Correlation between copy number variations of arm-level result and selected clinical features
Breast Invasive Carcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1Z60MWX
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 variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1Z60MWX
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.

Summary

Testing the association between copy number variation 80 arm-level events and 12 clinical features across 1025 patients, 28 significant findings detected with Q value < 0.25.

  • 2p gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 3q gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 6p gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 8q gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 10p gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 20p gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 20q gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 21q gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • xq gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 1p loss cnv correlated to 'AGE',  'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.

  • 4p loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 4q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 5p loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 5q loss cnv correlated to 'HISTOLOGICAL.TYPE' and 'RACE'.

  • 8p loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 9p loss cnv correlated to 'PATHOLOGY.T.STAGE' and 'HISTOLOGICAL.TYPE'.

  • 9q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 12q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 14q loss cnv correlated to 'HISTOLOGICAL.TYPE' and 'RACE'.

  • 16q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 18p loss cnv correlated to 'Time to Death'.

  • 19p loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 19q loss 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 80 arm-level events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 28 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
1p loss 233 (23%) 792 0.0627
(1.00) 		0.000219
(0.204) 		6e-05
(0.0563) 		2e-05
(0.0189) 		0.00321
(1.00) 		0.329
(1.00) 		1
(1.00) 		0.546
(1.00) 		0.677
(1.00) 		0.000414
(0.385) 		0.806
(1.00) 		0.677
(1.00)
5q loss 216 (21%) 809 0.372
(1.00) 		0.000688
(0.637) 		0.223
(1.00) 		0.00111
(1.00) 		0.372
(1.00) 		0.334
(1.00) 		0.133
(1.00) 		1e-05
(0.00959) 		0.441
(1.00) 		0.0822
(1.00) 		2e-05
(0.0189) 		0.306
(1.00)
9p loss 298 (29%) 727 0.015
(1.00) 		0.645
(1.00) 		0.00173
(1.00) 		0.0001
(0.0937) 		0.0136
(1.00) 		0.0349
(1.00) 		0.0895
(1.00) 		1e-05
(0.00959) 		0.054
(1.00) 		0.182
(1.00) 		0.304
(1.00) 		0.571
(1.00)
14q loss 250 (24%) 775 0.0279
(1.00) 		0.648
(1.00) 		0.841
(1.00) 		0.0456
(1.00) 		0.0826
(1.00) 		0.968
(1.00) 		0.312
(1.00) 		2e-05
(0.0189) 		0.329
(1.00) 		0.065
(1.00) 		0.00023
(0.215) 		0.427
(1.00)
2p gain 116 (11%) 909 0.292
(1.00) 		0.342
(1.00) 		0.798
(1.00) 		0.587
(1.00) 		0.971
(1.00) 		0.875
(1.00) 		0.624
(1.00) 		1e-05
(0.00959) 		0.378
(1.00) 		0.967
