Correlation between copy number variation genes (focal events) and selected clinical features
Breast Invasive Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1D799SN
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 70 focal events and 12 clinical features across 1079 patients, 224 significant findings detected with Q value < 0.25.

  • 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', 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 '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', and 'HISTOLOGICAL_TYPE'.

  • 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_1p21.2 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',  'HISTOLOGICAL_TYPE', and 'RACE'.

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

  • del_4q35.2 cnv correlated to 'Time to Death',  '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' 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', and 'HISTOLOGICAL_TYPE'.

  • del_9q21.11 cnv correlated to 'GENDER' 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 'Time to Death',  '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',  'HISTOLOGICAL_TYPE', 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 'PATHOLOGY_T_STAGE',  '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_14q32.12 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',  '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', 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 '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_22q11.1 cnv correlated to '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 70 focal events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 224 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 13 451 (42%) 628 0.0203
(0.112)
0.016
(0.0953)
0.00049
(0.00643)
1e-05
(0.000221)
0.00045
(0.006)
0.126
(0.368)
0.0346
(0.167)
0.172
(0.435)
0.00244
(0.0223)
0.00083
(0.00967)
0.79
(0.93)
0.742
(0.897)
del 9p23 325 (30%) 754 0.0138
(0.0833)
0.289
(0.559)
0.00621
(0.0442)
0.00058
(0.00738)
0.00083
(0.00967)
0.0641
(0.243)
0.201
(0.471)
0.362
(0.635)
1e-05
(0.000221)
0.0378
(0.176)
0.353
(0.629)
1
(1.00)
del 11q25 514 (48%) 565 0.979
(1.00)
0.0207
(0.114)
0.0397
(0.18)
0.00359
(0.0296)
0.0632
(0.241)
0.52
(0.756)
0.0173
(0.1)
0.7
(0.871)
0.0137
(0.0833)
0.247
(0.523)
0.00067
(0.00816)
1
(1.00)
del 1p21 2 355 (33%) 724 0.0198
(0.11)
0.0118
(0.0748)
0.0232
(0.12)
8e-05
(0.00146)
0.0173
(0.1)
0.819
(0.936)
0.544
(0.77)
0.374
(0.637)
0.144
(0.392)
0.00374
(0.0305)
0.936
(0.997)
0.484
(0.727)
amp 12q15 275 (25%) 804 0.2
(0.47)
0.26
(0.54)
0.322
(0.601)
0.0235
(0.12)
0.0131
(0.0808)
0.81
(0.936)
0.00301
(0.0253)
0.555
(0.778)
0.00036
(0.00513)
0.0147
(0.0881)
0.397
(0.654)
0.251
(0.526)
amp 19q12 283 (26%) 796 0.837
(0.937)
0.427
(0.674)
0.00902
(0.0606)
0.538
(0.77)
0.03
(0.15)
0.468
(0.716)
0.525
(0.756)
0.663
(0.847)
1e-05
(0.000221)
0.00604
(0.0438)
0.0341
(0.166)
0.853
(0.947)
del 5q11 2 280 (26%) 799 0.436
(0.684)
3.8e-06
(0.000221)
0.332
(0.608)
0.00101
(0.011)
0.281
(0.559)
0.34
(0.616)
0.0436
(0.194)
0.419
(0.668)
1e-05
(0.000221)
0.159
(0.416)
0.0001
(0.00179)
1
(1.00)
del 5q21 3 273 (25%) 806 0.949
(1.00)
0.000236
(0.00367)
0.206
(0.475)
0.00051
(0.00659)
0.0915
(0.31)
0.81
(0.936)
0.314
(0.592)
0.375
(0.637)
1e-05
(0.000221)
0.0024
(0.0223)
5e-05
(0.000955)
0.852
(0.947)
del 8p23 2 558 (52%) 521 0.0516
(0.214)
0.59
(0.798)
0.971
(1.00)
0.00287
(0.0246)
0.056
(0.225)
0.831
(0.936)
0.388
(0.65)
0.369
(0.637)
1e-05
(0.000221)
0.758
(0.908)
0.00083
(0.00967)
0.745
(0.899)
del 9q34 2 297 (28%) 782 0.558
(0.779)
0.9
(0.973)
0.15
(0.396)
0.0218
(0.117)
0.0664
(0.249)
0.81
(0.936)
0.00511
(0.038)
0.425
(0.673)
1e-05
(0.000221)
0.185
(0.453)
0.0493
(0.208)
0.363
(0.635)
del 15q13 1 374 (35%) 705 0.477
(0.721)
0.375
(0.637)
0.114
(0.348)
0.00134
(0.0137)
0.0225
(0.12)
0.368
(0.637)
0.761
(0.908)
0.311
(0.59)
1e-05
(0.000221)
0.0417
(0.187)
0.0219
(0.117)
0.866
(0.95)
amp 1q44 788 (73%) 291 0.0887
(0.306)
0.331
(0.608)
0.062
(0.24)
0.00432
(0.0342)
0.214
(0.478)
0.343
(0.617)
1
(1.00)
0.511
(0.747)
0.00585
(0.0427)
0.571
(0.788)
0.0463
(0.2)
0.141
(0.392)
amp 3p25 1 198 (18%) 881 0.0342
(0.166)
0.158
(0.413)
0.118
(0.353)
0.00037
(0.00518)
0.0458
(0.2)
0.423
(0.671)
0.706
(0.876)
0.563
(0.783)
1e-05
(0.000221)
0.348
(0.623)
0.505
(0.743)
1
(1.00)
amp 8p11 23 411 (38%) 668 0.0173
(0.1)
0.108
(0.34)
0.0512
(0.214)
0.568
(0.788)
0.0572
(0.228)
0.182
(0.45)
1
(1.00)
0.692
(0.863)
0.289
(0.559)
0.00454
(0.0346)
0.661
(0.847)
0.401
(0.657)
amp 8q24 21 677 (63%) 402 0.0853
(0.298)
0.0595
(0.234)
0.38
(0.643)
0.0624
(0.24)
0.256
(0.534)
0.653
(0.842)
0.228
(0.498)
0.428
(0.674)
1e-05
(0.000221)
0.794
(0.932)
0.00132
(0.0137)
0.239
(0.512)
amp 12p13 33 281 (26%) 798 0.864
(0.95)
0.389
(0.65)
0.523
(0.756)
0.00286
(0.0246)
0.566
(0.786)
0.81
(0.936)
0.202
(0.471)
0.211
(0.478)
1e-05
(0.000221)
0.321
(0.6)
0.0211
(0.115)
0.0617
(0.24)
amp 13q34 178 (16%) 901 0.385
(0.647)
0.0578
(0.228)
0.152
(0.4)
0.00663
(0.046)
0.281
(0.559)
0.572
(0.788)
0.702
(0.873)
0.0575
(0.228)
0.00108
(0.0115)
0.0752
(0.269)
0.571
(0.788)
0.829
(0.936)
amp 14q21 1 220 (20%) 859 0.506
(0.743)
0.181
(0.449)
0.251
(0.526)
0.0176
(0.1)
0.0326
(0.161)
0.437
(0.684)
0.718
(0.881)
0.385
(0.647)
0.00662
(0.046)
0.0105
(0.0684)
0.577
(0.789)
0.311
(0.59)
amp 17q12 333 (31%) 746 0.126
(0.368)
0.911
(0.979)
0.424
(0.671)
0.0889
(0.306)
0.0648
(0.245)
0.818
(0.936)
0.011
(0.0712)
0.889
(0.967)
0.00042
(0.00569)
0.364
(0.635)
0.00156
(0.0156)
1
(1.00)
amp 17q23 1 426 (39%) 653 0.149
(0.396)
0.202
(0.471)
0.0267
(0.134)
0.00034
(0.00506)
0.272
(0.552)
0.828
(0.936)
1.3e-05
(0.000281)
0.599
(0.805)
1e-05
(0.000221)
0.39
(0.65)
0.145
(0.392)
0.739
(0.895)
amp 20q13 2 547 (51%) 532 0.661
(0.847)
0.671
(0.85)
0.194
(0.464)
0.00226
(0.0213)
0.00112
(0.0118)
1
(1.00)
0.0377
(0.176)
0.223
(0.491)
1e-05
(0.000221)
0.189
(0.46)
0.289
(0.559)
0.417
(0.668)
del 3p21 31 347 (32%) 732 0.0702
(0.258)
0.00243
(0.0223)
0.206
(0.475)
4e-05
(8e-04)
0.457
(0.706)
0.65
(0.842)
1
(1.00)
0.0985
(0.325)
2e-05
(0.00041)
0.27
(0.551)
0.0125
(0.0776)
0.605
(0.808)
del 4p16 3 339 (31%) 740 0.892
(0.967)
0.0525
(0.215)
0.113
(0.348)
0.00016
(0.00264)
0.617
(0.821)
0.65
(0.842)
0.763
(0.908)
0.581
(0.793)
1e-05
(0.000221)
0.542
(0.77)
0.0189
(0.107)
0.726
(0.888)
del 4q35 2 347 (32%) 732 0.0416
(0.187)
0.604
(0.808)
0.365
(0.635)
0.00226
(0.0213)
0.648
(0.842)
0.499
(0.741)
0.357
(0.63)
0.63
(0.833)
1e-05
(0.000221)
0.484
(0.727)
0.00439
(0.0342)
0.0771
(0.274)
del 9p21 3 365 (34%) 714 0.192
(0.463)
0.417
(0.668)
0.0389
(0.178)
0.003
(0.0253)
0.00444
(0.0342)
0.173
(0.436)
0.12
(0.355)
0.415
(0.668)
1e-05
(0.000221)
0.0742
(0.269)
0.211
(0.478)
0.863
(0.95)
del 10q26 3 318 (29%) 761 0.0661
(0.249)
0.315
(0.592)
0.181
(0.449)
0.0387
(0.178)
0.191
(0.461)
0.347
(0.622)
0.526
(0.756)
0.944
(1.00)
1e-05
(0.000221)
0.393
(0.653)
0.105
(0.336)
0.0191
(0.107)
del 11q23 3 547 (51%) 532 0.971
(1.00)
0.198
(0.468)
0.144
(0.392)
0.049
(0.208)
0.115
(0.348)
0.395
(0.654)
0.0377
(0.176)
0.654
(0.842)
0.0526
(0.215)
0.179
(0.448)
0.0189
(0.107)
0.872
(0.952)
del 14q24 1 356 (33%) 723 0.0384
(0.177)
0.218
(0.483)
0.215
(0.478)
0.00021
(0.00333)
0.396
(0.654)
0.818
(0.936)
0.544
(0.77)
0.248
(0.523)
1e-05
(0.000221)
0.27
(0.551)
0.00035
(0.00507)
0.863
(0.95)
del 14q32 12 327 (30%) 752 0.0336
(0.165)
0.576
(0.789)
0.479
(0.721)
0.00171
(0.0165)
0.465
(0.716)
0.491
(0.736)
1
(1.00)
0.0946
(0.316)
1e-05
(0.000221)
0.544
(0.77)
0.00553
(0.0407)
1
(1.00)
del 17p12 649 (60%) 430 0.309
(0.59)
0.00266
(0.0238)
0.521
(0.756)
0.052
(0.214)
0.877
(0.957)
0.829
(0.936)
0.381
(0.643)
0.647
(0.842)
0.00278
(0.0243)
0.752
(0.906)
0.0461
(0.2)
0.868
(0.95)
del 19p13 3 362 (34%) 717 0.212
(0.478)
0.0017
(0.0165)
0.911
(0.979)
0.0568
(0.227)
0.801
(0.936)
0.824
(0.936)
0.356
(0.63)
0.586
(0.795)
1e-05
(0.000221)
0.23
(0.5)
0.00042
(0.00569)
0.733
(0.89)
del 21q11 2 215 (20%) 864 0.545
(0.77)
0.441
(0.687)
0.0105
(0.0684)
0.0132
(0.0811)
0.0113
(0.0722)
0.101
(0.328)
1
(1.00)
0.265
(0.547)
0.00249
(0.0225)
0.127
(0.368)
0.156
(0.41)
0.545
(0.77)
amp 3q26 32 339 (31%) 740 0.984
(1.00)
0.473
(0.72)
0.0912
(0.31)
0.00015
(0.00252)
0.373
(0.637)
0.82
(0.936)
1
(1.00)
0.945
(1.00)
1e-05
(0.000221)
0.12
(0.355)
0.0027
(0.0239)
0.109
(0.34)
amp 5p15 33 394 (37%) 685 0.0542
(0.22)
0.208
(0.476)
0.822
(0.936)
0.186
(0.454)
0.0175
(0.1)
0.825
(0.936)
0.767
(0.91)
0.0717
(0.262)
0.00479
(0.0362)
0.893
(0.967)
0.234
(0.506)
0.5
(0.741)
amp 6p23 298 (28%) 781 0.763
(0.908)
0.208
(0.476)
0.289
(0.559)
0.00421
(0.0337)
0.232
(0.503)
0.81
(0.936)
0.197
(0.468)
0.281
(0.559)
1e-05
(0.000221)
0.95
(1.00)
0.00141
(0.0143)
0.584
(0.793)
amp 6q21 202 (19%) 877 0.0751
(0.269)
0.281
(0.559)
0.08
(0.284)
0.00084
(0.00967)
0.139
(0.387)
1
(1.00)
0.708
(0.877)
0.934
(0.996)
1e-05
(0.000221)
0.045
(0.199)
0.101
(0.328)
0.676
(0.852)
amp 15q26 3 194 (18%) 885 0.18
(0.449)
0.0092
(0.0614)
0.79
(0.93)
0.323
(0.602)
0.899
(0.973)
1
(1.00)
0.245
(0.521)
0.803
(0.936)
1e-05
(0.000221)
0.641
(0.839)
0.0519
(0.214)
0.284
(0.559)
amp 19p13 12 229 (21%) 850 0.153
(0.402)
0.709
(0.877)
0.285
(0.559)
0.442
(0.687)
0.133
(0.38)
0.0623
(0.24)
0.145
(0.392)
0.279
(0.559)
0.0234
(0.12)
0.000613
(0.00757)
0.172
(0.435)
1
(1.00)
del 2q37 3 317 (29%) 762 0.647
(0.842)
0.556
(0.778)
0.214
(0.478)
0.00168
(0.0165)
0.41
(0.665)
0.246
(0.521)
1
(1.00)
0.622
(0.825)
1e-05
(0.000221)
0.283
(0.559)
0.0323
(0.161)
0.468
(0.716)
del 6p25 3 204 (19%) 875 0.867
(0.95)
0.0502
(0.211)
0.203
(0.471)
0.00948
(0.0627)
0.11
(0.343)
1
(1.00)
0.256
(0.534)
0.325
(0.603)
0.0232
(0.12)
0.581
(0.793)
0.476
(0.721)
0.679
(0.854)
del 6q15 358 (33%) 721 0.832
(0.936)
0.0372
(0.176)
0.128
(0.371)
0.339
(0.616)
0.0367
(0.175)
0.494
(0.739)
0.76
(0.908)
0.118
(0.353)
0.146
(0.394)
0.0228
(0.12)
0.137
(0.386)
0.604
(0.808)
del 7p22 3 138 (13%) 941 0.914
(0.98)
0.42
(0.668)
0.268
(0.549)
0.18
(0.449)
0.0428
(0.191)
1
(1.00)
1
(1.00)
1
(1.00)
1e-05
(0.000221)
0.00818
(0.0554)
0.797
(0.936)
0.808
(0.936)
del 10q23 31 320 (30%) 759 0.638
(0.839)
0.0744
(0.269)
0.176
(0.443)
0.0169
(0.1)
0.114
(0.348)
0.819
(0.936)
0.123
(0.363)
0.577
(0.789)
1e-05
(0.000221)
0.273
(0.553)
0.283
(0.559)
0.0486
(0.207)
del 11p15 5 309 (29%) 770 0.141
(0.392)
0.732
(0.89)
0.313
(0.592)
0.00653
(0.046)
0.415
(0.668)
0.344
(0.617)
0.34
(0.616)
0.672
(0.851)
1e-05
(0.000221)
0.836
(0.937)
0.00492
(0.0369)
0.364
(0.635)
del 12q23 1 200 (19%) 879 0.665
(0.847)
0.106
(0.336)
0.596
(0.803)
0.0232
(0.12)
0.847
(0.943)
0.403
(0.658)
1
(1.00)
0.506
(0.743)
0.00093
(0.0105)
0.529
(0.759)
0.00611
(0.0439)
1
(1.00)
del 12q24 31 210 (19%) 869 0.067
(0.25)
0.145
(0.392)
0.816
(0.936)
0.0626
(0.24)
0.668
(0.848)
1
(1.00)
0.479
(0.721)
0.807
(0.936)
0.0355
(0.17)
0.364
(0.635)
0.0463
(0.2)
0.681
(0.855)
del 16q24 3 692 (64%) 387 0.962
(1.00)
0.000283
(0.00432)
0.352
(0.627)
0.0708
(0.26)
0.438
(0.684)
0.115
(0.348)
1
(1.00)
0.548
(0.77)
1e-05
(0.000221)
0.329
(0.607)
0.00767
(0.0524)
0.24
(0.513)
del 17q21 31 371 (34%) 708 0.412
(0.666)
0.000343
(0.00506)
0.664
(0.847)
0.0918
(0.31)
0.144
(0.392)
0.367
(0.636)
0.761
(0.908)
1
(1.00)
1e-05
(0.000221)
0.833
(0.936)
0.00013
(0.00223)
1
(1.00)
del 18q23 355 (33%) 724 0.119
(0.354)
0.235
(0.506)
0.056
(0.225)
0.0214
(0.116)
0.0675
(0.25)
0.653
(0.842)
0.544
(0.77)
0.194
(0.464)
0.00012
(0.0021)
0.509
(0.746)
0.0868
(0.302)
0.863
(0.95)
amp 10p15 1 303 (28%) 776 0.166
(0.426)
0.646
(0.842)
0.391
(0.651)
0.104
(0.332)
0.474
(0.721)
0.477
(0.721)
1
(1.00)
0.52
(0.756)
1e-05
(0.000221)
0.212
(0.478)
2e-05
(0.00041)
0.713
(0.88)
amp 11q13 3 397 (37%) 682 0.501
(0.741)
0.261
(0.542)
0.593
(0.801)
0.047
(0.201)
0.662
(0.847)
0.266
(0.548)
0.0379
(0.176)
0.641
(0.839)
0.238
(0.512)
0.762
(0.908)
0.331
(0.608)
0.5
(0.741)
del 6q27 374 (35%) 705 0.133
(0.38)
1e-05
(0.000221)
0.366
(0.635)
0.635
(0.835)
0.115
(0.348)
0.654
(0.842)
0.235
(0.506)
0.00704
(0.0485)
0.189
(0.46)
0.2
(0.47)
0.587
(0.795)
0.302
(0.581)
del 9q21 11 295 (27%) 784 0.389
(0.65)
0.988
(1.00)
0.304
(0.582)
0.0752
(0.269)
0.207
(0.476)
0.343
(0.617)
0.0228
(0.12)
0.0955
(0.317)
1e-05
(0.000221)
0.466
(0.716)
0.202
(0.471)
0.354
(0.629)
del 20p13 160 (15%) 919 0.194
(0.464)
0.0453
(0.199)
0.546
(0.77)
0.42
(0.668)
0.982
(1.00)
0.129
(0.371)
0.402
(0.658)
0.145
(0.392)
6e-05
(0.00112)
0.89
(0.967)
0.17
(0.433)
0.64
(0.839)
del 22q13 32 492 (46%) 587 0.974
(1.00)
0.378
(0.642)
0.835
(0.937)
0.167
(0.429)
0.859
(0.95)
0.396
(0.654)
0.398
(0.654)
0.0243
(0.123)
0.0006
(0.00752)
1
(1.00)
0.417
(0.668)
0.625
(0.828)
amp 1q21 3 780 (72%) 299 0.912
(0.979)
0.921
(0.983)
0.242
(0.517)
0.0125
(0.0776)
0.356
(0.63)
1
(1.00)
0.104
(0.332)
0.72
(0.881)
0.1
(0.327)
0.712
(0.879)
0.206
(0.475)
0.0998
(0.327)
amp 4q13 3 163 (15%) 916 0.117
(0.353)
0.251
(0.526)
0.805
(0.936)
0.171
(0.435)
0.715
(0.88)
0.768
(0.91)
0.406
(0.659)
0.315
(0.592)
1e-05
(0.000221)
0.759
(0.908)
0.148
(0.396)
0.161
(0.417)
amp 8p11 21 420 (39%) 659 0.696
(0.868)
0.147
(0.396)
0.333
(0.608)
0.867
(0.95)
0.686
(0.86)
0.275
(0.555)
0.774
(0.916)
0.114
(0.348)
0.00094
(0.0105)
0.366
(0.635)
0.126
(0.367)
0.615
(0.818)
amp 10q22 3 149 (14%) 930 0.189
(0.46)
0.969
(1.00)
0.649
(0.842)
0.192
(0.463)
0.216
(0.48)
1
(1.00)
0.676
(0.852)
0.781
(0.922)
0.00019
(0.00307)
0.227
(0.496)
0.164
(0.425)
1
(1.00)
amp 11p13 222 (21%) 857 0.503
(0.743)
0.262
(0.542)
0.83
(0.936)
0.434
(0.683)
0.965
(1.00)
0.437
(0.684)
0.282
(0.559)
0.342
(0.617)
1e-05
(0.000221)
0.511
(0.747)
0.328
(0.606)
0.84
(0.939)
amp 11q14 1 267 (25%) 812 0.37
(0.637)
0.287
(0.559)
0.558
(0.779)
0.0948
(0.316)
0.111
(0.345)
0.467
(0.716)
0.184
(0.452)
0.404
(0.659)
0.0117
(0.0748)
0.818
(0.936)
0.115
(0.348)
0.446
(0.692)
amp 19q13 42 275 (25%) 804 0.919
(0.982)
0.577
(0.789)
0.824
(0.936)
0.214
(0.478)
0.498
(0.741)
0.223
(0.491)
0.0869
(0.302)
0.826
(0.936)
0.00441
(0.0342)
0.1
(0.327)
0.861
(0.95)
0.45
(0.697)
del 7q36 1 199 (18%) 880 0.215
(0.478)
0.979
(1.00)
0.768
(0.91)
0.162
(0.42)
0.338
(0.616)
0.405
(0.659)
0.472
(0.72)
1
(1.00)
5e-05
(0.000955)
0.919
(0.982)
0.603
(0.808)
0.523
(0.756)
del 8p11 21 200 (19%) 879 0.0853
(0.298)
0.287
(0.559)
0.732
(0.89)
0.145
(0.392)
0.225
(0.493)
0.165
(0.425)
0.138
(0.387)
0.867
(0.95)
0.00402
(0.0325)
0.124
(0.364)
0.138
(0.387)
0.832
(0.936)
del 11q13 1 241 (22%) 838 0.476
(0.721)
0.732
(0.89)
0.276
(0.556)
0.0903
(0.308)
0.548
(0.77)
0.799
(0.936)
0.736
(0.892)
0.539
(0.77)
0.717
(0.881)
0.519
(0.756)
0.00349
(0.029)
0.842
(0.94)
del 12p13 1 187 (17%) 892 0.373
(0.637)
0.372
(0.637)
0.329
(0.607)
0.131
(0.374)
0.907
(0.979)
0.782
(0.922)
0.139
(0.387)
1
(1.00)
0.00105
(0.0113)
0.632
(0.834)
0.69
(0.862)
0.524
(0.756)
del 13q14 2 498 (46%) 581 0.268
(0.549)
0.667
(0.848)
0.584
(0.793)
0.0902
(0.308)
0.381
(0.643)
0.668
(0.848)
1
(1.00)
0.198
(0.468)
1e-05
(0.000221)
0.687
(0.86)
0.0806
(0.285)
0.0988
(0.325)
del 19q13 32 216 (20%) 863 0.108
(0.34)
0.302
(0.581)
0.451
(0.698)
0.325
(0.603)
0.0676
(0.25)
0.412
(0.666)
0.715
(0.88)
0.631
(0.833)
1e-05
(0.000221)
0.839
(0.938)
0.0932
(0.313)
0.544
(0.77)
del 22q11 1 462 (43%) 617 0.91
(0.979)
0.884
(0.963)
0.733
(0.89)
0.285
(0.559)
0.559
(0.779)
0.287
(0.559)
0.571
(0.788)
0.106
(0.336)
0.00099
(0.0109)
0.915
(0.98)
0.319
(0.598)
0.87
(0.952)
amp 17p11 2 146 (14%) 933 0.311
(0.59)
0.304
(0.582)
0.674
(0.852)
0.149
(0.396)
0.606
(0.808)
0.756
(0.908)
0.214
(0.478)
0.134
(0.381)
0.497
(0.741)
0.274
(0.554)
0.595
(0.802)
1
(1.00)
'amp_1q21.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.0125 (Fisher's exact test), Q value = 0.078

