Correlation between copy number variation genes (focal events) and selected clinical features
Breast Invasive Carcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1Z899TD
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1Z899TD
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 68 focal events and 10 clinical features across 957 patients, 39 significant findings detected with Q value < 0.25.

  • amp_3p25.1 cnv correlated to 'PATHOLOGY.M.STAGE'.

  • amp_3q26.32 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • amp_4q13.3 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • amp_6p23 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • amp_6q21 cnv correlated to 'PATHOLOGY.T.STAGE' and 'HISTOLOGICAL.TYPE'.

  • amp_8q24.21 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • amp_10p15.1 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • amp_11p13 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • amp_12p13.33 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • amp_15q26.3 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • amp_17q23.1 cnv correlated to 'PATHOLOGY.T.STAGE' and 'GENDER'.

  • amp_19q12 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • amp_20q13.2 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • del_1p36.13 cnv correlated to 'PATHOLOGY.T.STAGE'.

  • del_1p21.2 cnv correlated to 'PATHOLOGY.T.STAGE'.

  • del_2q37.3 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • del_3p14.3 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • del_4p16.3 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • del_4q34.3 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • del_5q11.2 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • del_5q21.3 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • del_6q27 cnv correlated to 'AGE'.

  • del_7p22.3 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • del_8p23.2 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • del_9p23 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • del_9p21.3 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • del_9q34.3 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • del_10q26.3 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • del_13q14.2 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • del_14q24.1 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • del_15q13.1 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • del_16q24.3 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • del_17q21.31 cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