(1.00) 		0.00304
(1.00) 		0.0272
(1.00)
3q gain 204 (20%) 821 0.562
(1.00) 		0.539
(1.00) 		0.354
(1.00) 		0.0805
(1.00) 		0.448
(1.00) 		0.139
(1.00) 		0.703
(1.00) 		1e-05
(0.00959) 		0.255
(1.00) 		0.0153
(1.00) 		0.007
(1.00) 		0.831
(1.00)
6p gain 199 (19%) 826 0.343
(1.00) 		0.916
(1.00) 		0.549
(1.00) 		0.0763
(1.00) 		0.561
(1.00) 		0.887
(1.00) 		0.701
(1.00) 		0.00021
(0.197) 		0.216
(1.00) 		0.252
(1.00) 		0.0227
(1.00) 		0.388
(1.00)
8q gain 506 (49%) 519 0.814
(1.00) 		0.875
(1.00) 		0.498
(1.00) 		0.594
(1.00) 		0.53
(1.00) 		0.0862
(1.00) 		0.38
(1.00) 		1e-05
(0.00959) 		0.0209
(1.00) 		0.566
(1.00) 		0.0307
(1.00) 		0.173
(1.00)
10p gain 209 (20%) 816 0.872
(1.00) 		0.675
(1.00) 		0.271
(1.00) 		0.246
(1.00) 		0.266
(1.00) 		0.123
(1.00) 		1
(1.00) 		1e-05
(0.00959) 		0.0823
(1.00) 		0.346
(1.00) 		0.0008
(0.738) 		1
(1.00)
20p gain 397 (39%) 628 0.38
(1.00) 		0.221
(1.00) 		0.14
(1.00) 		0.29
(1.00) 		0.0109
(1.00) 		0.0181
(1.00) 		0.0276
(1.00) 		1e-05
(0.00959) 		0.0178
(1.00) 		0.518
(1.00) 		0.842
(1.00) 		0.383
(1.00)
20q gain 431 (42%) 594 0.348
(1.00) 		0.716
(1.00) 		0.527
(1.00) 		0.0162
(1.00) 		0.0539
(1.00) 		0.0402
(1.00) 		0.218
(1.00) 		1e-05
(0.00959) 		0.119
(1.00) 		0.261
(1.00) 		0.431
(1.00) 		0.171
(1.00)
21q gain 191 (19%) 834 0.0102
(1.00) 		0.0506
(1.00) 		0.623
(1.00) 		0.53
(1.00) 		0.642
(1.00) 		0.269
(1.00) 		1
(1.00) 		1e-05
(0.00959) 		0.0479
(1.00) 		0.606
(1.00) 		0.0201
(1.00) 		0.271
(1.00)
xq gain 137 (13%) 888 0.129
(1.00) 		0.0976
(1.00) 		0.461
(1.00) 		0.294
(1.00) 		0.683
(1.00) 		0.201
(1.00) 		1
(1.00) 		0.00021
(0.197) 		0.0998
(1.00) 		0.505
(1.00) 		0.114
(1.00) 		0.609
(1.00)
4p loss 335 (33%) 690 0.254
(1.00) 		0.192
(1.00) 		0.473
(1.00) 		0.019
(1.00) 		0.605
(1.00) 		0.429
(1.00) 		0.756
(1.00) 		1e-05
(0.00959) 		0.709
(1.00) 		0.826
(1.00) 		0.00653
(1.00) 		0.589
(1.00)
4q loss 295 (29%) 730 0.645
(1.00) 		0.788
(1.00) 		0.565
(1.00) 		0.0449
(1.00) 		0.751
(1.00) 		0.266
(1.00) 		0.738
(1.00) 		1e-05
(0.00959) 		0.396
(1.00) 		0.788
(1.00) 		0.0134
(1.00) 		0.85
(1.00)
5p loss 135 (13%) 890 0.215
(1.00) 		0.00526
(1.00) 		0.953
(1.00) 		0.022
(1.00) 		0.842
(1.00) 		0.986
(1.00) 		1
(1.00) 		1e-05
(0.00959) 		0.255
(1.00) 		0.332
(1.00) 		0.0454
(1.00) 		0.461
(1.00)
8p loss 377 (37%) 648 0.0458
(1.00) 		0.144
(1.00) 		1
(1.00) 		0.275
(1.00) 		0.655
(1.00) 		0.306
(1.00) 		0.755
(1.00) 		2e-05
(0.0189) 		0.384
(1.00) 		0.582
(1.00) 		0.0451
(1.00) 		0.482
(1.00)
9q loss 272 (27%) 753 0.427
(1.00) 		0.743
(1.00) 		0.166
(1.00) 		0.00392
(1.00) 		0.112
(1.00) 		0.277
(1.00) 		0.0773
(1.00) 		1e-05
(0.00959) 		0.0267
(1.00) 		0.962
(1.00) 		0.0249
(1.00) 		0.559
(1.00)
12q loss 123 (12%) 902 0.875
(1.00) 		0.0134
(1.00) 		0.243
(1.00) 		0.0131
(1.00) 		0.569
(1.00) 		0.342
(1.00) 		0.379
(1.00) 		7e-05
(0.0657) 		0.39
(1.00) 		0.0808
(1.00) 		0.0164
(1.00) 		0.609
(1.00)
16q loss 559 (55%) 466 0.15
(1.00) 		0.00185
(1.00) 		0.313
(1.00) 		0.633
(1.00) 		0.158
(1.00) 		0.0209
(1.00) 		0.241
(1.00) 		1e-05
(0.00959) 		0.14
(1.00) 		0.0853
(1.00) 		0.672
