Correlation between copy number variation genes (focal events) and selected clinical features
Breast Invasive Carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1PG1QVC
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1PG1QVC
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.

Summary

Testing the association between copy number variation 69 focal events and 12 clinical features across 1080 patients, 229 significant findings detected with Q value < 0.25.

  • amp_1p22.3 cnv correlated to 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'NUMBER_OF_LYMPH_NODES', and 'RACE'.

  • amp_1q21.3 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • amp_1q44 cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • amp_3p25.1 cnv correlated to 'Time to Death',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'HISTOLOGICAL_TYPE'.

  • amp_3q26.32 cnv correlated to 'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • amp_4q13.3 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • amp_5p15.33 cnv correlated to 'Time to Death',  'PATHOLOGY_N_STAGE',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

  • amp_6p23 cnv correlated to 'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • amp_6q21 cnv correlated to 'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • amp_8p11.23 cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • amp_8p11.21 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • amp_8q24.21 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • amp_10p15.1 cnv correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.

  • amp_10q22.3 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • amp_11p13 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • amp_11q13.3 cnv correlated to 'PATHOLOGY_T_STAGE' and 'GENDER'.

  • amp_11q14.1 cnv correlated to 'PATHOLOGY_T_STAGE' and 'HISTOLOGICAL_TYPE'.

  • amp_12p13.33 cnv correlated to 'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE',  'RACE', and 'ETHNICITY'.

  • amp_12q15 cnv correlated to 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'GENDER',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • amp_13q34 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'RADIATION_THERAPY',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • amp_14q21.1 cnv correlated to 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • amp_15q26.3 cnv correlated to 'YEARS_TO_BIRTH',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • amp_17q12 cnv correlated to 'PATHOLOGY_N_STAGE',  'GENDER',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • amp_17q23.1 cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'GENDER', and 'HISTOLOGICAL_TYPE'.

  • amp_19p13.12 cnv correlated to 'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • amp_19q12 cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE',  'NUMBER_OF_LYMPH_NODES', and 'RACE'.

  • amp_19q13.42 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • amp_20q13.2 cnv correlated to 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'GENDER', and 'HISTOLOGICAL_TYPE'.

  • del_1p36.13 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'GENDER',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • del_1p22.1 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • del_2q37.3 cnv correlated to 'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • del_3p21.31 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'RADIATION_THERAPY',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • del_4p16.3 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • del_4q35.1 cnv correlated to 'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • del_5q11.2 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'GENDER',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • del_5q21.3 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE',  'NUMBER_OF_LYMPH_NODES', and 'RACE'.

  • del_6p25.3 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE', and 'HISTOLOGICAL_TYPE'.

  • del_6q15 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_N_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • del_6q27 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_N_STAGE', and 'RADIATION_THERAPY'.

  • del_7p22.3 cnv correlated to 'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • del_7q36.1 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_8p23.2 cnv correlated to 'Time to Death',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • del_8p11.21 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_9p23 cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • del_9p21.3 cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • del_9q21.11 cnv correlated to 'GENDER',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

  • del_9q34.2 cnv correlated to 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'GENDER',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • del_10q23.31 cnv correlated to 'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'ETHNICITY'.

  • del_10q26.3 cnv correlated to 'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'ETHNICITY'.

  • del_11p15.5 cnv correlated to 'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • del_11q13.1 cnv correlated to 'RACE'.

  • del_11q23.3 cnv correlated to 'PATHOLOGY_T_STAGE',  'GENDER', and 'RACE'.

  • del_11q25 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'GENDER',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • del_12p13.1 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_12q23.1 cnv correlated to 'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • del_12q24.31 cnv correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.

  • del_13q14.2 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_14q24.1 cnv correlated to 'Time to Death',  'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • del_15q13.1 cnv correlated to 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE',  'NUMBER_OF_LYMPH_NODES', and 'RACE'.

  • del_16q24.3 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • del_17p12 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • del_17q21.31 cnv correlated to 'YEARS_TO_BIRTH',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • del_18q23 cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'HISTOLOGICAL_TYPE'.

  • del_19p13.3 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • del_19q13.32 cnv correlated to 'PATHOLOGY_N_STAGE' and 'HISTOLOGICAL_TYPE'.

  • del_20p13 cnv correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.

  • del_21q11.2 cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'HISTOLOGICAL_TYPE'.