Table S1.  Gene #1: 'amp_1q21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
AMP PEAK 1(1Q21.3) MUTATED 181 460 102 35
AMP PEAK 1(1Q21.3) WILD-TYPE 93 165 35 5

Figure S1.  Get High-res Image Gene #1: 'amp_1q21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_1q44' versus 'PATHOLOGIC_STAGE'

P value = 0.062 (Fisher's exact test), Q value = 0.24

Table S2.  Gene #2: '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 X
ALL 89 83 6 6 352 253 2 155 27 65 20 13
AMP PEAK 2(1Q44) MUTATED 56 55 3 6 264 188 1 110 23 53 13 8
AMP PEAK 2(1Q44) WILD-TYPE 33 28 3 0 88 65 1 45 4 12 7 5

Figure S2.  Get High-res Image Gene #2: 'amp_1q44' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_1q44' versus 'PATHOLOGY_T_STAGE'

P value = 0.00432 (Fisher's exact test), Q value = 0.034

Table S3.  Gene #2: 'amp_1q44' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
AMP PEAK 2(1Q44) MUTATED 178 474 101 33
AMP PEAK 2(1Q44) WILD-TYPE 96 151 36 7

Figure S3.  Get High-res Image Gene #2: 'amp_1q44' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_1q44' versus 'HISTOLOGICAL_TYPE'

P value = 0.00585 (Fisher's exact test), Q value = 0.043

Table S4.  Gene #2: '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 1 768 201 6 9 30 17 46
AMP PEAK 2(1Q44) MUTATED 1 548 167 5 5 21 9 32
AMP PEAK 2(1Q44) WILD-TYPE 0 220 34 1 4 9 8 14

Figure S4.  Get High-res Image Gene #2: 'amp_1q44' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_1q44' versus 'RACE'

P value = 0.0463 (Fisher's exact test), Q value = 0.2

Table S5.  Gene #2: 'amp_1q44' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
AMP PEAK 2(1Q44) MUTATED 1 35 133 553
AMP PEAK 2(1Q44) WILD-TYPE 0 25 48 191

Figure S5.  Get High-res Image Gene #2: 'amp_1q44' versus Clinical Feature #11: 'RACE'

'amp_3p25.1' versus 'Time to Death'

P value = 0.0342 (logrank test), Q value = 0.17

Table S6.  Gene #3: 'amp_3p25.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1065 148 0.0 - 282.9 (28.2)
AMP PEAK 3(3P25.1) MUTATED 197 35 0.3 - 282.9 (26.4)
AMP PEAK 3(3P25.1) WILD-TYPE 868 113 0.0 - 281.3 (28.5)

Figure S6.  Get High-res Image Gene #3: 'amp_3p25.1' versus Clinical Feature #1: 'Time to Death'

'amp_3p25.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00037 (Fisher's exact test), Q value = 0.0052

Table S7.  Gene #3: 'amp_3p25.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
AMP PEAK 3(3P25.1) MUTATED 37 132 15 13
AMP PEAK 3(3P25.1) WILD-TYPE 237 493 122 27

Figure S7.  Get High-res Image Gene #3: 'amp_3p25.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_3p25.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0458 (Fisher's exact test), Q value = 0.2

Table S8.  Gene #3: 'amp_3p25.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 506 358 119 77
AMP PEAK 3(3P25.1) MUTATED 95 55 32 12
AMP PEAK 3(3P25.1) WILD-TYPE 411 303 87 65

Figure S8.  Get High-res Image Gene #3: '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 = 0.00022

Table S9.  Gene #3: '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 1 768 201 6 9 30 17 46
AMP PEAK 3(3P25.1) MUTATED 1 168 14 1 2 5 1 6
AMP PEAK 3(3P25.1) WILD-TYPE 0 600 187 5 7 25 16 40

Figure S9.  Get High-res Image Gene #3: 'amp_3p25.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_3q26.32' versus 'PATHOLOGY_T_STAGE'

P value = 0.00015 (Fisher's exact test), Q value = 0.0025

Table S10.  Gene #4: 'amp_3q26.32' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
AMP PEAK 4(3Q26.32) MUTATED 65 225 31 17
AMP PEAK 4(3Q26.32) WILD-TYPE 209 400 106 23

Figure S10.  Get High-res Image Gene #4: '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 = 0.00022

Table S11.  Gene #4: '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 1 768 201 6 9 30 17 46
AMP PEAK 4(3Q26.32) MUTATED 1 292 16 5 7 6 1 10
AMP PEAK 4(3Q26.32) WILD-TYPE 0 476 185 1 2 24 16 36

Figure S11.  Get High-res Image Gene #4: 'amp_3q26.32' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_3q26.32' versus 'RACE'

