Correlation between copy number variation genes (focal events) and selected clinical features
Breast Invasive Carcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1TD9W52
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/C1TD9W52
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 67 focal events and 12 clinical features across 1025 patients, 51 significant findings detected with Q value < 0.25.

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

  • 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_1p22.1 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_4q35.1 cnv correlated to 'HISTOLOGICAL.TYPE'.

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

  • del_5q21.3 cnv correlated to 'PATHOLOGY.T.STAGE' and '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 'Time to Death',  'PATHOLOGY.T.STAGE', and '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_11p15.5 cnv correlated to 'HISTOLOGICAL.TYPE'.

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

  • del_14q24.1 cnv correlated to 'PATHOLOGY.T.STAGE' and '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 67 focal events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 51 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 1 407 (40%) 618 0.0827
(1.00) 		0.523
(1.00) 		0.0174
(1.00) 		0.00026
(0.197) 		0.374
(1.00) 		0.00041
(0.307) 		3.56e-05
(0.0273) 		2e-05
(0.0154) 		0.775
(1.00) 		0.331
(1.00) 		0.178
(1.00) 		0.728
(1.00)
del 5q11 2 267 (26%) 758 0.255
(1.00) 		6.28e-05
(0.048) 		0.273
(1.00) 		0.0008
(0.591) 		0.328
(1.00) 		0.0894
(1.00) 		0.0762
(1.00) 		1e-05
(0.00804) 		0.474
(1.00) 		0.0881
(1.00) 		0.00015
(0.114) 		0.701
(1.00)
del 9p23 311 (30%) 714 0.000221
(0.167) 		0.278
(1.00) 		0.00261
(1.00) 		0.00033
(0.249) 		0.00182
(1.00) 		0.0118
(1.00) 		0.0993
(1.00) 		1e-05
(0.00804) 		0.495
(1.00) 		0.0415
(1.00) 		0.495
(1.00) 		0.855
(1.00)
amp 3p25 1 193 (19%) 832 0.0175
(1.00) 		0.174
(1.00) 		0.0141
(1.00) 		0.00036
(0.271) 		0.0317
(1.00) 		0.00018
(0.137) 		0.7
(1.00) 		9e-05
(0.0687) 		0.476
(1.00) 		0.374
(1.00) 		0.414
(1.00) 		1
(1.00)
amp 6q21 192 (19%) 833 0.0994
(1.00) 		0.411
(1.00) 		0.0902
(1.00) 		0.00012
(0.0914) 		0.192
(1.00) 		0.615
(1.00) 		0.7
(1.00) 		1e-05
(0.00804) 		0.37
(1.00) 		0.0625
(1.00) 		0.178
(1.00) 		0.828
(1.00)
amp 10p15 1 297 (29%) 728 0.205
(1.00) 		0.589
(1.00) 		0.296
(1.00) 		0.152
(1.00) 		0.5
(1.00) 		0.492
(1.00) 		0.526
(1.00) 		1e-05
(0.00804) 		0.217
(1.00) 		0.16
(1.00) 		3e-05
(0.023) 		0.57
(1.00)
del 3p21 31 334 (33%) 691 0.00558
(1.00) 		0.00518
(1.00) 		0.148
(1.00) 		2e-05
(0.0154) 		0.723
(1.00) 		0.752
(1.00) 		0.755
(1.00) 		1e-05
(0.00804) 		0.233
(1.00) 		0.481
(1.00) 		0.0181
(1.00) 		0.589
(1.00)
del 5q21 3 259 (25%) 766 0.354
(1.00) 		0.00175
(1.00) 		0.157
(1.00) 		0.00012
(0.0914) 		0.0681
(1.00) 		0.25
(1.00) 		0.0751
(1.00) 		1e-05
(0.00804) 		0.171
(1.00) 		0.00171
(1.00) 		0.00046
(0.343) 		0.701
(1.00)
del 14q24 1 334 (33%) 691 0.0345
(1.00) 		0.271
(1.00) 		0.268
(1.00) 		0.00026
(0.197) 		0.269
(1.00) 		0.981
(1.00) 		0.755
(1.00) 		1e-05
(0.00804) 		0.0527
(1.00) 		0.256
(1.00) 		0.00379
(1.00) 		0.858
(1.00)
del 17q21 31 349 (34%) 676 0.515
(1.00) 		0.000312
(0.235) 		0.312
(1.00) 		0.0767
(1.00) 		0.114
(1.00) 		0.148
(1.00) 		0.35
(1.00) 		1e-05
(0.00804) 		0.462
(1.00) 		0.552
(1.00) 		0.00067
(0.498) 		1
(1.00)
amp 3q26 32 325 (32%) 700 0.953
(1.00) 		0.465
(1.00) 		0.15
(1.00) 		0.00045
(0.337) 		0.3
(1.00) 		0.00643
(1.00) 		0.75
(1.00) 		1e-05
(0.00804) 		0.0428
(1.00) 		0.107
(1.00) 		0.00481
(1.00) 		0.143
(1.00)
amp 4q13 3 158 (15%) 867 0.0331
(1.00) 		0.302
(1.00) 		0.855
(1.00) 		0.196
(1.00) 		0.605
(1.00) 		0.169
(1.00) 		0.39
(1.00) 		1e-05
(0.00804) 		0.288
(1.00) 		0.908
(1.00) 		0.175
(1.00) 		0.23
(1.00)
amp 6p23 285 (28%) 740 0.912
