Correlation between copy number variations of arm-level result and selected clinical features
Breast Invasive Carcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1M907CK
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 995 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 '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 'AGE',  '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'.

  • 13q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

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

  • 15q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 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
5q loss 212 (21%) 783 0.348
(1.00)
0.000261
(0.244)
0.273
(1.00)
0.00553
(1.00)
0.253
(1.00)
0.554
(1.00)
0.134
(1.00)
1e-05
(0.00959)
0.493
(1.00)
0.0672
(1.00)
9e-05
(0.0845)
0.304
(1.00)
1p loss 226 (23%) 769 0.0301
(1.00)
0.000588
(0.546)
6e-05
(0.0565)
3e-05
(0.0283)
0.00596
(1.00)
0.43
(1.00)
1
(1.00)
0.503
(1.00)
0.675
(1.00)
0.001
(0.922)
0.799
(1.00)
0.677
(1.00)
9p loss 296 (30%) 699 0.0226
(1.00)
0.872
(1.00)
0.00113
(1.00)
0.00014
(0.131)
0.0372
(1.00)
0.0459
(1.00)
0.0944
(1.00)
1e-05
(0.00959)
0.0909
(1.00)
0.354
(1.00)
0.203
(1.00)
0.575
(1.00)
2p gain 113 (11%) 882 0.275
(1.00)
0.536
(1.00)
0.705
(1.00)
0.604
(1.00)
0.993
(1.00)
0.974
(1.00)
0.624
(1.00)
1e-05
(0.00959)
0.377
(1.00)
0.645
(1.00)
0.00344
(1.00)
0.0161
(1.00)
3q gain 197 (20%) 798 0.572
(1.00)
0.385
(1.00)
0.721
(1.00)
0.163
(1.00)
0.536
(1.00)
0.227
(1.00)
0.703
(1.00)
1e-05
(0.00959)
0.217
(1.00)
0.0158
(1.00)
0.0226
(1.00)
0.83
(1.00)
6p gain 190 (19%) 805 0.308
(1.00)
0.927
(1.00)
0.76
(1.00)
0.128
(1.00)
0.458
(1.00)
0.864
(1.00)
0.701
(1.00)
0.00021
(0.196)
0.153
(1.00)
0.172
(1.00)
0.0572
(1.00)
0.382
(1.00)
8q gain 494 (50%) 501 0.55
(1.00)
0.755
(1.00)
0.359
(1.00)
0.707
(1.00)
0.447
(1.00)
0.0892
(1.00)
0.382
(1.00)
1e-05
(0.00959)
0.0291
(1.00)
0.539
(1.00)
0.0263
(1.00)
0.172
(1.00)
10p gain 200 (20%) 795 0.991
(1.00)
0.492
(1.00)
0.128
(1.00)
0.277
(1.00)
0.225
(1.00)
0.11
(1.00)
1
(1.00)
6e-05
(0.0565)
0.0534
(1.00)
0.437
(1.00)
0.00346
(1.00)
1
(1.00)
20p gain 383 (38%) 612 0.172
(1.00)
0.281
(1.00)
0.0871
(1.00)
0.606
(1.00)
0.00852
(1.00)
0.00596
(1.00)
0.0269
(1.00)
1e-05
(0.00959)
0.0206
(1.00)
0.476
(1.00)
0.914
(1.00)
0.383
(1.00)
20q gain 417 (42%) 578 0.32
(1.00)
0.798
(1.00)
0.287
(1.00)
0.0566
(1.00)
0.0495
(1.00)
0.0405
(1.00)
0.218
(1.00)
1e-05
(0.00959)
0.134
(1.00)
0.257
(1.00)
0.615
(1.00)
0.171
(1.00)
21q gain 187 (19%) 808 0.00378
(1.00)
0.0767
(1.00)
0.768
(1.00)
0.738
(1.00)
0.806
(1.00)
0.476
(1.00)
1
(1.00)