  • del_22q13.32 cnv correlated to 'RADIATION_THERAPY' and 'HISTOLOGICAL_TYPE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 69 focal events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 229 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		PATHOLOGIC
STAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER RADIATION
THERAPY 		HISTOLOGICAL
TYPE 		NUMBER
OF
LYMPH
NODES 		RACE ETHNICITY
nCNV (%) nWild-Type logrank test Wilcoxon-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 Wilcoxon-test Fisher's exact test Fisher's exact test
del 1p36 13 452 (42%) 628 0.0218
(0.117) 		0.0183
(0.101) 		0.00064
(0.00768) 		1e-05
(0.00023) 		0.00056
(0.00703) 		0.127
(0.359) 		0.0346
(0.164) 		0.186
(0.447) 		0.00278
(0.0245) 		0.00101
(0.0109) 		0.805
(0.939) 		0.743
(0.908)
del 9p23 325 (30%) 755 0.0133
(0.0824) 		0.278
(0.546) 		0.00558
(0.0405) 		0.00032
(0.00469) 		0.0007
(0.00816) 		0.0641
(0.238) 		0.201
(0.457) 		0.479
(0.715) 		1e-05
(0.00023) 		0.0369
(0.17) 		0.35
(0.61) 		1
(1.00)
del 11q25 513 (48%) 567 0.95
(1.00) 		0.0265
(0.134) 		0.0238
(0.125) 		0.00246
(0.0221) 		0.0677
(0.245) 		0.83
(0.943) 		0.0171
(0.1) 		0.896
(0.973) 		0.0111
(0.07) 		0.277
(0.546) 		0.00063
(0.00767) 		1
(1.00)
del 1p22 1 362 (34%) 718 0.000661
(0.00782) 		0.0412
(0.184) 		0.0104
(0.067) 		4e-05
(0.00077) 		0.00766
(0.0529) 		0.498
(0.732) 		0.232
(0.499) 		0.333
(0.606) 		0.118
(0.343) 		0.000895
(0.00988) 		0.667
(0.865) 		0.117
(0.343)
amp 12q15 276 (26%) 804 0.258
(0.524) 		0.235
(0.501) 		0.407
(0.655) 		0.0179
(0.101) 		0.0145
(0.0876) 		0.81
(0.939) 		0.00307
(0.0262) 		0.551
(0.77) 		0.0011
(0.0114) 		0.0179
(0.101) 		0.415
(0.659) 		0.251
(0.521)
amp 13q34 179 (17%) 901 0.394
(0.653) 		0.0539
(0.213) 		0.153
(0.398) 		0.00529
(0.0388) 		0.253
(0.521) 		0.573
(0.793) 		0.702
(0.886) 		0.0444
(0.195) 		0.00121
(0.0122) 		0.0645
(0.238) 		0.605
(0.82) 		0.83
(0.943)
amp 19q12 284 (26%) 796 0.777
(0.926) 		0.488
(0.724) 		0.00939
(0.0627) 		0.546
(0.768) 		0.0359
(0.169) 		0.468
(0.71) 		0.526
(0.755) 		0.941
(1.00) 		1e-05
(0.00023) 		0.00508
(0.0376) 		0.0369
(0.17) 		0.853
(0.954)
del 3p21 31 347 (32%) 733 0.0851
(0.284) 		0.00267
(0.0237) 		0.139
(0.38) 		3e-05
(0.000606) 		0.455
(0.698) 		0.65
(0.853) 		1
(1.00) 		0.0586
(0.226) 		2e-05
(0.000436) 		0.266
(0.536) 		0.0113
(0.0709) 		0.605
(0.82)
del 5q11 2 280 (26%) 800 0.431
(0.677) 		4.3e-06
(0.00023) 		0.201
(0.457) 		0.00037
(0.00502) 		0.284
(0.548) 		0.34
(0.61) 		0.0436
(0.194) 		0.553
(0.772) 		1e-05
(0.00023) 		0.163
(0.413) 		6e-05
(0.00108) 		1
(1.00)
del 5q21 3 272 (25%) 808 0.92
(0.99) 		0.000324
(0.00469) 		0.105
(0.325) 		0.00021
(0.00328) 		0.108
(0.333) 		0.811
(0.939) 		0.314
(0.58) 		0.5
(0.733) 		1e-05
(0.00023) 		0.00312
(0.0263) 		9e-05
(0.00159) 		0.852
(0.954)
del 8p23 2 558 (52%) 522 0.0521
(0.208) 		0.633
(0.845) 		0.978
(1.00) 		0.00387
(0.0312) 		0.061
(0.233) 		0.831
(0.943) 		0.388
(0.649) 		0.472
(0.712) 		1e-05
(0.00023) 		0.783
(0.926) 		0.00118
(0.0121) 		0.745
(0.909)
del 9p21 3 364 (34%) 716 0.188
(0.447) 		0.378
(0.639) 		0.0172
(0.1) 		0.00284
(0.0245) 		0.00408
(0.0322) 		0.172
(0.424) 		0.119
(0.344) 		0.68
(0.866) 		1e-05
(0.00023) 		0.0624
(0.234) 		0.2
(0.457) 		0.863
(0.957)
del 9q34 2 297 (28%) 783 0.577
(0.795) 		0.92
(0.99) 		0.118
(0.343) 		0.0197
(0.107) 		0.0669
(0.243) 		0.81
(0.939) 		0.00508
(0.0376) 		0.305
(0.571) 		1e-05
(0.00023) 		0.189
(0.447) 		0.0472
(0.2) 		0.363
(0.622)
del 15q13 1 375 (35%) 705 0.539
(0.768) 		0.347
(0.61) 		0.146
(0.39) 		0.0014
(0.014) 		0.0221
(0.117) 		0.369
(0.629) 		0.761
(0.916) 		0.411
(0.659) 		1e-05
(0.00023) 		0.037
(0.17) 		0.0239
(0.125) 		0.866
(0.958)
amp 1p22 3 250 (23%) 830 0.818
(0.943) 		0.28
(0.547) 		0.419
(0.66) 		0.0259
(0.132) 		0.0177
(0.101) 		0.61
(0.824) 		0.743
(0.908) 		0.54
(0.768) 		0.303
(0.567) 		0.0152
(0.091) 		0.0477
(0.2) 		0.847
(0.954)
amp 1q44 789 (73%) 291 0.114
(0.339) 		0.32
(0.589) 		0.0521
(0.208) 		0.00332
(0.0275) 		0.214
(0.475) 		0.342
(0.61) 		1
(1.00) 		0.505
(0.737) 		0.00406
(0.0322) 		0.602
(0.82) 		0.0455
(0.198) 		0.141
(0.382)
amp 3p25 1 198 (18%) 882 0.0307
(0.153) 		0.152
(0.397) 		0.0851
(0.284) 		0.00045
(0.00591) 		0.0459
(0.198) 		0.423
(0.666) 		0.706
(0.889) 		0.737
(0.908) 		1e-05
(0.00023) 		0.353
(0.612) 		0.503
(0.734) 		1
(1.00)
amp 5p15 33 394 (36%) 686 0.0586
(0.226) 		0.197
(0.456) 		0.806
(0.939) 		0.151
(0.397) 		0.0182
(0.101) 		0.825
(0.943) 		0.766
(0.92) 		0.0584
(0.226) 		0.00624
(0.0443) 		0.859
(0.956) 		0.236
(0.502) 		0.501
(0.733)
amp 8p11 23 412 (38%) 668 0.0243
(0.126) 		0.12
(0.345) 		0.0506
(0.208) 		0.589
(0.804) 		0.063
(0.235) 		0.182
(0.443) 		1
(1.00) 		0.893
(0.971) 		0.301
(0.566) 		0.00487
(0.037) 		0.667
(0.865) 		0.401
(0.655)
amp 8q24 21 678 (63%) 402 0.101
(0.322) 		0.0555
(0.219) 		0.405
(0.655) 		0.0521
(0.208) 		0.253
(0.521) 		0.653
(0.853) 		0.228
(0.497) 		0.459
(0.704) 		1e-05
(0.00023) 		0.761
(0.916) 		0.00151
(0.0149) 		0.239
(0.506)
amp 12p13 33 282 (26%) 798 0.728
(0.901) 		0.446
(0.692) 		0.514
(0.745) 		0.00192
(0.0177) 		0.64
(0.849) 		0.81
(0.939) 		0.202
(0.457) 		0.101
(0.322) 		1e-05
(0.00023) 		0.292
(0.556) 		0.0222
(0.117) 		0.0616
(0.233)
amp 14q21 1 220 (20%) 860 0.474
(0.712) 		0.188
(0.447) 		0.284
(0.548) 		0.0161
(0.0962) 		0.0321
(0.155) 		0.437
(0.683) 		0.718
(0.893) 		0.471
(0.712) 		0.00685
(0.0481) 		0.0103
(0.0666) 		0.569
(0.788) 		0.311
(0.577)
amp 17q12 333 (31%) 747 0.103
(0.323) 		0.932
(0.998) 		0.434
(0.679) 		0.0824
(0.281) 		0.0616
(0.233) 		0.818
(0.943) 		0.011
(0.0698) 		0.723
(0.898) 		0.0005
(0.00637) 		0.359
(0.617) 		0.00169
(0.0159) 		1
(1.00)
amp 17q23 1 426 (39%) 654 0.13
(0.364) 		0.214
(0.475) 		0.0291
(0.146) 		0.00034
(0.00469) 		0.265
(0.536) 		0.828
(0.943) 		1.29e-05
(0.000289) 		0.789
(0.93) 		1e-05
(0.00023) 		0.397
(0.653) 		0.144
(0.387) 		0.739
(0.908)
amp 20q13 2 548 (51%) 532 0.648
(0.853) 		0.671
(0.865) 		0.184
(0.445) 		0.00109
(0.0114) 		0.00105
(0.0111) 		1
(1.00) 		0.0378
(0.172) 		0.171
(0.423) 		1e-05
(0.00023) 		0.169
(0.419) 		0.225
(0.494) 		0.417
(0.659)
del 4p16 3 339 (31%) 741 0.984
(1.00) 		0.0561
(0.22) 		0.102
(0.323) 		0.00015
(0.00259) 		0.607
(0.821) 		0.65
(0.853) 		0.763
(0.917) 		0.674
(0.865) 		1e-05
(0.00023) 		0.535
(0.766) 		0.018
(0.101) 		0.727
(0.901)
del 14q24 1 353 (33%) 727 0.0509
(0.208) 		0.2
(0.457) 		0.222
(0.489) 		0.00017
(0.00287) 		0.394
(0.653) 		0.653
(0.853) 		0.542
(0.768) 		0.147
(0.39) 		1e-05
(0.00023) 		0.372
(0.633) 		0.00033
(0.00469) 		0.863
(0.957)
del 16q24 3 693 (64%) 387 0.95
(1.00) 		0.000319
(0.00469) 		0.377
(0.638) 		0.0602
(0.231) 		0.432
(0.677) 		0.114
(0.339) 		1
(1.00) 		0.684
(0.869) 		1e-05
(0.00023) 		0.309
(0.574) 		0.00765
(0.0529) 		0.239
(0.506)
del 17p12 650 (60%) 430 0.334
(0.606) 		0.0024
(0.0218) 		0.461
(0.704) 		0.047
(0.2) 		0.875
(0.96) 		0.829
(0.943) 		0.382
(0.641) 		0.947
(1.00) 		0.00428
(0.0331) 		0.743
(0.908) 		0.0457
(0.198) 		0.868
(0.958)
del 18q23 354 (33%) 726 0.084
(0.284) 		0.253
(0.521) 		0.0662
(0.243) 		0.0178
(0.101) 		0.0578
(0.226) 		0.653
(0.853) 		0.543
(0.768) 		0.237
(0.502) 		0.00021
(0.00328) 		0.461
(0.704) 		0.0818
(0.281) 		0.863
(0.957)
del 19p13 3 363 (34%) 717 0.269
(0.538) 		0.00162
(0.0156) 		0.928
(0.996) 		0.0473
(0.2) 		0.894
(0.971) 		0.824
(0.943) 		0.356
(0.616) 		0.783
(0.926) 		1e-05
(0.00023) 		0.21
(0.471) 		0.00021
(0.00328) 		1
(1.00)
del 21q11 2 217 (20%) 863 0.581
(0.797) 		0.402
(0.655) 		0.00928
(0.0625) 		0.00997
(0.065) 		0.0139
(0.0847) 		0.103
(0.323) 		1
(1.00) 		0.38
(0.639) 		0.00086
(0.00973) 		0.142
(0.382) 		0.181
(0.442) 		0.544
(0.768)
amp 3q26 32 340 (31%) 740 0.957
(1.00) 		0.448
(0.693) 		0.112
(0.338) 		0.0002
(0.00328) 		0.358
(0.617) 		0.82
(0.943) 		1
(1.00) 		0.944
(1.00) 		1e-05
(0.00023) 		0.107
(0.331) 		0.00315
(0.0263) 		0.109
(0.333)
amp 6p23 299 (28%) 781 0.914
(0.986) 		0.201
(0.457) 		0.337
(0.61) 		0.00281
(0.0245) 		0.234
(0.501) 		0.81
(0.939) 		0.196
(0.456) 		0.308
(0.574) 		1e-05
(0.00023) 		0.998
(1.00) 		0.00164
(0.0156) 		0.585
(0.8)
amp 6q21 202 (19%) 878 0.115
(0.339) 		0.29
(0.554) 		0.0809
(0.279) 		0.00059
(0.00729) 		0.141
(0.382) 		1
(1.00) 		0.707
(0.889) 		0.933
(0.998) 		1e-05
(0.00023) 		0.046
(0.198) 		0.0983
(0.319) 		0.676
(0.866)
amp 15q26 3 194 (18%) 886 0.19
(0.447) 		0.00973
(0.0639) 		0.807
(0.939) 		0.297
(0.561) 		0.902
(0.977) 		1
(1.00) 		0.245
(0.513) 		1
(1.00) 		1e-05
(0.00023) 		0.647
(0.853) 		0.0504
(0.208) 		0.284
(0.548)
amp 19p13 12 230 (21%) 850 0.121
(0.346) 		0.634
(0.846) 		0.343
(0.61) 		0.404
(0.655) 		0.159
(0.407) 		0.0623
(0.234) 		0.145
(0.388) 		0.181
(0.442) 		0.0313
(0.155) 		0.000495
(0.00637) 		0.172
(0.424) 		1
(1.00)
del 2q37 3 317 (29%) 763 0.612
(0.826) 		0.544
(0.768) 		0.35
(0.61) 		0.00158
(0.0154) 		0.416
(0.659) 		0.246
(0.513) 		1
(1.00) 		0.52
(0.75) 		1e-05
(0.00023) 		0.289
(0.554) 		0.0319
(0.155) 		0.468
(0.71)
del 4q35 1 345 (32%) 735 0.085
(0.284) 		0.55
(0.77) 		0.345
(0.61) 		0.00182
(0.0169) 		0.777
(0.926) 		0.497
(0.732) 		0.761
(0.916) 		0.673
(0.865) 		1e-05
(0.00023) 		0.75
(0.913) 		0.00599
(0.0431) 		0.0772
(0.271)
del 6p25 3 204 (19%) 876 0.887
(0.966) 		0.0526
(0.209) 		0.231
(0.499) 		0.0096
(0.0636) 		0.111
(0.336) 		1
(1.00) 		0.256
(0.523) 		0.136
(0.375) 		0.0258
(0.132) 		0.587
(0.802) 		0.472
(0.712) 		0.679
(0.866)
del 6q15 358 (33%) 722 0.79
(0.93) 		0.0399
(0.18) 		0.209
(0.468) 		0.375
(0.637) 		0.0335
(0.159) 		0.494
(0.73) 		0.76
(0.916) 		0.0977
(0.319) 		0.14
(0.382) 		0.0204
(0.11) 		0.135
(0.374) 		0.604
(0.82)
del 6q27 375 (35%) 705 0.101
(0.322) 		6.42e-06
(0.00023) 		0.246
(0.513) 		0.684
(0.869) 		0.0265
(0.134) 		1
(1.00) 		0.235
(0.501) 		0.00504
(0.0376) 		0.278
(0.546) 		0.289
(0.554) 		0.62
(0.834) 		0.302
(0.567)
del 7p22 3 137 (13%) 943 0.742
(0.908) 		0.345
(0.61) 		0.36
(0.619) 		0.192
(0.45) 		0.0521
(0.208) 		1
(1.00) 		1
(1.00) 		0.771
(0.923) 		1e-05
(0.00023) 		0.0137
(0.0839) 		0.658
(0.856) 		1
(1.00)
del 9q21 11 294 (27%) 786 0.38
(0.639) 		0.957
(1.00) 		0.273
(0.543) 		0.0718
(0.259) 		0.213
(0.475) 		0.342
(0.61) 		0.0222
(0.117) 		0.0477
(0.2) 		1e-05
(0.00023) 		0.516
(0.747) 		0.19
(0.447) 		0.353
(0.612)
del 10q23 31 320 (30%) 760 0.711
(0.89) 		0.0787
(0.273) 		0.231
(0.499) 		0.0165
(0.0975) 		0.115
(0.339) 		0.819
(0.943) 		0.123
(0.352) 		0.671
(0.865) 		3e-05
(0.000606) 		0.267
(0.536) 		0.28
(0.547) 		0.0486
(0.202)
del 10q26 3 319 (30%) 761 0.083
(0.282) 		0.388
(0.649) 		0.165
(0.413) 		0.0332
(0.159) 		0.189
(0.447) 		0.347
(0.61) 		0.526
(0.755) 		0.943
(1.00) 		1e-05
(0.00023) 		0.348
(0.61) 		0.114
(0.339) 		0.019
(0.104)
del 11p15 5 309 (29%) 771 0.203
(0.457) 		0.751
(0.913) 		0.241
(0.508) 		0.00413
(0.0323) 		0.414
(0.659) 		0.344
(0.61) 		0.34
(0.61) 		0.943
(1.00) 		1e-05
(0.00023) 		0.827
(0.943) 		0.0048
(0.0368) 		0.364
(0.623)
del 11q23 3 547 (51%) 533 0.944
(1.00) 		0.212
(0.473) 		0.1
(0.322) 		0.033
(0.159) 		0.111
(0.336) 		0.395
(0.653) 		0.0377
(0.172) 		0.794
(0.934) 		0.0778
(0.271) 		0.165
(0.413) 		0.0183
(0.101) 		0.871
(0.958)
del 12q23 1 201 (19%) 879 0.872
(0.958) 		0.0897
(0.293) 		0.565
(0.783) 		0.0316
(0.155) 		0.829
(0.943) 		0.403
(0.655) 		1
(1.00) 		0.451
(0.695) 		0.00099
(0.0108) 		0.484
(0.72) 		0.00626
(0.0443) 		1
(1.00)
del 17q21 31 371 (34%) 709 0.477
(0.715) 		0.000386
(0.00515) 		0.488
(0.724) 		0.0727
(0.261) 		0.145
(0.388) 		0.367
(0.626) 		0.761
(0.916) 		1
(1.00) 		1e-05
(0.00023) 		0.823
(0.943) 		5e-05
(0.00092) 		1
(1.00)
amp 10p15 1 304 (28%) 776 0.155
(0.4) 		0.632
(0.845) 		0.226
(0.494) 		0.0748
(0.264) 		0.461
(0.704) 		0.478
(0.715) 		1
(1.00) 		0.562
(0.78) 		1e-05
(0.00023) 		0.192
(0.45) 		3e-05
(0.000606) 		0.713
(0.892)
amp 11q13 3 398 (37%) 682 0.406
(0.655) 		0.267
(0.536) 		0.656
(0.855) 		0.0319
(0.155) 		0.672
(0.865) 		0.267
(0.536) 		0.0382
(0.173) 		0.417
(0.659) 		0.254
(0.522) 		0.779
(0.926) 		0.342
(0.61) 		0.501
(0.733)
amp 11q14 1 267 (25%) 813 0.29
(0.554) 		0.276
(0.546) 		0.439
(0.684) 		0.0668
(0.243) 		0.111
(0.336) 		0.467
(0.71) 		0.183
(0.444) 		0.281
(0.547) 		0.00849
(0.0576) 		0.853
(0.954) 		0.116
(0.339) 		0.446
(0.692)
del 12q24 31 211 (20%) 869 0.113
(0.339) 		0.125
(0.355) 		0.848
(0.954) 		0.0779
(0.271) 		0.64
(0.849) 		1
(1.00) 		0.479
(0.715) 		0.869
(0.958) 		0.0442
(0.195) 		0.329
(0.6) 		0.0509
(0.208) 		0.545
(0.768)
del 19q13 32 216 (20%) 864 0.118
(0.343) 		0.312
(0.578) 		0.452
(0.695) 		0.323
(0.593) 		0.0664
(0.243) 		0.412
(0.659) 		0.715
(0.892) 		0.517
(0.747) 		1e-05
(0.00023) 		0.831
(0.943) 		0.0895
(0.293) 		0.544
(0.768)
del 20p13 160 (15%) 920 0.197
(0.456) 		0.0472
(0.2) 		0.63
(0.844) 		0.413
(0.659) 		0.981
(1.00) 		0.129
(0.363) 		0.402
(0.655) 		0.167
(0.416) 		4e-05
(0.00077) 		0.886
(0.966) 		0.165
(0.413) 		0.64
(0.849)
del 22q13 32 492 (46%) 588 0.955
(1.00) 		0.399
(0.654) 		0.805
(0.939) 		0.159
(0.407) 		0.858
(0.956) 		0.396
(0.653) 		0.398
(0.653) 		0.0362
(0.169) 		0.00034
(0.00469) 		0.987
(1.00) 		0.416
(0.659) 		0.626
(0.84)
amp 1q21 3 781 (72%) 299 0.985
(1.00) 		0.902
(0.977) 		0.193
(0.452) 		0.0115
(0.0716) 		0.349
(0.61) 		1
(1.00) 		0.103
(0.323) 		0.715
(0.892) 		0.0746
(0.264) 		0.68
(0.866) 		0.198
(0.456) 		0.0997
(0.321)
amp 4q13 3 163 (15%) 917 0.114
(0.339) 		0.257
(0.523) 		0.872
(0.958) 		0.178
(0.435) 		0.71
(0.89) 		0.768
(0.921) 		0.406
(0.655) 		0.27
(0.538) 		1e-05
(0.00023) 		0.754
(0.915) 		0.149
(0.391) 		0.16
(0.408)
amp 8p11 21 421 (39%) 659 0.836
(0.945) 		0.162
(0.413) 		0.346
(0.61) 		0.879
(0.963) 		0.687
(0.871) 		0.274
(0.544) 		0.774
(0.925) 		0.203
(0.457) 		0.00087
(0.00973) 		0.394
(0.653) 		0.131
(0.367) 		0.508
(0.739)
amp 10q22 3 150 (14%) 930 0.153
(0.397) 		0.936
(1) 		0.3
(0.565) 		0.148
(0.391) 		0.198
(0.456) 		1
(1.00) 		0.678
(0.866) 		0.707
(0.889) 		0.00022
(0.00337) 		0.198
(0.456) 		0.169
(0.419) 		1
(1.00)
amp 11p13 223 (21%) 857 0.558
(0.776) 		0.251
(0.521) 		0.883
(0.965) 		0.392
(0.653) 		0.958
(1.00) 		0.44
(0.684) 		0.283
(0.548) 		0.295
(0.56) 		1e-05
(0.00023) 		0.492
(0.727) 		0.329
(0.6) 		0.84
(0.949)
amp 19q13 42 276 (26%) 804 0.885
(0.966) 		0.647
(0.853) 		0.854
(0.954) 		0.257
(0.523) 		0.558
(0.776) 		0.223
(0.491) 		0.0873
(0.289) 		0.94
(1.00) 		0.00774
(0.053) 		0.0887
(0.292) 		0.853
(0.954) 		0.45
(0.695)
del 7q36 1 200 (19%) 880 0.23
(0.498) 		0.912
(0.984) 		0.789
(0.93) 		0.186
(0.447) 		0.338
(0.61) 		0.406
(0.655) 		0.473
(0.712) 		0.867
(0.958) 		5e-05
(0.00092) 		0.859
(0.956) 		0.624
(0.839) 		0.523
(0.754)
del 8p11 21 200 (19%) 880 0.0748
(0.264) 		0.296
(0.56) 		0.809
(0.939) 		0.154
(0.399) 		0.228
(0.497) 		0.165
(0.413) 		0.138
(0.379) 		0.933
(0.998) 		0.00388
(0.0312) 		0.126
(0.357) 		0.134
(0.373) 		0.832
(0.943)
del 11q13 1 241 (22%) 839 0.54
(0.768) 		0.717
(0.892) 		0.395
(0.653) 		0.0857
(0.285) 		0.546
(0.768) 		0.799
(0.938) 		0.736
(0.908) 		0.641
(0.849) 		0.698
(0.884) 		0.49
(0.726) 		0.00346
(0.0284) 		0.842
(0.95)
del 12p13 1 188 (17%) 892 0.347
(0.61) 		0.327
(0.598) 		0.242
(0.508) 		0.147
(0.39) 		0.903
(0.977) 		0.782
(0.926) 		0.14
(0.382) 		1
(1.00) 		0.00085
(0.00973) 		0.579
(0.796) 		0.702
(0.886) 		0.665
(0.864)
del 13q14 2 495 (46%) 585 0.275
(0.544) 		0.547
(0.768) 		0.577
(0.795) 		0.0826
(0.281) 		0.255
(0.523) 		0.669
(0.865) 		0.78
(0.926) 		0.132
(0.367) 		1e-05
(0.00023) 		0.734
(0.907) 		0.0737
(0.263) 		0.0992
(0.321)
amp 17p11 2 147 (14%) 933 0.283
(0.548) 		0.355
(0.616) 		0.739
(0.908) 		0.16
(0.408) 		0.65
(0.853) 		0.756
(0.916) 		0.217
(0.478) 		0.104
(0.325) 		0.509
(0.74) 		0.314
(0.58) 		0.578
(0.795) 		1
(1.00)
'amp_1p22.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.0259 (Fisher's exact test), Q value = 0.13

Table S1.  Gene #1: 'amp_1p22.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
AMP PEAK 1(1P22.3) MUTATED 46 155 36 11
AMP PEAK 1(1P22.3) WILD-TYPE 230 469 100 29

Figure S1.  Get High-res Image Gene #1: 'amp_1p22.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_1p22.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.0177 (Fisher's exact test), Q value = 0.1

Table S2.  Gene #1: 'amp_1p22.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 507 358 119 77
AMP PEAK 1(1P22.3) MUTATED 137 68 21 20
AMP PEAK 1(1P22.3) WILD-TYPE 370 290 98 57

Figure S2.  Get High-res Image Gene #1: 'amp_1p22.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_1p22.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0152 (Wilcoxon-test), Q value = 0.091

Table S3.  Gene #1: 'amp_1p22.3' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 914 2.4 (4.7)
AMP PEAK 1(1P22.3) MUTATED 221 2.0 (4.1)
AMP PEAK 1(1P22.3) WILD-TYPE 693 2.5 (4.8)

Figure S3.  Get High-res Image Gene #1: 'amp_1p22.3' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'amp_1p22.3' versus 'RACE'

P value = 0.0477 (Fisher's exact test), Q value = 0.2

Table S4.  Gene #1: 'amp_1p22.3' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
AMP PEAK 1(1P22.3) MUTATED 0 9 54 166
AMP PEAK 1(1P22.3) WILD-TYPE 1 51 127 579