(1.00) 		0.341
(1.00) 		0.56
(1.00) 		0.0022
(1.00) 		0.259
(1.00) 		0.678
(1.00) 		0.307
(1.00) 		1e-05
(0.00804) 		0.185
(1.00) 		0.938
(1.00) 		0.00284
(1.00) 		0.703
(1.00)
amp 8q24 21 651 (64%) 374 0.145
(1.00) 		0.0596
(1.00) 		0.404
(1.00) 		0.0261
(1.00) 		0.423
(1.00) 		0.00637
(1.00) 		0.345
(1.00) 		1e-05
(0.00804) 		0.0947
(1.00) 		0.608
(1.00) 		0.00415
(1.00) 		0.292
(1.00)
amp 11p13 215 (21%) 810 0.664
(1.00) 		0.38
(1.00) 		0.675
(1.00) 		0.384
(1.00) 		0.98
(1.00) 		0.434
(1.00) 		0.256
(1.00) 		1e-05
(0.00804) 		0.264
(1.00) 		0.466
(1.00) 		0.29
(1.00) 		0.676
(1.00)
amp 12p13 33 271 (26%) 754 0.926
(1.00) 		0.423
(1.00) 		0.382
(1.00) 		0.00082
(0.605) 		0.762
(1.00) 		0.419
(1.00) 		0.305
(1.00) 		1e-05
(0.00804) 		0.267
(1.00) 		0.466
(1.00) 		0.0403
(1.00) 		0.0848
(1.00)
amp 15q26 3 187 (18%) 838 0.213
(1.00) 		0.00459
(1.00) 		0.592
(1.00) 		0.297
(1.00) 		0.986
(1.00) 		0.0272
(1.00) 		0.123
(1.00) 		1e-05
(0.00804) 		0.416
(1.00) 		0.532
(1.00) 		0.0321
(1.00) 		0.375
(1.00)
amp 19q12 271 (26%) 754 0.47
(1.00) 		0.432
(1.00) 		0.076
(1.00) 		0.651
(1.00) 		0.0626
(1.00) 		0.211
(1.00) 		0.494
(1.00) 		1e-05
(0.00804) 		0.477
(1.00) 		0.00756
(1.00) 		0.0528
(1.00) 		0.848
(1.00)
amp 20q13 2 523 (51%) 502 0.45
(1.00) 		0.656
(1.00) 		0.166
(1.00) 		0.0042
(1.00) 		0.00484
(1.00) 		0.053
(1.00) 		0.0646
(1.00) 		1e-05
(0.00804) 		0.000782
(0.579) 		0.161
(1.00) 		0.327
(1.00) 		0.498
(1.00)
del 1p36 13 427 (42%) 598 0.074
(1.00) 		0.0433
(1.00) 		0.00435
(1.00) 		1e-05
(0.00804) 		0.00073
(0.542) 		0.187
(1.00) 		0.0601
(1.00) 		0.0052
(1.00) 		0.137
(1.00) 		0.000912
(0.671) 		0.972
(1.00) 		0.729
(1.00)
del 1p22 1 345 (34%) 680 0.00325
(1.00) 		0.119
(1.00) 		0.00956
(1.00) 		1e-05
(0.00804) 		0.00456
(1.00) 		0.407
(1.00) 		0.522
(1.00) 		0.334
(1.00) 		0.824
(1.00) 		0.000943
(0.693) 		0.497
(1.00) 		0.206
(1.00)
del 2q37 3 304 (30%) 721 0.713
(1.00) 		0.563
(1.00) 		0.248
(1.00) 		0.00261
(1.00) 		0.348
(1.00) 		0.441
(1.00) 		1
(1.00) 		1e-05
(0.00804) 		0.092
(1.00) 		0.261
(1.00) 		0.0166
(1.00) 		0.344
(1.00)
del 4p16 3 323 (32%) 702 0.76
(1.00) 		0.0657
(1.00) 		0.102
(1.00) 		0.00039
(0.293) 		0.699
(1.00) 		0.27
(1.00) 		1
(1.00) 		1e-05
(0.00804) 		0.292
(1.00) 		0.752
(1.00) 		0.0317
(1.00) 		0.716
(1.00)
del 4q35 1 326 (32%) 699 0.0859
(1.00) 		0.403
(1.00) 		0.243
(1.00) 		0.00342
(1.00) 		0.768
(1.00) 		0.00312
(1.00) 		0.518
(1.00) 		1e-05
(0.00804) 		0.548
(1.00) 		0.828
(1.00) 		0.0142
(1.00) 		0.142
(1.00)
del 6q27 358 (35%) 667 0.0976
(1.00) 		1.52e-05
(0.0117) 		0.438
(1.00) 		0.655
(1.00) 		0.0317
(1.00) 		0.454
(1.00) 		0.346
(1.00) 		0.245
(1.00) 		0.0563
(1.00) 		0.367
(1.00) 		0.718
(1.00) 		0.283
(1.00)
del 7p22 3 133 (13%) 892 0.907
(1.00) 		0.273
(1.00) 		0.332
(1.00) 		0.223
(1.00) 		0.0612
(1.00) 		0.129
(1.00) 		0.377
(1.00) 		1e-05
(0.00804) 		0.604
(1.00) 		0.0291
(1.00) 		0.581
(1.00) 		0.609
(1.00)
del 8p23 2 532 (52%) 493 0.15
(1.00) 		0.554
(1.00) 		0.996
(1.00) 		0.0158
(1.00) 		0.177
(1.00) 		0.229
(1.00) 		0.55
(1.00) 		1e-05
(0.00804) 		0.889
(1.00) 		0.924
(1.00) 		0.0041
(1.00) 		0.866
(1.00)
del 9p21 3 346 (34%) 679 0.0357
(1.00) 		0.389
(1.00) 		0.0179
(1.00) 		0.00161
(1.00) 		0.00493
(1.00) 		0.0497
(1.00) 		0.051
(1.00) 		1e-05
(0.00804) 		0.416
(1.00) 		0.088
(1.00) 		0.246
(1.00) 		0.858
(1.00)
del 9q21 11 287 (28%) 738 0.267
(1.00) 		0.884
(1.00) 		0.256
(1.00) 		0.0603
(1.00) 		0.254
(1.00) 		0.544
(1.00) 		0.0831
(1.00) 		1e-05
(0.00804) 		0.0621
(1.00) 		0.562
(1.00) 		0.065
(1.00) 		0.25
(1.00)
del 9q34 2 285 (28%) 740 0.836
(1.00) 		0.975
(1.00) 		0.0771
(1.00) 		0.00844
(1.00) 		0.0938
(1.00) 		0.482
(1.00) 		0.0136
(1.00) 		1e-05
(0.00804) 		0.073
(1.00) 		0.202
(1.00) 		0.0364
(1.00) 		0.254
(1.00)
del 10q26 3 307 (30%) 718 0.0668
(1.00) 		0.667
