Correlation between copy number variation genes (focal events) and selected clinical features
Breast Invasive Carcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1GH9GPR
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/C1GH9GPR
Overview
Introduction

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

Summary

Testing the association between copy number variation 69 focal events and 12 clinical features across 995 patients, 44 significant findings detected with Q value < 0.25.

  • amp_3p25.1 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 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',  'GENDER', and 'HISTOLOGICAL.TYPE'.

  • 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 'HISTOLOGICAL.TYPE'.

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

  • del_5q11.2 cnv correlated to 'AGE',  'HISTOLOGICAL.TYPE', and 'RACE'.

  • 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 '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 69 focal events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 44 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 		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
amp 17q23 1 400 (40%) 595 0.103
(1.00) 		0.781
(1.00) 		0.00686
(1.00) 		0.00023
(0.181) 		0.329
(1.00) 		0.00052
(0.404) 		4.08e-05
(0.0324) 		2e-05
(0.0159) 		0.943
(1.00) 		0.278
(1.00) 		0.171
(1.00) 		0.862
(1.00)
del 5q11 2 261 (26%) 734 0.166
(1.00) 		0.000101
(0.0798) 		0.21
(1.00) 		0.00194
(1.00) 		0.44
(1.00) 		0.265
(1.00) 		0.0765
(1.00) 		1e-05
(0.00828) 		0.523
(1.00) 		0.154
(1.00) 		0.00025
(0.196) 		0.571
(1.00)
amp 6q21 187 (19%) 808 0.0226
(1.00) 		0.373
(1.00) 		0.0498
(1.00) 		0.00021
(0.165) 		0.0801
(1.00) 		0.741
(1.00) 		0.7
(1.00) 		1e-05
(0.00828) 		0.369
(1.00) 		0.0196
(1.00) 		0.149
(1.00) 		0.828
(1.00)
del 3p21 31 321 (32%) 674 0.0141
(1.00) 		0.00118
(0.899) 		0.204
(1.00) 		1e-05
(0.00828) 		0.48
(1.00) 		0.705
(1.00) 		0.753
(1.00) 		1e-05
(0.00828) 		0.177
(1.00) 		0.615
(1.00) 		0.0373
(1.00) 		0.589
(1.00)
del 17q21 31 344 (35%) 651 0.608
(1.00) 		9.25e-05
(0.073) 		0.161
(1.00) 		0.0784
(1.00) 		0.131
(1.00) 		0.111
(1.00) 		0.347
(1.00) 		2e-05
(0.0159) 		0.605
(1.00) 		0.553
(1.00) 		0.00038
(0.297) 		1
(1.00)
amp 3p25 1 192 (19%) 803 0.00913
(1.00) 		0.196
(1.00) 		0.0274
(1.00) 		0.00052
(0.404) 		0.0361
(1.00) 		0.00069
(0.533) 		0.701
(1.00) 		0.00016
(0.126) 		0.656
(1.00) 		0.433
(1.00) 		0.39
(1.00) 		1
(1.00)
amp 3q26 32 316 (32%) 679 0.859
(1.00) 		0.449
(1.00) 		0.219
(1.00) 		0.00153
(1.00) 		0.3
(1.00) 		0.0106
(1.00) 		0.75
(1.00) 		1e-05
(0.00828) 		0.0493
(1.00) 		0.0841
(1.00) 		0.0104
(1.00) 		0.142
(1.00)
amp 4q13 3 155 (16%) 840 0.00823
(1.00) 		0.461
(1.00) 		0.761
(1.00) 		0.117
(1.00) 		0.577
(1.00) 		0.237
(1.00) 		0.392
(1.00) 		1e-05
(0.00828) 		0.439
(1.00) 		0.715
(1.00) 		0.0982
(1.00) 		0.231
(1.00)
amp 6p23 274 (28%) 721 0.798
(1.00) 		0.299
(1.00) 		0.585
(1.00) 		0.00575
(1.00) 		0.279
(1.00) 		0.937
(1.00) 		0.307
(1.00) 		1e-05
(0.00828) 		0.156
(1.00) 		0.978
(1.00) 		0.0165
(1.00) 		0.701
(1.00)
amp 8q24 21 635 (64%) 360 0.0529
(1.00) 		0.0603