Figure S4.  Get High-res Image Gene #1: 'amp_1p22.3' versus Clinical Feature #11: 'RACE'

'amp_1q21.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.0115 (Fisher's exact test), Q value = 0.072

Table S5.  Gene #2: 'amp_1q21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
AMP PEAK 2(1Q21.3) MUTATED 182 460 101 35
AMP PEAK 2(1Q21.3) WILD-TYPE 94 164 35 5

Figure S5.  Get High-res Image Gene #2: 'amp_1q21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_1q44' versus 'PATHOLOGIC_STAGE'

P value = 0.0521 (Fisher's exact test), Q value = 0.21

Table S6.  Gene #3: 'amp_1q44' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
ALL 89 85 6 6 353 252 2 154 29 65 20 1 13
AMP PEAK 3(1Q44) MUTATED 56 56 3 6 266 187 1 109 25 53 13 1 8
AMP PEAK 3(1Q44) WILD-TYPE 33 29 3 0 87 65 1 45 4 12 7 0 5

Figure S6.  Get High-res Image Gene #3: 'amp_1q44' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_1q44' versus 'PATHOLOGY_T_STAGE'

P value = 0.00332 (Fisher's exact test), Q value = 0.027

Table S7.  Gene #3: 'amp_1q44' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
AMP PEAK 3(1Q44) MUTATED 179 474 100 33
AMP PEAK 3(1Q44) WILD-TYPE 97 150 36 7

Figure S7.  Get High-res Image Gene #3: 'amp_1q44' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_1q44' versus 'HISTOLOGICAL_TYPE'

P value = 0.00406 (Fisher's exact test), Q value = 0.032

Table S8.  Gene #3: 'amp_1q44' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
AMP PEAK 3(1Q44) MUTATED 1 549 167 5 5 20 9 33
AMP PEAK 3(1Q44) WILD-TYPE 0 221 33 1 4 9 8 14

Figure S8.  Get High-res Image Gene #3: 'amp_1q44' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_1q44' versus 'RACE'

P value = 0.0455 (Fisher's exact test), Q value = 0.2

Table S9.  Gene #3: 'amp_1q44' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
AMP PEAK 3(1Q44) MUTATED 1 35 133 554
AMP PEAK 3(1Q44) WILD-TYPE 0 25 48 191

Figure S9.  Get High-res Image Gene #3: 'amp_1q44' versus Clinical Feature #11: 'RACE'

'amp_3p25.1' versus 'Time to Death'

P value = 0.0307 (logrank test), Q value = 0.15

Table S10.  Gene #4: 'amp_3p25.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1064 147 0.0 - 282.9 (27.9)
AMP PEAK 4(3P25.1) MUTATED 196 35 0.3 - 282.9 (26.8)
AMP PEAK 4(3P25.1) WILD-TYPE 868 112 0.0 - 281.3 (28.2)

Figure S10.  Get High-res Image Gene #4: 'amp_3p25.1' versus Clinical Feature #1: 'Time to Death'

'amp_3p25.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00045 (Fisher's exact test), Q value = 0.0059

Table S11.  Gene #4: 'amp_3p25.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
AMP PEAK 4(3P25.1) MUTATED 37 132 15 13
AMP PEAK 4(3P25.1) WILD-TYPE 239 492 121 27

Figure S11.  Get High-res Image Gene #4: 'amp_3p25.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_3p25.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0459 (Fisher's exact test), Q value = 0.2

Table S12.  Gene #4: 'amp_3p25.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 507 358 119 77
AMP PEAK 4(3P25.1) MUTATED 95 55 32 12
AMP PEAK 4(3P25.1) WILD-TYPE 412 303 87 65

Figure S12.  Get High-res Image Gene #4: 'amp_3p25.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_3p25.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S13.  Gene #4: 'amp_3p25.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
AMP PEAK 4(3P25.1) MUTATED 1 168 14 1 2 5 1 6
AMP PEAK 4(3P25.1) WILD-TYPE 0 602 186 5 7 24 16 41

Figure S13.  Get High-res Image Gene #4: 'amp_3p25.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_3q26.32' versus 'PATHOLOGY_T_STAGE'

P value = 2e-04 (Fisher's exact test), Q value = 0.0033

Table S14.  Gene #5: 'amp_3q26.32' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
AMP PEAK 5(3Q26.32) MUTATED 66 225 31 17
AMP PEAK 5(3Q26.32) WILD-TYPE 210 399 105 23

Figure S14.  Get High-res Image Gene #5: 'amp_3q26.32' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_3q26.32' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S15.  Gene #5: 'amp_3q26.32' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
AMP PEAK 5(3Q26.32) MUTATED 1 293 16 5 7 6 1 10
AMP PEAK 5(3Q26.32) WILD-TYPE 0 477 184 1 2 23 16 37

Figure S15.  Get High-res Image Gene #5: 'amp_3q26.32' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_3q26.32' versus 'RACE'

P value = 0.00315 (Fisher's exact test), Q value = 0.026

Table S16.  Gene #5: 'amp_3q26.32' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
AMP PEAK 5(3Q26.32) MUTATED 1 27 65 208
AMP PEAK 5(3Q26.32) WILD-TYPE 0 33 116 537

Figure S16.  Get High-res Image Gene #5: 'amp_3q26.32' versus Clinical Feature #11: 'RACE'

'amp_4q13.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S17.  Gene #6: 'amp_4q13.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
AMP PEAK 6(4Q13.3) MUTATED 0 142 7 2 3 2 1 6
AMP PEAK 6(4Q13.3) WILD-TYPE 1 628 193 4 6 27 16 41

Figure S17.  Get High-res Image Gene #6: 'amp_4q13.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_5p15.33' versus 'Time to Death'

P value = 0.0586 (logrank test), Q value = 0.23

Table S18.  Gene #7: 'amp_5p15.33' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1064 147 0.0 - 282.9 (27.9)
AMP PEAK 7(5P15.33) MUTATED 390 59 0.0 - 255.7 (25.0)
AMP PEAK 7(5P15.33) WILD-TYPE 674 88 0.0 - 282.9 (29.2)

Figure S18.  Get High-res Image Gene #7: 'amp_5p15.33' versus Clinical Feature #1: 'Time to Death'

'amp_5p15.33' versus 'PATHOLOGY_N_STAGE'

P value = 0.0182 (Fisher's exact test), Q value = 0.1

Table S19.  Gene #7: 'amp_5p15.33' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 507 358 119 77
AMP PEAK 7(5P15.33) MUTATED 197 111 54 27
AMP PEAK 7(5P15.33) WILD-TYPE 310 247 65 50

Figure S19.  Get High-res Image Gene #7: 'amp_5p15.33' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_5p15.33' versus 'RADIATION_THERAPY'

P value = 0.0584 (Fisher's exact test), Q value = 0.23

Table S20.  Gene #7: 'amp_5p15.33' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients NO YES
ALL 429 518
AMP PEAK 7(5P15.33) MUTATED 144 205
AMP PEAK 7(5P15.33) WILD-TYPE 285 313

Figure S20.  Get High-res Image Gene #7: 'amp_5p15.33' versus Clinical Feature #8: 'RADIATION_THERAPY'

'amp_5p15.33' versus 'HISTOLOGICAL_TYPE'

P value = 0.00624 (Fisher's exact test), Q value = 0.044

Table S21.  Gene #7: 'amp_5p15.33' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
AMP PEAK 7(5P15.33) MUTATED 1 297 61 2 7 9 2 14
AMP PEAK 7(5P15.33) WILD-TYPE 0 473 139 4 2 20 15 33

Figure S21.  Get High-res Image Gene #7: 'amp_5p15.33' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_6p23' versus 'PATHOLOGY_T_STAGE'

P value = 0.00281 (Fisher's exact test), Q value = 0.024

Table S22.  Gene #8: 'amp_6p23' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
AMP PEAK 8(6P23) MUTATED 55 197 34 12
AMP PEAK 8(6P23) WILD-TYPE 221 427 102 28

Figure S22.  Get High-res Image Gene #8: 'amp_6p23' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_6p23' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S23.  Gene #8: 'amp_6p23' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
AMP PEAK 8(6P23) MUTATED 0 247 26 4 4 5 2 10
AMP PEAK 8(6P23) WILD-TYPE 1 523 174 2 5 24 15 37

Figure S23.  Get High-res Image Gene #8: 'amp_6p23' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_6p23' versus 'RACE'

P value = 0.00164 (Fisher's exact test), Q value = 0.016

Table S24.  Gene #8: 'amp_6p23' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
AMP PEAK 8(6P23) MUTATED 0 15 70 185
AMP PEAK 8(6P23) WILD-TYPE 1 45 111 560

Figure S24.  Get High-res Image Gene #8: 'amp_6p23' versus Clinical Feature #11: 'RACE'

'amp_6q21' versus 'PATHOLOGY_T_STAGE'

P value = 0.00059 (Fisher's exact test), Q value = 0.0073

Table S25.  Gene #9: 'amp_6q21' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
AMP PEAK 9(6Q21) MUTATED 34 142 22 4
AMP PEAK 9(6Q21) WILD-TYPE 242 482 114 36

Figure S25.  Get High-res Image Gene #9: 'amp_6q21' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_6q21' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S26.  Gene #9: 'amp_6q21' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
AMP PEAK 9(6Q21) MUTATED 1 171 15 3 5 1 0 6
AMP PEAK 9(6Q21) WILD-TYPE 0 599 185 3 4 28 17 41

Figure S26.  Get High-res Image Gene #9: 'amp_6q21' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_6q21' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.046 (Wilcoxon-test), Q value = 0.2

Table S27.  Gene #9: 'amp_6q21' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 914 2.4 (4.7)
AMP PEAK 9(6Q21) MUTATED 173 2.0 (4.4)
AMP PEAK 9(6Q21) WILD-TYPE 741 2.5 (4.7)

Figure S27.  Get High-res Image Gene #9: 'amp_6q21' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'amp_8p11.23' versus 'Time to Death'

P value = 0.0243 (logrank test), Q value = 0.13

Table S28.  Gene #10: 'amp_8p11.23' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1064 147 0.0 - 282.9 (27.9)
AMP PEAK 10(8P11.23) MUTATED 406 69 0.0 - 281.3 (26.2)
AMP PEAK 10(8P11.23) WILD-TYPE 658 78 0.0 - 282.9 (28.9)

Figure S28.  Get High-res Image Gene #10: 'amp_8p11.23' versus Clinical Feature #1: 'Time to Death'

'amp_8p11.23' versus 'PATHOLOGIC_STAGE'

P value = 0.0506 (Fisher's exact test), Q value = 0.21

Table S29.  Gene #10: 'amp_8p11.23' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
ALL 89 85 6 6 353 252 2 154 29 65 20 1 13
AMP PEAK 10(8P11.23) MUTATED 24 29 4 1 135 94 2 57 16 30 11 0 6
AMP PEAK 10(8P11.23) WILD-TYPE 65 56 2 5 218 158 0 97 13 35 9 1 7

Figure S29.  Get High-res Image Gene #10: 'amp_8p11.23' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_8p11.23' versus 'PATHOLOGY_N_STAGE'

P value = 0.063 (Fisher's exact test), Q value = 0.24

Table S30.  Gene #10: 'amp_8p11.23' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 507 358 119 77
AMP PEAK 10(8P11.23) MUTATED 173 146 48 36
AMP PEAK 10(8P11.23) WILD-TYPE 334 212 71 41

Figure S30.  Get High-res Image Gene #10: 'amp_8p11.23' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_8p11.23' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00487 (Wilcoxon-test), Q value = 0.037

Table S31.  Gene #10: 'amp_8p11.23' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 914 2.4 (4.7)
AMP PEAK 10(8P11.23) MUTATED 346 2.9 (5.3)
AMP PEAK 10(8P11.23) WILD-TYPE 568 2.1 (4.2)

Figure S31.  Get High-res Image Gene #10: 'amp_8p11.23' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'amp_8p11.21' versus 'HISTOLOGICAL_TYPE'

P value = 0.00087 (Fisher's exact test), Q value = 0.0097

Table S32.  Gene #11: 'amp_8p11.21' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
AMP PEAK 11(8P11.21) MUTATED 1 322 55 5 4 10 4 19
AMP PEAK 11(8P11.21) WILD-TYPE 0 448 145 1 5 19 13 28

Figure S32.  Get High-res Image Gene #11: 'amp_8p11.21' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_8q24.21' versus 'YEARS_TO_BIRTH'

P value = 0.0555 (Wilcoxon-test), Q value = 0.22

Table S33.  Gene #12: 'amp_8q24.21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1065 58.6 (13.2)
AMP PEAK 12(8Q24.21) MUTATED 670 58.0 (13.1)
AMP PEAK 12(8Q24.21) WILD-TYPE 395 59.7 (13.3)

Figure S33.  Get High-res Image Gene #12: 'amp_8q24.21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_8q24.21' versus 'PATHOLOGY_T_STAGE'

P value = 0.0521 (Fisher's exact test), Q value = 0.21

Table S34.  Gene #12: 'amp_8q24.21' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
AMP PEAK 12(8Q24.21) MUTATED 158 412 79 25
AMP PEAK 12(8Q24.21) WILD-TYPE 118 212 57 15

Figure S34.  Get High-res Image Gene #12: 'amp_8q24.21' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_8q24.21' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S35.  Gene #12: 'amp_8q24.21' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
AMP PEAK 12(8Q24.21) MUTATED 1 546 70 6 7 17 5 25
AMP PEAK 12(8Q24.21) WILD-TYPE 0 224 130 0 2 12 12 22

Figure S35.  Get High-res Image Gene #12: 'amp_8q24.21' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_8q24.21' versus 'RACE'

P value = 0.00151 (Fisher's exact test), Q value = 0.015

Table S36.  Gene #12: 'amp_8q24.21' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
AMP PEAK 12(8Q24.21) MUTATED 1 41 131 435
AMP PEAK 12(8Q24.21) WILD-TYPE 0 19 50 310

Figure S36.  Get High-res Image Gene #12: 'amp_8q24.21' versus Clinical Feature #11: 'RACE'

'amp_10p15.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S37.  Gene #13: 'amp_10p15.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
AMP PEAK 13(10P15.1) MUTATED 1 262 20 5 1 5 0 9
AMP PEAK 13(10P15.1) WILD-TYPE 0 508 180 1 8 24 17 38

Figure S37.  Get High-res Image Gene #13: 'amp_10p15.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_10p15.1' versus 'RACE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00061

Table S38.  Gene #13: 'amp_10p15.1' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
AMP PEAK 13(10P15.1) MUTATED 1 14 75 185
AMP PEAK 13(10P15.1) WILD-TYPE 0 46 106 560

Figure S38.  Get High-res Image Gene #13: 'amp_10p15.1' versus Clinical Feature #11: 'RACE'

'amp_10q22.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.00022 (Fisher's exact test), Q value = 0.0034

Table S39.  Gene #14: 'amp_10q22.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
AMP PEAK 14(10Q22.3) MUTATED 0 125 11 3 1 4 0 6
AMP PEAK 14(10Q22.3) WILD-TYPE 1 645 189 3 8 25 17 41

Figure S39.  Get High-res Image Gene #14: 'amp_10q22.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_11p13' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S40.  Gene #15: 'amp_11p13' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
AMP PEAK 15(11P13) MUTATED 1 187 18 3 2 2 2 8
AMP PEAK 15(11P13) WILD-TYPE 0 583 182 3 7 27 15 39

Figure S40.  Get High-res Image Gene #15: 'amp_11p13' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_11q13.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.0319 (Fisher's exact test), Q value = 0.16

Table S41.  Gene #16: 'amp_11q13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
AMP PEAK 16(11Q13.3) MUTATED 86 246 44 19
AMP PEAK 16(11Q13.3) WILD-TYPE 190 378 92 21

