PEAK 12(5Q35.3) WILD-TYPE | 489 | 410 | 641 | 324 |
Figure S70. Get High-res Image Gene #12: 'Amp Peak 12(5q35.3)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D12V10.png)
P value = 8.09e-08 (Fisher's exact test), Q value = 0.00011
Table S71. Gene #12: 'Amp Peak 12(5q35.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
AMP PEAK 12(5Q35.3) CNV | 116 | 838 |
AMP PEAK 12(5Q35.3) WILD-TYPE | 719 | 2978 |
Figure S71. Get High-res Image Gene #12: 'Amp Peak 12(5q35.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D12V11.png)
P value = 1.74e-115 (Chi-square test), Q value = 2.9e-112
Table S72. Gene #13: 'Amp Peak 13(6p22.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 13(6P22.3) CNV | 54 | 28 | 217 | 74 | 72 | 50 | 8 | 237 | 1 | 280 | 1 | 38 |
AMP PEAK 13(6P22.3) WILD-TYPE | 77 | 516 | 640 | 338 | 382 | 271 | 485 | 477 | 1 | 268 | 1 | 121 |
Figure S72. Get High-res Image Gene #13: 'Amp Peak 13(6p22.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D13V3.png)
P value = 6.53e-11 (Fisher's exact test), Q value = 9.4e-08
Table S73. Gene #13: 'Amp Peak 13(6p22.3)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
AMP PEAK 13(6P22.3) CNV | 758 | 303 |
AMP PEAK 13(6P22.3) WILD-TYPE | 2166 | 1414 |
Figure S73. Get High-res Image Gene #13: 'Amp Peak 13(6p22.3)' versus Clinical Feature #4: 'GENDER'
![](D13V4.png)
P value = 2.66e-91 (Chi-square test), Q value = 4.4e-88
Table S74. Gene #13: 'Amp Peak 13(6p22.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 13(6P22.3) CNV | 67 | 7 | 30 | 50 | 43 | 0 | 8 | 7 | 26 | 92 | 3 | 0 | 8 | 1 | 1 | 0 | 8 | 0 | 0 | 1 | 2 | 87 | 0 | 3 | 1 | 0 | 18 | 5 | 36 | 2 | 282 | 39 | 1 | 0 |
AMP PEAK 13(6P22.3) WILD-TYPE | 289 | 47 | 321 | 271 | 61 | 12 | 485 | 4 | 53 | 151 | 4 | 4 | 9 | 1 | 2 | 2 | 10 | 1 | 1 | 0 | 1 | 228 | 5 | 15 | 3 | 3 | 31 | 5 | 107 | 11 | 270 | 46 | 0 | 20 |
Figure S74. Get High-res Image Gene #13: 'Amp Peak 13(6p22.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D13V6.png)
P value = 0.00017 (Chi-square test), Q value = 0.21
Table S75. Gene #13: 'Amp Peak 13(6p22.3)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 1398 | 167 | 9 | 1 | 148 |
AMP PEAK 13(6P22.3) CNV | 236 | 26 | 3 | 0 | 47 |
AMP PEAK 13(6P22.3) WILD-TYPE | 1162 | 141 | 6 | 1 | 101 |
Figure S75. Get High-res Image Gene #13: 'Amp Peak 13(6p22.3)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'
![](D13V9.png)
P value = 3.21e-13 (Fisher's exact test), Q value = 4.7e-10
Table S76. Gene #13: 'Amp Peak 13(6p22.3)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
AMP PEAK 13(6P22.3) CNV | 132 | 97 | 303 | 93 |
AMP PEAK 13(6P22.3) WILD-TYPE | 553 | 390 | 573 | 327 |
Figure S76. Get High-res Image Gene #13: 'Amp Peak 13(6p22.3)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D13V10.png)
P value = 1.61e-10 (Fisher's exact test), Q value = 2.3e-07
Table S77. Gene #13: 'Amp Peak 13(6p22.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
AMP PEAK 13(6P22.3) CNV | 123 | 942 |
AMP PEAK 13(6P22.3) WILD-TYPE | 712 | 2874 |
Figure S77. Get High-res Image Gene #13: 'Amp Peak 13(6p22.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D13V11.png)
P value = 8.63e-74 (Chi-square test), Q value = 1.4e-70
Table S78. Gene #14: 'Amp Peak 14(6p21.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 14(6P21.1) CNV | 27 | 32 | 199 | 91 | 73 | 53 | 10 | 240 | 0 | 213 | 1 | 49 |
AMP PEAK 14(6P21.1) WILD-TYPE | 104 | 512 | 658 | 321 | 381 | 268 | 483 | 474 | 2 | 335 | 1 | 110 |
Figure S78. Get High-res Image Gene #14: 'Amp Peak 14(6p21.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D14V3.png)
P value = 2.33e-05 (Fisher's exact test), Q value = 0.03
Table S79. Gene #14: 'Amp Peak 14(6p21.1)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
AMP PEAK 14(6P21.1) CNV | 681 | 310 |
AMP PEAK 14(6P21.1) WILD-TYPE | 2243 | 1407 |
Figure S79. Get High-res Image Gene #14: 'Amp Peak 14(6p21.1)' versus Clinical Feature #4: 'GENDER'
![](D14V4.png)
P value = 1.64e-59 (Chi-square test), Q value = 2.6e-56
Table S80. Gene #14: 'Amp Peak 14(6p21.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 14(6P21.1) CNV | 85 | 6 | 35 | 53 | 36 | 0 | 10 | 6 | 27 | 92 | 2 | 0 | 9 | 0 | 1 | 0 | 8 | 1 | 0 | 1 | 1 | 91 | 0 | 0 | 1 | 0 | 6 | 4 | 48 | 1 | 214 | 38 | 0 | 0 |
AMP PEAK 14(6P21.1) WILD-TYPE | 271 | 48 | 316 | 268 | 68 | 12 | 483 | 5 | 52 | 151 | 5 | 4 | 8 | 2 | 2 | 2 | 10 | 0 | 1 | 0 | 2 | 224 | 5 | 18 | 3 | 3 | 43 | 6 | 95 | 12 | 338 | 47 | 1 | 20 |
Figure S80. Get High-res Image Gene #14: 'Amp Peak 14(6p21.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D14V6.png)
P value = 1.23e-07 (Fisher's exact test), Q value = 0.00017
Table S81. Gene #14: 'Amp Peak 14(6p21.1)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
AMP PEAK 14(6P21.1) CNV | 126 | 107 | 270 | 95 |
AMP PEAK 14(6P21.1) WILD-TYPE | 559 | 380 | 606 | 325 |
Figure S81. Get High-res Image Gene #14: 'Amp Peak 14(6p21.1)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D14V10.png)
P value = 2.11e-07 (Fisher's exact test), Q value = 0.00029
Table S82. Gene #14: 'Amp Peak 14(6p21.1)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
AMP PEAK 14(6P21.1) CNV | 124 | 870 |
AMP PEAK 14(6P21.1) WILD-TYPE | 711 | 2946 |
Figure S82. Get High-res Image Gene #14: 'Amp Peak 14(6p21.1)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D14V11.png)
P value = 6.27e-28 (Chi-square test), Q value = 9.7e-25
Table S83. Gene #15: 'Amp Peak 15(6q21)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 15(6Q21) CNV | 14 | 24 | 159 | 59 | 59 | 27 | 9 | 89 | 0 | 106 | 1 | 34 |
AMP PEAK 15(6Q21) WILD-TYPE | 117 | 520 | 698 | 353 | 395 | 294 | 484 | 625 | 2 | 442 | 1 | 125 |
Figure S83. Get High-res Image Gene #15: 'Amp Peak 15(6q21)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D15V3.png)
P value = 4.19e-07 (Fisher's exact test), Q value = 0.00057
Table S84. Gene #15: 'Amp Peak 15(6q21)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
AMP PEAK 15(6Q21) CNV | 421 | 161 |
AMP PEAK 15(6Q21) WILD-TYPE | 2503 | 1556 |
Figure S84. Get High-res Image Gene #15: 'Amp Peak 15(6q21)' versus Clinical Feature #4: 'GENDER'
![](D15V4.png)
P value = 1.03e-26 (Chi-square test), Q value = 1.6e-23
Table S85. Gene #15: 'Amp Peak 15(6q21)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 15(6Q21) CNV | 54 | 5 | 30 | 27 | 30 | 1 | 9 | 1 | 5 | 17 | 0 | 0 | 2 | 0 | 0 | 0 | 2 | 0 | 0 | 1 | 1 | 59 | 0 | 0 | 1 | 0 | 8 | 0 | 34 | 0 | 107 | 29 | 0 | 0 |
AMP PEAK 15(6Q21) WILD-TYPE | 302 | 49 | 321 | 294 | 74 | 11 | 484 | 10 | 74 | 226 | 7 | 4 | 15 | 2 | 3 | 2 | 16 | 1 | 1 | 0 | 2 | 256 | 5 | 18 | 3 | 3 | 41 | 10 | 109 | 13 | 445 | 56 | 1 | 20 |
Figure S85. Get High-res Image Gene #15: 'Amp Peak 15(6q21)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D15V6.png)
P value = 0 (logrank test), Q value = 0
Table S86. Gene #16: 'Amp Peak 16(7p11.2)' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4) |
AMP PEAK 16(7P11.2) CNV | 1927 | 780 | 0.0 - 224.0 (11.5) |
AMP PEAK 16(7P11.2) WILD-TYPE | 2443 | 626 | 0.0 - 220.9 (18.1) |
Figure S86. Get High-res Image Gene #16: 'Amp Peak 16(7p11.2)' versus Clinical Feature #1: 'Time to Death'
![](D16V1.png)
P value = 4.82e-156 (Chi-square test), Q value = 8.2e-153
Table S87. Gene #16: 'Amp Peak 16(7p11.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 16(7P11.2) CNV | 70 | 477 | 263 | 227 | 65 | 137 | 160 | 371 | 1 | 182 | 1 | 98 |
AMP PEAK 16(7P11.2) WILD-TYPE | 61 | 67 | 594 | 185 | 389 | 184 | 333 | 343 | 1 | 366 | 1 | 61 |
Figure S87. Get High-res Image Gene #16: 'Amp Peak 16(7p11.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D16V3.png)
P value = 4.27e-32 (Fisher's exact test), Q value = 6.7e-29
Table S88. Gene #16: 'Amp Peak 16(7p11.2)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
AMP PEAK 16(7P11.2) CNV | 1101 | 953 |
AMP PEAK 16(7P11.2) WILD-TYPE | 1823 | 764 |
Figure S88. Get High-res Image Gene #16: 'Amp Peak 16(7p11.2)' versus Clinical Feature #4: 'GENDER'
![](D16V4.png)
P value = 1.33e-52 (Chi-square test), Q value = 2.1e-49
Table S89. Gene #16: 'Amp Peak 16(7p11.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 16(7P11.2) CNV | 206 | 21 | 38 | 137 | 31 | 1 | 160 | 5 | 37 | 141 | 5 | 3 | 8 | 0 | 2 | 0 | 9 | 1 | 0 | 0 | 2 | 156 | 0 | 4 | 2 | 0 | 25 | 4 | 94 | 3 | 184 | 23 | 1 | 17 |
AMP PEAK 16(7P11.2) WILD-TYPE | 150 | 33 | 313 | 184 | 73 | 11 | 333 | 6 | 42 | 102 | 2 | 1 | 9 | 2 | 1 | 2 | 9 | 0 | 1 | 1 | 1 | 159 | 5 | 14 | 2 | 3 | 24 | 6 | 49 | 10 | 368 | 62 | 0 | 3 |
Figure S89. Get High-res Image Gene #16: 'Amp Peak 16(7p11.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D16V6.png)
P value = 2.1e-09 (Fisher's exact test), Q value = 3e-06
Table S90. Gene #16: 'Amp Peak 16(7p11.2)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
AMP PEAK 16(7P11.2) CNV | 151 | 308 | 360 | 101 |
AMP PEAK 16(7P11.2) WILD-TYPE | 297 | 303 | 328 | 107 |
Figure S90. Get High-res Image Gene #16: 'Amp Peak 16(7p11.2)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D16V7.png)
P value = 4.56e-07 (Fisher's exact test), Q value = 0.00062
Table S91. Gene #16: 'Amp Peak 16(7p11.2)' versus Clinical Feature #8: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 1036 | 343 | 279 | 11 |
AMP PEAK 16(7P11.2) CNV | 458 | 200 | 163 | 6 |
AMP PEAK 16(7P11.2) WILD-TYPE | 578 | 143 | 116 | 5 |
Figure S91. Get High-res Image Gene #16: 'Amp Peak 16(7p11.2)' versus Clinical Feature #8: 'PATHOLOGY.N'
![](D16V8.png)
P value = 7.18e-13 (Fisher's exact test), Q value = 1.1e-09
Table S92. Gene #16: 'Amp Peak 16(7p11.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
AMP PEAK 16(7P11.2) CNV | 463 | 1594 |
AMP PEAK 16(7P11.2) WILD-TYPE | 372 | 2222 |
Figure S92. Get High-res Image Gene #16: 'Amp Peak 16(7p11.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D16V11.png)
P value = 0 (logrank test), Q value = 0
Table S93. Gene #17: 'Amp Peak 17(7q21.2)' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4) |
AMP PEAK 17(7Q21.2) CNV | 1811 | 754 | 0.0 - 224.0 (12.0) |
AMP PEAK 17(7Q21.2) WILD-TYPE | 2559 | 652 | 0.0 - 220.9 (17.0) |
Figure S93. Get High-res Image Gene #17: 'Amp Peak 17(7q21.2)' versus Clinical Feature #1: 'Time to Death'
![](D17V1.png)
P value = 3.72e-139 (Chi-square test), Q value = 6.3e-136
Table S94. Gene #17: 'Amp Peak 17(7q21.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 17(7Q21.2) CNV | 52 | 453 | 222 | 203 | 59 | 109 | 165 | 345 | 1 | 223 | 1 | 83 |
AMP PEAK 17(7Q21.2) WILD-TYPE | 79 | 91 | 635 | 209 | 395 | 212 | 328 | 369 | 1 | 325 | 1 | 76 |
Figure S94. Get High-res Image Gene #17: 'Amp Peak 17(7q21.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D17V3.png)
P value = 8.63e-28 (Fisher's exact test), Q value = 1.3e-24
Table S95. Gene #17: 'Amp Peak 17(7q21.2)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
AMP PEAK 17(7Q21.2) CNV | 1031 | 887 |
AMP PEAK 17(7Q21.2) WILD-TYPE | 1893 | 830 |
Figure S95. Get High-res Image Gene #17: 'Amp Peak 17(7q21.2)' versus Clinical Feature #4: 'GENDER'
![](D17V4.png)
P value = 4.86e-38 (Chi-square test), Q value = 7.7e-35
Table S96. Gene #17: 'Amp Peak 17(7q21.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 17(7Q21.2) CNV | 185 | 18 | 40 | 109 | 26 | 1 | 165 | 3 | 30 | 114 | 4 | 2 | 8 | 0 | 2 | 0 | 8 | 1 | 0 | 0 | 1 | 172 | 1 | 4 | 0 | 0 | 18 | 1 | 79 | 3 | 225 | 15 | 1 | 14 |
AMP PEAK 17(7Q21.2) WILD-TYPE | 171 | 36 | 311 | 212 | 78 | 11 | 328 | 8 | 49 | 129 | 3 | 2 | 9 | 2 | 1 | 2 | 10 | 0 | 1 | 1 | 2 | 143 | 4 | 14 | 4 | 3 | 31 | 9 | 64 | 10 | 327 | 70 | 0 | 6 |
Figure S96. Get High-res Image Gene #17: 'Amp Peak 17(7q21.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D17V6.png)
P value = 5.62e-12 (Fisher's exact test), Q value = 8.2e-09
Table S97. Gene #17: 'Amp Peak 17(7q21.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
AMP PEAK 17(7Q21.2) CNV | 435 | 1488 |
AMP PEAK 17(7Q21.2) WILD-TYPE | 400 | 2328 |
Figure S97. Get High-res Image Gene #17: 'Amp Peak 17(7q21.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D17V11.png)
P value = 0 (logrank test), Q value = 0
Table S98. Gene #18: 'Amp Peak 18(7q36.3)' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4) |
AMP PEAK 18(7Q36.3) CNV | 1759 | 711 | 0.0 - 223.4 (12.0) |
AMP PEAK 18(7Q36.3) WILD-TYPE | 2611 | 695 | 0.0 - 224.0 (16.3) |
Figure S98. Get High-res Image Gene #18: 'Amp Peak 18(7q36.3)' versus Clinical Feature #1: 'Time to Death'
![](D18V1.png)
P value = 4.4e-158 (Chi-square test), Q value = 7.5e-155
Table S99. Gene #18: 'Amp Peak 18(7q36.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 18(7Q36.3) CNV | 40 | 447 | 209 | 201 | 58 | 60 | 164 | 306 | 1 | 293 | 1 | 82 |
AMP PEAK 18(7Q36.3) WILD-TYPE | 91 | 97 | 648 | 211 | 396 | 261 | 329 | 408 | 1 | 255 | 1 | 77 |
Figure S99. Get High-res Image Gene #18: 'Amp Peak 18(7q36.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D18V3.png)
P value = 2.93e-13 (Fisher's exact test), Q value = 4.3e-10
Table S100. Gene #18: 'Amp Peak 18(7q36.3)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
AMP PEAK 18(7Q36.3) CNV | 1056 | 808 |
AMP PEAK 18(7Q36.3) WILD-TYPE | 1868 | 909 |
Figure S100. Get High-res Image Gene #18: 'Amp Peak 18(7q36.3)' versus Clinical Feature #4: 'GENDER'
![](D18V4.png)
P value = 3.21e-53 (Chi-square test), Q value = 5.2e-50
Table S101. Gene #18: 'Amp Peak 18(7q36.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 18(7Q36.3) CNV | 181 | 19 | 38 | 60 | 25 | 0 | 164 | 4 | 29 | 115 | 2 | 2 | 9 | 0 | 1 | 0 | 7 | 1 | 0 | 1 | 2 | 132 | 1 | 3 | 1 | 0 | 9 | 3 | 79 | 2 | 295 | 17 | 1 | 14 |
AMP PEAK 18(7Q36.3) WILD-TYPE | 175 | 35 | 313 | 261 | 79 | 12 | 329 | 7 | 50 | 128 | 5 | 2 | 8 | 2 | 2 | 2 | 11 | 0 | 1 | 0 | 1 | 183 | 4 | 15 | 3 | 3 | 40 | 7 | 64 | 11 | 257 | 68 | 0 | 6 |
Figure S101. Get High-res Image Gene #18: 'Amp Peak 18(7q36.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D18V6.png)
P value = 1.84e-06 (Fisher's exact test), Q value = 0.0025
Table S102. Gene #18: 'Amp Peak 18(7q36.3)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
AMP PEAK 18(7Q36.3) CNV | 247 | 191 | 429 | 169 |
AMP PEAK 18(7Q36.3) WILD-TYPE | 438 | 296 | 447 | 251 |
Figure S102. Get High-res Image Gene #18: 'Amp Peak 18(7q36.3)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D18V10.png)
P value = 4.66e-08 (Fisher's exact test), Q value = 6.5e-05
Table S103. Gene #18: 'Amp Peak 18(7q36.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
AMP PEAK 18(7Q36.3) CNV | 406 | 1462 |
AMP PEAK 18(7Q36.3) WILD-TYPE | 429 | 2354 |
Figure S103. Get High-res Image Gene #18: 'Amp Peak 18(7q36.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D18V11.png)
P value = 3.4e-66 (Chi-square test), Q value = 5.5e-63
Table S104. Gene #19: 'Amp Peak 19(8p11.23)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 19(8P11.23) CNV | 46 | 41 | 319 | 143 | 106 | 102 | 27 | 266 | 0 | 125 | 1 | 52 |
AMP PEAK 19(8P11.23) WILD-TYPE | 85 | 503 | 538 | 269 | 348 | 219 | 466 | 448 | 2 | 423 | 1 | 107 |
Figure S104. Get High-res Image Gene #19: 'Amp Peak 19(8p11.23)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D19V3.png)
P value = 1.65e-37 (Chi-square test), Q value = 2.6e-34
Table S105. Gene #19: 'Amp Peak 19(8p11.23)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 19(8P11.23) CNV | 129 | 14 | 80 | 102 | 40 | 4 | 27 | 5 | 29 | 62 | 3 | 0 | 3 | 0 | 1 | 0 | 4 | 0 | 0 | 1 | 2 | 155 | 3 | 6 | 1 | 0 | 14 | 5 | 50 | 2 | 126 | 20 | 0 | 2 |
AMP PEAK 19(8P11.23) WILD-TYPE | 227 | 40 | 271 | 219 | 64 | 8 | 466 | 6 | 50 | 181 | 4 | 4 | 14 | 2 | 2 | 2 | 14 | 1 | 1 | 0 | 1 | 160 | 2 | 12 | 3 | 3 | 35 | 5 | 93 | 11 | 426 | 65 | 1 | 18 |
Figure S105. Get High-res Image Gene #19: 'Amp Peak 19(8p11.23)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D19V6.png)
P value = 7.37e-09 (Fisher's exact test), Q value = 1e-05
Table S106. Gene #19: 'Amp Peak 19(8p11.23)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
AMP PEAK 19(8P11.23) CNV | 82 | 213 | 183 | 71 |
AMP PEAK 19(8P11.23) WILD-TYPE | 366 | 398 | 505 | 137 |
Figure S106. Get High-res Image Gene #19: 'Amp Peak 19(8p11.23)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D19V7.png)
P value = 0.000163 (Fisher's exact test), Q value = 0.2
Table S107. Gene #19: 'Amp Peak 19(8p11.23)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
AMP PEAK 19(8P11.23) CNV | 178 | 1054 |
AMP PEAK 19(8P11.23) WILD-TYPE | 657 | 2762 |
Figure S107. Get High-res Image Gene #19: 'Amp Peak 19(8p11.23)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D19V11.png)
P value = 7.12e-06 (t-test), Q value = 0.0095
Table S108. Gene #20: 'Amp Peak 20(8p11.21)' versus Clinical Feature #2: 'AGE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 4585 | 61.9 (12.6) |
AMP PEAK 20(8P11.21) CNV | 1380 | 63.1 (12.0) |
AMP PEAK 20(8P11.21) WILD-TYPE | 3205 | 61.4 (12.8) |
Figure S108. Get High-res Image Gene #20: 'Amp Peak 20(8p11.21)' versus Clinical Feature #2: 'AGE'
![](D20V2.png)
P value = 7.88e-77 (Chi-square test), Q value = 1.3e-73
Table S109. Gene #20: 'Amp Peak 20(8p11.21)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 20(8P11.21) CNV | 45 | 42 | 337 | 173 | 135 | 89 | 29 | 281 | 0 | 194 | 2 | 72 |
AMP PEAK 20(8P11.21) WILD-TYPE | 86 | 502 | 520 | 239 | 319 | 232 | 464 | 433 | 2 | 354 | 0 | 87 |
Figure S109. Get High-res Image Gene #20: 'Amp Peak 20(8p11.21)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D20V3.png)
P value = 1.1e-45 (Chi-square test), Q value = 1.7e-42
Table S110. Gene #20: 'Amp Peak 20(8p11.21)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 20(8P11.21) CNV | 155 | 18 | 82 | 89 | 42 | 4 | 29 | 7 | 31 | 80 | 3 | 0 | 4 | 0 | 0 | 0 | 5 | 0 | 0 | 1 | 3 | 147 | 3 | 6 | 0 | 0 | 12 | 6 | 67 | 3 | 196 | 47 | 0 | 2 |
AMP PEAK 20(8P11.21) WILD-TYPE | 201 | 36 | 269 | 232 | 62 | 8 | 464 | 4 | 48 | 163 | 4 | 4 | 13 | 2 | 3 | 2 | 13 | 1 | 1 | 0 | 0 | 168 | 2 | 12 | 4 | 3 | 37 | 4 | 76 | 10 | 356 | 38 | 1 | 18 |
Figure S110. Get High-res Image Gene #20: 'Amp Peak 20(8p11.21)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D20V6.png)
P value = 1.34e-11 (Fisher's exact test), Q value = 2e-08
Table S111. Gene #20: 'Amp Peak 20(8p11.21)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
AMP PEAK 20(8P11.21) CNV | 78 | 227 | 222 | 67 |
AMP PEAK 20(8P11.21) WILD-TYPE | 370 | 384 | 466 | 141 |
Figure S111. Get High-res Image Gene #20: 'Amp Peak 20(8p11.21)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D20V7.png)
P value = 2.88e-05 (Fisher's exact test), Q value = 0.037
Table S112. Gene #20: 'Amp Peak 20(8p11.21)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
AMP PEAK 20(8P11.21) CNV | 181 | 186 | 292 | 113 |
AMP PEAK 20(8P11.21) WILD-TYPE | 504 | 301 | 584 | 307 |
Figure S112. Get High-res Image Gene #20: 'Amp Peak 20(8p11.21)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D20V10.png)
P value = 2.27e-08 (Fisher's exact test), Q value = 3.2e-05
Table S113. Gene #20: 'Amp Peak 20(8p11.21)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
AMP PEAK 20(8P11.21) CNV | 186 | 1219 |
AMP PEAK 20(8P11.21) WILD-TYPE | 649 | 2597 |
Figure S113. Get High-res Image Gene #20: 'Amp Peak 20(8p11.21)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D20V11.png)
P value = 1.94e-213 (Chi-square test), Q value = 3.4e-210
Table S114. Gene #21: 'Amp Peak 21(8q24.21)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 21(8Q24.21) CNV | 79 | 62 | 558 | 239 | 168 | 231 | 71 | 475 | 2 | 429 | 2 | 105 |
AMP PEAK 21(8Q24.21) WILD-TYPE | 52 | 482 | 299 | 173 | 286 | 90 | 422 | 239 | 0 | 119 | 0 | 54 |
Figure S114. Get High-res Image Gene #21: 'Amp Peak 21(8q24.21)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D21V3.png)
P value = 2.5e-08 (Fisher's exact test), Q value = 3.5e-05
Table S115. Gene #21: 'Amp Peak 21(8q24.21)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
AMP PEAK 21(8Q24.21) CNV | 1618 | 804 |
AMP PEAK 21(8Q24.21) WILD-TYPE | 1306 | 913 |
Figure S115. Get High-res Image Gene #21: 'Amp Peak 21(8q24.21)' versus Clinical Feature #4: 'GENDER'
![](D21V4.png)
P value = 1.3e-05 (t-test), Q value = 0.017
Table S116. Gene #21: 'Amp Peak 21(8q24.21)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 641 | 73.6 (23.9) |
AMP PEAK 21(8Q24.21) CNV | 194 | 66.2 (30.7) |
AMP PEAK 21(8Q24.21) WILD-TYPE | 447 | 76.8 (19.5) |
Figure S116. Get High-res Image Gene #21: 'Amp Peak 21(8q24.21)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'
![](D21V5.png)
P value = 2.05e-129 (Chi-square test), Q value = 3.5e-126
Table S117. Gene #21: 'Amp Peak 21(8q24.21)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 21(8Q24.21) CNV | 213 | 25 | 99 | 231 | 73 | 4 | 71 | 8 | 45 | 162 | 6 | 1 | 10 | 1 | 2 | 0 | 12 | 1 | 0 | 1 | 3 | 223 | 4 | 8 | 0 | 0 | 30 | 7 | 98 | 5 | 433 | 61 | 0 | 3 |
AMP PEAK 21(8Q24.21) WILD-TYPE | 143 | 29 | 252 | 90 | 31 | 8 | 422 | 3 | 34 | 81 | 1 | 3 | 7 | 1 | 1 | 2 | 6 | 0 | 1 | 0 | 0 | 92 | 1 | 10 | 4 | 3 | 19 | 3 | 45 | 8 | 119 | 24 | 1 | 17 |
Figure S117. Get High-res Image Gene #21: 'Amp Peak 21(8q24.21)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D21V6.png)
P value = 2.1e-26 (Fisher's exact test), Q value = 3.2e-23
Table S118. Gene #21: 'Amp Peak 21(8q24.21)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
AMP PEAK 21(8Q24.21) CNV | 141 | 378 | 369 | 141 |
AMP PEAK 21(8Q24.21) WILD-TYPE | 307 | 233 | 319 | 67 |
Figure S118. Get High-res Image Gene #21: 'Amp Peak 21(8q24.21)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D21V7.png)
P value = 4.03e-11 (Fisher's exact test), Q value = 5.8e-08
Table S119. Gene #21: 'Amp Peak 21(8q24.21)' versus Clinical Feature #8: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 1036 | 343 | 279 | 11 |
AMP PEAK 21(8Q24.21) CNV | 532 | 218 | 202 | 9 |
AMP PEAK 21(8Q24.21) WILD-TYPE | 504 | 125 | 77 | 2 |
Figure S119. Get High-res Image Gene #21: 'Amp Peak 21(8q24.21)' versus Clinical Feature #8: 'PATHOLOGY.N'
![](D21V8.png)
P value = 6.46e-19 (Fisher's exact test), Q value = 9.7e-16
Table S120. Gene #21: 'Amp Peak 21(8q24.21)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
AMP PEAK 21(8Q24.21) CNV | 296 | 294 | 570 | 272 |
AMP PEAK 21(8Q24.21) WILD-TYPE | 389 | 193 | 306 | 148 |
Figure S120. Get High-res Image Gene #21: 'Amp Peak 21(8q24.21)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D21V10.png)
P value = 4.46e-22 (Fisher's exact test), Q value = 6.8e-19
Table S121. Gene #21: 'Amp Peak 21(8q24.21)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
AMP PEAK 21(8Q24.21) CNV | 310 | 2120 |
AMP PEAK 21(8Q24.21) WILD-TYPE | 525 | 1696 |
Figure S121. Get High-res Image Gene #21: 'Amp Peak 21(8q24.21)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D21V11.png)
P value = 2.06e-34 (Chi-square test), Q value = 3.2e-31
Table S122. Gene #22: 'Amp Peak 22(9p13.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 22(9P13.3) CNV | 30 | 66 | 152 | 70 | 34 | 90 | 12 | 151 | 0 | 132 | 0 | 45 |
AMP PEAK 22(9P13.3) WILD-TYPE | 101 | 478 | 705 | 342 | 420 | 231 | 481 | 563 | 2 | 416 | 2 | 114 |
Figure S122. Get High-res Image Gene #22: 'Amp Peak 22(9p13.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D22V3.png)
P value = 2.44e-31 (Chi-square test), Q value = 3.8e-28
Table S123. Gene #22: 'Amp Peak 22(9p13.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 22(9P13.3) CNV | 56 | 14 | 16 | 90 | 25 | 1 | 12 | 3 | 16 | 36 | 4 | 0 | 3 | 0 | 1 | 0 | 4 | 0 | 0 | 1 | 0 | 83 | 0 | 2 | 0 | 0 | 14 | 3 | 39 | 5 | 132 | 16 | 1 | 1 |
AMP PEAK 22(9P13.3) WILD-TYPE | 300 | 40 | 335 | 231 | 79 | 11 | 481 | 8 | 63 | 207 | 3 | 4 | 14 | 2 | 2 | 2 | 14 | 1 | 1 | 0 | 3 | 232 | 5 | 16 | 4 | 3 | 35 | 7 | 104 | 8 | 420 | 69 | 0 | 19 |
Figure S123. Get High-res Image Gene #22: 'Amp Peak 22(9p13.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D22V6.png)
P value = 4.21e-07 (Fisher's exact test), Q value = 0.00058
Table S124. Gene #22: 'Amp Peak 22(9p13.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
AMP PEAK 22(9P13.3) CNV | 50 | 123 | 112 | 59 |
AMP PEAK 22(9P13.3) WILD-TYPE | 398 | 488 | 576 | 149 |
Figure S124. Get High-res Image Gene #22: 'Amp Peak 22(9p13.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D22V7.png)
P value = 8.14e-107 (Chi-square test), Q value = 1.4e-103
Table S125. Gene #23: 'Amp Peak 23(10p15.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 23(10P15.1) CNV | 54 | 17 | 242 | 38 | 112 | 29 | 16 | 170 | 0 | 239 | 2 | 15 |
AMP PEAK 23(10P15.1) WILD-TYPE | 77 | 527 | 615 | 374 | 342 | 292 | 477 | 544 | 2 | 309 | 0 | 144 |
Figure S125. Get High-res Image Gene #23: 'Amp Peak 23(10p15.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D23V3.png)
P value = 1.03e-21 (Fisher's exact test), Q value = 1.6e-18
Table S126. Gene #23: 'Amp Peak 23(10p15.1)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
AMP PEAK 23(10P15.1) CNV | 712 | 222 |
AMP PEAK 23(10P15.1) WILD-TYPE | 2212 | 1495 |
Figure S126. Get High-res Image Gene #23: 'Amp Peak 23(10p15.1)' versus Clinical Feature #4: 'GENDER'
![](D23V4.png)
P value = 2.93e-70 (Chi-square test), Q value = 4.8e-67
Table S127. Gene #23: 'Amp Peak 23(10p15.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 23(10P15.1) CNV | 34 | 3 | 84 | 29 | 45 | 0 | 16 | 4 | 27 | 62 | 2 | 0 | 4 | 0 | 2 | 0 | 7 | 0 | 0 | 0 | 2 | 59 | 2 | 4 | 1 | 0 | 20 | 2 | 14 | 1 | 241 | 24 | 0 | 0 |