(1.00) 		0.223
(1.00) 		0.0262
(1.00) 		0.53
(1.00) 		0.0237
(1.00) 		0.345
(1.00) 		1e-05
(0.00828) 		0.108
(1.00) 		0.369
(1.00) 		0.00303
(1.00) 		0.224
(1.00)
amp 10p15 1 285 (29%) 710 0.0977
(1.00) 		0.596
(1.00) 		0.123
(1.00) 		0.299
(1.00) 		0.53
(1.00) 		0.434
(1.00) 		0.738
(1.00) 		1e-05
(0.00828) 		0.162
(1.00) 		0.265
(1.00) 		0.00033
(0.259) 		0.569
(1.00)
amp 11p13 209 (21%) 786 0.82
(1.00) 		0.458
(1.00) 		0.793
(1.00) 		0.422
(1.00) 		0.977
(1.00) 		0.305
(1.00) 		0.257
(1.00) 		1e-05
(0.00828) 		0.262
(1.00) 		0.592
(1.00) 		0.295
(1.00) 		0.676
(1.00)
amp 12p13 33 266 (27%) 729 0.89
(1.00) 		0.293
(1.00) 		0.516
(1.00) 		0.00158
(1.00) 		0.779
(1.00) 		0.782
(1.00) 		0.305
(1.00) 		1e-05
(0.00828) 		0.302
(1.00) 		0.434
(1.00) 		0.00768
(1.00) 		0.0837
(1.00)
amp 15q26 3 182 (18%) 813 0.262
(1.00) 		0.00747
(1.00) 		0.407
(1.00) 		0.356
(1.00) 		0.96
(1.00) 		0.0381
(1.00) 		0.124
(1.00) 		1e-05
(0.00828) 		0.415
(1.00) 		0.447
(1.00) 		0.031
(1.00) 		0.375
(1.00)
amp 19q12 262 (26%) 733 0.331
(1.00) 		0.278
(1.00) 		0.0362
(1.00) 		0.596
(1.00) 		0.0197
(1.00) 		0.194
(1.00) 		0.493
(1.00) 		1e-05
(0.00828) 		0.472
(1.00) 		0.00305
(1.00) 		0.101
(1.00) 		0.848
(1.00)
amp 20q13 2 510 (51%) 485 0.465
(1.00) 		0.578
(1.00) 		0.0952
(1.00) 		0.0188
(1.00) 		0.00538
(1.00) 		0.095
(1.00) 		0.0649
(1.00) 		1e-05
(0.00828) 		0.00119
(0.906) 		0.148
(1.00) 		0.368
(1.00) 		0.496
(1.00)
del 1p36 13 416 (42%) 579 0.118
(1.00) 		0.0721
(1.00) 		0.0017
(1.00) 		1e-05
(0.00828) 		0.0014
(1.00) 		0.255
(1.00) 		0.0604
(1.00) 		0.00481
(1.00) 		0.154
(1.00) 		0.000998
(0.765) 		0.89
(1.00) 		0.73
(1.00)
del 1p21 2 328 (33%) 667 0.0347
(1.00) 		0.0698
(1.00) 		0.0115
(1.00) 		6e-05
(0.0476) 		0.00579
(1.00) 		0.427
(1.00) 		0.758
(1.00) 		0.243
(1.00) 		0.654
(1.00) 		0.00723
(1.00) 		0.792
(1.00) 		0.466
(1.00)
del 2q37 3 298 (30%) 697 0.59
(1.00) 		0.781
(1.00) 		0.313
(1.00) 		0.00284
(1.00) 		0.349
(1.00) 		0.477
(1.00) 		1
(1.00) 		1e-05
(0.00828) 		0.107
(1.00) 		0.342
(1.00) 		0.0132
(1.00) 		0.346
(1.00)
del 4p16 3 315 (32%) 680 0.646
(1.00) 		0.111
(1.00) 		0.104
(1.00) 		0.00052
(0.404) 		0.717
(1.00) 		0.43
(1.00) 		1
(1.00) 		1e-05
(0.00828) 		0.326
(1.00) 		0.562
(1.00) 		0.0443
(1.00) 		0.716
(1.00)
del 4q35 2 321 (32%) 674 0.0574
(1.00) 		0.611
(1.00) 		0.279
(1.00) 		0.00308
(1.00) 		0.614
(1.00) 		0.003
(1.00) 		0.116
(1.00) 		1e-05
(0.00828) 		0.548
(1.00) 		0.613
(1.00) 		0.00896
(1.00) 		0.142
(1.00)
del 5q21 3 252 (25%) 743 0.316
(1.00) 		0.00233
(1.00) 		0.0969
(1.00) 		0.00052
(0.404) 		0.0716
(1.00) 		0.316
(1.00) 		0.0751
(1.00) 		1e-05
(0.00828) 		0.17
(1.00) 		0.00495
(1.00) 		0.00076
(0.584) 		0.701
(1.00)
del 6q27 346 (35%) 649 0.0888
(1.00) 		1.59e-05
(0.0126) 		0.344
(1.00) 		0.701
(1.00) 		0.0206
(1.00) 		0.326
(1.00) 		0.347
(1.00) 		0.428
(1.00) 		0.046
(1.00) 		0.21
(1.00) 		0.685
(1.00) 		0.282
(1.00)
del 7p22 3 132 (13%) 863 0.885
(1.00) 		0.241
(1.00) 		0.569
(1.00) 		0.241
(1.00) 		0.101
(1.00) 		0.175
(1.00) 		0.377
(1.00) 		1e-05
(0.00828) 		0.756
(1.00) 		0.0396
(1.00) 		0.42
(1.00) 		0.61
(1.00)