Figure S41.  Get High-res Image Gene #16: 'amp_11q13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_11q13.3' versus 'GENDER'

P value = 0.0382 (Fisher's exact test), Q value = 0.17

Table S42.  Gene #16: 'amp_11q13.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1068 12
AMP PEAK 16(11Q13.3) MUTATED 390 8
AMP PEAK 16(11Q13.3) WILD-TYPE 678 4

Figure S42.  Get High-res Image Gene #16: 'amp_11q13.3' versus Clinical Feature #7: 'GENDER'

'amp_11q14.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.0668 (Fisher's exact test), Q value = 0.24

Table S43.  Gene #17: 'amp_11q14.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
AMP PEAK 17(11Q14.1) MUTATED 60 170 24 10
AMP PEAK 17(11Q14.1) WILD-TYPE 216 454 112 30

Figure S43.  Get High-res Image Gene #17: 'amp_11q14.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_11q14.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00849 (Fisher's exact test), Q value = 0.058

Table S44.  Gene #17: 'amp_11q14.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
AMP PEAK 17(11Q14.1) MUTATED 1 212 34 2 2 3 2 11
AMP PEAK 17(11Q14.1) WILD-TYPE 0 558 166 4 7 26 15 36

Figure S44.  Get High-res Image Gene #17: 'amp_11q14.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_12p13.33' versus 'PATHOLOGY_T_STAGE'

P value = 0.00192 (Fisher's exact test), Q value = 0.018

Table S45.  Gene #18: 'amp_12p13.33' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
AMP PEAK 18(12P13.33) MUTATED 49 184 35 12
AMP PEAK 18(12P13.33) WILD-TYPE 227 440 101 28

Figure S45.  Get High-res Image Gene #18: 'amp_12p13.33' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_12p13.33' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S46.  Gene #18: 'amp_12p13.33' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
AMP PEAK 18(12P13.33) MUTATED 1 230 28 4 2 10 1 6
AMP PEAK 18(12P13.33) WILD-TYPE 0 540 172 2 7 19 16 41

Figure S46.  Get High-res Image Gene #18: 'amp_12p13.33' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_12p13.33' versus 'RACE'

P value = 0.0222 (Fisher's exact test), Q value = 0.12

Table S47.  Gene #18: 'amp_12p13.33' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
AMP PEAK 18(12P13.33) MUTATED 0 13 62 178
AMP PEAK 18(12P13.33) WILD-TYPE 1 47 119 567

Figure S47.  Get High-res Image Gene #18: 'amp_12p13.33' versus Clinical Feature #11: 'RACE'

'amp_12p13.33' versus 'ETHNICITY'

P value = 0.0616 (Fisher's exact test), Q value = 0.23

Table S48.  Gene #18: 'amp_12p13.33' versus Clinical Feature #12: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 39 875
AMP PEAK 18(12P13.33) MUTATED 5 234
AMP PEAK 18(12P13.33) WILD-TYPE 34 641

Figure S48.  Get High-res Image Gene #18: 'amp_12p13.33' versus Clinical Feature #12: 'ETHNICITY'

'amp_12q15' versus 'PATHOLOGY_T_STAGE'

P value = 0.0179 (Fisher's exact test), Q value = 0.1

Table S49.  Gene #19: 'amp_12q15' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
AMP PEAK 19(12Q15) MUTATED 55 174 31 15
AMP PEAK 19(12Q15) WILD-TYPE 221 450 105 25

Figure S49.  Get High-res Image Gene #19: 'amp_12q15' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_12q15' versus 'PATHOLOGY_N_STAGE'

P value = 0.0145 (Fisher's exact test), Q value = 0.088

Table S50.  Gene #19: 'amp_12q15' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 507 358 119 77
AMP PEAK 19(12Q15) MUTATED 115 88 44 22
AMP PEAK 19(12Q15) WILD-TYPE 392 270 75 55

Figure S50.  Get High-res Image Gene #19: 'amp_12q15' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_12q15' versus 'GENDER'

P value = 0.00307 (Fisher's exact test), Q value = 0.026

Table S51.  Gene #19: 'amp_12q15' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1068 12
AMP PEAK 19(12Q15) MUTATED 268 8
AMP PEAK 19(12Q15) WILD-TYPE 800 4

Figure S51.  Get High-res Image Gene #19: 'amp_12q15' versus Clinical Feature #7: 'GENDER'

'amp_12q15' versus 'HISTOLOGICAL_TYPE'

P value = 0.0011 (Fisher's exact test), Q value = 0.011

Table S52.  Gene #19: 'amp_12q15' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
AMP PEAK 19(12Q15) MUTATED 0 224 34 1 1 9 2 5
AMP PEAK 19(12Q15) WILD-TYPE 1 546 166 5 8 20 15 42

Figure S52.  Get High-res Image Gene #19: 'amp_12q15' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_12q15' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0179 (Wilcoxon-test), Q value = 0.1

Table S53.  Gene #19: 'amp_12q15' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 914 2.4 (4.7)
AMP PEAK 19(12Q15) MUTATED 218 2.7 (4.6)
AMP PEAK 19(12Q15) WILD-TYPE 696 2.3 (4.7)

Figure S53.  Get High-res Image Gene #19: 'amp_12q15' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'amp_13q34' versus 'YEARS_TO_BIRTH'

P value = 0.0539 (Wilcoxon-test), Q value = 0.21

Table S54.  Gene #20: 'amp_13q34' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1065 58.6 (13.2)
AMP PEAK 20(13Q34) MUTATED 177 56.9 (12.7)
AMP PEAK 20(13Q34) WILD-TYPE 888 59.0 (13.3)

Figure S54.  Get High-res Image Gene #20: 'amp_13q34' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_13q34' versus 'PATHOLOGY_T_STAGE'

P value = 0.00529 (Fisher's exact test), Q value = 0.039

Table S55.  Gene #20: 'amp_13q34' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
AMP PEAK 20(13Q34) MUTATED 30 124 18 6
AMP PEAK 20(13Q34) WILD-TYPE 246 500 118 34

Figure S55.  Get High-res Image Gene #20: 'amp_13q34' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_13q34' versus 'RADIATION_THERAPY'

P value = 0.0444 (Fisher's exact test), Q value = 0.2

Table S56.  Gene #20: 'amp_13q34' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients NO YES
ALL 429 518
AMP PEAK 20(13Q34) MUTATED 84 75
AMP PEAK 20(13Q34) WILD-TYPE 345 443

Figure S56.  Get High-res Image Gene #20: 'amp_13q34' versus Clinical Feature #8: 'RADIATION_THERAPY'

'amp_13q34' versus 'HISTOLOGICAL_TYPE'

P value = 0.00121 (Fisher's exact test), Q value = 0.012

Table S57.  Gene #20: 'amp_13q34' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
AMP PEAK 20(13Q34) MUTATED 0 146 14 1 3 4 2 9
AMP PEAK 20(13Q34) WILD-TYPE 1 624 186 5 6 25 15 38

Figure S57.  Get High-res Image Gene #20: 'amp_13q34' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_13q34' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0645 (Wilcoxon-test), Q value = 0.24

Table S58.  Gene #20: 'amp_13q34' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 914 2.4 (4.7)
AMP PEAK 20(13Q34) MUTATED 154 1.9 (4.4)
AMP PEAK 20(13Q34) WILD-TYPE 760 2.5 (4.7)

Figure S58.  Get High-res Image Gene #20: 'amp_13q34' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'amp_14q21.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.0161 (Fisher's exact test), Q value = 0.096

Table S59.  Gene #21: 'amp_14q21.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
AMP PEAK 21(14Q21.1) MUTATED 43 148 21 8
AMP PEAK 21(14Q21.1) WILD-TYPE 233 476 115 32

Figure S59.  Get High-res Image Gene #21: 'amp_14q21.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_14q21.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0321 (Fisher's exact test), Q value = 0.16

Table S60.  Gene #21: 'amp_14q21.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 507 358 119 77
AMP PEAK 21(14Q21.1) MUTATED 87 75 32 21
AMP PEAK 21(14Q21.1) WILD-TYPE 420 283 87 56

Figure S60.  Get High-res Image Gene #21: 'amp_14q21.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_14q21.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00685 (Fisher's exact test), Q value = 0.048

Table S61.  Gene #21: 'amp_14q21.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
AMP PEAK 21(14Q21.1) MUTATED 0 174 23 0 3 9 2 9
AMP PEAK 21(14Q21.1) WILD-TYPE 1 596 177 6 6 20 15 38

Figure S61.  Get High-res Image Gene #21: 'amp_14q21.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_14q21.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0103 (Wilcoxon-test), Q value = 0.067

Table S62.  Gene #21: 'amp_14q21.1' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 914 2.4 (4.7)
AMP PEAK 21(14Q21.1) MUTATED 177 2.9 (4.8)
AMP PEAK 21(14Q21.1) WILD-TYPE 737 2.3 (4.6)

Figure S62.  Get High-res Image Gene #21: 'amp_14q21.1' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'amp_15q26.3' versus 'YEARS_TO_BIRTH'

P value = 0.00973 (Wilcoxon-test), Q value = 0.064

Table S63.  Gene #22: 'amp_15q26.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1065 58.6 (13.2)
AMP PEAK 22(15Q26.3) MUTATED 190 56.4 (12.9)
AMP PEAK 22(15Q26.3) WILD-TYPE 875 59.1 (13.2)

Figure S63.  Get High-res Image Gene #22: 'amp_15q26.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_15q26.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S64.  Gene #22: 'amp_15q26.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
AMP PEAK 22(15Q26.3) MUTATED 0 167 11 3 1 4 3 4
AMP PEAK 22(15Q26.3) WILD-TYPE 1 603 189 3 8 25 14 43

Figure S64.  Get High-res Image Gene #22: 'amp_15q26.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_15q26.3' versus 'RACE'

P value = 0.0504 (Fisher's exact test), Q value = 0.21

Table S65.  Gene #22: 'amp_15q26.3' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
AMP PEAK 22(15Q26.3) MUTATED 0 16 39 118
AMP PEAK 22(15Q26.3) WILD-TYPE 1 44 142 627

Figure S65.  Get High-res Image Gene #22: 'amp_15q26.3' versus Clinical Feature #11: 'RACE'

'amp_17q12' versus 'PATHOLOGY_N_STAGE'

P value = 0.0616 (Fisher's exact test), Q value = 0.23

Table S66.  Gene #24: 'amp_17q12' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 507 358 119 77
AMP PEAK 24(17Q12) MUTATED 138 128 35 22
AMP PEAK 24(17Q12) WILD-TYPE 369 230 84 55

Figure S66.  Get High-res Image Gene #24: 'amp_17q12' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_17q12' versus 'GENDER'

P value = 0.011 (Fisher's exact test), Q value = 0.07

Table S67.  Gene #24: 'amp_17q12' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1068 12
AMP PEAK 24(17Q12) MUTATED 325 8
AMP PEAK 24(17Q12) WILD-TYPE 743 4

Figure S67.  Get High-res Image Gene #24: 'amp_17q12' versus Clinical Feature #7: 'GENDER'

'amp_17q12' versus 'HISTOLOGICAL_TYPE'

P value = 5e-04 (Fisher's exact test), Q value = 0.0064

Table S68.  Gene #24: 'amp_17q12' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
AMP PEAK 24(17Q12) MUTATED 0 270 38 1 3 6 4 11
AMP PEAK 24(17Q12) WILD-TYPE 1 500 162 5 6 23 13 36

Figure S68.  Get High-res Image Gene #24: 'amp_17q12' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_17q12' versus 'RACE'

P value = 0.00169 (Fisher's exact test), Q value = 0.016

Table S69.  Gene #24: 'amp_17q12' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
AMP PEAK 24(17Q12) MUTATED 1 30 52 210
AMP PEAK 24(17Q12) WILD-TYPE 0 30 129 535

Figure S69.  Get High-res Image Gene #24: 'amp_17q12' versus Clinical Feature #11: 'RACE'

'amp_17q23.1' versus 'PATHOLOGIC_STAGE'

P value = 0.0291 (Fisher's exact test), Q value = 0.15

Table S70.  Gene #25: 'amp_17q23.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
ALL 89 85 6 6 353 252 2 154 29 65 20 1 13
AMP PEAK 25(17Q23.1) MUTATED 27 25 1 2 152 102 1 68 16 20 9 1 2
AMP PEAK 25(17Q23.1) WILD-TYPE 62 60 5 4 201 150 1 86 13 45 11 0 11

Figure S70.  Get High-res Image Gene #25: 'amp_17q23.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_17q23.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00034 (Fisher's exact test), Q value = 0.0047

Table S71.  Gene #25: 'amp_17q23.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
AMP PEAK 25(17Q23.1) MUTATED 81 276 49 18
AMP PEAK 25(17Q23.1) WILD-TYPE 195 348 87 22

Figure S71.  Get High-res Image Gene #25: 'amp_17q23.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_17q23.1' versus 'GENDER'

P value = 1.29e-05 (Fisher's exact test), Q value = 0.00029

Table S72.  Gene #25: 'amp_17q23.1' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1068 12
AMP PEAK 25(17Q23.1) MUTATED 414 12
AMP PEAK 25(17Q23.1) WILD-TYPE 654 0

Figure S72.  Get High-res Image Gene #25: 'amp_17q23.1' versus Clinical Feature #7: 'GENDER'

'amp_17q23.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S73.  Gene #25: 'amp_17q23.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
AMP PEAK 25(17Q23.1) MUTATED 1 341 44 3 6 12 5 13
AMP PEAK 25(17Q23.1) WILD-TYPE 0 429 156 3 3 17 12 34

Figure S73.  Get High-res Image Gene #25: 'amp_17q23.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_19p13.12' versus 'PATHOLOGY_M_STAGE'

P value = 0.0623 (Fisher's exact test), Q value = 0.23

Table S74.  Gene #26: 'amp_19p13.12' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 889 22
AMP PEAK 26(19P13.12) MUTATED 192 1
AMP PEAK 26(19P13.12) WILD-TYPE 697 21

Figure S74.  Get High-res Image Gene #26: 'amp_19p13.12' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_19p13.12' versus 'HISTOLOGICAL_TYPE'

P value = 0.0313 (Fisher's exact test), Q value = 0.16

Table S75.  Gene #26: 'amp_19p13.12' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
AMP PEAK 26(19P13.12) MUTATED 1 169 33 4 3 6 2 12
AMP PEAK 26(19P13.12) WILD-TYPE 0 601 167 2 6 23 15 35

Figure S75.  Get High-res Image Gene #26: 'amp_19p13.12' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_19p13.12' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000495 (Wilcoxon-test), Q value = 0.0064

Table S76.  Gene #26: 'amp_19p13.12' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 914 2.4 (4.7)
AMP PEAK 26(19P13.12) MUTATED 207 1.9 (4.5)
AMP PEAK 26(19P13.12) WILD-TYPE 707 2.5 (4.7)

Figure S76.  Get High-res Image Gene #26: 'amp_19p13.12' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'amp_19q12' versus 'PATHOLOGIC_STAGE'

P value = 0.00939 (Fisher's exact test), Q value = 0.063

Table S77.  Gene #27: 'amp_19q12' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
ALL 89 85 6 6 353 252 2 154 29 65 20 1 13
AMP PEAK 27(19Q12) MUTATED 23 18 2 2 121 56 0 36 8 12 3 0 0
AMP PEAK 27(19Q12) WILD-TYPE 66 67 4 4 232 196 2 118 21 53 17 1 13

Figure S77.  Get High-res Image Gene #27: 'amp_19q12' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_19q12' versus 'PATHOLOGY_N_STAGE'

P value = 0.0359 (Fisher's exact test), Q value = 0.17

Table S78.  Gene #27: 'amp_19q12' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 507 358 119 77
AMP PEAK 27(19Q12) MUTATED 155 86 28 14
AMP PEAK 27(19Q12) WILD-TYPE 352 272 91 63