  • del_19p13.3 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • del_19q13.32 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • del_20p13 cnv correlated to 'HISTOLOGICAL.TYPE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 68 focal events and 10 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 39 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		NUMBER
OF
LYMPH
NODES
nCNV (%) nWild-Type logrank test t-test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test t-test
amp 6q21 179 (19%) 778 0.0132
(1.00) 		0.373
(1.00) 		0.0734
(1.00) 		7.77e-05
(0.0506) 		0.159
(1.00) 		0.817
(1.00) 		0.698
(1.00) 		2e-05
(0.0131) 		0.414
(1.00) 		0.143
(1.00)
amp 17q23 1 388 (41%) 569 0.104
(1.00) 		0.693
(1.00) 		0.00986
(1.00) 		0.000156
(0.101) 		0.473
(1.00) 		0.00122
(0.763) 		0.000112
(0.0724) 		0.000539
(0.343) 		1
(1.00) 		0.144
(1.00)
del 17q21 31 332 (35%) 625 0.556
(1.00) 		0.000185
(0.119) 		0.163
(1.00) 		0.104
(1.00) 		0.118
(1.00) 		0.164
(1.00) 		0.508
(1.00) 		1.32e-05
(0.00874) 		0.603
(1.00) 		0.411
(1.00)
amp 3p25 1 186 (19%) 771 0.0144
(1.00) 		0.184
(1.00) 		0.0177
(1.00) 		0.0004
(0.256) 		0.0269
(1.00) 		0.000155
(0.0999) 		0.697
(1.00) 		0.00113
(0.711) 		0.591
(1.00) 		0.718
(1.00)
amp 3q26 32 305 (32%) 652 0.787
(1.00) 		0.401
(1.00) 		0.298
(1.00) 		0.00301
(1.00) 		0.359
(1.00) 		0.00357
(1.00) 		0.734
(1.00) 		2.09e-12
(1.41e-09) 		0.0674
(1.00) 		0.223
(1.00)
amp 4q13 3 149 (16%) 808 0.0574
(1.00) 		0.391
(1.00) 		0.896
(1.00) 		0.127
(1.00) 		0.673
(1.00) 		0.507
(1.00) 		0.66
(1.00) 		1.73e-05
(0.0114) 		0.328
(1.00) 		0.709
(1.00)
amp 6p23 258 (27%) 699 0.592
(1.00) 		0.179
(1.00) 		0.43
(1.00) 		0.00989
(1.00) 		0.232
(1.00) 		0.545
(1.00) 		0.303
(1.00) 		1.71e-05
(0.0113) 		0.11
(1.00) 		0.275
(1.00)
amp 8q24 21 608 (64%) 349 0.0538
(1.00) 		0.0515
(1.00) 		0.147
(1.00) 		0.0136
(1.00) 		0.399
(1.00) 		0.00973
(1.00) 		0.342
(1.00) 		1.73e-13
(1.17e-10) 		0.0767
(1.00) 		0.344
(1.00)
amp 10p15 1 271 (28%) 686 0.137
(1.00) 		0.764
(1.00) 		0.216
(1.00) 		0.382
(1.00) 		0.617
(1.00) 		0.638
(1.00) 		0.298
(1.00) 		1.33e-08
(8.91e-06) 		0.115
(1.00) 		0.88
(1.00)
amp 11p13 199 (21%) 758 0.453
(1.00) 		0.499
(1.00) 		0.804
(1.00) 		0.505
(1.00) 		0.982
(1.00) 		0.421
(1.00) 		0.442
(1.00) 		1.37e-05
(0.00903) 		0.19
(1.00) 		0.401
(1.00)
amp 12p13 33 251 (26%) 706 0.944
(1.00) 		0.238
(1.00) 		0.469
(1.00) 		0.00358
(1.00) 		0.761
(1.00) 		0.396
(1.00) 		0.469
(1.00) 		6.23e-05
(0.0407) 		0.146
(1.00) 		0.922
(1.00)
amp 15q26 3 175 (18%) 782 0.207
(1.00) 		0.00659
(1.00) 		0.454
(1.00) 		0.548
(1.00) 		0.956
(1.00) 		0.0222
(1.00) 		0.0916
(1.00) 		3.08e-05
(0.0202) 		0.409
(1.00) 		0.872
(1.00)
amp 19q12 247 (26%) 710 0.194
(1.00) 		0.29
(1.00) 		0.148
(1.00) 		0.755
(1.00) 		0.0726
(1.00) 		0.0352
(1.00) 		0.292
(1.00) 		6.32e-05
(0.0412) 		0.225
(1.00) 		0.135
(1.00)
amp 20q13 2 487 (51%) 470 0.498
(1.00) 		0.244
(1.00) 		0.145
(1.00) 		0.018
(1.00) 		0.00971
(1.00) 		0.0468
(1.00) 		0.108
(1.00) 		1.82e-13
(1.23e-10) 		0.000661
(0.419) 		1
(1.00)
del 1p36 13 400 (42%) 557 0.115
(1.00) 		0.197
(1.00) 		0.00206
(1.00) 		2.16e-06
(0.00144) 		0.000511
(0.325) 		0.229
(1.00) 		0.104
(1.00) 		0.0125
(1.00) 		0.222
(1.00) 		0.0112
(1.00)
del 1p21 2 319 (33%) 638 0.0475
(1.00) 		0.095
(1.00) 		0.0113
(1.00) 		3.13e-05
(0.0205) 		0.00659
(1.00) 		0.704
(1.00) 		1
(1.00) 		0.271
(1.00) 		0.652
(1.00) 		0.0342
(1.00)
del 2q37 3 287 (30%) 670 0.692
(1.00) 		0.652
(1.00) 		0.461
(1.00) 		0.00655
(1.00) 		0.323
(1.00) 		0.576
(1.00) 		0.732
(1.00) 		8.37e-05
(0.0543) 		0.0749
(1.00) 		0.601
(1.00)
del 3p14 3 300 (31%) 657 0.0178
(1.00) 		0.000614
(0.39) 		0.647
(1.00) 		0.000894
(0.564) 		0.453
(1.00) 		0.45
(1.00) 		1
(1.00) 		7.6e-06
(0.00504) 		0.146
(1.00) 		0.897
(1.00)
del 4p16 3 300 (31%) 657 0.733
(1.00) 		0.197
(1.00) 		0.164
(1.00) 		0.000393
(0.252) 		0.575
(1.00) 		0.566
(1.00) 		0.733
(1.00) 		3.93e-06
(0.00262) 		0.193
(1.00) 		0.882
(1.00)
del 4q34 3 310 (32%) 647 0.0489
(1.00) 		0.917
(1.00) 		0.328
(1.00) 		0.0045
(1.00) 		0.752
(1.00) 		0.0164
(1.00) 		0.514
(1.00) 		6.48e-07
(0.000434) 		0.65
(1.00) 		0.781
(1.00)
del 5q11 2 250 (26%) 707 0.228
(1.00) 		0.00107
(0.672) 		0.312
(1.00) 		0.00643