(1.00) 		0.737
(1.00)
18p loss 304 (30%) 721 8.95e-07
(0.000859) 		0.00339
(1.00) 		0.0295
(1.00) 		0.00442
(1.00) 		0.354
(1.00) 		0.666
(1.00) 		1
(1.00) 		0.00913
(1.00) 		1
(1.00) 		0.0992
(1.00) 		0.0298
(1.00) 		1
(1.00)
19p loss 182 (18%) 843 0.12
(1.00) 		0.0559
(1.00) 		0.866
(1.00) 		0.463
(1.00) 		0.402
(1.00) 		0.137
(1.00) 		1
(1.00) 		1e-05
(0.00959) 		0.584
(1.00) 		0.902
(1.00) 		0.00402
(1.00) 		0.377
(1.00)
19q loss 152 (15%) 873 0.118
(1.00) 		0.625
(1.00) 		0.697
(1.00) 		0.557
(1.00) 		0.278
(1.00) 		0.15
(1.00) 		0.672
(1.00) 		1e-05
(0.00959) 		0.116
(1.00) 		0.778
(1.00) 		0.041
(1.00) 		1
(1.00)
1p gain 194 (19%) 831 0.527
(1.00) 		0.0423
(1.00) 		0.878
(1.00) 		0.0638
(1.00) 		0.553
(1.00) 		0.772
(1.00) 		1
(1.00) 		0.0136
(1.00) 		0.0259
(1.00) 		0.237
(1.00) 		0.026
(1.00) 		0.52
(1.00)
1q gain 669 (65%) 356 0.347
(1.00) 		0.579
(1.00) 		0.0308
(1.00) 		0.0009
(0.827) 		0.506
(1.00) 		0.242
(1.00) 		0.528
(1.00) 		0.00086
(0.791) 		0.883
(1.00) 		0.437
(1.00) 		0.0729
(1.00) 		0.0744
(1.00)
2q gain 71 (7%) 954 0.901
(1.00) 		0.662
(1.00) 		0.653
(1.00) 		0.476
(1.00) 		0.825
(1.00) 		0.871
(1.00) 		1
(1.00) 		0.00954
(1.00) 		0.681
(1.00) 		0.411
(1.00) 		0.0713
(1.00) 		0.103
(1.00)
3p gain 132 (13%) 893 0.422
(1.00) 		0.307
(1.00) 		0.0512
(1.00) 		0.0471
(1.00) 		0.417
(1.00) 		0.00105
(0.964) 		1
(1.00) 		0.00085
(0.784) 		0.465
(1.00) 		0.322
(1.00) 		0.488
(1.00) 		0.792
(1.00)
4p gain 75 (7%) 950 0.358
(1.00) 		0.799
(1.00) 		0.0965
(1.00) 		0.0811
(1.00) 		0.701
(1.00) 		0.284
(1.00) 		0.568
(1.00) 		0.0133
(1.00) 		0.788
(1.00) 		0.764
(1.00) 		0.561
(1.00) 		0.736
(1.00)
4q gain 72 (7%) 953 0.228
(1.00) 		0.981
(1.00) 		0.204
(1.00) 		0.246
(1.00) 		0.462
(1.00) 		0.331
(1.00) 		0.553
(1.00) 		0.00719
(1.00) 		1
(1.00) 		0.721
(1.00) 		0.451
(1.00) 		0.731
(1.00)
5p gain 298 (29%) 727 0.223
(1.00) 		0.175
(1.00) 		0.564
(1.00) 		0.628
(1.00) 		0.00703
(1.00) 		0.111
(1.00) 		0.314
(1.00) 		0.523
(1.00) 		0.282
(1.00) 		0.816
(1.00) 		0.286
(1.00) 		1
(1.00)
5q gain 200 (20%) 825 0.954
(1.00) 		0.0125
(1.00) 		0.363
(1.00) 		0.206
(1.00) 		0.295
(1.00) 		0.36
(1.00) 		1
(1.00) 		0.666
(1.00) 		0.481
(1.00) 		0.585
(1.00) 		0.00582
(1.00) 		1
(1.00)
6q gain 141 (14%) 884 0.205
(1.00) 		0.972
(1.00) 		0.522
(1.00) 		0.0596
(1.00) 		0.156
(1.00) 		0.917
(1.00) 		1
(1.00) 		0.00184
(1.00) 		0.417
(1.00) 		0.0543
(1.00) 		0.298
(1.00) 		0.316
(1.00)
7p gain 293 (29%) 732 0.368
(1.00) 		0.183
(1.00) 		0.919
(1.00) 		0.816
(1.00) 		0.864
(1.00) 		0.524
(1.00) 		0.016
(1.00) 		0.0848
(1.00) 		0.215
(1.00) 		0.728
(1.00) 		0.47
(1.00) 		0.85
(1.00)
7q gain 250 (24%) 775 0.766
(1.00) 		0.991
(1.00) 		0.425
(1.00) 		0.352
(1.00) 		0.571
(1.00) 		0.243
(1.00) 		0.149
(1.00) 		0.15
(1.00) 		0.935
(1.00) 		0.798
(1.00) 		0.0965
(1.00) 		0.69
(1.00)
8p gain 276 (27%) 749 0.853
(1.00) 		0.889
(1.00) 		0.446
(1.00) 		0.89
(1.00) 		0.565
(1.00) 		0.262
(1.00) 		0.499
(1.00) 		0.212
(1.00) 		0.875
(1.00) 		0.669
(1.00) 		0.176
(1.00) 		1
(1.00)
9p gain 136 (13%) 889 0.768
(1.00) 		0.806