del 8p23 2 519 (52%) 476 0.138
(1.00) 		0.656
(1.00) 		0.956
(1.00) 		0.00713
(1.00) 		0.127
(1.00) 		0.141
(1.00) 		0.551
(1.00) 		1e-05
(0.00828) 		0.779
(1.00) 		0.826
(1.00) 		0.00182
(1.00) 		0.865
(1.00)
del 9p23 307 (31%) 688 0.000459
(0.358) 		0.231
(1.00) 		0.0028
(1.00) 		0.00042
(0.328) 		0.002
(1.00) 		0.0243
(1.00) 		0.104
(1.00) 		1e-05
(0.00828) 		0.648
(1.00) 		0.0754
(1.00) 		0.511
(1.00) 		0.854
(1.00)
del 9p21 3 343 (34%) 652 0.0359
(1.00) 		0.371
(1.00) 		0.00954
(1.00) 		0.00087
(0.668) 		0.00552
(1.00) 		0.1
(1.00) 		0.0546
(1.00) 		1e-05
(0.00828) 		0.605
(1.00) 		0.146
(1.00) 		0.183
(1.00) 		0.857
(1.00)
del 9q21 11 283 (28%) 712 0.344
(1.00) 		0.864
(1.00) 		0.124
(1.00) 		0.0364
(1.00) 		0.258
(1.00) 		0.322
(1.00) 		0.0855
(1.00) 		1e-05
(0.00828) 		0.102
(1.00) 		0.487
(1.00) 		0.0331
(1.00) 		0.255
(1.00)
del 9q34 2 283 (28%) 712 0.91
(1.00) 		0.965
(1.00) 		0.0458
(1.00) 		0.00792
(1.00) 		0.0795
(1.00) 		0.902
(1.00) 		0.0155
(1.00) 		1e-05
(0.00828) 		0.139
(1.00) 		0.123
(1.00) 		0.00475
(1.00) 		0.343
(1.00)
del 10q26 3 299 (30%) 696 0.0534
(1.00) 		0.735
(1.00) 		0.148
(1.00) 		0.0954
(1.00) 		0.152
(1.00) 		0.246
(1.00) 		0.52
(1.00) 		6e-05
(0.0476) 		0.443
(1.00) 		0.31
(1.00) 		0.178
(1.00) 		0.00891
(1.00)
del 13q14 2 464 (47%) 531 0.137
(1.00) 		0.537
(1.00) 		0.564
(1.00) 		0.0167
(1.00) 		0.501
(1.00) 		0.885
(1.00) 		0.763
(1.00) 		1e-05
(0.00828) 		0.232
(1.00) 		0.713
(1.00) 		0.0285
(1.00) 		0.172
(1.00)
del 14q24 1 323 (32%) 672 0.0393
(1.00) 		0.203
(1.00) 		0.299
(1.00) 		0.00042
(0.328) 		0.201
(1.00) 		0.986
(1.00) 		0.755
(1.00) 		1e-05
(0.00828) 		0.0507
(1.00) 		0.206
(1.00) 		0.00649
(1.00) 		0.858
(1.00)
del 15q13 1 349 (35%) 646 0.303
(1.00) 		0.155
(1.00) 		0.13
(1.00) 		0.00236
(1.00) 		0.0249
(1.00) 		0.382
(1.00) 		1
(1.00) 		1e-05
(0.00828) 		0.0773
(1.00) 		0.149
(1.00) 		0.0488
(1.00) 		0.86
(1.00)
del 16q24 3 633 (64%) 362 0.236
(1.00) 		0.00133
(1.00) 		0.077
(1.00) 		0.175
(1.00) 		0.3
(1.00) 		0.187
(1.00) 		1
(1.00) 		1e-05
(0.00828) 		0.465
(1.00) 		0.593
(1.00) 		0.013
(1.00) 		0.159
(1.00)
del 19p13 3 330 (33%) 665 0.0539
(1.00) 		0.00823
(1.00) 		0.625
(1.00) 		0.074
(1.00) 		0.859
(1.00) 		0.263
(1.00) 		0.355
(1.00) 		1e-05
(0.00828) 		0.941
(1.00) 		0.077
(1.00) 		0.0241
(1.00) 		0.857
(1.00)
del 19q13 32 194 (19%) 801 0.589
(1.00) 		0.598
(1.00) 		0.494
(1.00) 		0.369
(1.00) 		0.0939
(1.00) 		0.512
(1.00) 		1
(1.00) 		1e-05
(0.00828) 		0.00988
(1.00) 		0.911
(1.00) 		0.434
(1.00) 		0.521
(1.00)
del 20p13 151 (15%) 844 0.0766
(1.00) 		0.113
(1.00) 		0.397
(1.00) 		0.527
(1.00) 		0.878
(1.00) 		0.341
(1.00) 		0.226
(1.00) 		6e-05
(0.0476) 		0.117
(1.00) 		0.92
(1.00) 		0.179
(1.00) 		0.638
(1.00)
amp 1p22 3 226 (23%) 769 0.925
(1.00) 		0.334
(1.00) 		0.388
(1.00) 		0.0169
(1.00) 		0.00575
(1.00) 		0.86
(1.00) 		1
(1.00) 		0.202
(1.00) 		0.675
(1.00) 		0.00742
(1.00) 		0.0687
(1.00) 		1
(1.00)
amp 1q21 3 725 (73%) 270 0.965
(1.00) 		0.995
(1.00) 		0.277
(1.00) 		0.0191
(1.00) 		0.639
(1.00) 		0.64
(1.00) 		0.181
(1.00) 		0.0719
(1.00) 		0.635
(1.00) 		0.58
(1.00) 		0.195
(1.00) 		0.0579