(1.00) 		0.631
(1.00) 		0.226
(1.00) 		0.0715
(1.00) 		5.61e-11
(3.79e-08) 		0.375
(1.00) 		0.581
(1.00)
del 5q21 3 240 (25%) 717 0.308
(1.00) 		0.0105
(1.00) 		0.197
(1.00) 		0.002
(1.00) 		0.163
(1.00) 		0.367
(1.00) 		0.0743
(1.00) 		1.34e-14
(9.09e-12) 		0.0863
(1.00) 		0.0285
(1.00)
del 6q27 329 (34%) 628 0.087
(1.00) 		7.67e-06
(0.00508) 		0.358
(1.00) 		0.747
(1.00) 		0.0255
(1.00) 		0.106
(1.00) 		0.508
(1.00) 		0.376
(1.00) 		0.0167
(1.00) 		0.443
(1.00)
del 7p22 3 124 (13%) 833 0.942
(1.00) 		0.163
(1.00) 		0.529
(1.00) 		0.261
(1.00) 		0.0552
(1.00) 		0.308
(1.00) 		0.377
(1.00) 		0.000235
(0.151) 		0.46
(1.00) 		0.0589
(1.00)
del 8p23 2 499 (52%) 458 0.0786
(1.00) 		0.698
(1.00) 		0.96
(1.00) 		0.0112
(1.00) 		0.13
(1.00) 		0.181
(1.00) 		0.346
(1.00) 		2.29e-09
(1.54e-06) 		0.723
(1.00) 		0.72
(1.00)
del 9p23 299 (31%) 658 0.00109
(0.688) 		0.538
(1.00) 		0.00477
(1.00) 		0.000489
(0.312) 		0.00337
(1.00) 		0.0328
(1.00) 		0.301
(1.00) 		1.71e-05
(0.0112) 		0.878
(1.00) 		0.32
(1.00)
del 9p21 3 333 (35%) 624 0.0347
(1.00) 		0.782
(1.00) 		0.0111
(1.00) 		0.000693
(0.439) 		0.00548
(1.00) 		0.113
(1.00) 		0.105
(1.00) 		3.76e-09
(2.52e-06) 		0.655
(1.00) 		0.592
(1.00)
del 9q34 3 262 (27%) 695 0.893
(1.00) 		0.78
(1.00) 		0.0435
(1.00) 		0.00324
(1.00) 		0.0502
(1.00) 		0.979
(1.00) 		0.03
(1.00) 		2.2e-06
(0.00147) 		0.204
(1.00) 		0.319
(1.00)
del 10q26 3 286 (30%) 671 0.0424
(1.00) 		0.882
(1.00) 		0.18
(1.00) 		0.0906
(1.00) 		0.151
(1.00) 		0.3
(1.00) 		0.732
(1.00) 		0.000303
(0.195) 		0.439
(1.00) 		0.176
(1.00)
del 13q14 2 444 (46%) 513 0.0945
(1.00) 		0.399
(1.00) 		0.592
(1.00) 		0.0348
(1.00) 		0.422
(1.00) 		0.899
(1.00) 		0.527
(1.00) 		8.52e-05
(0.0552) 		0.177
(1.00) 		0.0988
(1.00)
del 14q24 1 312 (33%) 645 0.0601
(1.00) 		0.177
(1.00) 		0.449
(1.00) 		0.00238
(1.00) 		0.329
(1.00) 		0.976
(1.00) 		0.736
(1.00) 		2.6e-08
(1.74e-05) 		0.0339
(1.00) 		0.484
(1.00)
del 15q13 1 333 (35%) 624 0.173
(1.00) 		0.132
(1.00) 		0.183
(1.00) 		0.00385
(1.00) 		0.0826
(1.00) 		0.147
(1.00) 		0.746
(1.00) 		7.28e-06
(0.00483) 		0.037
(1.00) 		0.805
(1.00)
del 16q24 3 609 (64%) 348 0.132
(1.00) 		0.00152
(0.95) 		0.196
(1.00) 		0.214
(1.00) 		0.485
(1.00) 		0.178
(1.00) 		1
(1.00) 		1.92e-15
(1.31e-12) 		0.417
(1.00) 		0.778
(1.00)
del 19p13 3 318 (33%) 639 0.181
(1.00) 		0.00772
(1.00) 		0.743
(1.00) 		0.171
(1.00) 		0.904
(1.00) 		0.432
(1.00) 		0.178
(1.00) 		1.2e-10
(8.08e-08) 		0.598
(1.00) 		0.0427
(1.00)
del 19q13 32 188 (20%) 769 0.778
(1.00) 		0.569
(1.00) 		0.405
(1.00) 		0.408
(1.00) 		0.0728
(1.00) 		0.435
(1.00) 		0.697
(1.00) 		9.2e-07
(0.000614) 		0.00561
(1.00) 		0.369
(1.00)
del 20p13 145 (15%) 812 0.0917
(1.00) 		0.0667
(1.00) 		0.517
(1.00) 		0.612
(1.00) 		0.795
(1.00) 		0.314
(1.00) 		0.654
(1.00) 		7.99e-05
(0.0519) 		0.0744
(1.00) 		0.269
(1.00)
amp 1p22 3 210 (22%) 747 0.911
(1.00) 		0.379
(1.00) 		0.401
(1.00) 		0.027
(1.00) 		0.0251
(1.00) 		0.447
(1.00) 		1
(1.00) 		0.157
(1.00) 		0.932
(1.00) 		0.0488
(1.00)
amp 1q21 3 690 (72%) 267 0.772
(1.00) 		0.907
(1.00) 		0.313
(1.00) 		0.0157
(1.00) 		0.794
(1.00) 		0.476
(1.00) 		0.478
(1.00) 		0.163
(1.00) 		0.429
(1.00) 		0.877
(1.00)
amp 1q44 688 (72%) 269 0.0552
(1.00) 		0.563
(1.00) 		0.224
(1.00) 		0.0121
(1.00) 		0.533
(1.00) 		0.631
(1.00) 		1
(1.00) 		0.0178
(1.00) 		0.693
(1.00) 		0.972
(1.00)
amp 5p15 33 350 (37%) 607 0.126
(1.00) 		0.183
(1.00) 		0.65
(1.00) 		0.349
(1.00) 		0.00771
(1.00) 		0.0429
(1.00) 		1
(1.00) 		0.165
(1.00) 		0.0771
(1.00) 		0.981
(1.00)
amp 8p11 23 365 (38%) 592 0.0436
(1.00) 		0.184
(1.00) 		0.0748
(1.00) 		0.661
(1.00) 		0.195
(1.00) 		0.0248
(1.00) 		0.333
(1.00) 		0.637
(1.00) 		0.715
(1.00) 		0.0267
(1.00)
amp 8p11 21 371 (39%) 586 0.741
(1.00) 		0.108
(1.00) 		0.721
(1.00) 		0.916
(1.00) 		0.835
(1.00) 		0.276
(1.00) 		0.332
(1.00) 		0.0366
(1.00) 		0.191
(1.00) 		0.798
(1.00)
amp 10q22 3 137 (14%) 820 0.0876
(1.00) 		0.487
(1.00) 		0.119
(1.00) 		0.057
(1.00) 		0.404
(1.00) 		0.025
(1.00) 		1
(1.00) 		0.0164
(1.00) 		0.0848
(1.00) 		0.269
(1.00)
amp 11q13 3 356 (37%) 601 0.337
(1.00) 		0.281
(1.00) 		0.741
(1.00) 		0.139
(1.00) 		0.722
(1.00) 		0.404
(1.00) 		0.187
(1.00) 		0.114
(1.00) 		1
(1.00) 		0.987
(1.00)
amp 11q14 1 236 (25%) 721 0.348
