Correlation between copy number variation genes (focal events) and selected clinical features
Breast Invasive Carcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C14F1PBX
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/C14F1PBX
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 971 patients, 43 significant findings detected with Q value < 0.25.

  • amp_3p25.1 cnv correlated to 'PATHOLOGY.T.STAGE' and '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_3p21.31 cnv correlated to 'PATHOLOGY.T.STAGE' and 'HISTOLOGICAL.TYPE'.

  • del_4p16.3 cnv correlated to 'PATHOLOGY.T.STAGE' and 'HISTOLOGICAL.TYPE'.

  • del_4q35.2 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • del_5q11.2 cnv correlated to 'AGE' and '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_9q21.11 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • del_9q34.2 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 '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, 43 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 3p25 1 188 (19%) 783 0.00569
(1.00) 		0.184
(1.00) 		0.0256
(1.00) 		0.000376
(0.24) 		0.0296
(1.00) 		9.02e-05
(0.0583) 		0.697
(1.00) 		0.00107
(0.669) 		0.656
(1.00) 		0.845
(1.00)
amp 6q21 181 (19%) 790 0.019
(1.00) 		0.271
(1.00) 		0.0575
(1.00) 		7.95e-05
(0.0516) 		0.112
(1.00) 		0.75
(1.00) 		0.698
(1.00) 		1.22e-05
(0.00811) 		0.32
(1.00) 		0.126
(1.00)
amp 17q23 1 393 (40%) 578 0.105
(1.00) 		0.79
(1.00) 		0.0082
(1.00) 		0.000133
(0.086) 		0.402
(1.00) 		0.00128
(0.799) 		0.00011
(0.0711) 		0.000395
(0.251) 		1
(1.00) 		0.122
(1.00)
del 3p21 31 316 (33%) 655 0.0106
(1.00) 		0.000638
(0.402) 		0.243
(1.00) 		2.42e-05
(0.0159) 		0.419
(1.00) 		0.512
(1.00) 		0.736
(1.00) 		1.41e-05
(0.00931) 		0.228
(1.00) 		0.876
(1.00)
del 4p16 3 306 (32%) 665 0.682
(1.00) 		0.157
(1.00) 		0.138
(1.00) 		0.000228
(0.146) 		0.667
(1.00) 		0.47
(1.00) 		0.733
(1.00) 		2.04e-06
(0.00135) 		0.287
(1.00) 		0.885
(1.00)
del 5q11 2 255 (26%) 716 0.142
(1.00) 		0.000276
(0.177) 		0.251
(1.00) 		0.0041
(1.00) 		0.544
(1.00) 		0.158
(1.00) 		0.0712
(1.00) 		1.59e-11
(1.07e-08) 		0.522
(1.00) 		0.513
(1.00)
amp 3q26 32 310 (32%) 661 0.782
(1.00) 		0.422
(1.00) 		0.267
(1.00) 		0.00214
(1.00) 		0.343
(1.00) 		0.00178
(1.00) 		0.734
(1.00) 		1.13e-12
(7.61e-10) 		0.0579
(1.00) 		0.227
(1.00)
amp 4q13 3 153 (16%) 818 0.0168
(1.00) 		0.376
(1.00) 		0.888
(1.00) 		0.134
(1.00) 		0.678
(1.00) 		0.572
(1.00) 		0.662
(1.00) 		2.29e-05
(0.015) 		0.498
(1.00) 		0.791
(1.00)
amp 6p23 263 (27%) 708 0.707
(1.00) 		0.12
(1.00) 		0.418
(1.00) 		0.0069
(1.00) 		0.243
(1.00) 		0.561
(1.00) 		0.303
(1.00) 		2.91e-05
(0.019) 		0.0953
(1.00) 		0.277
(1.00)
amp 8q24 21 618 (64%) 353 0.042
(1.00) 		0.0452
(1.00) 		0.165
(1.00) 		0.012
(1.00) 		0.395
(1.00) 		0.0104
(1.00) 		0.343
(1.00) 		3.68e-14
(2.49e-11) 		0.0917
(1.00) 		0.41
(1.00)
amp 10p15 1 277 (29%) 694 0.126
(1.00) 		0.514
(1.00) 		0.218
(1.00) 		0.379
(1.00) 		0.588
(1.00) 		0.627
(1.00) 		0.297
(1.00) 		3.48e-09
(2.33e-06) 		0.138
(1.00) 		0.748
(1.00)
amp 11p13 205 (21%) 766 0.669
(1.00) 		0.316
(1.00) 		0.792
(1.00) 		0.395
(1.00) 		0.983
(1.00) 		0.37
(1.00) 		0.448
(1.00) 		1.36e-05
(0.00897) 		0.262
(1.00) 		0.4
(1.00)
amp 12p13 33 258 (27%) 713 0.829
(1.00) 		0.188
(1.00) 		0.426
(1.00) 		0.00207
(1.00) 		0.73