3e-05
(0.0283)
0.0583
(1.00)
0.801
(1.00)
0.0204
(1.00)
0.274
(1.00)
xq gain 130 (13%) 865 0.3
(1.00)
0.0968
(1.00)
0.573
(1.00)
0.435
(1.00)
0.716
(1.00)
0.136
(1.00)
1
(1.00)
0.00018
(0.169)
0.0606
(1.00)
0.569
(1.00)
0.249
(1.00)
0.609
(1.00)
4p loss 324 (33%) 671 0.302
(1.00)
0.298
(1.00)
0.45
(1.00)
0.0353
(1.00)
0.675
(1.00)
0.468
(1.00)
0.755
(1.00)
1e-05
(0.00959)
0.764
(1.00)
0.816
(1.00)
0.0187
(1.00)
0.589
(1.00)
4q loss 288 (29%) 707 0.819
(1.00)
0.871
(1.00)
0.598
(1.00)
0.0713
(1.00)
0.784
(1.00)
0.389
(1.00)
0.739
(1.00)
1e-05
(0.00959)
0.535
(1.00)
0.99
(1.00)
0.0171
(1.00)
0.71
(1.00)
5p loss 130 (13%) 865 0.348
(1.00)
0.00579
(1.00)
0.929
(1.00)
0.0565
(1.00)
0.941
(1.00)
0.91
(1.00)
1
(1.00)
1e-05
(0.00959)
0.144
(1.00)
0.552
(1.00)
0.104
(1.00)
0.461
(1.00)
8p loss 362 (36%) 633 0.0283
(1.00)
0.238
(1.00)
0.959
(1.00)
0.249
(1.00)
0.684
(1.00)
0.329
(1.00)
0.755
(1.00)
2e-05
(0.0189)
0.559
(1.00)
0.385
(1.00)
0.0351
(1.00)
0.482
(1.00)
9q loss 268 (27%) 727 0.276
(1.00)
0.829
(1.00)
0.142
(1.00)
0.00311
(1.00)
0.133
(1.00)
0.477
(1.00)
0.0785
(1.00)
1e-05
(0.00959)
0.0576
(1.00)
0.929
(1.00)
0.0111
(1.00)
0.562
(1.00)
13q loss 408 (41%) 587 0.0462
(1.00)
0.369
(1.00)
0.766
(1.00)
0.0711
(1.00)
0.855
(1.00)
0.986
(1.00)
0.767
(1.00)
0.00025
(0.233)
0.567
(1.00)
0.694
(1.00)
0.0122
(1.00)
0.3
(1.00)
14q loss 240 (24%) 755 0.0286
(1.00)
0.619
(1.00)
0.875
(1.00)
0.0328
(1.00)
0.0595
(1.00)
0.936
(1.00)
0.476
(1.00)
4e-05
(0.0377)
0.251
(1.00)
0.0505
(1.00)
0.00055
(0.511)
0.326
(1.00)
15q loss 296 (30%) 699 0.113
(1.00)
0.658
(1.00)
0.541
(1.00)
0.0106
(1.00)
0.0462
(1.00)
0.478
(1.00)
1
(1.00)
0.00018
(0.169)
0.0909
(1.00)
0.185
(1.00)
0.181
(1.00)
0.356
(1.00)
16q loss 546 (55%) 449 0.0592
(1.00)
0.000784
(0.726)
0.321
(1.00)
0.451
(1.00)
0.0651
(1.00)
0.113
(1.00)
0.238
(1.00)
1e-05
(0.00959)
0.0564
(1.00)
0.0997
(1.00)
0.703
(1.00)
0.734
(1.00)
18p loss 293 (29%) 702 9.48e-07
(0.00091)
0.00479
(1.00)
0.0572
(1.00)
0.0132
(1.00)
0.436
(1.00)
0.93
(1.00)
1
(1.00)
0.0104
(1.00)
0.878
(1.00)
0.171
(1.00)
0.0256
(1.00)
0.71
(1.00)
19p loss 176 (18%) 819 0.105
(1.00)
0.0885
(1.00)
0.858
(1.00)
0.585
(1.00)
0.409
(1.00)
0.183
(1.00)
1
(1.00)
1e-05
(0.00959)
0.461
(1.00)
0.721
(1.00)
0.00939
(1.00)
0.371
(1.00)
19q loss 149 (15%) 846 0.162
(1.00)
0.998
(1.00)
0.665
(1.00)
0.499
(1.00)
0.15
(1.00)
0.285
(1.00)
0.674
(1.00)
1e-05
(0.00959)
0.0937
(1.00)
0.436
(1.00)
0.146
(1.00)
1
(1.00)
1p gain 188 (19%) 807 0.392
(1.00)
0.0977
(1.00)
0.851
(1.00)
0.0719
(1.00)
0.309
(1.00)
0.941
(1.00)
1
(1.00)
0.0196
(1.00)
0.0388
(1.00)
0.11
(1.00)