(1.00) 		0.157
(1.00) 		0.212
(1.00) 		0.173
(1.00) 		0.937
(1.00) 		0.377
(1.00) 		0.243
(1.00) 		1
(1.00) 		0.633
(1.00) 		0.288
(1.00) 		1
(1.00)
9q gain 112 (11%) 913 0.205
(1.00) 		0.741
(1.00) 		0.497
(1.00) 		0.374
(1.00) 		0.305
(1.00) 		0.931
(1.00) 		0.62
(1.00) 		0.124
(1.00) 		0.654
(1.00) 		0.906
(1.00) 		0.349
(1.00) 		1
(1.00)
10q gain 122 (12%) 903 0.748
(1.00) 		0.621
(1.00) 		0.618
(1.00) 		0.331
(1.00) 		0.662
(1.00) 		0.374
(1.00) 		1
(1.00) 		0.00329
(1.00) 		0.0834
(1.00) 		0.226
(1.00) 		0.0755
(1.00) 		0.594
(1.00)
11p gain 131 (13%) 894 0.77
(1.00) 		0.768
(1.00) 		0.871
(1.00) 		0.766
(1.00) 		0.313
(1.00) 		0.619
(1.00) 		0.641
(1.00) 		0.00348
(1.00) 		0.835
(1.00) 		0.0119
(1.00) 		0.767
(1.00) 		0.452
(1.00)
11q gain 91 (9%) 934 0.138
(1.00) 		0.88
(1.00) 		0.486
(1.00) 		0.746
(1.00) 		0.503
(1.00) 		0.607
(1.00) 		1
(1.00) 		0.00079
(0.73) 		0.712
(1.00) 		0.128
(1.00) 		0.212
(1.00) 		0.559
(1.00)
12p gain 217 (21%) 808 0.272
(1.00) 		0.575
(1.00) 		0.538
(1.00) 		0.0665
(1.00) 		0.142
(1.00) 		0.653
(1.00) 		0.0616
(1.00) 		0.0316
(1.00) 		0.171
(1.00) 		0.383
(1.00) 		0.682
(1.00) 		0.402
(1.00)
12q gain 184 (18%) 841 0.194
(1.00) 		0.145
(1.00) 		0.0922
(1.00) 		0.0221
(1.00) 		0.00548
(1.00) 		0.544
(1.00) 		0.0322
(1.00) 		0.0857
(1.00) 		0.202
(1.00) 		0.00516
(1.00) 		0.851
(1.00) 		0.376
(1.00)
13q gain 87 (8%) 938 0.595
(1.00) 		0.404
(1.00) 		0.67
(1.00) 		0.335
(1.00) 		0.481
(1.00) 		0.163
(1.00) 		0.613
(1.00) 		0.00289
(1.00) 		0.317
(1.00) 		0.948
(1.00) 		0.359
(1.00) 		0.116
(1.00)
14q gain 137 (13%) 888 0.473
(1.00) 		0.113
(1.00) 		0.222
(1.00) 		0.172
(1.00) 		0.0646
(1.00) 		0.661
(1.00) 		0.377
(1.00) 		0.146
(1.00) 		0.537
(1.00) 		0.0411
(1.00) 		0.739
(1.00) 		0.213
(1.00)
15q gain 84 (8%) 941 0.488
(1.00) 		0.938
(1.00) 		0.585
(1.00) 		0.907
(1.00) 		0.956
(1.00) 		0.288
(1.00) 		0.611
(1.00) 		0.00109
(0.998) 		0.16
(1.00) 		0.991
(1.00) 		0.206
(1.00) 		0.761
(1.00)
16p gain 450 (44%) 575 0.555
(1.00) 		0.0365
(1.00) 		0.521
(1.00) 		0.705
(1.00) 		0.354
(1.00) 		0.794
(1.00) 		0.549
(1.00) 		0.0286
(1.00) 		0.438
(1.00) 		0.373
(1.00) 		0.0294
(1.00) 		0.0851
(1.00)
16q gain 135 (13%) 890 0.09
(1.00) 		0.617
(1.00) 		0.182
(1.00) 		0.205
(1.00) 		0.266
(1.00) 		0.441
(1.00) 		0.0452
(1.00) 		0.204
(1.00) 		0.605
(1.00) 		0.256
(1.00) 		0.708
(1.00) 		0.215
(1.00)
17p gain 102 (10%) 923 0.137
(1.00) 		0.964
(1.00) 		0.11
(1.00) 		0.0423
(1.00) 		0.0697
(1.00) 		0.726
(1.00) 		0.00252
(1.00) 		0.046
(1.00) 		0.0464
(1.00) 		0.894
(1.00) 		0.64
(1.00) 		0.776
(1.00)
17q gain 208 (20%) 817 0.0147
(1.00) 		0.735
(1.00) 		0.728
(1.00) 		0.298
(1.00) 		0.741
(1.00) 		0.446
(1.00) 		0.00202
(1.00) 		0.0423
(1.00) 		0.0678
(1.00) 		0.399
(1.00) 		0.893
(1.00) 		0.677
(1.00)
18p gain 168 (16%) 857 0.406
(1.00) 		0.361
(1.00) 		0.111
(1.00) 		0.529
(1.00) 		0.0422
(1.00) 		0.685
(1.00) 		0.699
(1.00) 		0.0017
(1.00) 		0.508
(1.00) 		0.0125
(1.00) 		0.00041
(0.382) 		0.251
(1.00)
18q gain 143 (14%) 882 0.984
(1.00) 		0.583
(1.00) 		0.215
(1.00) 		0.26
(1.00) 		0.187
(1.00) 		0.0455