P value = 0.0027 (Fisher's exact test), Q value = 0.024

Table S12.  Gene #4: 'amp_3q26.32' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
AMP PEAK 4(3Q26.32) MUTATED 1 27 65 207
AMP PEAK 4(3Q26.32) WILD-TYPE 0 33 116 537

Figure S12.  Get High-res Image Gene #4: 'amp_3q26.32' versus Clinical Feature #11: 'RACE'

'amp_4q13.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S13.  Gene #5: '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 1 768 201 6 9 30 17 46
AMP PEAK 5(4Q13.3) MUTATED 0 142 7 2 3 2 1 6
AMP PEAK 5(4Q13.3) WILD-TYPE 1 626 194 4 6 28 16 40

Figure S13.  Get High-res Image Gene #5: 'amp_4q13.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_5p15.33' versus 'Time to Death'

P value = 0.0542 (logrank test), Q value = 0.22

Table S14.  Gene #6: 'amp_5p15.33' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1065 148 0.0 - 282.9 (28.2)
AMP PEAK 6(5P15.33) MUTATED 391 60 0.0 - 255.7 (25.0)
AMP PEAK 6(5P15.33) WILD-TYPE 674 88 0.0 - 282.9 (29.9)

Figure S14.  Get High-res Image Gene #6: 'amp_5p15.33' versus Clinical Feature #1: 'Time to Death'

'amp_5p15.33' versus 'PATHOLOGY_N_STAGE'

P value = 0.0175 (Fisher's exact test), Q value = 0.1

Table S15.  Gene #6: 'amp_5p15.33' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 506 358 119 77
AMP PEAK 6(5P15.33) MUTATED 197 111 54 27
AMP PEAK 6(5P15.33) WILD-TYPE 309 247 65 50

Figure S15.  Get High-res Image Gene #6: 'amp_5p15.33' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_5p15.33' versus 'HISTOLOGICAL_TYPE'

P value = 0.00479 (Fisher's exact test), Q value = 0.036

Table S16.  Gene #6: '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 1 768 201 6 9 30 17 46
AMP PEAK 6(5P15.33) MUTATED 1 297 61 2 7 10 2 13
AMP PEAK 6(5P15.33) WILD-TYPE 0 471 140 4 2 20 15 33

Figure S16.  Get High-res Image Gene #6: 'amp_5p15.33' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_6p23' versus 'PATHOLOGY_T_STAGE'

P value = 0.00421 (Fisher's exact test), Q value = 0.034

Table S17.  Gene #7: 'amp_6p23' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
AMP PEAK 7(6P23) MUTATED 55 196 34 12
AMP PEAK 7(6P23) WILD-TYPE 219 429 103 28

Figure S17.  Get High-res Image Gene #7: 'amp_6p23' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_6p23' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S18.  Gene #7: '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 1 768 201 6 9 30 17 46
AMP PEAK 7(6P23) MUTATED 0 246 26 4 4 6 2 9
AMP PEAK 7(6P23) WILD-TYPE 1 522 175 2 5 24 15 37

Figure S18.  Get High-res Image Gene #7: 'amp_6p23' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_6p23' versus 'RACE'

P value = 0.00141 (Fisher's exact test), Q value = 0.014

Table S19.  Gene #7: 'amp_6p23' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
AMP PEAK 7(6P23) MUTATED 0 15 70 184
AMP PEAK 7(6P23) WILD-TYPE 1 45 111 560

Figure S19.  Get High-res Image Gene #7: 'amp_6p23' versus Clinical Feature #11: 'RACE'

'amp_6q21' versus 'PATHOLOGY_T_STAGE'

P value = 0.00084 (Fisher's exact test), Q value = 0.0097

Table S20.  Gene #8: 'amp_6q21' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
AMP PEAK 8(6Q21) MUTATED 34 142 22 4
AMP PEAK 8(6Q21) WILD-TYPE 240 483 115 36

Figure S20.  Get High-res Image Gene #8: 'amp_6q21' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_6q21' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S21.  Gene #8: '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 1 768 201 6 9 30 17 46
AMP PEAK 8(6Q21) MUTATED 1 171 15 3 5 2 0 5
AMP PEAK 8(6Q21) WILD-TYPE 0 597 186 3 4 28 17 41

Figure S21.  Get High-res Image Gene #8: 'amp_6q21' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_6q21' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.045 (Wilcoxon-test), Q value = 0.2

Table S22.  Gene #8: 'amp_6q21' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 913 2.4 (4.7)
AMP PEAK 8(6Q21) MUTATED 173 2.0 (4.4)
AMP PEAK 8(6Q21) WILD-TYPE 740 2.5 (4.7)

Figure S22.  Get High-res Image Gene #8: 'amp_6q21' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'amp_8p11.23' versus 'Time to Death'

P value = 0.0173 (logrank test), Q value = 0.1

Table S23.  Gene #9: 'amp_8p11.23' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1065 148 0.0 - 282.9 (28.2)
AMP PEAK 9(8P11.23) MUTATED 406 70 0.0 - 281.3 (26.2)
AMP PEAK 9(8P11.23) WILD-TYPE 659 78 0.0 - 282.9 (29.2)

Figure S23.  Get High-res Image Gene #9: 'amp_8p11.23' versus Clinical Feature #1: 'Time to Death'

'amp_8p11.23' versus 'PATHOLOGIC_STAGE'

P value = 0.0512 (Fisher's exact test), Q value = 0.21

Table S24.  Gene #9: '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 X
ALL 89 83 6 6 352 253 2 155 27 65 20 13
AMP PEAK 9(8P11.23) MUTATED 23 29 4 1 134 95 2 57 14 30 11 6
AMP PEAK 9(8P11.23) WILD-TYPE 66 54 2 5 218 158 0 98 13 35 9 7

Figure S24.  Get High-res Image Gene #9: 'amp_8p11.23' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_8p11.23' versus 'PATHOLOGY_N_STAGE'

P value = 0.0572 (Fisher's exact test), Q value = 0.23

Table S25.  Gene #9: 'amp_8p11.23' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 506 358 119 77
AMP PEAK 9(8P11.23) MUTATED 172 146 48 36
AMP PEAK 9(8P11.23) WILD-TYPE 334 212 71 41

Figure S25.  Get High-res Image Gene #9: 'amp_8p11.23' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_8p11.23' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00454 (Wilcoxon-test), Q value = 0.035

Table S26.  Gene #9: 'amp_8p11.23' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 913 2.4 (4.7)
AMP PEAK 9(8P11.23) MUTATED 345 2.9 (5.3)
AMP PEAK 9(8P11.23) WILD-TYPE 568 2.1 (4.2)

Figure S26.  Get High-res Image Gene #9: 'amp_8p11.23' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'amp_8p11.21' versus 'HISTOLOGICAL_TYPE'

P value = 0.00094 (Fisher's exact test), Q value = 0.011

Table S27.  Gene #10: '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 1 768 201 6 9 30 17 46
AMP PEAK 10(8P11.21) MUTATED 1 321 55 5 4 11 4 18
AMP PEAK 10(8P11.21) WILD-TYPE 0 447 146 1 5 19 13 28

Figure S27.  Get High-res Image Gene #10: 'amp_8p11.21' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_8q24.21' versus 'YEARS_TO_BIRTH'

P value = 0.0595 (Wilcoxon-test), Q value = 0.23

Table S28.  Gene #11: 'amp_8q24.21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1064 58.6 (13.2)
AMP PEAK 11(8Q24.21) MUTATED 669 58.0 (13.1)
AMP PEAK 11(8Q24.21) WILD-TYPE 395 59.7 (13.3)

Figure S28.  Get High-res Image Gene #11: 'amp_8q24.21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_8q24.21' versus 'PATHOLOGY_T_STAGE'

P value = 0.0624 (Fisher's exact test), Q value = 0.24

Table S29.  Gene #11: 'amp_8q24.21' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
AMP PEAK 11(8Q24.21) MUTATED 157 412 80 25
AMP PEAK 11(8Q24.21) WILD-TYPE 117 213 57 15

Figure S29.  Get High-res Image Gene #11: '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 = 0.00022

Table S30.  Gene #11: '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 1 768 201 6 9 30 17 46
AMP PEAK 11(8Q24.21) MUTATED 1 545 70 6 7 18 5 24
AMP PEAK 11(8Q24.21) WILD-TYPE 0 223 131 0 2 12 12 22

Figure S30.  Get High-res Image Gene #11: 'amp_8q24.21' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_8q24.21' versus 'RACE'

P value = 0.00132 (Fisher's exact test), Q value = 0.014

Table S31.  Gene #11: 'amp_8q24.21' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
AMP PEAK 11(8Q24.21) MUTATED 1 41 131 434
AMP PEAK 11(8Q24.21) WILD-TYPE 0 19 50 310

Figure S31.  Get High-res Image Gene #11: 'amp_8q24.21' versus Clinical Feature #11: 'RACE'

'amp_10p15.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S32.  Gene #12: '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 1 768 201 6 9 30 17 46
AMP PEAK 12(10P15.1) MUTATED 1 261 20 5 1 5 0 9
AMP PEAK 12(10P15.1) WILD-TYPE 0 507 181 1 8 25 17 37

Figure S32.  Get High-res Image Gene #12: 'amp_10p15.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_10p15.1' versus 'RACE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00041

Table S33.  Gene #12: 'amp_10p15.1' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
AMP PEAK 12(10P15.1) MUTATED 1 14 75 184
AMP PEAK 12(10P15.1) WILD-TYPE 0 46 106 560

Figure S33.  Get High-res Image Gene #12: 'amp_10p15.1' versus Clinical Feature #11: 'RACE'

'amp_10q22.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.00019 (Fisher's exact test), Q value = 0.0031

Table S34.  Gene #13: '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 1 768 201 6 9 30 17 46
AMP PEAK 13(10Q22.3) MUTATED 0 124 11 3 1 5 0 5
AMP PEAK 13(10Q22.3) WILD-TYPE 1 644 190 3 8 25 17 41

Figure S34.  Get High-res Image Gene #13: 'amp_10q22.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_11p13' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S35.  Gene #14: '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 1 768 201 6 9 30 17 46
AMP PEAK 14(11P13) MUTATED 1 186 18 3 2 3 2 7
AMP PEAK 14(11P13) WILD-TYPE 0 582 183 3 7 27 15 39

Figure S35.  Get High-res Image Gene #14: 'amp_11p13' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_11q13.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.047 (Fisher's exact test), Q value = 0.2

Table S36.  Gene #15: 'amp_11q13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
AMP PEAK 15(11Q13.3) MUTATED 86 245 45 19
AMP PEAK 15(11Q13.3) WILD-TYPE 188 380 92 21

Figure S36.  Get High-res Image Gene #15: 'amp_11q13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_11q13.3' versus 'GENDER'

P value = 0.0379 (Fisher's exact test), Q value = 0.18

Table S37.  Gene #15: 'amp_11q13.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1067 12
AMP PEAK 15(11Q13.3) MUTATED 389 8
AMP PEAK 15(11Q13.3) WILD-TYPE 678 4

Figure S37.  Get High-res Image Gene #15: 'amp_11q13.3' versus Clinical Feature #7: 'GENDER'

'amp_11q14.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.0117 (Fisher's exact test), Q value = 0.075

Table S38.  Gene #16: '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 1 768 201 6 9 30 17 46
AMP PEAK 16(11Q14.1) MUTATED 1 212 34 2 2 4 2 10
AMP PEAK 16(11Q14.1) WILD-TYPE 0 556 167 4 7 26 15 36

Figure S38.  Get High-res Image Gene #16: 'amp_11q14.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_12p13.33' versus 'PATHOLOGY_T_STAGE'

P value = 0.00286 (Fisher's exact test), Q value = 0.025

Table S39.  Gene #17: 'amp_12p13.33' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
AMP PEAK 17(12P13.33) MUTATED 49 184 34 12
AMP PEAK 17(12P13.33) WILD-TYPE 225 441 103 28

Figure S39.  Get High-res Image Gene #17: '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 = 0.00022

Table S40.  Gene #17: '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 1 768 201 6 9 30 17 46
AMP PEAK 17(12P13.33) MUTATED 1 230 27 4 2 11 1 5
AMP PEAK 17(12P13.33) WILD-TYPE 0 538 174 2 7 19 16 41

Figure S40.  Get High-res Image Gene #17: 'amp_12p13.33' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_12p13.33' versus 'RACE'

P value = 0.0211 (Fisher's exact test), Q value = 0.12

Table S41.  Gene #17: 'amp_12p13.33' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
AMP PEAK 17(12P13.33) MUTATED 0 13 62 177
AMP PEAK 17(12P13.33) WILD-TYPE 1 47 119 567

Figure S41.  Get High-res Image Gene #17: 'amp_12p13.33' versus Clinical Feature #11: 'RACE'

'amp_12p13.33' versus 'ETHNICITY'

P value = 0.0617 (Fisher's exact test), Q value = 0.24

Table S42.  Gene #17: 'amp_12p13.33' versus Clinical Feature #12: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 39 874
AMP PEAK 17(12P13.33) MUTATED 5 233
AMP PEAK 17(12P13.33) WILD-TYPE 34 641

Figure S42.  Get High-res Image Gene #17: 'amp_12p13.33' versus Clinical Feature #12: 'ETHNICITY'

'amp_12q15' versus 'PATHOLOGY_T_STAGE'

P value = 0.0235 (Fisher's exact test), Q value = 0.12

Table S43.  Gene #18: 'amp_12q15' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
AMP PEAK 18(12Q15) MUTATED 55 173 31 15
AMP PEAK 18(12Q15) WILD-TYPE 219 452 106 25

Figure S43.  Get High-res Image Gene #18: 'amp_12q15' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_12q15' versus 'PATHOLOGY_N_STAGE'

P value = 0.0131 (Fisher's exact test), Q value = 0.081

Table S44.  Gene #18: 'amp_12q15' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 506 358 119 77
AMP PEAK 18(12Q15) MUTATED 114 88 44 22
AMP PEAK 18(12Q15) WILD-TYPE 392 270 75 55

Figure S44.  Get High-res Image Gene #18: 'amp_12q15' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_12q15' versus 'GENDER'

P value = 0.00301 (Fisher's exact test), Q value = 0.025

Table S45.  Gene #18: 'amp_12q15' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1067 12
AMP PEAK 18(12Q15) MUTATED 267 8
AMP PEAK 18(12Q15) WILD-TYPE 800 4

Figure S45.  Get High-res Image Gene #18: 'amp_12q15' versus Clinical Feature #7: 'GENDER'

'amp_12q15' versus 'HISTOLOGICAL_TYPE'

P value = 0.00036 (Fisher's exact test), Q value = 0.0051

Table S46.  Gene #18: '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 1 768 201 6 9 30 17 46
AMP PEAK 18(12Q15) MUTATED 0 223 34 1 1 10 2 4
AMP PEAK 18(12Q15) WILD-TYPE 1 545 167 5 8 20 15 42