(1.00) 		0.286
(1.00) 		0.524
(1.00) 		0.145
(1.00) 		0.212
(1.00) 		0.0381
(1.00) 		0.273
(1.00) 		0.00298
(1.00) 		0.622
(1.00) 		0.581
(1.00)
amp 12q15 249 (26%) 708 0.132
(1.00) 		0.523
(1.00) 		0.139
(1.00) 		0.0124
(1.00) 		0.00868
(1.00) 		0.154
(1.00) 		0.00428
(1.00) 		0.0293
(1.00) 		1
(1.00) 		0.225
(1.00)
amp 13q34 163 (17%) 794 0.588
(1.00) 		0.0406
(1.00) 		0.188
(1.00) 		0.00991
(1.00) 		0.336
(1.00) 		0.0207
(1.00) 		0.227
(1.00) 		0.023
(1.00) 		1
(1.00) 		0.122
(1.00)
amp 14q21 1 195 (20%) 762 0.493
(1.00) 		0.075
(1.00) 		0.0898
(1.00) 		0.0126
(1.00) 		0.0126
(1.00) 		0.285
(1.00) 		0.697
(1.00) 		0.19
(1.00) 		0.66
(1.00) 		0.0734
(1.00)
amp 17q12 304 (32%) 653 0.134
(1.00) 		0.865
(1.00) 		0.416
(1.00) 		0.0602
(1.00) 		0.152
(1.00) 		0.146
(1.00) 		0.00229
(1.00) 		0.00536
(1.00) 		0.493
(1.00) 		0.944
(1.00)
amp 19p13 12 198 (21%) 759 0.746
(1.00) 		0.898
(1.00) 		0.676
(1.00) 		0.289
(1.00) 		0.277
(1.00) 		0.168
(1.00) 		0.0368
(1.00) 		0.00877
(1.00) 		0.00656
(1.00) 		0.0898
(1.00)
amp 19q13 42 247 (26%) 710 0.509
(1.00) 		0.139
(1.00) 		0.965
(1.00) 		0.434
(1.00) 		0.76
(1.00) 		0.00247
(1.00) 		0.137
(1.00) 		0.0359
(1.00) 		0.225
(1.00) 		0.618
(1.00)
del 6p25 3 184 (19%) 773 0.824
(1.00) 		0.01
(1.00) 		0.461
(1.00) 		0.0359
(1.00) 		0.283
(1.00) 		0.276
(1.00) 		0.415
(1.00) 		0.123
(1.00) 		0.0583
(1.00) 		0.291
(1.00)
del 6q15 316 (33%) 641 0.711
(1.00) 		0.0224
(1.00) 		0.108
(1.00) 		0.365
(1.00) 		0.0345
(1.00) 		0.483
(1.00) 		1
(1.00) 		0.463
(1.00) 		0.175
(1.00) 		0.253
(1.00)
del 7q36 1 184 (19%) 773 0.0792
(1.00) 		0.937
(1.00) 		0.647
(1.00) 		0.25
(1.00) 		0.231
(1.00) 		0.364
(1.00) 		1
(1.00) 		0.00986
(1.00) 		0.928
(1.00) 		0.924
(1.00)
del 8p11 21 183 (19%) 774 0.0429
(1.00) 		0.17
(1.00) 		0.647
(1.00) 		0.157
(1.00) 		0.244
(1.00) 		0.332
(1.00) 		0.223
(1.00) 		0.0109
(1.00) 		0.857
(1.00) 		0.37
(1.00)
del 9q21 11 271 (28%) 686 0.402
(1.00) 		0.861
(1.00) 		0.178
(1.00) 		0.0492
(1.00) 		0.174
(1.00) 		0.374
(1.00) 		0.157
(1.00) 		0.000436
(0.279) 		0.115
(1.00) 		0.375
(1.00)
del 10q23 31 284 (30%) 673 0.597
(1.00) 		0.344
(1.00) 		0.247
(1.00) 		0.0266
(1.00) 		0.235
(1.00) 		0.324
(1.00) 		0.297
(1.00) 		0.00154
(0.964) 		0.14
(1.00) 		0.291
(1.00)
del 11p15 5 276 (29%) 681 0.137
(1.00) 		0.622
(1.00) 		0.254
(1.00) 		0.0159
(1.00) 		0.441
(1.00) 		0.39
(1.00) 		0.486
(1.00) 		0.0042
(1.00) 		0.435
(1.00) 		0.192
(1.00)
del 11q13 1 210 (22%) 747 0.42
(1.00) 		0.952
(1.00) 		0.257
(1.00) 		0.128
(1.00) 		0.21
(1.00) 		0.657
(1.00) 		0.464
(1.00) 		0.737
(1.00) 		0.798
(1.00) 		0.954
(1.00)
del 11q23 2 485 (51%) 472 0.621
(1.00) 		0.171
(1.00) 		0.152
(1.00) 		0.019
(1.00) 		0.0604
(1.00) 		0.378
(1.00) 		0.108
(1.00) 		0.222
(1.00) 		0.944
(1.00) 		0.891
(1.00)
del 11q25 449 (47%) 508 0.362
(1.00) 		0.016
(1.00) 		0.1
(1.00) 		0.00473
(1.00) 		0.0985
(1.00) 		0.635
(1.00) 		0.0524
(1.00) 		0.0412
(1.00) 		0.67
(1.00) 		0.825
(1.00)
del 12p13 2 164 (17%) 793 0.746
(1.00) 		0.536
(1.00) 		0.138
(1.00) 		0.188
(1.00) 		0.903
(1.00) 		0.0175
(1.00) 		0.388
(1.00) 		0.0182
(1.00) 		0.778
(1.00) 		0.64
(1.00)
del 12q24 31 180 (19%) 777 0.198
(1.00) 		0.283
(1.00) 		0.689
(1.00) 		0.0402
(1.00) 		0.698
(1.00) 		0.636
(1.00) 		0.223
(1.00) 		0.0804
(1.00) 		0.856
(1.00) 		0.249
(1.00)
del 17p12 580 (61%) 377 0.578
(1.00) 		0.000804
(0.508) 		0.483
(1.00) 		0.0509
(1.00) 		0.675
(1.00) 		0.55
(1.00) 		0.331
(1.00) 		0.00299
(1.00) 		0.425
(1.00) 		0.989
(1.00)
del 18q23 311 (32%) 646 0.0328
(1.00) 		0.389
(1.00) 		0.116
(1.00) 		0.0648
(1.00) 		0.0902
(1.00) 		0.669
(1.00) 		0.736
(1.00) 		0.00941
(1.00) 		0.0816
(1.00) 		0.373
(1.00)
del 21q11 2 189 (20%) 768 0.478
(1.00) 		0.441
(1.00) 		0.0185
(1.00) 		0.0688
(1.00) 		0.0285
(1.00) 		0.454
(1.00) 		0.696
(1.00) 		0.0136
(1.00) 		0.328
(1.00) 		0.226
(1.00)
del 22q11 1 407 (43%) 550 0.525
(1.00) 		0.861
(1.00) 		0.591
(1.00) 		0.553
(1.00) 		0.377
(1.00) 		0.306
(1.00) 		0.53
(1.00) 		0.0294
(1.00) 		0.00156
(0.974) 		0.494
(1.00)
del 22q13 31 438 (46%) 519 0.425
(1.00) 		0.465
(1.00) 		0.799
(1.00) 		0.359
(1.00) 		0.573
(1.00) 		0.49
(1.00) 		0.526
(1.00) 		0.0327
(1.00) 		0.0017
(1.00) 		0.682
(1.00)
'amp_3p25.1' versus 'PATHOLOGY.M.STAGE'