(1.00) 		0.248
(1.00) 		0.0511
(1.00) 		0.174
(1.00) 		0.296
(1.00) 		0.521
(1.00) 		2e-05
(0.0154) 		0.402
(1.00) 		0.367
(1.00) 		0.148
(1.00) 		0.00904
(1.00)
del 11p15 5 296 (29%) 729 0.0446
(1.00) 		0.753
(1.00) 		0.133
(1.00) 		0.00281
(1.00) 		0.482
(1.00) 		0.127
(1.00) 		0.525
(1.00) 		5e-05
(0.0382) 		0.488
(1.00) 		0.867
(1.00) 		0.00951
(1.00) 		0.342
(1.00)
del 13q14 2 474 (46%) 551 0.111
(1.00) 		0.651
(1.00) 		0.669
(1.00) 		0.0168
(1.00) 		0.542
(1.00) 		0.735
(1.00) 		0.763
(1.00) 		1e-05
(0.00804) 		0.183
(1.00) 		0.713
(1.00) 		0.0947
(1.00) 		0.175
(1.00)
del 15q13 1 357 (35%) 668 0.395
(1.00) 		0.299
(1.00) 		0.0985
(1.00) 		0.00139
(1.00) 		0.0223
(1.00) 		0.534
(1.00) 		1
(1.00) 		1e-05
(0.00804) 		0.0665
(1.00) 		0.0781
(1.00) 		0.0912
(1.00) 		0.86
(1.00)
del 16q24 3 653 (64%) 372 0.461
(1.00) 		0.00055
(0.41) 		0.0568
(1.00) 		0.151
(1.00) 		0.489
(1.00) 		0.204
(1.00) 		1
(1.00) 		1e-05
(0.00804) 		0.424
(1.00) 		0.473
(1.00) 		0.0162
(1.00) 		0.159
(1.00)
del 19p13 3 343 (33%) 682 0.0847
(1.00) 		0.00637
(1.00) 		0.808
(1.00) 		0.0473
(1.00) 		0.796
(1.00) 		0.437
(1.00) 		0.353
(1.00) 		1e-05
(0.00804) 		0.824
(1.00) 		0.0645
(1.00) 		0.00644
(1.00) 		1
(1.00)
del 19q13 32 200 (20%) 825 0.386
(1.00) 		0.479
(1.00) 		0.538
(1.00) 		0.441
(1.00) 		0.0994
(1.00) 		0.42
(1.00) 		1
(1.00) 		1e-05
(0.00804) 		0.0104
(1.00) 		0.892
(1.00) 		0.366
(1.00) 		0.522
(1.00)
del 20p13 155 (15%) 870 0.187
(1.00) 		0.0725
(1.00) 		0.249
(1.00) 		0.434
(1.00) 		0.936
(1.00) 		0.177
(1.00) 		0.224
(1.00) 		1e-05
(0.00804) 		0.118
(1.00) 		0.95
(1.00) 		0.13
(1.00) 		0.809
(1.00)
amp 1p22 3 235 (23%) 790 0.786
(1.00) 		0.313
(1.00) 		0.271
(1.00) 		0.0134
(1.00) 		0.00805
(1.00) 		0.785
(1.00) 		1
(1.00) 		0.205
(1.00) 		0.561
(1.00) 		0.00782
(1.00) 		0.025
(1.00) 		1
(1.00)
amp 1q21 3 746 (73%) 279 0.751
(1.00) 		0.916
(1.00) 		0.256
(1.00) 		0.0153
(1.00) 		0.607
(1.00) 		0.423
(1.00) 		0.182
(1.00) 		0.0396
(1.00) 		0.583
(1.00) 		0.846
(1.00) 		0.23
(1.00) 		0.0588
(1.00)
amp 1q44 744 (73%) 281 0.0215
(1.00) 		0.396
(1.00) 		0.155
(1.00) 		0.00704
(1.00) 		0.338
(1.00) 		0.154
(1.00) 		1
(1.00) 		0.00152
(1.00) 		0.876
(1.00) 		0.535
(1.00) 		0.0173
(1.00) 		0.0855
(1.00)
amp 5p15 33 372 (36%) 653 0.274
(1.00) 		0.171
(1.00) 		0.458
(1.00) 		0.272
(1.00) 		0.0132
(1.00) 		0.0374
(1.00) 		0.54
(1.00) 		0.129
(1.00) 		0.0947
(1.00) 		0.909
(1.00) 		0.375
(1.00) 		0.596
(1.00)
amp 8p11 23 390 (38%) 635 0.0552
(1.00) 		0.0928
(1.00) 		0.0295
(1.00) 		0.618
(1.00) 		0.13
(1.00) 		0.12
(1.00) 		0.547
(1.00) 		0.468
(1.00) 		0.719
(1.00) 		0.0111
(1.00) 		0.824
(1.00) 		0.602
(1.00)
amp 8p11 21 402 (39%) 623 0.813
(1.00) 		0.0921
(1.00) 		0.693
(1.00) 		0.858
(1.00) 		0.805
(1.00) 		0.453
(1.00) 		0.542
(1.00) 		0.00553
(1.00) 		0.316
(1.00) 		0.588
(1.00) 		0.172
(1.00) 		0.601
(1.00)
amp 10q22 3 149 (15%) 876 0.0953
(1.00) 		0.924
(1.00) 		0.285
(1.00) 		0.162
(1.00) 		0.243
(1.00) 		0.0794
(1.00) 		0.667
(1.00) 		0.00075
(0.556) 		0.114
(1.00) 		0.158
(1.00) 		0.148
(1.00) 		1
(1.00)
amp 11q13 3 381 (37%) 644 0.258
(1.00) 		0.286
(1.00) 		0.462
(1.00) 		0.0608
(1.00) 		0.557
(1.00) 		0.269
(1.00) 		0.112
(1.00) 		0.237
(1.00) 		0.885
(1.00) 		0.801
(1.00) 		0.352
(1.00) 		0.596
(1.00)
amp 11q14 1 252 (25%) 773 0.309
(1.00) 		0.319
(1.00) 		0.364
(1.00) 		0.0774
(1.00) 		0.103
(1.00) 		0.102
(1.00) 		0.151
(1.00) 		0.00491
(1.00) 		0.746
(1.00) 		0.687
(1.00) 		0.195
(1.00) 		0.424
(1.00)
amp 12q15 265 (26%) 760 0.142
(1.00) 		0.276
(1.00) 		0.0988
(1.00) 		0.00846
(1.00) 		0.00367
(1.00) 		0.163
(1.00) 		0.00887
(1.00) 		0.015
(1.00) 		0.936
(1.00) 		0.00836
(1.00) 		0.512
(1.00) 		0.326
(1.00)
amp 13q34 172 (17%) 853 0.677
(1.00) 		0.0808
(1.00) 		0.248
(1.00) 		0.00929
(1.00) 		0.244
(1.00) 		0.0218
(1.00) 		0.228