(1.00) 		0.378
(1.00) 		0.306
(1.00) 		4.96e-05
(0.0323) 		0.263
(1.00) 		0.944
(1.00)
amp 15q26 3 179 (18%) 792 0.269
(1.00) 		0.00837
(1.00) 		0.425
(1.00) 		0.492
(1.00) 		0.964
(1.00) 		0.014
(1.00) 		0.0939
(1.00) 		1.4e-05
(0.00922) 		0.467
(1.00) 		0.776
(1.00)
amp 19q12 254 (26%) 717 0.254
(1.00) 		0.22
(1.00) 		0.0754
(1.00) 		0.618
(1.00) 		0.0389
(1.00) 		0.0368
(1.00) 		0.298
(1.00) 		4.62e-05
(0.0301) 		0.421
(1.00) 		0.0827
(1.00)
amp 20q13 2 494 (51%) 477 0.404
(1.00) 		0.28
(1.00) 		0.145
(1.00) 		0.0134
(1.00) 		0.0103
(1.00) 		0.0386
(1.00) 		0.108
(1.00) 		1.44e-13
(9.77e-11) 		0.000534
(0.338) 		0.996
(1.00)
del 1p36 13 406 (42%) 565 0.115
(1.00) 		0.249
(1.00) 		0.00175
(1.00) 		1.52e-06
(0.00101) 		0.000457
(0.291) 		0.218
(1.00) 		0.104
(1.00) 		0.0083
(1.00) 		0.152
(1.00) 		0.0147
(1.00)
del 1p21 2 322 (33%) 649 0.0392
(1.00) 		0.103
(1.00) 		0.0139
(1.00) 		3.15e-05
(0.0205) 		0.00519
(1.00) 		0.651
(1.00) 		1
(1.00) 		0.231
(1.00) 		0.708
(1.00) 		0.035
(1.00)
del 2q37 3 292 (30%) 679 0.675
(1.00) 		0.684
(1.00) 		0.449
(1.00) 		0.00529
(1.00) 		0.324
(1.00) 		0.581
(1.00) 		0.732
(1.00) 		8.37e-05
(0.0542) 		0.123
(1.00) 		0.631
(1.00)
del 4q35 2 313 (32%) 658 0.0313
(1.00) 		0.731
(1.00) 		0.337
(1.00) 		0.00169
(1.00) 		0.663
(1.00) 		0.00216
(1.00) 		0.181
(1.00) 		1.03e-07
(6.88e-05) 		0.546
(1.00) 		0.821
(1.00)
del 5q21 3 246 (25%) 725 0.277
(1.00) 		0.00302
(1.00) 		0.129
(1.00) 		0.000966
(0.607) 		0.12
(1.00) 		0.264
(1.00) 		0.0735
(1.00) 		3.11e-15
(2.11e-12) 		0.168
(1.00) 		0.0191
(1.00)
del 6q27 336 (35%) 635 0.143
(1.00) 		5.74e-06
(0.0038) 		0.389
(1.00) 		0.678
(1.00) 		0.028
(1.00) 		0.15
(1.00) 		0.508
(1.00) 		0.42
(1.00) 		0.0374
(1.00) 		0.452
(1.00)
del 7p22 3 128 (13%) 843 0.961
(1.00) 		0.193
(1.00) 		0.619
(1.00) 		0.19
(1.00) 		0.118
(1.00) 		0.218
(1.00) 		0.376
(1.00) 		0.000198
(0.127) 		0.754
(1.00) 		0.0852
(1.00)
del 8p23 2 508 (52%) 463 0.0895
(1.00) 		0.722
(1.00) 		0.963
(1.00) 		0.00802
(1.00) 		0.146
(1.00) 		0.219
(1.00) 		0.347
(1.00) 		3.39e-09
(2.28e-06) 		0.724
(1.00) 		0.748
(1.00)
del 9p23 300 (31%) 671 0.000427
(0.271) 		0.371
(1.00) 		0.00391
(1.00) 		0.000625
(0.395) 		0.00224
(1.00) 		0.0267
(1.00) 		0.299
(1.00) 		1.42e-05
(0.00937) 		0.702
(1.00) 		0.254
(1.00)
del 9p21 3 335 (35%) 636 0.0343
(1.00) 		0.654
(1.00) 		0.0097
(1.00) 		0.000781
(0.492) 		0.00393
(1.00) 		0.0944
(1.00) 		0.102
(1.00) 		2.2e-09
(1.48e-06) 		0.603
(1.00) 		0.496
(1.00)
del 9q21 11 274 (28%) 697 0.379
(1.00) 		0.985
(1.00) 		0.168
(1.00) 		0.0477
(1.00) 		0.155
(1.00) 		0.356
(1.00) 		0.156
(1.00) 		0.00024
(0.154) 		0.0839
(1.00) 		0.45
(1.00)
del 9q34 2 275 (28%) 696 0.964
(1.00) 		0.9
(1.00) 		0.0579
(1.00) 		0.0124
(1.00) 		0.0412
(1.00) 		0.845
(1.00) 		0.0353
(1.00) 		5.79e-07
(0.000387) 		0.117
(1.00) 		0.268
(1.00)
del 10q26 3 293 (30%) 678 0.0443
(1.00) 		0.787
(1.00) 		0.249
(1.00) 		0.0999
(1.00) 		0.178
(1.00) 		0.306
(1.00) 		0.732
(1.00) 		0.000162
(0.104) 		0.488
(1.00) 		0.185
(1.00)
del 13q14 2 455 (47%) 516 0.0959
(1.00) 		0.462
(1.00) 		0.65
(1.00) 		0.0277
(1.00) 		0.479
(1.00) 		0.9
(1.00) 		0.529
(1.00) 		7.32e-05
(0.0476) 		0.288
(1.00) 		0.113
(1.00)
del 14q24 1 318 (33%) 653 0.0356
(1.00) 		0.13
(1.00) 		0.393
(1.00) 		0.00143
(0.889) 		0.269
(1.00) 		0.976
