(primary solid tumor cohort)
This pipeline computes the correlation between significant copy number variation (cnv) genes and selected clinical features.
Testing the association between copy number variation of 62 peak regions and 9 clinical features across 162 patients, one significant finding detected with Q value < 0.25.
-
Del Peak 6(3q26.31) cnvs correlated to 'Time to Death'.
Clinical Features |
Time to Death |
AGE | GENDER |
HISTOLOGICAL TYPE |
PATHOLOGY T |
PATHOLOGY N |
PATHOLOGICSPREAD(M) |
TUMOR STAGE |
RADIATIONS RADIATION REGIMENINDICATION |
||
nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
Del Peak 6(3q26 31) | 17 (10%) | 145 |
8.16e-05 (0.0455) |
0.705 (1.00) |
0.0036 (1.00) |
0.0303 (1.00) |
0.216 (1.00) |
0.554 (1.00) |
0.2 (1.00) |
0.00256 (1.00) |
0.121 (1.00) |
Amp Peak 1(1q21 3) | 48 (30%) | 114 |
0.538 (1.00) |
0.951 (1.00) |
0.863 (1.00) |
1 (1.00) |
0.117 (1.00) |
0.443 (1.00) |
0.102 (1.00) |
0.843 (1.00) |
0.0639 (1.00) |
Amp Peak 2(1q32 2) | 48 (30%) | 114 |
0.0492 (1.00) |
0.645 (1.00) |
1 (1.00) |
1 (1.00) |
0.0291 (1.00) |
0.251 (1.00) |
0.36 (1.00) |
0.614 (1.00) |
0.362 (1.00) |
Amp Peak 3(5q22 3) | 19 (12%) | 143 |
0.529 (1.00) |
0.383 (1.00) |
0.81 (1.00) |
0.37 (1.00) |
0.881 (1.00) |
0.753 (1.00) |
0.743 (1.00) |
0.812 (1.00) |
1 (1.00) |
Amp Peak 4(6p21 1) | 52 (32%) | 110 |
0.178 (1.00) |
0.528 (1.00) |
0.4 (1.00) |
0.0626 (1.00) |
0.441 (1.00) |
0.00799 (1.00) |
0.00684 (1.00) |
0.0295 (1.00) |
0.0844 (1.00) |
Amp Peak 5(8p11 23) | 52 (32%) | 110 |
0.0852 (1.00) |
0.264 (1.00) |
0.0635 (1.00) |
0.222 (1.00) |
0.219 (1.00) |
0.449 (1.00) |
0.299 (1.00) |
0.223 (1.00) |
1 (1.00) |
Amp Peak 6(8p11 21) | 69 (43%) | 93 |
0.478 (1.00) |
0.541 (1.00) |
0.637 (1.00) |
0.154 (1.00) |
0.411 (1.00) |
0.828 (1.00) |
0.195 (1.00) |
0.0731 (1.00) |
0.241 (1.00) |
Amp Peak 7(8q24 21) | 107 (66%) | 55 |
0.693 (1.00) |
0.228 (1.00) |
0.868 (1.00) |
0.0326 (1.00) |
0.499 (1.00) |
0.702 (1.00) |
0.538 (1.00) |
0.29 (1.00) |
0.665 (1.00) |
Amp Peak 8(10q22 2) | 11 (7%) | 151 |
0.306 (1.00) |
0.686 (1.00) |
0.551 (1.00) |
0.592 (1.00) |
0.935 (1.00) |
0.914 (1.00) |
0.743 (1.00) |
0.969 (1.00) |
0.349 (1.00) |
Amp Peak 9(11p15 5) | 43 (27%) | 119 |
0.607 (1.00) |
0.969 (1.00) |
1 (1.00) |
0.188 (1.00) |
0.916 (1.00) |
0.191 (1.00) |
0.852 (1.00) |
0.269 (1.00) |
0.656 (1.00) |
Amp Peak 10(11q13 3) | 26 (16%) | 136 |
0.456 (1.00) |
0.0577 (1.00) |