(1.00) 		0.00419
(1.00) 		1
(1.00) 		0.0558
(1.00) 		0.69
(1.00) 		0.822
(1.00)
amp 14q21 1 207 (20%) 818 0.417
(1.00) 		0.142
(1.00) 		0.102
(1.00) 		0.0152
(1.00) 		0.0141
(1.00) 		0.097
(1.00) 		1
(1.00) 		0.04
(1.00) 		0.487
(1.00) 		0.00786
(1.00) 		0.716
(1.00) 		0.281
(1.00)
amp 17p11 2 143 (14%) 882 0.203
(1.00) 		0.356
(1.00) 		0.406
(1.00) 		0.104
(1.00) 		0.678
(1.00) 		0.552
(1.00) 		0.189
(1.00) 		0.539
(1.00) 		0.0554
(1.00) 		0.265
(1.00) 		0.626
(1.00) 		1
(1.00)
amp 17q12 319 (31%) 706 0.109
(1.00) 		0.783
(1.00) 		0.475
(1.00) 		0.111
(1.00) 		0.142
(1.00) 		0.0442
(1.00) 		0.0053
(1.00) 		0.00044
(0.33) 		0.29
(1.00) 		0.474
(1.00) 		0.00091
(0.671) 		1
(1.00)
amp 19p13 12 218 (21%) 807 0.547
(1.00) 		0.809
(1.00) 		0.466
(1.00) 		0.348
(1.00) 		0.187
(1.00) 		0.0578
(1.00) 		0.0627
(1.00) 		0.0645
(1.00) 		0.0324
(1.00) 		0.00122
(0.893) 		0.289
(1.00) 		0.838
(1.00)
amp 19q13 42 264 (26%) 761 0.482
(1.00) 		0.386
(1.00) 		0.916
(1.00) 		0.393
(1.00) 		0.753
(1.00) 		0.00442
(1.00) 		0.163
(1.00) 		0.00964
(1.00) 		0.201
(1.00) 		0.109
(1.00) 		0.748
(1.00) 		0.439
(1.00)
del 6p25 3 194 (19%) 831 0.441
(1.00) 		0.0585
(1.00) 		0.349
(1.00) 		0.00784
(1.00) 		0.139
(1.00) 		0.398
(1.00) 		0.137
(1.00) 		0.0685
(1.00) 		0.0611
(1.00) 		0.567
(1.00) 		0.646
(1.00) 		0.52
(1.00)
del 6q15 341 (33%) 684 0.529
(1.00) 		0.0647
(1.00) 		0.325
(1.00) 		0.439
(1.00) 		0.0589
(1.00) 		0.476
(1.00) 		1
(1.00) 		0.319
(1.00) 		0.182
(1.00) 		0.0236
(1.00) 		0.101
(1.00) 		0.589
(1.00)
del 7q36 1 195 (19%) 830 0.167
(1.00) 		0.994
(1.00) 		0.418
(1.00) 		0.143
(1.00) 		0.29
(1.00) 		0.173
(1.00) 		1
(1.00) 		0.00034
(0.256) 		1
(1.00) 		0.95
(1.00) 		0.581
(1.00) 		0.282
(1.00)
del 8p11 21 188 (18%) 837 0.0397
(1.00) 		0.128
(1.00) 		0.834
(1.00) 		0.294
(1.00) 		0.23
(1.00) 		0.192
(1.00) 		0.232
(1.00) 		0.00068
(0.505) 		0.366
(1.00) 		0.238
(1.00) 		0.183
(1.00) 		1
(1.00)
del 10q23 31 308 (30%) 717 0.529
(1.00) 		0.156
(1.00) 		0.236
(1.00) 		0.0148
(1.00) 		0.161
(1.00) 		0.43
(1.00) 		0.189
(1.00) 		0.00045
(0.337) 		0.222
(1.00) 		0.343
(1.00) 		0.16
(1.00) 		0.0264
(1.00)
del 11q23 3 520 (51%) 505 0.758
(1.00) 		0.211
(1.00) 		0.0781
(1.00) 		0.0204
(1.00) 		0.0997
(1.00) 		0.156
(1.00) 		0.0643
(1.00) 		0.126
(1.00) 		1
(1.00) 		0.229
(1.00) 		0.0223
(1.00) 		0.736
(1.00)
del 12p13 1 179 (17%) 846 0.539
(1.00) 		0.548
(1.00) 		0.118
(1.00) 		0.292
(1.00) 		0.873
(1.00) 		0.212
(1.00) 		0.418
(1.00) 		0.00553
(1.00) 		0.311
(1.00) 		0.434
(1.00) 		0.577
(1.00) 		1
(1.00)
del 12q23 1 194 (19%) 831 0.944
(1.00) 		0.168
(1.00) 		0.456
(1.00) 		0.0246
(1.00) 		0.701
(1.00) 		0.701
(1.00) 		0.7
(1.00) 		0.0057
(1.00) 		0.929
(1.00) 		0.271
(1.00) 		0.00621
(1.00) 		0.831
(1.00)
del 12q24 31 198 (19%) 827 0.222
(1.00) 		0.152
(1.00) 		0.661
(1.00) 		0.0361
(1.00) 		0.576
(1.00) 		0.484
(1.00) 		0.136
(1.00) 		0.0746
(1.00) 		1
(1.00) 		0.177
(1.00) 		0.149
(1.00) 		0.52
(1.00)
del 17p12 614 (60%) 411 0.503
(1.00) 		0.00188
(1.00) 		0.479
(1.00) 		0.0702
(1.00) 		0.751
(1.00) 		0.46
(1.00) 		0.54
(1.00) 		0.00171
(1.00) 		0.319
(1.00) 		0.669
(1.00) 		0.0823
(1.00) 		0.862
(1.00)
del 18q23 337 (33%) 688 0.0244
(1.00) 		0.359
(1.00) 		0.0475
(1.00) 		0.022
(1.00) 		0.0829
(1.00) 		0.885
(1.00) 		0.355
(1.00) 		0.00139
(1.00) 		0.101
(1.00) 		0.355
(1.00) 		0.0492
(1.00) 		0.857
(1.00)
del 21q11 2 203 (20%) 822 0.356
(1.00) 		0.514
(1.00) 		0.0131
(1.00) 		0.0096
(1.00) 		0.0295
(1.00) 		0.179
(1.00) 		0.703
(1.00) 		0.00101
(0.741) 		0.381
(1.00) 		0.274
(1.00) 		0.58
(1.00) 		0.207
(1.00)
del 22q13 32 464 (45%) 561 0.504
(1.00) 		0.509
(1.00) 		0.682
(1.00) 		0.288
(1.00) 		0.663
(1.00) 		0.623
(1.00) 		0.558
(1.00) 		0.00349
(1.00) 		0.00491
(1.00) 		0.971
(1.00) 		0.498
(1.00) 		0.735
(1.00)
'amp_3p25.1' versus 'PATHOLOGY.M.STAGE'