(1.00) 		0.737
(1.00) 		1.54e-08
(1.03e-05) 		0.06
(1.00) 		0.407
(1.00)
del 15q13 1 339 (35%) 632 0.246
(1.00) 		0.104
(1.00) 		0.143
(1.00) 		0.0025
(1.00) 		0.0675
(1.00) 		0.106
(1.00) 		0.746
(1.00) 		2.26e-06
(0.0015) 		0.0643
(1.00) 		0.91
(1.00)
del 16q24 3 617 (64%) 354 0.179
(1.00) 		0.00114
(0.713) 		0.166
(1.00) 		0.197
(1.00) 		0.425
(1.00) 		0.178
(1.00) 		1
(1.00) 		5.23e-16
(3.56e-13) 		0.463
(1.00) 		0.905
(1.00)
del 17q21 31 341 (35%) 630 0.552
(1.00) 		0.000532
(0.337) 		0.182
(1.00) 		0.093
(1.00) 		0.115
(1.00) 		0.209
(1.00) 		0.508
(1.00) 		1.68e-05
(0.011) 		0.768
(1.00) 		0.383
(1.00)
del 19p13 3 325 (33%) 646 0.129
(1.00) 		0.0115
(1.00) 		0.687
(1.00) 		0.112
(1.00) 		0.819
(1.00) 		0.357
(1.00) 		0.178
(1.00) 		4.25e-10
(2.86e-07) 		0.822
(1.00) 		0.0612
(1.00)
del 19q13 32 190 (20%) 781 0.705
(1.00) 		0.64
(1.00) 		0.454
(1.00) 		0.416
(1.00) 		0.0797
(1.00) 		0.5
(1.00) 		0.697
(1.00) 		8.37e-07
(0.000559) 		0.00973
(1.00) 		0.483
(1.00)
del 20p13 147 (15%) 824 0.118
(1.00) 		0.0526
(1.00) 		0.512
(1.00) 		0.595
(1.00) 		0.827
(1.00) 		0.383
(1.00) 		0.654
(1.00) 		0.00012
(0.0771) 		0.114
(1.00) 		0.283
(1.00)
amp 1p22 3 218 (22%) 753 0.852
(1.00) 		0.311
(1.00) 		0.353
(1.00) 		0.0233
(1.00) 		0.0121
(1.00) 		0.639
(1.00) 		1
(1.00) 		0.203
(1.00) 		0.735
(1.00) 		0.0609
(1.00)
amp 1q21 3 704 (73%) 267 0.694
(1.00) 		0.924
(1.00) 		0.299
(1.00) 		0.0139
(1.00) 		0.744
(1.00) 		0.492
(1.00) 		0.475
(1.00) 		0.149
(1.00) 		0.527
(1.00) 		0.903
(1.00)
amp 1q44 701 (72%) 270 0.0713
(1.00) 		0.545
(1.00) 		0.21
(1.00) 		0.0101
(1.00) 		0.458
(1.00) 		0.579
(1.00) 		1
(1.00) 		0.0128
(1.00) 		0.752
(1.00) 		0.965
(1.00)
amp 5p15 33 357 (37%) 614 0.121
(1.00) 		0.237
(1.00) 		0.601
(1.00) 		0.291
(1.00) 		0.00755
(1.00) 		0.0221
(1.00) 		1
(1.00) 		0.129
(1.00) 		0.143
(1.00) 		0.992
(1.00)
amp 8p11 23 369 (38%) 602 0.0257
(1.00) 		0.124
(1.00) 		0.0705
(1.00) 		0.642
(1.00) 		0.152
(1.00) 		0.0165
(1.00) 		0.334
(1.00) 		0.667
(1.00) 		0.716
(1.00) 		0.024
(1.00)
amp 8p11 21 377 (39%) 594 0.573
(1.00) 		0.105
(1.00) 		0.757
(1.00) 		0.877
(1.00) 		0.867
(1.00) 		0.176
(1.00) 		0.332
(1.00) 		0.0387
(1.00) 		0.219
(1.00) 		0.785
(1.00)
amp 10q22 3 138 (14%) 833 0.106
(1.00) 		0.493
(1.00) 		0.143
(1.00) 		0.104
(1.00) 		0.345
(1.00) 		0.0521
(1.00) 		1
(1.00) 		0.0135
(1.00) 		0.0848
(1.00) 		0.254
(1.00)
amp 11q13 3 363 (37%) 608 0.244
(1.00) 		0.252
(1.00) 		0.693
(1.00) 		0.0984
(1.00) 		0.743
(1.00) 		0.381
(1.00) 		0.188
(1.00) 		0.157
(1.00) 		0.942
(1.00) 		1
(1.00)
amp 11q14 1 240 (25%) 731 0.217
(1.00) 		0.32
(1.00) 		0.384
(1.00) 		0.12
(1.00) 		0.148
(1.00) 		0.0511
(1.00) 		0.274
(1.00) 		0.00609
(1.00) 		0.683
(1.00) 		0.558
(1.00)
amp 12q15 254 (26%) 717 0.0711
(1.00) 		0.447
(1.00) 		0.148
(1.00) 		0.00972
(1.00) 		0.00977
(1.00) 		0.163
(1.00) 		0.00443
(1.00) 		0.0292
(1.00) 		0.81
(1.00) 		0.224
(1.00)
amp 13q34 166 (17%) 805 0.531
(1.00) 		0.0363
(1.00) 		0.159
(1.00) 		0.00774
(1.00) 		0.317
(1.00) 		0.0335
(1.00) 		0.226
(1.00) 		0.0273
(1.00) 		0.852
(1.00) 		0.0999
(1.00)
amp 14q21 1 200 (21%) 771 0.315
(1.00) 		0.106
(1.00) 		0.115
(1.00) 		0.0135
(1.00) 		0.0146
(1.00) 		0.306
(1.00) 		0.697
(1.00) 		0.114
(1.00) 		0.601
(1.00) 		0.075
(1.00)
amp 17q12 308 (32%) 663 0.119
(1.00) 		0.75
(1.00) 		0.394