(1.00)
amp 1q44 722 (73%) 273 0.0529
(1.00) 		0.379
(1.00) 		0.161
(1.00) 		0.0157
(1.00) 		0.445
(1.00) 		0.549
(1.00) 		1
(1.00) 		0.0026
(1.00) 		0.875
(1.00) 		0.829
(1.00) 		0.0186
(1.00) 		0.0855
(1.00)
amp 5p15 33 364 (37%) 631 0.106
(1.00) 		0.15
(1.00) 		0.596
(1.00) 		0.243
(1.00) 		0.00747
(1.00) 		0.0427
(1.00) 		0.543
(1.00) 		0.101
(1.00) 		0.125
(1.00) 		0.644
(1.00) 		0.36
(1.00) 		0.484
(1.00)
amp 8p11 23 380 (38%) 615 0.0256
(1.00) 		0.146
(1.00) 		0.0736
(1.00) 		0.622
(1.00) 		0.133
(1.00) 		0.0313
(1.00) 		0.546
(1.00) 		0.613
(1.00) 		0.772
(1.00) 		0.0168
(1.00) 		0.833
(1.00) 		0.601
(1.00)
amp 8p11 21 390 (39%) 605 0.57
(1.00) 		0.0714
(1.00) 		0.852
(1.00) 		0.902
(1.00) 		0.978
(1.00) 		0.382
(1.00) 		0.542
(1.00) 		0.0104
(1.00) 		0.313
(1.00) 		0.821
(1.00) 		0.256
(1.00) 		0.601
(1.00)
amp 10q22 3 144 (14%) 851 0.0769
(1.00) 		0.869
(1.00) 		0.269
(1.00) 		0.182
(1.00) 		0.261
(1.00) 		0.142
(1.00) 		0.666
(1.00) 		0.00458
(1.00) 		0.11
(1.00) 		0.161
(1.00) 		0.21
(1.00) 		1
(1.00)
amp 11q13 3 369 (37%) 626 0.224
(1.00) 		0.181
(1.00) 		0.638
(1.00) 		0.0553
(1.00) 		0.685
(1.00) 		0.253
(1.00) 		0.112
(1.00) 		0.135
(1.00) 		0.884
(1.00) 		0.732
(1.00) 		0.343
(1.00) 		0.484
(1.00)
amp 11q14 1 245 (25%) 750 0.18
(1.00) 		0.262
(1.00) 		0.457
(1.00) 		0.108
(1.00) 		0.135
(1.00) 		0.0537
(1.00) 		0.151
(1.00) 		0.00407
(1.00) 		0.744
(1.00) 		0.623
(1.00) 		0.195
(1.00) 		0.424
(1.00)
amp 12q15 258 (26%) 737 0.0772
(1.00) 		0.407
(1.00) 		0.172
(1.00) 		0.00704
(1.00) 		0.00677
(1.00) 		0.224
(1.00) 		0.00901
(1.00) 		0.009
(1.00) 		0.873
(1.00) 		0.0166
(1.00) 		0.355
(1.00) 		0.326
(1.00)
amp 13q34 169 (17%) 826 0.531
(1.00) 		0.0747
(1.00) 		0.229
(1.00) 		0.0134
(1.00) 		0.302
(1.00) 		0.104
(1.00) 		0.228
(1.00) 		0.00753
(1.00) 		0.925
(1.00) 		0.0467
(1.00) 		0.669
(1.00) 		0.823
(1.00)
amp 14q21 1 204 (21%) 791 0.3
(1.00) 		0.105
(1.00) 		0.0559
(1.00) 		0.0168
(1.00) 		0.0116
(1.00) 		0.16
(1.00) 		1
(1.00) 		0.0473
(1.00) 		0.601
(1.00) 		0.00611
(1.00) 		0.66
(1.00) 		0.207
(1.00)
amp 17q12 311 (31%) 684 0.16
(1.00) 		0.655
(1.00) 		0.303
(1.00) 		0.0605
(1.00) 		0.115
(1.00) 		0.0265
(1.00) 		0.00545
(1.00) 		0.00073
(0.562) 		0.324
(1.00) 		0.381
(1.00) 		0.00107
(0.819) 		1
(1.00)
amp 19p13 12 211 (21%) 784 0.558
(1.00) 		0.918
(1.00) 		0.508
(1.00) 		0.327
(1.00) 		0.131
(1.00) 		0.124
(1.00) 		0.0619
(1.00) 		0.0234
(1.00) 		0.0254
(1.00) 		0.000705
(0.543) 		0.285
(1.00) 		0.837
(1.00)
amp 19q13 42 257 (26%) 738 0.417
(1.00) 		0.38
(1.00) 		0.98
(1.00) 		0.328
(1.00) 		0.781
(1.00) 		0.00906
(1.00) 		0.164
(1.00) 		0.0106
(1.00) 		0.199
(1.00) 		0.0975
(1.00) 		0.691
(1.00) 		0.44
(1.00)
del 2p25 1 189 (19%) 806 0.883
(1.00) 		0.223
(1.00) 		0.226
(1.00) 		0.245
(1.00) 		0.0379
(1.00) 		0.279
(1.00) 		0.446
(1.00) 		0.0692
(1.00) 		0.209
(1.00) 		0.699
(1.00) 		0.802
(1.00) 		0.501
(1.00)
del 6p25 3 194 (19%) 801 0.641
(1.00) 		0.0228
(1.00) 		0.336
(1.00) 		0.0267
(1.00) 		0.173
(1.00) 		0.683
(1.00) 		0.24
(1.00) 		0.077
(1.00) 		0.0766
(1.00) 		0.854
(1.00) 		0.441
(1.00) 		0.521
(1.00)
del 6q15 328 (33%) 667 0.713