AMP PEAK 23(10P15.1) WILD-TYPE | 322 | 51 | 267 | 292 | 59 | 12 | 477 | 7 | 52 | 181 | 5 | 4 | 13 | 2 | 1 | 2 | 11 | 1 | 1 | 1 | 1 | 256 | 3 | 14 | 3 | 3 | 29 | 8 | 129 | 12 | 311 | 61 | 1 | 20 |
Figure S127. Get High-res Image Gene #23: 'Amp Peak 23(10p15.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D23V6.png)
P value = 3.06e-06 (Fisher's exact test), Q value = 0.0041
Table S128. Gene #23: 'Amp Peak 23(10p15.1)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
AMP PEAK 23(10P15.1) CNV | 38 | 111 | 67 | 25 |
AMP PEAK 23(10P15.1) WILD-TYPE | 410 | 500 | 621 | 183 |
Figure S128. Get High-res Image Gene #23: 'Amp Peak 23(10p15.1)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D23V7.png)
P value = 5.14e-16 (Fisher's exact test), Q value = 7.6e-13
Table S129. Gene #23: 'Amp Peak 23(10p15.1)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
AMP PEAK 23(10P15.1) CNV | 88 | 76 | 250 | 61 |
AMP PEAK 23(10P15.1) WILD-TYPE | 597 | 411 | 626 | 359 |
Figure S129. Get High-res Image Gene #23: 'Amp Peak 23(10p15.1)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D23V10.png)
P value = 8.77e-07 (Fisher's exact test), Q value = 0.0012
Table S130. Gene #23: 'Amp Peak 23(10p15.1)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
AMP PEAK 23(10P15.1) CNV | 118 | 820 |
AMP PEAK 23(10P15.1) WILD-TYPE | 717 | 2996 |
Figure S130. Get High-res Image Gene #23: 'Amp Peak 23(10p15.1)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D23V11.png)
P value = 7.11e-07 (Chi-square test), Q value = 0.00097
Table S131. Gene #23: 'Amp Peak 23(10p15.1)' versus Clinical Feature #13: 'TOBACCOSMOKINGHISTORYINDICATOR'
nPatients | 1 | 2 | 3 | 4 | 5 | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER |
---|---|---|---|---|---|---|---|---|---|
ALL | 15 | 16 | 22 | 25 | 2 | 342 | 208 | 237 | 116 |
AMP PEAK 23(10P15.1) CNV | 7 | 6 | 12 | 8 | 0 | 78 | 35 | 47 | 8 |
AMP PEAK 23(10P15.1) WILD-TYPE | 8 | 10 | 10 | 17 | 2 | 264 | 173 | 190 | 108 |
Figure S131. Get High-res Image Gene #23: 'Amp Peak 23(10p15.1)' versus Clinical Feature #13: 'TOBACCOSMOKINGHISTORYINDICATOR'
![](D23V13.png)
P value = 3e-77 (Chi-square test), Q value = 4.9e-74
Table S132. Gene #24: 'Amp Peak 24(10q22.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 24(10Q22.2) CNV | 18 | 2 | 135 | 23 | 123 | 29 | 10 | 102 | 1 | 169 | 1 | 11 |
AMP PEAK 24(10Q22.2) WILD-TYPE | 113 | 542 | 722 | 389 | 331 | 292 | 483 | 612 | 1 | 379 | 1 | 148 |
Figure S132. Get High-res Image Gene #24: 'Amp Peak 24(10q22.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D24V3.png)
P value = 3.16e-20 (Fisher's exact test), Q value = 4.8e-17
Table S133. Gene #24: 'Amp Peak 24(10q22.2)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
AMP PEAK 24(10Q22.2) CNV | 493 | 131 |
AMP PEAK 24(10Q22.2) WILD-TYPE | 2431 | 1586 |
Figure S133. Get High-res Image Gene #24: 'Amp Peak 24(10q22.2)' versus Clinical Feature #4: 'GENDER'
![](D24V4.png)
P value = 4.23e-46 (Chi-square test), Q value = 6.7e-43
Table S134. Gene #24: 'Amp Peak 24(10q22.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 24(10Q22.2) CNV | 20 | 3 | 88 | 29 | 21 | 2 | 10 | 2 | 19 | 38 | 0 | 0 | 1 | 0 | 1 | 0 | 4 | 0 | 0 | 0 | 0 | 37 | 1 | 3 | 0 | 0 | 4 | 1 | 9 | 1 | 171 | 32 | 0 | 0 |
AMP PEAK 24(10Q22.2) WILD-TYPE | 336 | 51 | 263 | 292 | 83 | 10 | 483 | 9 | 60 | 205 | 7 | 4 | 16 | 2 | 2 | 2 | 14 | 1 | 1 | 1 | 3 | 278 | 4 | 15 | 4 | 3 | 45 | 9 | 134 | 12 | 381 | 53 | 1 | 20 |
Figure S134. Get High-res Image Gene #24: 'Amp Peak 24(10q22.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D24V6.png)
P value = 2.76e-10 (Fisher's exact test), Q value = 4e-07
Table S135. Gene #24: 'Amp Peak 24(10q22.2)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
AMP PEAK 24(10Q22.2) CNV | 58 | 45 | 169 | 54 |
AMP PEAK 24(10Q22.2) WILD-TYPE | 627 | 442 | 707 | 366 |
Figure S135. Get High-res Image Gene #24: 'Amp Peak 24(10q22.2)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D24V10.png)
P value = 2.29e-120 (Chi-square test), Q value = 3.9e-117
Table S136. Gene #25: 'Amp Peak 25(11q13.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 25(11Q13.3) CNV | 49 | 17 | 325 | 48 | 47 | 145 | 27 | 253 | 0 | 211 | 0 | 25 |
AMP PEAK 25(11Q13.3) WILD-TYPE | 82 | 527 | 532 | 364 | 407 | 176 | 466 | 461 | 2 | 337 | 2 | 134 |
Figure S136. Get High-res Image Gene #25: 'Amp Peak 25(11q13.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D25V3.png)
P value = 0.000162 (Fisher's exact test), Q value = 0.2
Table S137. Gene #25: 'Amp Peak 25(11q13.3)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
AMP PEAK 25(11Q13.3) CNV | 776 | 371 |
AMP PEAK 25(11Q13.3) WILD-TYPE | 2148 | 1346 |
Figure S137. Get High-res Image Gene #25: 'Amp Peak 25(11q13.3)' versus Clinical Feature #4: 'GENDER'
![](D25V4.png)
P value = 1.72e-67 (Chi-square test), Q value = 2.8e-64
Table S138. Gene #25: 'Amp Peak 25(11q13.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 25(11Q13.3) CNV | 47 | 1 | 28 | 145 | 40 | 3 | 27 | 4 | 26 | 92 | 2 | 1 | 5 | 1 | 2 | 0 | 2 | 1 | 0 | 0 | 1 | 116 | 3 | 1 | 0 | 0 | 18 | 3 | 24 | 1 | 211 | 18 | 0 | 0 |
AMP PEAK 25(11Q13.3) WILD-TYPE | 309 | 53 | 323 | 176 | 64 | 9 | 466 | 7 | 53 | 151 | 5 | 3 | 12 | 1 | 1 | 2 | 16 | 0 | 1 | 1 | 2 | 199 | 2 | 17 | 4 | 3 | 31 | 7 | 119 | 12 | 341 | 67 | 1 | 20 |
Figure S138. Get High-res Image Gene #25: 'Amp Peak 25(11q13.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D25V6.png)
P value = 3.36e-09 (Fisher's exact test), Q value = 4.8e-06
Table S139. Gene #25: 'Amp Peak 25(11q13.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
AMP PEAK 25(11Q13.3) CNV | 82 | 175 | 117 | 69 |
AMP PEAK 25(11Q13.3) WILD-TYPE | 366 | 436 | 571 | 139 |
Figure S139. Get High-res Image Gene #25: 'Amp Peak 25(11q13.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D25V7.png)
P value = 3.55e-06 (Fisher's exact test), Q value = 0.0048
Table S140. Gene #25: 'Amp Peak 25(11q13.3)' versus Clinical Feature #8: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 1036 | 343 | 279 | 11 |
AMP PEAK 25(11Q13.3) CNV | 224 | 86 | 100 | 6 |
AMP PEAK 25(11Q13.3) WILD-TYPE | 812 | 257 | 179 | 5 |
Figure S140. Get High-res Image Gene #25: 'Amp Peak 25(11q13.3)' versus Clinical Feature #8: 'PATHOLOGY.N'
![](D25V8.png)
P value = 2.61e-07 (Fisher's exact test), Q value = 0.00036
Table S141. Gene #25: 'Amp Peak 25(11q13.3)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
AMP PEAK 25(11Q13.3) CNV | 133 | 121 | 249 | 144 |
AMP PEAK 25(11Q13.3) WILD-TYPE | 552 | 366 | 627 | 276 |
Figure S141. Get High-res Image Gene #25: 'Amp Peak 25(11q13.3)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D25V10.png)
P value = 1.38e-05 (Fisher's exact test), Q value = 0.018
Table S142. Gene #25: 'Amp Peak 25(11q13.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
AMP PEAK 25(11Q13.3) CNV | 158 | 992 |
AMP PEAK 25(11Q13.3) WILD-TYPE | 677 | 2824 |
Figure S142. Get High-res Image Gene #25: 'Amp Peak 25(11q13.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D25V11.png)
P value = 1.48e-73 (Chi-square test), Q value = 2.4e-70
Table S143. Gene #26: 'Amp Peak 26(12p13.33)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 26(12P13.33) CNV | 44 | 64 | 224 | 103 | 67 | 108 | 115 | 278 | 2 | 306 | 1 | 38 |
AMP PEAK 26(12P13.33) WILD-TYPE | 87 | 480 | 633 | 309 | 387 | 213 | 378 | 436 | 0 | 242 | 1 | 121 |
Figure S143. Get High-res Image Gene #26: 'Amp Peak 26(12p13.33)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D26V3.png)
P value = 7.83e-52 (Chi-square test), Q value = 1.3e-48
Table S144. Gene #26: 'Amp Peak 26(12p13.33)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 26(12P13.33) CNV | 91 | 11 | 37 | 108 | 34 | 1 | 115 | 2 | 26 | 75 | 3 | 0 | 4 | 1 | 0 | 0 | 2 | 1 | 0 | 1 | 1 | 160 | 0 | 4 | 2 | 0 | 12 | 2 | 32 | 5 | 309 | 26 | 0 | 1 |
AMP PEAK 26(12P13.33) WILD-TYPE | 265 | 43 | 314 | 213 | 70 | 11 | 378 | 9 | 53 | 168 | 4 | 4 | 13 | 1 | 3 | 2 | 16 | 0 | 1 | 0 | 2 | 155 | 5 | 14 | 2 | 3 | 37 | 8 | 111 | 8 | 243 | 59 | 1 | 19 |
Figure S144. Get High-res Image Gene #26: 'Amp Peak 26(12p13.33)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D26V6.png)
P value = 9.81e-06 (Fisher's exact test), Q value = 0.013
Table S145. Gene #26: 'Amp Peak 26(12p13.33)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
AMP PEAK 26(12P13.33) CNV | 103 | 224 | 205 | 75 |
AMP PEAK 26(12P13.33) WILD-TYPE | 345 | 387 | 483 | 133 |
Figure S145. Get High-res Image Gene #26: 'Amp Peak 26(12p13.33)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D26V7.png)
P value = 1.28e-08 (Fisher's exact test), Q value = 1.8e-05
Table S146. Gene #26: 'Amp Peak 26(12p13.33)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
AMP PEAK 26(12P13.33) CNV | 190 | 183 | 377 | 153 |
AMP PEAK 26(12P13.33) WILD-TYPE | 495 | 304 | 499 | 267 |
Figure S146. Get High-res Image Gene #26: 'Amp Peak 26(12p13.33)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D26V10.png)
P value = 7.44e-13 (Fisher's exact test), Q value = 1.1e-09
Table S147. Gene #26: 'Amp Peak 26(12p13.33)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
AMP PEAK 26(12P13.33) CNV | 161 | 1198 |
AMP PEAK 26(12P13.33) WILD-TYPE | 674 | 2618 |
Figure S147. Get High-res Image Gene #26: 'Amp Peak 26(12p13.33)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D26V11.png)
P value = 7.8e-71 (Chi-square test), Q value = 1.3e-67
Table S148. Gene #27: 'Amp Peak 27(12p12.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 27(12P12.1) CNV | 42 | 62 | 217 | 90 | 70 | 96 | 113 | 293 | 2 | 288 | 2 | 38 |
AMP PEAK 27(12P12.1) WILD-TYPE | 89 | 482 | 640 | 322 | 384 | 225 | 380 | 421 | 0 | 260 | 0 | 121 |
Figure S148. Get High-res Image Gene #27: 'Amp Peak 27(12p12.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D27V3.png)
P value = 2.71e-47 (Chi-square test), Q value = 4.3e-44
Table S149. Gene #27: 'Amp Peak 27(12p12.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 27(12P12.1) CNV | 76 | 13 | 36 | 96 | 31 | 1 | 113 | 3 | 22 | 93 | 3 | 0 | 7 | 1 | 1 | 0 | 3 | 1 | 0 | 0 | 1 | 156 | 0 | 2 | 2 | 0 | 13 | 2 | 32 | 5 | 292 | 32 | 0 | 2 |
AMP PEAK 27(12P12.1) WILD-TYPE | 280 | 41 | 315 | 225 | 73 | 11 | 380 | 8 | 57 | 150 | 4 | 4 | 10 | 1 | 2 | 2 | 15 | 0 | 1 | 1 | 2 | 159 | 5 | 16 | 2 | 3 | 36 | 8 | 111 | 8 | 260 | 53 | 1 | 18 |
Figure S149. Get High-res Image Gene #27: 'Amp Peak 27(12p12.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D27V6.png)
P value = 1.78e-05 (Fisher's exact test), Q value = 0.023
Table S150. Gene #27: 'Amp Peak 27(12p12.1)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
AMP PEAK 27(12P12.1) CNV | 104 | 226 | 196 | 64 |
AMP PEAK 27(12P12.1) WILD-TYPE | 344 | 385 | 492 | 144 |
Figure S150. Get High-res Image Gene #27: 'Amp Peak 27(12p12.1)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D27V7.png)
P value = 5.86e-08 (Fisher's exact test), Q value = 8.2e-05
Table S151. Gene #27: 'Amp Peak 27(12p12.1)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
AMP PEAK 27(12P12.1) CNV | 198 | 165 | 375 | 133 |
AMP PEAK 27(12P12.1) WILD-TYPE | 487 | 322 | 501 | 287 |
Figure S151. Get High-res Image Gene #27: 'Amp Peak 27(12p12.1)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D27V10.png)
P value = 1.86e-10 (Fisher's exact test), Q value = 2.7e-07
Table S152. Gene #27: 'Amp Peak 27(12p12.1)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
AMP PEAK 27(12P12.1) CNV | 164 | 1158 |
AMP PEAK 27(12P12.1) WILD-TYPE | 671 | 2658 |
Figure S152. Get High-res Image Gene #27: 'Amp Peak 27(12p12.1)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D27V11.png)
P value = 7.95e-05 (logrank test), Q value = 0.1
Table S153. Gene #28: 'Amp Peak 28(12q14.1)' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4) |
AMP PEAK 28(12Q14.1) CNV | 1032 | 375 | 0.1 - 180.2 (14.1) |
AMP PEAK 28(12Q14.1) WILD-TYPE | 3338 | 1031 | 0.0 - 224.0 (14.5) |
Figure S153. Get High-res Image Gene #28: 'Amp Peak 28(12q14.1)' versus Clinical Feature #1: 'Time to Death'
![](D28V1.png)
P value = 0.00011 (t-test), Q value = 0.14
Table S154. Gene #28: 'Amp Peak 28(12q14.1)' versus Clinical Feature #2: 'AGE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 4585 | 61.9 (12.6) |
AMP PEAK 28(12Q14.1) CNV | 1072 | 63.2 (12.5) |
AMP PEAK 28(12Q14.1) WILD-TYPE | 3513 | 61.5 (12.6) |
Figure S154. Get High-res Image Gene #28: 'Amp Peak 28(12q14.1)' versus Clinical Feature #2: 'AGE'
![](D28V2.png)
P value = 5.75e-23 (Chi-square test), Q value = 8.8e-20
Table S155. Gene #28: 'Amp Peak 28(12q14.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 28(12Q14.1) CNV | 30 | 125 | 189 | 85 | 48 | 56 | 113 | 235 | 1 | 184 | 2 | 23 |
AMP PEAK 28(12Q14.1) WILD-TYPE | 101 | 419 | 668 | 327 | 406 | 265 | 380 | 479 | 1 | 364 | 0 | 136 |
Figure S155. Get High-res Image Gene #28: 'Amp Peak 28(12q14.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D28V3.png)
P value = 1.56e-17 (Chi-square test), Q value = 2.4e-14
Table S156. Gene #28: 'Amp Peak 28(12q14.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 28(12Q14.1) CNV | 72 | 12 | 30 | 56 | 32 | 1 | 113 | 4 | 23 | 84 | 2 | 0 | 4 | 1 | 0 | 0 | 3 | 1 | 0 | 0 | 2 | 109 | 0 | 2 | 2 | 0 | 12 | 1 | 21 | 2 | 187 | 16 | 0 | 3 |
AMP PEAK 28(12Q14.1) WILD-TYPE | 284 | 42 | 321 | 265 | 72 | 11 | 380 | 7 | 56 | 159 | 5 | 4 | 13 | 1 | 3 | 2 | 15 | 0 | 1 | 1 | 1 | 206 | 5 | 16 | 2 | 3 | 37 | 9 | 122 | 11 | 365 | 69 | 1 | 17 |
Figure S156. Get High-res Image Gene #28: 'Amp Peak 28(12q14.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D28V6.png)
P value = 9.74e-05 (Fisher's exact test), Q value = 0.12
Table S157. Gene #28: 'Amp Peak 28(12q14.1)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
AMP PEAK 28(12Q14.1) CNV | 150 | 133 | 275 | 96 |
AMP PEAK 28(12Q14.1) WILD-TYPE | 535 | 354 | 601 | 324 |
Figure S157. Get High-res Image Gene #28: 'Amp Peak 28(12q14.1)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D28V10.png)
P value = 3.48e-05 (t-test), Q value = 0.045
Table S158. Gene #29: 'Amp Peak 29(12q15)' versus Clinical Feature #2: 'AGE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 4585 | 61.9 (12.6) |
AMP PEAK 29(12Q15) CNV | 1085 | 63.3 (12.3) |
AMP PEAK 29(12Q15) WILD-TYPE | 3500 | 61.5 (12.7) |
Figure S158. Get High-res Image Gene #29: 'Amp Peak 29(12q15)' versus Clinical Feature #2: 'AGE'
![](D29V2.png)
P value = 1.88e-32 (Chi-square test), Q value = 2.9e-29
Table S159. Gene #29: 'Amp Peak 29(12q15)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 29(12Q15) CNV | 42 | 87 | 219 | 81 | 46 | 62 | 114 | 247 | 2 | 184 | 2 | 19 |
AMP PEAK 29(12Q15) WILD-TYPE | 89 | 457 | 638 | 331 | 408 | 259 | 379 | 467 | 0 | 364 | 0 | 140 |
Figure S159. Get High-res Image Gene #29: 'Amp Peak 29(12q15)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D29V3.png)
P value = 9.77e-22 (Chi-square test), Q value = 1.5e-18
Table S160. Gene #29: 'Amp Peak 29(12q15)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 29(12Q15) CNV | 68 | 12 | 31 | 62 | 35 | 1 | 114 | 4 | 26 | 84 | 2 | 0 | 3 | 1 | 0 | 0 | 4 | 1 | 0 | 0 | 2 | 118 | 0 | 2 | 2 | 0 | 20 | 1 | 17 | 2 | 188 | 13 | 0 | 4 |
AMP PEAK 29(12Q15) WILD-TYPE | 288 | 42 | 320 | 259 | 69 | 11 | 379 | 7 | 53 | 159 | 5 | 4 | 14 | 1 | 3 | 2 | 14 | 0 | 1 | 1 | 1 | 197 | 5 | 16 | 2 | 3 | 29 | 9 | 126 | 11 | 364 | 72 | 1 | 16 |
Figure S160. Get High-res Image Gene #29: 'Amp Peak 29(12q15)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D29V6.png)
P value = 9.9e-07 (Fisher's exact test), Q value = 0.0013
Table S161. Gene #29: 'Amp Peak 29(12q15)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
AMP PEAK 29(12Q15) CNV | 146 | 966 |
AMP PEAK 29(12Q15) WILD-TYPE | 689 | 2850 |
Figure S161. Get High-res Image Gene #29: 'Amp Peak 29(12q15)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D29V11.png)
P value = 5.94e-06 (t-test), Q value = 0.0079
Table S162. Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #2: 'AGE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 4585 | 61.9 (12.6) |
AMP PEAK 30(13Q34) CNV | 954 | 63.5 (12.4) |
AMP PEAK 30(13Q34) WILD-TYPE | 3631 | 61.5 (12.6) |
Figure S162. Get High-res Image Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #2: 'AGE'
![](D30V2.png)
P value = 3.58e-172 (Chi-square test), Q value = 6.1e-169
Table S163. Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 30(13Q34) CNV | 49 | 29 | 143 | 242 | 42 | 59 | 27 | 117 | 1 | 135 | 0 | 112 |
AMP PEAK 30(13Q34) WILD-TYPE | 82 | 515 | 714 | 170 | 412 | 262 | 466 | 597 | 1 | 413 | 2 | 47 |
Figure S163. Get High-res Image Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D30V3.png)
P value = 3.68e-134 (Chi-square test), Q value = 6.3e-131
Table S164. Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 30(13Q34) CNV | 224 | 18 | 13 | 59 | 29 | 0 | 27 | 3 | 13 | 38 | 3 | 0 | 2 | 1 | 0 | 0 | 3 | 1 | 0 | 1 | 0 | 51 | 0 | 2 | 1 | 0 | 14 | 3 | 107 | 4 | 136 | 27 | 0 | 1 |
AMP PEAK 30(13Q34) WILD-TYPE | 132 | 36 | 338 | 262 | 75 | 12 | 466 | 8 | 66 | 205 | 4 | 4 | 15 | 1 | 3 | 2 | 15 | 0 | 1 | 0 | 3 | 264 | 5 | 16 | 3 | 3 | 35 | 7 | 36 | 9 | 416 | 58 | 1 | 19 |
Figure S164. Get High-res Image Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D30V6.png)
P value = 5.87e-27 (Fisher's exact test), Q value = 9e-24
Table S165. Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
AMP PEAK 30(13Q34) CNV | 53 | 144 | 280 | 57 |
AMP PEAK 30(13Q34) WILD-TYPE | 395 | 467 | 408 | 151 |
Figure S165. Get High-res Image Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D30V7.png)
P value = 5.81e-08 (Fisher's exact test), Q value = 8.1e-05
Table S166. Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #8: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 1036 | 343 | 279 | 11 |
AMP PEAK 30(13Q34) CNV | 261 | 134 | 107 | 1 |
AMP PEAK 30(13Q34) WILD-TYPE | 775 | 209 | 172 | 10 |
Figure S166. Get High-res Image Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #8: 'PATHOLOGY.N'
![](D30V8.png)
P value = 3.46e-05 (Chi-square test), Q value = 0.044
Table S167. Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 1398 | 167 | 9 | 1 | 148 |
AMP PEAK 30(13Q34) CNV | 371 | 62 | 8 | 0 | 46 |
AMP PEAK 30(13Q34) WILD-TYPE | 1027 | 105 | 1 | 1 | 102 |
Figure S167. Get High-res Image Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'
![](D30V9.png)
P value = 9.81e-11 (Fisher's exact test), Q value = 1.4e-07
Table S168. Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
AMP PEAK 30(13Q34) CNV | 118 | 159 | 268 | 107 |
AMP PEAK 30(13Q34) WILD-TYPE | 567 | 328 | 608 | 313 |
Figure S168. Get High-res Image Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D30V10.png)
P value = 2.15e-15 (Fisher's exact test), Q value = 3.2e-12
Table S169. Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
AMP PEAK 30(13Q34) CNV | 93 | 871 |
AMP PEAK 30(13Q34) WILD-TYPE | 742 | 2945 |
Figure S169. Get High-res Image Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D30V11.png)
P value = 9.51e-08 (Chi-square test), Q value = 0.00013
Table S170. Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #13: 'TOBACCOSMOKINGHISTORYINDICATOR'
nPatients | 1 | 2 | 3 | 4 | 5 | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER |
---|---|---|---|---|---|---|---|---|---|
ALL | 15 | 16 | 22 | 25 | 2 | 342 | 208 | 237 | 116 |
AMP PEAK 30(13Q34) CNV | 2 | 8 | 9 | 13 | 2 | 52 | 33 | 45 | 26 |
AMP PEAK 30(13Q34) WILD-TYPE | 13 | 8 | 13 | 12 | 0 | 290 | 175 | 192 | 90 |
Figure S170. Get High-res Image Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #13: 'TOBACCOSMOKINGHISTORYINDICATOR'
![](D30V13.png)
P value = 2.86e-06 (Chi-square test), Q value = 0.0038
Table S171. Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #20: 'NEOPLASM.DISEASESTAGE'
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 71 | 45 | 2 | 34 | 246 | 165 | 29 | 107 | 22 | 36 | 35 | 12 |
AMP PEAK 30(13Q34) CNV | 6 | 4 | 0 | 11 | 51 | 21 | 9 | 15 | 1 | 8 | 17 | 3 |
AMP PEAK 30(13Q34) WILD-TYPE | 65 | 41 | 2 | 23 | 195 | 144 | 20 | 92 | 21 | 28 | 18 | 9 |
Figure S171. Get High-res Image Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #20: 'NEOPLASM.DISEASESTAGE'
![](D30V20.png)
P value = 3.33e-93 (Chi-square test), Q value = 5.5e-90
Table S172. Gene #31: 'Amp Peak 31(14q13.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 31(14Q13.3) CNV | 23 | 20 | 169 | 38 | 30 | 91 | 14 | 270 | 1 | 95 | 0 | 12 |
AMP PEAK 31(14Q13.3) WILD-TYPE | 108 | 524 | 688 | 374 | 424 | 230 | 479 | 444 | 1 | 453 | 2 | 147 |
Figure S172. Get High-res Image Gene #31: 'Amp Peak 31(14q13.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D31V3.png)
P value = 1.21e-71 (Chi-square test), Q value = 2e-68
Table S173. Gene #31: 'Amp Peak 31(14q13.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 31(14Q13.3) CNV | 28 | 10 | 14 | 91 | 24 | 1 | 14 | 6 | 27 | 116 | 1 | 1 | 6 | 1 | 2 | 0 | 6 | 1 | 0 | 0 | 2 | 100 | 0 | 1 | 1 | 0 | 11 | 3 | 12 | 0 | 96 | 15 | 1 | 0 |
AMP PEAK 31(14Q13.3) WILD-TYPE | 328 | 44 | 337 | 230 | 80 | 11 | 479 | 5 | 52 | 127 | 6 | 3 | 11 | 1 | 1 | 2 | 12 | 0 | 1 | 1 | 1 | 215 | 5 | 17 | 3 | 3 | 38 | 7 | 131 | 13 | 456 | 70 | 0 | 20 |
Figure S173. Get High-res Image Gene #31: 'Amp Peak 31(14q13.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D31V6.png)
P value = 1.82e-11 (Fisher's exact test), Q value = 2.6e-08
Table S174. Gene #31: 'Amp Peak 31(14q13.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
AMP PEAK 31(14Q13.3) CNV | 75 | 163 | 83 | 54 |
AMP PEAK 31(14Q13.3) WILD-TYPE | 373 | 448 | 605 | 154 |
Figure S174. Get High-res Image Gene #31: 'Amp Peak 31(14q13.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D31V7.png)
P value = 4.45e-08 (Chi-square test), Q value = 6.2e-05
Table S175. Gene #31: 'Amp Peak 31(14q13.3)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 1398 | 167 | 9 | 1 | 148 |
AMP PEAK 31(14Q13.3) CNV | 234 | 14 | 4 | 0 | 49 |
AMP PEAK 31(14Q13.3) WILD-TYPE | 1164 | 153 | 5 | 1 | 99 |
Figure S175. Get High-res Image Gene #31: 'Amp Peak 31(14q13.3)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'
![](D31V9.png)
P value = 2.98e-07 (Fisher's exact test), Q value = 0.00041
Table S176. Gene #31: 'Amp Peak 31(14q13.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
AMP PEAK 31(14Q13.3) CNV | 89 | 674 |
AMP PEAK 31(14Q13.3) WILD-TYPE | 746 | 3142 |
Figure S176. Get High-res Image Gene #31: 'Amp Peak 31(14q13.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D31V11.png)
P value = 1.14e-50 (Chi-square test), Q value = 1.8e-47
Table S177. Gene #32: 'Amp Peak 32(15q26.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 32(15Q26.3) CNV | 20 | 31 | 161 | 26 | 29 | 70 | 24 | 165 | 1 | 153 | 0 | 13 |
AMP PEAK 32(15Q26.3) WILD-TYPE | 111 | 513 | 696 | 386 | 425 | 251 | 469 | 549 | 1 | 395 | 2 | 146 |
Figure S177. Get High-res Image Gene #32: 'Amp Peak 32(15q26.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D32V3.png)
P value = 3.88e-47 (Chi-square test), Q value = 6.2e-44
Table S178. Gene #32: 'Amp Peak 32(15q26.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 32(15Q26.3) CNV | 22 | 4 | 16 | 70 | 23 | 0 | 24 | 1 | 15 | 26 | 4 | 1 | 1 | 0 | 0 | 0 | 4 | 0 | 0 | 0 | 1 | 109 | 0 | 0 | 3 | 0 | 7 | 1 | 11 | 2 | 154 | 13 | 0 | 1 |
AMP PEAK 32(15Q26.3) WILD-TYPE | 334 | 50 | 335 | 251 | 81 | 12 | 469 | 10 | 64 | 217 | 3 | 3 | 16 | 2 | 3 | 2 | 14 | 1 | 1 | 1 | 2 | 206 | 5 | 18 | 1 | 3 | 42 | 9 | 132 | 11 | 398 | 72 | 1 | 19 |
Figure S178. Get High-res Image Gene #32: 'Amp Peak 32(15q26.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D32V6.png)
P value = 1.68e-10 (Fisher's exact test), Q value = 2.4e-07
Table S179. Gene #32: 'Amp Peak 32(15q26.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
AMP PEAK 32(15Q26.3) CNV | 49 | 126 | 60 | 43 |
AMP PEAK 32(15Q26.3) WILD-TYPE | 399 | 485 | 628 | 165 |
Figure S179. Get High-res Image Gene #32: 'Amp Peak 32(15q26.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D32V7.png)
P value = 2.33e-07 (Fisher's exact test), Q value = 0.00032
Table S180. Gene #32: 'Amp Peak 32(15q26.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
AMP PEAK 32(15Q26.3) CNV | 78 | 616 |
AMP PEAK 32(15Q26.3) WILD-TYPE | 757 | 3200 |
Figure S180. Get High-res Image Gene #32: 'Amp Peak 32(15q26.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D32V11.png)
P value = 4.28e-05 (t-test), Q value = 0.055
Table S181. Gene #33: 'Amp Peak 33(17q12)' versus Clinical Feature #2: 'AGE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 4585 | 61.9 (12.6) |
AMP PEAK 33(17Q12) CNV | 988 | 63.3 (12.1) |
AMP PEAK 33(17Q12) WILD-TYPE | 3597 | 61.5 (12.7) |
Figure S181. Get High-res Image Gene #33: 'Amp Peak 33(17q12)' versus Clinical Feature #2: 'AGE'
![](D33V2.png)
P value = 1.47e-88 (Chi-square test), Q value = 2.4e-85
Table S182. Gene #33: 'Amp Peak 33(17q12)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 33(17Q12) CNV | 55 | 48 | 281 | 101 | 57 | 56 | 25 | 284 | 0 | 52 | 0 | 43 |
AMP PEAK 33(17Q12) WILD-TYPE | 76 | 496 | 576 | 311 | 397 | 265 | 468 | 430 | 2 | 496 | 2 | 116 |
Figure S182. Get High-res Image Gene #33: 'Amp Peak 33(17q12)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D33V3.png)