(1.00) 		0.0537
(1.00) 		0.188
(1.00) 		0.159
(1.00) 		0.00227
(1.00) 		0.00439
(1.00) 		0.404
(1.00) 		0.962
(1.00)
amp 19p13 12 203 (21%) 768 0.668
(1.00) 		0.758
(1.00) 		0.591
(1.00) 		0.234
(1.00) 		0.227
(1.00) 		0.168
(1.00) 		0.0383
(1.00) 		0.0112
(1.00) 		0.0187
(1.00) 		0.0602
(1.00)
amp 19q13 42 251 (26%) 720 0.474
(1.00) 		0.225
(1.00) 		0.962
(1.00) 		0.383
(1.00) 		0.763
(1.00) 		0.00135
(0.841) 		0.137
(1.00) 		0.0212
(1.00) 		0.197
(1.00) 		0.534
(1.00)
del 6p25 3 186 (19%) 785 0.705
(1.00) 		0.011
(1.00) 		0.427
(1.00) 		0.0346
(1.00) 		0.239
(1.00) 		0.241
(1.00) 		0.414
(1.00) 		0.0982
(1.00) 		0.059
(1.00) 		0.267
(1.00)
del 6q15 321 (33%) 650 0.532
(1.00) 		0.0253
(1.00) 		0.113
(1.00) 		0.372
(1.00) 		0.0341
(1.00) 		0.484
(1.00) 		1
(1.00) 		0.481
(1.00) 		0.153
(1.00) 		0.236
(1.00)
del 7q36 1 189 (19%) 782 0.113
(1.00) 		0.999
(1.00) 		0.687
(1.00) 		0.181
(1.00) 		0.288
(1.00) 		0.359
(1.00) 		1
(1.00) 		0.00595
(1.00) 		0.929
(1.00) 		0.957
(1.00)
del 8p11 21 188 (19%) 783 0.0605
(1.00) 		0.123
(1.00) 		0.66
(1.00) 		0.154
(1.00) 		0.248
(1.00) 		0.418
(1.00) 		0.224
(1.00) 		0.0105
(1.00) 		0.789
(1.00) 		0.452
(1.00)
del 10q23 31 291 (30%) 680 0.459
(1.00) 		0.24
(1.00) 		0.299
(1.00) 		0.0271
(1.00) 		0.256
(1.00) 		0.31
(1.00) 		0.297
(1.00) 		0.000868
(0.546) 		0.191
(1.00) 		0.305
(1.00)
del 11p15 5 284 (29%) 687 0.121
(1.00) 		0.561
(1.00) 		0.207
(1.00) 		0.00763
(1.00) 		0.495
(1.00) 		0.359
(1.00) 		0.49
(1.00) 		0.00283
(1.00) 		0.587
(1.00) 		0.204
(1.00)
del 11q13 1 214 (22%) 757 0.346
(1.00) 		0.82
(1.00) 		0.236
(1.00) 		0.147
(1.00) 		0.15
(1.00) 		0.729
(1.00) 		0.466
(1.00) 		0.765
(1.00) 		0.734
(1.00) 		0.892
(1.00)
del 11q23 2 496 (51%) 475 0.758
(1.00) 		0.18
(1.00) 		0.115
(1.00) 		0.0209
(1.00) 		0.0523
(1.00) 		0.308
(1.00) 		0.108
(1.00) 		0.211
(1.00) 		1
(1.00) 		0.721
(1.00)
del 12p13 2 171 (18%) 800 0.858
(1.00) 		0.49
(1.00) 		0.0856
(1.00) 		0.29
(1.00) 		0.838
(1.00) 		0.0292
(1.00) 		0.394
(1.00) 		0.0134
(1.00) 		0.458
(1.00) 		0.539
(1.00)
del 12q23 1 185 (19%) 786 0.976
(1.00) 		0.234
(1.00) 		0.349
(1.00) 		0.0106
(1.00) 		0.746
(1.00) 		0.627
(1.00) 		0.697
(1.00) 		0.00793
(1.00) 		0.857
(1.00) 		0.273
(1.00)
del 12q24 31 188 (19%) 783 0.25
(1.00) 		0.245
(1.00) 		0.641
(1.00) 		0.0197
(1.00) 		0.603
(1.00) 		0.611
(1.00) 		0.224
(1.00) 		0.0979
(1.00) 		1
(1.00) 		0.312
(1.00)
del 17p12 587 (60%) 384 0.498
(1.00) 		0.00143
(0.889) 		0.564
(1.00) 		0.0727
(1.00) 		0.668
(1.00) 		0.583
(1.00) 		0.331
(1.00) 		0.0033
(1.00) 		0.47
(1.00) 		0.859
(1.00)
del 18q23 319 (33%) 652 0.0312
(1.00) 		0.354
(1.00) 		0.134
(1.00) 		0.0668
(1.00) 		0.108
(1.00) 		0.669
(1.00) 		0.737
(1.00) 		0.00872
(1.00) 		0.0977
(1.00) 		0.413
(1.00)
del 21q11 2 193 (20%) 778 0.425
(1.00) 		0.461
(1.00) 		0.0245
(1.00) 		0.056
(1.00) 		0.0359
(1.00) 		0.408
(1.00) 		0.696
(1.00) 		0.00704
(1.00) 		0.377
(1.00) 		0.264
(1.00)
del 22q11 1 416 (43%) 555 0.664
(1.00) 		0.973
(1.00) 		0.576
(1.00) 		0.454
(1.00) 		0.411
(1.00) 		0.344
(1.00) 		0.529
(1.00) 		0.0199
(1.00) 		0.00167
(1.00) 		0.536
(1.00)
del 22q13 32 440 (45%) 531 0.506
(1.00) 		0.456
(1.00) 		0.797
(1.00) 		0.352
(1.00) 		0.696
(1.00) 		0.638
(1.00) 		0.362
(1.00) 		0.01
(1.00) 		0.0045
(1.00) 		0.697
(1.00)
'amp_3p25.1' versus 'PATHOLOGY.T.STAGE'