P value = 0.000155 (Fisher's exact test), Q value = 0.1

Table S1.  Gene #4: 'amp_3p25.1' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients CM0 (I+) M0 M1 MX
ALL 2 825 15 115
AMP PEAK 4(3P25.1) MUTATED 0 172 6 8
AMP PEAK 4(3P25.1) WILD-TYPE 2 653 9 107

Figure S1.  Get High-res Image Gene #4: 'amp_3p25.1' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'amp_3q26.32' versus 'HISTOLOGICAL.TYPE'

P value = 2.09e-12 (Chi-square test), Q value = 1.4e-09

Table S2.  Gene #5: 'amp_3q26.32' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
AMP PEAK 5(3Q26.32) MUTATED 1 268 12 4 5 1 13
AMP PEAK 5(3Q26.32) WILD-TYPE 0 442 142 1 23 13 31

Figure S2.  Get High-res Image Gene #5: 'amp_3q26.32' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'amp_4q13.3' versus 'HISTOLOGICAL.TYPE'

P value = 1.73e-05 (Chi-square test), Q value = 0.011

Table S3.  Gene #6: 'amp_4q13.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
AMP PEAK 6(4Q13.3) MUTATED 0 134 4 2 1 1 7
AMP PEAK 6(4Q13.3) WILD-TYPE 1 576 150 3 27 13 37

Figure S3.  Get High-res Image Gene #6: 'amp_4q13.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'amp_6p23' versus 'HISTOLOGICAL.TYPE'

P value = 1.71e-05 (Chi-square test), Q value = 0.011

Table S4.  Gene #8: 'amp_6p23' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
AMP PEAK 8(6P23) MUTATED 0 219 17 3 4 2 12
AMP PEAK 8(6P23) WILD-TYPE 1 491 137 2 24 12 32

Figure S4.  Get High-res Image Gene #8: 'amp_6p23' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'amp_6q21' versus 'PATHOLOGY.T.STAGE'

P value = 7.77e-05 (Fisher's exact test), Q value = 0.051

Table S5.  Gene #9: 'amp_6q21' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 248 556 114 36
AMP PEAK 9(6Q21) MUTATED 27 130 19 3
AMP PEAK 9(6Q21) WILD-TYPE 221 426 95 33

Figure S5.  Get High-res Image Gene #9: 'amp_6q21' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'amp_6q21' versus 'HISTOLOGICAL.TYPE'