0.215
(1.00)
0.519
(1.00)
1q gain 649 (65%) 346 0.314
(1.00)
0.478
(1.00)
0.0324
(1.00)
0.00379
(1.00)
0.596
(1.00)
0.635
(1.00)
0.528
(1.00)
0.0032
(1.00)
1
(1.00)
0.847
(1.00)
0.0791
(1.00)
0.0746
(1.00)
2q gain 71 (7%) 924 0.857
(1.00)
0.882
(1.00)
0.886
(1.00)
0.463
(1.00)
0.885
(1.00)
1
(1.00)
1
(1.00)
0.0112
(1.00)
0.786
(1.00)
0.653
(1.00)
0.0503
(1.00)
0.102
(1.00)
3p gain 131 (13%) 864 0.335
(1.00)
0.313
(1.00)
0.0864
(1.00)
0.0396
(1.00)
0.431
(1.00)
0.00072
(0.667)
1
(1.00)
0.00125
(1.00)
0.535
(1.00)
0.38
(1.00)
0.457
(1.00)
0.795
(1.00)
4p gain 74 (7%) 921 0.105
(1.00)
0.765
(1.00)
0.18
(1.00)
0.0745
(1.00)
0.698
(1.00)
0.262
(1.00)
0.575
(1.00)
0.00586
(1.00)
0.688
(1.00)
0.664
(1.00)
0.656
(1.00)
0.739
(1.00)
4q gain 70 (7%) 925 0.0554
(1.00)
0.884
(1.00)
0.242
(1.00)
0.193
(1.00)
0.499
(1.00)
0.275
(1.00)
0.554
(1.00)
0.00276
(1.00)
1
(1.00)
0.813
(1.00)
0.471
(1.00)
0.731
(1.00)
5p gain 290 (29%) 705 0.0768
(1.00)
0.123
(1.00)
0.384
(1.00)
0.613
(1.00)
0.00123
(1.00)
0.0219
(1.00)
0.314
(1.00)
0.514
(1.00)
0.395
(1.00)
0.414
(1.00)
0.379
(1.00)
1
(1.00)
5q gain 194 (19%) 801 0.561
(1.00)
0.00823
(1.00)
0.475
(1.00)
0.35
(1.00)
0.179
(1.00)
0.211
(1.00)
1
(1.00)
0.75
(1.00)
0.479
(1.00)
0.957
(1.00)
0.0149
(1.00)
1
(1.00)
6q gain 136 (14%) 859 0.268
(1.00)
0.989
(1.00)
0.579
(1.00)
0.0992
(1.00)
0.0955
(1.00)
0.977
(1.00)
1
(1.00)
0.00067
(0.622)
0.358
(1.00)
0.02
(1.00)
0.26
(1.00)
0.314
(1.00)
7p gain 283 (28%) 712 0.531
(1.00)
0.14
(1.00)
0.903
(1.00)
0.832
(1.00)
0.926
(1.00)
0.511
(1.00)
0.0155
(1.00)
0.124
(1.00)
0.242
(1.00)
0.989
(1.00)
0.554
(1.00)
0.85
(1.00)
7q gain 239 (24%) 756 0.729
(1.00)
0.871
(1.00)
0.599
(1.00)
0.536
(1.00)
0.582
(1.00)
0.595
(1.00)
0.307
(1.00)
0.223
(1.00)
0.935
(1.00)
0.393
(1.00)
0.245
(1.00)
0.689
(1.00)
8p gain 270 (27%) 725 0.787
(1.00)
0.878
(1.00)
0.569
(1.00)
0.814
(1.00)
0.726
(1.00)
0.252
(1.00)
0.502
(1.00)
0.384
(1.00)
0.937
(1.00)
0.79
(1.00)
0.168
(1.00)
1
(1.00)
9p gain 128 (13%) 867 0.767
(1.00)
0.95
(1.00)
0.167
(1.00)
0.479
(1.00)
0.146
(1.00)
0.794
(1.00)
0.377
(1.00)
0.553
(1.00)
1
(1.00)
0.714
(1.00)
0.622
(1.00)
0.803
(1.00)
9q gain 108 (11%) 887 0.18
(1.00)
0.73
(1.00)
0.513
(1.00)
0.46
(1.00)
0.206
(1.00)
0.972
(1.00)
0.62
(1.00)
0.319
(1.00)
0.574
(1.00)
0.874
(1.00)
0.366
(1.00)
1
(1.00)
10q gain 117 (12%) 878 0.638
(1.00)
0.414
(1.00)
0.623
(1.00)
0.325
(1.00)
0.819
(1.00)
0.566
(1.00)
1
(1.00)
0.0217
(1.00)
0.063
(1.00)
0.319
(1.00)
0.102
(1.00)
0.592
(1.00)
11p gain 129 (13%) 866 0.465
(1.00)
0.991
(1.00)
0.938
(1.00)
0.729
(1.00)
0.231
(1.00)
0.706
(1.00)
0.643
(1.00)