P value = 3.07e-71 (Chi-square test), Q value = 5e-68
Table S183. Gene #33: 'Amp Peak 33(17q12)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 33(17Q12) CNV | 90 | 10 | 16 | 56 | 31 | 2 | 25 | 5 | 39 | 110 | 2 | 1 | 5 | 2 | 1 | 1 | 5 | 1 | 0 | 0 | 2 | 109 | 0 | 3 | 1 | 0 | 21 | 2 | 41 | 2 | 52 | 38 | 0 | 1 |
AMP PEAK 33(17Q12) WILD-TYPE | 266 | 44 | 335 | 265 | 73 | 10 | 468 | 6 | 40 | 133 | 5 | 3 | 12 | 0 | 2 | 1 | 13 | 0 | 1 | 1 | 1 | 206 | 5 | 15 | 3 | 3 | 28 | 8 | 102 | 11 | 500 | 47 | 1 | 19 |
Figure S183. Get High-res Image Gene #33: 'Amp Peak 33(17q12)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D33V6.png)
P value = 1.44e-06 (Fisher's exact test), Q value = 0.0019
Table S184. Gene #33: 'Amp Peak 33(17q12)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
AMP PEAK 33(17Q12) CNV | 79 | 189 | 142 | 48 |
AMP PEAK 33(17Q12) WILD-TYPE | 369 | 422 | 546 | 160 |
Figure S184. Get High-res Image Gene #33: 'Amp Peak 33(17q12)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D33V7.png)
P value = 2.21e-06 (Chi-square test), Q value = 0.003
Table S185. Gene #33: 'Amp Peak 33(17q12)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 1398 | 167 | 9 | 1 | 148 |
AMP PEAK 33(17Q12) CNV | 311 | 38 | 4 | 1 | 61 |
AMP PEAK 33(17Q12) WILD-TYPE | 1087 | 129 | 5 | 0 | 87 |
Figure S185. Get High-res Image Gene #33: 'Amp Peak 33(17q12)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'
![](D33V9.png)
P value = 8.39e-95 (Chi-square test), Q value = 1.4e-91
Table S186. Gene #34: 'Amp Peak 34(17q25.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 34(17Q25.3) CNV | 70 | 67 | 338 | 95 | 72 | 68 | 38 | 346 | 1 | 200 | 1 | 34 |
AMP PEAK 34(17Q25.3) WILD-TYPE | 61 | 477 | 519 | 317 | 382 | 253 | 455 | 368 | 1 | 348 | 1 | 125 |
Figure S186. Get High-res Image Gene #34: 'Amp Peak 34(17q25.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D34V3.png)
P value = 1.85e-74 (Chi-square test), Q value = 3e-71
Table S187. Gene #34: 'Amp Peak 34(17q25.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 34(17Q25.3) CNV | 88 | 6 | 27 | 68 | 46 | 1 | 38 | 4 | 41 | 134 | 3 | 1 | 5 | 2 | 2 | 1 | 7 | 1 | 0 | 0 | 3 | 141 | 1 | 5 | 1 | 0 | 28 | 2 | 33 | 0 | 202 | 40 | 1 | 2 |
AMP PEAK 34(17Q25.3) WILD-TYPE | 268 | 48 | 324 | 253 | 58 | 11 | 455 | 7 | 38 | 109 | 4 | 3 | 12 | 0 | 1 | 1 | 11 | 0 | 1 | 1 | 0 | 174 | 4 | 13 | 3 | 3 | 21 | 8 | 110 | 13 | 350 | 45 | 0 | 18 |
Figure S187. Get High-res Image Gene #34: 'Amp Peak 34(17q25.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D34V6.png)
P value = 1.94e-07 (Fisher's exact test), Q value = 0.00027
Table S188. Gene #34: 'Amp Peak 34(17q25.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
AMP PEAK 34(17Q25.3) CNV | 95 | 213 | 153 | 54 |
AMP PEAK 34(17Q25.3) WILD-TYPE | 353 | 398 | 535 | 154 |
Figure S188. Get High-res Image Gene #34: 'Amp Peak 34(17q25.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D34V7.png)
P value = 5.94e-09 (Chi-square test), Q value = 8.4e-06
Table S189. Gene #34: 'Amp Peak 34(17q25.3)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 1398 | 167 | 9 | 1 | 148 |
AMP PEAK 34(17Q25.3) CNV | 352 | 36 | 4 | 1 | 72 |
AMP PEAK 34(17Q25.3) WILD-TYPE | 1046 | 131 | 5 | 0 | 76 |
Figure S189. Get High-res Image Gene #34: 'Amp Peak 34(17q25.3)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'
![](D34V9.png)
P value = 3.76e-07 (Fisher's exact test), Q value = 0.00052
Table S190. Gene #34: 'Amp Peak 34(17q25.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
AMP PEAK 34(17Q25.3) CNV | 180 | 1152 |
AMP PEAK 34(17Q25.3) WILD-TYPE | 655 | 2664 |
Figure S190. Get High-res Image Gene #34: 'Amp Peak 34(17q25.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D34V11.png)
P value = 1.36e-38 (Chi-square test), Q value = 2.1e-35
Table S191. Gene #35: 'Amp Peak 35(18q11.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 35(18Q11.2) CNV | 29 | 54 | 148 | 20 | 56 | 53 | 25 | 178 | 0 | 132 | 2 | 7 |
AMP PEAK 35(18Q11.2) WILD-TYPE | 102 | 490 | 709 | 392 | 398 | 268 | 468 | 536 | 2 | 416 | 0 | 152 |
Figure S191. Get High-res Image Gene #35: 'Amp Peak 35(18q11.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D35V3.png)
P value = 5.07e-47 (Chi-square test), Q value = 8.1e-44
Table S192. Gene #35: 'Amp Peak 35(18q11.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 35(18Q11.2) CNV | 13 | 7 | 18 | 53 | 21 | 1 | 25 | 5 | 12 | 42 | 3 | 0 | 3 | 2 | 1 | 0 | 5 | 1 | 0 | 0 | 1 | 103 | 0 | 3 | 0 | 0 | 10 | 3 | 6 | 1 | 134 | 35 | 0 | 2 |
AMP PEAK 35(18Q11.2) WILD-TYPE | 343 | 47 | 333 | 268 | 83 | 11 | 468 | 6 | 67 | 201 | 4 | 4 | 14 | 0 | 2 | 2 | 13 | 0 | 1 | 1 | 2 | 212 | 5 | 15 | 4 | 3 | 39 | 7 | 137 | 12 | 418 | 50 | 1 | 18 |
Figure S192. Get High-res Image Gene #35: 'Amp Peak 35(18q11.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D35V6.png)
P value = 6.41e-12 (Fisher's exact test), Q value = 9.3e-09
Table S193. Gene #35: 'Amp Peak 35(18q11.2)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
AMP PEAK 35(18Q11.2) CNV | 59 | 119 | 42 | 29 |
AMP PEAK 35(18Q11.2) WILD-TYPE | 389 | 492 | 646 | 179 |
Figure S193. Get High-res Image Gene #35: 'Amp Peak 35(18q11.2)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D35V7.png)
P value = 1.09e-09 (logrank test), Q value = 1.5e-06
Table S194. Gene #36: 'Amp Peak 36(19p13.2)' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4) |
AMP PEAK 36(19P13.2) CNV | 818 | 338 | 0.1 - 224.0 (14.1) |
AMP PEAK 36(19P13.2) WILD-TYPE | 3552 | 1068 | 0.0 - 223.4 (14.7) |
Figure S194. Get High-res Image Gene #36: 'Amp Peak 36(19p13.2)' versus Clinical Feature #1: 'Time to Death'
![](D36V1.png)
P value = 2.35e-71 (Chi-square test), Q value = 3.8e-68
Table S195. Gene #36: 'Amp Peak 36(19p13.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 36(19P13.2) CNV | 20 | 231 | 144 | 65 | 24 | 37 | 43 | 95 | 0 | 160 | 1 | 32 |
AMP PEAK 36(19P13.2) WILD-TYPE | 111 | 313 | 713 | 347 | 430 | 284 | 450 | 619 | 2 | 388 | 1 | 127 |
Figure S195. Get High-res Image Gene #36: 'Amp Peak 36(19p13.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D36V3.png)
P value = 1.17e-30 (Chi-square test), Q value = 1.8e-27
Table S196. Gene #36: 'Amp Peak 36(19p13.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 36(19P13.2) CNV | 60 | 5 | 11 | 37 | 19 | 1 | 43 | 0 | 7 | 15 | 3 | 0 | 1 | 0 | 1 | 0 | 1 | 1 | 0 | 0 | 0 | 66 | 0 | 3 | 0 | 0 | 8 | 2 | 32 | 0 | 161 | 10 | 1 | 10 |
AMP PEAK 36(19P13.2) WILD-TYPE | 296 | 49 | 340 | 284 | 85 | 11 | 450 | 11 | 72 | 228 | 4 | 4 | 16 | 2 | 2 | 2 | 17 | 0 | 1 | 1 | 3 | 249 | 5 | 15 | 4 | 3 | 41 | 8 | 111 | 13 | 391 | 75 | 0 | 10 |
Figure S196. Get High-res Image Gene #36: 'Amp Peak 36(19p13.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D36V6.png)
P value = 7.78e-09 (Fisher's exact test), Q value = 1.1e-05
Table S197. Gene #36: 'Amp Peak 36(19p13.2)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
AMP PEAK 36(19P13.2) CNV | 70 | 79 | 194 | 68 |
AMP PEAK 36(19P13.2) WILD-TYPE | 615 | 408 | 682 | 352 |
Figure S197. Get High-res Image Gene #36: 'Amp Peak 36(19p13.2)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D36V10.png)
P value = 3.08e-11 (Fisher's exact test), Q value = 4.5e-08
Table S198. Gene #36: 'Amp Peak 36(19p13.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
AMP PEAK 36(19P13.2) CNV | 224 | 633 |
AMP PEAK 36(19P13.2) WILD-TYPE | 611 | 3183 |
Figure S198. Get High-res Image Gene #36: 'Amp Peak 36(19p13.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D36V11.png)
P value = 3.26e-105 (Chi-square test), Q value = 5.4e-102
Table S199. Gene #37: 'Amp Peak 37(19p13.12)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 37(19P13.12) CNV | 21 | 210 | 182 | 65 | 75 | 42 | 43 | 98 | 0 | 299 | 1 | 30 |
AMP PEAK 37(19P13.12) WILD-TYPE | 110 | 334 | 675 | 347 | 379 | 279 | 450 | 616 | 2 | 249 | 1 | 129 |
Figure S199. Get High-res Image Gene #37: 'Amp Peak 37(19p13.12)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D37V3.png)
P value = 3.65e-107 (Chi-square test), Q value = 6.1e-104
Table S200. Gene #37: 'Amp Peak 37(19p13.12)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 37(19P13.12) CNV | 59 | 6 | 24 | 42 | 23 | 1 | 43 | 0 | 5 | 14 | 3 | 0 | 0 | 0 | 1 | 0 | 2 | 1 | 0 | 0 | 0 | 71 | 0 | 6 | 1 | 0 | 8 | 3 | 30 | 0 | 300 | 45 | 1 | 9 |
AMP PEAK 37(19P13.12) WILD-TYPE | 297 | 48 | 327 | 279 | 81 | 11 | 450 | 11 | 74 | 229 | 4 | 4 | 17 | 2 | 2 | 2 | 16 | 0 | 1 | 1 | 3 | 244 | 5 | 12 | 3 | 3 | 41 | 7 | 113 | 13 | 252 | 40 | 0 | 11 |
Figure S200. Get High-res Image Gene #37: 'Amp Peak 37(19p13.12)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D37V6.png)
P value = 8.9e-29 (Fisher's exact test), Q value = 1.4e-25
Table S201. Gene #37: 'Amp Peak 37(19p13.12)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
AMP PEAK 37(19P13.12) CNV | 76 | 92 | 305 | 83 |
AMP PEAK 37(19P13.12) WILD-TYPE | 609 | 395 | 571 | 337 |
Figure S201. Get High-res Image Gene #37: 'Amp Peak 37(19p13.12)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D37V10.png)
P value = 9.43e-05 (Fisher's exact test), Q value = 0.12
Table S202. Gene #37: 'Amp Peak 37(19p13.12)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
AMP PEAK 37(19P13.12) CNV | 236 | 835 |
AMP PEAK 37(19P13.12) WILD-TYPE | 599 | 2981 |
Figure S202. Get High-res Image Gene #37: 'Amp Peak 37(19p13.12)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D37V11.png)
P value = 7.8e-78 (Chi-square test), Q value = 1.3e-74
Table S203. Gene #38: 'Amp Peak 38(19q12)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 38(19Q12) CNV | 56 | 195 | 218 | 83 | 84 | 44 | 51 | 245 | 0 | 303 | 2 | 38 |
AMP PEAK 38(19Q12) WILD-TYPE | 75 | 349 | 639 | 329 | 370 | 277 | 442 | 469 | 2 | 245 | 0 | 121 |
Figure S203. Get High-res Image Gene #38: 'Amp Peak 38(19q12)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D38V3.png)
P value = 7.99e-96 (Chi-square test), Q value = 1.3e-92
Table S204. Gene #38: 'Amp Peak 38(19q12)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 38(19Q12) CNV | 76 | 7 | 18 | 44 | 33 | 2 | 51 | 5 | 24 | 62 | 5 | 0 | 6 | 1 | 1 | 0 | 8 | 1 | 0 | 0 | 1 | 129 | 0 | 9 | 2 | 0 | 22 | 3 | 38 | 0 | 305 | 57 | 1 | 8 |
AMP PEAK 38(19Q12) WILD-TYPE | 280 | 47 | 333 | 277 | 71 | 10 | 442 | 6 | 55 | 181 | 2 | 4 | 11 | 1 | 2 | 2 | 10 | 0 | 1 | 1 | 2 | 186 | 5 | 9 | 2 | 3 | 27 | 7 | 105 | 13 | 247 | 28 | 0 | 12 |
Figure S204. Get High-res Image Gene #38: 'Amp Peak 38(19q12)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D38V6.png)
P value = 3.69e-06 (Fisher's exact test), Q value = 0.0049
Table S205. Gene #38: 'Amp Peak 38(19q12)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
AMP PEAK 38(19Q12) CNV | 68 | 172 | 136 | 41 |
AMP PEAK 38(19Q12) WILD-TYPE | 380 | 439 | 552 | 167 |
Figure S205. Get High-res Image Gene #38: 'Amp Peak 38(19q12)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D38V7.png)
P value = 7.63e-17 (Fisher's exact test), Q value = 1.1e-13
Table S206. Gene #38: 'Amp Peak 38(19q12)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
AMP PEAK 38(19Q12) CNV | 142 | 125 | 347 | 99 |
AMP PEAK 38(19Q12) WILD-TYPE | 543 | 362 | 529 | 321 |
Figure S206. Get High-res Image Gene #38: 'Amp Peak 38(19q12)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D38V10.png)
P value = 0.00019 (logrank test), Q value = 0.23
Table S207. Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4) |
AMP PEAK 39(20Q11.21) CNV | 2002 | 670 | 0.0 - 224.0 (13.0) |
AMP PEAK 39(20Q11.21) WILD-TYPE | 2368 | 736 | 0.0 - 223.4 (15.5) |
Figure S207. Get High-res Image Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #1: 'Time to Death'
![](D39V1.png)
P value = 1.91e-15 (t-test), Q value = 2.8e-12
Table S208. Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #2: 'AGE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 4585 | 61.9 (12.6) |
AMP PEAK 39(20Q11.21) CNV | 2146 | 63.5 (12.1) |
AMP PEAK 39(20Q11.21) WILD-TYPE | 2439 | 60.5 (12.9) |
Figure S208. Get High-res Image Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #2: 'AGE'
![](D39V2.png)
P value = 4.96e-100 (Chi-square test), Q value = 8.2e-97
Table S209. Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 39(20Q11.21) CNV | 92 | 211 | 369 | 295 | 116 | 147 | 109 | 363 | 1 | 320 | 1 | 141 |
AMP PEAK 39(20Q11.21) WILD-TYPE | 39 | 333 | 488 | 117 | 338 | 174 | 384 | 351 | 1 | 228 | 1 | 18 |
Figure S209. Get High-res Image Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D39V3.png)
P value = 8.43e-05 (Fisher's exact test), Q value = 0.11
Table S210. Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
AMP PEAK 39(20Q11.21) CNV | 1301 | 867 |
AMP PEAK 39(20Q11.21) WILD-TYPE | 1623 | 850 |
Figure S210. Get High-res Image Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #4: 'GENDER'
![](D39V4.png)
P value = 3.74e-112 (Chi-square test), Q value = 6.3e-109
Table S211. Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 39(20Q11.21) CNV | 269 | 24 | 48 | 147 | 50 | 1 | 109 | 5 | 27 | 119 | 6 | 1 | 7 | 0 | 2 | 0 | 6 | 0 | 0 | 0 | 2 | 187 | 0 | 6 | 1 | 0 | 34 | 2 | 132 | 7 | 322 | 62 | 1 | 7 |
AMP PEAK 39(20Q11.21) WILD-TYPE | 87 | 30 | 303 | 174 | 54 | 11 | 384 | 6 | 52 | 124 | 1 | 3 | 10 | 2 | 1 | 2 | 12 | 1 | 1 | 1 | 1 | 128 | 5 | 12 | 3 | 3 | 15 | 8 | 11 | 6 | 230 | 23 | 0 | 13 |
Figure S211. Get High-res Image Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D39V6.png)
P value = 1.33e-23 (Fisher's exact test), Q value = 2e-20
Table S212. Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
AMP PEAK 39(20Q11.21) CNV | 133 | 329 | 415 | 110 |
AMP PEAK 39(20Q11.21) WILD-TYPE | 315 | 282 | 273 | 98 |
Figure S212. Get High-res Image Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D39V7.png)
P value = 1.18e-05 (Fisher's exact test), Q value = 0.016
Table S213. Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #8: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 1036 | 343 | 279 | 11 |
AMP PEAK 39(20Q11.21) CNV | 525 | 224 | 160 | 4 |
AMP PEAK 39(20Q11.21) WILD-TYPE | 511 | 119 | 119 | 7 |
Figure S213. Get High-res Image Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #8: 'PATHOLOGY.N'
![](D39V8.png)
P value = 7.69e-10 (Fisher's exact test), Q value = 1.1e-06
Table S214. Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
AMP PEAK 39(20Q11.21) CNV | 285 | 272 | 508 | 214 |
AMP PEAK 39(20Q11.21) WILD-TYPE | 400 | 215 | 368 | 206 |
Figure S214. Get High-res Image Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D39V10.png)
P value = 1.76e-05 (Fisher's exact test), Q value = 0.023
Table S215. Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
AMP PEAK 39(20Q11.21) CNV | 334 | 1840 |
AMP PEAK 39(20Q11.21) WILD-TYPE | 501 | 1976 |
Figure S215. Get High-res Image Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D39V11.png)
P value = 2.73e-08 (t-test), Q value = 3.8e-05
Table S216. Gene #40: 'Amp Peak 40(20q13.2)' versus Clinical Feature #2: 'AGE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 4585 | 61.9 (12.6) |
AMP PEAK 40(20Q13.2) CNV | 2228 | 63.0 (12.2) |
AMP PEAK 40(20Q13.2) WILD-TYPE | 2357 | 60.9 (12.9) |
Figure S216. Get High-res Image Gene #40: 'Amp Peak 40(20q13.2)' versus Clinical Feature #2: 'AGE'
![](D40V2.png)
P value = 3.02e-111 (Chi-square test), Q value = 5.1e-108
Table S217. Gene #40: 'Amp Peak 40(20q13.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 40(20Q13.2) CNV | 86 | 206 | 447 | 299 | 122 | 123 | 111 | 343 | 1 | 367 | 2 | 141 |
AMP PEAK 40(20Q13.2) WILD-TYPE | 45 | 338 | 410 | 113 | 332 | 198 | 382 | 371 | 1 | 181 | 0 | 18 |
Figure S217. Get High-res Image Gene #40: 'Amp Peak 40(20q13.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D40V3.png)
P value = 2.81e-119 (Chi-square test), Q value = 4.7e-116
Table S218. Gene #40: 'Amp Peak 40(20q13.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 40(20Q13.2) CNV | 273 | 24 | 54 | 123 | 61 | 1 | 111 | 8 | 33 | 121 | 5 | 1 | 7 | 1 | 2 | 0 | 7 | 0 | 0 | 1 | 3 | 154 | 1 | 6 | 0 | 0 | 31 | 3 | 132 | 7 | 370 | 62 | 1 | 6 |
AMP PEAK 40(20Q13.2) WILD-TYPE | 83 | 30 | 297 | 198 | 43 | 11 | 382 | 3 | 46 | 122 | 2 | 3 | 10 | 1 | 1 | 2 | 11 | 1 | 1 | 0 | 0 | 161 | 4 | 12 | 4 | 3 | 18 | 7 | 11 | 6 | 182 | 23 | 0 | 14 |
Figure S218. Get High-res Image Gene #40: 'Amp Peak 40(20q13.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D40V6.png)
P value = 1.02e-23 (Fisher's exact test), Q value = 1.6e-20
Table S219. Gene #40: 'Amp Peak 40(20q13.2)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
AMP PEAK 40(20Q13.2) CNV | 130 | 303 | 415 | 108 |
AMP PEAK 40(20Q13.2) WILD-TYPE | 318 | 308 | 273 | 100 |
Figure S219. Get High-res Image Gene #40: 'Amp Peak 40(20q13.2)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D40V7.png)
P value = 0.000166 (Chi-square test), Q value = 0.21
Table S220. Gene #40: 'Amp Peak 40(20q13.2)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 1398 | 167 | 9 | 1 | 148 |
AMP PEAK 40(20Q13.2) CNV | 668 | 97 | 9 | 0 | 88 |
AMP PEAK 40(20Q13.2) WILD-TYPE | 730 | 70 | 0 | 1 | 60 |
Figure S220. Get High-res Image Gene #40: 'Amp Peak 40(20q13.2)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'
![](D40V9.png)
P value = 3.26e-13 (Fisher's exact test), Q value = 4.8e-10
Table S221. Gene #40: 'Amp Peak 40(20q13.2)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
AMP PEAK 40(20Q13.2) CNV | 280 | 265 | 531 | 220 |
AMP PEAK 40(20Q13.2) WILD-TYPE | 405 | 222 | 345 | 200 |
Figure S221. Get High-res Image Gene #40: 'Amp Peak 40(20q13.2)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D40V10.png)
P value = 6.37e-06 (Fisher's exact test), Q value = 0.0085
Table S222. Gene #40: 'Amp Peak 40(20q13.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
AMP PEAK 40(20Q13.2) CNV | 346 | 1910 |
AMP PEAK 40(20Q13.2) WILD-TYPE | 489 | 1906 |
Figure S222. Get High-res Image Gene #40: 'Amp Peak 40(20q13.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D40V11.png)
P value = 2.19e-57 (Chi-square test), Q value = 3.5e-54
Table S223. Gene #41: 'Amp Peak 41(Xq28)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
AMP PEAK 41(XQ28) CNV | 25 | 30 | 167 | 82 | 75 | 97 | 38 | 207 | 0 | 217 | 1 | 36 |
AMP PEAK 41(XQ28) WILD-TYPE | 106 | 514 | 690 | 330 | 379 | 224 | 455 | 507 | 2 | 331 | 1 | 123 |
Figure S223. Get High-res Image Gene #41: 'Amp Peak 41(Xq28)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D41V3.png)
P value = 4.22e-30 (Chi-square test), Q value = 6.5e-27
Table S224. Gene #41: 'Amp Peak 41(Xq28)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
AMP PEAK 41(XQ28) CNV | 77 | 5 | 46 | 97 | 25 | 1 | 38 | 4 | 24 | 85 | 2 | 1 | 3 | 1 | 1 | 0 | 5 | 1 | 0 | 0 | 0 | 80 | 1 | 2 | 0 | 0 | 11 | 1 | 34 | 1 | 218 | 27 | 0 | 1 |
AMP PEAK 41(XQ28) WILD-TYPE | 279 | 49 | 305 | 224 | 79 | 11 | 455 | 7 | 55 | 158 | 5 | 3 | 14 | 1 | 2 | 2 | 13 | 0 | 1 | 1 | 3 | 235 | 4 | 16 | 4 | 3 | 38 | 9 | 109 | 12 | 334 | 58 | 1 | 19 |
Figure S224. Get High-res Image Gene #41: 'Amp Peak 41(Xq28)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D41V6.png)
P value = 2.67e-08 (Fisher's exact test), Q value = 3.7e-05
Table S225. Gene #41: 'Amp Peak 41(Xq28)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
AMP PEAK 41(XQ28) CNV | 57 | 167 | 144 | 56 |
AMP PEAK 41(XQ28) WILD-TYPE | 391 | 444 | 544 | 152 |
Figure S225. Get High-res Image Gene #41: 'Amp Peak 41(Xq28)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D41V7.png)
P value = 8.82e-05 (Fisher's exact test), Q value = 0.11
Table S226. Gene #41: 'Amp Peak 41(Xq28)' versus Clinical Feature #8: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 1036 | 343 | 279 | 11 |
AMP PEAK 41(XQ28) CNV | 212 | 93 | 92 | 2 |
AMP PEAK 41(XQ28) WILD-TYPE | 824 | 250 | 187 | 9 |
Figure S226. Get High-res Image Gene #41: 'Amp Peak 41(Xq28)' versus Clinical Feature #8: 'PATHOLOGY.N'
![](D41V8.png)
P value = 2.91e-07 (Fisher's exact test), Q value = 4e-04
Table S227. Gene #41: 'Amp Peak 41(Xq28)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
AMP PEAK 41(XQ28) CNV | 125 | 120 | 255 | 131 |
AMP PEAK 41(XQ28) WILD-TYPE | 560 | 367 | 621 | 289 |
Figure S227. Get High-res Image Gene #41: 'Amp Peak 41(Xq28)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D41V10.png)
P value = 8.82e-39 (Chi-square test), Q value = 1.4e-35
Table S228. Gene #42: 'Del Peak 1(1p36.23)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 1(1P36.23) CNV | 22 | 129 | 352 | 135 | 55 | 65 | 97 | 223 | 2 | 200 | 0 | 65 |
DEL PEAK 1(1P36.23) WILD-TYPE | 109 | 415 | 505 | 277 | 399 | 256 | 396 | 491 | 0 | 348 | 2 | 94 |
Figure S228. Get High-res Image Gene #42: 'Del Peak 1(1p36.23)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D42V3.png)
P value = 3.35e-32 (Chi-square test), Q value = 5.2e-29
Table S229. Gene #42: 'Del Peak 1(1p36.23)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 1(1P36.23) CNV | 125 | 10 | 23 | 65 | 45 | 5 | 97 | 3 | 21 | 53 | 4 | 0 | 3 | 1 | 0 | 0 | 1 | 1 | 0 | 1 | 0 | 134 | 1 | 4 | 1 | 0 | 7 | 5 | 57 | 7 | 202 | 28 | 0 | 6 |
DEL PEAK 1(1P36.23) WILD-TYPE | 231 | 44 | 328 | 256 | 59 | 7 | 396 | 8 | 58 | 190 | 3 | 4 | 14 | 1 | 3 | 2 | 17 | 0 | 1 | 0 | 3 | 181 | 4 | 14 | 3 | 3 | 42 | 5 | 86 | 6 | 350 | 57 | 1 | 14 |
Figure S229. Get High-res Image Gene #42: 'Del Peak 1(1p36.23)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D42V6.png)
P value = 2.35e-75 (Chi-square test), Q value = 3.8e-72
Table S230. Gene #43: 'Del Peak 2(1p36.11)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 2(1P36.11) CNV | 25 | 47 | 357 | 150 | 63 | 64 | 95 | 245 | 1 | 255 | 0 | 69 |
DEL PEAK 2(1P36.11) WILD-TYPE | 106 | 497 | 500 | 262 | 391 | 257 | 398 | 469 | 1 | 293 | 2 | 90 |
Figure S230. Get High-res Image Gene #43: 'Del Peak 2(1p36.11)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D43V3.png)
P value = 1.16e-45 (Chi-square test), Q value = 1.8e-42
Table S231. Gene #43: 'Del Peak 2(1p36.11)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 2(1P36.11) CNV | 139 | 10 | 24 | 64 | 46 | 5 | 95 | 5 | 22 | 63 | 3 | 0 | 3 | 1 | 0 | 0 | 2 | 1 | 0 | 1 | 1 | 142 | 1 | 4 | 1 | 0 | 11 | 4 | 61 | 7 | 256 | 35 | 0 | 3 |
DEL PEAK 2(1P36.11) WILD-TYPE | 217 | 44 | 327 | 257 | 58 | 7 | 398 | 6 | 57 | 180 | 4 | 4 | 14 | 1 | 3 | 2 | 16 | 0 | 1 | 0 | 2 | 173 | 4 | 14 | 3 | 3 | 38 | 6 | 82 | 6 | 296 | 50 | 1 | 17 |
Figure S231. Get High-res Image Gene #43: 'Del Peak 2(1p36.11)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D43V6.png)
P value = 1.02e-05 (Fisher's exact test), Q value = 0.014
Table S232. Gene #43: 'Del Peak 2(1p36.11)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 2(1P36.11) CNV | 193 | 149 | 348 | 147 |
DEL PEAK 2(1P36.11) WILD-TYPE | 492 | 338 | 528 | 273 |
Figure S232. Get High-res Image Gene #43: 'Del Peak 2(1p36.11)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D43V10.png)
P value = 2.95e-10 (Fisher's exact test), Q value = 4.2e-07
Table S233. Gene #43: 'Del Peak 2(1p36.11)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
DEL PEAK 2(1P36.11) CNV | 173 | 1202 |
DEL PEAK 2(1P36.11) WILD-TYPE | 662 | 2614 |
Figure S233. Get High-res Image Gene #43: 'Del Peak 2(1p36.11)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D43V11.png)
P value = 0.000119 (Chi-square test), Q value = 0.15
Table S234. Gene #43: 'Del Peak 2(1p36.11)' versus Clinical Feature #13: 'TOBACCOSMOKINGHISTORYINDICATOR'
nPatients | 1 | 2 | 3 | 4 | 5 | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER |
---|---|---|---|---|---|---|---|---|---|
ALL | 15 | 16 | 22 | 25 | 2 | 342 | 208 | 237 | 116 |
DEL PEAK 2(1P36.11) CNV | 1 | 3 | 7 | 3 | 0 | 122 | 57 | 86 | 18 |
DEL PEAK 2(1P36.11) WILD-TYPE | 14 | 13 | 15 | 22 | 2 | 220 | 151 | 151 | 98 |
Figure S234. Get High-res Image Gene #43: 'Del Peak 2(1p36.11)' versus Clinical Feature #13: 'TOBACCOSMOKINGHISTORYINDICATOR'
![](D43V13.png)
P value = 4.02e-05 (t-test), Q value = 0.051
Table S235. Gene #43: 'Del Peak 2(1p36.11)' versus Clinical Feature #18: 'NUMBER.OF.LYMPH.NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 1592 | 2.3 (4.6) |
DEL PEAK 2(1P36.11) CNV | 573 | 3.0 (5.8) |
DEL PEAK 2(1P36.11) WILD-TYPE | 1019 | 1.9 (3.7) |
Figure S235. Get High-res Image Gene #43: 'Del Peak 2(1p36.11)' versus Clinical Feature #18: 'NUMBER.OF.LYMPH.NODES'
![](D43V18.png)
P value = 5.18e-05 (Chi-square test), Q value = 0.066
Table S236. Gene #43: 'Del Peak 2(1p36.11)' versus Clinical Feature #20: 'NEOPLASM.DISEASESTAGE'
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 71 | 45 | 2 | 34 | 246 | 165 | 29 | 107 | 22 | 36 | 35 | 12 |
DEL PEAK 2(1P36.11) CNV | 18 | 12 | 1 | 4 | 102 | 72 | 7 | 54 | 14 | 16 | 9 | 6 |
DEL PEAK 2(1P36.11) WILD-TYPE | 53 | 33 | 1 | 30 | 144 | 93 | 22 | 53 | 8 | 20 | 26 | 6 |
Figure S236. Get High-res Image Gene #43: 'Del Peak 2(1p36.11)' versus Clinical Feature #20: 'NEOPLASM.DISEASESTAGE'
![](D43V20.png)
P value = 2.26e-05 (t-test), Q value = 0.029
Table S237. Gene #44: 'Del Peak 3(1p13.2)' versus Clinical Feature #2: 'AGE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 4585 | 61.9 (12.6) |
DEL PEAK 3(1P13.2) CNV | 964 | 63.4 (12.1) |
DEL PEAK 3(1P13.2) WILD-TYPE | 3621 | 61.5 (12.7) |
Figure S237. Get High-res Image Gene #44: 'Del Peak 3(1p13.2)' versus Clinical Feature #2: 'AGE'
![](D44V2.png)