P value = 0.000376 (Fisher's exact test), Q value = 0.24

Table S1.  Gene #4: 'amp_3p25.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 249 568 115 36
AMP PEAK 4(3P25.1) MUTATED 34 126 14 13
AMP PEAK 4(3P25.1) WILD-TYPE 215 442 101 23

Figure S1.  Get High-res Image Gene #4: 'amp_3p25.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'amp_3p25.1' versus 'PATHOLOGY.M.STAGE'

P value = 9.02e-05 (Fisher's exact test), Q value = 0.058

Table S2.  Gene #4: 'amp_3p25.1' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients CM0 (I+) M0 M1 MX
ALL 2 836 15 118
AMP PEAK 4(3P25.1) MUTATED 0 174 6 8
AMP PEAK 4(3P25.1) WILD-TYPE 2 662 9 110

Figure S2.  Get High-res Image Gene #4: 'amp_3p25.1' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'amp_3q26.32' versus 'HISTOLOGICAL.TYPE'

P value = 1.13e-12 (Chi-square test), Q value = 7.6e-10

Table S3.  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 1 719 158 5 29 14 44
AMP PEAK 5(3Q26.32) MUTATED 1 272 12 4 6 1 13
AMP PEAK 5(3Q26.32) WILD-TYPE 0 447 146 1 23 13 31

Figure S3.  Get High-res Image Gene #5: 'amp_3q26.32' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'amp_4q13.3' versus 'HISTOLOGICAL.TYPE'

P value = 2.29e-05 (Chi-square test), Q value = 0.015

Table S4.  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 1 719 158 5 29 14 44
AMP PEAK 6(4Q13.3) MUTATED 0 137 5 2 1 1 7
AMP PEAK 6(4Q13.3) WILD-TYPE 1 582 153 3 28 13 37

Figure S4.  Get High-res Image Gene #6: 'amp_4q13.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'amp_6p23' versus 'HISTOLOGICAL.TYPE'

P value = 2.91e-05 (Chi-square test), Q value = 0.019

Table S5.  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 1 719 158 5 29 14 44
AMP PEAK 8(6P23) MUTATED 0 222 18 3 5 2 12
AMP PEAK 8(6P23) WILD-TYPE 1 497 140 2 24 12 32

Figure S5.  Get High-res Image Gene #8: 'amp_6p23' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'amp_6q21' versus 'PATHOLOGY.T.STAGE'

P value = 7.95e-05 (Fisher's exact test), Q value = 0.052

Table S6.  Gene #9: 'amp_6q21' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 249 568 115 36
AMP PEAK 9(6Q21) MUTATED 27 132 19 3
AMP PEAK 9(6Q21) WILD-TYPE 222 436 96 33

Figure S6.  Get High-res Image Gene #9: 'amp_6q21' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'amp_6q21' versus 'HISTOLOGICAL.TYPE'

P value = 1.22e-05 (Chi-square test), Q value = 0.0081

Table S7.  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 1 719 158 5 29 14 44
AMP PEAK 9(6Q21) MUTATED 1 154 13 3 1 0 9
AMP PEAK 9(6Q21) WILD-TYPE 0 565 145 2 28 14 35

Figure S7.  Get High-res Image Gene #9: 'amp_6q21' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'amp_8q24.21' versus 'HISTOLOGICAL.TYPE'

P value = 3.68e-14 (Chi-square test), Q value = 2.5e-11

Table S8.  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 1 719 158 5 29 14 44
AMP PEAK 12(8Q24.21) MUTATED 1 506 57 5 16 5 27
AMP PEAK 12(8Q24.21) WILD-TYPE 0 213 101 0 13 9 17