(1.00) 		0.658
(1.00) 		0.0223
(1.00) 		0.48
(1.00) 		0.234
(1.00) 		0.263
(1.00) 		0.612
(1.00)
19p gain 181 (18%) 844 0.978
(1.00) 		0.456
(1.00) 		0.326
(1.00) 		0.196
(1.00) 		0.254
(1.00) 		0.122
(1.00) 		0.112
(1.00) 		0.251
(1.00) 		0.359
(1.00) 		0.0212
(1.00) 		0.694
(1.00) 		1
(1.00)
19q gain 214 (21%) 811 0.647
(1.00) 		0.197
(1.00) 		0.259
(1.00) 		0.594
(1.00) 		0.123
(1.00) 		0.0263
(1.00) 		0.255
(1.00) 		0.205
(1.00) 		0.606
(1.00) 		0.0138
(1.00) 		0.982
(1.00) 		0.837
(1.00)
22q gain 97 (9%) 928 0.199
(1.00) 		0.759
(1.00) 		0.156
(1.00) 		0.0438
(1.00) 		0.375
(1.00) 		0.874
(1.00) 		1
(1.00) 		0.0007
(0.647) 		0.19
(1.00) 		0.153
(1.00) 		0.0173
(1.00) 		1
(1.00)
1q loss 49 (5%) 976 0.353
(1.00) 		0.344
(1.00) 		0.909
(1.00) 		0.405
(1.00) 		0.0928
(1.00) 		0.31
(1.00) 		1
(1.00) 		0.228
(1.00) 		0.624
(1.00) 		0.198
(1.00) 		0.641
(1.00) 		1
(1.00)
2p loss 172 (17%) 853 0.488
(1.00) 		0.427
(1.00) 		0.235
(1.00) 		0.374
(1.00) 		0.0651
(1.00) 		0.0366
(1.00) 		1
(1.00) 		0.271
(1.00) 		0.0194
(1.00) 		0.449
(1.00) 		0.324
(1.00) 		0.0528
(1.00)
2q loss 199 (19%) 826 0.278
(1.00) 		0.593
(1.00) 		0.0999
(1.00) 		0.276
(1.00) 		0.0688
(1.00) 		0.047
(1.00) 		1
(1.00) 		0.0638
(1.00) 		0.112
(1.00) 		0.286
(1.00) 		0.495
(1.00) 		0.0465
(1.00)
3p loss 176 (17%) 849 0.252
(1.00) 		0.141
(1.00) 		0.847
(1.00) 		0.00147
(1.00) 		0.925
(1.00) 		0.375
(1.00) 		0.228
(1.00) 		0.0149
(1.00) 		0.0157
(1.00) 		0.745
(1.00) 		0.14
(1.00) 		0.0462
(1.00)
3q loss 98 (10%) 927 0.122
(1.00) 		0.675
(1.00) 		0.396
(1.00) 		0.00085
(0.784) 		0.932
(1.00) 		0.978
(1.00) 		0.613
(1.00) 		0.167
(1.00) 		0.0425
(1.00) 		0.757
(1.00) 		0.287
(1.00) 		0.0426
(1.00)
6p loss 175 (17%) 850 0.932
(1.00) 		0.046
(1.00) 		0.994
(1.00) 		0.438
(1.00) 		0.935
(1.00) 		0.169
(1.00) 		0.701
(1.00) 		0.497
(1.00) 		0.227
(1.00) 		0.824
(1.00) 		0.583
(1.00) 		0.494
(1.00)
6q loss 260 (25%) 765 0.53
(1.00) 		0.00197
(1.00) 		0.953
(1.00) 		0.315
(1.00) 		0.697
(1.00) 		0.755
(1.00) 		0.308
(1.00) 		0.437
(1.00) 		0.0365
(1.00) 		0.457
(1.00) 		0.629
(1.00) 		0.556
(1.00)
7p loss 108 (11%) 917 0.688
(1.00) 		0.51
(1.00) 		0.44
(1.00) 		0.282
(1.00) 		0.104
(1.00) 		0.083
(1.00) 		0.618
(1.00) 		0.00064
(0.593) 		0.649
(1.00) 		0.3
(1.00) 		0.238
(1.00) 		0.25
(1.00)
7q loss 116 (11%) 909 0.117
(1.00) 		0.126
(1.00) 		0.638
(1.00) 		0.3
(1.00) 		0.378
(1.00) 		0.247
(1.00) 		1
(1.00) 		0.138
(1.00) 		0.508
(1.00) 		0.941
(1.00) 		0.734
(1.00) 		0.0257
(1.00)
8q loss 85 (8%) 940 0.0621
(1.00) 		0.107
(1.00) 		0.976
(1.00) 		0.751
(1.00) 		0.541
(1.00) 		0.252
(1.00) 		0.614
(1.00) 		0.605
(1.00) 		0.205
(1.00) 		0.938
(1.00) 		0.0573
(1.00) 		0.549
(1.00)
10p loss 162 (16%) 863 0.00734
(1.00) 		0.809
(1.00) 		0.0989
(1.00) 		0.00441
(1.00) 		0.116
(1.00) 		0.0259
(1.00) 		0.23
(1.00) 		0.0827
(1.00) 		1
(1.00) 		0.226
(1.00) 		0.345
(1.00) 		0.344
(1.00)
10q loss 219 (21%) 806 0.014
(1.00) 		0.772
(1.00) 		0.241
(1.00) 		0.00741
(1.00) 		0.116
(1.00) 		0.114
(1.00) 		0.474
(1.00) 		0.00943
(1.00) 		1
(1.00) 		0.316
(1.00) 		0.0363