0.00523
(1.00)
0.917
(1.00)
0.0482
(1.00)
0.709
(1.00)
0.455
(1.00)
11q gain 89 (9%) 906 0.103
(1.00)
0.972
(1.00)
0.654
(1.00)
0.71
(1.00)
0.393
(1.00)
0.753
(1.00)
1
(1.00)
0.00123
(1.00)
0.624
(1.00)
0.192
(1.00)
0.201
(1.00)
0.562
(1.00)
12p gain 214 (22%) 781 0.252
(1.00)
0.805
(1.00)
0.648
(1.00)
0.12
(1.00)
0.114
(1.00)
0.736
(1.00)
0.0653
(1.00)
0.0172
(1.00)
0.231
(1.00)
0.452
(1.00)
0.62
(1.00)
0.403
(1.00)
12q gain 181 (18%) 814 0.155
(1.00)
0.303
(1.00)
0.137
(1.00)
0.0428
(1.00)
0.00631
(1.00)
0.523
(1.00)
0.034
(1.00)
0.0618
(1.00)
0.172
(1.00)
0.0068
(1.00)
0.71
(1.00)
0.375
(1.00)
13q gain 86 (9%) 909 0.777
(1.00)
0.423
(1.00)
0.674
(1.00)
0.422
(1.00)
0.469
(1.00)
0.297
(1.00)
0.613
(1.00)
0.004
(1.00)
0.382
(1.00)
0.789
(1.00)
0.417
(1.00)
0.121
(1.00)
14q gain 134 (13%) 861 0.43
(1.00)
0.0845
(1.00)
0.196
(1.00)
0.164
(1.00)
0.057
(1.00)
0.676
(1.00)
0.377
(1.00)
0.142
(1.00)
0.537
(1.00)
0.0339
(1.00)
0.719
(1.00)
0.212
(1.00)
15q gain 83 (8%) 912 0.37
(1.00)
0.812
(1.00)
0.696
(1.00)
0.835
(1.00)
0.931
(1.00)
0.548
(1.00)
1
(1.00)
0.00135
(1.00)
0.164
(1.00)
0.997
(1.00)
0.204
(1.00)
1
(1.00)
16p gain 443 (45%) 552 0.897
(1.00)
0.0163
(1.00)
0.616
(1.00)
0.8
(1.00)
0.402
(1.00)
0.909
(1.00)
0.553
(1.00)
0.0419
(1.00)
0.437
(1.00)
0.716
(1.00)
0.164
(1.00)
0.126
(1.00)
16q gain 129 (13%) 866 0.0707
(1.00)
0.783
(1.00)
0.21
(1.00)
0.301
(1.00)
0.188
(1.00)
0.158
(1.00)
0.0429
(1.00)
0.143
(1.00)
1
(1.00)
0.273
(1.00)
0.51
(1.00)
0.213
(1.00)
17p gain 101 (10%) 894 0.157
(1.00)
0.913
(1.00)
0.155
(1.00)
0.0243
(1.00)
0.0814
(1.00)
0.477
(1.00)
0.00275
(1.00)
0.123
(1.00)
0.0618
(1.00)
0.879
(1.00)
0.656
(1.00)
0.777
(1.00)
17q gain 208 (21%) 787 0.0498
(1.00)
0.663
(1.00)
0.806
(1.00)
0.272
(1.00)
0.675
(1.00)
0.18
(1.00)
0.00243
(1.00)
0.0653
(1.00)
0.0464
(1.00)
0.293
(1.00)
0.856
(1.00)
0.676
(1.00)
18p gain 163 (16%) 832 0.287
(1.00)
0.298
(1.00)
0.0636
(1.00)
0.391
(1.00)
0.0249
(1.00)
0.607
(1.00)
0.699
(1.00)
0.00394
(1.00)
0.506
(1.00)
0.0163
(1.00)
0.00043
(0.401)
0.102
(1.00)
18q gain 138 (14%) 857 0.813
(1.00)
0.692
(1.00)
0.139
(1.00)
0.247
(1.00)
0.249
(1.00)
0.0686
(1.00)
0.656
(1.00)
0.0449
(1.00)
0.418
(1.00)
0.281
(1.00)
0.207
(1.00)
0.213
(1.00)
19p gain 170 (17%) 825 0.971
(1.00)
0.721
(1.00)
0.311
(1.00)
0.199
(1.00)
0.205
(1.00)
0.16
(1.00)
0.102
(1.00)
0.196
(1.00)
0.224
(1.00)
0.0175
(1.00)
0.865
(1.00)
1
(1.00)
19q gain 201 (20%) 794 0.543
(1.00)
0.105
(1.00)
0.273
(1.00)
0.68
(1.00)
0.107
(1.00)
0.0435
(1.00)
0.247
(1.00)
0.442
(1.00)
0.382
(1.00)
0.014
(1.00)
0.935
(1.00)
0.833
(1.00)
22q gain 94 (9%) 901 0.127