P value = 0.00018 (Fisher's exact test), Q value = 0.14

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

nPatients CM0 (I+) M0 M1 MX
ALL 5 854 19 147
AMP PEAK 4(3P25.1) MUTATED 0 176 6 11
AMP PEAK 4(3P25.1) WILD-TYPE 5 678 13 136

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

'amp_3p25.1' versus 'HISTOLOGICAL.TYPE'

P value = 9e-05 (Fisher's exact test), Q value = 0.069

Table S2.  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 1 754 175 6 29 15 44
AMP PEAK 4(3P25.1) MUTATED 1 165 13 1 5 1 7
AMP PEAK 4(3P25.1) WILD-TYPE 0 589 162 5 24 14 37

Figure S2.  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 = 0.008

Table S3.  Gene #5: 'amp_3q26.32' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 754 175 6 29 15 44
AMP PEAK 5(3Q26.32) MUTATED 1 286 12 5 6 1 13
AMP PEAK 5(3Q26.32) WILD-TYPE 0 468 163 1 23 14 31

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

'amp_4q13.3' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S4.  Gene #6: 'amp_4q13.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 754 175 6 29 15 44
AMP PEAK 6(4Q13.3) MUTATED 0 140 6 2 1 1 8
AMP PEAK 6(4Q13.3) WILD-TYPE 1 614 169 4 28 14 36

Figure S4.  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 = 0.008

Table S5.  Gene #8: 'amp_6p23' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 754 175 6 29 15 44
AMP PEAK 8(6P23) MUTATED 0 239 22 4 5 2 12
AMP PEAK 8(6P23) WILD-TYPE 1 515 153 2 24 13 32

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

'amp_6q21' versus 'PATHOLOGY.T.STAGE'