Figure S8.  Get High-res Image Gene #12: 'amp_8q24.21' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'amp_10p15.1' versus 'HISTOLOGICAL.TYPE'

P value = 3.48e-09 (Chi-square test), Q value = 2.3e-06

Table S9.  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 1 719 158 5 29 14 44
AMP PEAK 13(10P15.1) MUTATED 1 240 17 4 5 0 9
AMP PEAK 13(10P15.1) WILD-TYPE 0 479 141 1 24 14 35

Figure S9.  Get High-res Image Gene #13: 'amp_10p15.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'amp_11p13' versus 'HISTOLOGICAL.TYPE'

P value = 1.36e-05 (Chi-square test), Q value = 0.009

Table S10.  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 1 719 158 5 29 14 44
AMP PEAK 15(11P13) MUTATED 1 175 13 3 2 2 9
AMP PEAK 15(11P13) WILD-TYPE 0 544 145 2 27 12 35

Figure S10.  Get High-res Image Gene #15: 'amp_11p13' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'amp_12p13.33' versus 'HISTOLOGICAL.TYPE'

P value = 4.96e-05 (Chi-square test), Q value = 0.032

Table S11.  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 1 719 158 5 29 14 44
AMP PEAK 18(12P13.33) MUTATED 1 212 23 4 9 1 8
AMP PEAK 18(12P13.33) WILD-TYPE 0 507 135 1 20 13 36

Figure S11.  Get High-res Image Gene #18: 'amp_12p13.33' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'amp_15q26.3' versus 'HISTOLOGICAL.TYPE'

P value = 1.4e-05 (Chi-square test), Q value = 0.0092

Table S12.  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 1 719 158 5 29 14 44
AMP PEAK 22(15Q26.3) MUTATED 0 158 6 2 4 3 5
AMP PEAK 22(15Q26.3) WILD-TYPE 1 561 152 3 25 11 39

Figure S12.  Get High-res Image Gene #22: 'amp_15q26.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

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

P value = 0.000133 (Fisher's exact test), Q value = 0.086

Table S13.  Gene #24: 'amp_17q23.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 249 568 115 36
AMP PEAK 24(17Q23.1) MUTATED 72 257 45 17
AMP PEAK 24(17Q23.1) WILD-TYPE 177 311 70 19

Figure S13.  Get High-res Image Gene #24: 'amp_17q23.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'amp_17q23.1' versus 'GENDER'

P value = 0.00011 (Fisher's exact test), Q value = 0.071

Table S14.  Gene #24: 'amp_17q23.1' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 961 10
AMP PEAK 24(17Q23.1) MUTATED 383 10
AMP PEAK 24(17Q23.1) WILD-TYPE 578 0

Figure S14.  Get High-res Image Gene #24: 'amp_17q23.1' versus Clinical Feature #7: 'GENDER'

'amp_19q12' versus 'HISTOLOGICAL.TYPE'

P value = 4.62e-05 (Chi-square test), Q value = 0.03

Table S15.  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 1 719 158 5 29 14 44
AMP PEAK 26(19Q12) MUTATED 0 208 24 5 5 2 10
AMP PEAK 26(19Q12) WILD-TYPE 1 511 134 0 24 12 34

Figure S15.  Get High-res Image Gene #26: 'amp_19q12' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'amp_20q13.2' versus 'HISTOLOGICAL.TYPE'

P value = 1.44e-13 (Chi-square test), Q value = 9.8e-11

Table S16.  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 1 719 158 5 29 14 44
AMP PEAK 28(20Q13.2) MUTATED 1 420 41 1 11 1 19
AMP PEAK 28(20Q13.2) WILD-TYPE 0 299 117 4 18 13 25

Figure S16.  Get High-res Image Gene #28: 'amp_20q13.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

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

P value = 1.52e-06 (Fisher's exact test), Q value = 0.001

Table S17.  Gene #29: 'del_1p36.13' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 249 568 115 36
DEL PEAK 1(1P36.13) MUTATED 74 263 44 24
DEL PEAK 1(1P36.13) WILD-TYPE 175 305 71 12

Figure S17.  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 = 3.15e-05 (Fisher's exact test), Q value = 0.021

Table S18.  Gene #30: 'del_1p21.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 249 568 115 36
DEL PEAK 2(1P21.2) MUTATED 57 208 36 20
DEL PEAK 2(1P21.2) WILD-TYPE 192 360 79 16

Figure S18.  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 S19.  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 1 719 158 5 29 14 44
DEL PEAK 3(2Q37.3) MUTATED 0 244 21 2 10 3 11
DEL PEAK 3(2Q37.3) WILD-TYPE 1 475 137 3 19 11 33

Figure S19.  Get High-res Image Gene #31: 'del_2q37.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_3p21.31' versus 'PATHOLOGY.T.STAGE'

P value = 2.42e-05 (Fisher's exact test), Q value = 0.016

Table S20.  Gene #32: 'del_3p21.31' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 249 568 115 36
DEL PEAK 4(3P21.31) MUTATED 53 217 35 10
DEL PEAK 4(3P21.31) WILD-TYPE 196 351 80 26

Figure S20.  Get High-res Image Gene #32: 'del_3p21.31' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_3p21.31' versus 'HISTOLOGICAL.TYPE'