(1.00) 		0.06
(1.00)
11p loss 266 (26%) 759 0.113
(1.00) 		0.625
(1.00) 		0.0156
(1.00) 		0.0101
(1.00) 		0.0616
(1.00) 		0.613
(1.00) 		0.738
(1.00) 		0.105
(1.00) 		0.69
(1.00) 		0.0759
(1.00) 		0.0011
(1.00) 		0.0731
(1.00)
11q loss 353 (34%) 672 0.971
(1.00) 		0.85
(1.00) 		0.122
(1.00) 		0.0934
(1.00) 		0.0442
(1.00) 		0.313
(1.00) 		0.202
(1.00) 		0.312
(1.00) 		0.606
(1.00) 		0.263
(1.00) 		0.00124
(1.00) 		1
(1.00)
12p loss 144 (14%) 881 0.725
(1.00) 		0.432
(1.00) 		0.254
(1.00) 		0.0158
(1.00) 		0.688
(1.00) 		0.186
(1.00) 		1
(1.00) 		0.00044
(0.409) 		0.367
(1.00) 		0.351
(1.00) 		0.282
(1.00) 		0.464
(1.00)
13q loss 415 (40%) 610 0.0469
(1.00) 		0.257
(1.00) 		0.796
(1.00) 		0.089
(1.00) 		0.773
(1.00) 		0.996
(1.00) 		0.764
(1.00) 		0.00033
(0.308) 		0.433
(1.00) 		0.604
(1.00) 		0.0956
(1.00) 		0.383
(1.00)
15q loss 303 (30%) 722 0.125
(1.00) 		0.861
(1.00) 		0.345
(1.00) 		0.00562
(1.00) 		0.0364
(1.00) 		0.498
(1.00) 		1
(1.00) 		0.00046
(0.427) 		0.0782
(1.00) 		0.129
(1.00) 		0.37
(1.00) 		0.358
(1.00)
16p loss 163 (16%) 862 0.367
(1.00) 		0.912
(1.00) 		0.28
(1.00) 		0.972
(1.00) 		0.078
(1.00) 		0.459
(1.00) 		0.69
(1.00) 		0.0524
(1.00) 		0.504
(1.00) 		0.0278
(1.00) 		0.00263
(1.00) 		0.645
(1.00)
17p loss 546 (53%) 479 0.249
(1.00) 		0.0265
(1.00) 		0.223
(1.00) 		0.00476
(1.00) 		0.777
(1.00) 		0.524
(1.00) 		0.364
(1.00) 		0.00629
(1.00) 		0.834
(1.00) 		0.88
(1.00) 		0.173
(1.00) 		1
(1.00)
17q loss 258 (25%) 767 0.914
(1.00) 		0.134
(1.00) 		0.986
(1.00) 		0.627
(1.00) 		0.174
(1.00) 		0.193
(1.00) 		0.0751
(1.00) 		0.00108
(0.99) 		0.629
(1.00) 		0.354
(1.00) 		0.00818
(1.00) 		1
(1.00)
18q loss 304 (30%) 721 0.00346
(1.00) 		0.0189
(1.00) 		0.0382
(1.00) 		0.0222
(1.00) 		0.107
(1.00) 		0.735
(1.00) 		1
(1.00) 		0.0109
(1.00) 		0.444
(1.00) 		0.211
(1.00) 		0.129
(1.00) 		0.711
(1.00)
20p loss 90 (9%) 935 0.203
(1.00) 		0.118
(1.00) 		0.413
(1.00) 		0.0797
(1.00) 		0.833
(1.00) 		0.0782
(1.00) 		1
(1.00) 		0.0372
(1.00) 		0.458
(1.00) 		0.936
(1.00) 		0.0532
(1.00) 		0.22
(1.00)
20q loss 52 (5%) 973 0.35
(1.00) 		0.0575
(1.00) 		0.262
(1.00) 		0.0349
(1.00) 		0.959
(1.00) 		0.53
(1.00) 		1
(1.00) 		0.0225
(1.00) 		0.633
(1.00) 		0.243
(1.00) 		0.0244
(1.00) 		0.105
(1.00)
21q loss 170 (17%) 855 0.674
(1.00) 		0.435
(1.00) 		0.0175
(1.00) 		0.164
(1.00) 		0.0314
(1.00) 		0.0974
(1.00) 		0.228
(1.00) 		0.0137
(1.00) 		0.452
(1.00) 		0.211
(1.00) 		0.086
(1.00) 		0.25
(1.00)
22q loss 454 (44%) 571 0.0804
(1.00) 		0.572
(1.00) 		0.617
(1.00) 		0.5
(1.00) 		0.231
(1.00) 		0.57
(1.00) 		0.551
(1.00) 		0.00121
(1.00) 		0.00121
(1.00) 		0.248
(1.00) 		0.401
(1.00) 		0.865
(1.00)
xq loss 171 (17%) 854 0.41
(1.00) 		0.144
(1.00) 		0.432
(1.00) 		0.0724
(1.00) 		0.653
(1.00) 		0.08
(1.00) 		0.406
(1.00) 		0.0618
(1.00) 		0.852
(1.00) 		0.341
(1.00) 		0.23
(1.00) 		1
(1.00)
'2p gain' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S1.  Gene #3: '2p gain' 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 1 754 175 6 29 15 44
2P GAIN MUTATED 1 104 4 2 0 0 5
2P GAIN WILD-TYPE 0 650 171 4 29 15 39