(1.00) 		0.0305
(1.00) 		0.0957
(1.00) 		0.382
(1.00) 		0.0258
(1.00) 		0.655
(1.00) 		1
(1.00) 		0.446
(1.00) 		0.135
(1.00) 		0.0142
(1.00) 		0.094
(1.00) 		0.591
(1.00)
del 7q36 1 191 (19%) 804 0.143
(1.00) 		0.995
(1.00) 		0.568
(1.00) 		0.18
(1.00) 		0.307
(1.00) 		0.259
(1.00) 		1
(1.00) 		0.00097
(0.744) 		1
(1.00) 		0.886
(1.00) 		0.629
(1.00) 		0.28
(1.00)
del 8p11 21 191 (19%) 804 0.0654
(1.00) 		0.0854
(1.00) 		0.599
(1.00) 		0.144
(1.00) 		0.229
(1.00) 		0.283
(1.00) 		0.137
(1.00) 		0.00553
(1.00) 		0.789
(1.00) 		0.368
(1.00) 		0.0711
(1.00) 		0.831
(1.00)
del 10q23 31 298 (30%) 697 0.504
(1.00) 		0.177
(1.00) 		0.183
(1.00) 		0.0249
(1.00) 		0.159
(1.00) 		0.287
(1.00) 		0.189
(1.00) 		0.00065
(0.502) 		0.193
(1.00) 		0.283
(1.00) 		0.225
(1.00) 		0.0265
(1.00)
del 11p15 5 289 (29%) 706 0.146
(1.00) 		0.639
(1.00) 		0.158
(1.00) 		0.00435
(1.00) 		0.467
(1.00) 		0.274
(1.00) 		0.739
(1.00) 		0.00033
(0.259) 		0.536
(1.00) 		0.96
(1.00) 		0.00772
(1.00) 		0.342
(1.00)
del 11q13 1 222 (22%) 773 0.443
(1.00) 		0.745
(1.00) 		0.318
(1.00) 		0.174
(1.00) 		0.217
(1.00) 		0.681
(1.00) 		0.717
(1.00) 		0.757
(1.00) 		0.673
(1.00) 		0.824
(1.00) 		0.00727
(1.00) 		0.54
(1.00)
del 11q23 2 509 (51%) 486 0.633
(1.00) 		0.29
(1.00) 		0.0809
(1.00) 		0.0191
(1.00) 		0.0572
(1.00) 		0.159
(1.00) 		0.0647
(1.00) 		0.194
(1.00) 		1
(1.00) 		0.25
(1.00) 		0.00453
(1.00) 		0.865
(1.00)
del 12p13 2 171 (17%) 824 0.876
(1.00) 		0.413
(1.00) 		0.263
(1.00) 		0.182
(1.00) 		0.816
(1.00) 		0.105
(1.00) 		0.414
(1.00) 		0.00968
(1.00) 		0.642
(1.00) 		0.589
(1.00) 		0.538
(1.00) 		1
(1.00)
del 12q23 1 190 (19%) 805 0.909
(1.00) 		0.097
(1.00) 		0.353
(1.00) 		0.0232
(1.00) 		0.633
(1.00) 		0.764
(1.00) 		0.701
(1.00) 		0.00443
(1.00) 		0.858
(1.00) 		0.215
(1.00) 		0.00485
(1.00) 		0.831
(1.00)
del 12q24 31 192 (19%) 803 0.28
(1.00) 		0.0929
(1.00) 		0.699
(1.00) 		0.0481
(1.00) 		0.529
(1.00) 		0.447
(1.00) 		0.136
(1.00) 		0.0836
(1.00) 		1
(1.00) 		0.153
(1.00) 		0.266
(1.00) 		0.52
(1.00)
del 17p12 600 (60%) 395 0.624
(1.00) 		0.00047
(0.365) 		0.578
(1.00) 		0.0802
(1.00) 		0.78
(1.00) 		0.692
(1.00) 		0.541
(1.00) 		0.00181
(1.00) 		0.429
(1.00) 		0.706
(1.00) 		0.0622
(1.00) 		0.862
(1.00)
del 18q23 324 (33%) 671 0.0221
(1.00) 		0.396
(1.00) 		0.154
(1.00) 		0.061
(1.00) 		0.124
(1.00) 		0.801
(1.00) 		0.351
(1.00) 		0.00206
(1.00) 		0.0718
(1.00) 		0.429
(1.00) 		0.0485
(1.00) 		0.857
(1.00)
del 21q11 2 196 (20%) 799 0.478
(1.00) 		0.539
(1.00) 		0.0257
(1.00) 		0.0488
(1.00) 		0.0203
(1.00) 		0.545
(1.00) 		0.702
(1.00) 		0.00244
(1.00) 		0.332
(1.00) 		0.289
(1.00) 		0.609
(1.00) 		0.282
(1.00)
del 22q11 1 426 (43%) 569 0.681
(1.00) 		0.906
(1.00) 		0.687
(1.00) 		0.548
(1.00) 		0.44
(1.00) 		0.634
(1.00) 		0.369
(1.00) 		0.014
(1.00) 		0.00175
(1.00) 		0.931
(1.00) 		0.559
(1.00) 		0.864
(1.00)
del 22q13 32 451 (45%) 544 0.532
(1.00) 		0.525
(1.00) 		0.656
(1.00) 		0.355
(1.00) 		0.668
(1.00) 		0.502
(1.00) 		0.559
(1.00) 		0.00432
(1.00) 		0.00471
(1.00) 		0.908
(1.00) 		0.501
(1.00) 		0.734
(1.00)
'amp_3p25.1' versus 'HISTOLOGICAL.TYPE'