Figure S46.  Get High-res Image Gene #18: 'amp_12q15' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_12q15' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0147 (Wilcoxon-test), Q value = 0.088

Table S47.  Gene #18: 'amp_12q15' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 913 2.4 (4.7)
AMP PEAK 18(12Q15) MUTATED 217 2.7 (4.6)
AMP PEAK 18(12Q15) WILD-TYPE 696 2.3 (4.7)

Figure S47.  Get High-res Image Gene #18: 'amp_12q15' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'amp_13q34' versus 'YEARS_TO_BIRTH'

P value = 0.0578 (Wilcoxon-test), Q value = 0.23

Table S48.  Gene #19: 'amp_13q34' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1064 58.6 (13.2)
AMP PEAK 19(13Q34) MUTATED 176 56.9 (12.7)
AMP PEAK 19(13Q34) WILD-TYPE 888 59.0 (13.3)

Figure S48.  Get High-res Image Gene #19: 'amp_13q34' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_13q34' versus 'PATHOLOGY_T_STAGE'

P value = 0.00663 (Fisher's exact test), Q value = 0.046

Table S49.  Gene #19: 'amp_13q34' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
AMP PEAK 19(13Q34) MUTATED 30 123 18 6
AMP PEAK 19(13Q34) WILD-TYPE 244 502 119 34

Figure S49.  Get High-res Image Gene #19: 'amp_13q34' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_13q34' versus 'RADIATION_THERAPY'

P value = 0.0575 (Fisher's exact test), Q value = 0.23

Table S50.  Gene #19: 'amp_13q34' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients NO YES
ALL 437 547
AMP PEAK 19(13Q34) MUTATED 83 79
AMP PEAK 19(13Q34) WILD-TYPE 354 468

Figure S50.  Get High-res Image Gene #19: 'amp_13q34' versus Clinical Feature #8: 'RADIATION_THERAPY'

'amp_13q34' versus 'HISTOLOGICAL_TYPE'

P value = 0.00108 (Fisher's exact test), Q value = 0.011

Table S51.  Gene #19: '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 1 768 201 6 9 30 17 46
AMP PEAK 19(13Q34) MUTATED 0 145 14 1 3 4 2 9
AMP PEAK 19(13Q34) WILD-TYPE 1 623 187 5 6 26 15 37

Figure S51.  Get High-res Image Gene #19: 'amp_13q34' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_14q21.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.0176 (Fisher's exact test), Q value = 0.1

Table S52.  Gene #20: 'amp_14q21.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
AMP PEAK 20(14Q21.1) MUTATED 43 148 21 8
AMP PEAK 20(14Q21.1) WILD-TYPE 231 477 116 32

Figure S52.  Get High-res Image Gene #20: 'amp_14q21.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_14q21.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0326 (Fisher's exact test), Q value = 0.16

Table S53.  Gene #20: 'amp_14q21.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 506 358 119 77
AMP PEAK 20(14Q21.1) MUTATED 87 75 32 21
AMP PEAK 20(14Q21.1) WILD-TYPE 419 283 87 56

Figure S53.  Get High-res Image Gene #20: 'amp_14q21.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_14q21.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00662 (Fisher's exact test), Q value = 0.046

Table S54.  Gene #20: '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 1 768 201 6 9 30 17 46
AMP PEAK 20(14Q21.1) MUTATED 0 174 23 0 3 9 2 9
AMP PEAK 20(14Q21.1) WILD-TYPE 1 594 178 6 6 21 15 37

Figure S54.  Get High-res Image Gene #20: 'amp_14q21.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_14q21.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0105 (Wilcoxon-test), Q value = 0.068

Table S55.  Gene #20: 'amp_14q21.1' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 913 2.4 (4.7)
AMP PEAK 20(14Q21.1) MUTATED 177 2.9 (4.8)
AMP PEAK 20(14Q21.1) WILD-TYPE 736 2.3 (4.6)

Figure S55.  Get High-res Image Gene #20: 'amp_14q21.1' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'amp_15q26.3' versus 'YEARS_TO_BIRTH'

P value = 0.0092 (Wilcoxon-test), Q value = 0.061

Table S56.  Gene #21: 'amp_15q26.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1064 58.6 (13.2)
AMP PEAK 21(15Q26.3) MUTATED 190 56.4 (12.9)
AMP PEAK 21(15Q26.3) WILD-TYPE 874 59.1 (13.2)

Figure S56.  Get High-res Image Gene #21: '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 = 0.00022

Table S57.  Gene #21: '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 1 768 201 6 9 30 17 46
AMP PEAK 21(15Q26.3) MUTATED 0 167 11 3 1 4 3 4
AMP PEAK 21(15Q26.3) WILD-TYPE 1 601 190 3 8 26 14 42

Figure S57.  Get High-res Image Gene #21: 'amp_15q26.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_15q26.3' versus 'RACE'

P value = 0.0519 (Fisher's exact test), Q value = 0.21

Table S58.  Gene #21: 'amp_15q26.3' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
AMP PEAK 21(15Q26.3) MUTATED 0 16 39 118
AMP PEAK 21(15Q26.3) WILD-TYPE 1 44 142 626

Figure S58.  Get High-res Image Gene #21: 'amp_15q26.3' versus Clinical Feature #11: 'RACE'

'amp_17q12' versus 'PATHOLOGY_N_STAGE'

P value = 0.0648 (Fisher's exact test), Q value = 0.25

Table S59.  Gene #23: 'amp_17q12' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 506 358 119 77
AMP PEAK 23(17Q12) MUTATED 138 128 35 22
AMP PEAK 23(17Q12) WILD-TYPE 368 230 84 55

Figure S59.  Get High-res Image Gene #23: 'amp_17q12' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_17q12' versus 'GENDER'

P value = 0.011 (Fisher's exact test), Q value = 0.071

Table S60.  Gene #23: 'amp_17q12' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1067 12
AMP PEAK 23(17Q12) MUTATED 325 8
AMP PEAK 23(17Q12) WILD-TYPE 742 4

Figure S60.  Get High-res Image Gene #23: 'amp_17q12' versus Clinical Feature #7: 'GENDER'

'amp_17q12' versus 'HISTOLOGICAL_TYPE'

P value = 0.00042 (Fisher's exact test), Q value = 0.0057

Table S61.  Gene #23: '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 1 768 201 6 9 30 17 46
AMP PEAK 23(17Q12) MUTATED 0 270 38 1 3 6 4 11
AMP PEAK 23(17Q12) WILD-TYPE 1 498 163 5 6 24 13 35

Figure S61.  Get High-res Image Gene #23: 'amp_17q12' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_17q12' versus 'RACE'

P value = 0.00156 (Fisher's exact test), Q value = 0.016

Table S62.  Gene #23: 'amp_17q12' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
AMP PEAK 23(17Q12) MUTATED 1 30 52 210
AMP PEAK 23(17Q12) WILD-TYPE 0 30 129 534

Figure S62.  Get High-res Image Gene #23: 'amp_17q12' versus Clinical Feature #11: 'RACE'

'amp_17q23.1' versus 'PATHOLOGIC_STAGE'

P value = 0.0267 (Fisher's exact test), Q value = 0.13

Table S63.  Gene #24: '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 X
ALL 89 83 6 6 352 253 2 155 27 65 20 13
AMP PEAK 24(17Q23.1) MUTATED 27 25 1 2 151 102 1 69 16 20 9 2
AMP PEAK 24(17Q23.1) WILD-TYPE 62 58 5 4 201 151 1 86 11 45 11 11

Figure S63.  Get High-res Image Gene #24: '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 = 0.0051

Table S64.  Gene #24: 'amp_17q23.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
AMP PEAK 24(17Q23.1) MUTATED 81 276 50 18
AMP PEAK 24(17Q23.1) WILD-TYPE 193 349 87 22

Figure S64.  Get High-res Image Gene #24: 'amp_17q23.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_17q23.1' versus 'GENDER'

P value = 1.3e-05 (Fisher's exact test), Q value = 0.00028

Table S65.  Gene #24: 'amp_17q23.1' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1067 12
AMP PEAK 24(17Q23.1) MUTATED 414 12
AMP PEAK 24(17Q23.1) WILD-TYPE 653 0

Figure S65.  Get High-res Image Gene #24: 'amp_17q23.1' versus Clinical Feature #7: 'GENDER'

'amp_17q23.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S66.  Gene #24: '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 1 768 201 6 9 30 17 46
AMP PEAK 24(17Q23.1) MUTATED 1 341 44 3 6 12 5 13
AMP PEAK 24(17Q23.1) WILD-TYPE 0 427 157 3 3 18 12 33

Figure S66.  Get High-res Image Gene #24: '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 = 0.24

Table S67.  Gene #25: 'amp_19p13.12' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 889 22
AMP PEAK 25(19P13.12) MUTATED 192 1
AMP PEAK 25(19P13.12) WILD-TYPE 697 21

Figure S67.  Get High-res Image Gene #25: 'amp_19p13.12' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_19p13.12' versus 'HISTOLOGICAL_TYPE'

P value = 0.0234 (Fisher's exact test), Q value = 0.12

Table S68.  Gene #25: '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 1 768 201 6 9 30 17 46
AMP PEAK 25(19P13.12) MUTATED 1 169 32 4 3 7 2 11
AMP PEAK 25(19P13.12) WILD-TYPE 0 599 169 2 6 23 15 35

Figure S68.  Get High-res Image Gene #25: 'amp_19p13.12' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_19p13.12' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000613 (Wilcoxon-test), Q value = 0.0076

Table S69.  Gene #25: 'amp_19p13.12' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 913 2.4 (4.7)
AMP PEAK 25(19P13.12) MUTATED 206 1.9 (4.5)
AMP PEAK 25(19P13.12) WILD-TYPE 707 2.5 (4.7)

Figure S69.  Get High-res Image Gene #25: 'amp_19p13.12' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'amp_19q12' versus 'PATHOLOGIC_STAGE'

P value = 0.00902 (Fisher's exact test), Q value = 0.061

Table S70.  Gene #26: '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 X
ALL 89 83 6 6 352 253 2 155 27 65 20 13
AMP PEAK 26(19Q12) MUTATED 23 18 2 2 120 57 0 35 8 12 3 0
AMP PEAK 26(19Q12) WILD-TYPE 66 65 4 4 232 196 2 120 19 53 17 13

Figure S70.  Get High-res Image Gene #26: 'amp_19q12' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_19q12' versus 'PATHOLOGY_N_STAGE'

P value = 0.03 (Fisher's exact test), Q value = 0.15

Table S71.  Gene #26: 'amp_19q12' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 506 358 119 77
AMP PEAK 26(19Q12) MUTATED 155 85 28 14
AMP PEAK 26(19Q12) WILD-TYPE 351 273 91 63

Figure S71.  Get High-res Image Gene #26: 'amp_19q12' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_19q12' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S72.  Gene #26: '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 1 768 201 6 9 30 17 46
AMP PEAK 26(19Q12) MUTATED 0 226 29 6 3 7 2 10
AMP PEAK 26(19Q12) WILD-TYPE 1 542 172 0 6 23 15 36

Figure S72.  Get High-res Image Gene #26: 'amp_19q12' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_19q12' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00604 (Wilcoxon-test), Q value = 0.044

Table S73.  Gene #26: 'amp_19q12' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 913 2.4 (4.7)
AMP PEAK 26(19Q12) MUTATED 245 2.0 (4.6)
AMP PEAK 26(19Q12) WILD-TYPE 668 2.5 (4.7)

Figure S73.  Get High-res Image Gene #26: 'amp_19q12' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'amp_19q12' versus 'RACE'

P value = 0.0341 (Fisher's exact test), Q value = 0.17

Table S74.  Gene #26: 'amp_19q12' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
AMP PEAK 26(19Q12) MUTATED 0 13 63 187
AMP PEAK 26(19Q12) WILD-TYPE 1 47 118 557

Figure S74.  Get High-res Image Gene #26: 'amp_19q12' versus Clinical Feature #11: 'RACE'

'amp_19q13.42' versus 'HISTOLOGICAL_TYPE'

P value = 0.00441 (Fisher's exact test), Q value = 0.034

Table S75.  Gene #27: '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 1 768 201 6 9 30 17 46
AMP PEAK 27(19Q13.42) MUTATED 1 217 32 2 3 6 2 12
AMP PEAK 27(19Q13.42) WILD-TYPE 0 551 169 4 6 24 15 34

Figure S75.  Get High-res Image Gene #27: 'amp_19q13.42' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_20q13.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00226 (Fisher's exact test), Q value = 0.021

Table S76.  Gene #28: 'amp_20q13.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
AMP PEAK 28(20Q13.2) MUTATED 120 345 58 22
AMP PEAK 28(20Q13.2) WILD-TYPE 154 280 79 18

Figure S76.  Get High-res Image Gene #28: 'amp_20q13.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_20q13.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.00112 (Fisher's exact test), Q value = 0.012

Table S77.  Gene #28: 'amp_20q13.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 506 358 119 77
AMP PEAK 28(20Q13.2) MUTATED 248 178 79 31
AMP PEAK 28(20Q13.2) WILD-TYPE 258 180 40 46

Figure S77.  Get High-res Image Gene #28: 'amp_20q13.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_20q13.2' versus 'GENDER'

P value = 0.0377 (Fisher's exact test), Q value = 0.18

Table S78.  Gene #28: 'amp_20q13.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1067 12
AMP PEAK 28(20Q13.2) MUTATED 537 10
AMP PEAK 28(20Q13.2) WILD-TYPE 530 2

Figure S78.  Get High-res Image Gene #28: 'amp_20q13.2' versus Clinical Feature #7: 'GENDER'

'amp_20q13.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S79.  Gene #28: '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 1 768 201 6 9 30 17 46
AMP PEAK 28(20Q13.2) MUTATED 1 451 55 1 7 12 1 19
AMP PEAK 28(20Q13.2) WILD-TYPE 0 317 146 5 2 18 16 27

Figure S79.  Get High-res Image Gene #28: 'amp_20q13.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_1p36.13' versus 'Time to Death'

P value = 0.0203 (logrank test), Q value = 0.11

Table S80.  Gene #29: 'del_1p36.13' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1065 148 0.0 - 282.9 (28.2)
DEL PEAK 1(1P36.13) MUTATED 447 69 0.2 - 282.9 (25.1)
DEL PEAK 1(1P36.13) WILD-TYPE 618 79 0.0 - 281.3 (30.8)

Figure S80.  Get High-res Image Gene #29: 'del_1p36.13' versus Clinical Feature #1: 'Time to Death'

'del_1p36.13' versus 'YEARS_TO_BIRTH'

P value = 0.016 (Wilcoxon-test), Q value = 0.095

Table S81.  Gene #29: 'del_1p36.13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1064 58.6 (13.2)
DEL PEAK 1(1P36.13) MUTATED 445 59.6 (13.1)
DEL PEAK 1(1P36.13) WILD-TYPE 619 58.0 (13.3)