P value = 0.00012 (Fisher's exact test), Q value = 0.091

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

nPatients T1 T2 T3 T4
ALL 265 594 124 39
AMP PEAK 9(6Q21) MUTATED 30 138 20 4
AMP PEAK 9(6Q21) WILD-TYPE 235 456 104 35

Figure S6.  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 = 0.008

Table S7.  Gene #9: 'amp_6q21' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 754 175 6 29 15 44
AMP PEAK 9(6Q21) MUTATED 1 164 14 3 1 0 9
AMP PEAK 9(6Q21) WILD-TYPE 0 590 161 3 28 15 35

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

'amp_8q24.21' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S8.  Gene #12: 'amp_8q24.21' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 754 175 6 29 15 44
AMP PEAK 12(8Q24.21) MUTATED 1 532 63 6 16 5 27
AMP PEAK 12(8Q24.21) WILD-TYPE 0 222 112 0 13 10 17

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

'amp_10p15.1' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S9.  Gene #13: 'amp_10p15.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 754 175 6 29 15 44
AMP PEAK 13(10P15.1) MUTATED 1 257 19 5 5 0 9
AMP PEAK 13(10P15.1) WILD-TYPE 0 497 156 1 24 15 35

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

'amp_10p15.1' versus 'RACE'

P value = 3e-05 (Fisher's exact test), Q value = 0.023

Table S10.  Gene #13: 'amp_10p15.1' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 56 158 717
AMP PEAK 13(10P15.1) MUTATED 1 14 69 184
AMP PEAK 13(10P15.1) WILD-TYPE 0 42 89 533

Figure S10.  Get High-res Image Gene #13: 'amp_10p15.1' versus Clinical Feature #11: 'RACE'

'amp_11p13' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S11.  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 1 754 175 6 29 15 44
AMP PEAK 15(11P13) MUTATED 1 184 14 3 2 2 9
AMP PEAK 15(11P13) WILD-TYPE 0 570 161 3 27 13 35

Figure S11.  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 = 0.008

Table S12.  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 1 754 175 6 29 15 44
AMP PEAK 18(12P13.33) MUTATED 1 223 25 4 9 1 8
AMP PEAK 18(12P13.33) WILD-TYPE 0 531 150 2 20 14 36

Figure S12.  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 = 0.008

Table S13.  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 1 754 175 6 29 15 44
AMP PEAK 22(15Q26.3) MUTATED 0 163 8 3 4 3 5
AMP PEAK 22(15Q26.3) WILD-TYPE 1 591 167 3 25 12 39

Figure S13.  Get High-res Image Gene #22: 'amp_15q26.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

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

P value = 0.00026 (Fisher's exact test), Q value = 0.2

Table S14.  Gene #25: 'amp_17q23.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 265 594 124 39
AMP PEAK 25(17Q23.1) MUTATED 77 263 47 18
AMP PEAK 25(17Q23.1) WILD-TYPE 188 331 77 21

Figure S14.  Get High-res Image Gene #25: 'amp_17q23.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'amp_17q23.1' versus 'GENDER'

P value = 3.56e-05 (Fisher's exact test), Q value = 0.027

Table S15.  Gene #25: 'amp_17q23.1' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1014 11
AMP PEAK 25(17Q23.1) MUTATED 396 11
AMP PEAK 25(17Q23.1) WILD-TYPE 618 0

Figure S15.  Get High-res Image Gene #25: 'amp_17q23.1' versus Clinical Feature #7: 'GENDER'

'amp_17q23.1' versus 'HISTOLOGICAL.TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S16.  Gene #25: '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 1 754 175 6 29 15 44
AMP PEAK 25(17Q23.1) MUTATED 1 332 40 3 9 5 16
AMP PEAK 25(17Q23.1) WILD-TYPE 0 422 135 3 20 10 28

Figure S16.  Get High-res Image Gene #25: 'amp_17q23.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'amp_19q12' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S17.  Gene #27: '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 1 754 175 6 29 15 44
AMP PEAK 27(19Q12) MUTATED 0 221 27 6 5 2 10
AMP PEAK 27(19Q12) WILD-TYPE 1 533 148 0 24 13 34

Figure S17.  Get High-res Image Gene #27: 'amp_19q12' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'amp_20q13.2' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S18.  Gene #29: '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 1 754 175 6 29 15 44
AMP PEAK 29(20Q13.2) MUTATED 1 442 48 1 11 1 19
AMP PEAK 29(20Q13.2) WILD-TYPE 0 312 127 5 18 14 25

Figure S18.  Get High-res Image Gene #29: '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 = 0.008

Table S19.  Gene #30: 'del_1p36.13' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 265 594 124 39
DEL PEAK 1(1P36.13) MUTATED 78 275 48 25
DEL PEAK 1(1P36.13) WILD-TYPE 187 319 76 14

Figure S19.  Get High-res Image Gene #30: 'del_1p36.13' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_1p22.1' versus 'PATHOLOGY.T.STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S20.  Gene #31: 'del_1p22.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 265 594 124 39
DEL PEAK 2(1P22.1) MUTATED 64 216 41 24
DEL PEAK 2(1P22.1) WILD-TYPE 201 378 83 15

Figure S20.  Get High-res Image Gene #31: 'del_1p22.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_2q37.3' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S21.  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 1 754 175 6 29 15 44
DEL PEAK 3(2Q37.3) MUTATED 0 254 22 3 10 3 11
DEL PEAK 3(2Q37.3) WILD-TYPE 1 500 153 3 19 12 33

Figure S21.  Get High-res Image Gene #32: 'del_2q37.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