P value = 2e-05 (Chi-square test), Q value = 0.013

Table S6.  Gene #9: 'amp_6q21' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
AMP PEAK 9(6Q21) MUTATED 1 152 13 3 1 0 9
AMP PEAK 9(6Q21) WILD-TYPE 0 558 141 2 27 14 35

Figure S6.  Get High-res Image Gene #9: 'amp_6q21' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'amp_8q24.21' versus 'HISTOLOGICAL.TYPE'

P value = 1.73e-13 (Chi-square test), Q value = 1.2e-10

Table S7.  Gene #12: 'amp_8q24.21' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
AMP PEAK 12(8Q24.21) MUTATED 1 498 56 5 15 5 27
AMP PEAK 12(8Q24.21) WILD-TYPE 0 212 98 0 13 9 17

Figure S7.  Get High-res Image Gene #12: 'amp_8q24.21' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'amp_10p15.1' versus 'HISTOLOGICAL.TYPE'

P value = 1.33e-08 (Chi-square test), Q value = 8.9e-06

Table S8.  Gene #13: 'amp_10p15.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
AMP PEAK 13(10P15.1) MUTATED 1 234 17 4 5 0 9
AMP PEAK 13(10P15.1) WILD-TYPE 0 476 137 1 23 14 35

Figure S8.  Get High-res Image Gene #13: 'amp_10p15.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'amp_11p13' versus 'HISTOLOGICAL.TYPE'

P value = 1.37e-05 (Chi-square test), Q value = 0.009

Table S9.  Gene #15: 'amp_11p13' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
AMP PEAK 15(11P13) MUTATED 1 170 13 3 1 2 9
AMP PEAK 15(11P13) WILD-TYPE 0 540 141 2 27 12 35

Figure S9.  Get High-res Image Gene #15: 'amp_11p13' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'amp_12p13.33' versus 'HISTOLOGICAL.TYPE'

P value = 6.23e-05 (Chi-square test), Q value = 0.041

Table S10.  Gene #18: 'amp_12p13.33' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
AMP PEAK 18(12P13.33) MUTATED 1 207 22 4 8 1 8
AMP PEAK 18(12P13.33) WILD-TYPE 0 503 132 1 20 13 36

Figure S10.  Get High-res Image Gene #18: 'amp_12p13.33' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'amp_15q26.3' versus 'HISTOLOGICAL.TYPE'

P value = 3.08e-05 (Chi-square test), Q value = 0.02

Table S11.  Gene #22: 'amp_15q26.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
AMP PEAK 22(15Q26.3) MUTATED 0 154 6 2 4 3 5
AMP PEAK 22(15Q26.3) WILD-TYPE 1 556 148 3 24 11 39

Figure S11.  Get High-res Image Gene #22: 'amp_15q26.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'amp_17q23.1' versus 'PATHOLOGY.T.STAGE'

P value = 0.000156 (Fisher's exact test), Q value = 0.1

Table S12.  Gene #24: 'amp_17q23.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 248 556 114 36
AMP PEAK 24(17Q23.1) MUTATED 72 252 45 17
AMP PEAK 24(17Q23.1) WILD-TYPE 176 304 69 19

Figure S12.  Get High-res Image Gene #24: 'amp_17q23.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'amp_17q23.1' versus 'GENDER'

P value = 0.000112 (Fisher's exact test), Q value = 0.072

Table S13.  Gene #24: 'amp_17q23.1' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 947 10
AMP PEAK 24(17Q23.1) MUTATED 378 10
AMP PEAK 24(17Q23.1) WILD-TYPE 569 0

Figure S13.  Get High-res Image Gene #24: 'amp_17q23.1' versus Clinical Feature #7: 'GENDER'

'amp_19q12' versus 'HISTOLOGICAL.TYPE'

P value = 6.32e-05 (Chi-square test), Q value = 0.041

Table S14.  Gene #26: 'amp_19q12' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
AMP PEAK 26(19Q12) MUTATED 0 202 23 5 5 2 10
AMP PEAK 26(19Q12) WILD-TYPE 1 508 131 0 23 12 34

Figure S14.  Get High-res Image Gene #26: 'amp_19q12' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'amp_20q13.2' versus 'HISTOLOGICAL.TYPE'

P value = 1.82e-13 (Chi-square test), Q value = 1.2e-10

Table S15.  Gene #28: 'amp_20q13.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
AMP PEAK 28(20Q13.2) MUTATED 1 415 40 1 10 1 19
AMP PEAK 28(20Q13.2) WILD-TYPE 0 295 114 4 18 13 25

Figure S15.  Get High-res Image Gene #28: 'amp_20q13.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_1p36.13' versus 'PATHOLOGY.T.STAGE'

P value = 2.16e-06 (Fisher's exact test), Q value = 0.0014

Table S16.  Gene #29: 'del_1p36.13' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 248 556 114 36
DEL PEAK 1(1P36.13) MUTATED 74 257 44 24
DEL PEAK 1(1P36.13) WILD-TYPE 174 299 70 12

Figure S16.  Get High-res Image Gene #29: 'del_1p36.13' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_1p21.2' versus 'PATHOLOGY.T.STAGE'

P value = 3.13e-05 (Fisher's exact test), Q value = 0.021

Table S17.  Gene #30: 'del_1p21.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 248 556 114 36
DEL PEAK 2(1P21.2) MUTATED 57 205 36 20
DEL PEAK 2(1P21.2) WILD-TYPE 191 351 78 16