P value = 0.00016 (Fisher's exact test), Q value = 0.13

Table S1.  Gene #4: 'amp_3p25.1' 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 1 735 166 5 29 14 44
AMP PEAK 4(3P25.1) MUTATED 1 164 13 1 5 1 7
AMP PEAK 4(3P25.1) WILD-TYPE 0 571 153 4 24 13 37

Figure S1.  Get High-res Image Gene #4: 'amp_3p25.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'amp_3q26.32' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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 1 735 166 5 29 14 44
AMP PEAK 5(3Q26.32) MUTATED 1 278 12 4 6 1 13
AMP PEAK 5(3Q26.32) WILD-TYPE 0 457 154 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 = 1e-05 (Fisher's exact test), Q value = 0.0083

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 1 735 166 5 29 14 44
AMP PEAK 6(4Q13.3) MUTATED 0 139 5 2 1 1 7
AMP PEAK 6(4Q13.3) WILD-TYPE 1 596 161 3 28 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 = 1e-05 (Fisher's exact test), Q value = 0.0083

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 1 735 166 5 29 14 44
AMP PEAK 8(6P23) MUTATED 0 230 21 3 5 2 12
AMP PEAK 8(6P23) WILD-TYPE 1 505 145 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 = 0.00021 (Fisher's exact test), Q value = 0.17

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

nPatients T1 T2 T3 T4
ALL 258 581 117 36
AMP PEAK 9(6Q21) MUTATED 30 135 19 3
AMP PEAK 9(6Q21) WILD-TYPE 228 446 98 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 = 1e-05 (Fisher's exact test), Q value = 0.0083

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 1 735 166 5 29 14 44
AMP PEAK 9(6Q21) MUTATED 1 160 13 3 1 0 9
AMP PEAK 9(6Q21) WILD-TYPE 0 575 153 2 28 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 = 1e-05 (Fisher's exact test), Q value = 0.0083

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 1 735 166 5 29 14 44
AMP PEAK 12(8Q24.21) MUTATED 1 521 59 5 16 5 27
AMP PEAK 12(8Q24.21) WILD-TYPE 0 214 107 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 = 1e-05 (Fisher's exact test), Q value = 0.0083

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 1 735 166 5 29 14 44
AMP PEAK 13(10P15.1) MUTATED 1 247 18 4 5 0 9
AMP PEAK 13(10P15.1) WILD-TYPE 0 488 148 1 24 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 = 1e-05 (Fisher's exact test), Q value = 0.0083

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 1 735 166 5 29 14 44
AMP PEAK 15(11P13) MUTATED 1 179 13 3 2 2 9
AMP PEAK 15(11P13) WILD-TYPE 0 556 153 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 = 1e-05 (Fisher's exact test), Q value = 0.0083

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 1 735 166 5 29 14 44
AMP PEAK 18(12P13.33) MUTATED 1 220 23 4 9 1 8
AMP PEAK 18(12P13.33) WILD-TYPE 0 515 143 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 = 1e-05 (Fisher's exact test), Q value = 0.0083

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 1 735 166 5 29 14 44
AMP PEAK 22(15Q26.3) MUTATED 0 160 7 2 4 3 5
AMP PEAK 22(15Q26.3) WILD-TYPE 1 575 159 3 25 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 = 0.00023 (Fisher's exact test), Q value = 0.18

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

nPatients T1 T2 T3 T4
ALL 258 581 117 36
AMP PEAK 24(17Q23.1) MUTATED 76 260 45 17
AMP PEAK 24(17Q23.1) WILD-TYPE 182 321 72 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 = 4.08e-05 (Fisher's exact test), Q value = 0.032

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

nPatients FEMALE MALE
ALL 984 11
AMP PEAK 24(17Q23.1) MUTATED 389 11
AMP PEAK 24(17Q23.1) WILD-TYPE 595 0

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

'amp_17q23.1' versus 'HISTOLOGICAL.TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.016

Table S14.  Gene #24: 'amp_17q23.1' 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 1 735 166 5 29 14 44
AMP PEAK 24(17Q23.1) MUTATED 1 326 39 3 9 5 16
AMP PEAK 24(17Q23.1) WILD-TYPE 0 409 127 2 20 9 28

Figure S14.  Get High-res Image Gene #24: 'amp_17q23.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'amp_19q12' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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 1 735 166 5 29 14 44
AMP PEAK 26(19Q12) MUTATED 0 215 25 5 5 2 10
AMP PEAK 26(19Q12) WILD-TYPE 1 520 141 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 = 1e-05 (Fisher's exact test), Q value = 0.0083

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 1 735 166 5 29 14 44
AMP PEAK 28(20Q13.2) MUTATED 1 432 45 1 11 1 19
AMP PEAK 28(20Q13.2) WILD-TYPE 0 303 121 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 = 1e-05 (Fisher's exact test), Q value = 0.0083