Figure S81.  Get High-res Image Gene #29: 'del_1p36.13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_1p36.13' versus 'PATHOLOGIC_STAGE'

P value = 0.00049 (Fisher's exact test), Q value = 0.0064

Table S82.  Gene #29: '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 X
ALL 89 83 6 6 352 253 2 155 27 65 20 13
DEL PEAK 1(1P36.13) MUTATED 27 24 0 3 135 118 1 74 17 33 12 5
DEL PEAK 1(1P36.13) WILD-TYPE 62 59 6 3 217 135 1 81 10 32 8 8

Figure S82.  Get High-res Image Gene #29: '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 = 0.00022

Table S83.  Gene #29: 'del_1p36.13' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
DEL PEAK 1(1P36.13) MUTATED 82 287 55 26
DEL PEAK 1(1P36.13) WILD-TYPE 192 338 82 14

Figure S83.  Get High-res Image Gene #29: 'del_1p36.13' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_1p36.13' versus 'PATHOLOGY_N_STAGE'

P value = 0.00045 (Fisher's exact test), Q value = 0.006

Table S84.  Gene #29: 'del_1p36.13' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 506 358 119 77
DEL PEAK 1(1P36.13) MUTATED 179 166 57 41
DEL PEAK 1(1P36.13) WILD-TYPE 327 192 62 36

Figure S84.  Get High-res Image Gene #29: '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 = 0.17

Table S85.  Gene #29: 'del_1p36.13' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1067 12
DEL PEAK 1(1P36.13) MUTATED 442 9
DEL PEAK 1(1P36.13) WILD-TYPE 625 3

Figure S85.  Get High-res Image Gene #29: 'del_1p36.13' versus Clinical Feature #7: 'GENDER'

'del_1p36.13' versus 'HISTOLOGICAL_TYPE'

P value = 0.00244 (Fisher's exact test), Q value = 0.022

Table S86.  Gene #29: '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 1 768 201 6 9 30 17 46
DEL PEAK 1(1P36.13) MUTATED 1 346 74 1 0 8 4 17
DEL PEAK 1(1P36.13) WILD-TYPE 0 422 127 5 9 22 13 29

Figure S86.  Get High-res Image Gene #29: 'del_1p36.13' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_1p36.13' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00083 (Wilcoxon-test), Q value = 0.0097

Table S87.  Gene #29: 'del_1p36.13' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 913 2.4 (4.7)
DEL PEAK 1(1P36.13) MUTATED 371 2.9 (5.1)
DEL PEAK 1(1P36.13) WILD-TYPE 542 2.0 (4.3)

Figure S87.  Get High-res Image Gene #29: 'del_1p36.13' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'del_1p21.2' versus 'Time to Death'

P value = 0.0198 (logrank test), Q value = 0.11

Table S88.  Gene #30: 'del_1p21.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1065 148 0.0 - 282.9 (28.2)
DEL PEAK 2(1P21.2) MUTATED 349 59 0.2 - 255.7 (25.1)
DEL PEAK 2(1P21.2) WILD-TYPE 716 89 0.0 - 282.9 (29.8)

Figure S88.  Get High-res Image Gene #30: 'del_1p21.2' versus Clinical Feature #1: 'Time to Death'

'del_1p21.2' versus 'YEARS_TO_BIRTH'

P value = 0.0118 (Wilcoxon-test), Q value = 0.075

Table S89.  Gene #30: 'del_1p21.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1064 58.6 (13.2)
DEL PEAK 2(1P21.2) MUTATED 349 59.9 (13.0)
DEL PEAK 2(1P21.2) WILD-TYPE 715 58.0 (13.3)

Figure S89.  Get High-res Image Gene #30: 'del_1p21.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_1p21.2' versus 'PATHOLOGIC_STAGE'

P value = 0.0232 (Fisher's exact test), Q value = 0.12

Table S90.  Gene #30: 'del_1p21.2' 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 X
ALL 89 83 6 6 352 253 2 155 27 65 20 13
DEL PEAK 2(1P21.2) MUTATED 21 20 0 1 110 86 1 59 15 25 8 6
DEL PEAK 2(1P21.2) WILD-TYPE 68 63 6 5 242 167 1 96 12 40 12 7

Figure S90.  Get High-res Image Gene #30: 'del_1p21.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_1p21.2' versus 'PATHOLOGY_T_STAGE'

P value = 8e-05 (Fisher's exact test), Q value = 0.0015

Table S91.  Gene #30: 'del_1p21.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
DEL PEAK 2(1P21.2) MUTATED 65 223 44 22
DEL PEAK 2(1P21.2) WILD-TYPE 209 402 93 18

Figure S91.  Get High-res Image Gene #30: 'del_1p21.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_1p21.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.0173 (Fisher's exact test), Q value = 0.1

Table S92.  Gene #30: 'del_1p21.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 506 358 119 77
DEL PEAK 2(1P21.2) MUTATED 146 122 51 29
DEL PEAK 2(1P21.2) WILD-TYPE 360 236 68 48

Figure S92.  Get High-res Image Gene #30: 'del_1p21.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_1p21.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00374 (Wilcoxon-test), Q value = 0.031

Table S93.  Gene #30: 'del_1p21.2' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 913 2.4 (4.7)
DEL PEAK 2(1P21.2) MUTATED 287 2.9 (5.3)
DEL PEAK 2(1P21.2) WILD-TYPE 626 2.1 (4.3)

Figure S93.  Get High-res Image Gene #30: 'del_1p21.2' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'del_2q37.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00168 (Fisher's exact test), Q value = 0.017

Table S94.  Gene #31: 'del_2q37.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
DEL PEAK 3(2Q37.3) MUTATED 60 198 38 19
DEL PEAK 3(2Q37.3) WILD-TYPE 214 427 99 21

Figure S94.  Get High-res Image Gene #31: '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 = 0.00022

Table S95.  Gene #31: '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 1 768 201 6 9 30 17 46
DEL PEAK 3(2Q37.3) MUTATED 0 261 26 3 5 10 3 8
DEL PEAK 3(2Q37.3) WILD-TYPE 1 507 175 3 4 20 14 38

Figure S95.  Get High-res Image Gene #31: 'del_2q37.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_2q37.3' versus 'RACE'

P value = 0.0323 (Fisher's exact test), Q value = 0.16

Table S96.  Gene #31: 'del_2q37.3' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
DEL PEAK 3(2Q37.3) MUTATED 0 25 58 197
DEL PEAK 3(2Q37.3) WILD-TYPE 1 35 123 547

Figure S96.  Get High-res Image Gene #31: 'del_2q37.3' versus Clinical Feature #11: 'RACE'

'del_3p21.31' versus 'YEARS_TO_BIRTH'

P value = 0.00243 (Wilcoxon-test), Q value = 0.022

Table S97.  Gene #32: 'del_3p21.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1064 58.6 (13.2)
DEL PEAK 4(3P21.31) MUTATED 341 56.8 (13.1)
DEL PEAK 4(3P21.31) WILD-TYPE 723 59.5 (13.2)

Figure S97.  Get High-res Image Gene #32: 'del_3p21.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_3p21.31' versus 'PATHOLOGY_T_STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 8e-04

Table S98.  Gene #32: 'del_3p21.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
DEL PEAK 4(3P21.31) MUTATED 60 236 40 10
DEL PEAK 4(3P21.31) WILD-TYPE 214 389 97 30

Figure S98.  Get High-res Image Gene #32: 'del_3p21.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_3p21.31' versus 'HISTOLOGICAL_TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00041

Table S99.  Gene #32: '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 1 768 201 6 9 30 17 46
DEL PEAK 4(3P21.31) MUTATED 1 285 41 1 2 6 1 10
DEL PEAK 4(3P21.31) WILD-TYPE 0 483 160 5 7 24 16 36

Figure S99.  Get High-res Image Gene #32: 'del_3p21.31' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_3p21.31' versus 'RACE'

P value = 0.0125 (Fisher's exact test), Q value = 0.078

Table S100.  Gene #32: 'del_3p21.31' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
DEL PEAK 4(3P21.31) MUTATED 0 26 72 224
DEL PEAK 4(3P21.31) WILD-TYPE 1 34 109 520

Figure S100.  Get High-res Image Gene #32: 'del_3p21.31' versus Clinical Feature #11: 'RACE'

'del_4p16.3' versus 'YEARS_TO_BIRTH'

P value = 0.0525 (Wilcoxon-test), Q value = 0.21

Table S101.  Gene #33: 'del_4p16.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1064 58.6 (13.2)
DEL PEAK 5(4P16.3) MUTATED 332 57.6 (12.7)
DEL PEAK 5(4P16.3) WILD-TYPE 732 59.1 (13.4)

Figure S101.  Get High-res Image Gene #33: 'del_4p16.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_4p16.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00016 (Fisher's exact test), Q value = 0.0026

Table S102.  Gene #33: 'del_4p16.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
DEL PEAK 5(4P16.3) MUTATED 59 226 39 13
DEL PEAK 5(4P16.3) WILD-TYPE 215 399 98 27

Figure S102.  Get High-res Image Gene #33: '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 = 0.00022

Table S103.  Gene #33: '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 1 768 201 6 9 30 17 46
DEL PEAK 5(4P16.3) MUTATED 1 281 32 4 3 6 0 12
DEL PEAK 5(4P16.3) WILD-TYPE 0 487 169 2 6 24 17 34

Figure S103.  Get High-res Image Gene #33: 'del_4p16.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_4p16.3' versus 'RACE'

P value = 0.0189 (Fisher's exact test), Q value = 0.11

Table S104.  Gene #33: 'del_4p16.3' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
DEL PEAK 5(4P16.3) MUTATED 1 17 73 225
DEL PEAK 5(4P16.3) WILD-TYPE 0 43 108 519

Figure S104.  Get High-res Image Gene #33: 'del_4p16.3' versus Clinical Feature #11: 'RACE'

'del_4q35.2' versus 'Time to Death'

P value = 0.0416 (logrank test), Q value = 0.19

Table S105.  Gene #34: 'del_4q35.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1065 148 0.0 - 282.9 (28.2)
DEL PEAK 6(4Q35.2) MUTATED 342 58 0.0 - 255.7 (25.1)
DEL PEAK 6(4Q35.2) WILD-TYPE 723 90 0.0 - 282.9 (28.9)

Figure S105.  Get High-res Image Gene #34: 'del_4q35.2' versus Clinical Feature #1: 'Time to Death'

'del_4q35.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00226 (Fisher's exact test), Q value = 0.021

Table S106.  Gene #34: 'del_4q35.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
DEL PEAK 6(4Q35.2) MUTATED 65 223 41 16
DEL PEAK 6(4Q35.2) WILD-TYPE 209 402 96 24

Figure S106.  Get High-res Image Gene #34: 'del_4q35.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_4q35.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S107.  Gene #34: 'del_4q35.2' 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 1 768 201 6 9 30 17 46
DEL PEAK 6(4Q35.2) MUTATED 1 288 36 4 5 5 0 7
DEL PEAK 6(4Q35.2) WILD-TYPE 0 480 165 2 4 25 17 39

Figure S107.  Get High-res Image Gene #34: 'del_4q35.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_4q35.2' versus 'RACE'

P value = 0.00439 (Fisher's exact test), Q value = 0.034

Table S108.  Gene #34: 'del_4q35.2' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
DEL PEAK 6(4Q35.2) MUTATED 1 22 75 220
DEL PEAK 6(4Q35.2) WILD-TYPE 0 38 106 524

Figure S108.  Get High-res Image Gene #34: 'del_4q35.2' versus Clinical Feature #11: 'RACE'

'del_5q11.2' versus 'YEARS_TO_BIRTH'

P value = 3.8e-06 (Wilcoxon-test), Q value = 0.00022

Table S109.  Gene #35: 'del_5q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1064 58.6 (13.2)
DEL PEAK 7(5Q11.2) MUTATED 277 55.6 (13.2)
DEL PEAK 7(5Q11.2) WILD-TYPE 787 59.7 (13.0)

Figure S109.  Get High-res Image Gene #35: 'del_5q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_5q11.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00101 (Fisher's exact test), Q value = 0.011

Table S110.  Gene #35: 'del_5q11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
DEL PEAK 7(5Q11.2) MUTATED 60 187 21 12
DEL PEAK 7(5Q11.2) WILD-TYPE 214 438 116 28

Figure S110.  Get High-res Image Gene #35: '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 S111.  Gene #35: 'del_5q11.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1067 12
DEL PEAK 7(5Q11.2) MUTATED 280 0
DEL PEAK 7(5Q11.2) WILD-TYPE 787 12

Figure S111.  Get High-res Image Gene #35: 'del_5q11.2' versus Clinical Feature #7: 'GENDER'

'del_5q11.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S112.  Gene #35: '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 1 768 201 6 9 30 17 46
DEL PEAK 7(5Q11.2) MUTATED 1 244 12 5 1 6 1 9
DEL PEAK 7(5Q11.2) WILD-TYPE 0 524 189 1 8 24 16 37

Figure S112.  Get High-res Image Gene #35: 'del_5q11.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_5q11.2' versus 'RACE'

P value = 1e-04 (Fisher's exact test), Q value = 0.0018

Table S113.  Gene #35: 'del_5q11.2' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
DEL PEAK 7(5Q11.2) MUTATED 1 20 68 170
DEL PEAK 7(5Q11.2) WILD-TYPE 0 40 113 574

Figure S113.  Get High-res Image Gene #35: 'del_5q11.2' versus Clinical Feature #11: 'RACE'

'del_5q21.3' versus 'YEARS_TO_BIRTH'

P value = 0.000236 (Wilcoxon-test), Q value = 0.0037

Table S114.  Gene #36: 'del_5q21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1064 58.6 (13.2)
DEL PEAK 8(5Q21.3) MUTATED 270 56.2 (13.4)
DEL PEAK 8(5Q21.3) WILD-TYPE 794 59.5 (13.1)

Figure S114.  Get High-res Image Gene #36: 'del_5q21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_5q21.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00051 (Fisher's exact test), Q value = 0.0066

Table S115.  Gene #36: 'del_5q21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
DEL PEAK 8(5Q21.3) MUTATED 55 184 21 12
DEL PEAK 8(5Q21.3) WILD-TYPE 219 441 116 28

Figure S115.  Get High-res Image Gene #36: '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 = 0.00022

Table S116.  Gene #36: '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 1 768 201 6 9 30 17 46
DEL PEAK 8(5Q21.3) MUTATED 1 243 6 6 2 6 0 8
DEL PEAK 8(5Q21.3) WILD-TYPE 0 525 195 0 7 24 17 38

Figure S116.  Get High-res Image Gene #36: 'del_5q21.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_5q21.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0024 (Wilcoxon-test), Q value = 0.022