(1.00)
0.714
(1.00)
0.304
(1.00)
0.101
(1.00)
0.384
(1.00)
0.786
(1.00)
1
(1.00)
0.00196
(1.00)
0.188
(1.00)
0.144
(1.00)
0.027
(1.00)
1
(1.00)
1q loss 50 (5%) 945 0.378
(1.00)
0.275
(1.00)
0.795
(1.00)
0.314
(1.00)
0.0424
(1.00)
0.333
(1.00)
1
(1.00)
0.199
(1.00)
1
(1.00)
0.14
(1.00)
0.456
(1.00)
1
(1.00)
2p loss 168 (17%) 827 0.703
(1.00)
0.324
(1.00)
0.318
(1.00)
0.475
(1.00)
0.0604
(1.00)
0.094
(1.00)
1
(1.00)
0.309
(1.00)
0.024
(1.00)
0.419
(1.00)
0.435
(1.00)
0.0531
(1.00)
2q loss 190 (19%) 805 0.265
(1.00)
0.413
(1.00)
0.143
(1.00)
0.373
(1.00)
0.0693
(1.00)
0.0696
(1.00)
1
(1.00)
0.134
(1.00)
0.108
(1.00)
0.166
(1.00)
0.564
(1.00)
0.044
(1.00)
3p loss 170 (17%) 825 0.362
(1.00)
0.0735
(1.00)
0.843
(1.00)
0.00089
(0.821)
0.862
(1.00)
0.756
(1.00)
0.228
(1.00)
0.00536
(1.00)
0.0116
(1.00)
0.827
(1.00)
0.0967
(1.00)
0.0461
(1.00)
3q loss 93 (9%) 902 0.137
(1.00)
0.326
(1.00)
0.326
(1.00)
0.00045
(0.419)
0.707
(1.00)
0.61
(1.00)
0.613
(1.00)
0.0698
(1.00)
0.022
(1.00)
0.836
(1.00)
0.2
(1.00)
0.0414
(1.00)
6p loss 170 (17%) 825 0.843
(1.00)
0.0591
(1.00)
0.888
(1.00)
0.434
(1.00)
0.697
(1.00)
0.0446
(1.00)
0.701
(1.00)
0.576
(1.00)
0.161
(1.00)
0.99
(1.00)
0.689
(1.00)
0.494
(1.00)
6q loss 250 (25%) 745 0.604
(1.00)
0.00129
(1.00)
0.667
(1.00)
0.309
(1.00)
0.403
(1.00)
0.404
(1.00)
0.308
(1.00)
0.682
(1.00)
0.0151
(1.00)
0.307
(1.00)
0.959
(1.00)
0.556
(1.00)
7p loss 104 (10%) 891 0.581
(1.00)
0.576
(1.00)
0.448
(1.00)
0.458
(1.00)
0.0634
(1.00)
0.143
(1.00)
0.617
(1.00)
0.00369
(1.00)
0.422
(1.00)
0.264
(1.00)
0.396
(1.00)
0.165
(1.00)
7q loss 113 (11%) 882 0.0884
(1.00)
0.161
(1.00)
0.524
(1.00)
0.447
(1.00)
0.306
(1.00)
0.139
(1.00)
1
(1.00)
0.22
(1.00)
0.377
(1.00)
0.887
(1.00)
0.875
(1.00)
0.0256
(1.00)
8q loss 81 (8%) 914 0.044
(1.00)
0.23
(1.00)
0.934
(1.00)
0.496
(1.00)
0.36
(1.00)
0.497
(1.00)
1
(1.00)
0.823
(1.00)
0.156
(1.00)
0.664
(1.00)
0.0145
(1.00)
0.543
(1.00)
10p loss 159 (16%) 836 0.0214
(1.00)
0.661
(1.00)
0.0387
(1.00)
0.0111
(1.00)
0.124
(1.00)
0.00863
(1.00)
0.229
(1.00)
0.0942
(1.00)
0.924
(1.00)
0.182
(1.00)
0.395
(1.00)
0.345
(1.00)
10q loss 213 (21%) 782 0.0265
(1.00)
0.972
(1.00)
0.151
(1.00)
0.0113
(1.00)
0.168
(1.00)
0.0148
(1.00)
0.473
(1.00)
0.0141
(1.00)
1
(1.00)
0.42
(1.00)
0.0615
(1.00)
0.0597
(1.00)
11p loss 253 (25%) 742 0.259
(1.00)
0.689
(1.00)
0.147
(1.00)
0.0781
(1.00)
0.0392
(1.00)
0.872
(1.00)
0.739
(1.00)
0.125
(1.00)
0.518
(1.00)
0.159
(1.00)
0.00242
(1.00)
0.0724
(1.00)
11q loss 338 (34%) 657 0.893
(1.00)
0.811
(1.00)
0.265
(1.00)
0.235
(1.00)
0.0228
(1.00)
0.483
(1.00)
0.199
(1.00)
0.411
(1.00)