P value = 1.18e-68 (Chi-square test), Q value = 1.9e-65
Table S238. Gene #44: 'Del Peak 3(1p13.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 3(1P13.2) CNV | 19 | 23 | 252 | 107 | 25 | 78 | 59 | 261 | 0 | 97 | 1 | 51 |
DEL PEAK 3(1P13.2) WILD-TYPE | 112 | 521 | 605 | 305 | 429 | 243 | 434 | 453 | 2 | 451 | 1 | 108 |
Figure S238. Get High-res Image Gene #44: 'Del Peak 3(1p13.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D44V3.png)
P value = 3.6e-38 (Chi-square test), Q value = 5.7e-35
Table S239. Gene #44: 'Del Peak 3(1p13.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 3(1P13.2) CNV | 98 | 9 | 11 | 78 | 34 | 3 | 59 | 5 | 26 | 68 | 3 | 1 | 6 | 1 | 0 | 0 | 6 | 1 | 0 | 0 | 1 | 141 | 1 | 3 | 1 | 1 | 9 | 2 | 48 | 2 | 98 | 11 | 0 | 0 |
DEL PEAK 3(1P13.2) WILD-TYPE | 258 | 45 | 340 | 243 | 70 | 9 | 434 | 6 | 53 | 175 | 4 | 3 | 11 | 1 | 3 | 2 | 12 | 0 | 1 | 1 | 2 | 174 | 4 | 15 | 3 | 2 | 40 | 8 | 95 | 11 | 454 | 74 | 1 | 20 |
Figure S239. Get High-res Image Gene #44: 'Del Peak 3(1p13.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D44V6.png)
P value = 1.14e-11 (Fisher's exact test), Q value = 1.7e-08
Table S240. Gene #44: 'Del Peak 3(1p13.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
DEL PEAK 3(1P13.2) CNV | 106 | 872 |
DEL PEAK 3(1P13.2) WILD-TYPE | 729 | 2944 |
Figure S240. Get High-res Image Gene #44: 'Del Peak 3(1p13.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D44V11.png)
P value = 8.76e-05 (Chi-square test), Q value = 0.11
Table S241. Gene #44: 'Del Peak 3(1p13.2)' versus Clinical Feature #13: 'TOBACCOSMOKINGHISTORYINDICATOR'
nPatients | 1 | 2 | 3 | 4 | 5 | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER |
---|---|---|---|---|---|---|---|---|---|
ALL | 15 | 16 | 22 | 25 | 2 | 342 | 208 | 237 | 116 |
DEL PEAK 3(1P13.2) CNV | 1 | 2 | 3 | 4 | 0 | 134 | 61 | 89 | 25 |
DEL PEAK 3(1P13.2) WILD-TYPE | 14 | 14 | 19 | 21 | 2 | 208 | 147 | 148 | 91 |
Figure S241. Get High-res Image Gene #44: 'Del Peak 3(1p13.2)' versus Clinical Feature #13: 'TOBACCOSMOKINGHISTORYINDICATOR'
![](D44V13.png)
P value = 0.000101 (t-test), Q value = 0.13
Table S242. Gene #44: 'Del Peak 3(1p13.2)' versus Clinical Feature #18: 'NUMBER.OF.LYMPH.NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 1592 | 2.3 (4.6) |
DEL PEAK 3(1P13.2) CNV | 426 | 3.1 (5.5) |
DEL PEAK 3(1P13.2) WILD-TYPE | 1166 | 1.9 (4.2) |
Figure S242. Get High-res Image Gene #44: 'Del Peak 3(1p13.2)' versus Clinical Feature #18: 'NUMBER.OF.LYMPH.NODES'
![](D44V18.png)
P value = 1.6e-44 (Chi-square test), Q value = 2.5e-41
Table S243. Gene #45: 'Del Peak 4(2q22.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 4(2Q22.1) CNV | 40 | 43 | 195 | 24 | 35 | 65 | 19 | 130 | 0 | 128 | 1 | 10 |
DEL PEAK 4(2Q22.1) WILD-TYPE | 91 | 501 | 662 | 388 | 419 | 256 | 474 | 584 | 2 | 420 | 1 | 149 |
Figure S243. Get High-res Image Gene #45: 'Del Peak 4(2q22.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D45V3.png)
P value = 1.03e-36 (Chi-square test), Q value = 1.6e-33
Table S244. Gene #45: 'Del Peak 4(2q22.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 4(2Q22.1) CNV | 22 | 2 | 15 | 65 | 25 | 2 | 19 | 4 | 7 | 24 | 0 | 0 | 3 | 0 | 0 | 0 | 4 | 1 | 0 | 1 | 0 | 85 | 0 | 1 | 1 | 0 | 16 | 2 | 9 | 0 | 129 | 19 | 0 | 1 |
DEL PEAK 4(2Q22.1) WILD-TYPE | 334 | 52 | 336 | 256 | 79 | 10 | 474 | 7 | 72 | 219 | 7 | 4 | 14 | 2 | 3 | 2 | 14 | 0 | 1 | 0 | 3 | 230 | 5 | 17 | 3 | 3 | 33 | 8 | 134 | 13 | 423 | 66 | 1 | 19 |
Figure S244. Get High-res Image Gene #45: 'Del Peak 4(2q22.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D45V6.png)
P value = 1.24e-05 (Fisher's exact test), Q value = 0.016
Table S245. Gene #45: 'Del Peak 4(2q22.1)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 4(2Q22.1) CNV | 39 | 93 | 58 | 37 |
DEL PEAK 4(2Q22.1) WILD-TYPE | 409 | 518 | 630 | 171 |
Figure S245. Get High-res Image Gene #45: 'Del Peak 4(2q22.1)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D45V7.png)
P value = 1.08e-05 (Fisher's exact test), Q value = 0.014
Table S246. Gene #45: 'Del Peak 4(2q22.1)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 4(2Q22.1) CNV | 62 | 72 | 155 | 66 |
DEL PEAK 4(2Q22.1) WILD-TYPE | 623 | 415 | 721 | 354 |
Figure S246. Get High-res Image Gene #45: 'Del Peak 4(2q22.1)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D45V10.png)
P value = 3.31e-67 (Chi-square test), Q value = 5.4e-64
Table S247. Gene #46: 'Del Peak 5(2q37.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 5(2Q37.3) CNV | 63 | 58 | 255 | 21 | 43 | 92 | 47 | 160 | 1 | 169 | 1 | 12 |
DEL PEAK 5(2Q37.3) WILD-TYPE | 68 | 486 | 602 | 391 | 411 | 229 | 446 | 554 | 1 | 379 | 1 | 147 |
Figure S247. Get High-res Image Gene #46: 'Del Peak 5(2q37.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D46V3.png)
P value = 2.82e-45 (Chi-square test), Q value = 4.5e-42
Table S248. Gene #46: 'Del Peak 5(2q37.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 5(2Q37.3) CNV | 19 | 1 | 24 | 92 | 38 | 2 | 47 | 3 | 7 | 35 | 2 | 0 | 5 | 1 | 0 | 0 | 5 | 1 | 0 | 0 | 0 | 100 | 0 | 2 | 1 | 0 | 20 | 3 | 11 | 0 | 171 | 17 | 0 | 2 |
DEL PEAK 5(2Q37.3) WILD-TYPE | 337 | 53 | 327 | 229 | 66 | 10 | 446 | 8 | 72 | 208 | 5 | 4 | 12 | 1 | 3 | 2 | 13 | 0 | 1 | 1 | 3 | 215 | 5 | 16 | 3 | 3 | 29 | 7 | 132 | 13 | 381 | 68 | 1 | 18 |
Figure S248. Get High-res Image Gene #46: 'Del Peak 5(2q37.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D46V6.png)
P value = 2.28e-06 (Chi-square test), Q value = 0.0031
Table S249. Gene #46: 'Del Peak 5(2q37.3)' versus Clinical Feature #13: 'TOBACCOSMOKINGHISTORYINDICATOR'
nPatients | 1 | 2 | 3 | 4 | 5 | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER |
---|---|---|---|---|---|---|---|---|---|
ALL | 15 | 16 | 22 | 25 | 2 | 342 | 208 | 237 | 116 |
DEL PEAK 5(2Q37.3) CNV | 9 | 6 | 11 | 14 | 2 | 86 | 40 | 77 | 29 |
DEL PEAK 5(2Q37.3) WILD-TYPE | 6 | 10 | 11 | 11 | 0 | 256 | 168 | 160 | 87 |
Figure S249. Get High-res Image Gene #46: 'Del Peak 5(2q37.3)' versus Clinical Feature #13: 'TOBACCOSMOKINGHISTORYINDICATOR'
![](D46V13.png)
P value = 0 (Chi-square test), Q value = 0
Table S250. Gene #47: 'Del Peak 6(3p25.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 6(3P25.3) CNV | 25 | 42 | 138 | 60 | 48 | 227 | 432 | 435 | 2 | 196 | 0 | 19 |
DEL PEAK 6(3P25.3) WILD-TYPE | 106 | 502 | 719 | 352 | 406 | 94 | 61 | 279 | 0 | 352 | 2 | 140 |
Figure S250. Get High-res Image Gene #47: 'Del Peak 6(3p25.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D47V3.png)
P value = 1.72e-36 (Fisher's exact test), Q value = 2.7e-33
Table S251. Gene #47: 'Del Peak 6(3p25.3)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
DEL PEAK 6(3P25.3) CNV | 825 | 801 |
DEL PEAK 6(3P25.3) WILD-TYPE | 2099 | 916 |
Figure S251. Get High-res Image Gene #47: 'Del Peak 6(3p25.3)' versus Clinical Feature #4: 'GENDER'
![](D47V4.png)
P value = 5.86e-225 (Chi-square test), Q value = 1e-221
Table S252. Gene #47: 'Del Peak 6(3p25.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 6(3P25.3) CNV | 56 | 4 | 16 | 227 | 18 | 0 | 432 | 5 | 35 | 114 | 6 | 0 | 7 | 1 | 2 | 0 | 8 | 1 | 0 | 1 | 1 | 251 | 1 | 6 | 2 | 1 | 10 | 2 | 15 | 3 | 198 | 26 | 0 | 2 |
DEL PEAK 6(3P25.3) WILD-TYPE | 300 | 50 | 335 | 94 | 86 | 12 | 61 | 6 | 44 | 129 | 1 | 4 | 10 | 1 | 1 | 2 | 10 | 0 | 1 | 0 | 2 | 64 | 4 | 12 | 2 | 2 | 39 | 8 | 128 | 10 | 354 | 59 | 1 | 18 |
Figure S252. Get High-res Image Gene #47: 'Del Peak 6(3p25.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D47V6.png)
P value = 2.3e-21 (Fisher's exact test), Q value = 3.5e-18
Table S253. Gene #47: 'Del Peak 6(3p25.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 6(3P25.3) CNV | 334 | 340 | 310 | 118 |
DEL PEAK 6(3P25.3) WILD-TYPE | 114 | 271 | 378 | 90 |
Figure S253. Get High-res Image Gene #47: 'Del Peak 6(3p25.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D47V7.png)
P value = 1.54e-14 (Fisher's exact test), Q value = 2.3e-11
Table S254. Gene #47: 'Del Peak 6(3p25.3)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 6(3P25.3) CNV | 425 | 206 | 408 | 252 |
DEL PEAK 6(3P25.3) WILD-TYPE | 260 | 281 | 468 | 168 |
Figure S254. Get High-res Image Gene #47: 'Del Peak 6(3p25.3)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D47V10.png)
P value = 2.46e-27 (Fisher's exact test), Q value = 3.8e-24
Table S255. Gene #47: 'Del Peak 6(3p25.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
DEL PEAK 6(3P25.3) CNV | 162 | 1468 |
DEL PEAK 6(3P25.3) WILD-TYPE | 673 | 2348 |
Figure S255. Get High-res Image Gene #47: 'Del Peak 6(3p25.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D47V11.png)
P value = 8.43e-18 (Chi-square test), Q value = 1.3e-14
Table S256. Gene #47: 'Del Peak 6(3p25.3)' versus Clinical Feature #13: 'TOBACCOSMOKINGHISTORYINDICATOR'
nPatients | 1 | 2 | 3 | 4 | 5 | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER |
---|---|---|---|---|---|---|---|---|---|
ALL | 15 | 16 | 22 | 25 | 2 | 342 | 208 | 237 | 116 |
DEL PEAK 6(3P25.3) CNV | 0 | 4 | 5 | 4 | 1 | 240 | 119 | 174 | 63 |
DEL PEAK 6(3P25.3) WILD-TYPE | 15 | 12 | 17 | 21 | 1 | 102 | 89 | 63 | 53 |
Figure S256. Get High-res Image Gene #47: 'Del Peak 6(3p25.3)' versus Clinical Feature #13: 'TOBACCOSMOKINGHISTORYINDICATOR'
![](D47V13.png)
P value = 2.82e-247 (Chi-square test), Q value = 4.9e-244
Table S257. Gene #48: 'Del Peak 7(3p14.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 7(3P14.2) CNV | 43 | 51 | 260 | 75 | 59 | 242 | 387 | 456 | 1 | 162 | 0 | 27 |
DEL PEAK 7(3P14.2) WILD-TYPE | 88 | 493 | 597 | 337 | 395 | 79 | 106 | 258 | 1 | 386 | 2 | 132 |
Figure S257. Get High-res Image Gene #48: 'Del Peak 7(3p14.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D48V3.png)
P value = 3.08e-34 (Fisher's exact test), Q value = 4.8e-31
Table S258. Gene #48: 'Del Peak 7(3p14.2)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
DEL PEAK 7(3P14.2) CNV | 916 | 849 |
DEL PEAK 7(3P14.2) WILD-TYPE | 2008 | 868 |
Figure S258. Get High-res Image Gene #48: 'Del Peak 7(3p14.2)' versus Clinical Feature #4: 'GENDER'
![](D48V4.png)
P value = 2.12e-05 (t-test), Q value = 0.028
Table S259. Gene #48: 'Del Peak 7(3p14.2)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 641 | 73.6 (23.9) |
DEL PEAK 7(3P14.2) CNV | 161 | 64.1 (35.4) |
DEL PEAK 7(3P14.2) WILD-TYPE | 480 | 76.8 (17.5) |
Figure S259. Get High-res Image Gene #48: 'Del Peak 7(3p14.2)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'
![](D48V5.png)
P value = 1.54e-199 (Chi-square test), Q value = 2.7e-196
Table S260. Gene #48: 'Del Peak 7(3p14.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 7(3P14.2) CNV | 69 | 6 | 19 | 242 | 39 | 0 | 387 | 4 | 39 | 115 | 6 | 0 | 6 | 1 | 1 | 0 | 7 | 1 | 0 | 1 | 1 | 270 | 0 | 6 | 3 | 1 | 16 | 4 | 23 | 3 | 163 | 34 | 0 | 2 |
DEL PEAK 7(3P14.2) WILD-TYPE | 287 | 48 | 332 | 79 | 65 | 12 | 106 | 7 | 40 | 128 | 1 | 4 | 11 | 1 | 2 | 2 | 11 | 0 | 1 | 0 | 2 | 45 | 5 | 12 | 1 | 2 | 33 | 6 | 120 | 10 | 389 | 51 | 1 | 18 |
Figure S260. Get High-res Image Gene #48: 'Del Peak 7(3p14.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D48V6.png)
P value = 8.81e-20 (Fisher's exact test), Q value = 1.3e-16
Table S261. Gene #48: 'Del Peak 7(3p14.2)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 7(3P14.2) CNV | 324 | 360 | 304 | 124 |
DEL PEAK 7(3P14.2) WILD-TYPE | 124 | 251 | 384 | 84 |
Figure S261. Get High-res Image Gene #48: 'Del Peak 7(3p14.2)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D48V7.png)
P value = 3.07e-17 (Fisher's exact test), Q value = 4.6e-14
Table S262. Gene #48: 'Del Peak 7(3p14.2)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 7(3P14.2) CNV | 426 | 208 | 379 | 248 |
DEL PEAK 7(3P14.2) WILD-TYPE | 259 | 279 | 497 | 172 |
Figure S262. Get High-res Image Gene #48: 'Del Peak 7(3p14.2)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D48V10.png)
P value = 4.04e-20 (Fisher's exact test), Q value = 6.1e-17
Table S263. Gene #48: 'Del Peak 7(3p14.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
DEL PEAK 7(3P14.2) CNV | 203 | 1563 |
DEL PEAK 7(3P14.2) WILD-TYPE | 632 | 2253 |
Figure S263. Get High-res Image Gene #48: 'Del Peak 7(3p14.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D48V11.png)
P value = 2.41e-17 (Chi-square test), Q value = 3.6e-14
Table S264. Gene #48: 'Del Peak 7(3p14.2)' versus Clinical Feature #13: 'TOBACCOSMOKINGHISTORYINDICATOR'
nPatients | 1 | 2 | 3 | 4 | 5 | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER |
---|---|---|---|---|---|---|---|---|---|
ALL | 15 | 16 | 22 | 25 | 2 | 342 | 208 | 237 | 116 |
DEL PEAK 7(3P14.2) CNV | 1 | 9 | 11 | 4 | 2 | 255 | 126 | 188 | 63 |
DEL PEAK 7(3P14.2) WILD-TYPE | 14 | 7 | 11 | 21 | 0 | 87 | 82 | 49 | 53 |
Figure S264. Get High-res Image Gene #48: 'Del Peak 7(3p14.2)' versus Clinical Feature #13: 'TOBACCOSMOKINGHISTORYINDICATOR'
![](D48V13.png)
P value = 3.49e-53 (Chi-square test), Q value = 5.6e-50
Table S265. Gene #49: 'Del Peak 8(4p16.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 8(4P16.3) CNV | 46 | 78 | 269 | 117 | 69 | 137 | 67 | 286 | 2 | 223 | 0 | 59 |
DEL PEAK 8(4P16.3) WILD-TYPE | 85 | 466 | 588 | 295 | 385 | 184 | 426 | 428 | 0 | 325 | 2 | 100 |
Figure S265. Get High-res Image Gene #49: 'Del Peak 8(4p16.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D49V3.png)
P value = 6.2e-60 (Chi-square test), Q value = 1e-56
Table S266. Gene #49: 'Del Peak 8(4p16.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 8(4P16.3) CNV | 108 | 9 | 27 | 137 | 36 | 0 | 67 | 3 | 19 | 65 | 3 | 0 | 1 | 1 | 0 | 1 | 2 | 1 | 0 | 1 | 1 | 187 | 0 | 4 | 1 | 0 | 18 | 4 | 54 | 4 | 225 | 38 | 0 | 2 |
DEL PEAK 8(4P16.3) WILD-TYPE | 248 | 45 | 324 | 184 | 68 | 12 | 426 | 8 | 60 | 178 | 4 | 4 | 16 | 1 | 3 | 1 | 16 | 0 | 1 | 0 | 2 | 128 | 5 | 14 | 3 | 3 | 31 | 6 | 89 | 9 | 327 | 47 | 1 | 18 |
Figure S266. Get High-res Image Gene #49: 'Del Peak 8(4p16.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D49V6.png)
P value = 9.16e-07 (Fisher's exact test), Q value = 0.0012
Table S267. Gene #49: 'Del Peak 8(4p16.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 8(4P16.3) CNV | 104 | 224 | 216 | 86 |
DEL PEAK 8(4P16.3) WILD-TYPE | 344 | 387 | 472 | 122 |
Figure S267. Get High-res Image Gene #49: 'Del Peak 8(4p16.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D49V7.png)
P value = 0.000126 (Fisher's exact test), Q value = 0.16
Table S268. Gene #49: 'Del Peak 8(4p16.3)' versus Clinical Feature #8: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 1036 | 343 | 279 | 11 |
DEL PEAK 8(4P16.3) CNV | 321 | 130 | 120 | 7 |
DEL PEAK 8(4P16.3) WILD-TYPE | 715 | 213 | 159 | 4 |
Figure S268. Get High-res Image Gene #49: 'Del Peak 8(4p16.3)' versus Clinical Feature #8: 'PATHOLOGY.N'
![](D49V8.png)
P value = 0.000177 (Fisher's exact test), Q value = 0.22
Table S269. Gene #49: 'Del Peak 8(4p16.3)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 8(4P16.3) CNV | 202 | 146 | 324 | 168 |
DEL PEAK 8(4P16.3) WILD-TYPE | 483 | 341 | 552 | 252 |
Figure S269. Get High-res Image Gene #49: 'Del Peak 8(4p16.3)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D49V10.png)
P value = 0.000184 (Fisher's exact test), Q value = 0.23
Table S270. Gene #49: 'Del Peak 8(4p16.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
DEL PEAK 8(4P16.3) CNV | 200 | 1160 |
DEL PEAK 8(4P16.3) WILD-TYPE | 635 | 2656 |
Figure S270. Get High-res Image Gene #49: 'Del Peak 8(4p16.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D49V11.png)
P value = 1.3e-123 (Chi-square test), Q value = 2.2e-120
Table S271. Gene #50: 'Del Peak 9(4q22.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 9(4Q22.1) CNV | 52 | 58 | 237 | 125 | 79 | 102 | 67 | 304 | 2 | 367 | 1 | 69 |
DEL PEAK 9(4Q22.1) WILD-TYPE | 79 | 486 | 620 | 287 | 375 | 219 | 426 | 410 | 0 | 181 | 1 | 90 |
Figure S271. Get High-res Image Gene #50: 'Del Peak 9(4q22.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D50V3.png)
P value = 3.96e-108 (Chi-square test), Q value = 6.6e-105
Table S272. Gene #50: 'Del Peak 9(4q22.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 9(4Q22.1) CNV | 116 | 9 | 25 | 102 | 29 | 0 | 67 | 2 | 21 | 85 | 3 | 0 | 3 | 2 | 1 | 0 | 4 | 1 | 0 | 1 | 1 | 179 | 0 | 5 | 1 | 0 | 24 | 3 | 64 | 4 | 370 | 49 | 0 | 0 |
DEL PEAK 9(4Q22.1) WILD-TYPE | 240 | 45 | 326 | 219 | 75 | 12 | 426 | 9 | 58 | 158 | 4 | 4 | 14 | 0 | 2 | 2 | 14 | 0 | 1 | 0 | 2 | 136 | 5 | 13 | 3 | 3 | 25 | 7 | 79 | 9 | 182 | 36 | 1 | 20 |
Figure S272. Get High-res Image Gene #50: 'Del Peak 9(4q22.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D50V6.png)
P value = 3.4e-08 (Fisher's exact test), Q value = 4.7e-05
Table S273. Gene #50: 'Del Peak 9(4q22.1)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 9(4Q22.1) CNV | 93 | 227 | 231 | 75 |
DEL PEAK 9(4Q22.1) WILD-TYPE | 355 | 384 | 457 | 133 |
Figure S273. Get High-res Image Gene #50: 'Del Peak 9(4q22.1)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D50V7.png)
P value = 8.59e-22 (Fisher's exact test), Q value = 1.3e-18
Table S274. Gene #50: 'Del Peak 9(4q22.1)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 9(4Q22.1) CNV | 206 | 154 | 461 | 159 |
DEL PEAK 9(4Q22.1) WILD-TYPE | 479 | 333 | 415 | 261 |
Figure S274. Get High-res Image Gene #50: 'Del Peak 9(4q22.1)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D50V10.png)
P value = 1.72e-14 (Fisher's exact test), Q value = 2.5e-11
Table S275. Gene #50: 'Del Peak 9(4q22.1)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
DEL PEAK 9(4Q22.1) CNV | 174 | 1303 |
DEL PEAK 9(4Q22.1) WILD-TYPE | 661 | 2513 |
Figure S275. Get High-res Image Gene #50: 'Del Peak 9(4q22.1)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D50V11.png)
P value = 2.74e-125 (Chi-square test), Q value = 4.6e-122
Table S276. Gene #51: 'Del Peak 10(4q34.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 10(4Q34.3) CNV | 56 | 89 | 274 | 132 | 97 | 118 | 76 | 357 | 2 | 396 | 1 | 70 |
DEL PEAK 10(4Q34.3) WILD-TYPE | 75 | 455 | 583 | 280 | 357 | 203 | 417 | 357 | 0 | 152 | 1 | 89 |
Figure S276. Get High-res Image Gene #51: 'Del Peak 10(4q34.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D51V3.png)
P value = 1.47e-119 (Chi-square test), Q value = 2.5e-116
Table S277. Gene #51: 'Del Peak 10(4q34.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 10(4Q34.3) CNV | 121 | 11 | 35 | 118 | 39 | 0 | 76 | 3 | 32 | 94 | 3 | 0 | 4 | 2 | 1 | 0 | 4 | 1 | 0 | 1 | 2 | 209 | 0 | 6 | 1 | 0 | 23 | 3 | 66 | 3 | 399 | 56 | 0 | 3 |
DEL PEAK 10(4Q34.3) WILD-TYPE | 235 | 43 | 316 | 203 | 65 | 12 | 417 | 8 | 47 | 149 | 4 | 4 | 13 | 0 | 2 | 2 | 14 | 0 | 1 | 0 | 1 | 106 | 5 | 12 | 3 | 3 | 26 | 7 | 77 | 10 | 153 | 29 | 1 | 17 |
Figure S277. Get High-res Image Gene #51: 'Del Peak 10(4q34.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D51V6.png)
P value = 5.9e-09 (Fisher's exact test), Q value = 8.3e-06
Table S278. Gene #51: 'Del Peak 10(4q34.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 10(4Q34.3) CNV | 112 | 267 | 245 | 82 |
DEL PEAK 10(4Q34.3) WILD-TYPE | 336 | 344 | 443 | 126 |
Figure S278. Get High-res Image Gene #51: 'Del Peak 10(4q34.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D51V7.png)
P value = 8.71e-16 (Fisher's exact test), Q value = 1.3e-12
Table S279. Gene #51: 'Del Peak 10(4q34.3)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 10(4Q34.3) CNV | 241 | 183 | 482 | 180 |
DEL PEAK 10(4Q34.3) WILD-TYPE | 444 | 304 | 394 | 240 |
Figure S279. Get High-res Image Gene #51: 'Del Peak 10(4q34.3)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D51V10.png)
P value = 7.92e-11 (Fisher's exact test), Q value = 1.1e-07
Table S280. Gene #51: 'Del Peak 10(4q34.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
DEL PEAK 10(4Q34.3) CNV | 221 | 1459 |
DEL PEAK 10(4Q34.3) WILD-TYPE | 614 | 2357 |
Figure S280. Get High-res Image Gene #51: 'Del Peak 10(4q34.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D51V11.png)
P value = 5.24e-169 (Chi-square test), Q value = 9e-166
Table S281. Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 11(5Q11.2) CNV | 68 | 43 | 216 | 91 | 81 | 134 | 10 | 377 | 2 | 326 | 1 | 49 |
DEL PEAK 11(5Q11.2) WILD-TYPE | 63 | 501 | 641 | 321 | 373 | 187 | 483 | 337 | 0 | 222 | 1 | 110 |
Figure S281. Get High-res Image Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D52V3.png)
P value = 8.31e-05 (t-test), Q value = 0.1
Table S282. Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 641 | 73.6 (23.9) |
DEL PEAK 11(5Q11.2) CNV | 152 | 65.3 (31.2) |
DEL PEAK 11(5Q11.2) WILD-TYPE | 489 | 76.2 (20.6) |
Figure S282. Get High-res Image Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'
![](D52V5.png)
P value = 1.1e-150 (Chi-square test), Q value = 1.9e-147
Table S283. Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 11(5Q11.2) CNV | 84 | 7 | 29 | 134 | 35 | 0 | 10 | 4 | 28 | 91 | 5 | 0 | 3 | 0 | 2 | 1 | 5 | 1 | 0 | 0 | 3 | 233 | 2 | 2 | 1 | 0 | 20 | 3 | 46 | 2 | 329 | 50 | 0 | 0 |
DEL PEAK 11(5Q11.2) WILD-TYPE | 272 | 47 | 322 | 187 | 69 | 12 | 483 | 7 | 51 | 152 | 2 | 4 | 14 | 2 | 1 | 1 | 13 | 0 | 1 | 1 | 0 | 82 | 3 | 16 | 3 | 3 | 29 | 7 | 97 | 11 | 223 | 35 | 1 | 20 |
Figure S283. Get High-res Image Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D52V6.png)
P value = 3.14e-17 (Fisher's exact test), Q value = 4.7e-14
Table S284. Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 11(5Q11.2) CNV | 107 | 261 | 157 | 85 |
DEL PEAK 11(5Q11.2) WILD-TYPE | 341 | 350 | 531 | 123 |
Figure S284. Get High-res Image Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D52V7.png)
P value = 2.66e-05 (Fisher's exact test), Q value = 0.034
Table S285. Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #8: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 1036 | 343 | 279 | 11 |
DEL PEAK 11(5Q11.2) CNV | 320 | 150 | 113 | 5 |
DEL PEAK 11(5Q11.2) WILD-TYPE | 716 | 193 | 166 | 6 |
Figure S285. Get High-res Image Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #8: 'PATHOLOGY.N'
![](D52V8.png)
P value = 4.37e-06 (Fisher's exact test), Q value = 0.0058
Table S286. Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 11(5Q11.2) CNV | 214 | 164 | 378 | 168 |
DEL PEAK 11(5Q11.2) WILD-TYPE | 471 | 323 | 498 | 252 |
Figure S286. Get High-res Image Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D52V10.png)
P value = 9.91e-14 (Fisher's exact test), Q value = 1.5e-10
Table S287. Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
DEL PEAK 11(5Q11.2) CNV | 165 | 1239 |
DEL PEAK 11(5Q11.2) WILD-TYPE | 670 | 2577 |
Figure S287. Get High-res Image Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D52V11.png)
P value = 6.24e-06 (t-test), Q value = 0.0083
Table S288. Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #12: 'NUMBERPACKYEARSSMOKED'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 804 | 46.7 (32.6) |
DEL PEAK 11(5Q11.2) CNV | 415 | 51.7 (34.6) |
DEL PEAK 11(5Q11.2) WILD-TYPE | 389 | 41.4 (29.6) |
Figure S288. Get High-res Image Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #12: 'NUMBERPACKYEARSSMOKED'
![](D52V12.png)
P value = 5.67e-05 (Chi-square test), Q value = 0.072
Table S289. Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #13: 'TOBACCOSMOKINGHISTORYINDICATOR'
nPatients | 1 | 2 | 3 | 4 | 5 | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER |
---|---|---|---|---|---|---|---|---|---|
ALL | 15 | 16 | 22 | 25 | 2 | 342 | 208 | 237 | 116 |
DEL PEAK 11(5Q11.2) CNV | 9 | 6 | 15 | 16 | 0 | 200 | 95 | 130 | 39 |
DEL PEAK 11(5Q11.2) WILD-TYPE | 6 | 10 | 7 | 9 | 2 | 142 | 113 | 107 | 77 |
Figure S289. Get High-res Image Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #13: 'TOBACCOSMOKINGHISTORYINDICATOR'
![](D52V13.png)
P value = 2.6e-05 (Chi-square test), Q value = 0.034
Table S290. Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #20: 'NEOPLASM.DISEASESTAGE'
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 71 | 45 | 2 | 34 | 246 | 165 | 29 | 107 | 22 | 36 | 35 | 12 |
DEL PEAK 11(5Q11.2) CNV | 18 | 7 | 1 | 17 | 67 | 42 | 10 | 25 | 4 | 5 | 22 | 3 |
DEL PEAK 11(5Q11.2) WILD-TYPE | 53 | 38 | 1 | 17 | 179 | 123 | 19 | 82 | 18 | 31 | 13 | 9 |
Figure S290. Get High-res Image Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #20: 'NEOPLASM.DISEASESTAGE'
![](D52V20.png)
P value = 8.65e-176 (Chi-square test), Q value = 1.5e-172
Table S291. Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 12(5Q21.3) CNV | 67 | 43 | 213 | 117 | 70 | 128 | 5 | 406 | 2 | 311 | 1 | 51 |
DEL PEAK 12(5Q21.3) WILD-TYPE | 64 | 501 | 644 | 295 | 384 | 193 | 488 | 308 | 0 | 237 | 1 | 108 |
Figure S291. Get High-res Image Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D53V3.png)
P value = 1.8e-05 (t-test), Q value = 0.023
Table S292. Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 641 | 73.6 (23.9) |
DEL PEAK 12(5Q21.3) CNV | 149 | 64.2 (32.2) |
DEL PEAK 12(5Q21.3) WILD-TYPE | 492 | 76.4 (20.0) |
Figure S292. Get High-res Image Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'
![](D53V5.png)
P value = 8.17e-150 (Chi-square test), Q value = 1.4e-146
Table S293. Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 12(5Q21.3) CNV | 107 | 10 | 23 | 128 | 34 | 0 | 5 | 5 | 34 | 99 | 5 | 0 | 4 | 1 | 2 | 1 | 6 | 1 | 0 | 1 | 3 | 243 | 2 | 3 | 1 | 0 | 17 | 3 | 48 | 2 | 314 | 44 | 0 | 0 |