P value = 1.41e-05 (Chi-square test), Q value = 0.0093

Table S21.  Gene #32: 'del_3p21.31' 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 1 719 158 5 29 14 44
DEL PEAK 4(3P21.31) MUTATED 1 267 31 1 5 0 11
DEL PEAK 4(3P21.31) WILD-TYPE 0 452 127 4 24 14 33

Figure S21.  Get High-res Image Gene #32: 'del_3p21.31' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_4p16.3' versus 'PATHOLOGY.T.STAGE'

P value = 0.000228 (Fisher's exact test), Q value = 0.15

Table S22.  Gene #33: 'del_4p16.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 249 568 115 36
DEL PEAK 5(4P16.3) MUTATED 53 207 35 10
DEL PEAK 5(4P16.3) WILD-TYPE 196 361 80 26

Figure S22.  Get High-res Image Gene #33: 'del_4p16.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_4p16.3' versus 'HISTOLOGICAL.TYPE'

P value = 2.04e-06 (Chi-square test), Q value = 0.0014

Table S23.  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 1 719 158 5 29 14 44
DEL PEAK 5(4P16.3) MUTATED 1 257 24 3 7 0 14
DEL PEAK 5(4P16.3) WILD-TYPE 0 462 134 2 22 14 30

Figure S23.  Get High-res Image Gene #33: 'del_4p16.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_4q35.2' versus 'HISTOLOGICAL.TYPE'

P value = 1.03e-07 (Chi-square test), Q value = 6.9e-05

Table S24.  Gene #34: 'del_4q35.2' 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 1 719 158 5 29 14 44
DEL PEAK 6(4Q35.2) MUTATED 1 268 26 3 4 0 10
DEL PEAK 6(4Q35.2) WILD-TYPE 0 451 132 2 25 14 34

Figure S24.  Get High-res Image Gene #34: 'del_4q35.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_5q11.2' versus 'AGE'

P value = 0.000276 (t-test), Q value = 0.18

Table S25.  Gene #35: 'del_5q11.2' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 958 58.7 (13.1)
DEL PEAK 7(5Q11.2) MUTATED 253 56.1 (13.2)
DEL PEAK 7(5Q11.2) WILD-TYPE 705 59.6 (13.0)

Figure S25.  Get High-res Image Gene #35: 'del_5q11.2' versus Clinical Feature #2: 'AGE'

'del_5q11.2' versus 'HISTOLOGICAL.TYPE'

P value = 1.59e-11 (Chi-square test), Q value = 1.1e-08

Table S26.  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 1 719 158 5 29 14 44
DEL PEAK 7(5Q11.2) MUTATED 1 226 8 4 4 1 10
DEL PEAK 7(5Q11.2) WILD-TYPE 0 493 150 1 25 13 34

Figure S26.  Get High-res Image Gene #35: 'del_5q11.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_5q21.3' versus 'HISTOLOGICAL.TYPE'

P value = 3.11e-15 (Chi-square test), Q value = 2.1e-12

Table S27.  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 1 719 158 5 29 14 44
DEL PEAK 8(5Q21.3) MUTATED 1 222 4 5 4 0 9
DEL PEAK 8(5Q21.3) WILD-TYPE 0 497 154 0 25 14 35

Figure S27.  Get High-res Image Gene #36: 'del_5q21.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_6q27' versus 'AGE'

P value = 5.74e-06 (t-test), Q value = 0.0038

Table S28.  Gene #39: 'del_6q27' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 958 58.7 (13.1)
DEL PEAK 11(6Q27) MUTATED 332 56.1 (12.6)
DEL PEAK 11(6Q27) WILD-TYPE 626 60.0 (13.2)

Figure S28.  Get High-res Image Gene #39: 'del_6q27' versus Clinical Feature #2: 'AGE'

'del_7p22.3' versus 'HISTOLOGICAL.TYPE'

P value = 0.000198 (Chi-square test), Q value = 0.13

Table S29.  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 1 719 158 5 29 14 44
DEL PEAK 12(7P22.3) MUTATED 0 116 3 0 3 0 6
DEL PEAK 12(7P22.3) WILD-TYPE 1 603 155 5 26 14 38

Figure S29.  Get High-res Image Gene #40: 'del_7p22.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_8p23.2' versus 'HISTOLOGICAL.TYPE'

P value = 3.39e-09 (Chi-square test), Q value = 2.3e-06

Table S30.  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 1 719 158 5 29 14 44
DEL PEAK 14(8P23.2) MUTATED 1 417 47 3 11 3 25
DEL PEAK 14(8P23.2) WILD-TYPE 0 302 111 2 18 11 19

Figure S30.  Get High-res Image Gene #42: 'del_8p23.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_9p23' versus 'HISTOLOGICAL.TYPE'

P value = 1.42e-05 (Chi-square test), Q value = 0.0094

Table S31.  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 1 719 158 5 29 14 44
DEL PEAK 16(9P23) MUTATED 0 253 20 2 9 5 11
DEL PEAK 16(9P23) WILD-TYPE 1 466 138 3 20 9 33

Figure S31.  Get High-res Image Gene #44: 'del_9p23' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_9p21.3' versus 'HISTOLOGICAL.TYPE'

P value = 2.2e-09 (Chi-square test), Q value = 1.5e-06

Table S32.  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 1 719 158 5 29 14 44
DEL PEAK 17(9P21.3) MUTATED 1 284 19 4 11 5 11
DEL PEAK 17(9P21.3) WILD-TYPE 0 435 139 1 18 9 33