0.553
(1.00)
0.265
(1.00)
0.00313
(1.00)
0.857
(1.00)
12p loss 139 (14%) 856 0.462
(1.00)
0.331
(1.00)
0.326
(1.00)
0.0282
(1.00)
0.553
(1.00)
0.147
(1.00)
1
(1.00)
0.00201
(1.00)
0.362
(1.00)
0.304
(1.00)
0.319
(1.00)
0.463
(1.00)
12q loss 117 (12%) 878 0.693
(1.00)
0.0139
(1.00)
0.263
(1.00)
0.0187
(1.00)
0.577
(1.00)
0.21
(1.00)
0.628
(1.00)
0.00088
(0.813)
0.445
(1.00)
0.0706
(1.00)
0.0401
(1.00)
0.608
(1.00)
16p loss 154 (15%) 841 0.689
(1.00)
0.557
(1.00)
0.249
(1.00)
0.982
(1.00)
0.0986
(1.00)
0.592
(1.00)
0.683
(1.00)
0.132
(1.00)
0.383
(1.00)
0.066
(1.00)
0.00646
(1.00)
0.818
(1.00)
17p loss 532 (53%) 463 0.343
(1.00)
0.0139
(1.00)
0.102
(1.00)
0.00609
(1.00)
0.844
(1.00)
0.801
(1.00)
0.364
(1.00)
0.00856
(1.00)
0.888
(1.00)
0.986
(1.00)
0.121
(1.00)
0.866
(1.00)
17q loss 250 (25%) 745 0.952
(1.00)
0.0881
(1.00)
0.891
(1.00)
0.461
(1.00)
0.292
(1.00)
0.22
(1.00)
0.075
(1.00)
0.00085
(0.786)
1
(1.00)
0.594
(1.00)
0.00347
(1.00)
1
(1.00)
18q loss 294 (30%) 701 0.00126
(1.00)
0.0178
(1.00)
0.0607
(1.00)
0.0584
(1.00)
0.134
(1.00)
0.767
(1.00)
1
(1.00)
0.0101
(1.00)
0.397
(1.00)
0.331
(1.00)
0.156
(1.00)
0.458
(1.00)
20p loss 85 (9%) 910 0.24
(1.00)
0.189
(1.00)
0.494
(1.00)
0.0679
(1.00)
0.691
(1.00)
0.414
(1.00)
1
(1.00)
0.0556
(1.00)
0.317
(1.00)
0.932
(1.00)
0.2
(1.00)
0.207
(1.00)
20q loss 47 (5%) 948 0.195
(1.00)
0.0751
(1.00)
0.0716
(1.00)
0.012
(1.00)
0.917
(1.00)
0.307
(1.00)
1
(1.00)
0.122
(1.00)
0.619
(1.00)
0.152
(1.00)
0.0951
(1.00)
0.0822
(1.00)
21q loss 164 (16%) 831 0.731
(1.00)
0.431
(1.00)
0.0527
(1.00)
0.437
(1.00)
0.0267
(1.00)
0.423
(1.00)
0.228
(1.00)
0.028
(1.00)
0.395
(1.00)
0.167
(1.00)
0.112
(1.00)
0.25
(1.00)
22q loss 440 (44%) 555 0.152
(1.00)
0.618
(1.00)
0.699
(1.00)
0.552
(1.00)
0.312
(1.00)
0.475
(1.00)
0.551
(1.00)
0.00204
(1.00)
0.00111
(1.00)
0.258
(1.00)
0.382
(1.00)
0.865
(1.00)
xq loss 164 (16%) 831 0.65
(1.00)
0.127
(1.00)
0.469
(1.00)
0.0257
(1.00)
0.623
(1.00)
0.106
(1.00)
0.403
(1.00)
0.0366
(1.00)
0.777
(1.00)
0.433
(1.00)
0.365
(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 1 735 166 5 29 14 44
2P GAIN MUTATED 1 102 4 1 0 0 5
2P GAIN WILD-TYPE 0 633 162 4 29 14 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 1 735 166 5 29 14 44
3Q GAIN MUTATED 0 170 8 3 6 1 9
3Q GAIN WILD-TYPE 1 565 158 2 23 13 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 1 735 166 5 29 14 44
6P GAIN MUTATED 0 155 16 4 3 1 10
6P GAIN WILD-TYPE 1 580 150 1 26 13 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 1 735 166 5 29 14 44
8Q GAIN MUTATED 1 400 47 4 12 4 25
8Q GAIN WILD-TYPE 0 335 119 1 17 10 19