Figure S78.  Get High-res Image Gene #27: 'amp_19q12' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_19q12' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S79.  Gene #27: 'amp_19q12' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
AMP PEAK 27(19Q12) MUTATED 0 226 30 6 3 6 2 11
AMP PEAK 27(19Q12) WILD-TYPE 1 544 170 0 6 23 15 36

Figure S79.  Get High-res Image Gene #27: 'amp_19q12' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_19q12' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00508 (Wilcoxon-test), Q value = 0.038

Table S80.  Gene #27: 'amp_19q12' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 914 2.4 (4.7)
AMP PEAK 27(19Q12) MUTATED 246 2.0 (4.6)
AMP PEAK 27(19Q12) WILD-TYPE 668 2.5 (4.7)

Figure S80.  Get High-res Image Gene #27: 'amp_19q12' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'amp_19q12' versus 'RACE'

P value = 0.0369 (Fisher's exact test), Q value = 0.17

Table S81.  Gene #27: 'amp_19q12' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
AMP PEAK 27(19Q12) MUTATED 0 13 63 188
AMP PEAK 27(19Q12) WILD-TYPE 1 47 118 557

Figure S81.  Get High-res Image Gene #27: 'amp_19q12' versus Clinical Feature #11: 'RACE'

'amp_19q13.42' versus 'HISTOLOGICAL_TYPE'

P value = 0.00774 (Fisher's exact test), Q value = 0.053

Table S82.  Gene #28: 'amp_19q13.42' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
AMP PEAK 28(19Q13.42) MUTATED 1 217 33 2 3 5 2 13
AMP PEAK 28(19Q13.42) WILD-TYPE 0 553 167 4 6 24 15 34

Figure S82.  Get High-res Image Gene #28: 'amp_19q13.42' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_20q13.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00109 (Fisher's exact test), Q value = 0.011

Table S83.  Gene #29: 'amp_20q13.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
AMP PEAK 29(20Q13.2) MUTATED 120 346 57 22
AMP PEAK 29(20Q13.2) WILD-TYPE 156 278 79 18

Figure S83.  Get High-res Image Gene #29: 'amp_20q13.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_20q13.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.00105 (Fisher's exact test), Q value = 0.011

Table S84.  Gene #29: 'amp_20q13.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 507 358 119 77
AMP PEAK 29(20Q13.2) MUTATED 248 179 79 31
AMP PEAK 29(20Q13.2) WILD-TYPE 259 179 40 46

Figure S84.  Get High-res Image Gene #29: 'amp_20q13.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_20q13.2' versus 'GENDER'

P value = 0.0378 (Fisher's exact test), Q value = 0.17

Table S85.  Gene #29: 'amp_20q13.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1068 12
AMP PEAK 29(20Q13.2) MUTATED 538 10
AMP PEAK 29(20Q13.2) WILD-TYPE 530 2

Figure S85.  Get High-res Image Gene #29: 'amp_20q13.2' versus Clinical Feature #7: 'GENDER'

'amp_20q13.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S86.  Gene #29: 'amp_20q13.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
AMP PEAK 29(20Q13.2) MUTATED 1 452 55 1 7 11 1 20
AMP PEAK 29(20Q13.2) WILD-TYPE 0 318 145 5 2 18 16 27

Figure S86.  Get High-res Image Gene #29: 'amp_20q13.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_1p36.13' versus 'Time to Death'

P value = 0.0218 (logrank test), Q value = 0.12

Table S87.  Gene #30: 'del_1p36.13' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1064 147 0.0 - 282.9 (27.9)
DEL PEAK 1(1P36.13) MUTATED 448 68 0.2 - 282.9 (25.0)
DEL PEAK 1(1P36.13) WILD-TYPE 616 79 0.0 - 281.3 (30.0)

Figure S87.  Get High-res Image Gene #30: 'del_1p36.13' versus Clinical Feature #1: 'Time to Death'

'del_1p36.13' versus 'YEARS_TO_BIRTH'

P value = 0.0183 (Wilcoxon-test), Q value = 0.1

Table S88.  Gene #30: 'del_1p36.13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1065 58.6 (13.2)
DEL PEAK 1(1P36.13) MUTATED 446 59.5 (13.1)
DEL PEAK 1(1P36.13) WILD-TYPE 619 58.0 (13.3)

Figure S88.  Get High-res Image Gene #30: 'del_1p36.13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_1p36.13' versus 'PATHOLOGIC_STAGE'

P value = 0.00064 (Fisher's exact test), Q value = 0.0077

Table S89.  Gene #30: 'del_1p36.13' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
ALL 89 85 6 6 353 252 2 154 29 65 20 1 13
DEL PEAK 1(1P36.13) MUTATED 28 24 0 3 136 117 1 74 18 33 12 0 5
DEL PEAK 1(1P36.13) WILD-TYPE 61 61 6 3 217 135 1 80 11 32 8 1 8

Figure S89.  Get High-res Image Gene #30: 'del_1p36.13' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_1p36.13' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S90.  Gene #30: 'del_1p36.13' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
DEL PEAK 1(1P36.13) MUTATED 83 287 55 26
DEL PEAK 1(1P36.13) WILD-TYPE 193 337 81 14

Figure S90.  Get High-res Image Gene #30: 'del_1p36.13' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_1p36.13' versus 'PATHOLOGY_N_STAGE'

P value = 0.00056 (Fisher's exact test), Q value = 0.007

Table S91.  Gene #30: 'del_1p36.13' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 507 358 119 77
DEL PEAK 1(1P36.13) MUTATED 180 166 57 41
DEL PEAK 1(1P36.13) WILD-TYPE 327 192 62 36

Figure S91.  Get High-res Image Gene #30: 'del_1p36.13' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_1p36.13' versus 'GENDER'

P value = 0.0346 (Fisher's exact test), Q value = 0.16

Table S92.  Gene #30: 'del_1p36.13' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1068 12
DEL PEAK 1(1P36.13) MUTATED 443 9
DEL PEAK 1(1P36.13) WILD-TYPE 625 3

Figure S92.  Get High-res Image Gene #30: 'del_1p36.13' versus Clinical Feature #7: 'GENDER'

'del_1p36.13' versus 'HISTOLOGICAL_TYPE'

P value = 0.00278 (Fisher's exact test), Q value = 0.024

Table S93.  Gene #30: 'del_1p36.13' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
DEL PEAK 1(1P36.13) MUTATED 1 347 74 1 0 8 4 17
DEL PEAK 1(1P36.13) WILD-TYPE 0 423 126 5 9 21 13 30

Figure S93.  Get High-res Image Gene #30: 'del_1p36.13' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_1p36.13' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00101 (Wilcoxon-test), Q value = 0.011

Table S94.  Gene #30: 'del_1p36.13' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 914 2.4 (4.7)
DEL PEAK 1(1P36.13) MUTATED 372 2.9 (5.1)
DEL PEAK 1(1P36.13) WILD-TYPE 542 2.1 (4.3)

Figure S94.  Get High-res Image Gene #30: 'del_1p36.13' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'del_1p22.1' versus 'Time to Death'

P value = 0.000661 (logrank test), Q value = 0.0078

Table S95.  Gene #31: 'del_1p22.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1064 147 0.0 - 282.9 (27.9)
DEL PEAK 2(1P22.1) MUTATED 357 62 0.2 - 165.8 (25.2)
DEL PEAK 2(1P22.1) WILD-TYPE 707 85 0.0 - 282.9 (29.1)

Figure S95.  Get High-res Image Gene #31: 'del_1p22.1' versus Clinical Feature #1: 'Time to Death'

'del_1p22.1' versus 'YEARS_TO_BIRTH'

P value = 0.0412 (Wilcoxon-test), Q value = 0.18

Table S96.  Gene #31: 'del_1p22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1065 58.6 (13.2)
DEL PEAK 2(1P22.1) MUTATED 356 59.7 (13.0)
DEL PEAK 2(1P22.1) WILD-TYPE 709 58.1 (13.3)

Figure S96.  Get High-res Image Gene #31: 'del_1p22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_1p22.1' versus 'PATHOLOGIC_STAGE'

P value = 0.0104 (Fisher's exact test), Q value = 0.067

Table S97.  Gene #31: 'del_1p22.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
ALL 89 85 6 6 353 252 2 154 29 65 20 1 13
DEL PEAK 2(1P22.1) MUTATED 20 21 0 1 115 84 1 60 16 28 9 0 5
DEL PEAK 2(1P22.1) WILD-TYPE 69 64 6 5 238 168 1 94 13 37 11 1 8

Figure S97.  Get High-res Image Gene #31: 'del_1p22.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_1p22.1' versus 'PATHOLOGY_T_STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.00077

Table S98.  Gene #31: 'del_1p22.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
DEL PEAK 2(1P22.1) MUTATED 67 226 45 24
DEL PEAK 2(1P22.1) WILD-TYPE 209 398 91 16

Figure S98.  Get High-res Image Gene #31: 'del_1p22.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_1p22.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.00766 (Fisher's exact test), Q value = 0.053

Table S99.  Gene #31: 'del_1p22.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 507 358 119 77
DEL PEAK 2(1P22.1) MUTATED 146 127 50 32
DEL PEAK 2(1P22.1) WILD-TYPE 361 231 69 45

Figure S99.  Get High-res Image Gene #31: 'del_1p22.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_1p22.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000895 (Wilcoxon-test), Q value = 0.0099

Table S100.  Gene #31: 'del_1p22.1' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 914 2.4 (4.7)
DEL PEAK 2(1P22.1) MUTATED 291 3.0 (5.3)
DEL PEAK 2(1P22.1) WILD-TYPE 623 2.1 (4.3)

Figure S100.  Get High-res Image Gene #31: 'del_1p22.1' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'del_2q37.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00158 (Fisher's exact test), Q value = 0.015

Table S101.  Gene #32: 'del_2q37.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
DEL PEAK 3(2Q37.3) MUTATED 61 197 38 19
DEL PEAK 3(2Q37.3) WILD-TYPE 215 427 98 21

Figure S101.  Get High-res Image Gene #32: 'del_2q37.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_2q37.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S102.  Gene #32: 'del_2q37.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
DEL PEAK 3(2Q37.3) MUTATED 0 261 26 3 5 10 3 8
DEL PEAK 3(2Q37.3) WILD-TYPE 1 509 174 3 4 19 14 39

Figure S102.  Get High-res Image Gene #32: 'del_2q37.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_2q37.3' versus 'RACE'

P value = 0.0319 (Fisher's exact test), Q value = 0.16

Table S103.  Gene #32: 'del_2q37.3' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
DEL PEAK 3(2Q37.3) MUTATED 0 25 58 197
DEL PEAK 3(2Q37.3) WILD-TYPE 1 35 123 548

Figure S103.  Get High-res Image Gene #32: 'del_2q37.3' versus Clinical Feature #11: 'RACE'

'del_3p21.31' versus 'YEARS_TO_BIRTH'

P value = 0.00267 (Wilcoxon-test), Q value = 0.024

Table S104.  Gene #33: 'del_3p21.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1065 58.6 (13.2)
DEL PEAK 4(3P21.31) MUTATED 341 56.8 (13.1)
DEL PEAK 4(3P21.31) WILD-TYPE 724 59.5 (13.2)

Figure S104.  Get High-res Image Gene #33: 'del_3p21.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_3p21.31' versus 'PATHOLOGY_T_STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00061

Table S105.  Gene #33: 'del_3p21.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
DEL PEAK 4(3P21.31) MUTATED 60 236 39 10
DEL PEAK 4(3P21.31) WILD-TYPE 216 388 97 30

Figure S105.  Get High-res Image Gene #33: 'del_3p21.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_3p21.31' versus 'RADIATION_THERAPY'

P value = 0.0586 (Fisher's exact test), Q value = 0.23

Table S106.  Gene #33: 'del_3p21.31' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients NO YES
ALL 429 518
DEL PEAK 4(3P21.31) MUTATED 123 179
DEL PEAK 4(3P21.31) WILD-TYPE 306 339

Figure S106.  Get High-res Image Gene #33: 'del_3p21.31' versus Clinical Feature #8: 'RADIATION_THERAPY'

'del_3p21.31' versus 'HISTOLOGICAL_TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00044

Table S107.  Gene #33: 'del_3p21.31' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
DEL PEAK 4(3P21.31) MUTATED 1 285 41 1 2 6 1 10
DEL PEAK 4(3P21.31) WILD-TYPE 0 485 159 5 7 23 16 37

Figure S107.  Get High-res Image Gene #33: 'del_3p21.31' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_3p21.31' versus 'RACE'

P value = 0.0113 (Fisher's exact test), Q value = 0.071

Table S108.  Gene #33: 'del_3p21.31' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
DEL PEAK 4(3P21.31) MUTATED 0 26 72 224
DEL PEAK 4(3P21.31) WILD-TYPE 1 34 109 521

Figure S108.  Get High-res Image Gene #33: 'del_3p21.31' versus Clinical Feature #11: 'RACE'

'del_4p16.3' versus 'YEARS_TO_BIRTH'

P value = 0.0561 (Wilcoxon-test), Q value = 0.22

Table S109.  Gene #34: 'del_4p16.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1065 58.6 (13.2)
DEL PEAK 5(4P16.3) MUTATED 332 57.6 (12.7)
DEL PEAK 5(4P16.3) WILD-TYPE 733 59.1 (13.4)

Figure S109.  Get High-res Image Gene #34: 'del_4p16.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_4p16.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00015 (Fisher's exact test), Q value = 0.0026

Table S110.  Gene #34: 'del_4p16.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
DEL PEAK 5(4P16.3) MUTATED 59 226 39 13
DEL PEAK 5(4P16.3) WILD-TYPE 217 398 97 27

Figure S110.  Get High-res Image Gene #34: 'del_4p16.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_4p16.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S111.  Gene #34: 'del_4p16.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
DEL PEAK 5(4P16.3) MUTATED 1 281 32 4 3 6 0 12
DEL PEAK 5(4P16.3) WILD-TYPE 0 489 168 2 6 23 17 35

Figure S111.  Get High-res Image Gene #34: 'del_4p16.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_4p16.3' versus 'RACE'

P value = 0.018 (Fisher's exact test), Q value = 0.1

Table S112.  Gene #34: 'del_4p16.3' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
DEL PEAK 5(4P16.3) MUTATED 1 17 73 225
DEL PEAK 5(4P16.3) WILD-TYPE 0 43 108 520

Figure S112.  Get High-res Image Gene #34: 'del_4p16.3' versus Clinical Feature #11: 'RACE'

'del_4q35.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00182 (Fisher's exact test), Q value = 0.017

Table S113.  Gene #35: 'del_4q35.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
DEL PEAK 6(4Q35.1) MUTATED 66 223 38 16
DEL PEAK 6(4Q35.1) WILD-TYPE 210 401 98 24

Figure S113.  Get High-res Image Gene #35: 'del_4q35.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_4q35.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S114.  Gene #35: 'del_4q35.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
DEL PEAK 6(4Q35.1) MUTATED 1 287 36 4 4 4 0 8
DEL PEAK 6(4Q35.1) WILD-TYPE 0 483 164 2 5 25 17 39

Figure S114.  Get High-res Image Gene #35: 'del_4q35.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_4q35.1' versus 'RACE'

P value = 0.00599 (Fisher's exact test), Q value = 0.043

Table S115.  Gene #35: 'del_4q35.1' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
DEL PEAK 6(4Q35.1) MUTATED 1 23 73 218
DEL PEAK 6(4Q35.1) WILD-TYPE 0 37 108 527

Figure S115.  Get High-res Image Gene #35: 'del_4q35.1' versus Clinical Feature #11: 'RACE'

'del_5q11.2' versus 'YEARS_TO_BIRTH'

P value = 4.3e-06 (Wilcoxon-test), Q value = 0.00023

Table S116.  Gene #36: 'del_5q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1065 58.6 (13.2)
DEL PEAK 7(5Q11.2) MUTATED 277 55.6 (13.2)
DEL PEAK 7(5Q11.2) WILD-TYPE 788 59.7 (13.0)