DEL PEAK 12(5Q21.3) WILD-TYPE | 249 | 44 | 328 | 193 | 70 | 12 | 488 | 6 | 45 | 144 | 2 | 4 | 13 | 1 | 1 | 1 | 12 | 0 | 1 | 0 | 0 | 72 | 3 | 15 | 3 | 3 | 32 | 7 | 95 | 11 | 238 | 41 | 1 | 20 |
Figure S293. Get High-res Image Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D53V6.png)
P value = 3.33e-16 (Fisher's exact test), Q value = 5e-13
Table S294. Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 12(5Q21.3) CNV | 113 | 276 | 177 | 86 |
DEL PEAK 12(5Q21.3) WILD-TYPE | 335 | 335 | 511 | 122 |
Figure S294. Get High-res Image Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D53V7.png)
P value = 1.5e-05 (Fisher's exact test), Q value = 0.02
Table S295. Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #8: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 1036 | 343 | 279 | 11 |
DEL PEAK 12(5Q21.3) CNV | 346 | 162 | 116 | 6 |
DEL PEAK 12(5Q21.3) WILD-TYPE | 690 | 181 | 163 | 5 |
Figure S295. Get High-res Image Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #8: 'PATHOLOGY.N'
![](D53V8.png)
P value = 4.4e-05 (Chi-square test), Q value = 0.056
Table S296. Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 1398 | 167 | 9 | 1 | 148 |
DEL PEAK 12(5Q21.3) CNV | 437 | 40 | 6 | 0 | 69 |
DEL PEAK 12(5Q21.3) WILD-TYPE | 961 | 127 | 3 | 1 | 79 |
Figure S296. Get High-res Image Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'
![](D53V9.png)
P value = 1.72e-14 (Fisher's exact test), Q value = 2.5e-11
Table S297. Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
DEL PEAK 12(5Q21.3) CNV | 165 | 1256 |
DEL PEAK 12(5Q21.3) WILD-TYPE | 670 | 2560 |
Figure S297. Get High-res Image Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D53V11.png)
P value = 3.54e-05 (Chi-square test), Q value = 0.045
Table S298. Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #13: 'TOBACCOSMOKINGHISTORYINDICATOR'
nPatients | 1 | 2 | 3 | 4 | 5 | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER |
---|---|---|---|---|---|---|---|---|---|
ALL | 15 | 16 | 22 | 25 | 2 | 342 | 208 | 237 | 116 |
DEL PEAK 12(5Q21.3) CNV | 10 | 8 | 15 | 14 | 1 | 206 | 100 | 139 | 38 |
DEL PEAK 12(5Q21.3) WILD-TYPE | 5 | 8 | 7 | 11 | 1 | 136 | 108 | 98 | 78 |
Figure S298. Get High-res Image Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #13: 'TOBACCOSMOKINGHISTORYINDICATOR'
![](D53V13.png)
P value = 9.36e-06 (Chi-square test), Q value = 0.012
Table S299. Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #20: 'NEOPLASM.DISEASESTAGE'
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 71 | 45 | 2 | 34 | 246 | 165 | 29 | 107 | 22 | 36 | 35 | 12 |
DEL PEAK 12(5Q21.3) CNV | 17 | 6 | 1 | 16 | 72 | 39 | 11 | 22 | 3 | 7 | 22 | 4 |
DEL PEAK 12(5Q21.3) WILD-TYPE | 54 | 39 | 1 | 18 | 174 | 126 | 18 | 85 | 19 | 29 | 13 | 8 |
Figure S299. Get High-res Image Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #20: 'NEOPLASM.DISEASESTAGE'
![](D53V20.png)
P value = 3.78e-16 (Chi-square test), Q value = 5.6e-13
Table S300. Gene #54: 'Del Peak 13(6p25.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 13(6P25.3) CNV | 34 | 84 | 160 | 54 | 14 | 64 | 93 | 134 | 0 | 126 | 0 | 21 |
DEL PEAK 13(6P25.3) WILD-TYPE | 97 | 460 | 697 | 358 | 440 | 257 | 400 | 580 | 2 | 422 | 2 | 138 |
Figure S300. Get High-res Image Gene #54: 'Del Peak 13(6p25.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D54V3.png)
P value = 7.04e-05 (Fisher's exact test), Q value = 0.089
Table S301. Gene #54: 'Del Peak 13(6p25.3)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
DEL PEAK 13(6P25.3) CNV | 446 | 341 |
DEL PEAK 13(6P25.3) WILD-TYPE | 2478 | 1376 |
Figure S301. Get High-res Image Gene #54: 'Del Peak 13(6p25.3)' versus Clinical Feature #4: 'GENDER'
![](D54V4.png)
P value = 1.05e-13 (Chi-square test), Q value = 1.5e-10
Table S302. Gene #54: 'Del Peak 13(6p25.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 13(6P25.3) CNV | 49 | 5 | 6 | 64 | 15 | 2 | 93 | 1 | 9 | 33 | 2 | 0 | 2 | 0 | 0 | 0 | 3 | 1 | 0 | 0 | 0 | 82 | 0 | 1 | 1 | 0 | 12 | 4 | 18 | 3 | 126 | 7 | 0 | 5 |
DEL PEAK 13(6P25.3) WILD-TYPE | 307 | 49 | 345 | 257 | 89 | 10 | 400 | 10 | 70 | 210 | 5 | 4 | 15 | 2 | 3 | 2 | 15 | 0 | 1 | 1 | 3 | 233 | 5 | 17 | 3 | 3 | 37 | 6 | 125 | 10 | 426 | 78 | 1 | 15 |
Figure S302. Get High-res Image Gene #54: 'Del Peak 13(6p25.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D54V6.png)
P value = 3.9e-93 (Chi-square test), Q value = 6.4e-90
Table S303. Gene #55: 'Del Peak 14(6q22.31)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 14(6Q22.31) CNV | 52 | 152 | 260 | 57 | 25 | 54 | 138 | 274 | 2 | 315 | 2 | 25 |
DEL PEAK 14(6Q22.31) WILD-TYPE | 79 | 392 | 597 | 355 | 429 | 267 | 355 | 440 | 0 | 233 | 0 | 134 |
Figure S303. Get High-res Image Gene #55: 'Del Peak 14(6q22.31)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D55V3.png)
P value = 1.53e-94 (Chi-square test), Q value = 2.5e-91
Table S304. Gene #55: 'Del Peak 14(6q22.31)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 14(6Q22.31) CNV | 49 | 8 | 5 | 54 | 28 | 3 | 138 | 5 | 44 | 120 | 2 | 2 | 9 | 1 | 1 | 0 | 9 | 1 | 0 | 0 | 1 | 77 | 2 | 2 | 1 | 1 | 17 | 5 | 19 | 6 | 319 | 18 | 1 | 8 |
DEL PEAK 14(6Q22.31) WILD-TYPE | 307 | 46 | 346 | 267 | 76 | 9 | 355 | 6 | 35 | 123 | 5 | 2 | 8 | 1 | 2 | 2 | 9 | 0 | 1 | 1 | 2 | 238 | 3 | 16 | 3 | 2 | 32 | 5 | 124 | 7 | 233 | 67 | 0 | 12 |
Figure S304. Get High-res Image Gene #55: 'Del Peak 14(6q22.31)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D55V6.png)
P value = 3.81e-10 (Fisher's exact test), Q value = 5.4e-07
Table S305. Gene #55: 'Del Peak 14(6q22.31)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 14(6Q22.31) CNV | 202 | 118 | 356 | 121 |
DEL PEAK 14(6Q22.31) WILD-TYPE | 483 | 369 | 520 | 299 |
Figure S305. Get High-res Image Gene #55: 'Del Peak 14(6q22.31)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D55V10.png)
P value = 6.33e-06 (t-test), Q value = 0.0084
Table S306. Gene #56: 'Del Peak 15(6q26)' versus Clinical Feature #2: 'AGE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 4585 | 61.9 (12.6) |
DEL PEAK 15(6Q26) CNV | 1451 | 60.7 (12.4) |
DEL PEAK 15(6Q26) WILD-TYPE | 3134 | 62.5 (12.7) |
Figure S306. Get High-res Image Gene #56: 'Del Peak 15(6q26)' versus Clinical Feature #2: 'AGE'
![](D56V2.png)
P value = 2.31e-104 (Chi-square test), Q value = 3.8e-101
Table S307. Gene #56: 'Del Peak 15(6q26)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 15(6Q26) CNV | 57 | 162 | 295 | 60 | 37 | 55 | 142 | 285 | 1 | 351 | 1 | 28 |
DEL PEAK 15(6Q26) WILD-TYPE | 74 | 382 | 562 | 352 | 417 | 266 | 351 | 429 | 1 | 197 | 1 | 131 |
Figure S307. Get High-res Image Gene #56: 'Del Peak 15(6q26)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D56V3.png)
P value = 3.37e-104 (Chi-square test), Q value = 5.6e-101
Table S308. Gene #56: 'Del Peak 15(6q26)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 15(6Q26) CNV | 52 | 8 | 12 | 55 | 37 | 3 | 142 | 5 | 43 | 123 | 2 | 2 | 7 | 1 | 1 | 0 | 11 | 1 | 0 | 0 | 1 | 86 | 2 | 3 | 1 | 1 | 19 | 5 | 22 | 6 | 353 | 22 | 1 | 11 |
DEL PEAK 15(6Q26) WILD-TYPE | 304 | 46 | 339 | 266 | 67 | 9 | 351 | 6 | 36 | 120 | 5 | 2 | 10 | 1 | 2 | 2 | 7 | 0 | 1 | 1 | 2 | 229 | 3 | 15 | 3 | 2 | 30 | 5 | 121 | 7 | 199 | 63 | 0 | 9 |
Figure S308. Get High-res Image Gene #56: 'Del Peak 15(6q26)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D56V6.png)
P value = 1.02e-13 (Fisher's exact test), Q value = 1.5e-10
Table S309. Gene #56: 'Del Peak 15(6q26)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 15(6Q26) CNV | 209 | 120 | 388 | 136 |
DEL PEAK 15(6Q26) WILD-TYPE | 476 | 367 | 488 | 284 |
Figure S309. Get High-res Image Gene #56: 'Del Peak 15(6q26)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D56V10.png)
P value = 1.33e-144 (Chi-square test), Q value = 2.3e-141
Table S310. Gene #57: 'Del Peak 16(7p22.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 16(7P22.3) CNV | 8 | 13 | 115 | 2 | 57 | 17 | 2 | 70 | 0 | 229 | 1 | 2 |
DEL PEAK 16(7P22.3) WILD-TYPE | 123 | 531 | 742 | 410 | 397 | 304 | 491 | 644 | 2 | 319 | 1 | 157 |
Figure S310. Get High-res Image Gene #57: 'Del Peak 16(7p22.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D57V3.png)
P value = 4.91e-27 (Fisher's exact test), Q value = 7.6e-24
Table S311. Gene #57: 'Del Peak 16(7p22.3)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
DEL PEAK 16(7P22.3) CNV | 431 | 85 |
DEL PEAK 16(7P22.3) WILD-TYPE | 2493 | 1632 |
Figure S311. Get High-res Image Gene #57: 'Del Peak 16(7p22.3)' versus Clinical Feature #4: 'GENDER'
![](D57V4.png)
P value = 8.12e-126 (Chi-square test), Q value = 1.4e-122
Table S312. Gene #57: 'Del Peak 16(7p22.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 16(7P22.3) CNV | 2 | 0 | 21 | 17 | 22 | 0 | 2 | 0 | 4 | 17 | 1 | 0 | 0 | 0 | 0 | 0 | 2 | 1 | 0 | 0 | 0 | 45 | 0 | 4 | 0 | 0 | 2 | 2 | 1 | 1 | 230 | 32 | 0 | 0 |
DEL PEAK 16(7P22.3) WILD-TYPE | 354 | 54 | 330 | 304 | 82 | 12 | 491 | 11 | 75 | 226 | 6 | 4 | 17 | 2 | 3 | 2 | 16 | 0 | 1 | 1 | 3 | 270 | 5 | 14 | 4 | 3 | 47 | 8 | 142 | 12 | 322 | 53 | 1 | 20 |
Figure S312. Get High-res Image Gene #57: 'Del Peak 16(7p22.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D57V6.png)
P value = 3.04e-07 (Fisher's exact test), Q value = 0.00042
Table S313. Gene #57: 'Del Peak 16(7p22.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 16(7P22.3) CNV | 15 | 48 | 11 | 12 |
DEL PEAK 16(7P22.3) WILD-TYPE | 433 | 563 | 677 | 196 |
Figure S313. Get High-res Image Gene #57: 'Del Peak 16(7p22.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D57V7.png)
P value = 2.28e-28 (Fisher's exact test), Q value = 3.5e-25
Table S314. Gene #57: 'Del Peak 16(7p22.3)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 16(7P22.3) CNV | 38 | 29 | 200 | 45 |
DEL PEAK 16(7P22.3) WILD-TYPE | 647 | 458 | 676 | 375 |
Figure S314. Get High-res Image Gene #57: 'Del Peak 16(7p22.3)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D57V10.png)
P value = 9.82e-56 (Chi-square test), Q value = 1.6e-52
Table S315. Gene #58: 'Del Peak 17(7q36.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 17(7Q36.1) CNV | 15 | 8 | 172 | 8 | 51 | 80 | 6 | 122 | 0 | 67 | 1 | 8 |
DEL PEAK 17(7Q36.1) WILD-TYPE | 116 | 536 | 685 | 404 | 403 | 241 | 487 | 592 | 2 | 481 | 1 | 151 |
Figure S315. Get High-res Image Gene #58: 'Del Peak 17(7q36.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D58V3.png)
P value = 1.46e-49 (Chi-square test), Q value = 2.3e-46
Table S316. Gene #58: 'Del Peak 17(7q36.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 17(7Q36.1) CNV | 7 | 1 | 12 | 80 | 22 | 1 | 6 | 0 | 6 | 36 | 2 | 1 | 2 | 1 | 1 | 0 | 3 | 0 | 0 | 0 | 0 | 67 | 0 | 4 | 2 | 1 | 4 | 2 | 5 | 3 | 68 | 35 | 0 | 0 |
DEL PEAK 17(7Q36.1) WILD-TYPE | 349 | 53 | 339 | 241 | 82 | 11 | 487 | 11 | 73 | 207 | 5 | 3 | 15 | 1 | 2 | 2 | 15 | 1 | 1 | 1 | 3 | 248 | 5 | 14 | 2 | 2 | 45 | 8 | 138 | 10 | 484 | 50 | 1 | 20 |
Figure S316. Get High-res Image Gene #58: 'Del Peak 17(7q36.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D58V6.png)
P value = 7.27e-11 (Fisher's exact test), Q value = 1.1e-07
Table S317. Gene #58: 'Del Peak 17(7q36.1)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 17(7Q36.1) CNV | 33 | 95 | 38 | 36 |
DEL PEAK 17(7Q36.1) WILD-TYPE | 415 | 516 | 650 | 172 |
Figure S317. Get High-res Image Gene #58: 'Del Peak 17(7q36.1)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D58V7.png)
P value = 0.000181 (Chi-square test), Q value = 0.22
Table S318. Gene #58: 'Del Peak 17(7q36.1)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 1398 | 167 | 9 | 1 | 148 |
DEL PEAK 17(7Q36.1) CNV | 126 | 3 | 0 | 1 | 12 |
DEL PEAK 17(7Q36.1) WILD-TYPE | 1272 | 164 | 9 | 0 | 136 |
Figure S318. Get High-res Image Gene #58: 'Del Peak 17(7q36.1)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'
![](D58V9.png)
P value = 4.6e-129 (Chi-square test), Q value = 7.8e-126
Table S319. Gene #59: 'Del Peak 18(8p23.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 18(8P23.2) CNV | 71 | 65 | 456 | 172 | 87 | 184 | 146 | 411 | 2 | 367 | 2 | 98 |
DEL PEAK 18(8P23.2) WILD-TYPE | 60 | 479 | 401 | 240 | 367 | 137 | 347 | 303 | 0 | 181 | 0 | 61 |
Figure S319. Get High-res Image Gene #59: 'Del Peak 18(8p23.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D59V3.png)
P value = 7.36e-05 (t-test), Q value = 0.093
Table S320. Gene #59: 'Del Peak 18(8p23.2)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 641 | 73.6 (23.9) |
DEL PEAK 18(8P23.2) CNV | 183 | 66.2 (32.4) |
DEL PEAK 18(8P23.2) WILD-TYPE | 458 | 76.5 (18.8) |
Figure S320. Get High-res Image Gene #59: 'Del Peak 18(8p23.2)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'
![](D59V5.png)
P value = 9.65e-91 (Chi-square test), Q value = 1.6e-87
Table S321. Gene #59: 'Del Peak 18(8p23.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 18(8P23.2) CNV | 156 | 15 | 28 | 184 | 60 | 2 | 146 | 4 | 31 | 126 | 4 | 1 | 9 | 2 | 3 | 0 | 7 | 1 | 0 | 0 | 3 | 220 | 2 | 4 | 0 | 0 | 22 | 8 | 89 | 7 | 371 | 55 | 0 | 4 |
DEL PEAK 18(8P23.2) WILD-TYPE | 200 | 39 | 323 | 137 | 44 | 10 | 347 | 7 | 48 | 117 | 3 | 3 | 8 | 0 | 0 | 2 | 11 | 0 | 1 | 1 | 0 | 95 | 3 | 14 | 4 | 3 | 27 | 2 | 54 | 6 | 181 | 30 | 1 | 16 |
Figure S321. Get High-res Image Gene #59: 'Del Peak 18(8p23.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D59V6.png)
P value = 3.31e-05 (Fisher's exact test), Q value = 0.043
Table S322. Gene #59: 'Del Peak 18(8p23.2)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 18(8P23.2) CNV | 181 | 327 | 325 | 117 |
DEL PEAK 18(8P23.2) WILD-TYPE | 267 | 284 | 363 | 91 |
Figure S322. Get High-res Image Gene #59: 'Del Peak 18(8p23.2)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D59V7.png)
P value = 5.54e-09 (Fisher's exact test), Q value = 7.8e-06
Table S323. Gene #59: 'Del Peak 18(8p23.2)' versus Clinical Feature #8: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 1036 | 343 | 279 | 11 |
DEL PEAK 18(8P23.2) CNV | 462 | 199 | 174 | 8 |
DEL PEAK 18(8P23.2) WILD-TYPE | 574 | 144 | 105 | 3 |
Figure S323. Get High-res Image Gene #59: 'Del Peak 18(8p23.2)' versus Clinical Feature #8: 'PATHOLOGY.N'
![](D59V8.png)
P value = 2.21e-08 (Fisher's exact test), Q value = 3.1e-05
Table S324. Gene #59: 'Del Peak 18(8p23.2)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 18(8P23.2) CNV | 306 | 238 | 514 | 245 |
DEL PEAK 18(8P23.2) WILD-TYPE | 379 | 249 | 362 | 175 |
Figure S324. Get High-res Image Gene #59: 'Del Peak 18(8p23.2)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D59V10.png)
P value = 3.83e-21 (Fisher's exact test), Q value = 5.8e-18
Table S325. Gene #59: 'Del Peak 18(8p23.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
DEL PEAK 18(8P23.2) CNV | 250 | 1818 |
DEL PEAK 18(8P23.2) WILD-TYPE | 585 | 1998 |
Figure S325. Get High-res Image Gene #59: 'Del Peak 18(8p23.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D59V11.png)
P value = 5.87e-133 (Chi-square test), Q value = 1e-129
Table S326. Gene #60: 'Del Peak 19(8p21.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 19(8P21.2) CNV | 73 | 66 | 470 | 179 | 86 | 161 | 148 | 415 | 2 | 382 | 2 | 94 |
DEL PEAK 19(8P21.2) WILD-TYPE | 58 | 478 | 387 | 233 | 368 | 160 | 345 | 299 | 0 | 166 | 0 | 65 |
Figure S326. Get High-res Image Gene #60: 'Del Peak 19(8p21.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D60V3.png)
P value = 8.03e-05 (Fisher's exact test), Q value = 0.1
Table S327. Gene #60: 'Del Peak 19(8p21.2)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
DEL PEAK 19(8P21.2) CNV | 1375 | 705 |
DEL PEAK 19(8P21.2) WILD-TYPE | 1549 | 1012 |
Figure S327. Get High-res Image Gene #60: 'Del Peak 19(8p21.2)' versus Clinical Feature #4: 'GENDER'
![](D60V4.png)
P value = 1.51e-05 (t-test), Q value = 0.02
Table S328. Gene #60: 'Del Peak 19(8p21.2)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 641 | 73.6 (23.9) |
DEL PEAK 19(8P21.2) CNV | 188 | 65.7 (32.3) |
DEL PEAK 19(8P21.2) WILD-TYPE | 453 | 76.8 (18.5) |
Figure S328. Get High-res Image Gene #60: 'Del Peak 19(8p21.2)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'
![](D60V5.png)
P value = 5.32e-94 (Chi-square test), Q value = 8.8e-91
Table S329. Gene #60: 'Del Peak 19(8p21.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 19(8P21.2) CNV | 163 | 15 | 22 | 161 | 63 | 1 | 148 | 4 | 36 | 133 | 4 | 1 | 9 | 2 | 3 | 0 | 10 | 1 | 0 | 0 | 3 | 209 | 2 | 5 | 0 | 0 | 21 | 8 | 85 | 7 | 386 | 59 | 0 | 5 |
DEL PEAK 19(8P21.2) WILD-TYPE | 193 | 39 | 329 | 160 | 41 | 11 | 345 | 7 | 43 | 110 | 3 | 3 | 8 | 0 | 0 | 2 | 8 | 0 | 1 | 1 | 0 | 106 | 3 | 13 | 4 | 3 | 28 | 2 | 58 | 6 | 166 | 26 | 1 | 15 |
Figure S329. Get High-res Image Gene #60: 'Del Peak 19(8p21.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D60V6.png)
P value = 6.31e-09 (Fisher's exact test), Q value = 8.9e-06
Table S330. Gene #60: 'Del Peak 19(8p21.2)' versus Clinical Feature #8: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 1036 | 343 | 279 | 11 |
DEL PEAK 19(8P21.2) CNV | 452 | 197 | 170 | 8 |
DEL PEAK 19(8P21.2) WILD-TYPE | 584 | 146 | 109 | 3 |
Figure S330. Get High-res Image Gene #60: 'Del Peak 19(8p21.2)' versus Clinical Feature #8: 'PATHOLOGY.N'
![](D60V8.png)
P value = 2.83e-11 (Fisher's exact test), Q value = 4.1e-08
Table S331. Gene #60: 'Del Peak 19(8p21.2)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 19(8P21.2) CNV | 302 | 227 | 530 | 239 |
DEL PEAK 19(8P21.2) WILD-TYPE | 383 | 260 | 346 | 181 |
Figure S331. Get High-res Image Gene #60: 'Del Peak 19(8p21.2)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D60V10.png)
P value = 6.66e-22 (Fisher's exact test), Q value = 1e-18
Table S332. Gene #60: 'Del Peak 19(8p21.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
DEL PEAK 19(8P21.2) CNV | 251 | 1835 |
DEL PEAK 19(8P21.2) WILD-TYPE | 584 | 1981 |
Figure S332. Get High-res Image Gene #60: 'Del Peak 19(8p21.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D60V11.png)
P value = 0 (logrank test), Q value = 0
Table S333. Gene #61: 'Del Peak 20(9p23)' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4) |
DEL PEAK 20(9P23) CNV | 1564 | 625 | 0.0 - 163.1 (14.0) |
DEL PEAK 20(9P23) WILD-TYPE | 2806 | 781 | 0.0 - 224.0 (14.9) |
Figure S333. Get High-res Image Gene #61: 'Del Peak 20(9p23)' versus Clinical Feature #1: 'Time to Death'
![](D61V1.png)
P value = 3.56e-93 (Chi-square test), Q value = 5.9e-90
Table S334. Gene #61: 'Del Peak 20(9p23)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 20(9P23) CNV | 58 | 232 | 266 | 53 | 53 | 151 | 144 | 415 | 1 | 245 | 2 | 25 |
DEL PEAK 20(9P23) WILD-TYPE | 73 | 312 | 591 | 359 | 401 | 170 | 349 | 299 | 1 | 303 | 0 | 134 |
Figure S334. Get High-res Image Gene #61: 'Del Peak 20(9p23)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D61V3.png)
P value = 1.64e-10 (Fisher's exact test), Q value = 2.4e-07
Table S335. Gene #61: 'Del Peak 20(9p23)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
DEL PEAK 20(9P23) CNV | 936 | 710 |
DEL PEAK 20(9P23) WILD-TYPE | 1988 | 1007 |
Figure S335. Get High-res Image Gene #61: 'Del Peak 20(9p23)' versus Clinical Feature #4: 'GENDER'
![](D61V4.png)
P value = 2.59e-84 (Chi-square test), Q value = 4.2e-81
Table S336. Gene #61: 'Del Peak 20(9p23)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 20(9P23) CNV | 49 | 4 | 20 | 151 | 37 | 2 | 144 | 6 | 44 | 129 | 3 | 2 | 11 | 1 | 3 | 1 | 7 | 1 | 0 | 0 | 2 | 203 | 1 | 3 | 2 | 0 | 21 | 2 | 24 | 1 | 248 | 30 | 0 | 10 |
DEL PEAK 20(9P23) WILD-TYPE | 307 | 50 | 331 | 170 | 67 | 10 | 349 | 5 | 35 | 114 | 4 | 2 | 6 | 1 | 0 | 1 | 11 | 0 | 1 | 1 | 1 | 112 | 4 | 15 | 2 | 3 | 28 | 8 | 119 | 12 | 304 | 55 | 1 | 10 |
Figure S336. Get High-res Image Gene #61: 'Del Peak 20(9p23)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D61V6.png)
P value = 1.05e-09 (Fisher's exact test), Q value = 1.5e-06
Table S337. Gene #61: 'Del Peak 20(9p23)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 20(9P23) CNV | 163 | 280 | 194 | 84 |
DEL PEAK 20(9P23) WILD-TYPE | 285 | 331 | 494 | 124 |
Figure S337. Get High-res Image Gene #61: 'Del Peak 20(9p23)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D61V7.png)
P value = 0 (logrank test), Q value = 0
Table S338. Gene #62: 'Del Peak 21(9p21.3)' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4) |
DEL PEAK 21(9P21.3) CNV | 1831 | 792 | 0.0 - 177.0 (13.1) |
DEL PEAK 21(9P21.3) WILD-TYPE | 2539 | 614 | 0.0 - 224.0 (15.6) |
Figure S338. Get High-res Image Gene #62: 'Del Peak 21(9p21.3)' versus Clinical Feature #1: 'Time to Death'
![](D62V1.png)
P value = 5.76e-162 (Chi-square test), Q value = 9.9e-159
Table S339. Gene #62: 'Del Peak 21(9p21.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 21(9P21.3) CNV | 73 | 405 | 294 | 56 | 59 | 162 | 148 | 454 | 1 | 245 | 2 | 24 |
DEL PEAK 21(9P21.3) WILD-TYPE | 58 | 139 | 563 | 356 | 395 | 159 | 345 | 260 | 1 | 303 | 0 | 135 |
Figure S339. Get High-res Image Gene #62: 'Del Peak 21(9p21.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D62V3.png)
P value = 2.67e-22 (Fisher's exact test), Q value = 4.1e-19
Table S340. Gene #62: 'Del Peak 21(9p21.3)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
DEL PEAK 21(9P21.3) CNV | 1054 | 870 |
DEL PEAK 21(9P21.3) WILD-TYPE | 1870 | 847 |
Figure S340. Get High-res Image Gene #62: 'Del Peak 21(9p21.3)' versus Clinical Feature #4: 'GENDER'
![](D62V4.png)
P value = 3.34e-109 (Chi-square test), Q value = 5.6e-106
Table S341. Gene #62: 'Del Peak 21(9p21.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 21(9P21.3) CNV | 52 | 4 | 21 | 162 | 43 | 2 | 148 | 5 | 43 | 133 | 3 | 4 | 10 | 1 | 3 | 1 | 8 | 1 | 0 | 0 | 3 | 237 | 1 | 3 | 2 | 0 | 27 | 2 | 23 | 1 | 248 | 35 | 1 | 16 |
DEL PEAK 21(9P21.3) WILD-TYPE | 304 | 50 | 330 | 159 | 61 | 10 | 345 | 6 | 36 | 110 | 4 | 0 | 7 | 1 | 0 | 1 | 10 | 0 | 1 | 1 | 0 | 78 | 4 | 15 | 2 | 3 | 22 | 8 | 120 | 12 | 304 | 50 | 0 | 4 |
Figure S341. Get High-res Image Gene #62: 'Del Peak 21(9p21.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D62V6.png)
P value = 2.4e-16 (Fisher's exact test), Q value = 3.6e-13
Table S342. Gene #62: 'Del Peak 21(9p21.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 21(9P21.3) CNV | 176 | 321 | 199 | 85 |
DEL PEAK 21(9P21.3) WILD-TYPE | 272 | 290 | 489 | 123 |
Figure S342. Get High-res Image Gene #62: 'Del Peak 21(9p21.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D62V7.png)
P value = 8.2e-07 (Fisher's exact test), Q value = 0.0011
Table S343. Gene #62: 'Del Peak 21(9p21.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
DEL PEAK 21(9P21.3) CNV | 411 | 1521 |
DEL PEAK 21(9P21.3) WILD-TYPE | 424 | 2295 |
Figure S343. Get High-res Image Gene #62: 'Del Peak 21(9p21.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D62V11.png)
P value = 3.24e-07 (t-test), Q value = 0.00045
Table S344. Gene #63: 'Del Peak 22(9q21.11)' versus Clinical Feature #2: 'AGE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 4585 | 61.9 (12.6) |
DEL PEAK 22(9Q21.11) CNV | 1310 | 63.3 (11.9) |
DEL PEAK 22(9Q21.11) WILD-TYPE | 3275 | 61.3 (12.8) |
Figure S344. Get High-res Image Gene #63: 'Del Peak 22(9q21.11)' versus Clinical Feature #2: 'AGE'
![](D63V2.png)
P value = 4.8e-86 (Chi-square test), Q value = 7.9e-83
Table S345. Gene #63: 'Del Peak 22(9q21.11)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 22(9Q21.11) CNV | 56 | 72 | 237 | 49 | 94 | 50 | 143 | 346 | 2 | 262 | 2 | 23 |
DEL PEAK 22(9Q21.11) WILD-TYPE | 75 | 472 | 620 | 363 | 360 | 271 | 350 | 368 | 0 | 286 | 0 | 136 |
Figure S345. Get High-res Image Gene #63: 'Del Peak 22(9q21.11)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D63V3.png)
P value = 4.54e-71 (Chi-square test), Q value = 7.4e-68
Table S346. Gene #63: 'Del Peak 22(9q21.11)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 22(9Q21.11) CNV | 47 | 2 | 38 | 50 | 37 | 3 | 143 | 5 | 29 | 131 | 3 | 1 | 9 | 1 | 3 | 0 | 6 | 0 | 0 | 1 | 3 | 152 | 1 | 7 | 2 | 0 | 21 | 3 | 21 | 1 | 266 | 49 | 0 | 5 |
DEL PEAK 22(9Q21.11) WILD-TYPE | 309 | 52 | 313 | 271 | 67 | 9 | 350 | 6 | 50 | 112 | 4 | 3 | 8 | 1 | 0 | 2 | 12 | 1 | 1 | 0 | 0 | 163 | 4 | 11 | 2 | 3 | 28 | 7 | 122 | 12 | 286 | 36 | 1 | 15 |
Figure S346. Get High-res Image Gene #63: 'Del Peak 22(9q21.11)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D63V6.png)
P value = 1.48e-09 (Fisher's exact test), Q value = 2.1e-06
Table S347. Gene #63: 'Del Peak 22(9q21.11)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 22(9Q21.11) CNV | 142 | 223 | 151 | 41 |
DEL PEAK 22(9Q21.11) WILD-TYPE | 306 | 388 | 537 | 167 |
Figure S347. Get High-res Image Gene #63: 'Del Peak 22(9q21.11)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D63V7.png)
P value = 2.63e-09 (Fisher's exact test), Q value = 3.7e-06
Table S348. Gene #63: 'Del Peak 22(9q21.11)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 22(9Q21.11) CNV | 227 | 129 | 352 | 104 |
DEL PEAK 22(9Q21.11) WILD-TYPE | 458 | 358 | 524 | 316 |
Figure S348. Get High-res Image Gene #63: 'Del Peak 22(9q21.11)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D63V10.png)
P value = 9.63e-14 (Fisher's exact test), Q value = 1.4e-10
Table S349. Gene #63: 'Del Peak 22(9q21.11)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
DEL PEAK 22(9Q21.11) CNV | 156 | 1190 |