Table S117.  Gene #36: 'del_5q21.3' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 913 2.4 (4.7)
DEL PEAK 8(5Q21.3) MUTATED 233 1.7 (3.6)
DEL PEAK 8(5Q21.3) WILD-TYPE 680 2.6 (4.9)

Figure S117.  Get High-res Image Gene #36: 'del_5q21.3' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'del_5q21.3' versus 'RACE'

P value = 5e-05 (Fisher's exact test), Q value = 0.00095

Table S118.  Gene #36: 'del_5q21.3' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
DEL PEAK 8(5Q21.3) MUTATED 0 18 70 164
DEL PEAK 8(5Q21.3) WILD-TYPE 1 42 111 580

Figure S118.  Get High-res Image Gene #36: 'del_5q21.3' versus Clinical Feature #11: 'RACE'

'del_6p25.3' versus 'YEARS_TO_BIRTH'

P value = 0.0502 (Wilcoxon-test), Q value = 0.21

Table S119.  Gene #37: 'del_6p25.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1064 58.6 (13.2)
DEL PEAK 9(6P25.3) MUTATED 201 56.9 (13.0)
DEL PEAK 9(6P25.3) WILD-TYPE 863 59.0 (13.2)

Figure S119.  Get High-res Image Gene #37: 'del_6p25.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_6p25.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00948 (Fisher's exact test), Q value = 0.063

Table S120.  Gene #37: 'del_6p25.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
DEL PEAK 9(6P25.3) MUTATED 45 138 15 6
DEL PEAK 9(6P25.3) WILD-TYPE 229 487 122 34

Figure S120.  Get High-res Image Gene #37: 'del_6p25.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_6p25.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0232 (Fisher's exact test), Q value = 0.12

Table S121.  Gene #37: '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 1 768 201 6 9 30 17 46
DEL PEAK 9(6P25.3) MUTATED 1 161 24 2 0 5 3 8
DEL PEAK 9(6P25.3) WILD-TYPE 0 607 177 4 9 25 14 38

Figure S121.  Get High-res Image Gene #37: 'del_6p25.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_6q15' versus 'YEARS_TO_BIRTH'

P value = 0.0372 (Wilcoxon-test), Q value = 0.18

Table S122.  Gene #38: 'del_6q15' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1064 58.6 (13.2)
DEL PEAK 10(6Q15) MUTATED 355 57.4 (13.2)
DEL PEAK 10(6Q15) WILD-TYPE 709 59.3 (13.2)

Figure S122.  Get High-res Image Gene #38: 'del_6q15' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_6q15' versus 'PATHOLOGY_N_STAGE'

P value = 0.0367 (Fisher's exact test), Q value = 0.17

Table S123.  Gene #38: 'del_6q15' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 506 358 119 77
DEL PEAK 10(6Q15) MUTATED 149 130 49 23
DEL PEAK 10(6Q15) WILD-TYPE 357 228 70 54

Figure S123.  Get High-res Image Gene #38: 'del_6q15' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_6q15' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0228 (Wilcoxon-test), Q value = 0.12

Table S124.  Gene #38: 'del_6q15' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 913 2.4 (4.7)
DEL PEAK 10(6Q15) MUTATED 293 2.5 (4.6)
DEL PEAK 10(6Q15) WILD-TYPE 620 2.3 (4.7)

Figure S124.  Get High-res Image Gene #38: 'del_6q15' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'del_6q27' versus 'YEARS_TO_BIRTH'

P value = 1e-05 (Wilcoxon-test), Q value = 0.00022

Table S125.  Gene #39: 'del_6q27' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1064 58.6 (13.2)
DEL PEAK 11(6Q27) MUTATED 370 56.1 (12.6)
DEL PEAK 11(6Q27) WILD-TYPE 694 60.0 (13.3)

Figure S125.  Get High-res Image Gene #39: 'del_6q27' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_6q27' versus 'RADIATION_THERAPY'

P value = 0.00704 (Fisher's exact test), Q value = 0.048

Table S126.  Gene #39: 'del_6q27' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients NO YES
ALL 437 547
DEL PEAK 11(6Q27) MUTATED 131 209
DEL PEAK 11(6Q27) WILD-TYPE 306 338

Figure S126.  Get High-res Image Gene #39: 'del_6q27' versus Clinical Feature #8: 'RADIATION_THERAPY'

'del_7p22.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.0428 (Fisher's exact test), Q value = 0.19

Table S127.  Gene #40: 'del_7p22.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 506 358 119 77
DEL PEAK 12(7P22.3) MUTATED 77 36 17 5
DEL PEAK 12(7P22.3) WILD-TYPE 429 322 102 72

Figure S127.  Get High-res Image Gene #40: '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 = 0.00022

Table S128.  Gene #40: '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 1 768 201 6 9 30 17 46
DEL PEAK 12(7P22.3) MUTATED 0 121 4 1 2 5 0 5
DEL PEAK 12(7P22.3) WILD-TYPE 1 647 197 5 7 25 17 41

Figure S128.  Get High-res Image Gene #40: 'del_7p22.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_7p22.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00818 (Wilcoxon-test), Q value = 0.055

Table S129.  Gene #40: 'del_7p22.3' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 913 2.4 (4.7)
DEL PEAK 12(7P22.3) MUTATED 111 1.6 (3.5)
DEL PEAK 12(7P22.3) WILD-TYPE 802 2.5 (4.8)

Figure S129.  Get High-res Image Gene #40: '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 = 0.00095

Table S130.  Gene #41: '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 1 768 201 6 9 30 17 46
DEL PEAK 13(7Q36.1) MUTATED 0 165 15 0 2 7 0 10
DEL PEAK 13(7Q36.1) WILD-TYPE 1 603 186 6 7 23 17 36

Figure S130.  Get High-res Image Gene #41: 'del_7q36.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_8p23.2' versus 'Time to Death'

P value = 0.0516 (logrank test), Q value = 0.21

Table S131.  Gene #42: 'del_8p23.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1065 148 0.0 - 282.9 (28.2)
DEL PEAK 14(8P23.2) MUTATED 555 91 0.2 - 282.9 (27.2)
DEL PEAK 14(8P23.2) WILD-TYPE 510 57 0.0 - 281.3 (28.4)

Figure S131.  Get High-res Image Gene #42: 'del_8p23.2' versus Clinical Feature #1: 'Time to Death'

'del_8p23.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00287 (Fisher's exact test), Q value = 0.025

Table S132.  Gene #42: 'del_8p23.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
DEL PEAK 14(8P23.2) MUTATED 156 325 52 23
DEL PEAK 14(8P23.2) WILD-TYPE 118 300 85 17

Figure S132.  Get High-res Image Gene #42: 'del_8p23.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_8p23.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.056 (Fisher's exact test), Q value = 0.23

Table S133.  Gene #42: 'del_8p23.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 506 358 119 77
DEL PEAK 14(8P23.2) MUTATED 246 187 74 37
DEL PEAK 14(8P23.2) WILD-TYPE 260 171 45 40

Figure S133.  Get High-res Image Gene #42: '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 = 0.00022

Table S134.  Gene #42: '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 1 768 201 6 9 30 17 46
DEL PEAK 14(8P23.2) MUTATED 1 446 64 3 3 11 4 25
DEL PEAK 14(8P23.2) WILD-TYPE 0 322 137 3 6 19 13 21

Figure S134.  Get High-res Image Gene #42: 'del_8p23.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_8p23.2' versus 'RACE'

P value = 0.00083 (Fisher's exact test), Q value = 0.0097

Table S135.  Gene #42: 'del_8p23.2' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
DEL PEAK 14(8P23.2) MUTATED 1 41 106 356
DEL PEAK 14(8P23.2) WILD-TYPE 0 19 75 388

Figure S135.  Get High-res Image Gene #42: 'del_8p23.2' versus Clinical Feature #11: 'RACE'

'del_8p11.21' versus 'HISTOLOGICAL_TYPE'

P value = 0.00402 (Fisher's exact test), Q value = 0.032

Table S136.  Gene #43: '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 1 768 201 6 9 30 17 46
DEL PEAK 15(8P11.21) MUTATED 0 166 20 0 2 5 1 6
DEL PEAK 15(8P11.21) WILD-TYPE 1 602 181 6 7 25 16 40

Figure S136.  Get High-res Image Gene #43: 'del_8p11.21' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_9p23' versus 'Time to Death'

P value = 0.0138 (logrank test), Q value = 0.083

Table S137.  Gene #44: 'del_9p23' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1065 148 0.0 - 282.9 (28.2)
DEL PEAK 16(9P23) MUTATED 320 50 0.0 - 165.8 (24.7)
DEL PEAK 16(9P23) WILD-TYPE 745 98 0.0 - 282.9 (30.2)

Figure S137.  Get High-res Image Gene #44: 'del_9p23' versus Clinical Feature #1: 'Time to Death'

'del_9p23' versus 'PATHOLOGIC_STAGE'

P value = 0.00621 (Fisher's exact test), Q value = 0.044

Table S138.  Gene #44: '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 X
ALL 89 83 6 6 352 253 2 155 27 65 20 13
DEL PEAK 16(9P23) MUTATED 21 19 1 1 98 71 1 62 15 19 10 4
DEL PEAK 16(9P23) WILD-TYPE 68 64 5 5 254 182 1 93 12 46 10 9

Figure S138.  Get High-res Image Gene #44: 'del_9p23' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_9p23' versus 'PATHOLOGY_T_STAGE'

P value = 0.00058 (Fisher's exact test), Q value = 0.0074

Table S139.  Gene #44: 'del_9p23' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
DEL PEAK 16(9P23) MUTATED 60 207 38 19
DEL PEAK 16(9P23) WILD-TYPE 214 418 99 21

Figure S139.  Get High-res Image Gene #44: 'del_9p23' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_9p23' versus 'PATHOLOGY_N_STAGE'

P value = 0.00083 (Fisher's exact test), Q value = 0.0097

Table S140.  Gene #44: 'del_9p23' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 506 358 119 77
DEL PEAK 16(9P23) MUTATED 137 103 55 24
DEL PEAK 16(9P23) WILD-TYPE 369 255 64 53

Figure S140.  Get High-res Image Gene #44: '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 S141.  Gene #44: '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 S141.  Get High-res Image Gene #44: 'del_9p23' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_9p23' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S142.  Gene #44: '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 1 768 201 6 9 30 17 46
DEL PEAK 16(9P23) MUTATED 0 269 26 3 5 9 5 8
DEL PEAK 16(9P23) WILD-TYPE 1 499 175 3 4 21 12 38

Figure S142.  Get High-res Image Gene #44: 'del_9p23' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_9p23' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0378 (Wilcoxon-test), Q value = 0.18

Table S143.  Gene #44: 'del_9p23' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 913 2.4 (4.7)
DEL PEAK 16(9P23) MUTATED 263 2.7 (4.9)
DEL PEAK 16(9P23) WILD-TYPE 650 2.3 (4.6)

Figure S143.  Get High-res Image Gene #44: 'del_9p23' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'del_9p21.3' versus 'PATHOLOGIC_STAGE'

P value = 0.0389 (Fisher's exact test), Q value = 0.18

Table S144.  Gene #45: '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 X
ALL 89 83 6 6 352 253 2 155 27 65 20 13
DEL PEAK 17(9P21.3) MUTATED 24 22 3 1 115 78 1 64 15 23 10 6
DEL PEAK 17(9P21.3) WILD-TYPE 65 61 3 5 237 175 1 91 12 42 10 7

Figure S144.  Get High-res Image Gene #45: 'del_9p21.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_9p21.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.003 (Fisher's exact test), Q value = 0.025

Table S145.  Gene #45: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
DEL PEAK 17(9P21.3) MUTATED 73 229 42 20
DEL PEAK 17(9P21.3) WILD-TYPE 201 396 95 20

Figure S145.  Get High-res Image Gene #45: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_9p21.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.00444 (Fisher's exact test), Q value = 0.034

Table S146.  Gene #45: 'del_9p21.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 506 358 119 77
DEL PEAK 17(9P21.3) MUTATED 162 111 57 30
DEL PEAK 17(9P21.3) WILD-TYPE 344 247 62 47

Figure S146.  Get High-res Image Gene #45: '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 = 0.00022

Table S147.  Gene #45: '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 1 768 201 6 9 30 17 46
DEL PEAK 17(9P21.3) MUTATED 1 303 24 4 6 12 5 10
DEL PEAK 17(9P21.3) WILD-TYPE 0 465 177 2 3 18 12 36

Figure S147.  Get High-res Image Gene #45: 'del_9p21.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_9q21.11' versus 'GENDER'

P value = 0.0228 (Fisher's exact test), Q value = 0.12

Table S148.  Gene #46: 'del_9q21.11' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1067 12
DEL PEAK 18(9Q21.11) MUTATED 288 7
DEL PEAK 18(9Q21.11) WILD-TYPE 779 5

Figure S148.  Get High-res Image Gene #46: 'del_9q21.11' versus Clinical Feature #7: 'GENDER'

'del_9q21.11' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S149.  Gene #46: '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 1 768 201 6 9 30 17 46
DEL PEAK 18(9Q21.11) MUTATED 0 246 23 2 4 10 3 7
DEL PEAK 18(9Q21.11) WILD-TYPE 1 522 178 4 5 20 14 39

Figure S149.  Get High-res Image Gene #46: 'del_9q21.11' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_9q34.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.0218 (Fisher's exact test), Q value = 0.12

Table S150.  Gene #47: 'del_9q34.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
DEL PEAK 19(9Q34.2) MUTATED 60 188 32 15
DEL PEAK 19(9Q34.2) WILD-TYPE 214 437 105 25

Figure S150.  Get High-res Image Gene #47: 'del_9q34.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_9q34.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.0664 (Fisher's exact test), Q value = 0.25

Table S151.  Gene #47: 'del_9q34.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 506 358 119 77
DEL PEAK 19(9Q34.2) MUTATED 149 83 41 21
DEL PEAK 19(9Q34.2) WILD-TYPE 357 275 78 56

Figure S151.  Get High-res Image Gene #47: 'del_9q34.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_9q34.2' versus 'GENDER'

P value = 0.00511 (Fisher's exact test), Q value = 0.038

Table S152.  Gene #47: 'del_9q34.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1067 12
DEL PEAK 19(9Q34.2) MUTATED 289 8
DEL PEAK 19(9Q34.2) WILD-TYPE 778 4

Figure S152.  Get High-res Image Gene #47: 'del_9q34.2' versus Clinical Feature #7: 'GENDER'

'del_9q34.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S153.  Gene #47: '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 1 768 201 6 9 30 17 46
DEL PEAK 19(9Q34.2) MUTATED 0 251 22 4 3 7 3 6
DEL PEAK 19(9Q34.2) WILD-TYPE 1 517 179 2 6 23 14 40

Figure S153.  Get High-res Image Gene #47: 'del_9q34.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_9q34.2' versus 'RACE'