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

'10p gain' versus 'HISTOLOGICAL.TYPE'

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

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 1 735 166 5 29 14 44
10P GAIN MUTATED 0 171 16 3 4 0 6
10P GAIN WILD-TYPE 1 564 150 2 25 14 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 1 735 166 5 29 14 44
20P GAIN MUTATED 0 321 37 1 9 1 13
20P GAIN WILD-TYPE 1 414 129 4 20 13 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 1 735 166 5 29 14 44
20Q GAIN MUTATED 0 350 41 1 9 1 15
20Q GAIN WILD-TYPE 1 385 125 4 20 13 29

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

'21q gain' versus 'HISTOLOGICAL.TYPE'

P value = 3e-05 (Fisher's exact test), Q value = 0.028

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 1 735 166 5 29 14 44
21Q GAIN MUTATED 0 160 15 2 0 1 9
21Q GAIN WILD-TYPE 1 575 151 3 29 13 35

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

'xq gain' versus 'HISTOLOGICAL.TYPE'

P value = 0.00018 (Fisher's exact test), Q value = 0.17

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 1 735 166 5 29 14 44
XQ GAIN MUTATED 1 110 8 2 1 3 4
XQ GAIN WILD-TYPE 0 625 158 3 28 11 40

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

'1p loss' versus 'NEOPLASM.DISEASESTAGE'

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

Table S10.  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 80 77 9 9 335 224 2 138 27 59 17 1 16
1P LOSS MUTATED 12 11 1 3 73 39 1 42 16 18 6 0 4
1P LOSS WILD-TYPE 68 66 8 6 262 185 1 96 11 41 11 1 12

Figure S10.  Get High-res Image Gene #41: '1p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 3e-05 (Fisher's exact test), Q value = 0.028

Table S11.  Gene #41: '1p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 258 581 117 36
1P LOSS MUTATED 46 133 27 20
1P LOSS WILD-TYPE 212 448 90 16

Figure S11.  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 S12.  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 1 735 166 5 29 14 44
4P LOSS MUTATED 1 271 27 2 7 0 15
4P LOSS WILD-TYPE 0 464 139 3 22 14 29