DEL PEAK 22(9Q21.11) WILD-TYPE | 679 | 2626 |
Figure S349. Get High-res Image Gene #63: 'Del Peak 22(9q21.11)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D63V11.png)
P value = 7.74e-05 (t-test), Q value = 0.098
Table S350. Gene #64: 'Del Peak 23(9q34.13)' versus Clinical Feature #2: 'AGE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 4585 | 61.9 (12.6) |
DEL PEAK 23(9Q34.13) CNV | 1337 | 63.0 (11.9) |
DEL PEAK 23(9Q34.13) WILD-TYPE | 3248 | 61.4 (12.8) |
Figure S350. Get High-res Image Gene #64: 'Del Peak 23(9q34.13)' versus Clinical Feature #2: 'AGE'
![](D64V2.png)
P value = 7.47e-104 (Chi-square test), Q value = 1.2e-100
Table S351. Gene #64: 'Del Peak 23(9q34.13)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 23(9Q34.13) CNV | 46 | 70 | 227 | 51 | 103 | 43 | 149 | 315 | 1 | 328 | 2 | 30 |
DEL PEAK 23(9Q34.13) WILD-TYPE | 85 | 474 | 630 | 361 | 351 | 278 | 344 | 399 | 1 | 220 | 0 | 129 |
Figure S351. Get High-res Image Gene #64: 'Del Peak 23(9q34.13)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D64V3.png)
P value = 1.92e-84 (Chi-square test), Q value = 3.2e-81
Table S352. Gene #64: 'Del Peak 23(9q34.13)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 23(9Q34.13) CNV | 49 | 2 | 45 | 43 | 31 | 2 | 149 | 4 | 26 | 111 | 3 | 1 | 9 | 1 | 3 | 0 | 5 | 0 | 0 | 0 | 3 | 147 | 1 | 8 | 2 | 0 | 20 | 1 | 29 | 1 | 331 | 50 | 0 | 6 |
DEL PEAK 23(9Q34.13) WILD-TYPE | 307 | 52 | 306 | 278 | 73 | 10 | 344 | 7 | 53 | 132 | 4 | 3 | 8 | 1 | 0 | 2 | 13 | 1 | 1 | 1 | 0 | 168 | 4 | 10 | 2 | 3 | 29 | 9 | 114 | 12 | 221 | 35 | 1 | 14 |
Figure S352. Get High-res Image Gene #64: 'Del Peak 23(9q34.13)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D64V6.png)
P value = 1.73e-08 (Fisher's exact test), Q value = 2.4e-05
Table S353. Gene #64: 'Del Peak 23(9q34.13)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 23(9Q34.13) CNV | 138 | 212 | 158 | 34 |
DEL PEAK 23(9Q34.13) WILD-TYPE | 310 | 399 | 530 | 174 |
Figure S353. Get High-res Image Gene #64: 'Del Peak 23(9q34.13)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D64V7.png)
P value = 2.46e-13 (Fisher's exact test), Q value = 3.6e-10
Table S354. Gene #64: 'Del Peak 23(9q34.13)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 23(9Q34.13) CNV | 217 | 129 | 393 | 123 |
DEL PEAK 23(9Q34.13) WILD-TYPE | 468 | 358 | 483 | 297 |
Figure S354. Get High-res Image Gene #64: 'Del Peak 23(9q34.13)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D64V10.png)
P value = 1.9e-14 (Fisher's exact test), Q value = 2.8e-11
Table S355. Gene #64: 'Del Peak 23(9q34.13)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
DEL PEAK 23(9Q34.13) CNV | 158 | 1216 |
DEL PEAK 23(9Q34.13) WILD-TYPE | 677 | 2600 |
Figure S355. Get High-res Image Gene #64: 'Del Peak 23(9q34.13)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D64V11.png)
P value = 0.000148 (t-test), Q value = 0.18
Table S356. Gene #65: 'Del Peak 24(9q34.3)' versus Clinical Feature #2: 'AGE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 4585 | 61.9 (12.6) |
DEL PEAK 24(9Q34.3) CNV | 1341 | 63.0 (12.0) |
DEL PEAK 24(9Q34.3) WILD-TYPE | 3244 | 61.5 (12.8) |
Figure S356. Get High-res Image Gene #65: 'Del Peak 24(9q34.3)' versus Clinical Feature #2: 'AGE'
![](D65V2.png)
P value = 8.36e-98 (Chi-square test), Q value = 1.4e-94
Table S357. Gene #65: 'Del Peak 24(9q34.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 24(9Q34.3) CNV | 47 | 73 | 235 | 49 | 102 | 45 | 149 | 313 | 1 | 321 | 2 | 30 |
DEL PEAK 24(9Q34.3) WILD-TYPE | 84 | 471 | 622 | 363 | 352 | 276 | 344 | 401 | 1 | 227 | 0 | 129 |
Figure S357. Get High-res Image Gene #65: 'Del Peak 24(9q34.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D65V3.png)
P value = 9.53e-81 (Chi-square test), Q value = 1.6e-77
Table S358. Gene #65: 'Del Peak 24(9q34.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 24(9Q34.3) CNV | 47 | 2 | 45 | 45 | 33 | 2 | 149 | 4 | 25 | 107 | 3 | 1 | 9 | 1 | 3 | 0 | 5 | 0 | 0 | 0 | 3 | 150 | 1 | 8 | 2 | 0 | 20 | 1 | 29 | 1 | 324 | 49 | 0 | 6 |
DEL PEAK 24(9Q34.3) WILD-TYPE | 309 | 52 | 306 | 276 | 71 | 10 | 344 | 7 | 54 | 136 | 4 | 3 | 8 | 1 | 0 | 2 | 13 | 1 | 1 | 1 | 0 | 165 | 4 | 10 | 2 | 3 | 29 | 9 | 114 | 12 | 228 | 36 | 1 | 14 |
Figure S358. Get High-res Image Gene #65: 'Del Peak 24(9q34.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D65V6.png)
P value = 9.21e-09 (Fisher's exact test), Q value = 1.3e-05
Table S359. Gene #65: 'Del Peak 24(9q34.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 24(9Q34.3) CNV | 132 | 216 | 158 | 34 |
DEL PEAK 24(9Q34.3) WILD-TYPE | 316 | 395 | 530 | 174 |
Figure S359. Get High-res Image Gene #65: 'Del Peak 24(9q34.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D65V7.png)
P value = 2.71e-12 (Fisher's exact test), Q value = 4e-09
Table S360. Gene #65: 'Del Peak 24(9q34.3)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 24(9Q34.3) CNV | 212 | 131 | 387 | 123 |
DEL PEAK 24(9Q34.3) WILD-TYPE | 473 | 356 | 489 | 297 |
Figure S360. Get High-res Image Gene #65: 'Del Peak 24(9q34.3)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D65V10.png)
P value = 7.05e-14 (Fisher's exact test), Q value = 1e-10
Table S361. Gene #65: 'Del Peak 24(9q34.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
DEL PEAK 24(9Q34.3) CNV | 160 | 1216 |
DEL PEAK 24(9Q34.3) WILD-TYPE | 675 | 2600 |
Figure S361. Get High-res Image Gene #65: 'Del Peak 24(9q34.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D65V11.png)
P value = 0 (logrank test), Q value = 0
Table S362. Gene #66: 'Del Peak 25(10p15.3)' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4) |
DEL PEAK 25(10P15.3) CNV | 1197 | 570 | 0.0 - 177.4 (11.5) |
DEL PEAK 25(10P15.3) WILD-TYPE | 3173 | 836 | 0.0 - 224.0 (16.1) |
Figure S362. Get High-res Image Gene #66: 'Del Peak 25(10p15.3)' versus Clinical Feature #1: 'Time to Death'
![](D66V1.png)
P value = 4.91e-243 (Chi-square test), Q value = 8.5e-240
Table S363. Gene #66: 'Del Peak 25(10p15.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 25(10P15.3) CNV | 22 | 449 | 109 | 68 | 30 | 108 | 62 | 242 | 1 | 114 | 0 | 33 |
DEL PEAK 25(10P15.3) WILD-TYPE | 109 | 95 | 748 | 344 | 424 | 213 | 431 | 472 | 1 | 434 | 2 | 126 |
Figure S363. Get High-res Image Gene #66: 'Del Peak 25(10p15.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D66V3.png)
P value = 1.84e-25 (Fisher's exact test), Q value = 2.8e-22
Table S364. Gene #66: 'Del Peak 25(10p15.3)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
DEL PEAK 25(10P15.3) CNV | 627 | 612 |
DEL PEAK 25(10P15.3) WILD-TYPE | 2297 | 1105 |
Figure S364. Get High-res Image Gene #66: 'Del Peak 25(10p15.3)' versus Clinical Feature #4: 'GENDER'
![](D66V4.png)
P value = 2.64e-48 (Chi-square test), Q value = 4.2e-45
Table S365. Gene #66: 'Del Peak 25(10p15.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 25(10P15.3) CNV | 61 | 7 | 11 | 108 | 11 | 1 | 62 | 3 | 12 | 68 | 5 | 1 | 4 | 0 | 1 | 0 | 3 | 1 | 0 | 0 | 0 | 142 | 0 | 1 | 1 | 1 | 11 | 2 | 29 | 4 | 115 | 18 | 1 | 16 |
DEL PEAK 25(10P15.3) WILD-TYPE | 295 | 47 | 340 | 213 | 93 | 11 | 431 | 8 | 67 | 175 | 2 | 3 | 13 | 2 | 2 | 2 | 15 | 0 | 1 | 1 | 3 | 173 | 5 | 17 | 3 | 2 | 38 | 8 | 114 | 9 | 437 | 67 | 0 | 4 |
Figure S365. Get High-res Image Gene #66: 'Del Peak 25(10p15.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D66V6.png)
P value = 4.26e-07 (Fisher's exact test), Q value = 0.00058
Table S366. Gene #66: 'Del Peak 25(10p15.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 25(10P15.3) CNV | 94 | 186 | 132 | 68 |
DEL PEAK 25(10P15.3) WILD-TYPE | 354 | 425 | 556 | 140 |
Figure S366. Get High-res Image Gene #66: 'Del Peak 25(10p15.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D66V7.png)
P value = 1.22e-34 (Fisher's exact test), Q value = 1.9e-31
Table S367. Gene #66: 'Del Peak 25(10p15.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
DEL PEAK 25(10P15.3) CNV | 371 | 871 |
DEL PEAK 25(10P15.3) WILD-TYPE | 464 | 2945 |
Figure S367. Get High-res Image Gene #66: 'Del Peak 25(10p15.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D66V11.png)
P value = 0 (logrank test), Q value = 0
Table S368. Gene #67: 'Del Peak 26(10q23.31)' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4) |
DEL PEAK 26(10Q23.31) CNV | 1570 | 690 | 0.0 - 211.5 (12.0) |
DEL PEAK 26(10Q23.31) WILD-TYPE | 2800 | 716 | 0.0 - 224.0 (16.3) |
Figure S368. Get High-res Image Gene #67: 'Del Peak 26(10q23.31)' versus Clinical Feature #1: 'Time to Death'
![](D67V1.png)
P value = 5.8e-192 (Chi-square test), Q value = 1e-188
Table S369. Gene #67: 'Del Peak 26(10q23.31)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 26(10Q23.31) CNV | 57 | 486 | 247 | 94 | 56 | 82 | 90 | 268 | 1 | 212 | 1 | 50 |
DEL PEAK 26(10Q23.31) WILD-TYPE | 74 | 58 | 610 | 318 | 398 | 239 | 403 | 446 | 1 | 336 | 1 | 109 |
Figure S369. Get High-res Image Gene #67: 'Del Peak 26(10q23.31)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D67V3.png)
P value = 2.92e-11 (Fisher's exact test), Q value = 4.2e-08
Table S370. Gene #67: 'Del Peak 26(10q23.31)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
DEL PEAK 26(10Q23.31) CNV | 931 | 714 |
DEL PEAK 26(10Q23.31) WILD-TYPE | 1993 | 1003 |
Figure S370. Get High-res Image Gene #67: 'Del Peak 26(10q23.31)' versus Clinical Feature #4: 'GENDER'
![](D67V4.png)
P value = 2.27e-44 (Chi-square test), Q value = 3.6e-41
Table S371. Gene #67: 'Del Peak 26(10q23.31)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 26(10Q23.31) CNV | 85 | 8 | 28 | 82 | 33 | 3 | 90 | 3 | 13 | 72 | 4 | 1 | 4 | 0 | 3 | 0 | 3 | 1 | 0 | 1 | 2 | 159 | 0 | 3 | 1 | 1 | 18 | 1 | 41 | 7 | 214 | 25 | 1 | 19 |
DEL PEAK 26(10Q23.31) WILD-TYPE | 271 | 46 | 323 | 239 | 71 | 9 | 403 | 8 | 66 | 171 | 3 | 3 | 13 | 2 | 0 | 2 | 15 | 0 | 1 | 0 | 1 | 156 | 5 | 15 | 3 | 2 | 31 | 9 | 102 | 6 | 338 | 60 | 0 | 1 |
Figure S371. Get High-res Image Gene #67: 'Del Peak 26(10q23.31)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D67V6.png)
P value = 2.29e-29 (Fisher's exact test), Q value = 3.5e-26
Table S372. Gene #67: 'Del Peak 26(10q23.31)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
DEL PEAK 26(10Q23.31) CNV | 440 | 1210 |
DEL PEAK 26(10Q23.31) WILD-TYPE | 395 | 2606 |
Figure S372. Get High-res Image Gene #67: 'Del Peak 26(10q23.31)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D67V11.png)
P value = 7.23e-05 (t-test), Q value = 0.092
Table S373. Gene #67: 'Del Peak 26(10q23.31)' versus Clinical Feature #14: 'YEAROFTOBACCOSMOKINGONSET'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 605 | 1962.9 (12.6) |
DEL PEAK 26(10Q23.31) CNV | 202 | 1960.2 (10.9) |
DEL PEAK 26(10Q23.31) WILD-TYPE | 403 | 1964.2 (13.1) |
Figure S373. Get High-res Image Gene #67: 'Del Peak 26(10q23.31)' versus Clinical Feature #14: 'YEAROFTOBACCOSMOKINGONSET'
![](D67V14.png)
P value = 0 (logrank test), Q value = 0
Table S374. Gene #68: 'Del Peak 27(10q26.3)' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4) |
DEL PEAK 27(10Q26.3) CNV | 1493 | 677 | 0.0 - 211.5 (11.8) |
DEL PEAK 27(10Q26.3) WILD-TYPE | 2877 | 729 | 0.0 - 224.0 (16.4) |
Figure S374. Get High-res Image Gene #68: 'Del Peak 27(10q26.3)' versus Clinical Feature #1: 'Time to Death'
![](D68V1.png)
P value = 6.56e-206 (Chi-square test), Q value = 1.1e-202
Table S375. Gene #68: 'Del Peak 27(10q26.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 27(10Q26.3) CNV | 47 | 487 | 251 | 89 | 37 | 74 | 94 | 254 | 0 | 185 | 1 | 46 |
DEL PEAK 27(10Q26.3) WILD-TYPE | 84 | 57 | 606 | 323 | 417 | 247 | 399 | 460 | 2 | 363 | 1 | 113 |
Figure S375. Get High-res Image Gene #68: 'Del Peak 27(10q26.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D68V3.png)
P value = 1.1e-12 (Fisher's exact test), Q value = 1.6e-09
Table S376. Gene #68: 'Del Peak 27(10q26.3)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
DEL PEAK 27(10Q26.3) CNV | 875 | 691 |
DEL PEAK 27(10Q26.3) WILD-TYPE | 2049 | 1026 |
Figure S376. Get High-res Image Gene #68: 'Del Peak 27(10q26.3)' versus Clinical Feature #4: 'GENDER'
![](D68V4.png)
P value = 3.27e-38 (Chi-square test), Q value = 5.2e-35
Table S377. Gene #68: 'Del Peak 27(10q26.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 27(10Q26.3) CNV | 81 | 8 | 20 | 74 | 28 | 1 | 94 | 3 | 16 | 71 | 3 | 1 | 5 | 0 | 2 | 0 | 3 | 0 | 0 | 1 | 1 | 146 | 0 | 2 | 1 | 1 | 13 | 2 | 38 | 6 | 186 | 15 | 1 | 20 |
DEL PEAK 27(10Q26.3) WILD-TYPE | 275 | 46 | 331 | 247 | 76 | 11 | 399 | 8 | 63 | 172 | 4 | 3 | 12 | 2 | 1 | 2 | 15 | 1 | 1 | 0 | 2 | 169 | 5 | 16 | 3 | 2 | 36 | 8 | 105 | 7 | 366 | 70 | 0 | 0 |
Figure S377. Get High-res Image Gene #68: 'Del Peak 27(10q26.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D68V6.png)
P value = 1.05e-33 (Fisher's exact test), Q value = 1.6e-30
Table S378. Gene #68: 'Del Peak 27(10q26.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
DEL PEAK 27(10Q26.3) CNV | 435 | 1134 |
DEL PEAK 27(10Q26.3) WILD-TYPE | 400 | 2682 |
Figure S378. Get High-res Image Gene #68: 'Del Peak 27(10q26.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D68V11.png)
P value = 6.24e-116 (Chi-square test), Q value = 1e-112
Table S379. Gene #69: 'Del Peak 28(11p15.5)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 28(11P15.5) CNV | 66 | 125 | 249 | 54 | 78 | 101 | 17 | 259 | 0 | 327 | 0 | 23 |
DEL PEAK 28(11P15.5) WILD-TYPE | 65 | 419 | 608 | 358 | 376 | 220 | 476 | 455 | 2 | 221 | 2 | 136 |
Figure S379. Get High-res Image Gene #69: 'Del Peak 28(11p15.5)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D69V3.png)
P value = 2.96e-119 (Chi-square test), Q value = 5e-116
Table S380. Gene #69: 'Del Peak 28(11p15.5)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 28(11P15.5) CNV | 47 | 7 | 28 | 101 | 38 | 3 | 17 | 1 | 21 | 71 | 4 | 0 | 5 | 2 | 0 | 0 | 3 | 1 | 0 | 1 | 0 | 149 | 1 | 5 | 1 | 0 | 25 | 2 | 19 | 3 | 327 | 45 | 0 | 6 |
DEL PEAK 28(11P15.5) WILD-TYPE | 309 | 47 | 323 | 220 | 66 | 9 | 476 | 10 | 58 | 172 | 3 | 4 | 12 | 0 | 3 | 2 | 15 | 0 | 1 | 0 | 3 | 166 | 4 | 13 | 3 | 3 | 24 | 8 | 124 | 10 | 225 | 40 | 1 | 14 |
Figure S380. Get High-res Image Gene #69: 'Del Peak 28(11p15.5)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D69V6.png)
P value = 3.58e-10 (Fisher's exact test), Q value = 5.1e-07
Table S381. Gene #69: 'Del Peak 28(11p15.5)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 28(11P15.5) CNV | 70 | 173 | 106 | 59 |
DEL PEAK 28(11P15.5) WILD-TYPE | 378 | 438 | 582 | 149 |
Figure S381. Get High-res Image Gene #69: 'Del Peak 28(11p15.5)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D69V7.png)
P value = 0.000168 (Fisher's exact test), Q value = 0.21
Table S382. Gene #69: 'Del Peak 28(11p15.5)' versus Clinical Feature #8: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 1036 | 343 | 279 | 11 |
DEL PEAK 28(11P15.5) CNV | 207 | 98 | 76 | 6 |
DEL PEAK 28(11P15.5) WILD-TYPE | 829 | 245 | 203 | 5 |
Figure S382. Get High-res Image Gene #69: 'Del Peak 28(11p15.5)' versus Clinical Feature #8: 'PATHOLOGY.N'
![](D69V8.png)
P value = 1.79e-16 (Fisher's exact test), Q value = 2.7e-13
Table S383. Gene #69: 'Del Peak 28(11p15.5)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 28(11P15.5) CNV | 149 | 105 | 346 | 127 |
DEL PEAK 28(11P15.5) WILD-TYPE | 536 | 382 | 530 | 293 |
Figure S383. Get High-res Image Gene #69: 'Del Peak 28(11p15.5)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D69V10.png)
P value = 2.27e-95 (Chi-square test), Q value = 3.8e-92
Table S384. Gene #70: 'Del Peak 29(11q22.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 29(11Q22.3) CNV | 48 | 90 | 408 | 63 | 68 | 149 | 27 | 189 | 2 | 165 | 2 | 35 |
DEL PEAK 29(11Q22.3) WILD-TYPE | 83 | 454 | 449 | 349 | 386 | 172 | 466 | 525 | 0 | 383 | 0 | 124 |
Figure S384. Get High-res Image Gene #70: 'Del Peak 29(11q22.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D70V3.png)
P value = 6e-56 (Chi-square test), Q value = 9.7e-53
Table S385. Gene #70: 'Del Peak 29(11q22.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 29(11Q22.3) CNV | 56 | 7 | 27 | 149 | 50 | 6 | 27 | 2 | 19 | 55 | 4 | 0 | 4 | 1 | 0 | 0 | 4 | 0 | 0 | 0 | 0 | 98 | 2 | 5 | 2 | 0 | 18 | 6 | 28 | 6 | 169 | 36 | 0 | 5 |
DEL PEAK 29(11Q22.3) WILD-TYPE | 300 | 47 | 324 | 172 | 54 | 6 | 466 | 9 | 60 | 188 | 3 | 4 | 13 | 1 | 3 | 2 | 14 | 1 | 1 | 1 | 3 | 217 | 3 | 13 | 2 | 3 | 31 | 4 | 115 | 7 | 383 | 49 | 1 | 15 |
Figure S385. Get High-res Image Gene #70: 'Del Peak 29(11q22.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D70V6.png)
P value = 4.74e-09 (Fisher's exact test), Q value = 6.7e-06
Table S386. Gene #70: 'Del Peak 29(11q22.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 29(11Q22.3) CNV | 66 | 154 | 125 | 72 |
DEL PEAK 29(11Q22.3) WILD-TYPE | 382 | 457 | 563 | 136 |
Figure S386. Get High-res Image Gene #70: 'Del Peak 29(11q22.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D70V7.png)
P value = 3.12e-08 (Fisher's exact test), Q value = 4.4e-05
Table S387. Gene #70: 'Del Peak 29(11q22.3)' versus Clinical Feature #8: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 1036 | 343 | 279 | 11 |
DEL PEAK 29(11Q22.3) CNV | 193 | 95 | 97 | 4 |
DEL PEAK 29(11Q22.3) WILD-TYPE | 843 | 248 | 182 | 7 |
Figure S387. Get High-res Image Gene #70: 'Del Peak 29(11q22.3)' versus Clinical Feature #8: 'PATHOLOGY.N'
![](D70V8.png)
P value = 2.74e-05 (Fisher's exact test), Q value = 0.035
Table S388. Gene #70: 'Del Peak 29(11q22.3)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 29(11Q22.3) CNV | 124 | 102 | 219 | 126 |
DEL PEAK 29(11Q22.3) WILD-TYPE | 561 | 385 | 657 | 294 |
Figure S388. Get High-res Image Gene #70: 'Del Peak 29(11q22.3)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D70V10.png)
P value = 4.75e-90 (Chi-square test), Q value = 7.8e-87
Table S389. Gene #71: 'Del Peak 30(11q25)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 30(11Q25) CNV | 42 | 91 | 401 | 59 | 72 | 141 | 26 | 206 | 1 | 189 | 2 | 32 |
DEL PEAK 30(11Q25) WILD-TYPE | 89 | 453 | 456 | 353 | 382 | 180 | 467 | 508 | 1 | 359 | 0 | 127 |
Figure S389. Get High-res Image Gene #71: 'Del Peak 30(11q25)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D71V3.png)
P value = 0.000114 (Fisher's exact test), Q value = 0.14
Table S390. Gene #71: 'Del Peak 30(11q25)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
DEL PEAK 30(11Q25) CNV | 854 | 412 |
DEL PEAK 30(11Q25) WILD-TYPE | 2070 | 1305 |
Figure S390. Get High-res Image Gene #71: 'Del Peak 30(11q25)' versus Clinical Feature #4: 'GENDER'
![](D71V4.png)
P value = 1.71e-62 (Chi-square test), Q value = 2.8e-59
Table S391. Gene #71: 'Del Peak 30(11q25)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 30(11Q25) CNV | 53 | 6 | 27 | 141 | 51 | 6 | 26 | 2 | 20 | 50 | 4 | 0 | 3 | 1 | 0 | 0 | 4 | 0 | 0 | 1 | 1 | 118 | 2 | 5 | 2 | 0 | 12 | 4 | 25 | 6 | 192 | 40 | 0 | 4 |
DEL PEAK 30(11Q25) WILD-TYPE | 303 | 48 | 324 | 180 | 53 | 6 | 467 | 9 | 59 | 193 | 3 | 4 | 14 | 1 | 3 | 2 | 14 | 1 | 1 | 0 | 2 | 197 | 3 | 13 | 2 | 3 | 37 | 6 | 118 | 7 | 360 | 45 | 1 | 16 |
Figure S391. Get High-res Image Gene #71: 'Del Peak 30(11q25)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D71V6.png)
P value = 9.7e-11 (Fisher's exact test), Q value = 1.4e-07
Table S392. Gene #71: 'Del Peak 30(11q25)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 30(11Q25) CNV | 70 | 170 | 117 | 71 |
DEL PEAK 30(11Q25) WILD-TYPE | 378 | 441 | 571 | 137 |
Figure S392. Get High-res Image Gene #71: 'Del Peak 30(11q25)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D71V7.png)
P value = 3.1e-09 (Fisher's exact test), Q value = 4.4e-06
Table S393. Gene #71: 'Del Peak 30(11q25)' versus Clinical Feature #8: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 1036 | 343 | 279 | 11 |
DEL PEAK 30(11Q25) CNV | 195 | 105 | 98 | 3 |
DEL PEAK 30(11Q25) WILD-TYPE | 841 | 238 | 181 | 8 |
Figure S393. Get High-res Image Gene #71: 'Del Peak 30(11q25)' versus Clinical Feature #8: 'PATHOLOGY.N'
![](D71V8.png)
P value = 2.59e-05 (Fisher's exact test), Q value = 0.034
Table S394. Gene #71: 'Del Peak 30(11q25)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 30(11Q25) CNV | 136 | 102 | 235 | 131 |
DEL PEAK 30(11Q25) WILD-TYPE | 549 | 385 | 641 | 289 |
Figure S394. Get High-res Image Gene #71: 'Del Peak 30(11q25)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D71V10.png)
P value = 5.87e-21 (Chi-square test), Q value = 8.9e-18
Table S395. Gene #72: 'Del Peak 31(12p13.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 31(12P13.1) CNV | 17 | 72 | 150 | 45 | 37 | 30 | 6 | 134 | 0 | 90 | 1 | 29 |
DEL PEAK 31(12P13.1) WILD-TYPE | 114 | 472 | 707 | 367 | 417 | 291 | 487 | 580 | 2 | 458 | 1 | 130 |
Figure S395. Get High-res Image Gene #72: 'Del Peak 31(12p13.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D72V3.png)
P value = 2.28e-07 (Fisher's exact test), Q value = 0.00031
Table S396. Gene #72: 'Del Peak 31(12p13.1)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
DEL PEAK 31(12P13.1) CNV | 444 | 170 |
DEL PEAK 31(12P13.1) WILD-TYPE | 2480 | 1547 |
Figure S396. Get High-res Image Gene #72: 'Del Peak 31(12p13.1)' versus Clinical Feature #4: 'GENDER'
![](D72V4.png)
P value = 2.52e-36 (Chi-square test), Q value = 4e-33
Table S397. Gene #72: 'Del Peak 31(12p13.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 31(12P13.1) CNV | 45 | 0 | 13 | 30 | 24 | 1 | 6 | 1 | 25 | 69 | 1 | 0 | 7 | 1 | 1 | 0 | 5 | 0 | 0 | 0 | 1 | 21 | 2 | 2 | 1 | 1 | 5 | 1 | 28 | 1 | 91 | 22 | 0 | 3 |
DEL PEAK 31(12P13.1) WILD-TYPE | 311 | 54 | 338 | 291 | 80 | 11 | 487 | 10 | 54 | 174 | 6 | 4 | 10 | 1 | 2 | 2 | 13 | 1 | 1 | 1 | 2 | 294 | 3 | 16 | 3 | 2 | 44 | 9 | 115 | 12 | 461 | 63 | 1 | 17 |
Figure S397. Get High-res Image Gene #72: 'Del Peak 31(12p13.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D72V6.png)
P value = 4.66e-53 (Chi-square test), Q value = 7.5e-50
Table S398. Gene #73: 'Del Peak 32(12q23.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 32(12Q23.1) CNV | 21 | 61 | 149 | 48 | 34 | 36 | 6 | 138 | 1 | 187 | 0 | 24 |
DEL PEAK 32(12Q23.1) WILD-TYPE | 110 | 483 | 708 | 364 | 420 | 285 | 487 | 576 | 1 | 361 | 2 | 135 |
Figure S398. Get High-res Image Gene #73: 'Del Peak 32(12q23.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D73V3.png)
P value = 1.3e-08 (Fisher's exact test), Q value = 1.8e-05
Table S399. Gene #73: 'Del Peak 32(12q23.1)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
DEL PEAK 32(12Q23.1) CNV | 511 | 195 |
DEL PEAK 32(12Q23.1) WILD-TYPE | 2413 | 1522 |
Figure S399. Get High-res Image Gene #73: 'Del Peak 32(12q23.1)' versus Clinical Feature #4: 'GENDER'
![](D73V4.png)
P value = 2.77e-55 (Chi-square test), Q value = 4.5e-52
Table S400. Gene #73: 'Del Peak 32(12q23.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 32(12Q23.1) CNV | 44 | 3 | 10 | 36 | 18 | 0 | 6 | 0 | 17 | 54 | 2 | 0 | 9 | 1 | 0 | 0 | 8 | 0 | 0 | 0 | 1 | 44 | 1 | 1 | 0 | 2 | 4 | 1 | 23 | 1 | 188 | 23 | 0 | 3 |
DEL PEAK 32(12Q23.1) WILD-TYPE | 312 | 51 | 341 | 285 | 86 | 12 | 487 | 11 | 62 | 189 | 5 | 4 | 8 | 1 | 3 | 2 | 10 | 1 | 1 | 1 | 2 | 271 | 4 | 17 | 4 | 1 | 45 | 9 | 120 | 12 | 364 | 62 | 1 | 17 |
Figure S400. Get High-res Image Gene #73: 'Del Peak 32(12q23.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D73V6.png)
P value = 3.72e-05 (Fisher's exact test), Q value = 0.048
Table S401. Gene #73: 'Del Peak 32(12q23.1)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 32(12Q23.1) CNV | 29 | 96 | 82 | 20 |
DEL PEAK 32(12Q23.1) WILD-TYPE | 419 | 515 | 606 | 188 |
Figure S401. Get High-res Image Gene #73: 'Del Peak 32(12q23.1)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D73V7.png)
P value = 1.39e-05 (Chi-square test), Q value = 0.018
Table S402. Gene #73: 'Del Peak 32(12q23.1)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 1398 | 167 | 9 | 1 | 148 |
DEL PEAK 32(12Q23.1) CNV | 145 | 15 | 1 | 1 | 33 |
DEL PEAK 32(12Q23.1) WILD-TYPE | 1253 | 152 | 8 | 0 | 115 |
Figure S402. Get High-res Image Gene #73: 'Del Peak 32(12q23.1)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'
![](D73V9.png)
P value = 1.58e-06 (Fisher's exact test), Q value = 0.0021
Table S403. Gene #73: 'Del Peak 32(12q23.1)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 32(12Q23.1) CNV | 85 | 62 | 189 | 74 |
DEL PEAK 32(12Q23.1) WILD-TYPE | 600 | 425 | 687 | 346 |
Figure S403. Get High-res Image Gene #73: 'Del Peak 32(12q23.1)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D73V10.png)
P value = 2.68e-59 (Chi-square test), Q value = 4.3e-56
Table S404. Gene #74: 'Del Peak 33(12q24.33)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 33(12Q24.33) CNV | 24 | 68 | 150 | 45 | 46 | 42 | 8 | 152 | 2 | 205 | 0 | 26 |
DEL PEAK 33(12Q24.33) WILD-TYPE | 107 | 476 | 707 | 367 | 408 | 279 | 485 | 562 | 0 | 343 | 2 | 133 |
Figure S404. Get High-res Image Gene #74: 'Del Peak 33(12q24.33)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D74V3.png)
P value = 1.54e-08 (Fisher's exact test), Q value = 2.2e-05
Table S405. Gene #74: 'Del Peak 33(12q24.33)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
DEL PEAK 33(12Q24.33) CNV | 553 | 216 |
DEL PEAK 33(12Q24.33) WILD-TYPE | 2371 | 1501 |