Figure S116.  Get High-res Image Gene #36: 'del_5q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_5q11.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00037 (Fisher's exact test), Q value = 0.005

Table S117.  Gene #36: 'del_5q11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
DEL PEAK 7(5Q11.2) MUTATED 60 187 20 12
DEL PEAK 7(5Q11.2) WILD-TYPE 216 437 116 28

Figure S117.  Get High-res Image Gene #36: 'del_5q11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_5q11.2' versus 'GENDER'

P value = 0.0436 (Fisher's exact test), Q value = 0.19

Table S118.  Gene #36: 'del_5q11.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1068 12
DEL PEAK 7(5Q11.2) MUTATED 280 0
DEL PEAK 7(5Q11.2) WILD-TYPE 788 12

Figure S118.  Get High-res Image Gene #36: 'del_5q11.2' versus Clinical Feature #7: 'GENDER'

'del_5q11.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S119.  Gene #36: 'del_5q11.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
DEL PEAK 7(5Q11.2) MUTATED 1 244 12 5 1 6 1 9
DEL PEAK 7(5Q11.2) WILD-TYPE 0 526 188 1 8 23 16 38

Figure S119.  Get High-res Image Gene #36: 'del_5q11.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_5q11.2' versus 'RACE'

P value = 6e-05 (Fisher's exact test), Q value = 0.0011

Table S120.  Gene #36: 'del_5q11.2' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
DEL PEAK 7(5Q11.2) MUTATED 1 20 68 170
DEL PEAK 7(5Q11.2) WILD-TYPE 0 40 113 575

Figure S120.  Get High-res Image Gene #36: 'del_5q11.2' versus Clinical Feature #11: 'RACE'

'del_5q21.3' versus 'YEARS_TO_BIRTH'

P value = 0.000324 (Wilcoxon-test), Q value = 0.0047

Table S121.  Gene #37: 'del_5q21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1065 58.6 (13.2)
DEL PEAK 8(5Q21.3) MUTATED 269 56.2 (13.4)
DEL PEAK 8(5Q21.3) WILD-TYPE 796 59.5 (13.1)

Figure S121.  Get High-res Image Gene #37: 'del_5q21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_5q21.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00021 (Fisher's exact test), Q value = 0.0033

Table S122.  Gene #37: 'del_5q21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
DEL PEAK 8(5Q21.3) MUTATED 54 184 20 12
DEL PEAK 8(5Q21.3) WILD-TYPE 222 440 116 28

Figure S122.  Get High-res Image Gene #37: 'del_5q21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_5q21.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S123.  Gene #37: 'del_5q21.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
DEL PEAK 8(5Q21.3) MUTATED 1 243 6 6 1 6 0 8
DEL PEAK 8(5Q21.3) WILD-TYPE 0 527 194 0 8 23 17 39

Figure S123.  Get High-res Image Gene #37: 'del_5q21.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_5q21.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00312 (Wilcoxon-test), Q value = 0.026

Table S124.  Gene #37: 'del_5q21.3' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 914 2.4 (4.7)
DEL PEAK 8(5Q21.3) MUTATED 232 1.7 (3.7)
DEL PEAK 8(5Q21.3) WILD-TYPE 682 2.6 (4.9)

Figure S124.  Get High-res Image Gene #37: 'del_5q21.3' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'del_5q21.3' versus 'RACE'

P value = 9e-05 (Fisher's exact test), Q value = 0.0016

Table S125.  Gene #37: 'del_5q21.3' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
DEL PEAK 8(5Q21.3) MUTATED 0 18 70 163
DEL PEAK 8(5Q21.3) WILD-TYPE 1 42 111 582

Figure S125.  Get High-res Image Gene #37: 'del_5q21.3' versus Clinical Feature #11: 'RACE'

'del_6p25.3' versus 'YEARS_TO_BIRTH'

P value = 0.0526 (Wilcoxon-test), Q value = 0.21

Table S126.  Gene #38: 'del_6p25.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1065 58.6 (13.2)
DEL PEAK 9(6P25.3) MUTATED 201 56.9 (13.0)
DEL PEAK 9(6P25.3) WILD-TYPE 864 59.0 (13.2)

Figure S126.  Get High-res Image Gene #38: 'del_6p25.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_6p25.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.0096 (Fisher's exact test), Q value = 0.064

Table S127.  Gene #38: 'del_6p25.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
DEL PEAK 9(6P25.3) MUTATED 45 138 15 6
DEL PEAK 9(6P25.3) WILD-TYPE 231 486 121 34

Figure S127.  Get High-res Image Gene #38: 'del_6p25.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_6p25.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0258 (Fisher's exact test), Q value = 0.13

Table S128.  Gene #38: 'del_6p25.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
DEL PEAK 9(6P25.3) MUTATED 1 161 24 2 0 5 3 8
DEL PEAK 9(6P25.3) WILD-TYPE 0 609 176 4 9 24 14 39

Figure S128.  Get High-res Image Gene #38: 'del_6p25.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_6q15' versus 'YEARS_TO_BIRTH'

P value = 0.0399 (Wilcoxon-test), Q value = 0.18

Table S129.  Gene #39: 'del_6q15' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1065 58.6 (13.2)
DEL PEAK 10(6Q15) MUTATED 355 57.4 (13.2)
DEL PEAK 10(6Q15) WILD-TYPE 710 59.3 (13.2)

Figure S129.  Get High-res Image Gene #39: 'del_6q15' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_6q15' versus 'PATHOLOGY_N_STAGE'

P value = 0.0335 (Fisher's exact test), Q value = 0.16

Table S130.  Gene #39: 'del_6q15' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 507 358 119 77
DEL PEAK 10(6Q15) MUTATED 149 130 49 23
DEL PEAK 10(6Q15) WILD-TYPE 358 228 70 54

Figure S130.  Get High-res Image Gene #39: 'del_6q15' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_6q15' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0204 (Wilcoxon-test), Q value = 0.11

Table S131.  Gene #39: 'del_6q15' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 914 2.4 (4.7)
DEL PEAK 10(6Q15) MUTATED 293 2.5 (4.6)
DEL PEAK 10(6Q15) WILD-TYPE 621 2.3 (4.7)

Figure S131.  Get High-res Image Gene #39: 'del_6q15' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'del_6q27' versus 'YEARS_TO_BIRTH'

P value = 6.42e-06 (Wilcoxon-test), Q value = 0.00023

Table S132.  Gene #40: 'del_6q27' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1065 58.6 (13.2)
DEL PEAK 11(6Q27) MUTATED 371 56.0 (12.7)
DEL PEAK 11(6Q27) WILD-TYPE 694 60.0 (13.3)

Figure S132.  Get High-res Image Gene #40: 'del_6q27' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_6q27' versus 'PATHOLOGY_N_STAGE'

P value = 0.0265 (Fisher's exact test), Q value = 0.13

Table S133.  Gene #40: 'del_6q27' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 507 358 119 77
DEL PEAK 11(6Q27) MUTATED 168 138 46 17
DEL PEAK 11(6Q27) WILD-TYPE 339 220 73 60

Figure S133.  Get High-res Image Gene #40: 'del_6q27' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_6q27' versus 'RADIATION_THERAPY'

P value = 0.00504 (Fisher's exact test), Q value = 0.038

Table S134.  Gene #40: 'del_6q27' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients NO YES
ALL 429 518
DEL PEAK 11(6Q27) MUTATED 130 203
DEL PEAK 11(6Q27) WILD-TYPE 299 315

Figure S134.  Get High-res Image Gene #40: 'del_6q27' versus Clinical Feature #8: 'RADIATION_THERAPY'

'del_7p22.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.0521 (Fisher's exact test), Q value = 0.21

Table S135.  Gene #41: 'del_7p22.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 507 358 119 77
DEL PEAK 12(7P22.3) MUTATED 76 36 17 5
DEL PEAK 12(7P22.3) WILD-TYPE 431 322 102 72

Figure S135.  Get High-res Image Gene #41: 'del_7p22.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_7p22.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S136.  Gene #41: 'del_7p22.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
DEL PEAK 12(7P22.3) MUTATED 0 121 4 1 2 4 0 5
DEL PEAK 12(7P22.3) WILD-TYPE 1 649 196 5 7 25 17 42

Figure S136.  Get High-res Image Gene #41: 'del_7p22.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_7p22.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0137 (Wilcoxon-test), Q value = 0.084

Table S137.  Gene #41: 'del_7p22.3' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 914 2.4 (4.7)
DEL PEAK 12(7P22.3) MUTATED 109 1.6 (3.5)
DEL PEAK 12(7P22.3) WILD-TYPE 805 2.5 (4.8)

Figure S137.  Get High-res Image Gene #41: 'del_7p22.3' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'del_7q36.1' versus 'HISTOLOGICAL_TYPE'

P value = 5e-05 (Fisher's exact test), Q value = 0.00092

Table S138.  Gene #42: 'del_7q36.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
DEL PEAK 13(7Q36.1) MUTATED 0 166 15 0 2 7 0 10
DEL PEAK 13(7Q36.1) WILD-TYPE 1 604 185 6 7 22 17 37

Figure S138.  Get High-res Image Gene #42: 'del_7q36.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_8p23.2' versus 'Time to Death'

P value = 0.0521 (logrank test), Q value = 0.21

Table S139.  Gene #43: 'del_8p23.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1064 147 0.0 - 282.9 (27.9)
DEL PEAK 14(8P23.2) MUTATED 553 91 0.2 - 282.9 (27.2)
DEL PEAK 14(8P23.2) WILD-TYPE 511 56 0.0 - 281.3 (28.2)

Figure S139.  Get High-res Image Gene #43: 'del_8p23.2' versus Clinical Feature #1: 'Time to Death'

'del_8p23.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00387 (Fisher's exact test), Q value = 0.031

Table S140.  Gene #43: 'del_8p23.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
DEL PEAK 14(8P23.2) MUTATED 157 324 52 23
DEL PEAK 14(8P23.2) WILD-TYPE 119 300 84 17

Figure S140.  Get High-res Image Gene #43: 'del_8p23.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_8p23.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.061 (Fisher's exact test), Q value = 0.23

Table S141.  Gene #43: 'del_8p23.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 507 358 119 77
DEL PEAK 14(8P23.2) MUTATED 247 186 74 37
DEL PEAK 14(8P23.2) WILD-TYPE 260 172 45 40

Figure S141.  Get High-res Image Gene #43: 'del_8p23.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_8p23.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S142.  Gene #43: 'del_8p23.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
DEL PEAK 14(8P23.2) MUTATED 1 446 64 3 3 10 4 26
DEL PEAK 14(8P23.2) WILD-TYPE 0 324 136 3 6 19 13 21

Figure S142.  Get High-res Image Gene #43: 'del_8p23.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_8p23.2' versus 'RACE'

P value = 0.00118 (Fisher's exact test), Q value = 0.012

Table S143.  Gene #43: 'del_8p23.2' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
DEL PEAK 14(8P23.2) MUTATED 1 41 105 357
DEL PEAK 14(8P23.2) WILD-TYPE 0 19 76 388

Figure S143.  Get High-res Image Gene #43: 'del_8p23.2' versus Clinical Feature #11: 'RACE'

'del_8p11.21' versus 'HISTOLOGICAL_TYPE'

P value = 0.00388 (Fisher's exact test), Q value = 0.031

Table S144.  Gene #44: 'del_8p11.21' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
DEL PEAK 15(8P11.21) MUTATED 0 166 20 0 2 5 1 6
DEL PEAK 15(8P11.21) WILD-TYPE 1 604 180 6 7 24 16 41

Figure S144.  Get High-res Image Gene #44: 'del_8p11.21' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_9p23' versus 'Time to Death'

P value = 0.0133 (logrank test), Q value = 0.082

Table S145.  Gene #45: 'del_9p23' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1064 147 0.0 - 282.9 (27.9)
DEL PEAK 16(9P23) MUTATED 320 50 0.0 - 165.8 (24.6)
DEL PEAK 16(9P23) WILD-TYPE 744 97 0.0 - 282.9 (30.0)

Figure S145.  Get High-res Image Gene #45: 'del_9p23' versus Clinical Feature #1: 'Time to Death'

'del_9p23' versus 'PATHOLOGIC_STAGE'

P value = 0.00558 (Fisher's exact test), Q value = 0.041

Table S146.  Gene #45: 'del_9p23' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
ALL 89 85 6 6 353 252 2 154 29 65 20 1 13
DEL PEAK 16(9P23) MUTATED 21 19 1 1 98 71 1 62 16 19 10 0 4
DEL PEAK 16(9P23) WILD-TYPE 68 66 5 5 255 181 1 92 13 46 10 1 9

Figure S146.  Get High-res Image Gene #45: 'del_9p23' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_9p23' versus 'PATHOLOGY_T_STAGE'

P value = 0.00032 (Fisher's exact test), Q value = 0.0047

Table S147.  Gene #45: 'del_9p23' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
DEL PEAK 16(9P23) MUTATED 60 207 38 19
DEL PEAK 16(9P23) WILD-TYPE 216 417 98 21

Figure S147.  Get High-res Image Gene #45: 'del_9p23' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_9p23' versus 'PATHOLOGY_N_STAGE'

P value = 7e-04 (Fisher's exact test), Q value = 0.0082

Table S148.  Gene #45: 'del_9p23' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 507 358 119 77
DEL PEAK 16(9P23) MUTATED 137 103 55 24
DEL PEAK 16(9P23) WILD-TYPE 370 255 64 53

Figure S148.  Get High-res Image Gene #45: 'del_9p23' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_9p23' versus 'PATHOLOGY_M_STAGE'

P value = 0.0641 (Fisher's exact test), Q value = 0.24

Table S149.  Gene #45: 'del_9p23' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 889 22
DEL PEAK 16(9P23) MUTATED 274 11
DEL PEAK 16(9P23) WILD-TYPE 615 11

Figure S149.  Get High-res Image Gene #45: 'del_9p23' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_9p23' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S150.  Gene #45: 'del_9p23' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
DEL PEAK 16(9P23) MUTATED 0 269 26 3 5 9 5 8
DEL PEAK 16(9P23) WILD-TYPE 1 501 174 3 4 20 12 39

Figure S150.  Get High-res Image Gene #45: 'del_9p23' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_9p23' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0369 (Wilcoxon-test), Q value = 0.17

Table S151.  Gene #45: 'del_9p23' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 914 2.4 (4.7)
DEL PEAK 16(9P23) MUTATED 263 2.7 (4.9)
DEL PEAK 16(9P23) WILD-TYPE 651 2.3 (4.5)

Figure S151.  Get High-res Image Gene #45: 'del_9p23' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'del_9p21.3' versus 'PATHOLOGIC_STAGE'

P value = 0.0172 (Fisher's exact test), Q value = 0.1

Table S152.  Gene #46: 'del_9p21.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
ALL 89 85 6 6 353 252 2 154 29 65 20 1 13
DEL PEAK 17(9P21.3) MUTATED 24 22 3 1 114 78 1 64 17 23 10 0 6
DEL PEAK 17(9P21.3) WILD-TYPE 65 63 3 5 239 174 1 90 12 42 10 1 7

Figure S152.  Get High-res Image Gene #46: 'del_9p21.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_9p21.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00284 (Fisher's exact test), Q value = 0.024

Table S153.  Gene #46: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
DEL PEAK 17(9P21.3) MUTATED 73 228 42 20
DEL PEAK 17(9P21.3) WILD-TYPE 203 396 94 20

Figure S153.  Get High-res Image Gene #46: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_9p21.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.00408 (Fisher's exact test), Q value = 0.032

Table S154.  Gene #46: 'del_9p21.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 507 358 119 77
DEL PEAK 17(9P21.3) MUTATED 161 111 57 30
DEL PEAK 17(9P21.3) WILD-TYPE 346 247 62 47