1 (1.00) |
0.697 (1.00) |
0.499 (1.00) |
0.377 (1.00) |
0.288 (1.00) |
0.103 (1.00) |
0.591 (1.00) |
Amp Peak 11(12p13 33) | 41 (25%) | 121 |
0.984 (1.00) |
0.246 (1.00) |
0.589 (1.00) |
0.308 (1.00) |
0.425 (1.00) |
0.548 (1.00) |
0.102 (1.00) |
0.653 (1.00) |
0.171 (1.00) |
Amp Peak 12(12p12 1) | 40 (25%) | 122 |
0.702 (1.00) |
0.334 (1.00) |
0.716 (1.00) |
0.191 (1.00) |
0.376 (1.00) |
0.542 (1.00) |
0.0879 (1.00) |
0.449 (1.00) |
0.161 (1.00) |
Amp Peak 13(13q12 13) | 121 (75%) | 41 |
0.0417 (1.00) |
0.113 (1.00) |
0.718 (1.00) |
0.00387 (1.00) |
0.0666 (1.00) |
0.0178 (1.00) |
0.239 (1.00) |
0.269 (1.00) |
0.171 (1.00) |
Amp Peak 14(13q12 2) | 120 (74%) | 42 |
0.052 (1.00) |
0.0514 (1.00) |
0.369 (1.00) |
0.00467 (1.00) |
0.0629 (1.00) |
0.0276 (1.00) |
0.303 (1.00) |
0.307 (1.00) |
0.181 (1.00) |
Amp Peak 15(13q22 1) | 117 (72%) | 45 |
0.202 (1.00) |
0.337 (1.00) |
0.482 (1.00) |
0.00132 (0.732) |
0.201 (1.00) |
0.134 (1.00) |
0.279 (1.00) |
0.441 (1.00) |
0.67 (1.00) |
Amp Peak 16(15q26 1) | 15 (9%) | 147 |
0.854 (1.00) |
0.944 (1.00) |
0.106 (1.00) |
0.362 (1.00) |
0.221 (1.00) |
0.423 (1.00) |
0.446 (1.00) |
0.568 (1.00) |
0.0967 (1.00) |
Amp Peak 17(16p11 2) | 45 (28%) | 117 |
0.183 (1.00) |
0.323 (1.00) |
0.862 (1.00) |
0.0205 (1.00) |
0.624 (1.00) |
0.146 (1.00) |
0.0796 (1.00) |
0.367 (1.00) |
0.67 (1.00) |
Amp Peak 18(17q12) | 43 (27%) | 119 |
0.653 (1.00) |
0.676 (1.00) |
0.215 (1.00) |
0.517 (1.00) |
0.745 (1.00) |
0.357 (1.00) |
0.348 (1.00) |
0.437 (1.00) |
0.343 (1.00) |
Amp Peak 19(17q24 1) | 37 (23%) | 125 |
0.659 (1.00) |
0.423 (1.00) |
1 (1.00) |
0.0401 (1.00) |
0.255 (1.00) |
0.265 (1.00) |
0.185 (1.00) |
0.196 (1.00) |
0.338 (1.00) |
Amp Peak 20(19p13 2) | 32 (20%) | 130 |
0.0245 (1.00) |
0.451 (1.00) |
0.693 (1.00) |
0.0717 (1.00) |
0.242 (1.00) |
0.543 (1.00) |
0.578 (1.00) |
0.723 (1.00) |
0.599 (1.00) |
Amp Peak 21(20q11 21) | 143 (88%) | 19 |
0.209 (1.00) |
0.099 (1.00) |
1 (1.00) |
0.000738 (0.409) |
0.55 (1.00) |
0.0991 (1.00) |
0.547 (1.00) |
0.0951 (1.00) |
0.533 (1.00) |
Amp Peak 22(20q11 23) | 144 (89%) | 18 |
0.211 (1.00) |
0.179 (1.00) |
1 (1.00) |
0.000498 (0.277) |
0.603 (1.00) |
0.0305 (1.00) |
0.433 (1.00) |
0.0815 (1.00) |
0.513 (1.00) |
Amp Peak 23(20q13 31) | 145 (90%) | 17 |
0.217 (1.00) |
0.239 (1.00) |
0.8 (1.00) |
0.000498 (0.277) |
0.614 (1.00) |
0.0498 (1.00) |
0.493 (1.00) |
0.133 (1.00) |
0.492 (1.00) |