Figure S17.  Get High-res Image Gene #30: 'del_1p21.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_2q37.3' versus 'HISTOLOGICAL.TYPE'

P value = 8.37e-05 (Chi-square test), Q value = 0.054

Table S18.  Gene #31: 'del_2q37.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
DEL PEAK 3(2Q37.3) MUTATED 0 241 20 2 9 3 11
DEL PEAK 3(2Q37.3) WILD-TYPE 1 469 134 3 19 11 33

Figure S18.  Get High-res Image Gene #31: 'del_2q37.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_3p14.3' versus 'HISTOLOGICAL.TYPE'

P value = 7.6e-06 (Chi-square test), Q value = 0.005

Table S19.  Gene #32: 'del_3p14.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
DEL PEAK 4(3P14.3) MUTATED 0 257 27 2 4 0 10
DEL PEAK 4(3P14.3) WILD-TYPE 1 453 127 3 24 14 34

Figure S19.  Get High-res Image Gene #32: 'del_3p14.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_4p16.3' versus 'HISTOLOGICAL.TYPE'

P value = 3.93e-06 (Chi-square test), Q value = 0.0026

Table S20.  Gene #33: 'del_4p16.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
DEL PEAK 5(4P16.3) MUTATED 1 252 24 3 6 0 14
DEL PEAK 5(4P16.3) WILD-TYPE 0 458 130 2 22 14 30

Figure S20.  Get High-res Image Gene #33: 'del_4p16.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_4q34.3' versus 'HISTOLOGICAL.TYPE'

P value = 6.48e-07 (Chi-square test), Q value = 0.00043

Table S21.  Gene #34: 'del_4q34.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
DEL PEAK 6(4Q34.3) MUTATED 1 263 26 3 4 0 12
DEL PEAK 6(4Q34.3) WILD-TYPE 0 447 128 2 24 14 32

Figure S21.  Get High-res Image Gene #34: 'del_4q34.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_5q11.2' versus 'HISTOLOGICAL.TYPE'

P value = 5.61e-11 (Chi-square test), Q value = 3.8e-08

Table S22.  Gene #35: 'del_5q11.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
DEL PEAK 7(5Q11.2) MUTATED 1 221 8 4 4 1 10
DEL PEAK 7(5Q11.2) WILD-TYPE 0 489 146 1 24 13 34

Figure S22.  Get High-res Image Gene #35: 'del_5q11.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_5q21.3' versus 'HISTOLOGICAL.TYPE'

P value = 1.34e-14 (Chi-square test), Q value = 9.1e-12

Table S23.  Gene #36: 'del_5q21.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
DEL PEAK 8(5Q21.3) MUTATED 1 216 4 5 4 0 9
DEL PEAK 8(5Q21.3) WILD-TYPE 0 494 150 0 24 14 35

Figure S23.  Get High-res Image Gene #36: 'del_5q21.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_6q27' versus 'AGE'

P value = 7.67e-06 (t-test), Q value = 0.0051

Table S24.  Gene #39: 'del_6q27' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 954 58.6 (13.2)
DEL PEAK 11(6Q27) MUTATED 328 56.0 (12.7)
DEL PEAK 11(6Q27) WILD-TYPE 626 60.0 (13.3)

Figure S24.  Get High-res Image Gene #39: 'del_6q27' versus Clinical Feature #2: 'AGE'

'del_7p22.3' versus 'HISTOLOGICAL.TYPE'

P value = 0.000235 (Chi-square test), Q value = 0.15

Table S25.  Gene #40: 'del_7p22.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
DEL PEAK 12(7P22.3) MUTATED 0 113 3 0 2 0 6
DEL PEAK 12(7P22.3) WILD-TYPE 1 597 151 5 26 14 38

Figure S25.  Get High-res Image Gene #40: 'del_7p22.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_8p23.2' versus 'HISTOLOGICAL.TYPE'

P value = 2.29e-09 (Chi-square test), Q value = 1.5e-06

Table S26.  Gene #42: 'del_8p23.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
DEL PEAK 14(8P23.2) MUTATED 1 411 45 3 10 3 25
DEL PEAK 14(8P23.2) WILD-TYPE 0 299 109 2 18 11 19

Figure S26.  Get High-res Image Gene #42: 'del_8p23.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_9p23' versus 'HISTOLOGICAL.TYPE'

P value = 1.71e-05 (Chi-square test), Q value = 0.011

Table S27.  Gene #44: 'del_9p23' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
DEL PEAK 16(9P23) MUTATED 0 253 20 2 8 5 11
DEL PEAK 16(9P23) WILD-TYPE 1 457 134 3 20 9 33

Figure S27.  Get High-res Image Gene #44: 'del_9p23' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_9p21.3' versus 'HISTOLOGICAL.TYPE'

P value = 3.76e-09 (Chi-square test), Q value = 2.5e-06

Table S28.  Gene #45: 'del_9p21.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
DEL PEAK 17(9P21.3) MUTATED 1 283 19 4 10 5 11
DEL PEAK 17(9P21.3) WILD-TYPE 0 427 135 1 18 9 33

Figure S28.  Get High-res Image Gene #45: 'del_9p21.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_9q34.3' versus 'HISTOLOGICAL.TYPE'