Figure S154.  Get High-res Image Gene #46: 'del_9p21.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_9p21.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S155.  Gene #46: 'del_9p21.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
DEL PEAK 17(9P21.3) MUTATED 1 302 24 4 6 12 5 10
DEL PEAK 17(9P21.3) WILD-TYPE 0 468 176 2 3 17 12 37

Figure S155.  Get High-res Image Gene #46: 'del_9p21.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_9p21.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0624 (Wilcoxon-test), Q value = 0.23

Table S156.  Gene #46: 'del_9p21.3' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 914 2.4 (4.7)
DEL PEAK 17(9P21.3) MUTATED 295 2.6 (4.5)
DEL PEAK 17(9P21.3) WILD-TYPE 619 2.3 (4.8)

Figure S156.  Get High-res Image Gene #46: 'del_9p21.3' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'del_9q21.11' versus 'GENDER'

P value = 0.0222 (Fisher's exact test), Q value = 0.12

Table S157.  Gene #47: 'del_9q21.11' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1068 12
DEL PEAK 18(9Q21.11) MUTATED 287 7
DEL PEAK 18(9Q21.11) WILD-TYPE 781 5

Figure S157.  Get High-res Image Gene #47: 'del_9q21.11' versus Clinical Feature #7: 'GENDER'

'del_9q21.11' versus 'RADIATION_THERAPY'

P value = 0.0477 (Fisher's exact test), Q value = 0.2

Table S158.  Gene #47: 'del_9q21.11' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients NO YES
ALL 429 518
DEL PEAK 18(9Q21.11) MUTATED 103 155
DEL PEAK 18(9Q21.11) WILD-TYPE 326 363

Figure S158.  Get High-res Image Gene #47: 'del_9q21.11' versus Clinical Feature #8: 'RADIATION_THERAPY'

'del_9q21.11' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S159.  Gene #47: 'del_9q21.11' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
DEL PEAK 18(9Q21.11) MUTATED 0 245 23 2 4 10 3 7
DEL PEAK 18(9Q21.11) WILD-TYPE 1 525 177 4 5 19 14 40

Figure S159.  Get High-res Image Gene #47: 'del_9q21.11' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_9q34.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.0197 (Fisher's exact test), Q value = 0.11

Table S160.  Gene #48: 'del_9q34.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
DEL PEAK 19(9Q34.2) MUTATED 60 188 32 15
DEL PEAK 19(9Q34.2) WILD-TYPE 216 436 104 25

Figure S160.  Get High-res Image Gene #48: 'del_9q34.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_9q34.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.0669 (Fisher's exact test), Q value = 0.24

Table S161.  Gene #48: 'del_9q34.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 507 358 119 77
DEL PEAK 19(9Q34.2) MUTATED 149 83 41 21
DEL PEAK 19(9Q34.2) WILD-TYPE 358 275 78 56

Figure S161.  Get High-res Image Gene #48: 'del_9q34.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_9q34.2' versus 'GENDER'

P value = 0.00508 (Fisher's exact test), Q value = 0.038

Table S162.  Gene #48: 'del_9q34.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1068 12
DEL PEAK 19(9Q34.2) MUTATED 289 8
DEL PEAK 19(9Q34.2) WILD-TYPE 779 4

Figure S162.  Get High-res Image Gene #48: 'del_9q34.2' versus Clinical Feature #7: 'GENDER'

'del_9q34.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S163.  Gene #48: 'del_9q34.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
DEL PEAK 19(9Q34.2) MUTATED 0 251 22 4 3 7 3 6
DEL PEAK 19(9Q34.2) WILD-TYPE 1 519 178 2 6 22 14 41

Figure S163.  Get High-res Image Gene #48: 'del_9q34.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_9q34.2' versus 'RACE'

P value = 0.0472 (Fisher's exact test), Q value = 0.2

Table S164.  Gene #48: 'del_9q34.2' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
DEL PEAK 19(9Q34.2) MUTATED 0 17 63 187
DEL PEAK 19(9Q34.2) WILD-TYPE 1 43 118 558

Figure S164.  Get High-res Image Gene #48: 'del_9q34.2' versus Clinical Feature #11: 'RACE'

'del_10q23.31' versus 'PATHOLOGY_T_STAGE'

P value = 0.0165 (Fisher's exact test), Q value = 0.097

Table S165.  Gene #49: 'del_10q23.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
DEL PEAK 20(10Q23.31) MUTATED 70 190 38 20
DEL PEAK 20(10Q23.31) WILD-TYPE 206 434 98 20

Figure S165.  Get High-res Image Gene #49: 'del_10q23.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_10q23.31' versus 'HISTOLOGICAL_TYPE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00061

Table S166.  Gene #49: 'del_10q23.31' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
DEL PEAK 20(10Q23.31) MUTATED 0 246 41 5 7 8 1 11
DEL PEAK 20(10Q23.31) WILD-TYPE 1 524 159 1 2 21 16 36

Figure S166.  Get High-res Image Gene #49: 'del_10q23.31' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_10q23.31' versus 'ETHNICITY'

P value = 0.0486 (Fisher's exact test), Q value = 0.2

Table S167.  Gene #49: 'del_10q23.31' versus Clinical Feature #12: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 39 875
DEL PEAK 20(10Q23.31) MUTATED 6 267
DEL PEAK 20(10Q23.31) WILD-TYPE 33 608

Figure S167.  Get High-res Image Gene #49: 'del_10q23.31' versus Clinical Feature #12: 'ETHNICITY'

'del_10q26.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.0332 (Fisher's exact test), Q value = 0.16

Table S168.  Gene #50: 'del_10q26.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
DEL PEAK 21(10Q26.3) MUTATED 67 192 40 18
DEL PEAK 21(10Q26.3) WILD-TYPE 209 432 96 22

Figure S168.  Get High-res Image Gene #50: 'del_10q26.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_10q26.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S169.  Gene #50: 'del_10q26.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
DEL PEAK 21(10Q26.3) MUTATED 0 255 32 5 7 8 2 9
DEL PEAK 21(10Q26.3) WILD-TYPE 1 515 168 1 2 21 15 38

Figure S169.  Get High-res Image Gene #50: 'del_10q26.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_10q26.3' versus 'ETHNICITY'

P value = 0.019 (Fisher's exact test), Q value = 0.1

Table S170.  Gene #50: 'del_10q26.3' versus Clinical Feature #12: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 39 875
DEL PEAK 21(10Q26.3) MUTATED 5 265
DEL PEAK 21(10Q26.3) WILD-TYPE 34 610

Figure S170.  Get High-res Image Gene #50: 'del_10q26.3' versus Clinical Feature #12: 'ETHNICITY'

'del_11p15.5' versus 'PATHOLOGY_T_STAGE'

P value = 0.00413 (Fisher's exact test), Q value = 0.032

Table S171.  Gene #51: 'del_11p15.5' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
DEL PEAK 22(11P15.5) MUTATED 60 200 33 15
DEL PEAK 22(11P15.5) WILD-TYPE 216 424 103 25

Figure S171.  Get High-res Image Gene #51: 'del_11p15.5' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_11p15.5' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S172.  Gene #51: 'del_11p15.5' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
DEL PEAK 22(11P15.5) MUTATED 0 250 30 4 2 12 2 9
DEL PEAK 22(11P15.5) WILD-TYPE 1 520 170 2 7 17 15 38

Figure S172.  Get High-res Image Gene #51: 'del_11p15.5' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_11p15.5' versus 'RACE'

P value = 0.0048 (Fisher's exact test), Q value = 0.037

Table S173.  Gene #51: 'del_11p15.5' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
DEL PEAK 22(11P15.5) MUTATED 0 19 69 190
DEL PEAK 22(11P15.5) WILD-TYPE 1 41 112 555

Figure S173.  Get High-res Image Gene #51: 'del_11p15.5' versus Clinical Feature #11: 'RACE'

'del_11q13.1' versus 'RACE'

P value = 0.00346 (Fisher's exact test), Q value = 0.028

Table S174.  Gene #52: 'del_11q13.1' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
DEL PEAK 23(11Q13.1) MUTATED 0 21 50 143
DEL PEAK 23(11Q13.1) WILD-TYPE 1 39 131 602

Figure S174.  Get High-res Image Gene #52: 'del_11q13.1' versus Clinical Feature #11: 'RACE'

'del_11q23.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.033 (Fisher's exact test), Q value = 0.16

Table S175.  Gene #53: 'del_11q23.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
DEL PEAK 24(11Q23.3) MUTATED 120 327 77 22
DEL PEAK 24(11Q23.3) WILD-TYPE 156 297 59 18

Figure S175.  Get High-res Image Gene #53: 'del_11q23.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_11q23.3' versus 'GENDER'

P value = 0.0377 (Fisher's exact test), Q value = 0.17

Table S176.  Gene #53: 'del_11q23.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1068 12
DEL PEAK 24(11Q23.3) MUTATED 537 10
DEL PEAK 24(11Q23.3) WILD-TYPE 531 2

Figure S176.  Get High-res Image Gene #53: 'del_11q23.3' versus Clinical Feature #7: 'GENDER'

'del_11q23.3' versus 'RACE'

P value = 0.0183 (Fisher's exact test), Q value = 0.1

Table S177.  Gene #53: 'del_11q23.3' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
DEL PEAK 24(11Q23.3) MUTATED 1 33 106 353
DEL PEAK 24(11Q23.3) WILD-TYPE 0 27 75 392

Figure S177.  Get High-res Image Gene #53: 'del_11q23.3' versus Clinical Feature #11: 'RACE'

'del_11q25' versus 'YEARS_TO_BIRTH'

P value = 0.0265 (Wilcoxon-test), Q value = 0.13

Table S178.  Gene #54: 'del_11q25' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1065 58.6 (13.2)
DEL PEAK 25(11Q25) MUTATED 506 57.6 (13.5)
DEL PEAK 25(11Q25) WILD-TYPE 559 59.6 (12.9)

Figure S178.  Get High-res Image Gene #54: 'del_11q25' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_11q25' versus 'PATHOLOGIC_STAGE'

P value = 0.0238 (Fisher's exact test), Q value = 0.12

Table S179.  Gene #54: 'del_11q25' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
ALL 89 85 6 6 353 252 2 154 29 65 20 1 13
DEL PEAK 25(11Q25) MUTATED 31 33 2 2 162 137 1 86 12 27 10 0 8
DEL PEAK 25(11Q25) WILD-TYPE 58 52 4 4 191 115 1 68 17 38 10 1 5

Figure S179.  Get High-res Image Gene #54: 'del_11q25' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_11q25' versus 'PATHOLOGY_T_STAGE'

P value = 0.00246 (Fisher's exact test), Q value = 0.022

Table S180.  Gene #54: 'del_11q25' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
DEL PEAK 25(11Q25) MUTATED 106 316 73 17
DEL PEAK 25(11Q25) WILD-TYPE 170 308 63 23

Figure S180.  Get High-res Image Gene #54: 'del_11q25' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_11q25' versus 'PATHOLOGY_N_STAGE'

P value = 0.0677 (Fisher's exact test), Q value = 0.24

Table S181.  Gene #54: 'del_11q25' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 507 358 119 77
DEL PEAK 25(11Q25) MUTATED 226 181 65 31
DEL PEAK 25(11Q25) WILD-TYPE 281 177 54 46

Figure S181.  Get High-res Image Gene #54: 'del_11q25' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_11q25' versus 'GENDER'

P value = 0.0171 (Fisher's exact test), Q value = 0.1

Table S182.  Gene #54: 'del_11q25' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1068 12
DEL PEAK 25(11Q25) MUTATED 503 10
DEL PEAK 25(11Q25) WILD-TYPE 565 2

Figure S182.  Get High-res Image Gene #54: 'del_11q25' versus Clinical Feature #7: 'GENDER'

'del_11q25' versus 'HISTOLOGICAL_TYPE'

P value = 0.0111 (Fisher's exact test), Q value = 0.07

Table S183.  Gene #54: 'del_11q25' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
DEL PEAK 25(11Q25) MUTATED 1 377 92 5 4 16 5 12
DEL PEAK 25(11Q25) WILD-TYPE 0 393 108 1 5 13 12 35

Figure S183.  Get High-res Image Gene #54: 'del_11q25' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_11q25' versus 'RACE'

P value = 0.00063 (Fisher's exact test), Q value = 0.0077

Table S184.  Gene #54: 'del_11q25' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
DEL PEAK 25(11Q25) MUTATED 1 29 107 323
DEL PEAK 25(11Q25) WILD-TYPE 0 31 74 422

Figure S184.  Get High-res Image Gene #54: 'del_11q25' versus Clinical Feature #11: 'RACE'

'del_12p13.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00085 (Fisher's exact test), Q value = 0.0097

Table S185.  Gene #55: 'del_12p13.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
DEL PEAK 26(12P13.1) MUTATED 0 157 19 1 3 3 1 3
DEL PEAK 26(12P13.1) WILD-TYPE 1 613 181 5 6 26 16 44

Figure S185.  Get High-res Image Gene #55: 'del_12p13.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_12q23.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.0316 (Fisher's exact test), Q value = 0.16

Table S186.  Gene #56: 'del_12q23.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
DEL PEAK 27(12Q23.1) MUTATED 37 130 22 10
DEL PEAK 27(12Q23.1) WILD-TYPE 239 494 114 30

Figure S186.  Get High-res Image Gene #56: 'del_12q23.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_12q23.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00099 (Fisher's exact test), Q value = 0.011

Table S187.  Gene #56: 'del_12q23.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
DEL PEAK 27(12Q23.1) MUTATED 0 162 21 3 3 4 0 8
DEL PEAK 27(12Q23.1) WILD-TYPE 1 608 179 3 6 25 17 39

Figure S187.  Get High-res Image Gene #56: 'del_12q23.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_12q23.1' versus 'RACE'

P value = 0.00626 (Fisher's exact test), Q value = 0.044

Table S188.  Gene #56: 'del_12q23.1' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
DEL PEAK 27(12Q23.1) MUTATED 0 13 50 125
DEL PEAK 27(12Q23.1) WILD-TYPE 1 47 131 620

Figure S188.  Get High-res Image Gene #56: 'del_12q23.1' versus Clinical Feature #11: 'RACE'

'del_12q24.31' versus 'HISTOLOGICAL_TYPE'

P value = 0.0442 (Fisher's exact test), Q value = 0.2

Table S189.  Gene #57: 'del_12q24.31' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
DEL PEAK 28(12Q24.31) MUTATED 0 161 30 3 3 6 0 8
DEL PEAK 28(12Q24.31) WILD-TYPE 1 609 170 3 6 23 17 39

Figure S189.  Get High-res Image Gene #57: 'del_12q24.31' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_12q24.31' versus 'RACE'

P value = 0.0509 (Fisher's exact test), Q value = 0.21

Table S190.  Gene #57: 'del_12q24.31' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
DEL PEAK 28(12Q24.31) MUTATED 0 11 49 136
DEL PEAK 28(12Q24.31) WILD-TYPE 1 49 132 609

Figure S190.  Get High-res Image Gene #57: 'del_12q24.31' versus Clinical Feature #11: 'RACE'

'del_13q14.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S191.  Gene #58: 'del_13q14.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
DEL PEAK 29(13Q14.2) MUTATED 0 389 67 5 5 13 2 13
DEL PEAK 29(13Q14.2) WILD-TYPE 1 381 133 1 4 16 15 34

Figure S191.  Get High-res Image Gene #58: 'del_13q14.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_14q24.1' versus 'Time to Death'

P value = 0.0509 (logrank test), Q value = 0.21

Table S192.  Gene #59: 'del_14q24.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1064 147 0.0 - 282.9 (27.9)
DEL PEAK 30(14Q24.1) MUTATED 349 60 0.0 - 255.7 (28.2)
DEL PEAK 30(14Q24.1) WILD-TYPE 715 87 0.0 - 282.9 (27.0)

Figure S192.  Get High-res Image Gene #59: 'del_14q24.1' versus Clinical Feature #1: 'Time to Death'