Amp Peak 24(Xp22 2) | 33 (20%) | 129 |
0.945 (1.00) |
0.427 (1.00) |
0.0771 (1.00) |
0.303 (1.00) |
0.722 (1.00) |
0.677 (1.00) |
0.465 (1.00) |
0.602 (1.00) |
0.348 (1.00) |
Amp Peak 25(Xq27 3) | 38 (23%) | 124 |
0.459 (1.00) |
0.225 (1.00) |
0.356 (1.00) |
0.3 (1.00) |
0.343 (1.00) |
0.749 (1.00) |
0.688 (1.00) |
0.652 (1.00) |
0.337 (1.00) |
Del Peak 1(1p36 11) | 71 (44%) | 91 |
0.939 (1.00) |
0.617 (1.00) |
0.751 (1.00) |
0.56 (1.00) |
0.0983 (1.00) |
0.223 (1.00) |
0.412 (1.00) |
0.639 (1.00) |
1 (1.00) |
Del Peak 2(1p33) | 49 (30%) | 113 |
0.522 (1.00) |
0.652 (1.00) |
1 (1.00) |
0.11 (1.00) |
0.537 (1.00) |
0.253 (1.00) |
0.778 (1.00) |
0.649 (1.00) |
0.368 (1.00) |
Del Peak 3(1p13 2) | 51 (31%) | 111 |
0.944 (1.00) |
0.646 (1.00) |
0.735 (1.00) |
0.347 (1.00) |
0.144 (1.00) |
0.807 (1.00) |
0.518 (1.00) |
0.177 (1.00) |
0.38 (1.00) |
Del Peak 4(2p12) | 17 (10%) | 145 |
0.498 (1.00) |
0.175 (1.00) |
0.8 (1.00) |
1 (1.00) |
0.364 (1.00) |
0.66 (1.00) |
0.285 (1.00) |
0.251 (1.00) |
0.492 (1.00) |
Del Peak 5(3p14 2) | 29 (18%) | 133 |
0.052 (1.00) |
0.811 (1.00) |
0.013 (1.00) |
0.456 (1.00) |
0.186 (1.00) |
0.962 (1.00) |
0.285 (1.00) |
0.039 (1.00) |
0.292 (1.00) |
Del Peak 7(4p13) | 58 (36%) | 104 |
0.215 (1.00) |
0.877 (1.00) |
0.0996 (1.00) |
0.38 (1.00) |
0.769 (1.00) |
0.326 (1.00) |
0.98 (1.00) |
0.685 (1.00) |
0.00177 (0.977) |
Del Peak 8(4q22 1) | 72 (44%) | 90 |
0.107 (1.00) |
0.378 (1.00) |
0.153 (1.00) |
0.393 (1.00) |
0.288 (1.00) |
0.722 (1.00) |
0.858 (1.00) |
0.642 (1.00) |
0.0892 (1.00) |
Del Peak 9(4q35 1) | 72 (44%) | 90 |
0.294 (1.00) |
0.645 (1.00) |
0.428 (1.00) |
0.15 (1.00) |
0.455 (1.00) |
0.573 (1.00) |
0.98 (1.00) |
0.807 (1.00) |
0.0892 (1.00) |
Del Peak 10(5q11 2) | 49 (30%) | 113 |
0.708 (1.00) |
0.836 (1.00) |
0.233 (1.00) |
0.347 (1.00) |
0.966 (1.00) |
0.874 (1.00) |
0.339 (1.00) |
0.253 (1.00) |
0.01 (1.00) |
Del Peak 11(5q22 2) | 55 (34%) | 107 |
0.58 (1.00) |
0.56 (1.00) |
0.405 (1.00) |
0.222 (1.00) |
0.51 (1.00) |
0.432 (1.00) |
0.922 (1.00) |
0.578 (1.00) |
0.0176 (1.00) |
Del Peak 12(6p25 3) | 24 (15%) | 138 |
0.409 (1.00) |
0.391 (1.00) |
0.825 (1.00) |
0.386 (1.00) |
0.216 (1.00) |
0.388 (1.00) |
0.67 (1.00) |
0.0752 (1.00) |
0.217 (1.00) |
Del Peak 13(6q26) | 30 (19%) | 132 |
0.4 (1.00) |
0.852 (1.00) |
0.158 (1.00) |
0.0138 (1.00) |
0.395 (1.00) |
0.077 (1.00) |
0.677 (1.00) |
0.527 (1.00) |
0.308 (1.00) |