Figure S405. Get High-res Image Gene #74: 'Del Peak 33(12q24.33)' versus Clinical Feature #4: 'GENDER'
![](D74V4.png)
P value = 1.4e-61 (Chi-square test), Q value = 2.3e-58
Table S406. Gene #74: 'Del Peak 33(12q24.33)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 33(12Q24.33) CNV | 42 | 2 | 14 | 42 | 21 | 0 | 8 | 2 | 17 | 60 | 4 | 0 | 7 | 0 | 1 | 0 | 7 | 0 | 0 | 0 | 1 | 51 | 3 | 1 | 0 | 2 | 7 | 1 | 25 | 1 | 207 | 31 | 0 | 3 |
DEL PEAK 33(12Q24.33) WILD-TYPE | 314 | 52 | 337 | 279 | 83 | 12 | 485 | 9 | 62 | 183 | 3 | 4 | 10 | 2 | 2 | 2 | 11 | 1 | 1 | 1 | 2 | 264 | 2 | 17 | 4 | 1 | 42 | 9 | 118 | 12 | 345 | 54 | 1 | 17 |
Figure S406. Get High-res Image Gene #74: 'Del Peak 33(12q24.33)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D74V6.png)
P value = 9.64e-06 (Fisher's exact test), Q value = 0.013
Table S407. Gene #74: 'Del Peak 33(12q24.33)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 33(12Q24.33) CNV | 33 | 106 | 77 | 30 |
DEL PEAK 33(12Q24.33) WILD-TYPE | 415 | 505 | 611 | 178 |
Figure S407. Get High-res Image Gene #74: 'Del Peak 33(12q24.33)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D74V7.png)
P value = 2.17e-08 (Fisher's exact test), Q value = 3e-05
Table S408. Gene #74: 'Del Peak 33(12q24.33)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 33(12Q24.33) CNV | 94 | 61 | 208 | 82 |
DEL PEAK 33(12Q24.33) WILD-TYPE | 591 | 426 | 668 | 338 |
Figure S408. Get High-res Image Gene #74: 'Del Peak 33(12q24.33)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D74V10.png)
P value = 9.08e-157 (Chi-square test), Q value = 1.6e-153
Table S409. Gene #75: 'Del Peak 34(13q11)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 34(13Q11) CNV | 31 | 177 | 345 | 10 | 69 | 132 | 73 | 431 | 1 | 308 | 2 | 9 |
DEL PEAK 34(13Q11) WILD-TYPE | 100 | 367 | 512 | 402 | 385 | 189 | 420 | 283 | 1 | 240 | 0 | 150 |
Figure S409. Get High-res Image Gene #75: 'Del Peak 34(13q11)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D75V3.png)
P value = 2.19e-151 (Chi-square test), Q value = 3.7e-148
Table S410. Gene #75: 'Del Peak 34(13q11)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 34(13Q11) CNV | 8 | 2 | 32 | 132 | 35 | 2 | 73 | 6 | 42 | 140 | 4 | 1 | 13 | 2 | 0 | 0 | 8 | 1 | 0 | 1 | 2 | 210 | 3 | 3 | 1 | 0 | 13 | 3 | 5 | 4 | 311 | 34 | 0 | 9 |
DEL PEAK 34(13Q11) WILD-TYPE | 348 | 52 | 319 | 189 | 69 | 10 | 420 | 5 | 37 | 103 | 3 | 3 | 4 | 0 | 3 | 2 | 10 | 0 | 1 | 0 | 1 | 105 | 2 | 15 | 3 | 3 | 36 | 7 | 138 | 9 | 241 | 51 | 1 | 11 |
Figure S410. Get High-res Image Gene #75: 'Del Peak 34(13q11)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D75V6.png)
P value = 1.89e-28 (Fisher's exact test), Q value = 2.9e-25
Table S411. Gene #75: 'Del Peak 34(13q11)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 34(13Q11) CNV | 122 | 266 | 109 | 80 |
DEL PEAK 34(13Q11) WILD-TYPE | 326 | 345 | 579 | 128 |
Figure S411. Get High-res Image Gene #75: 'Del Peak 34(13q11)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D75V7.png)
P value = 7.09e-06 (Chi-square test), Q value = 0.0094
Table S412. Gene #75: 'Del Peak 34(13q11)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 1398 | 167 | 9 | 1 | 148 |
DEL PEAK 34(13Q11) CNV | 384 | 32 | 0 | 0 | 65 |
DEL PEAK 34(13Q11) WILD-TYPE | 1014 | 135 | 9 | 1 | 83 |
Figure S412. Get High-res Image Gene #75: 'Del Peak 34(13q11)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'
![](D75V9.png)
P value = 9.02e-08 (Fisher's exact test), Q value = 0.00013
Table S413. Gene #75: 'Del Peak 34(13q11)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 34(13Q11) CNV | 234 | 126 | 364 | 158 |
DEL PEAK 34(13Q11) WILD-TYPE | 451 | 361 | 512 | 262 |
Figure S413. Get High-res Image Gene #75: 'Del Peak 34(13q11)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D75V10.png)
P value = 1.62e-06 (Chi-square test), Q value = 0.0022
Table S414. Gene #75: 'Del Peak 34(13q11)' versus Clinical Feature #13: 'TOBACCOSMOKINGHISTORYINDICATOR'
nPatients | 1 | 2 | 3 | 4 | 5 | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER |
---|---|---|---|---|---|---|---|---|---|
ALL | 15 | 16 | 22 | 25 | 2 | 342 | 208 | 237 | 116 |
DEL PEAK 34(13Q11) CNV | 3 | 4 | 6 | 4 | 1 | 205 | 101 | 129 | 52 |
DEL PEAK 34(13Q11) WILD-TYPE | 12 | 12 | 16 | 21 | 1 | 137 | 107 | 108 | 64 |
Figure S414. Get High-res Image Gene #75: 'Del Peak 34(13q11)' versus Clinical Feature #13: 'TOBACCOSMOKINGHISTORYINDICATOR'
![](D75V13.png)
P value = 5.46e-06 (logrank test), Q value = 0.0073
Table S415. Gene #76: 'Del Peak 35(13q14.2)' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4) |
DEL PEAK 35(13Q14.2) CNV | 1689 | 634 | 0.0 - 211.5 (15.1) |
DEL PEAK 35(13Q14.2) WILD-TYPE | 2681 | 772 | 0.0 - 224.0 (14.1) |
Figure S415. Get High-res Image Gene #76: 'Del Peak 35(13q14.2)' versus Clinical Feature #1: 'Time to Death'
![](D76V1.png)
P value = 1.57e-163 (Chi-square test), Q value = 2.7e-160
Table S416. Gene #76: 'Del Peak 35(13q14.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 35(13Q14.2) CNV | 51 | 230 | 396 | 15 | 74 | 136 | 77 | 434 | 1 | 340 | 2 | 10 |
DEL PEAK 35(13Q14.2) WILD-TYPE | 80 | 314 | 461 | 397 | 380 | 185 | 416 | 280 | 1 | 208 | 0 | 149 |
Figure S416. Get High-res Image Gene #76: 'Del Peak 35(13q14.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D76V3.png)
P value = 7.05e-156 (Chi-square test), Q value = 1.2e-152
Table S417. Gene #76: 'Del Peak 35(13q14.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 35(13Q14.2) CNV | 12 | 2 | 42 | 136 | 44 | 3 | 77 | 7 | 40 | 136 | 3 | 1 | 11 | 2 | 1 | 0 | 7 | 1 | 0 | 1 | 2 | 221 | 3 | 4 | 1 | 0 | 20 | 4 | 6 | 4 | 343 | 28 | 0 | 11 |
DEL PEAK 35(13Q14.2) WILD-TYPE | 344 | 52 | 309 | 185 | 60 | 9 | 416 | 4 | 39 | 107 | 4 | 3 | 6 | 0 | 2 | 2 | 11 | 0 | 1 | 0 | 1 | 94 | 2 | 14 | 3 | 3 | 29 | 6 | 137 | 9 | 209 | 57 | 1 | 9 |
Figure S417. Get High-res Image Gene #76: 'Del Peak 35(13q14.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D76V6.png)
P value = 2.06e-27 (Fisher's exact test), Q value = 3.2e-24
Table S418. Gene #76: 'Del Peak 35(13q14.2)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 35(13Q14.2) CNV | 141 | 266 | 109 | 74 |
DEL PEAK 35(13Q14.2) WILD-TYPE | 307 | 345 | 579 | 134 |
Figure S418. Get High-res Image Gene #76: 'Del Peak 35(13q14.2)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D76V7.png)
P value = 2.6e-05 (Chi-square test), Q value = 0.034
Table S419. Gene #76: 'Del Peak 35(13q14.2)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 1398 | 167 | 9 | 1 | 148 |
DEL PEAK 35(13Q14.2) CNV | 400 | 32 | 1 | 1 | 64 |
DEL PEAK 35(13Q14.2) WILD-TYPE | 998 | 135 | 8 | 0 | 84 |
Figure S419. Get High-res Image Gene #76: 'Del Peak 35(13q14.2)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'
![](D76V9.png)
P value = 1.27e-08 (Fisher's exact test), Q value = 1.8e-05
Table S420. Gene #76: 'Del Peak 35(13q14.2)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 35(13Q14.2) CNV | 247 | 134 | 389 | 156 |
DEL PEAK 35(13Q14.2) WILD-TYPE | 438 | 353 | 487 | 264 |
Figure S420. Get High-res Image Gene #76: 'Del Peak 35(13q14.2)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D76V10.png)
P value = 1.3e-49 (Chi-square test), Q value = 2.1e-46
Table S421. Gene #77: 'Del Peak 36(14q24.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 36(14Q24.1) CNV | 40 | 168 | 267 | 125 | 55 | 40 | 218 | 229 | 1 | 273 | 1 | 66 |
DEL PEAK 36(14Q24.1) WILD-TYPE | 91 | 376 | 590 | 287 | 399 | 281 | 275 | 485 | 1 | 275 | 1 | 93 |
Figure S421. Get High-res Image Gene #77: 'Del Peak 36(14q24.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D77V3.png)
P value = 2.93e-51 (Chi-square test), Q value = 4.7e-48
Table S422. Gene #77: 'Del Peak 36(14q24.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 36(14Q24.1) CNV | 119 | 5 | 21 | 40 | 36 | 1 | 218 | 5 | 21 | 70 | 3 | 0 | 4 | 1 | 0 | 1 | 3 | 0 | 0 | 1 | 0 | 117 | 0 | 4 | 2 | 1 | 16 | 2 | 64 | 1 | 275 | 30 | 0 | 5 |
DEL PEAK 36(14Q24.1) WILD-TYPE | 237 | 49 | 330 | 281 | 68 | 11 | 275 | 6 | 58 | 173 | 4 | 4 | 13 | 1 | 3 | 1 | 15 | 1 | 1 | 0 | 3 | 198 | 5 | 14 | 2 | 2 | 33 | 8 | 79 | 12 | 277 | 55 | 1 | 15 |
Figure S422. Get High-res Image Gene #77: 'Del Peak 36(14q24.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D77V6.png)
P value = 2.02e-05 (Fisher's exact test), Q value = 0.026
Table S423. Gene #77: 'Del Peak 36(14q24.1)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 36(14Q24.1) CNV | 149 | 191 | 257 | 41 |
DEL PEAK 36(14Q24.1) WILD-TYPE | 299 | 420 | 431 | 167 |
Figure S423. Get High-res Image Gene #77: 'Del Peak 36(14q24.1)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D77V7.png)
P value = 3.01e-05 (Fisher's exact test), Q value = 0.039
Table S424. Gene #77: 'Del Peak 36(14q24.1)' versus Clinical Feature #8: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 1036 | 343 | 279 | 11 |
DEL PEAK 36(14Q24.1) CNV | 327 | 133 | 59 | 4 |
DEL PEAK 36(14Q24.1) WILD-TYPE | 709 | 210 | 220 | 7 |
Figure S424. Get High-res Image Gene #77: 'Del Peak 36(14q24.1)' versus Clinical Feature #8: 'PATHOLOGY.N'
![](D77V8.png)
P value = 2.81e-08 (Fisher's exact test), Q value = 3.9e-05
Table S425. Gene #77: 'Del Peak 36(14q24.1)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 36(14Q24.1) CNV | 227 | 152 | 389 | 130 |
DEL PEAK 36(14Q24.1) WILD-TYPE | 458 | 335 | 487 | 290 |
Figure S425. Get High-res Image Gene #77: 'Del Peak 36(14q24.1)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D77V10.png)
P value = 7.95e-75 (Chi-square test), Q value = 1.3e-71
Table S426. Gene #78: 'Del Peak 37(15q11.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 37(15Q11.2) CNV | 49 | 116 | 295 | 159 | 93 | 68 | 39 | 314 | 2 | 283 | 2 | 71 |
DEL PEAK 37(15Q11.2) WILD-TYPE | 82 | 428 | 562 | 253 | 361 | 253 | 454 | 400 | 0 | 265 | 0 | 88 |
Figure S426. Get High-res Image Gene #78: 'Del Peak 37(15q11.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D78V3.png)
P value = 3.56e-05 (Fisher's exact test), Q value = 0.046
Table S427. Gene #78: 'Del Peak 37(15q11.2)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
DEL PEAK 37(15Q11.2) CNV | 1005 | 489 |
DEL PEAK 37(15Q11.2) WILD-TYPE | 1919 | 1228 |
Figure S427. Get High-res Image Gene #78: 'Del Peak 37(15q11.2)' versus Clinical Feature #4: 'GENDER'
![](D78V4.png)
P value = 3.04e-80 (Chi-square test), Q value = 5e-77
Table S428. Gene #78: 'Del Peak 37(15q11.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 37(15Q11.2) CNV | 145 | 13 | 38 | 68 | 40 | 4 | 39 | 4 | 33 | 143 | 2 | 0 | 9 | 1 | 3 | 0 | 11 | 0 | 0 | 1 | 2 | 104 | 1 | 5 | 1 | 0 | 16 | 3 | 64 | 6 | 287 | 50 | 0 | 6 |
DEL PEAK 37(15Q11.2) WILD-TYPE | 211 | 41 | 313 | 253 | 64 | 8 | 454 | 7 | 46 | 100 | 5 | 4 | 8 | 1 | 0 | 2 | 7 | 1 | 1 | 0 | 1 | 211 | 4 | 13 | 3 | 3 | 33 | 7 | 79 | 7 | 265 | 35 | 1 | 14 |
Figure S428. Get High-res Image Gene #78: 'Del Peak 37(15q11.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D78V6.png)
P value = 7.04e-07 (Fisher's exact test), Q value = 0.00096
Table S429. Gene #78: 'Del Peak 37(15q11.2)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 37(15Q11.2) CNV | 92 | 215 | 229 | 60 |
DEL PEAK 37(15Q11.2) WILD-TYPE | 356 | 396 | 459 | 148 |
Figure S429. Get High-res Image Gene #78: 'Del Peak 37(15q11.2)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D78V7.png)
P value = 7.75e-07 (Fisher's exact test), Q value = 0.0011
Table S430. Gene #78: 'Del Peak 37(15q11.2)' versus Clinical Feature #8: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 1036 | 343 | 279 | 11 |
DEL PEAK 37(15Q11.2) CNV | 299 | 144 | 117 | 5 |
DEL PEAK 37(15Q11.2) WILD-TYPE | 737 | 199 | 162 | 6 |
Figure S430. Get High-res Image Gene #78: 'Del Peak 37(15q11.2)' versus Clinical Feature #8: 'PATHOLOGY.N'
![](D78V8.png)
P value = 3.67e-10 (Fisher's exact test), Q value = 5.3e-07
Table S431. Gene #78: 'Del Peak 37(15q11.2)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 37(15Q11.2) CNV | 182 | 170 | 377 | 140 |
DEL PEAK 37(15Q11.2) WILD-TYPE | 503 | 317 | 499 | 280 |
Figure S431. Get High-res Image Gene #78: 'Del Peak 37(15q11.2)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D78V10.png)
P value = 1.66e-06 (Fisher's exact test), Q value = 0.0022
Table S432. Gene #78: 'Del Peak 37(15q11.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
DEL PEAK 37(15Q11.2) CNV | 211 | 1288 |
DEL PEAK 37(15Q11.2) WILD-TYPE | 624 | 2528 |
Figure S432. Get High-res Image Gene #78: 'Del Peak 37(15q11.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D78V11.png)
P value = 4.09e-92 (Chi-square test), Q value = 6.7e-89
Table S433. Gene #79: 'Del Peak 38(15q15.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 38(15Q15.1) CNV | 50 | 140 | 313 | 149 | 108 | 74 | 38 | 322 | 2 | 343 | 2 | 74 |
DEL PEAK 38(15Q15.1) WILD-TYPE | 81 | 404 | 544 | 263 | 346 | 247 | 455 | 392 | 0 | 205 | 0 | 85 |
Figure S433. Get High-res Image Gene #79: 'Del Peak 38(15q15.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D79V3.png)
P value = 1.95e-07 (Fisher's exact test), Q value = 0.00027
Table S434. Gene #79: 'Del Peak 38(15q15.1)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
DEL PEAK 38(15Q15.1) CNV | 1101 | 517 |
DEL PEAK 38(15Q15.1) WILD-TYPE | 1823 | 1200 |
Figure S434. Get High-res Image Gene #79: 'Del Peak 38(15q15.1)' versus Clinical Feature #4: 'GENDER'
![](D79V4.png)
P value = 2.29e-101 (Chi-square test), Q value = 3.8e-98
Table S435. Gene #79: 'Del Peak 38(15q15.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 38(15Q15.1) CNV | 136 | 12 | 46 | 74 | 43 | 4 | 38 | 4 | 34 | 147 | 2 | 0 | 9 | 1 | 3 | 0 | 11 | 0 | 0 | 1 | 1 | 108 | 1 | 7 | 1 | 0 | 18 | 3 | 67 | 6 | 347 | 55 | 0 | 6 |
DEL PEAK 38(15Q15.1) WILD-TYPE | 220 | 42 | 305 | 247 | 61 | 8 | 455 | 7 | 45 | 96 | 5 | 4 | 8 | 1 | 0 | 2 | 7 | 1 | 1 | 0 | 2 | 207 | 4 | 11 | 3 | 3 | 31 | 7 | 76 | 7 | 205 | 30 | 1 | 14 |
Figure S435. Get High-res Image Gene #79: 'Del Peak 38(15q15.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D79V6.png)
P value = 4.02e-07 (Fisher's exact test), Q value = 0.00055
Table S436. Gene #79: 'Del Peak 38(15q15.1)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 38(15Q15.1) CNV | 92 | 220 | 225 | 62 |
DEL PEAK 38(15Q15.1) WILD-TYPE | 356 | 391 | 463 | 146 |
Figure S436. Get High-res Image Gene #79: 'Del Peak 38(15q15.1)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D79V7.png)
P value = 9.24e-07 (Fisher's exact test), Q value = 0.0013
Table S437. Gene #79: 'Del Peak 38(15q15.1)' versus Clinical Feature #8: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 1036 | 343 | 279 | 11 |
DEL PEAK 38(15Q15.1) CNV | 300 | 146 | 115 | 5 |
DEL PEAK 38(15Q15.1) WILD-TYPE | 736 | 197 | 164 | 6 |
Figure S437. Get High-res Image Gene #79: 'Del Peak 38(15q15.1)' versus Clinical Feature #8: 'PATHOLOGY.N'
![](D79V8.png)
P value = 1.31e-16 (Fisher's exact test), Q value = 2e-13
Table S438. Gene #79: 'Del Peak 38(15q15.1)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 38(15Q15.1) CNV | 187 | 174 | 424 | 145 |
DEL PEAK 38(15Q15.1) WILD-TYPE | 498 | 313 | 452 | 275 |
Figure S438. Get High-res Image Gene #79: 'Del Peak 38(15q15.1)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D79V10.png)
P value = 2.13e-05 (Fisher's exact test), Q value = 0.028
Table S439. Gene #79: 'Del Peak 38(15q15.1)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
DEL PEAK 38(15Q15.1) CNV | 239 | 1385 |
DEL PEAK 38(15Q15.1) WILD-TYPE | 596 | 2431 |
Figure S439. Get High-res Image Gene #79: 'Del Peak 38(15q15.1)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D79V11.png)
P value = 3.06e-05 (logrank test), Q value = 0.039
Table S440. Gene #80: 'Del Peak 39(16p13.3)' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4) |
DEL PEAK 39(16P13.3) CNV | 722 | 291 | 0.0 - 211.5 (15.3) |
DEL PEAK 39(16P13.3) WILD-TYPE | 3648 | 1115 | 0.0 - 224.0 (14.3) |
Figure S440. Get High-res Image Gene #80: 'Del Peak 39(16p13.3)' versus Clinical Feature #1: 'Time to Death'
![](D80V1.png)
P value = 3.17e-130 (Chi-square test), Q value = 5.4e-127
Table S441. Gene #80: 'Del Peak 39(16p13.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 39(16P13.3) CNV | 39 | 66 | 49 | 45 | 58 | 37 | 12 | 172 | 2 | 264 | 1 | 13 |
DEL PEAK 39(16P13.3) WILD-TYPE | 92 | 478 | 808 | 367 | 396 | 284 | 481 | 542 | 0 | 284 | 1 | 146 |
Figure S441. Get High-res Image Gene #80: 'Del Peak 39(16p13.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D80V3.png)
P value = 1.02e-100 (Chi-square test), Q value = 1.7e-97
Table S442. Gene #80: 'Del Peak 39(16p13.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 39(16P13.3) CNV | 39 | 6 | 20 | 37 | 4 | 0 | 12 | 2 | 15 | 44 | 4 | 0 | 3 | 0 | 0 | 0 | 2 | 1 | 0 | 0 | 1 | 99 | 0 | 4 | 1 | 0 | 15 | 1 | 10 | 2 | 267 | 34 | 0 | 3 |
DEL PEAK 39(16P13.3) WILD-TYPE | 317 | 48 | 331 | 284 | 100 | 12 | 481 | 9 | 64 | 199 | 3 | 4 | 14 | 2 | 3 | 2 | 16 | 0 | 1 | 1 | 2 | 216 | 5 | 14 | 3 | 3 | 34 | 9 | 133 | 11 | 285 | 51 | 1 | 17 |
Figure S442. Get High-res Image Gene #80: 'Del Peak 39(16p13.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D80V6.png)
P value = 8.54e-13 (Fisher's exact test), Q value = 1.2e-09
Table S443. Gene #80: 'Del Peak 39(16p13.3)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 39(16P13.3) CNV | 103 | 81 | 260 | 79 |
DEL PEAK 39(16P13.3) WILD-TYPE | 582 | 406 | 616 | 341 |
Figure S443. Get High-res Image Gene #80: 'Del Peak 39(16p13.3)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D80V10.png)
P value = 3.38e-09 (Fisher's exact test), Q value = 4.8e-06
Table S444. Gene #80: 'Del Peak 39(16p13.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
DEL PEAK 39(16P13.3) CNV | 82 | 681 |
DEL PEAK 39(16P13.3) WILD-TYPE | 753 | 3135 |
Figure S444. Get High-res Image Gene #80: 'Del Peak 39(16p13.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D80V11.png)
P value = 7.08e-09 (Chi-square test), Q value = 1e-05
Table S445. Gene #80: 'Del Peak 39(16p13.3)' versus Clinical Feature #20: 'NEOPLASM.DISEASESTAGE'
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 71 | 45 | 2 | 34 | 246 | 165 | 29 | 107 | 22 | 36 | 35 | 12 |
DEL PEAK 39(16P13.3) CNV | 5 | 0 | 0 | 4 | 18 | 11 | 12 | 4 | 1 | 3 | 8 | 2 |
DEL PEAK 39(16P13.3) WILD-TYPE | 66 | 45 | 2 | 30 | 228 | 154 | 17 | 103 | 21 | 33 | 27 | 10 |
Figure S445. Get High-res Image Gene #80: 'Del Peak 39(16p13.3)' versus Clinical Feature #20: 'NEOPLASM.DISEASESTAGE'
![](D80V20.png)
P value = 2.05e-249 (Chi-square test), Q value = 3.6e-246
Table S446. Gene #81: 'Del Peak 40(16q23.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 40(16Q23.1) CNV | 37 | 96 | 543 | 49 | 132 | 60 | 19 | 257 | 1 | 426 | 2 | 23 |
DEL PEAK 40(16Q23.1) WILD-TYPE | 94 | 448 | 314 | 363 | 322 | 261 | 474 | 457 | 1 | 122 | 0 | 136 |
Figure S446. Get High-res Image Gene #81: 'Del Peak 40(16q23.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D81V3.png)
P value = 5.49e-72 (Fisher's exact test), Q value = 8.9e-69
Table S447. Gene #81: 'Del Peak 40(16q23.1)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
DEL PEAK 40(16Q23.1) CNV | 1312 | 333 |
DEL PEAK 40(16Q23.1) WILD-TYPE | 1612 | 1384 |
Figure S447. Get High-res Image Gene #81: 'Del Peak 40(16q23.1)' versus Clinical Feature #4: 'GENDER'
![](D81V4.png)
P value = 8.25e-194 (Chi-square test), Q value = 1.4e-190
Table S448. Gene #81: 'Del Peak 40(16q23.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 40(16Q23.1) CNV | 40 | 9 | 59 | 60 | 49 | 12 | 19 | 5 | 26 | 79 | 3 | 1 | 7 | 2 | 1 | 0 | 6 | 0 | 0 | 0 | 1 | 123 | 4 | 6 | 2 | 1 | 10 | 6 | 20 | 2 | 429 | 67 | 0 | 6 |
DEL PEAK 40(16Q23.1) WILD-TYPE | 316 | 45 | 292 | 261 | 55 | 0 | 474 | 6 | 53 | 164 | 4 | 3 | 10 | 0 | 2 | 2 | 12 | 1 | 1 | 1 | 2 | 192 | 1 | 12 | 2 | 2 | 39 | 4 | 123 | 11 | 123 | 18 | 1 | 14 |
Figure S448. Get High-res Image Gene #81: 'Del Peak 40(16q23.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D81V6.png)
P value = 4.44e-10 (Fisher's exact test), Q value = 6.4e-07
Table S449. Gene #81: 'Del Peak 40(16q23.1)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 40(16Q23.1) CNV | 63 | 161 | 88 | 45 |
DEL PEAK 40(16Q23.1) WILD-TYPE | 385 | 450 | 600 | 163 |
Figure S449. Get High-res Image Gene #81: 'Del Peak 40(16q23.1)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D81V7.png)
P value = 3.97e-34 (Fisher's exact test), Q value = 6.2e-31
Table S450. Gene #81: 'Del Peak 40(16q23.1)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 40(16Q23.1) CNV | 139 | 108 | 412 | 116 |
DEL PEAK 40(16Q23.1) WILD-TYPE | 546 | 379 | 464 | 304 |
Figure S450. Get High-res Image Gene #81: 'Del Peak 40(16q23.1)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D81V10.png)
P value = 9.07e-05 (Fisher's exact test), Q value = 0.11
Table S451. Gene #81: 'Del Peak 40(16q23.1)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
DEL PEAK 40(16Q23.1) CNV | 248 | 1405 |
DEL PEAK 40(16Q23.1) WILD-TYPE | 587 | 2411 |
Figure S451. Get High-res Image Gene #81: 'Del Peak 40(16q23.1)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D81V11.png)
P value = 1.07e-240 (Chi-square test), Q value = 1.8e-237
Table S452. Gene #82: 'Del Peak 41(17p12)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 41(17P12) CNV | 67 | 68 | 519 | 228 | 102 | 76 | 50 | 405 | 2 | 463 | 1 | 110 |
DEL PEAK 41(17P12) WILD-TYPE | 64 | 476 | 338 | 184 | 352 | 245 | 443 | 309 | 0 | 85 | 1 | 49 |
Figure S452. Get High-res Image Gene #82: 'Del Peak 41(17p12)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D82V3.png)
P value = 1.18e-26 (Fisher's exact test), Q value = 1.8e-23
Table S453. Gene #82: 'Del Peak 41(17p12)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
DEL PEAK 41(17P12) CNV | 1494 | 601 |
DEL PEAK 41(17P12) WILD-TYPE | 1430 | 1116 |
Figure S453. Get High-res Image Gene #82: 'Del Peak 41(17p12)' versus Clinical Feature #4: 'GENDER'
![](D82V4.png)
P value = 2.8e-05 (t-test), Q value = 0.036
Table S454. Gene #82: 'Del Peak 41(17p12)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 641 | 73.6 (23.9) |
DEL PEAK 41(17P12) CNV | 199 | 66.7 (30.4) |
DEL PEAK 41(17P12) WILD-TYPE | 442 | 76.7 (19.6) |
Figure S454. Get High-res Image Gene #82: 'Del Peak 41(17p12)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'
![](D82V5.png)
P value = 1e-188 (Chi-square test), Q value = 1.7e-185
Table S455. Gene #82: 'Del Peak 41(17p12)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 41(17P12) CNV | 213 | 14 | 36 | 76 | 65 | 7 | 50 | 6 | 35 | 139 | 5 | 2 | 10 | 2 | 3 | 0 | 5 | 0 | 0 | 1 | 2 | 193 | 3 | 9 | 1 | 1 | 28 | 6 | 102 | 6 | 466 | 57 | 0 | 2 |
DEL PEAK 41(17P12) WILD-TYPE | 143 | 40 | 315 | 245 | 39 | 5 | 443 | 5 | 44 | 104 | 2 | 2 | 7 | 0 | 0 | 2 | 13 | 1 | 1 | 0 | 1 | 122 | 2 | 9 | 3 | 2 | 21 | 4 | 41 | 7 | 86 | 28 | 1 | 18 |
Figure S455. Get High-res Image Gene #82: 'Del Peak 41(17p12)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D82V6.png)
P value = 1.09e-12 (Fisher's exact test), Q value = 1.6e-09
Table S456. Gene #82: 'Del Peak 41(17p12)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 41(17P12) CNV | 126 | 300 | 317 | 72 |
DEL PEAK 41(17P12) WILD-TYPE | 322 | 311 | 371 | 136 |
Figure S456. Get High-res Image Gene #82: 'Del Peak 41(17p12)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D82V7.png)
P value = 1.42e-07 (Fisher's exact test), Q value = 2e-04
Table S457. Gene #82: 'Del Peak 41(17p12)' versus Clinical Feature #8: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 1036 | 343 | 279 | 11 |
DEL PEAK 41(17P12) CNV | 421 | 196 | 146 | 5 |
DEL PEAK 41(17P12) WILD-TYPE | 615 | 147 | 133 | 6 |
Figure S457. Get High-res Image Gene #82: 'Del Peak 41(17p12)' versus Clinical Feature #8: 'PATHOLOGY.N'
![](D82V8.png)
P value = 9.6e-31 (Fisher's exact test), Q value = 1.5e-27
Table S458. Gene #82: 'Del Peak 41(17p12)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 41(17P12) CNV | 256 | 235 | 581 | 189 |
DEL PEAK 41(17P12) WILD-TYPE | 429 | 252 | 295 | 231 |
Figure S458. Get High-res Image Gene #82: 'Del Peak 41(17p12)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D82V10.png)
P value = 1.53e-27 (Fisher's exact test), Q value = 2.4e-24
Table S459. Gene #82: 'Del Peak 41(17p12)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
DEL PEAK 41(17P12) CNV | 238 | 1866 |
DEL PEAK 41(17P12) WILD-TYPE | 597 | 1950 |
Figure S459. Get High-res Image Gene #82: 'Del Peak 41(17p12)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D82V11.png)
P value = 1.14e-05 (t-test), Q value = 0.015
Table S460. Gene #83: 'Del Peak 42(17q11.2)' versus Clinical Feature #2: 'AGE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 4585 | 61.9 (12.6) |
DEL PEAK 42(17Q11.2) CNV | 1123 | 60.5 (12.2) |
DEL PEAK 42(17Q11.2) WILD-TYPE | 3462 | 62.3 (12.7) |
Figure S460. Get High-res Image Gene #83: 'Del Peak 42(17q11.2)' versus Clinical Feature #2: 'AGE'
![](D83V2.png)
P value = 1.98e-263 (Chi-square test), Q value = 3.4e-260
Table S461. Gene #83: 'Del Peak 42(17q11.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 42(17Q11.2) CNV | 12 | 67 | 265 | 47 | 81 | 30 | 33 | 128 | 2 | 448 | 0 | 21 |
DEL PEAK 42(17Q11.2) WILD-TYPE | 119 | 477 | 592 | 365 | 373 | 291 | 460 | 586 | 0 | 100 | 2 | 138 |
Figure S461. Get High-res Image Gene #83: 'Del Peak 42(17q11.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D83V3.png)