P value = 2.2e-06 (Chi-square test), Q value = 0.0015

Table S29.  Gene #47: 'del_9q34.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
DEL PEAK 19(9Q34.3) MUTATED 0 223 17 4 6 3 8
DEL PEAK 19(9Q34.3) WILD-TYPE 1 487 137 1 22 11 36

Figure S29.  Get High-res Image Gene #47: 'del_9q34.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_10q26.3' versus 'HISTOLOGICAL.TYPE'

P value = 0.000303 (Chi-square test), Q value = 0.19

Table S30.  Gene #49: 'del_10q26.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
DEL PEAK 21(10Q26.3) MUTATED 0 234 27 4 6 1 13
DEL PEAK 21(10Q26.3) WILD-TYPE 1 476 127 1 22 13 31

Figure S30.  Get High-res Image Gene #49: 'del_10q26.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_13q14.2' versus 'HISTOLOGICAL.TYPE'

P value = 8.52e-05 (Chi-square test), Q value = 0.055

Table S31.  Gene #56: 'del_13q14.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
DEL PEAK 28(13Q14.2) MUTATED 0 360 51 4 10 2 16
DEL PEAK 28(13Q14.2) WILD-TYPE 1 350 103 1 18 12 28

Figure S31.  Get High-res Image Gene #56: 'del_13q14.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_14q24.1' versus 'HISTOLOGICAL.TYPE'

P value = 2.6e-08 (Chi-square test), Q value = 1.7e-05

Table S32.  Gene #57: 'del_14q24.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
DEL PEAK 29(14Q24.1) MUTATED 1 267 25 4 3 1 10
DEL PEAK 29(14Q24.1) WILD-TYPE 0 443 129 1 25 13 34

Figure S32.  Get High-res Image Gene #57: 'del_14q24.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_15q13.1' versus 'HISTOLOGICAL.TYPE'

P value = 7.28e-06 (Chi-square test), Q value = 0.0048

Table S33.  Gene #58: 'del_15q13.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
DEL PEAK 30(15Q13.1) MUTATED 1 276 30 4 8 1 12
DEL PEAK 30(15Q13.1) WILD-TYPE 0 434 124 1 20 13 32

Figure S33.  Get High-res Image Gene #58: 'del_15q13.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_16q24.3' versus 'HISTOLOGICAL.TYPE'

P value = 1.92e-15 (Chi-square test), Q value = 1.3e-12

Table S34.  Gene #59: 'del_16q24.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
DEL PEAK 31(16Q24.3) MUTATED 0 434 137 2 19 1 16
DEL PEAK 31(16Q24.3) WILD-TYPE 1 276 17 3 9 13 28

Figure S34.  Get High-res Image Gene #59: 'del_16q24.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_17q21.31' versus 'AGE'

P value = 0.000185 (t-test), Q value = 0.12

Table S35.  Gene #61: 'del_17q21.31' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 954 58.6 (13.2)
DEL PEAK 33(17Q21.31) MUTATED 331 56.4 (13.4)
DEL PEAK 33(17Q21.31) WILD-TYPE 623 59.8 (12.9)

Figure S35.  Get High-res Image Gene #61: 'del_17q21.31' versus Clinical Feature #2: 'AGE'

'del_17q21.31' versus 'HISTOLOGICAL.TYPE'

P value = 1.32e-05 (Chi-square test), Q value = 0.0087

Table S36.  Gene #61: 'del_17q21.31' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
DEL PEAK 33(17Q21.31) MUTATED 0 272 28 4 10 1 16
DEL PEAK 33(17Q21.31) WILD-TYPE 1 438 126 1 18 13 28

Figure S36.  Get High-res Image Gene #61: 'del_17q21.31' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_19p13.3' versus 'HISTOLOGICAL.TYPE'

P value = 1.2e-10 (Chi-square test), Q value = 8.1e-08

Table S37.  Gene #63: 'del_19p13.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
DEL PEAK 35(19P13.3) MUTATED 1 274 14 4 7 4 13
DEL PEAK 35(19P13.3) WILD-TYPE 0 436 140 1 21 10 31

Figure S37.  Get High-res Image Gene #63: 'del_19p13.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_19q13.32' versus 'HISTOLOGICAL.TYPE'

P value = 9.2e-07 (Chi-square test), Q value = 0.00061

Table S38.  Gene #64: 'del_19q13.32' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
DEL PEAK 36(19Q13.32) MUTATED 0 166 6 3 4 3 5
DEL PEAK 36(19Q13.32) WILD-TYPE 1 544 148 2 24 11 39

Figure S38.  Get High-res Image Gene #64: 'del_19q13.32' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_20p13' versus 'HISTOLOGICAL.TYPE'

P value = 7.99e-05 (Chi-square test), Q value = 0.052

Table S39.  Gene #65: 'del_20p13' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
DEL PEAK 37(20P13) MUTATED 1 127 8 2 2 0 5
DEL PEAK 37(20P13) WILD-TYPE 0 583 146 3 26 14 39

Figure S39.  Get High-res Image Gene #65: 'del_20p13' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

  • Clinical data file = BRCA-TP.merged_data.txt

  • Number of patients = 957

  • Number of significantly focal cnvs = 68

  • Number of selected clinical features = 10

  • 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

Student's t-test analysis

For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' function in R

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

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] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[4] 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)
[5] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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