Del Peak 14(7q31 1) | 4 (2%) | 158 |
0.174 (1.00) |
1 (1.00) |
0.296 (1.00) |
1 (1.00) |
0.528 (1.00) |
1 (1.00) |
0.919 (1.00) |
1 (1.00) |
|
Del Peak 15(8p23 2) | 100 (62%) | 62 |
0.71 (1.00) |
0.494 (1.00) |
0.872 (1.00) |
0.564 (1.00) |
0.205 (1.00) |
0.557 (1.00) |
0.827 (1.00) |
0.818 (1.00) |
0.0831 (1.00) |
Del Peak 16(8p11 21) | 24 (15%) | 138 |
0.847 (1.00) |
0.184 (1.00) |
0.506 (1.00) |
1 (1.00) |
0.755 (1.00) |
0.837 (1.00) |
0.0829 (1.00) |
0.339 (1.00) |
0.217 (1.00) |
Del Peak 17(10q21 1) | 37 (23%) | 125 |
0.498 (1.00) |
0.261 (1.00) |
0.574 (1.00) |
0.179 (1.00) |
0.858 (1.00) |
0.579 (1.00) |
0.102 (1.00) |
0.194 (1.00) |
0.0249 (1.00) |
Del Peak 18(10q25 2) | 47 (29%) | 115 |
0.422 (1.00) |
0.369 (1.00) |
0.864 (1.00) |
0.0535 (1.00) |
0.14 (1.00) |
0.895 (1.00) |
0.599 (1.00) |
0.303 (1.00) |
0.00819 (1.00) |
Del Peak 19(11q22 3) | 37 (23%) | 125 |
0.298 (1.00) |
0.453 (1.00) |
0.71 (1.00) |
0.0322 (1.00) |
0.647 (1.00) |
0.967 (1.00) |
0.0597 (1.00) |
0.273 (1.00) |
0.133 (1.00) |
Del Peak 20(12p13 1) | 33 (20%) | 129 |
0.0863 (1.00) |
0.894 (1.00) |
0.845 (1.00) |
0.465 (1.00) |
0.936 (1.00) |
0.142 (1.00) |
0.28 (1.00) |
0.763 (1.00) |
1 (1.00) |
Del Peak 21(12q21 33) | 28 (17%) | 134 |
0.626 (1.00) |
0.292 (1.00) |
1 (1.00) |
0.469 (1.00) |
0.735 (1.00) |
0.888 (1.00) |
0.677 (1.00) |
0.254 (1.00) |
0.277 (1.00) |
Del Peak 22(14q11 2) | 67 (41%) | 95 |
0.23 (1.00) |
0.427 (1.00) |
0.427 (1.00) |
0.0746 (1.00) |
0.615 (1.00) |
0.278 (1.00) |
0.714 (1.00) |
0.332 (1.00) |
0.232 (1.00) |
Del Peak 23(14q31 1) | 69 (43%) | 93 |
0.607 (1.00) |
0.84 (1.00) |
0.27 (1.00) |
0.00787 (1.00) |
0.166 (1.00) |
0.0557 (1.00) |
0.622 (1.00) |
0.269 (1.00) |
1 (1.00) |
Del Peak 24(15q22 33) | 75 (46%) | 87 |
0.558 (1.00) |
0.86 (1.00) |
0.344 (1.00) |
1 (1.00) |
0.0108 (1.00) |
0.268 (1.00) |
0.767 (1.00) |
0.0731 (1.00) |
0.0966 (1.00) |
Del Peak 25(16p13 3) | 13 (8%) | 149 |
0.00338 (1.00) |
0.433 (1.00) |
1 (1.00) |
0.263 (1.00) |
0.788 (1.00) |
0.181 (1.00) |
0.797 (1.00) |
0.134 (1.00) |
1 (1.00) |
Del Peak 26(16q23 1) | 23 (14%) | 139 |
0.925 (1.00) |
0.585 (1.00) |
0.826 (1.00) |
1 (1.00) |
0.606 (1.00) |
0.0146 (1.00) |
0.841 (1.00) |
0.338 (1.00) |
1 (1.00) |
Del Peak 27(17p12) | 110 (68%) | 52 |
0.4 (1.00) |
0.0943 (1.00) |
0.866 (1.00) |
0.122 (1.00) |
0.0145 (1.00) |
0.924 (1.00) |
0.918 (1.00) |
0.206 (1.00) |
1 (1.00) |
Del Peak 28(17p11 2) | 102 (63%) | 60 |