P value = 1.06e-51 (Fisher's exact test), Q value = 1.7e-48
Table S462. Gene #83: 'Del Peak 42(17q11.2)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
DEL PEAK 42(17Q11.2) CNV | 923 | 214 |
DEL PEAK 42(17Q11.2) WILD-TYPE | 2001 | 1503 |
Figure S462. Get High-res Image Gene #83: 'Del Peak 42(17q11.2)' versus Clinical Feature #4: 'GENDER'
![](D83V4.png)
P value = 9.39e-235 (Chi-square test), Q value = 1.6e-231
Table S463. Gene #83: 'Del Peak 42(17q11.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 42(17Q11.2) CNV | 41 | 6 | 38 | 30 | 36 | 2 | 33 | 0 | 9 | 35 | 1 | 0 | 2 | 0 | 1 | 0 | 1 | 0 | 0 | 1 | 0 | 77 | 1 | 5 | 1 | 0 | 5 | 4 | 20 | 1 | 450 | 38 | 0 | 2 |
DEL PEAK 42(17Q11.2) WILD-TYPE | 315 | 48 | 313 | 291 | 68 | 10 | 460 | 11 | 70 | 208 | 6 | 4 | 15 | 2 | 2 | 2 | 17 | 1 | 1 | 0 | 3 | 238 | 4 | 13 | 3 | 3 | 44 | 6 | 123 | 12 | 102 | 47 | 1 | 18 |
Figure S463. Get High-res Image Gene #83: 'Del Peak 42(17q11.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D83V6.png)
P value = 6.83e-59 (Fisher's exact test), Q value = 1.1e-55
Table S464. Gene #83: 'Del Peak 42(17q11.2)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 42(17Q11.2) CNV | 100 | 72 | 418 | 100 |
DEL PEAK 42(17Q11.2) WILD-TYPE | 585 | 415 | 458 | 320 |
Figure S464. Get High-res Image Gene #83: 'Del Peak 42(17q11.2)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D83V10.png)
P value = 3.35e-09 (Fisher's exact test), Q value = 4.8e-06
Table S465. Gene #83: 'Del Peak 42(17q11.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
DEL PEAK 42(17Q11.2) CNV | 141 | 1006 |
DEL PEAK 42(17Q11.2) WILD-TYPE | 694 | 2810 |
Figure S465. Get High-res Image Gene #83: 'Del Peak 42(17q11.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D83V11.png)
P value = 1.98e-06 (t-test), Q value = 0.0027
Table S466. Gene #84: 'Del Peak 43(18q21.2)' versus Clinical Feature #2: 'AGE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 4585 | 61.9 (12.6) |
DEL PEAK 43(18Q21.2) CNV | 1777 | 63.0 (12.0) |
DEL PEAK 43(18Q21.2) WILD-TYPE | 2808 | 61.2 (12.9) |
Figure S466. Get High-res Image Gene #84: 'Del Peak 43(18q21.2)' versus Clinical Feature #2: 'AGE'
![](D84V2.png)
P value = 2.16e-160 (Chi-square test), Q value = 3.7e-157
Table S467. Gene #84: 'Del Peak 43(18q21.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 43(18Q21.2) CNV | 61 | 67 | 279 | 260 | 67 | 170 | 97 | 329 | 1 | 331 | 0 | 140 |
DEL PEAK 43(18Q21.2) WILD-TYPE | 70 | 477 | 578 | 152 | 387 | 151 | 396 | 385 | 1 | 217 | 2 | 19 |
Figure S467. Get High-res Image Gene #84: 'Del Peak 43(18q21.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D84V3.png)
P value = 3.7e-112 (Chi-square test), Q value = 6.2e-109
Table S468. Gene #84: 'Del Peak 43(18q21.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 43(18Q21.2) CNV | 245 | 14 | 29 | 170 | 34 | 3 | 97 | 5 | 39 | 130 | 1 | 1 | 7 | 2 | 2 | 1 | 4 | 1 | 0 | 0 | 2 | 130 | 1 | 5 | 3 | 1 | 24 | 2 | 126 | 12 | 332 | 33 | 0 | 5 |
DEL PEAK 43(18Q21.2) WILD-TYPE | 111 | 40 | 322 | 151 | 70 | 9 | 396 | 6 | 40 | 113 | 6 | 3 | 10 | 0 | 1 | 1 | 14 | 0 | 1 | 1 | 1 | 185 | 4 | 13 | 1 | 2 | 25 | 8 | 17 | 1 | 220 | 52 | 1 | 15 |
Figure S468. Get High-res Image Gene #84: 'Del Peak 43(18q21.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D84V6.png)
P value = 1.41e-23 (Fisher's exact test), Q value = 2.1e-20
Table S469. Gene #84: 'Del Peak 43(18q21.2)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 43(18Q21.2) CNV | 124 | 296 | 393 | 122 |
DEL PEAK 43(18Q21.2) WILD-TYPE | 324 | 315 | 295 | 86 |
Figure S469. Get High-res Image Gene #84: 'Del Peak 43(18q21.2)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D84V7.png)
P value = 2.41e-10 (Fisher's exact test), Q value = 3.5e-07
Table S470. Gene #84: 'Del Peak 43(18q21.2)' versus Clinical Feature #8: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 1036 | 343 | 279 | 11 |
DEL PEAK 43(18Q21.2) CNV | 473 | 210 | 180 | 5 |
DEL PEAK 43(18Q21.2) WILD-TYPE | 563 | 133 | 99 | 6 |
Figure S470. Get High-res Image Gene #84: 'Del Peak 43(18q21.2)' versus Clinical Feature #8: 'PATHOLOGY.N'
![](D84V8.png)
P value = 8.73e-07 (Chi-square test), Q value = 0.0012
Table S471. Gene #84: 'Del Peak 43(18q21.2)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 1398 | 167 | 9 | 1 | 148 |
DEL PEAK 43(18Q21.2) CNV | 608 | 99 | 8 | 1 | 88 |
DEL PEAK 43(18Q21.2) WILD-TYPE | 790 | 68 | 1 | 0 | 60 |
Figure S471. Get High-res Image Gene #84: 'Del Peak 43(18q21.2)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'
![](D84V9.png)
P value = 3.65e-17 (Fisher's exact test), Q value = 5.5e-14
Table S472. Gene #84: 'Del Peak 43(18q21.2)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 43(18Q21.2) CNV | 249 | 260 | 478 | 254 |
DEL PEAK 43(18Q21.2) WILD-TYPE | 436 | 227 | 398 | 166 |
Figure S472. Get High-res Image Gene #84: 'Del Peak 43(18q21.2)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D84V10.png)
P value = 6.39e-27 (Fisher's exact test), Q value = 9.8e-24
Table S473. Gene #84: 'Del Peak 43(18q21.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
DEL PEAK 43(18Q21.2) CNV | 192 | 1621 |
DEL PEAK 43(18Q21.2) WILD-TYPE | 643 | 2195 |
Figure S473. Get High-res Image Gene #84: 'Del Peak 43(18q21.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D84V11.png)
P value = 4.93e-163 (Chi-square test), Q value = 8.4e-160
Table S474. Gene #85: 'Del Peak 44(18q23)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 44(18Q23) CNV | 58 | 73 | 279 | 258 | 75 | 181 | 101 | 341 | 1 | 360 | 0 | 136 |
DEL PEAK 44(18Q23) WILD-TYPE | 73 | 471 | 578 | 154 | 379 | 140 | 392 | 373 | 1 | 188 | 2 | 23 |
Figure S474. Get High-res Image Gene #85: 'Del Peak 44(18q23)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D85V3.png)
P value = 2.15e-116 (Chi-square test), Q value = 3.6e-113
Table S475. Gene #85: 'Del Peak 44(18q23)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 44(18Q23) CNV | 244 | 13 | 30 | 181 | 34 | 4 | 101 | 6 | 39 | 124 | 1 | 1 | 8 | 2 | 2 | 1 | 3 | 1 | 0 | 0 | 1 | 148 | 1 | 5 | 3 | 1 | 22 | 1 | 124 | 11 | 361 | 40 | 0 | 5 |
DEL PEAK 44(18Q23) WILD-TYPE | 112 | 41 | 321 | 140 | 70 | 8 | 392 | 5 | 40 | 119 | 6 | 3 | 9 | 0 | 1 | 1 | 15 | 0 | 1 | 1 | 2 | 167 | 4 | 13 | 1 | 2 | 27 | 9 | 19 | 2 | 191 | 45 | 1 | 15 |
Figure S475. Get High-res Image Gene #85: 'Del Peak 44(18q23)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D85V6.png)
P value = 1.9e-22 (Fisher's exact test), Q value = 2.9e-19
Table S476. Gene #85: 'Del Peak 44(18q23)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 44(18Q23) CNV | 131 | 297 | 397 | 126 |
DEL PEAK 44(18Q23) WILD-TYPE | 317 | 314 | 291 | 82 |
Figure S476. Get High-res Image Gene #85: 'Del Peak 44(18q23)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D85V7.png)
P value = 6.46e-10 (Fisher's exact test), Q value = 9.2e-07
Table S477. Gene #85: 'Del Peak 44(18q23)' versus Clinical Feature #8: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 1036 | 343 | 279 | 11 |
DEL PEAK 44(18Q23) CNV | 482 | 206 | 185 | 6 |
DEL PEAK 44(18Q23) WILD-TYPE | 554 | 137 | 94 | 5 |
Figure S477. Get High-res Image Gene #85: 'Del Peak 44(18q23)' versus Clinical Feature #8: 'PATHOLOGY.N'
![](D85V8.png)
P value = 6.05e-05 (Chi-square test), Q value = 0.077
Table S478. Gene #85: 'Del Peak 44(18q23)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 1398 | 167 | 9 | 1 | 148 |
DEL PEAK 44(18Q23) CNV | 623 | 96 | 8 | 1 | 85 |
DEL PEAK 44(18Q23) WILD-TYPE | 775 | 71 | 1 | 0 | 63 |
Figure S478. Get High-res Image Gene #85: 'Del Peak 44(18q23)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'
![](D85V9.png)
P value = 2.49e-19 (Fisher's exact test), Q value = 3.8e-16
Table S479. Gene #85: 'Del Peak 44(18q23)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 44(18Q23) CNV | 255 | 261 | 512 | 257 |
DEL PEAK 44(18Q23) WILD-TYPE | 430 | 226 | 364 | 163 |
Figure S479. Get High-res Image Gene #85: 'Del Peak 44(18q23)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D85V10.png)
P value = 1.11e-25 (Fisher's exact test), Q value = 1.7e-22
Table S480. Gene #85: 'Del Peak 44(18q23)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
DEL PEAK 44(18Q23) CNV | 205 | 1668 |
DEL PEAK 44(18Q23) WILD-TYPE | 630 | 2148 |
Figure S480. Get High-res Image Gene #85: 'Del Peak 44(18q23)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D85V11.png)
P value = 6.56e-269 (Chi-square test), Q value = 1.1e-265
Table S481. Gene #86: 'Del Peak 45(19p13.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 45(19P13.3) CNV | 50 | 36 | 296 | 56 | 112 | 108 | 18 | 360 | 2 | 478 | 2 | 34 |
DEL PEAK 45(19P13.3) WILD-TYPE | 81 | 508 | 561 | 356 | 342 | 213 | 475 | 354 | 0 | 70 | 0 | 125 |
Figure S481. Get High-res Image Gene #86: 'Del Peak 45(19p13.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D86V3.png)
P value = 1.22e-22 (Fisher's exact test), Q value = 1.9e-19
Table S482. Gene #86: 'Del Peak 45(19p13.3)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
DEL PEAK 45(19P13.3) CNV | 1129 | 424 |
DEL PEAK 45(19P13.3) WILD-TYPE | 1795 | 1293 |
Figure S482. Get High-res Image Gene #86: 'Del Peak 45(19p13.3)' versus Clinical Feature #4: 'GENDER'
![](D86V4.png)
P value = 2.22e-237 (Chi-square test), Q value = 3.8e-234
Table S483. Gene #86: 'Del Peak 45(19p13.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 45(19P13.3) CNV | 51 | 4 | 35 | 108 | 47 | 0 | 18 | 5 | 45 | 132 | 3 | 0 | 9 | 1 | 3 | 1 | 12 | 1 | 0 | 1 | 2 | 143 | 0 | 7 | 2 | 0 | 19 | 4 | 31 | 2 | 482 | 70 | 0 | 1 |
DEL PEAK 45(19P13.3) WILD-TYPE | 305 | 50 | 316 | 213 | 57 | 12 | 475 | 6 | 34 | 111 | 4 | 4 | 8 | 1 | 0 | 1 | 6 | 0 | 1 | 0 | 1 | 172 | 5 | 11 | 2 | 3 | 30 | 6 | 112 | 11 | 70 | 15 | 1 | 19 |
Figure S483. Get High-res Image Gene #86: 'Del Peak 45(19p13.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D86V6.png)
P value = 7.92e-17 (Fisher's exact test), Q value = 1.2e-13
Table S484. Gene #86: 'Del Peak 45(19p13.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 45(19P13.3) CNV | 84 | 230 | 130 | 70 |
DEL PEAK 45(19P13.3) WILD-TYPE | 364 | 381 | 558 | 138 |
Figure S484. Get High-res Image Gene #86: 'Del Peak 45(19p13.3)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D86V7.png)
P value = 4.24e-06 (Fisher's exact test), Q value = 0.0057
Table S485. Gene #86: 'Del Peak 45(19p13.3)' versus Clinical Feature #8: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 1036 | 343 | 279 | 11 |
DEL PEAK 45(19P13.3) CNV | 261 | 112 | 112 | 5 |
DEL PEAK 45(19P13.3) WILD-TYPE | 775 | 231 | 167 | 6 |
Figure S485. Get High-res Image Gene #86: 'Del Peak 45(19p13.3)' versus Clinical Feature #8: 'PATHOLOGY.N'
![](D86V8.png)
P value = 8.26e-44 (Fisher's exact test), Q value = 1.3e-40
Table S486. Gene #86: 'Del Peak 45(19p13.3)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 45(19P13.3) CNV | 180 | 134 | 507 | 165 |
DEL PEAK 45(19P13.3) WILD-TYPE | 505 | 353 | 369 | 255 |
Figure S486. Get High-res Image Gene #86: 'Del Peak 45(19p13.3)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D86V10.png)
P value = 7.2e-19 (Fisher's exact test), Q value = 1.1e-15
Table S487. Gene #86: 'Del Peak 45(19p13.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
DEL PEAK 45(19P13.3) CNV | 174 | 1389 |
DEL PEAK 45(19P13.3) WILD-TYPE | 661 | 2427 |
Figure S487. Get High-res Image Gene #86: 'Del Peak 45(19p13.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D86V11.png)
P value = 5.86e-114 (Chi-square test), Q value = 9.8e-111
Table S488. Gene #87: 'Del Peak 46(19q13.32)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 46(19Q13.32) CNV | 14 | 96 | 177 | 43 | 48 | 62 | 7 | 234 | 1 | 286 | 1 | 22 |
DEL PEAK 46(19Q13.32) WILD-TYPE | 117 | 448 | 680 | 369 | 406 | 259 | 486 | 480 | 1 | 262 | 1 | 137 |
Figure S488. Get High-res Image Gene #87: 'Del Peak 46(19q13.32)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D87V3.png)
P value = 1.1e-07 (Fisher's exact test), Q value = 0.00015
Table S489. Gene #87: 'Del Peak 46(19q13.32)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
DEL PEAK 46(19Q13.32) CNV | 696 | 296 |
DEL PEAK 46(19Q13.32) WILD-TYPE | 2228 | 1421 |
Figure S489. Get High-res Image Gene #87: 'Del Peak 46(19q13.32)' versus Clinical Feature #4: 'GENDER'
![](D87V4.png)
P value = 6.78e-107 (Chi-square test), Q value = 1.1e-103
Table S490. Gene #87: 'Del Peak 46(19q13.32)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 46(19Q13.32) CNV | 37 | 5 | 15 | 62 | 20 | 0 | 7 | 4 | 32 | 86 | 4 | 0 | 5 | 1 | 1 | 0 | 10 | 1 | 0 | 0 | 2 | 87 | 1 | 5 | 1 | 0 | 5 | 1 | 20 | 1 | 288 | 28 | 0 | 5 |
DEL PEAK 46(19Q13.32) WILD-TYPE | 319 | 49 | 336 | 259 | 84 | 12 | 486 | 7 | 47 | 157 | 3 | 4 | 12 | 1 | 2 | 2 | 8 | 0 | 1 | 1 | 1 | 228 | 4 | 13 | 3 | 3 | 44 | 9 | 123 | 12 | 264 | 57 | 1 | 15 |
Figure S490. Get High-res Image Gene #87: 'Del Peak 46(19q13.32)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D87V6.png)
P value = 6.59e-06 (Fisher's exact test), Q value = 0.0088
Table S491. Gene #87: 'Del Peak 46(19q13.32)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 46(19Q13.32) CNV | 56 | 140 | 94 | 38 |
DEL PEAK 46(19Q13.32) WILD-TYPE | 392 | 471 | 594 | 170 |
Figure S491. Get High-res Image Gene #87: 'Del Peak 46(19q13.32)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D87V7.png)
P value = 2.14e-20 (Fisher's exact test), Q value = 3.2e-17
Table S492. Gene #87: 'Del Peak 46(19q13.32)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 46(19Q13.32) CNV | 119 | 86 | 316 | 87 |
DEL PEAK 46(19Q13.32) WILD-TYPE | 566 | 401 | 560 | 333 |
Figure S492. Get High-res Image Gene #87: 'Del Peak 46(19q13.32)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D87V10.png)
P value = 7.62e-104 (Chi-square test), Q value = 1.3e-100
Table S493. Gene #88: 'Del Peak 47(19q13.43)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 47(19Q13.43) CNV | 14 | 82 | 146 | 42 | 49 | 64 | 5 | 213 | 1 | 267 | 1 | 25 |
DEL PEAK 47(19Q13.43) WILD-TYPE | 117 | 462 | 711 | 370 | 405 | 257 | 488 | 501 | 1 | 281 | 1 | 134 |
Figure S493. Get High-res Image Gene #88: 'Del Peak 47(19q13.43)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D88V3.png)
P value = 2e-06 (Fisher's exact test), Q value = 0.0027
Table S494. Gene #88: 'Del Peak 47(19q13.43)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
DEL PEAK 47(19Q13.43) CNV | 635 | 275 |
DEL PEAK 47(19Q13.43) WILD-TYPE | 2289 | 1442 |
Figure S494. Get High-res Image Gene #88: 'Del Peak 47(19q13.43)' versus Clinical Feature #4: 'GENDER'
![](D88V4.png)
P value = 8.06e-97 (Chi-square test), Q value = 1.3e-93
Table S495. Gene #88: 'Del Peak 47(19q13.43)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 47(19Q13.43) CNV | 36 | 5 | 13 | 64 | 18 | 0 | 5 | 4 | 29 | 77 | 4 | 0 | 6 | 0 | 2 | 0 | 9 | 1 | 0 | 0 | 1 | 79 | 0 | 4 | 1 | 0 | 4 | 1 | 23 | 1 | 269 | 32 | 0 | 6 |
DEL PEAK 47(19Q13.43) WILD-TYPE | 320 | 49 | 338 | 257 | 86 | 12 | 488 | 7 | 50 | 166 | 3 | 4 | 11 | 2 | 1 | 2 | 9 | 0 | 1 | 1 | 2 | 236 | 5 | 14 | 3 | 3 | 45 | 9 | 120 | 12 | 283 | 53 | 1 | 14 |
Figure S495. Get High-res Image Gene #88: 'Del Peak 47(19q13.43)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D88V6.png)
P value = 3.89e-06 (Fisher's exact test), Q value = 0.0052
Table S496. Gene #88: 'Del Peak 47(19q13.43)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 47(19Q13.43) CNV | 47 | 130 | 94 | 41 |
DEL PEAK 47(19Q13.43) WILD-TYPE | 401 | 481 | 594 | 167 |
Figure S496. Get High-res Image Gene #88: 'Del Peak 47(19q13.43)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D88V7.png)
P value = 2.97e-17 (Fisher's exact test), Q value = 4.5e-14
Table S497. Gene #88: 'Del Peak 47(19q13.43)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 47(19Q13.43) CNV | 105 | 88 | 291 | 88 |
DEL PEAK 47(19Q13.43) WILD-TYPE | 580 | 399 | 585 | 332 |
Figure S497. Get High-res Image Gene #88: 'Del Peak 47(19q13.43)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D88V10.png)
P value = 5.06e-36 (Chi-square test), Q value = 7.9e-33
Table S498. Gene #89: 'Del Peak 48(20p12.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 48(20P12.1) CNV | 9 | 18 | 104 | 79 | 26 | 45 | 9 | 120 | 0 | 68 | 0 | 46 |
DEL PEAK 48(20P12.1) WILD-TYPE | 122 | 526 | 753 | 333 | 428 | 276 | 484 | 594 | 2 | 480 | 2 | 113 |
Figure S498. Get High-res Image Gene #89: 'Del Peak 48(20p12.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D89V3.png)
P value = 3.04e-28 (Chi-square test), Q value = 4.7e-25
Table S499. Gene #89: 'Del Peak 48(20p12.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 48(20P12.1) CNV | 73 | 6 | 12 | 45 | 18 | 2 | 9 | 2 | 20 | 56 | 0 | 0 | 5 | 2 | 1 | 0 | 2 | 0 | 0 | 0 | 1 | 29 | 0 | 2 | 1 | 1 | 4 | 0 | 41 | 5 | 68 | 12 | 0 | 0 |
DEL PEAK 48(20P12.1) WILD-TYPE | 283 | 48 | 339 | 276 | 86 | 10 | 484 | 9 | 59 | 187 | 7 | 4 | 12 | 0 | 2 | 2 | 16 | 1 | 1 | 1 | 2 | 286 | 5 | 16 | 3 | 2 | 45 | 10 | 102 | 8 | 484 | 73 | 1 | 20 |
Figure S499. Get High-res Image Gene #89: 'Del Peak 48(20p12.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D89V6.png)
P value = 2.98e-05 (Fisher's exact test), Q value = 0.038
Table S500. Gene #89: 'Del Peak 48(20p12.1)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
DEL PEAK 48(20P12.1) CNV | 61 | 465 |
DEL PEAK 48(20P12.1) WILD-TYPE | 774 | 3351 |
Figure S500. Get High-res Image Gene #89: 'Del Peak 48(20p12.1)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D89V11.png)
P value = 1.48e-67 (Chi-square test), Q value = 2.4e-64
Table S501. Gene #90: 'Del Peak 49(21q11.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 49(21Q11.2) CNV | 21 | 53 | 173 | 124 | 50 | 105 | 54 | 288 | 2 | 180 | 0 | 68 |
DEL PEAK 49(21Q11.2) WILD-TYPE | 110 | 491 | 684 | 288 | 404 | 216 | 439 | 426 | 0 | 368 | 2 | 91 |
Figure S501. Get High-res Image Gene #90: 'Del Peak 49(21q11.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D90V3.png)
P value = 6.88e-46 (Chi-square test), Q value = 1.1e-42
Table S502. Gene #90: 'Del Peak 49(21q11.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 49(21Q11.2) CNV | 115 | 8 | 17 | 105 | 22 | 1 | 54 | 7 | 23 | 85 | 3 | 0 | 5 | 0 | 1 | 0 | 6 | 1 | 0 | 1 | 1 | 152 | 2 | 5 | 2 | 1 | 8 | 2 | 63 | 3 | 182 | 28 | 0 | 2 |
DEL PEAK 49(21Q11.2) WILD-TYPE | 241 | 46 | 334 | 216 | 82 | 11 | 439 | 4 | 56 | 158 | 4 | 4 | 12 | 2 | 2 | 2 | 12 | 0 | 1 | 0 | 2 | 163 | 3 | 13 | 2 | 2 | 41 | 8 | 80 | 10 | 370 | 57 | 1 | 18 |
Figure S502. Get High-res Image Gene #90: 'Del Peak 49(21q11.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D90V6.png)
P value = 8.93e-06 (Fisher's exact test), Q value = 0.012
Table S503. Gene #90: 'Del Peak 49(21q11.2)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 49(21Q11.2) CNV | 102 | 222 | 202 | 75 |
DEL PEAK 49(21Q11.2) WILD-TYPE | 346 | 389 | 486 | 133 |
Figure S503. Get High-res Image Gene #90: 'Del Peak 49(21q11.2)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D90V7.png)
P value = 8.8e-05 (Fisher's exact test), Q value = 0.11
Table S504. Gene #90: 'Del Peak 49(21q11.2)' versus Clinical Feature #8: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 1036 | 343 | 279 | 11 |
DEL PEAK 49(21Q11.2) CNV | 302 | 142 | 104 | 5 |
DEL PEAK 49(21Q11.2) WILD-TYPE | 734 | 201 | 175 | 6 |
Figure S504. Get High-res Image Gene #90: 'Del Peak 49(21q11.2)' versus Clinical Feature #8: 'PATHOLOGY.N'
![](D90V8.png)
P value = 1.78e-11 (Fisher's exact test), Q value = 2.6e-08
Table S505. Gene #90: 'Del Peak 49(21q11.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 835 | 3816 |
DEL PEAK 49(21Q11.2) CNV | 129 | 996 |
DEL PEAK 49(21Q11.2) WILD-TYPE | 706 | 2820 |
Figure S505. Get High-res Image Gene #90: 'Del Peak 49(21q11.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D90V11.png)
P value = 1.85e-172 (Chi-square test), Q value = 3.2e-169
Table S506. Gene #91: 'Del Peak 50(22q13.32)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 50(22Q13.32) CNV | 54 | 206 | 384 | 143 | 110 | 64 | 37 | 264 | 2 | 474 | 1 | 63 |
DEL PEAK 50(22Q13.32) WILD-TYPE | 77 | 338 | 473 | 269 | 344 | 257 | 456 | 450 | 0 | 74 | 1 | 96 |
Figure S506. Get High-res Image Gene #91: 'Del Peak 50(22q13.32)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D91V3.png)
P value = 4.14e-26 (Fisher's exact test), Q value = 6.4e-23
Table S507. Gene #91: 'Del Peak 50(22q13.32)' versus Clinical Feature #4: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 2924 | 1717 |
DEL PEAK 50(22Q13.32) CNV | 1306 | 500 |
DEL PEAK 50(22Q13.32) WILD-TYPE | 1618 | 1217 |
Figure S507. Get High-res Image Gene #91: 'Del Peak 50(22q13.32)' versus Clinical Feature #4: 'GENDER'
![](D91V4.png)
P value = 8.76e-187 (Chi-square test), Q value = 1.5e-183
Table S508. Gene #91: 'Del Peak 50(22q13.32)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 50(22Q13.32) CNV | 133 | 10 | 48 | 64 | 47 | 7 | 37 | 5 | 34 | 124 | 4 | 1 | 10 | 0 | 2 | 0 | 8 | 1 | 0 | 1 | 3 | 70 | 1 | 8 | 1 | 0 | 17 | 4 | 59 | 4 | 477 | 54 | 0 | 9 |
DEL PEAK 50(22Q13.32) WILD-TYPE | 223 | 44 | 303 | 257 | 57 | 5 | 456 | 6 | 45 | 119 | 3 | 3 | 7 | 2 | 1 | 2 | 10 | 0 | 1 | 0 | 0 | 245 | 4 | 10 | 3 | 3 | 32 | 6 | 84 | 9 | 75 | 31 | 1 | 11 |
Figure S508. Get High-res Image Gene #91: 'Del Peak 50(22q13.32)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D91V6.png)
P value = 7.66e-05 (Fisher's exact test), Q value = 0.097
Table S509. Gene #91: 'Del Peak 50(22q13.32)' versus Clinical Feature #7: 'PATHOLOGY.T'
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 448 | 611 | 688 | 208 |
DEL PEAK 50(22Q13.32) CNV | 83 | 184 | 198 | 52 |
DEL PEAK 50(22Q13.32) WILD-TYPE | 365 | 427 | 490 | 156 |
Figure S509. Get High-res Image Gene #91: 'Del Peak 50(22q13.32)' versus Clinical Feature #7: 'PATHOLOGY.T'
![](D91V7.png)
P value = 2.75e-45 (Fisher's exact test), Q value = 4.4e-42
Table S510. Gene #91: 'Del Peak 50(22q13.32)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 50(22Q13.32) CNV | 165 | 147 | 506 | 158 |
DEL PEAK 50(22Q13.32) WILD-TYPE | 520 | 340 | 370 | 262 |
Figure S510. Get High-res Image Gene #91: 'Del Peak 50(22q13.32)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D91V10.png)
P value = 0.000108 (Fisher's exact test), Q value = 0.14
Table S511. Gene #91: 'Del Peak 50(22q13.32)' versus Clinical Feature #17: 'COMPLETENESS.OF.RESECTION'
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 1221 | 69 | 59 | 80 |
DEL PEAK 50(22Q13.32) CNV | 399 | 41 | 23 | 31 |
DEL PEAK 50(22Q13.32) WILD-TYPE | 822 | 28 | 36 | 49 |
Figure S511. Get High-res Image Gene #91: 'Del Peak 50(22q13.32)' versus Clinical Feature #17: 'COMPLETENESS.OF.RESECTION'
![](D91V17.png)
P value = 1.5e-05 (logrank test), Q value = 0.02
Table S512. Gene #92: 'Del Peak 51(Xp21.1)' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4) |
DEL PEAK 51(XP21.1) CNV | 1133 | 440 | 0.0 - 173.8 (16.6) |
DEL PEAK 51(XP21.1) WILD-TYPE | 3237 | 966 | 0.0 - 224.0 (13.9) |
Figure S512. Get High-res Image Gene #92: 'Del Peak 51(Xp21.1)' versus Clinical Feature #1: 'Time to Death'
![](D92V1.png)
P value = 1.34e-113 (Chi-square test), Q value = 2.3e-110
Table S513. Gene #92: 'Del Peak 51(Xp21.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159 |
DEL PEAK 51(XP21.1) CNV | 33 | 121 | 176 | 63 | 66 | 104 | 51 | 206 | 1 | 350 | 1 | 28 |
DEL PEAK 51(XP21.1) WILD-TYPE | 98 | 423 | 681 | 349 | 388 | 217 | 442 | 508 | 1 | 198 | 1 | 131 |
Figure S513. Get High-res Image Gene #92: 'Del Peak 51(Xp21.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D92V3.png)
P value = 6.27e-103 (Chi-square test), Q value = 1e-99
Table S514. Gene #92: 'Del Peak 51(Xp21.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20 |
DEL PEAK 51(XP21.1) CNV | 59 | 4 | 26 | 104 | 21 | 1 | 51 | 3 | 20 | 70 | 1 | 1 | 2 | 0 | 2 | 1 | 3 | 1 | 0 | 0 | 0 | 100 | 1 | 2 | 1 | 1 | 11 | 3 | 23 | 4 | 352 | 38 | 0 | 7 |
DEL PEAK 51(XP21.1) WILD-TYPE | 297 | 50 | 325 | 217 | 83 | 11 | 442 | 8 | 59 | 173 | 6 | 3 | 15 | 2 | 1 | 1 | 15 | 0 | 1 | 1 | 3 | 215 | 4 | 16 | 3 | 2 | 38 | 7 | 120 | 9 | 200 | 47 | 1 | 13 |
Figure S514. Get High-res Image Gene #92: 'Del Peak 51(Xp21.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'
![](D92V6.png)
P value = 1.1e-18 (Fisher's exact test), Q value = 1.7e-15
Table S515. Gene #92: 'Del Peak 51(Xp21.1)' versus Clinical Feature #10: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 685 | 487 | 876 | 420 |
DEL PEAK 51(XP21.1) CNV | 142 | 115 | 357 | 138 |
DEL PEAK 51(XP21.1) WILD-TYPE | 543 | 372 | 519 | 282 |
Figure S515. Get High-res Image Gene #92: 'Del Peak 51(Xp21.1)' versus Clinical Feature #10: 'TUMOR.STAGE'
![](D92V10.png)
-
Mutation data file = all_lesions.conf_99.cnv.cluster.txt
-
Clinical data file = PANCAN12-TP.clin.merged.picked.txt
-
Number of patients = 4651
-
Number of significantly arm-level cnvs = 92
-
Number of selected clinical features = 20
-
Exclude genes that fewer than K tumors have mutations, K = 3
For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R
For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' function in R
For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R
For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R
For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.