Figure S12.  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 S13.  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 1 735 166 5 29 14 44
4Q LOSS MUTATED 0 240 24 1 7 0 15
4Q LOSS WILD-TYPE 1 495 142 4 22 14 29

Figure S13.  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 S14.  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 1 735 166 5 29 14 44
5P LOSS MUTATED 0 114 2 3 4 0 6
5P LOSS WILD-TYPE 1 621 164 2 25 14 38

Figure S14.  Get High-res Image Gene #49: '5p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'5q loss' versus 'AGE'

P value = 0.000261 (Wilcoxon-test), Q value = 0.24

Table S15.  Gene #50: '5q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 982 58.7 (13.1)
5Q LOSS MUTATED 210 55.9 (13.4)
5Q LOSS WILD-TYPE 772 59.4 (12.9)

Figure S15.  Get High-res Image Gene #50: '5q loss' versus Clinical Feature #2: 'AGE'

'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 1 735 166 5 29 14 44
5Q LOSS MUTATED 1 192 3 3 4 0 8
5Q LOSS WILD-TYPE 0 543 163 2 25 14 36

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

'5q loss' versus 'RACE'

P value = 9e-05 (Fisher's exact test), Q value = 0.085

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 56 137 708
5Q LOSS MUTATED 0 17 48 131
5Q LOSS WILD-TYPE 1 39 89 577

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 1 735 166 5 29 14 44
8P LOSS MUTATED 1 297 35 2 8 1 17
8P LOSS WILD-TYPE 0 438 131 3 21 13 27

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

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

P value = 0.00014 (Fisher's exact test), Q value = 0.13

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

nPatients T1 T2 T3 T4
ALL 258 581 117 36
9P LOSS MUTATED 55 194 29 18
9P LOSS WILD-TYPE 203 387 88 18

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 1 735 166 5 29 14 44
9P LOSS MUTATED 0 252 20 3 9 3 9
9P LOSS WILD-TYPE 1 483 146 2 20 11 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 1 735 166 5 29 14 44
9Q LOSS MUTATED 0 225 18 2 9 3 11
9Q LOSS WILD-TYPE 1 510 148 3 20 11 33

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

'13q loss' versus 'HISTOLOGICAL.TYPE'

P value = 0.00025 (Fisher's exact test), Q value = 0.23

Table S22.  Gene #65: '13q 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 1 735 166 5 29 14 44
13Q LOSS MUTATED 0 329 48 4 10 2 14
13Q LOSS WILD-TYPE 1 406 118 1 19 12 30

Figure S22.  Get High-res Image Gene #65: '13q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'14q loss' versus 'HISTOLOGICAL.TYPE'

P value = 4e-05 (Fisher's exact test), Q value = 0.038

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 1 735 166 5 29 14 44
14Q LOSS MUTATED 0 200 22 4 3 1 9
14Q LOSS WILD-TYPE 1 535 144 1 26 13 35

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

'15q loss' versus 'HISTOLOGICAL.TYPE'

P value = 0.00018 (Fisher's exact test), Q value = 0.17

Table S24.  Gene #67: '15q 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 1 735 166 5 29 14 44
15Q LOSS MUTATED 0 242 26 3 9 2 14
15Q LOSS WILD-TYPE 1 493 140 2 20 12 30

Figure S24.  Get High-res Image Gene #67: '15q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'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 1 735 166 5 29 14 44
16Q LOSS MUTATED 0 379 130 2 19 1 14
16Q LOSS WILD-TYPE 1 356 36 3 10 13 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 = 9.48e-07 (logrank test), Q value = 0.00091

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

nPatients nDeath Duration Range (Median), Month
ALL 974 114 0.0 - 234.3 (21.4)
18P LOSS MUTATED 285 51 0.0 - 189.0 (20.3)
18P LOSS WILD-TYPE 689 63 0.0 - 234.3 (22.4)

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 1 735 166 5 29 14 44
19P LOSS MUTATED 0 157 6 1 3 3 5
19P LOSS WILD-TYPE 1 578 160 4 26 11 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 1 735 166 5 29 14 44
19Q LOSS MUTATED 0 133 4 1 3 3 4
19Q LOSS WILD-TYPE 1 602 162 4 26 11 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 = 995

  • 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)