Figure S1.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'3q gain' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S2.  Gene #6: '3q gain' 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 1 754 175 6 29 15 44
3Q GAIN MUTATED 0 176 8 4 6 1 9
3Q GAIN WILD-TYPE 1 578 167 2 23 14 35

Figure S2.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'6p gain' versus 'HISTOLOGICAL.TYPE'

P value = 0.00021 (Fisher's exact test), Q value = 0.2

Table S3.  Gene #11: '6p gain' 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 1 754 175 6 29 15 44
6P GAIN MUTATED 0 163 17 4 3 1 10
6P GAIN WILD-TYPE 1 591 158 2 26 14 34

Figure S3.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'8q gain' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S4.  Gene #16: '8q gain' 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 1 754 175 6 29 15 44
8Q GAIN MUTATED 1 407 51 5 12 4 25
8Q GAIN WILD-TYPE 0 347 124 1 17 11 19

Figure S4.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'10p gain' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S5.  Gene #19: '10p gain' 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 1 754 175 6 29 15 44
10P GAIN MUTATED 0 179 16 4 4 0 6
10P GAIN WILD-TYPE 1 575 159 2 25 15 38

Figure S5.  Get High-res Image Gene #19: '10p gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'20p gain' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S6.  Gene #36: '20p gain' 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 1 754 175 6 29 15 44
20P GAIN MUTATED 0 331 40 2 9 1 13
20P GAIN WILD-TYPE 1 423 135 4 20 14 31

Figure S6.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'20q gain' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S7.  Gene #37: '20q gain' 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 1 754 175 6 29 15 44
20Q GAIN MUTATED 0 361 44 1 9 1 15
20Q GAIN WILD-TYPE 1 393 131 5 20 14 29

Figure S7.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'21q gain' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S8.  Gene #38: '21q gain' 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 1 754 175 6 29 15 44
21Q GAIN MUTATED 0 164 15 2 0 1 9
21Q GAIN WILD-TYPE 1 590 160 4 29 14 35

Figure S8.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'xq gain' versus 'HISTOLOGICAL.TYPE'

P value = 0.00021 (Fisher's exact test), Q value = 0.2

Table S9.  Gene #40: 'xq gain' 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 1 754 175 6 29 15 44
XQ GAIN MUTATED 1 116 9 2 1 3 4
XQ GAIN WILD-TYPE 0 638 166 4 28 12 40

Figure S9.  Get High-res Image Gene #40: 'xq gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'1p loss' versus 'AGE'

P value = 0.000219 (Wilcoxon-test), Q value = 0.2

Table S10.  Gene #41: '1p loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 1012 58.6 (13.2)
1P LOSS MUTATED 229 61.3 (13.0)
1P LOSS WILD-TYPE 783 57.8 (13.2)

Figure S10.  Get High-res Image Gene #41: '1p loss' versus Clinical Feature #2: 'AGE'

'1p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 6e-05 (Fisher's exact test), Q value = 0.056

Table S11.  Gene #41: '1p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
ALL 83 80 9 5 342 234 2 142 29 63 18 1 16
1P LOSS MUTATED 12 12 2 1 75 40 1 42 17 19 7 0 5
1P LOSS WILD-TYPE 71 68 7 4 267 194 1 100 12 44 11 1 11

Figure S11.  Get High-res Image Gene #41: '1p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'1p loss' versus 'PATHOLOGY.T.STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.019

Table S12.  Gene #41: '1p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 265 594 124 39
1P LOSS MUTATED 48 135 27 22
1P LOSS WILD-TYPE 217 459 97 17

Figure S12.  Get High-res Image Gene #41: '1p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'4p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S13.  Gene #47: '4p loss' 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 1 754 175 6 29 15 44
4P LOSS MUTATED 1 281 27 3 7 0 15
4P LOSS WILD-TYPE 0 473 148 3 22 15 29

Figure S13.  Get High-res Image Gene #47: '4p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'4q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S14.  Gene #48: '4q loss' 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 1 754 175 6 29 15 44
4Q LOSS MUTATED 0 246 24 2 7 0 15
4Q LOSS WILD-TYPE 1 508 151 4 22 15 29