Figure S32.  Get High-res Image Gene #45: 'del_9p21.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_9q21.11' versus 'HISTOLOGICAL.TYPE'

P value = 0.00024 (Chi-square test), Q value = 0.15

Table S33.  Gene #46: 'del_9q21.11' 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 1 719 158 5 29 14 44
DEL PEAK 18(9Q21.11) MUTATED 0 229 20 2 10 3 10
DEL PEAK 18(9Q21.11) WILD-TYPE 1 490 138 3 19 11 34

Figure S33.  Get High-res Image Gene #46: 'del_9q21.11' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_9q34.2' versus 'HISTOLOGICAL.TYPE'

P value = 5.79e-07 (Chi-square test), Q value = 0.00039

Table S34.  Gene #47: 'del_9q34.2' 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 1 719 158 5 29 14 44
DEL PEAK 19(9Q34.2) MUTATED 0 235 18 4 6 3 8
DEL PEAK 19(9Q34.2) WILD-TYPE 1 484 140 1 23 11 36

Figure S34.  Get High-res Image Gene #47: 'del_9q34.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_10q26.3' versus 'HISTOLOGICAL.TYPE'

P value = 0.000162 (Chi-square test), Q value = 0.1

Table S35.  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 1 719 158 5 29 14 44
DEL PEAK 21(10Q26.3) MUTATED 0 240 27 4 7 1 13
DEL PEAK 21(10Q26.3) WILD-TYPE 1 479 131 1 22 13 31

Figure S35.  Get High-res Image Gene #49: 'del_10q26.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_13q14.2' versus 'HISTOLOGICAL.TYPE'

P value = 7.32e-05 (Chi-square test), Q value = 0.048

Table S36.  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 1 719 158 5 29 14 44
DEL PEAK 28(13Q14.2) MUTATED 0 368 53 4 11 2 16
DEL PEAK 28(13Q14.2) WILD-TYPE 1 351 105 1 18 12 28

Figure S36.  Get High-res Image Gene #56: 'del_13q14.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_14q24.1' versus 'HISTOLOGICAL.TYPE'

P value = 1.54e-08 (Chi-square test), Q value = 1e-05

Table S37.  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 1 719 158 5 29 14 44
DEL PEAK 29(14Q24.1) MUTATED 1 272 26 4 3 1 10
DEL PEAK 29(14Q24.1) WILD-TYPE 0 447 132 1 26 13 34

Figure S37.  Get High-res Image Gene #57: 'del_14q24.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_15q13.1' versus 'HISTOLOGICAL.TYPE'

P value = 2.26e-06 (Chi-square test), Q value = 0.0015

Table S38.  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 1 719 158 5 29 14 44
DEL PEAK 30(15Q13.1) MUTATED 1 282 30 4 8 1 12
DEL PEAK 30(15Q13.1) WILD-TYPE 0 437 128 1 21 13 32

Figure S38.  Get High-res Image Gene #58: 'del_15q13.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_16q24.3' versus 'HISTOLOGICAL.TYPE'

P value = 5.23e-16 (Chi-square test), Q value = 3.6e-13

Table S39.  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 1 719 158 5 29 14 44
DEL PEAK 31(16Q24.3) MUTATED 0 437 141 2 20 1 16
DEL PEAK 31(16Q24.3) WILD-TYPE 1 282 17 3 9 13 28

Figure S39.  Get High-res Image Gene #59: 'del_16q24.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_17q21.31' versus 'HISTOLOGICAL.TYPE'

P value = 1.68e-05 (Chi-square test), Q value = 0.011

Table S40.  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 1 719 158 5 29 14 44
DEL PEAK 33(17Q21.31) MUTATED 0 278 30 4 11 1 16
DEL PEAK 33(17Q21.31) WILD-TYPE 1 441 128 1 18 13 28

Figure S40.  Get High-res Image Gene #61: 'del_17q21.31' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_19p13.3' versus 'HISTOLOGICAL.TYPE'

P value = 4.25e-10 (Chi-square test), Q value = 2.9e-07

Table S41.  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 1 719 158 5 29 14 44
DEL PEAK 35(19P13.3) MUTATED 1 278 16 4 8 4 13
DEL PEAK 35(19P13.3) WILD-TYPE 0 441 142 1 21 10 31

Figure S41.  Get High-res Image Gene #63: 'del_19p13.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_19q13.32' versus 'HISTOLOGICAL.TYPE'

P value = 8.37e-07 (Chi-square test), Q value = 0.00056

Table S42.  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 1 719 158 5 29 14 44
DEL PEAK 36(19Q13.32) MUTATED 0 167 6 3 5 3 5
DEL PEAK 36(19Q13.32) WILD-TYPE 1 552 152 2 24 11 39

Figure S42.  Get High-res Image Gene #64: 'del_19q13.32' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_20p13' versus 'HISTOLOGICAL.TYPE'

P value = 0.00012 (Chi-square test), Q value = 0.077

Table S43.  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 1 719 158 5 29 14 44
DEL PEAK 37(20P13) MUTATED 1 128 9 2 2 0 5
DEL PEAK 37(20P13) WILD-TYPE 0 591 149 3 27 14 39

Figure S43.  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 = 971

  • 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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