P value = 0.0493 (Fisher's exact test), Q value = 0.21

Table S154.  Gene #47: 'del_9q34.2' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
DEL PEAK 19(9Q34.2) MUTATED 0 17 63 187
DEL PEAK 19(9Q34.2) WILD-TYPE 1 43 118 557

Figure S154.  Get High-res Image Gene #47: 'del_9q34.2' versus Clinical Feature #11: 'RACE'

'del_10q23.31' versus 'PATHOLOGY_T_STAGE'

P value = 0.0169 (Fisher's exact test), Q value = 0.1

Table S155.  Gene #48: 'del_10q23.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
DEL PEAK 20(10Q23.31) MUTATED 70 190 38 20
DEL PEAK 20(10Q23.31) WILD-TYPE 204 435 99 20

Figure S155.  Get High-res Image Gene #48: 'del_10q23.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_10q23.31' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S156.  Gene #48: '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 1 768 201 6 9 30 17 46
DEL PEAK 20(10Q23.31) MUTATED 0 246 41 5 7 9 1 10
DEL PEAK 20(10Q23.31) WILD-TYPE 1 522 160 1 2 21 16 36

Figure S156.  Get High-res Image Gene #48: 'del_10q23.31' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_10q23.31' versus 'ETHNICITY'

P value = 0.0486 (Fisher's exact test), Q value = 0.21

Table S157.  Gene #48: 'del_10q23.31' versus Clinical Feature #12: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 39 874
DEL PEAK 20(10Q23.31) MUTATED 6 267
DEL PEAK 20(10Q23.31) WILD-TYPE 33 607

Figure S157.  Get High-res Image Gene #48: 'del_10q23.31' versus Clinical Feature #12: 'ETHNICITY'

'del_10q26.3' versus 'Time to Death'

P value = 0.0661 (logrank test), Q value = 0.25

Table S158.  Gene #49: 'del_10q26.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1065 148 0.0 - 282.9 (28.2)
DEL PEAK 21(10Q26.3) MUTATED 315 51 0.0 - 282.9 (26.7)
DEL PEAK 21(10Q26.3) WILD-TYPE 750 97 0.0 - 281.3 (28.9)

Figure S158.  Get High-res Image Gene #49: 'del_10q26.3' versus Clinical Feature #1: 'Time to Death'

'del_10q26.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.0387 (Fisher's exact test), Q value = 0.18

Table S159.  Gene #49: 'del_10q26.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
DEL PEAK 21(10Q26.3) MUTATED 67 192 39 18
DEL PEAK 21(10Q26.3) WILD-TYPE 207 433 98 22

Figure S159.  Get High-res Image Gene #49: '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 = 0.00022

Table S160.  Gene #49: '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 1 768 201 6 9 30 17 46
DEL PEAK 21(10Q26.3) MUTATED 0 255 31 5 7 9 2 8
DEL PEAK 21(10Q26.3) WILD-TYPE 1 513 170 1 2 21 15 38

Figure S160.  Get High-res Image Gene #49: 'del_10q26.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_10q26.3' versus 'ETHNICITY'

P value = 0.0191 (Fisher's exact test), Q value = 0.11

Table S161.  Gene #49: 'del_10q26.3' versus Clinical Feature #12: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 39 874
DEL PEAK 21(10Q26.3) MUTATED 5 264
DEL PEAK 21(10Q26.3) WILD-TYPE 34 610

Figure S161.  Get High-res Image Gene #49: 'del_10q26.3' versus Clinical Feature #12: 'ETHNICITY'

'del_11p15.5' versus 'PATHOLOGY_T_STAGE'

P value = 0.00653 (Fisher's exact test), Q value = 0.046

Table S162.  Gene #50: 'del_11p15.5' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
DEL PEAK 22(11P15.5) MUTATED 60 200 34 15
DEL PEAK 22(11P15.5) WILD-TYPE 214 425 103 25

Figure S162.  Get High-res Image Gene #50: '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 = 0.00022

Table S163.  Gene #50: '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 1 768 201 6 9 30 17 46
DEL PEAK 22(11P15.5) MUTATED 0 250 30 4 2 12 2 9
DEL PEAK 22(11P15.5) WILD-TYPE 1 518 171 2 7 18 15 37

Figure S163.  Get High-res Image Gene #50: 'del_11p15.5' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_11p15.5' versus 'RACE'

P value = 0.00492 (Fisher's exact test), Q value = 0.037

Table S164.  Gene #50: 'del_11p15.5' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
DEL PEAK 22(11P15.5) MUTATED 0 19 69 190
DEL PEAK 22(11P15.5) WILD-TYPE 1 41 112 554

Figure S164.  Get High-res Image Gene #50: 'del_11p15.5' versus Clinical Feature #11: 'RACE'

'del_11q13.1' versus 'RACE'

P value = 0.00349 (Fisher's exact test), Q value = 0.029

Table S165.  Gene #51: 'del_11q13.1' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
DEL PEAK 23(11Q13.1) MUTATED 0 21 50 143
DEL PEAK 23(11Q13.1) WILD-TYPE 1 39 131 601

Figure S165.  Get High-res Image Gene #51: 'del_11q13.1' versus Clinical Feature #11: 'RACE'

'del_11q23.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.049 (Fisher's exact test), Q value = 0.21

Table S166.  Gene #52: 'del_11q23.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
DEL PEAK 24(11Q23.3) MUTATED 120 327 77 22
DEL PEAK 24(11Q23.3) WILD-TYPE 154 298 60 18

Figure S166.  Get High-res Image Gene #52: '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 = 0.18

Table S167.  Gene #52: 'del_11q23.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1067 12
DEL PEAK 24(11Q23.3) MUTATED 537 10
DEL PEAK 24(11Q23.3) WILD-TYPE 530 2

Figure S167.  Get High-res Image Gene #52: 'del_11q23.3' versus Clinical Feature #7: 'GENDER'

'del_11q23.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0526 (Fisher's exact test), Q value = 0.21

Table S168.  Gene #52: 'del_11q23.3' 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 1 768 201 6 9 30 17 46
DEL PEAK 24(11Q23.3) MUTATED 1 396 102 5 5 17 5 15
DEL PEAK 24(11Q23.3) WILD-TYPE 0 372 99 1 4 13 12 31

Figure S168.  Get High-res Image Gene #52: 'del_11q23.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_11q23.3' versus 'RACE'

P value = 0.0189 (Fisher's exact test), Q value = 0.11

Table S169.  Gene #52: 'del_11q23.3' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
DEL PEAK 24(11Q23.3) MUTATED 1 33 106 353
DEL PEAK 24(11Q23.3) WILD-TYPE 0 27 75 391

Figure S169.  Get High-res Image Gene #52: 'del_11q23.3' versus Clinical Feature #11: 'RACE'

'del_11q25' versus 'YEARS_TO_BIRTH'

P value = 0.0207 (Wilcoxon-test), Q value = 0.11

Table S170.  Gene #53: 'del_11q25' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1064 58.6 (13.2)
DEL PEAK 25(11Q25) MUTATED 507 57.6 (13.5)
DEL PEAK 25(11Q25) WILD-TYPE 557 59.6 (12.9)

Figure S170.  Get High-res Image Gene #53: 'del_11q25' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_11q25' versus 'PATHOLOGIC_STAGE'

P value = 0.0397 (Fisher's exact test), Q value = 0.18

Table S171.  Gene #53: '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 X
ALL 89 83 6 6 352 253 2 155 27 65 20 13
DEL PEAK 25(11Q25) MUTATED 31 33 2 2 162 137 1 86 12 27 10 8
DEL PEAK 25(11Q25) WILD-TYPE 58 50 4 4 190 116 1 69 15 38 10 5

Figure S171.  Get High-res Image Gene #53: 'del_11q25' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_11q25' versus 'PATHOLOGY_T_STAGE'

P value = 0.00359 (Fisher's exact test), Q value = 0.03

Table S172.  Gene #53: 'del_11q25' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
DEL PEAK 25(11Q25) MUTATED 106 317 73 17
DEL PEAK 25(11Q25) WILD-TYPE 168 308 64 23

Figure S172.  Get High-res Image Gene #53: 'del_11q25' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_11q25' versus 'PATHOLOGY_N_STAGE'

P value = 0.0632 (Fisher's exact test), Q value = 0.24

Table S173.  Gene #53: 'del_11q25' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 506 358 119 77
DEL PEAK 25(11Q25) MUTATED 226 182 65 31
DEL PEAK 25(11Q25) WILD-TYPE 280 176 54 46

Figure S173.  Get High-res Image Gene #53: 'del_11q25' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_11q25' versus 'GENDER'

P value = 0.0173 (Fisher's exact test), Q value = 0.1

Table S174.  Gene #53: 'del_11q25' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1067 12
DEL PEAK 25(11Q25) MUTATED 504 10
DEL PEAK 25(11Q25) WILD-TYPE 563 2

Figure S174.  Get High-res Image Gene #53: 'del_11q25' versus Clinical Feature #7: 'GENDER'

'del_11q25' versus 'HISTOLOGICAL_TYPE'

P value = 0.0137 (Fisher's exact test), Q value = 0.083

Table S175.  Gene #53: '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 1 768 201 6 9 30 17 46
DEL PEAK 25(11Q25) MUTATED 1 378 92 5 4 16 5 12
DEL PEAK 25(11Q25) WILD-TYPE 0 390 109 1 5 14 12 34

Figure S175.  Get High-res Image Gene #53: 'del_11q25' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_11q25' versus 'RACE'

P value = 0.00067 (Fisher's exact test), Q value = 0.0082

Table S176.  Gene #53: 'del_11q25' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
DEL PEAK 25(11Q25) MUTATED 1 29 107 324
DEL PEAK 25(11Q25) WILD-TYPE 0 31 74 420

Figure S176.  Get High-res Image Gene #53: 'del_11q25' versus Clinical Feature #11: 'RACE'

'del_12p13.1' versus 'HISTOLOGICAL_TYPE'

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

Table S177.  Gene #54: '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 1 768 201 6 9 30 17 46
DEL PEAK 26(12P13.1) MUTATED 0 156 19 1 3 3 1 3
DEL PEAK 26(12P13.1) WILD-TYPE 1 612 182 5 6 27 16 43

Figure S177.  Get High-res Image Gene #54: 'del_12p13.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_12q23.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.0232 (Fisher's exact test), Q value = 0.12

Table S178.  Gene #55: 'del_12q23.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
DEL PEAK 27(12Q23.1) MUTATED 36 130 22 10
DEL PEAK 27(12Q23.1) WILD-TYPE 238 495 115 30

Figure S178.  Get High-res Image Gene #55: 'del_12q23.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_12q23.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00093 (Fisher's exact test), Q value = 0.011

Table S179.  Gene #55: '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 1 768 201 6 9 30 17 46
DEL PEAK 27(12Q23.1) MUTATED 0 161 21 3 3 5 0 7
DEL PEAK 27(12Q23.1) WILD-TYPE 1 607 180 3 6 25 17 39

Figure S179.  Get High-res Image Gene #55: 'del_12q23.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_12q23.1' versus 'RACE'

P value = 0.00611 (Fisher's exact test), Q value = 0.044

Table S180.  Gene #55: 'del_12q23.1' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
DEL PEAK 27(12Q23.1) MUTATED 0 13 50 124
DEL PEAK 27(12Q23.1) WILD-TYPE 1 47 131 620

Figure S180.  Get High-res Image Gene #55: 'del_12q23.1' versus Clinical Feature #11: 'RACE'

'del_12q24.31' versus 'PATHOLOGY_T_STAGE'

P value = 0.0626 (Fisher's exact test), Q value = 0.24

Table S181.  Gene #56: 'del_12q24.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
DEL PEAK 28(12Q24.31) MUTATED 39 135 25 9
DEL PEAK 28(12Q24.31) WILD-TYPE 235 490 112 31

Figure S181.  Get High-res Image Gene #56: 'del_12q24.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_12q24.31' versus 'HISTOLOGICAL_TYPE'

P value = 0.0355 (Fisher's exact test), Q value = 0.17

Table S182.  Gene #56: '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 1 768 201 6 9 30 17 46
DEL PEAK 28(12Q24.31) MUTATED 0 160 30 3 3 7 0 7
DEL PEAK 28(12Q24.31) WILD-TYPE 1 608 171 3 6 23 17 39

Figure S182.  Get High-res Image Gene #56: 'del_12q24.31' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_12q24.31' versus 'RACE'

P value = 0.0463 (Fisher's exact test), Q value = 0.2

Table S183.  Gene #56: 'del_12q24.31' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
DEL PEAK 28(12Q24.31) MUTATED 0 11 49 135
DEL PEAK 28(12Q24.31) WILD-TYPE 1 49 132 609

Figure S183.  Get High-res Image Gene #56: 'del_12q24.31' versus Clinical Feature #11: 'RACE'

'del_13q14.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S184.  Gene #57: '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 1 768 201 6 9 30 17 46
DEL PEAK 29(13Q14.2) MUTATED 0 391 67 5 5 13 2 14
DEL PEAK 29(13Q14.2) WILD-TYPE 1 377 134 1 4 17 15 32

Figure S184.  Get High-res Image Gene #57: 'del_13q14.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_14q24.1' versus 'Time to Death'

P value = 0.0384 (logrank test), Q value = 0.18

Table S185.  Gene #58: 'del_14q24.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1065 148 0.0 - 282.9 (28.2)
DEL PEAK 30(14Q24.1) MUTATED 353 61 0.0 - 255.7 (28.0)
DEL PEAK 30(14Q24.1) WILD-TYPE 712 87 0.0 - 282.9 (28.3)

Figure S185.  Get High-res Image Gene #58: 'del_14q24.1' versus Clinical Feature #1: 'Time to Death'

'del_14q24.1' versus 'PATHOLOGY_T_STAGE'

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

Table S186.  Gene #58: 'del_14q24.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
DEL PEAK 30(14Q24.1) MUTATED 66 239 38 11
DEL PEAK 30(14Q24.1) WILD-TYPE 208 386 99 29

Figure S186.  Get High-res Image Gene #58: '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 = 0.00022

Table S187.  Gene #58: '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 1 768 201 6 9 30 17 46
DEL PEAK 30(14Q24.1) MUTATED 1 297 35 4 5 4 1 8
DEL PEAK 30(14Q24.1) WILD-TYPE 0 471 166 2 4 26 16 38

Figure S187.  Get High-res Image Gene #58: 'del_14q24.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_14q24.1' versus 'RACE'

P value = 0.00035 (Fisher's exact test), Q value = 0.0051

Table S188.  Gene #58: 'del_14q24.1' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
DEL PEAK 30(14Q24.1) MUTATED 0 18 83 223
DEL PEAK 30(14Q24.1) WILD-TYPE 1 42 98 521

Figure S188.  Get High-res Image Gene #58: 'del_14q24.1' versus Clinical Feature #11: 'RACE'

'del_14q32.12' versus 'Time to Death'