Figure S14.  Get High-res Image Gene #48: '4q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'5p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S15.  Gene #49: '5p loss' 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 1 754 175 6 29 15 44
5P LOSS MUTATED 0 118 2 4 4 0 6
5P LOSS WILD-TYPE 1 636 173 2 25 15 38

Figure S15.  Get High-res Image Gene #49: '5p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'5q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S16.  Gene #50: '5q loss' 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 1 754 175 6 29 15 44
5Q LOSS MUTATED 1 195 3 4 4 0 8
5Q LOSS WILD-TYPE 0 559 172 2 25 15 36

Figure S16.  Get High-res Image Gene #50: '5q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'5q loss' versus 'RACE'

P value = 2e-05 (Fisher's exact test), Q value = 0.019

Table S17.  Gene #50: '5q loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 56 158 717
5Q LOSS MUTATED 0 17 54 129
5Q LOSS WILD-TYPE 1 39 104 588

Figure S17.  Get High-res Image Gene #50: '5q loss' versus Clinical Feature #11: 'RACE'

'8p loss' versus 'HISTOLOGICAL.TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.019

Table S18.  Gene #55: '8p loss' 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 1 754 175 6 29 15 44
8P LOSS MUTATED 1 307 39 2 7 2 18
8P LOSS WILD-TYPE 0 447 136 4 22 13 26

Figure S18.  Get High-res Image Gene #55: '8p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'9p loss' versus 'PATHOLOGY.T.STAGE'

P value = 1e-04 (Fisher's exact test), Q value = 0.094

Table S19.  Gene #57: '9p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 265 594 124 39
9P LOSS MUTATED 54 195 31 18
9P LOSS WILD-TYPE 211 399 93 21

Figure S19.  Get High-res Image Gene #57: '9p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'9p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S20.  Gene #57: '9p loss' 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 1 754 175 6 29 15 44
9P LOSS MUTATED 0 254 20 3 9 3 9
9P LOSS WILD-TYPE 1 500 155 3 20 12 35

Figure S20.  Get High-res Image Gene #57: '9p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'9q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S21.  Gene #58: '9q loss' 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 1 754 175 6 29 15 44
9Q LOSS MUTATED 0 229 18 2 9 3 11
9Q LOSS WILD-TYPE 1 525 157 4 20 12 33

Figure S21.  Get High-res Image Gene #58: '9q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'12q loss' versus 'HISTOLOGICAL.TYPE'

P value = 7e-05 (Fisher's exact test), Q value = 0.066

Table S22.  Gene #64: '12q loss' 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 1 754 175 6 29 15 44
12Q LOSS MUTATED 0 105 7 3 1 0 7
12Q LOSS WILD-TYPE 1 649 168 3 28 15 37

Figure S22.  Get High-res Image Gene #64: '12q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'14q loss' versus 'HISTOLOGICAL.TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.019

Table S23.  Gene #66: '14q loss' 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 1 754 175 6 29 15 44
14Q LOSS MUTATED 0 207 24 5 3 1 9
14Q LOSS WILD-TYPE 1 547 151 1 26 14 35

Figure S23.  Get High-res Image Gene #66: '14q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'14q loss' versus 'RACE'

P value = 0.00023 (Fisher's exact test), Q value = 0.21

Table S24.  Gene #66: '14q loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 56 158 717
14Q LOSS MUTATED 0 13 60 155
14Q LOSS WILD-TYPE 1 43 98 562

Figure S24.  Get High-res Image Gene #66: '14q loss' versus Clinical Feature #11: 'RACE'

'16q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S25.  Gene #69: '16q loss' 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 1 754 175 6 29 15 44
16Q LOSS MUTATED 0 386 136 3 18 1 14
16Q LOSS WILD-TYPE 1 368 39 3 11 14 30

Figure S25.  Get High-res Image Gene #69: '16q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'18p loss' versus 'Time to Death'

P value = 8.95e-07 (logrank test), Q value = 0.00086

Table S26.  Gene #72: '18p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1005 119 0.0 - 234.3 (22.4)
18P LOSS MUTATED 296 52 0.0 - 189.0 (20.4)
18P LOSS WILD-TYPE 709 67 0.0 - 234.3 (23.5)

Figure S26.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #1: 'Time to Death'

'19p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S27.  Gene #74: '19p loss' 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 1 754 175 6 29 15 44
19P LOSS MUTATED 0 162 7 1 3 3 5
19P LOSS WILD-TYPE 1 592 168 5 26 12 39

Figure S27.  Get High-res Image Gene #74: '19p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'19q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S28.  Gene #75: '19q loss' 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 1 754 175 6 29 15 44
19Q LOSS MUTATED 0 136 4 1 3 3 4
19Q LOSS WILD-TYPE 1 618 171 5 26 12 40

Figure S28.  Get High-res Image Gene #75: '19q loss' 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 = 1025

  • Number of significantly arm-level cnvs = 80

  • Number of selected clinical features = 12

  • Exclude regions 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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