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

nPatients T1 T2 T3 T4
ALL 258 581 117 36
DEL PEAK 1(1P36.13) MUTATED 77 270 44 24
DEL PEAK 1(1P36.13) WILD-TYPE 181 311 73 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 = 6e-05 (Fisher's exact test), Q value = 0.048

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

nPatients T1 T2 T3 T4
ALL 258 581 117 36
DEL PEAK 2(1P21.2) MUTATED 60 211 36 20
DEL PEAK 2(1P21.2) WILD-TYPE 198 370 81 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 = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S19.  Gene #32: '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 1 735 166 5 29 14 44
DEL PEAK 4(2Q37.3) MUTATED 0 250 21 2 10 3 11
DEL PEAK 4(2Q37.3) WILD-TYPE 1 485 145 3 19 11 33

Figure S19.  Get High-res Image Gene #32: 'del_2q37.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

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

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S20.  Gene #33: 'del_3p21.31' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 258 581 117 36
DEL PEAK 5(3P21.31) MUTATED 53 222 35 10
DEL PEAK 5(3P21.31) WILD-TYPE 205 359 82 26

Figure S20.  Get High-res Image Gene #33: 'del_3p21.31' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_3p21.31' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S21.  Gene #33: '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 1 735 166 5 29 14 44
DEL PEAK 5(3P21.31) MUTATED 1 270 33 1 5 0 11
DEL PEAK 5(3P21.31) WILD-TYPE 0 465 133 4 24 14 33

Figure S21.  Get High-res Image Gene #33: 'del_3p21.31' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_4p16.3' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S22.  Gene #34: '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 1 735 166 5 29 14 44
DEL PEAK 6(4P16.3) MUTATED 1 265 25 3 7 0 14
DEL PEAK 6(4P16.3) WILD-TYPE 0 470 141 2 22 14 30

Figure S22.  Get High-res Image Gene #34: 'del_4p16.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_4q35.2' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S23.  Gene #35: '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 1 735 166 5 29 14 44
DEL PEAK 7(4Q35.2) MUTATED 1 274 28 3 4 0 10
DEL PEAK 7(4Q35.2) WILD-TYPE 0 461 138 2 25 14 34

Figure S23.  Get High-res Image Gene #35: 'del_4q35.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_5q11.2' versus 'AGE'

P value = 0.000101 (Wilcoxon-test), Q value = 0.08

Table S24.  Gene #36: 'del_5q11.2' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 982 58.7 (13.1)
DEL PEAK 8(5Q11.2) MUTATED 259 56.1 (13.2)
DEL PEAK 8(5Q11.2) WILD-TYPE 723 59.6 (13.0)

Figure S24.  Get High-res Image Gene #36: 'del_5q11.2' versus Clinical Feature #2: 'AGE'

'del_5q11.2' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S25.  Gene #36: '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 1 735 166 5 29 14 44
DEL PEAK 8(5Q11.2) MUTATED 1 232 8 4 4 1 10
DEL PEAK 8(5Q11.2) WILD-TYPE 0 503 158 1 25 13 34

Figure S25.  Get High-res Image Gene #36: 'del_5q11.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_5q11.2' versus 'RACE'

P value = 0.00025 (Fisher's exact test), Q value = 0.2

Table S26.  Gene #36: 'del_5q11.2' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 56 137 708
DEL PEAK 8(5Q11.2) MUTATED 1 19 54 167
DEL PEAK 8(5Q11.2) WILD-TYPE 0 37 83 541

Figure S26.  Get High-res Image Gene #36: 'del_5q11.2' versus Clinical Feature #11: 'RACE'

'del_5q21.3' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S27.  Gene #37: '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 1 735 166 5 29 14 44
DEL PEAK 9(5Q21.3) MUTATED 1 228 4 5 4 0 9
DEL PEAK 9(5Q21.3) WILD-TYPE 0 507 162 0 25 14 35

Figure S27.  Get High-res Image Gene #37: 'del_5q21.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_6q27' versus 'AGE'

P value = 1.59e-05 (Wilcoxon-test), Q value = 0.013

Table S28.  Gene #40: 'del_6q27' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 982 58.7 (13.1)
DEL PEAK 12(6Q27) MUTATED 342 56.1 (12.5)
DEL PEAK 12(6Q27) WILD-TYPE 640 60.1 (13.2)

Figure S28.  Get High-res Image Gene #40: 'del_6q27' versus Clinical Feature #2: 'AGE'

'del_7p22.3' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S29.  Gene #41: '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 1 735 166 5 29 14 44
DEL PEAK 13(7P22.3) MUTATED 0 120 3 0 3 0 6
DEL PEAK 13(7P22.3) WILD-TYPE 1 615 163 5 26 14 38

Figure S29.  Get High-res Image Gene #41: 'del_7p22.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_8p23.2' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S30.  Gene #43: '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 1 735 166 5 29 14 44
DEL PEAK 15(8P23.2) MUTATED 1 427 48 3 11 3 25
DEL PEAK 15(8P23.2) WILD-TYPE 0 308 118 2 18 11 19

Figure S30.  Get High-res Image Gene #43: 'del_8p23.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_9p23' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S31.  Gene #45: '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 1 735 166 5 29 14 44
DEL PEAK 17(9P23) MUTATED 0 260 20 2 9 5 11
DEL PEAK 17(9P23) WILD-TYPE 1 475 146 3 20 9 33