P value = 0.0336 (logrank test), Q value = 0.17

Table S189.  Gene #59: 'del_14q32.12' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1065 148 0.0 - 282.9 (28.2)
DEL PEAK 31(14Q32.12) MUTATED 323 56 0.0 - 255.7 (27.5)
DEL PEAK 31(14Q32.12) WILD-TYPE 742 92 0.0 - 282.9 (28.4)

Figure S189.  Get High-res Image Gene #59: 'del_14q32.12' versus Clinical Feature #1: 'Time to Death'

'del_14q32.12' versus 'PATHOLOGY_T_STAGE'

P value = 0.00171 (Fisher's exact test), Q value = 0.017

Table S190.  Gene #59: 'del_14q32.12' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
DEL PEAK 31(14Q32.12) MUTATED 63 216 33 13
DEL PEAK 31(14Q32.12) WILD-TYPE 211 409 104 27

Figure S190.  Get High-res Image Gene #59: 'del_14q32.12' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_14q32.12' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S191.  Gene #59: 'del_14q32.12' 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 1 768 201 6 9 30 17 46
DEL PEAK 31(14Q32.12) MUTATED 0 267 37 5 5 5 1 6
DEL PEAK 31(14Q32.12) WILD-TYPE 1 501 164 1 4 25 16 40

Figure S191.  Get High-res Image Gene #59: 'del_14q32.12' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_14q32.12' versus 'RACE'

P value = 0.00553 (Fisher's exact test), Q value = 0.041

Table S192.  Gene #59: 'del_14q32.12' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
DEL PEAK 31(14Q32.12) MUTATED 0 17 74 209
DEL PEAK 31(14Q32.12) WILD-TYPE 1 43 107 535

Figure S192.  Get High-res Image Gene #59: 'del_14q32.12' versus Clinical Feature #11: 'RACE'

'del_15q13.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00134 (Fisher's exact test), Q value = 0.014

Table S193.  Gene #60: 'del_15q13.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
DEL PEAK 32(15Q13.1) MUTATED 72 246 43 12
DEL PEAK 32(15Q13.1) WILD-TYPE 202 379 94 28

Figure S193.  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 = 0.0225 (Fisher's exact test), Q value = 0.12

Table S194.  Gene #60: 'del_15q13.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 506 358 119 77
DEL PEAK 32(15Q13.1) MUTATED 192 110 49 20
DEL PEAK 32(15Q13.1) WILD-TYPE 314 248 70 57

Figure S194.  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 = 0.00022

Table S195.  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 1 768 201 6 9 30 17 46
DEL PEAK 32(15Q13.1) MUTATED 1 304 39 4 3 11 1 10
DEL PEAK 32(15Q13.1) WILD-TYPE 0 464 162 2 6 19 16 36

Figure S195.  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 = 0.0417 (Wilcoxon-test), Q value = 0.19

Table S196.  Gene #60: 'del_15q13.1' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 913 2.4 (4.7)
DEL PEAK 32(15Q13.1) MUTATED 318 2.2 (4.8)
DEL PEAK 32(15Q13.1) WILD-TYPE 595 2.5 (4.6)

Figure S196.  Get High-res Image Gene #60: 'del_15q13.1' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'del_15q13.1' versus 'RACE'

P value = 0.0219 (Fisher's exact test), Q value = 0.12

Table S197.  Gene #60: 'del_15q13.1' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
DEL PEAK 32(15Q13.1) MUTATED 0 23 79 242
DEL PEAK 32(15Q13.1) WILD-TYPE 1 37 102 502

Figure S197.  Get High-res Image Gene #60: 'del_15q13.1' versus Clinical Feature #11: 'RACE'

'del_16q24.3' versus 'YEARS_TO_BIRTH'

P value = 0.000283 (Wilcoxon-test), Q value = 0.0043

Table S198.  Gene #61: 'del_16q24.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1064 58.6 (13.2)
DEL PEAK 33(16Q24.3) MUTATED 683 59.8 (13.0)
DEL PEAK 33(16Q24.3) WILD-TYPE 381 56.6 (13.3)

Figure S198.  Get High-res Image Gene #61: 'del_16q24.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_16q24.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S199.  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 1 768 201 6 9 30 17 46
DEL PEAK 33(16Q24.3) MUTATED 0 463 180 3 1 22 3 20
DEL PEAK 33(16Q24.3) WILD-TYPE 1 305 21 3 8 8 14 26

Figure S199.  Get High-res Image Gene #61: 'del_16q24.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_16q24.3' versus 'RACE'

P value = 0.00767 (Fisher's exact test), Q value = 0.052

Table S200.  Gene #61: 'del_16q24.3' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
DEL PEAK 33(16Q24.3) MUTATED 1 34 97 489
DEL PEAK 33(16Q24.3) WILD-TYPE 0 26 84 255

Figure S200.  Get High-res Image Gene #61: 'del_16q24.3' versus Clinical Feature #11: 'RACE'

'del_17p12' versus 'YEARS_TO_BIRTH'

P value = 0.00266 (Wilcoxon-test), Q value = 0.024

Table S201.  Gene #62: 'del_17p12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1064 58.6 (13.2)
DEL PEAK 34(17P12) MUTATED 639 57.7 (13.1)
DEL PEAK 34(17P12) WILD-TYPE 425 60.1 (13.3)

Figure S201.  Get High-res Image Gene #62: 'del_17p12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_17p12' versus 'PATHOLOGY_T_STAGE'

P value = 0.052 (Fisher's exact test), Q value = 0.21

Table S202.  Gene #62: 'del_17p12' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
DEL PEAK 34(17P12) MUTATED 147 395 83 22
DEL PEAK 34(17P12) WILD-TYPE 127 230 54 18

Figure S202.  Get High-res Image Gene #62: 'del_17p12' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_17p12' versus 'HISTOLOGICAL_TYPE'

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

Table S203.  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 1 768 201 6 9 30 17 46
DEL PEAK 34(17P12) MUTATED 0 488 103 5 5 19 6 22
DEL PEAK 34(17P12) WILD-TYPE 1 280 98 1 4 11 11 24

Figure S203.  Get High-res Image Gene #62: 'del_17p12' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_17p12' versus 'RACE'

P value = 0.0461 (Fisher's exact test), Q value = 0.2

Table S204.  Gene #62: 'del_17p12' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
DEL PEAK 34(17P12) MUTATED 1 44 115 432
DEL PEAK 34(17P12) WILD-TYPE 0 16 66 312

Figure S204.  Get High-res Image Gene #62: 'del_17p12' versus Clinical Feature #11: 'RACE'

'del_17q21.31' versus 'YEARS_TO_BIRTH'

P value = 0.000343 (Wilcoxon-test), Q value = 0.0051

Table S205.  Gene #63: 'del_17q21.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1064 58.6 (13.2)
DEL PEAK 35(17Q21.31) MUTATED 363 56.8 (13.4)
DEL PEAK 35(17Q21.31) WILD-TYPE 701 59.6 (13.0)

Figure S205.  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 = 0.00022

Table S206.  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 1 768 201 6 9 30 17 46
DEL PEAK 35(17Q21.31) MUTATED 0 297 39 4 5 11 1 13
DEL PEAK 35(17Q21.31) WILD-TYPE 1 471 162 2 4 19 16 33

Figure S206.  Get High-res Image Gene #63: 'del_17q21.31' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_17q21.31' versus 'RACE'

P value = 0.00013 (Fisher's exact test), Q value = 0.0022

Table S207.  Gene #63: 'del_17q21.31' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
DEL PEAK 35(17Q21.31) MUTATED 0 34 75 233
DEL PEAK 35(17Q21.31) WILD-TYPE 1 26 106 511

Figure S207.  Get High-res Image Gene #63: 'del_17q21.31' versus Clinical Feature #11: 'RACE'

'del_18q23' versus 'PATHOLOGIC_STAGE'

P value = 0.056 (Fisher's exact test), Q value = 0.23

Table S208.  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 X
ALL 89 83 6 6 352 253 2 155 27 65 20 13
DEL PEAK 36(18Q23) MUTATED 23 29 0 0 112 78 0 57 14 29 6 3
DEL PEAK 36(18Q23) WILD-TYPE 66 54 6 6 240 175 2 98 13 36 14 10

Figure S208.  Get High-res Image Gene #64: 'del_18q23' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_18q23' versus 'PATHOLOGY_T_STAGE'

P value = 0.0214 (Fisher's exact test), Q value = 0.12

Table S209.  Gene #64: 'del_18q23' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
DEL PEAK 36(18Q23) MUTATED 75 215 44 20
DEL PEAK 36(18Q23) WILD-TYPE 199 410 93 20

Figure S209.  Get High-res Image Gene #64: 'del_18q23' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_18q23' versus 'HISTOLOGICAL_TYPE'

P value = 0.00012 (Fisher's exact test), Q value = 0.0021

Table S210.  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 1 768 201 6 9 30 17 46
DEL PEAK 36(18Q23) MUTATED 1 274 55 3 5 9 0 7
DEL PEAK 36(18Q23) WILD-TYPE 0 494 146 3 4 21 17 39

Figure S210.  Get High-res Image Gene #64: 'del_18q23' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_19p13.3' versus 'YEARS_TO_BIRTH'

P value = 0.0017 (Wilcoxon-test), Q value = 0.017

Table S211.  Gene #65: 'del_19p13.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1064 58.6 (13.2)
DEL PEAK 37(19P13.3) MUTATED 354 56.9 (13.6)
DEL PEAK 37(19P13.3) WILD-TYPE 710 59.5 (12.9)

Figure S211.  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 = 0.0568 (Fisher's exact test), Q value = 0.23

Table S212.  Gene #65: 'del_19p13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
DEL PEAK 37(19P13.3) MUTATED 81 229 37 15
DEL PEAK 37(19P13.3) WILD-TYPE 193 396 100 25

Figure S212.  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 = 0.00022

Table S213.  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 1 768 201 6 9 30 17 46
DEL PEAK 37(19P13.3) MUTATED 1 301 24 5 4 9 5 12
DEL PEAK 37(19P13.3) WILD-TYPE 0 467 177 1 5 21 12 34

Figure S213.  Get High-res Image Gene #65: 'del_19p13.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_19p13.3' versus 'RACE'

P value = 0.00042 (Fisher's exact test), Q value = 0.0057

Table S214.  Gene #65: 'del_19p13.3' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
DEL PEAK 37(19P13.3) MUTATED 0 28 78 223
DEL PEAK 37(19P13.3) WILD-TYPE 1 32 103 521

Figure S214.  Get High-res Image Gene #65: 'del_19p13.3' versus Clinical Feature #11: 'RACE'

'del_19q13.32' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S215.  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 1 768 201 6 9 30 17 46
DEL PEAK 38(19Q13.32) MUTATED 0 185 10 3 1 6 4 6
DEL PEAK 38(19Q13.32) WILD-TYPE 1 583 191 3 8 24 13 40

Figure S215.  Get High-res Image Gene #66: 'del_19q13.32' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_20p13' versus 'YEARS_TO_BIRTH'

P value = 0.0453 (Wilcoxon-test), Q value = 0.2

Table S216.  Gene #67: 'del_20p13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1064 58.6 (13.2)
DEL PEAK 39(20P13) MUTATED 157 56.7 (12.2)
DEL PEAK 39(20P13) WILD-TYPE 907 59.0 (13.3)

Figure S216.  Get High-res Image Gene #67: 'del_20p13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_20p13' versus 'HISTOLOGICAL_TYPE'

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

Table S217.  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 1 768 201 6 9 30 17 46
DEL PEAK 39(20P13) MUTATED 1 137 11 2 0 2 1 6
DEL PEAK 39(20P13) WILD-TYPE 0 631 190 4 9 28 16 40

Figure S217.  Get High-res Image Gene #67: 'del_20p13' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_21q11.2' versus 'PATHOLOGIC_STAGE'

P value = 0.0105 (Fisher's exact test), Q value = 0.068

Table S218.  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 X
ALL 89 83 6 6 352 253 2 155 27 65 20 13
DEL PEAK 40(21Q11.2) MUTATED 11 12 0 1 64 54 1 41 11 9 7 3
DEL PEAK 40(21Q11.2) WILD-TYPE 78 71 6 5 288 199 1 114 16 56 13 10

Figure S218.  Get High-res Image Gene #68: 'del_21q11.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_21q11.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.0132 (Fisher's exact test), Q value = 0.081

Table S219.  Gene #68: 'del_21q11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
DEL PEAK 40(21Q11.2) MUTATED 40 137 25 13
DEL PEAK 40(21Q11.2) WILD-TYPE 234 488 112 27

Figure S219.  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 = 0.0113 (Fisher's exact test), Q value = 0.072

Table S220.  Gene #68: 'del_21q11.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 506 358 119 77
DEL PEAK 40(21Q11.2) MUTATED 88 74 37 13
DEL PEAK 40(21Q11.2) WILD-TYPE 418 284 82 64

Figure S220.  Get High-res Image Gene #68: 'del_21q11.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_21q11.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.00249 (Fisher's exact test), Q value = 0.022

Table S221.  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 1 768 201 6 9 30 17 46
DEL PEAK 40(21Q11.2) MUTATED 0 173 22 2 2 9 2 5
DEL PEAK 40(21Q11.2) WILD-TYPE 1 595 179 4 7 21 15 41

Figure S221.  Get High-res Image Gene #68: 'del_21q11.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_22q11.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00099 (Fisher's exact test), Q value = 0.011

Table S222.  Gene #69: 'del_22q11.1' 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 1 768 201 6 9 30 17 46
DEL PEAK 41(22Q11.1) MUTATED 1 346 80 2 2 18 2 11
DEL PEAK 41(22Q11.1) WILD-TYPE 0 422 121 4 7 12 15 35

Figure S222.  Get High-res Image Gene #69: 'del_22q11.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_22q13.32' versus 'RADIATION_THERAPY'

P value = 0.0243 (Fisher's exact test), Q value = 0.12

Table S223.  Gene #70: 'del_22q13.32' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients NO YES
ALL 437 547
DEL PEAK 42(22Q13.32) MUTATED 183 269
DEL PEAK 42(22Q13.32) WILD-TYPE 254 278

Figure S223.  Get High-res Image Gene #70: 'del_22q13.32' versus Clinical Feature #8: 'RADIATION_THERAPY'

'del_22q13.32' versus 'HISTOLOGICAL_TYPE'

P value = 6e-04 (Fisher's exact test), Q value = 0.0075

Table S224.  Gene #70: '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 1 768 201 6 9 30 17 46
DEL PEAK 42(22Q13.32) MUTATED 1 361 90 3 3 19 1 13
DEL PEAK 42(22Q13.32) WILD-TYPE 0 407 111 3 6 11 16 33

Figure S224.  Get High-res Image Gene #70: '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/22531239/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BRCA-TP/22506573/BRCA-TP.merged_data.txt

  • Number of patients = 1079

  • Number of significantly focal cnvs = 70

  • 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)