0.775 (1.00) |
0.201 (1.00) |
0.514 (1.00) |
0.0783 (1.00) |
0.0845 (1.00) |
0.705 (1.00) |
0.372 (1.00) |
0.617 (1.00) |
0.671 (1.00) |
Del Peak 29(17q25 3) | 24 (15%) | 138 |
0.103 (1.00) |
0.696 (1.00) |
0.119 (1.00) |
1 (1.00) |
0.366 (1.00) |
0.874 (1.00) |
0.13 (1.00) |
0.361 (1.00) |
0.217 (1.00) |
Del Peak 30(18q21 2) | 143 (88%) | 19 |
0.653 (1.00) |
0.443 (1.00) |
1 (1.00) |
1 (1.00) |
0.00589 (1.00) |
0.0607 (1.00) |
0.208 (1.00) |
0.0198 (1.00) |
1 (1.00) |
Del Peak 31(18q22 1) | 138 (85%) | 24 |
0.653 (1.00) |
0.227 (1.00) |
0.825 (1.00) |
0.397 (1.00) |
0.0487 (1.00) |
0.353 (1.00) |
0.567 (1.00) |
0.123 (1.00) |
0.593 (1.00) |
Del Peak 32(19p13 3) | 38 (23%) | 124 |
0.816 (1.00) |
0.795 (1.00) |
1 (1.00) |
0.734 (1.00) |
0.295 (1.00) |
0.567 (1.00) |
0.249 (1.00) |
0.751 (1.00) |
1 (1.00) |
Del Peak 33(20p12 1) | 60 (37%) | 102 |
0.131 (1.00) |
0.23 (1.00) |
0.257 (1.00) |
1 (1.00) |
0.84 (1.00) |
0.885 (1.00) |
0.468 (1.00) |
0.853 (1.00) |
0.0855 (1.00) |
Del Peak 34(20p12 1) | 60 (37%) | 102 |
0.131 (1.00) |
0.23 (1.00) |
0.257 (1.00) |
1 (1.00) |
0.84 (1.00) |
0.885 (1.00) |
0.468 (1.00) |
0.853 (1.00) |
0.0855 (1.00) |
Del Peak 35(21q11 2) | 70 (43%) | 92 |
0.996 (1.00) |
0.454 (1.00) |
0.633 (1.00) |
0.24 (1.00) |
0.139 (1.00) |
0.332 (1.00) |
0.778 (1.00) |
0.602 (1.00) |
1 (1.00) |
Del Peak 36(22q13 31) | 66 (41%) | 96 |
0.0572 (1.00) |
0.255 (1.00) |
0.339 (1.00) |
0.563 (1.00) |
0.278 (1.00) |
0.00849 (1.00) |
0.209 (1.00) |
0.331 (1.00) |
0.688 (1.00) |
Del Peak 37(Xp22 33) | 33 (20%) | 129 |
0.626 (1.00) |
0.681 (1.00) |
0.845 (1.00) |
0.716 (1.00) |
0.722 (1.00) |
0.869 (1.00) |
0.596 (1.00) |
0.902 (1.00) |
1 (1.00) |
P value = 8.16e-05 (logrank test), Q value = 0.045
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 125 | 11 | 0.2 - 121.1 (6.3) |
DEL PEAK 6(3Q26.31) MUTATED | 15 | 3 | 0.2 - 38.9 (2.8) |
DEL PEAK 6(3Q26.31) WILD-TYPE | 110 | 8 | 0.4 - 121.1 (7.0) |
-
Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
-
Clinical data file = READ-TP.clin.merged.picked.txt
-
Number of patients = 162
-
Number of copy number variation regions = 62
-
Number of selected clinical features = 9
-
Exclude regions that fewer than K tumors have alterations, K = 3
For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene cnvs 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 cnvs using 't.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.