Figure S31.  Get High-res Image Gene #45: 'del_9p23' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_9p21.3' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S32.  Gene #46: '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 1 735 166 5 29 14 44
DEL PEAK 18(9P21.3) MUTATED 1 292 19 4 11 5 11
DEL PEAK 18(9P21.3) WILD-TYPE 0 443 147 1 18 9 33

Figure S32.  Get High-res Image Gene #46: 'del_9p21.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_9q21.11' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S33.  Gene #47: '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 1 735 166 5 29 14 44
DEL PEAK 19(9Q21.11) MUTATED 0 238 20 2 10 3 10
DEL PEAK 19(9Q21.11) WILD-TYPE 1 497 146 3 19 11 34

Figure S33.  Get High-res Image Gene #47: 'del_9q21.11' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_9q34.2' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S34.  Gene #48: '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 1 735 166 5 29 14 44
DEL PEAK 20(9Q34.2) MUTATED 0 243 18 4 6 3 8
DEL PEAK 20(9Q34.2) WILD-TYPE 1 492 148 1 23 11 36

Figure S34.  Get High-res Image Gene #48: 'del_9q34.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_10q26.3' versus 'HISTOLOGICAL.TYPE'

P value = 6e-05 (Fisher's exact test), Q value = 0.048

Table S35.  Gene #50: '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 1 735 166 5 29 14 44
DEL PEAK 22(10Q26.3) MUTATED 0 245 28 4 7 1 13
DEL PEAK 22(10Q26.3) WILD-TYPE 1 490 138 1 22 13 31

Figure S35.  Get High-res Image Gene #50: 'del_10q26.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_13q14.2' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S36.  Gene #57: '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 1 735 166 5 29 14 44
DEL PEAK 29(13Q14.2) MUTATED 0 375 55 4 11 2 16
DEL PEAK 29(13Q14.2) WILD-TYPE 1 360 111 1 18 12 28

Figure S36.  Get High-res Image Gene #57: 'del_13q14.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_14q24.1' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S37.  Gene #58: '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 1 735 166 5 29 14 44
DEL PEAK 30(14Q24.1) MUTATED 1 276 27 4 3 1 10
DEL PEAK 30(14Q24.1) WILD-TYPE 0 459 139 1 26 13 34

Figure S37.  Get High-res Image Gene #58: 'del_14q24.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_15q13.1' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S38.  Gene #59: '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 1 735 166 5 29 14 44
DEL PEAK 31(15Q13.1) MUTATED 1 290 32 4 8 1 12
DEL PEAK 31(15Q13.1) WILD-TYPE 0 445 134 1 21 13 32

Figure S38.  Get High-res Image Gene #59: 'del_15q13.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_16q24.3' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S39.  Gene #60: '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 1 735 166 5 29 14 44
DEL PEAK 32(16Q24.3) MUTATED 0 445 149 2 20 1 16
DEL PEAK 32(16Q24.3) WILD-TYPE 1 290 17 3 9 13 28

Figure S39.  Get High-res Image Gene #60: 'del_16q24.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_17q21.31' versus 'AGE'

P value = 9.25e-05 (Wilcoxon-test), Q value = 0.073

Table S40.  Gene #62: 'del_17q21.31' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 982 58.7 (13.1)
DEL PEAK 34(17Q21.31) MUTATED 337 56.6 (13.2)
DEL PEAK 34(17Q21.31) WILD-TYPE 645 59.8 (12.9)

Figure S40.  Get High-res Image Gene #62: 'del_17q21.31' versus Clinical Feature #2: 'AGE'

'del_17q21.31' versus 'HISTOLOGICAL.TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.016

Table S41.  Gene #62: '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 1 735 166 5 29 14 44
DEL PEAK 34(17Q21.31) MUTATED 0 280 31 4 11 1 16
DEL PEAK 34(17Q21.31) WILD-TYPE 1 455 135 1 18 13 28

Figure S41.  Get High-res Image Gene #62: 'del_17q21.31' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_19p13.3' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S42.  Gene #64: '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 1 735 166 5 29 14 44
DEL PEAK 36(19P13.3) MUTATED 1 282 17 4 8 4 13
DEL PEAK 36(19P13.3) WILD-TYPE 0 453 149 1 21 10 31

Figure S42.  Get High-res Image Gene #64: 'del_19p13.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_19q13.32' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S43.  Gene #65: '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 1 735 166 5 29 14 44
DEL PEAK 37(19Q13.32) MUTATED 0 171 6 3 5 3 5
DEL PEAK 37(19Q13.32) WILD-TYPE 1 564 160 2 24 11 39

Figure S43.  Get High-res Image Gene #65: 'del_19q13.32' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_20p13' versus 'HISTOLOGICAL.TYPE'

P value = 6e-05 (Fisher's exact test), Q value = 0.048

Table S44.  Gene #66: '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 1 735 166 5 29 14 44
DEL PEAK 38(20P13) MUTATED 1 132 9 2 2 0 5
DEL PEAK 38(20P13) WILD-TYPE 0 603 157 3 27 14 39

Figure S44.  Get High-res Image Gene #66: '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 = 995

  • Number of significantly focal cnvs = 69

  • Number of selected clinical features = 12

  • Exclude genes that fewer than K tumors have mutations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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