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

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S22.  Gene #33: 'del_3p21.31' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 265 594 124 39
DEL PEAK 4(3P21.31) MUTATED 55 229 39 10
DEL PEAK 4(3P21.31) WILD-TYPE 210 365 85 29

Figure S22.  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 = 0.008

Table S23.  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 1 754 175 6 29 15 44
DEL PEAK 4(3P21.31) MUTATED 1 279 37 1 5 0 11
DEL PEAK 4(3P21.31) WILD-TYPE 0 475 138 5 24 15 33

Figure S23.  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 = 0.008

Table S24.  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 1 754 175 6 29 15 44
DEL PEAK 5(4P16.3) MUTATED 1 272 25 4 7 0 14
DEL PEAK 5(4P16.3) WILD-TYPE 0 482 150 2 22 15 30

Figure S24.  Get High-res Image Gene #34: 'del_4p16.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_4q35.1' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S25.  Gene #35: 'del_4q35.1' 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 1 754 175 6 29 15 44
DEL PEAK 6(4Q35.1) MUTATED 1 279 28 4 3 0 10
DEL PEAK 6(4Q35.1) WILD-TYPE 0 475 147 2 26 15 34

Figure S25.  Get High-res Image Gene #35: 'del_4q35.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_5q11.2' versus 'AGE'

P value = 6.28e-05 (Wilcoxon-test), Q value = 0.048

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

nPatients Mean (Std.Dev)
ALL 1012 58.6 (13.2)
DEL PEAK 7(5Q11.2) MUTATED 265 56.0 (13.3)
DEL PEAK 7(5Q11.2) WILD-TYPE 747 59.6 (13.1)

Figure S26.  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 = 0.008

Table S27.  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 1 754 175 6 29 15 44
DEL PEAK 7(5Q11.2) MUTATED 1 237 8 5 4 1 10
DEL PEAK 7(5Q11.2) WILD-TYPE 0 517 167 1 25 14 34

Figure S27.  Get High-res Image Gene #36: 'del_5q11.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_5q11.2' versus 'RACE'

P value = 0.00015 (Fisher's exact test), Q value = 0.11

Table S28.  Gene #36: 'del_5q11.2' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 56 158 717
DEL PEAK 7(5Q11.2) MUTATED 1 19 60 167
DEL PEAK 7(5Q11.2) WILD-TYPE 0 37 98 550

Figure S28.  Get High-res Image Gene #36: 'del_5q11.2' versus Clinical Feature #11: 'RACE'

'del_5q21.3' versus 'PATHOLOGY.T.STAGE'

P value = 0.00012 (Fisher's exact test), Q value = 0.091

Table S29.  Gene #37: 'del_5q21.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 265 594 124 39
DEL PEAK 8(5Q21.3) MUTATED 52 176 17 12
DEL PEAK 8(5Q21.3) WILD-TYPE 213 418 107 27

Figure S29.  Get High-res Image Gene #37: 'del_5q21.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_5q21.3' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S30.  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 1 754 175 6 29 15 44
DEL PEAK 8(5Q21.3) MUTATED 1 234 4 6 4 0 9
DEL PEAK 8(5Q21.3) WILD-TYPE 0 520 171 0 25 15 35

Figure S30.  Get High-res Image Gene #37: 'del_5q21.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_6q27' versus 'AGE'

P value = 1.52e-05 (Wilcoxon-test), Q value = 0.012

Table S31.  Gene #40: 'del_6q27' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 1012 58.6 (13.2)
DEL PEAK 11(6Q27) MUTATED 354 56.0 (12.7)
DEL PEAK 11(6Q27) WILD-TYPE 658 60.0 (13.3)

Figure S31.  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 = 0.008

Table S32.  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 1 754 175 6 29 15 44
DEL PEAK 12(7P22.3) MUTATED 0 120 3 1 3 0 6
DEL PEAK 12(7P22.3) WILD-TYPE 1 634 172 5 26 15 38

Figure S32.  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 = 0.008

Table S33.  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 1 754 175 6 29 15 44
DEL PEAK 14(8P23.2) MUTATED 1 435 53 3 11 3 25
DEL PEAK 14(8P23.2) WILD-TYPE 0 319 122 3 18 12 19

Figure S33.  Get High-res Image Gene #43: 'del_8p23.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_9p23' versus 'Time to Death'

P value = 0.000221 (logrank test), Q value = 0.17

Table S34.  Gene #45: 'del_9p23' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1005 119 0.0 - 234.3 (22.4)
DEL PEAK 16(9P23) MUTATED 306 45 0.1 - 162.1 (20.8)
DEL PEAK 16(9P23) WILD-TYPE 699 74 0.0 - 234.3 (23.6)

Figure S34.  Get High-res Image Gene #45: 'del_9p23' versus Clinical Feature #1: 'Time to Death'

'del_9p23' versus 'PATHOLOGY.T.STAGE'

P value = 0.00033 (Fisher's exact test), Q value = 0.25

Table S35.  Gene #45: 'del_9p23' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 265 594 124 39
DEL PEAK 16(9P23) MUTATED 58 200 34 19
DEL PEAK 16(9P23) WILD-TYPE 207 394 90 20

Figure S35.  Get High-res Image Gene #45: 'del_9p23' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_9p23' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S36.  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 1 754 175 6 29 15 44
DEL PEAK 16(9P23) MUTATED 0 263 20 3 9 5 11
DEL PEAK 16(9P23) WILD-TYPE 1 491 155 3 20 10 33