'del_14q24.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00017 (Fisher's exact test), Q value = 0.0029

Table S193.  Gene #59: 'del_14q24.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
DEL PEAK 30(14Q24.1) MUTATED 66 237 37 11
DEL PEAK 30(14Q24.1) WILD-TYPE 210 387 99 29

Figure S193.  Get High-res Image Gene #59: 'del_14q24.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_14q24.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S194.  Gene #59: 'del_14q24.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
DEL PEAK 30(14Q24.1) MUTATED 1 296 34 4 4 4 1 8
DEL PEAK 30(14Q24.1) WILD-TYPE 0 474 166 2 5 25 16 39

Figure S194.  Get High-res Image Gene #59: 'del_14q24.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_14q24.1' versus 'RACE'

P value = 0.00033 (Fisher's exact test), Q value = 0.0047

Table S195.  Gene #59: 'del_14q24.1' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
DEL PEAK 30(14Q24.1) MUTATED 0 18 83 220
DEL PEAK 30(14Q24.1) WILD-TYPE 1 42 98 525

Figure S195.  Get High-res Image Gene #59: 'del_14q24.1' versus Clinical Feature #11: 'RACE'

'del_15q13.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.0014 (Fisher's exact test), Q value = 0.014

Table S196.  Gene #60: 'del_15q13.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
DEL PEAK 31(15Q13.1) MUTATED 73 246 43 12
DEL PEAK 31(15Q13.1) WILD-TYPE 203 378 93 28

Figure S196.  Get High-res Image Gene #60: 'del_15q13.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_15q13.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0221 (Fisher's exact test), Q value = 0.12

Table S197.  Gene #60: 'del_15q13.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 507 358 119 77
DEL PEAK 31(15Q13.1) MUTATED 193 110 49 20
DEL PEAK 31(15Q13.1) WILD-TYPE 314 248 70 57

Figure S197.  Get High-res Image Gene #60: 'del_15q13.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_15q13.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S198.  Gene #60: 'del_15q13.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
DEL PEAK 31(15Q13.1) MUTATED 1 305 39 4 3 10 1 11
DEL PEAK 31(15Q13.1) WILD-TYPE 0 465 161 2 6 19 16 36

Figure S198.  Get High-res Image Gene #60: 'del_15q13.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_15q13.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.037 (Wilcoxon-test), Q value = 0.17

Table S199.  Gene #60: 'del_15q13.1' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 914 2.4 (4.7)
DEL PEAK 31(15Q13.1) MUTATED 319 2.2 (4.8)
DEL PEAK 31(15Q13.1) WILD-TYPE 595 2.5 (4.6)

Figure S199.  Get High-res Image Gene #60: 'del_15q13.1' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'del_15q13.1' versus 'RACE'

P value = 0.0239 (Fisher's exact test), Q value = 0.12

Table S200.  Gene #60: 'del_15q13.1' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
DEL PEAK 31(15Q13.1) MUTATED 0 23 79 243
DEL PEAK 31(15Q13.1) WILD-TYPE 1 37 102 502

Figure S200.  Get High-res Image Gene #60: 'del_15q13.1' versus Clinical Feature #11: 'RACE'

'del_16q24.3' versus 'YEARS_TO_BIRTH'

P value = 0.000319 (Wilcoxon-test), Q value = 0.0047

Table S201.  Gene #61: 'del_16q24.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1065 58.6 (13.2)
DEL PEAK 32(16Q24.3) MUTATED 684 59.8 (13.0)
DEL PEAK 32(16Q24.3) WILD-TYPE 381 56.6 (13.3)

Figure S201.  Get High-res Image Gene #61: 'del_16q24.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_16q24.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.0602 (Fisher's exact test), Q value = 0.23

Table S202.  Gene #61: 'del_16q24.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
DEL PEAK 32(16Q24.3) MUTATED 182 392 97 20
DEL PEAK 32(16Q24.3) WILD-TYPE 94 232 39 20

Figure S202.  Get High-res Image Gene #61: 'del_16q24.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_16q24.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S203.  Gene #61: 'del_16q24.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
DEL PEAK 32(16Q24.3) MUTATED 0 464 180 3 1 21 3 21
DEL PEAK 32(16Q24.3) WILD-TYPE 1 306 20 3 8 8 14 26

Figure S203.  Get High-res Image Gene #61: 'del_16q24.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_16q24.3' versus 'RACE'

P value = 0.00765 (Fisher's exact test), Q value = 0.053

Table S204.  Gene #61: 'del_16q24.3' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
DEL PEAK 32(16Q24.3) MUTATED 1 34 97 490
DEL PEAK 32(16Q24.3) WILD-TYPE 0 26 84 255

Figure S204.  Get High-res Image Gene #61: 'del_16q24.3' versus Clinical Feature #11: 'RACE'

'del_17p12' versus 'YEARS_TO_BIRTH'

P value = 0.0024 (Wilcoxon-test), Q value = 0.022

Table S205.  Gene #62: 'del_17p12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1065 58.6 (13.2)
DEL PEAK 33(17P12) MUTATED 640 57.7 (13.1)
DEL PEAK 33(17P12) WILD-TYPE 425 60.1 (13.3)

Figure S205.  Get High-res Image Gene #62: 'del_17p12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_17p12' versus 'PATHOLOGY_T_STAGE'

P value = 0.047 (Fisher's exact test), Q value = 0.2

Table S206.  Gene #62: 'del_17p12' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
DEL PEAK 33(17P12) MUTATED 148 395 82 22
DEL PEAK 33(17P12) WILD-TYPE 128 229 54 18

Figure S206.  Get High-res Image Gene #62: 'del_17p12' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_17p12' versus 'HISTOLOGICAL_TYPE'

P value = 0.00428 (Fisher's exact test), Q value = 0.033

Table S207.  Gene #62: 'del_17p12' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
DEL PEAK 33(17P12) MUTATED 0 489 103 5 5 18 6 23
DEL PEAK 33(17P12) WILD-TYPE 1 281 97 1 4 11 11 24

Figure S207.  Get High-res Image Gene #62: 'del_17p12' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_17p12' versus 'RACE'

P value = 0.0457 (Fisher's exact test), Q value = 0.2

Table S208.  Gene #62: 'del_17p12' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
DEL PEAK 33(17P12) MUTATED 1 44 115 433
DEL PEAK 33(17P12) WILD-TYPE 0 16 66 312

Figure S208.  Get High-res Image Gene #62: 'del_17p12' versus Clinical Feature #11: 'RACE'

'del_17q21.31' versus 'YEARS_TO_BIRTH'

P value = 0.000386 (Wilcoxon-test), Q value = 0.0052

Table S209.  Gene #63: 'del_17q21.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1065 58.6 (13.2)
DEL PEAK 34(17Q21.31) MUTATED 363 56.8 (13.4)
DEL PEAK 34(17Q21.31) WILD-TYPE 702 59.6 (13.0)

Figure S209.  Get High-res Image Gene #63: 'del_17q21.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_17q21.31' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S210.  Gene #63: 'del_17q21.31' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
DEL PEAK 34(17Q21.31) MUTATED 0 297 39 4 5 11 1 13
DEL PEAK 34(17Q21.31) WILD-TYPE 1 473 161 2 4 18 16 34

Figure S210.  Get High-res Image Gene #63: 'del_17q21.31' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_17q21.31' versus 'RACE'

P value = 5e-05 (Fisher's exact test), Q value = 0.00092

Table S211.  Gene #63: 'del_17q21.31' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
DEL PEAK 34(17Q21.31) MUTATED 0 34 75 233
DEL PEAK 34(17Q21.31) WILD-TYPE 1 26 106 512

Figure S211.  Get High-res Image Gene #63: 'del_17q21.31' versus Clinical Feature #11: 'RACE'

'del_18q23' versus 'PATHOLOGIC_STAGE'

P value = 0.0662 (Fisher's exact test), Q value = 0.24

Table S212.  Gene #64: 'del_18q23' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
ALL 89 85 6 6 353 252 2 154 29 65 20 1 13
DEL PEAK 35(18Q23) MUTATED 23 29 0 0 113 77 0 56 15 29 6 0 3
DEL PEAK 35(18Q23) WILD-TYPE 66 56 6 6 240 175 2 98 14 36 14 1 10

Figure S212.  Get High-res Image Gene #64: 'del_18q23' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_18q23' versus 'PATHOLOGY_T_STAGE'

P value = 0.0178 (Fisher's exact test), Q value = 0.1

Table S213.  Gene #64: 'del_18q23' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
DEL PEAK 35(18Q23) MUTATED 75 215 43 20
DEL PEAK 35(18Q23) WILD-TYPE 201 409 93 20

Figure S213.  Get High-res Image Gene #64: 'del_18q23' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_18q23' versus 'PATHOLOGY_N_STAGE'

P value = 0.0578 (Fisher's exact test), Q value = 0.23

Table S214.  Gene #64: 'del_18q23' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 507 358 119 77
DEL PEAK 35(18Q23) MUTATED 160 107 49 31
DEL PEAK 35(18Q23) WILD-TYPE 347 251 70 46

Figure S214.  Get High-res Image Gene #64: 'del_18q23' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_18q23' versus 'HISTOLOGICAL_TYPE'

P value = 0.00021 (Fisher's exact test), Q value = 0.0033

Table S215.  Gene #64: 'del_18q23' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
DEL PEAK 35(18Q23) MUTATED 1 274 54 3 5 8 0 8
DEL PEAK 35(18Q23) WILD-TYPE 0 496 146 3 4 21 17 39

Figure S215.  Get High-res Image Gene #64: 'del_18q23' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_19p13.3' versus 'YEARS_TO_BIRTH'

P value = 0.00162 (Wilcoxon-test), Q value = 0.016

Table S216.  Gene #65: 'del_19p13.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1065 58.6 (13.2)
DEL PEAK 36(19P13.3) MUTATED 355 56.9 (13.6)
DEL PEAK 36(19P13.3) WILD-TYPE 710 59.5 (12.9)

Figure S216.  Get High-res Image Gene #65: 'del_19p13.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_19p13.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.0473 (Fisher's exact test), Q value = 0.2

Table S217.  Gene #65: 'del_19p13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
DEL PEAK 36(19P13.3) MUTATED 81 230 37 15
DEL PEAK 36(19P13.3) WILD-TYPE 195 394 99 25

Figure S217.  Get High-res Image Gene #65: 'del_19p13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_19p13.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S218.  Gene #65: 'del_19p13.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
DEL PEAK 36(19P13.3) MUTATED 1 302 24 5 4 9 5 12
DEL PEAK 36(19P13.3) WILD-TYPE 0 468 176 1 5 20 12 35

Figure S218.  Get High-res Image Gene #65: 'del_19p13.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_19p13.3' versus 'RACE'

P value = 0.00021 (Fisher's exact test), Q value = 0.0033

Table S219.  Gene #65: 'del_19p13.3' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
DEL PEAK 36(19P13.3) MUTATED 0 28 79 223
DEL PEAK 36(19P13.3) WILD-TYPE 1 32 102 522

Figure S219.  Get High-res Image Gene #65: 'del_19p13.3' versus Clinical Feature #11: 'RACE'

'del_19q13.32' versus 'PATHOLOGY_N_STAGE'

P value = 0.0664 (Fisher's exact test), Q value = 0.24

Table S220.  Gene #66: 'del_19q13.32' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 507 358 119 77
DEL PEAK 37(19Q13.32) MUTATED 98 70 35 12
DEL PEAK 37(19Q13.32) WILD-TYPE 409 288 84 65

Figure S220.  Get High-res Image Gene #66: 'del_19q13.32' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_19q13.32' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S221.  Gene #66: 'del_19q13.32' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
DEL PEAK 37(19Q13.32) MUTATED 0 185 10 3 1 6 4 6
DEL PEAK 37(19Q13.32) WILD-TYPE 1 585 190 3 8 23 13 41

Figure S221.  Get High-res Image Gene #66: 'del_19q13.32' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_20p13' versus 'YEARS_TO_BIRTH'

P value = 0.0472 (Wilcoxon-test), Q value = 0.2

Table S222.  Gene #67: 'del_20p13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1065 58.6 (13.2)
DEL PEAK 38(20P13) MUTATED 157 56.7 (12.2)
DEL PEAK 38(20P13) WILD-TYPE 908 59.0 (13.3)

Figure S222.  Get High-res Image Gene #67: 'del_20p13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_20p13' versus 'HISTOLOGICAL_TYPE'

P value = 4e-05 (Fisher's exact test), Q value = 0.00077

Table S223.  Gene #67: 'del_20p13' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
DEL PEAK 38(20P13) MUTATED 1 137 11 2 0 2 1 6
DEL PEAK 38(20P13) WILD-TYPE 0 633 189 4 9 27 16 41

Figure S223.  Get High-res Image Gene #67: 'del_20p13' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_21q11.2' versus 'PATHOLOGIC_STAGE'

P value = 0.00928 (Fisher's exact test), Q value = 0.062

Table S224.  Gene #68: 'del_21q11.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
ALL 89 85 6 6 353 252 2 154 29 65 20 1 13
DEL PEAK 39(21Q11.2) MUTATED 12 12 0 1 66 54 1 39 12 9 7 1 3
DEL PEAK 39(21Q11.2) WILD-TYPE 77 73 6 5 287 198 1 115 17 56 13 0 10

Figure S224.  Get High-res Image Gene #68: 'del_21q11.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_21q11.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00997 (Fisher's exact test), Q value = 0.065

Table S225.  Gene #68: 'del_21q11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
DEL PEAK 39(21Q11.2) MUTATED 41 139 23 13
DEL PEAK 39(21Q11.2) WILD-TYPE 235 485 113 27

Figure S225.  Get High-res Image Gene #68: 'del_21q11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_21q11.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.0139 (Fisher's exact test), Q value = 0.085

Table S226.  Gene #68: 'del_21q11.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 507 358 119 77
DEL PEAK 39(21Q11.2) MUTATED 90 74 37 13
DEL PEAK 39(21Q11.2) WILD-TYPE 417 284 82 64

Figure S226.  Get High-res Image Gene #68: 'del_21q11.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_21q11.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.00086 (Fisher's exact test), Q value = 0.0097

Table S227.  Gene #68: 'del_21q11.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
DEL PEAK 39(21Q11.2) MUTATED 0 176 21 2 2 9 2 5
DEL PEAK 39(21Q11.2) WILD-TYPE 1 594 179 4 7 20 15 42

Figure S227.  Get High-res Image Gene #68: 'del_21q11.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_22q13.32' versus 'RADIATION_THERAPY'

P value = 0.0362 (Fisher's exact test), Q value = 0.17

Table S228.  Gene #69: 'del_22q13.32' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients NO YES
ALL 429 518
DEL PEAK 40(22Q13.32) MUTATED 183 257
DEL PEAK 40(22Q13.32) WILD-TYPE 246 261

Figure S228.  Get High-res Image Gene #69: 'del_22q13.32' versus Clinical Feature #8: 'RADIATION_THERAPY'

'del_22q13.32' versus 'HISTOLOGICAL_TYPE'

P value = 0.00034 (Fisher's exact test), Q value = 0.0047

Table S229.  Gene #69: 'del_22q13.32' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 770 200 6 9 29 17 47
DEL PEAK 40(22Q13.32) MUTATED 1 361 90 3 3 19 1 13
DEL PEAK 40(22Q13.32) WILD-TYPE 0 409 110 3 6 10 16 34

Figure S229.  Get High-res Image Gene #69: 'del_22q13.32' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

Methods & Data
Input

  • Copy number data file = all_lesions.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BRCA-TP/19785968/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BRCA-TP/19775058/BRCA-TP.merged_data.txt

  • Number of patients = 1080

  • Number of significantly focal cnvs = 69

  • Number of selected clinical features = 12

  • Exclude genes that fewer than K tumors have mutations, K = 3

Survival analysis

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

Fisher's exact test

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

Q value calculation

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.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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