Figure S36.  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 = 0.008

Table S37.  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 1 754 175 6 29 15 44
DEL PEAK 17(9P21.3) MUTATED 1 295 19 4 11 5 11
DEL PEAK 17(9P21.3) WILD-TYPE 0 459 156 2 18 10 33

Figure S37.  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 = 0.008

Table S38.  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 1 754 175 6 29 15 44
DEL PEAK 18(9Q21.11) MUTATED 0 242 20 2 10 3 10
DEL PEAK 18(9Q21.11) WILD-TYPE 1 512 155 4 19 12 34

Figure S38.  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 = 0.008

Table S39.  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 1 754 175 6 29 15 44
DEL PEAK 19(9Q34.2) MUTATED 0 245 18 4 6 3 8
DEL PEAK 19(9Q34.2) WILD-TYPE 1 509 157 2 23 12 36

Figure S39.  Get High-res Image Gene #48: 'del_9q34.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_10q26.3' versus 'HISTOLOGICAL.TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S40.  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 1 754 175 6 29 15 44
DEL PEAK 21(10Q26.3) MUTATED 0 251 29 5 7 1 13
DEL PEAK 21(10Q26.3) WILD-TYPE 1 503 146 1 22 14 31

Figure S40.  Get High-res Image Gene #50: 'del_10q26.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_11p15.5' versus 'HISTOLOGICAL.TYPE'

P value = 5e-05 (Fisher's exact test), Q value = 0.038

Table S41.  Gene #51: 'del_11p15.5' 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
DEL PEAK 22(11P15.5) MUTATED 0 242 28 4 10 2 10
DEL PEAK 22(11P15.5) WILD-TYPE 1 512 147 2 19 13 34

Figure S41.  Get High-res Image Gene #51: 'del_11p15.5' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_13q14.2' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S42.  Gene #56: 'del_13q14.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 754 175 6 29 15 44
DEL PEAK 27(13Q14.2) MUTATED 0 380 59 5 11 2 16
DEL PEAK 27(13Q14.2) WILD-TYPE 1 374 116 1 18 13 28

Figure S42.  Get High-res Image Gene #56: 'del_13q14.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_14q24.1' versus 'PATHOLOGY.T.STAGE'

P value = 0.00026 (Fisher's exact test), Q value = 0.2

Table S43.  Gene #57: 'del_14q24.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 265 594 124 39
DEL PEAK 28(14Q24.1) MUTATED 64 226 33 10
DEL PEAK 28(14Q24.1) WILD-TYPE 201 368 91 29

Figure S43.  Get High-res Image Gene #57: 'del_14q24.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_14q24.1' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S44.  Gene #57: 'del_14q24.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 754 175 6 29 15 44
DEL PEAK 28(14Q24.1) MUTATED 1 285 29 4 3 1 10
DEL PEAK 28(14Q24.1) WILD-TYPE 0 469 146 2 26 14 34

Figure S44.  Get High-res Image Gene #57: '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 = 0.008

Table S45.  Gene #58: 'del_15q13.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 754 175 6 29 15 44
DEL PEAK 29(15Q13.1) MUTATED 1 295 35 4 8 1 12
DEL PEAK 29(15Q13.1) WILD-TYPE 0 459 140 2 21 14 32

Figure S45.  Get High-res Image Gene #58: '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 = 0.008

Table S46.  Gene #59: 'del_16q24.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 754 175 6 29 15 44
DEL PEAK 30(16Q24.3) MUTATED 0 456 157 3 20 1 16
DEL PEAK 30(16Q24.3) WILD-TYPE 1 298 18 3 9 14 28

Figure S46.  Get High-res Image Gene #59: 'del_16q24.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_17q21.31' versus 'AGE'

P value = 0.000312 (Wilcoxon-test), Q value = 0.24

Table S47.  Gene #61: 'del_17q21.31' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 1012 58.6 (13.2)
DEL PEAK 32(17Q21.31) MUTATED 342 56.8 (13.4)
DEL PEAK 32(17Q21.31) WILD-TYPE 670 59.6 (13.0)

Figure S47.  Get High-res Image Gene #61: 'del_17q21.31' versus Clinical Feature #2: 'AGE'

'del_17q21.31' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S48.  Gene #61: 'del_17q21.31' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 754 175 6 29 15 44
DEL PEAK 32(17Q21.31) MUTATED 0 283 33 4 11 1 16
DEL PEAK 32(17Q21.31) WILD-TYPE 1 471 142 2 18 14 28

Figure S48.  Get High-res Image Gene #61: '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 = 0.008

Table S49.  Gene #63: 'del_19p13.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 754 175 6 29 15 44
DEL PEAK 34(19P13.3) MUTATED 1 292 19 5 8 4 13
DEL PEAK 34(19P13.3) WILD-TYPE 0 462 156 1 21 11 31

Figure S49.  Get High-res Image Gene #63: '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 = 0.008

Table S50.  Gene #64: 'del_19q13.32' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 754 175 6 29 15 44
DEL PEAK 35(19Q13.32) MUTATED 0 177 6 3 5 3 5
DEL PEAK 35(19Q13.32) WILD-TYPE 1 577 169 3 24 12 39

Figure S50.  Get High-res Image Gene #64: 'del_19q13.32' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_20p13' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S51.  Gene #65: 'del_20p13' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 754 175 6 29 15 44
DEL PEAK 36(20P13) MUTATED 1 136 9 2 2 0 5
DEL PEAK 36(20P13) WILD-TYPE 0 618 166 4 27 15 39

Figure S51.  Get High-res Image Gene #65: 'del_20p13' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

Methods & Data
Input

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

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

  • Number of patients = 1025

  • Number of significantly focal cnvs = 67

  • 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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