Correlation between copy number variation genes (focal events) and selected clinical features
Breast Invasive Carcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1B27SKN
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1B27SKN
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 70 focal events and 10 clinical features across 949 patients, 40 significant findings detected with Q value < 0.25.

  • AMP PEAK 4(3P26.1) MUTATION ANALYSIS cnv correlated to 'PATHOLOGY.T.STAGE'.

  • AMP PEAK 5(3Q26.32) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • AMP PEAK 6(4Q13.3) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • AMP PEAK 8(6P23) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • AMP PEAK 9(6Q21) MUTATION ANALYSIS cnv correlated to 'PATHOLOGY.T.STAGE' and 'HISTOLOGICAL.TYPE'.

  • AMP PEAK 12(8Q24.21) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • AMP PEAK 13(10P15.1) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • AMP PEAK 15(11P13) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • AMP PEAK 18(12P13.33) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • AMP PEAK 23(15Q26.3) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • AMP PEAK 25(17Q23.1) MUTATION ANALYSIS cnv correlated to 'PATHOLOGY.T.STAGE' and 'GENDER'.

  • AMP PEAK 27(19Q12) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • AMP PEAK 29(20Q13.2) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 1(1P36.13) MUTATION ANALYSIS cnv correlated to 'PATHOLOGY.T.STAGE'.

  • DEL PEAK 2(1P22.1) MUTATION ANALYSIS cnv correlated to 'PATHOLOGY.T.STAGE'.

  • DEL PEAK 3(2Q37.3) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 4(3P14.3) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 5(4P16.3) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 6(4Q35.2) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 7(5Q11.2) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 8(5Q21.3) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 11(6Q27) MUTATION ANALYSIS cnv correlated to 'AGE'.

  • DEL PEAK 12(7P22.3) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 14(8P23.2) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 16(9P23) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 17(9P21.3) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 19(9Q34.2) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 21(10Q26.3) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 28(13Q11) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 29(13Q14.2) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 30(14Q24.1) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 31(15Q13.1) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 32(16Q24.3) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 34(17Q21.31) MUTATION ANALYSIS cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 36(19P13.3) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 37(19Q13.32) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 38(20P13) MUTATION ANALYSIS 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 70 focal events and 10 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 40 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		NUMBER
OF
LYMPH
NODES
nCNV (%) nWild-Type logrank test t-test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test t-test
AMP PEAK 9(6Q21) MUTATION ANALYSIS 178 (19%) 771 0.0184
(1.00) 		0.364
(1.00) 		0.142
(1.00) 		9.41e-05
(0.0629) 		0.221
(1.00) 		0.932
(1.00) 		0.698
(1.00) 		1.24e-05
(0.00839) 		1
(1.00) 		0.418
(1.00)
AMP PEAK 25(17Q23 1) MUTATION ANALYSIS 383 (40%) 566 0.0903
(1.00) 		0.65
(1.00) 		0.0183
(1.00) 		0.000156
(0.103) 		0.414
(1.00) 		0.00302
(1.00) 		0.000107
(0.0712) 		0.00111
(0.722) 		0.878
(1.00) 		0.169
(1.00)
DEL PEAK 34(17Q21 31) MUTATION ANALYSIS 327 (34%) 622 0.744
(1.00) 		0.000368
(0.243) 		0.146
(1.00) 		0.136
(1.00) 		0.0921
(1.00) 		0.173
(1.00) 		0.508
(1.00) 		1.53e-05
(0.0104) 		1
(1.00) 		0.482
(1.00)
AMP PEAK 4(3P26 1) MUTATION ANALYSIS 192 (20%) 757 0.00473
(1.00) 		0.537
(1.00) 		0.0598
(1.00) 		5.03e-05
(0.0338) 		0.0135
(1.00) 		0.0105
(1.00) 		0.696
(1.00) 		0.0013
(0.844) 		0.346
(1.00) 		0.794
(1.00)
AMP PEAK 5(3Q26 32) MUTATION ANALYSIS 295 (31%) 654 0.789
(1.00) 		0.276
(1.00) 		0.343
(1.00) 		0.00182
(1.00) 		0.544
(1.00) 		0.00884
(1.00) 		1
(1.00) 		1.61e-11
(1.12e-08) 		0.0724
(1.00) 		0.31
(1.00)
AMP PEAK 6(4Q13 3) MUTATION ANALYSIS 146 (15%) 803 0.0484
(1.00) 		0.384
(1.00) 		0.613
(1.00) 		0.0361
(1.00) 		0.486
(1.00) 		0.622
(1.00) 		0.657
(1.00) 		2.48e-05
(0.0168) 		0.464
(1.00) 		0.615
(1.00)
AMP PEAK 8(6P23) MUTATION ANALYSIS 252 (27%) 697 0.485
(1.00) 		0.119
(1.00) 		0.551
(1.00) 		0.016
(1.00) 		0.191
(1.00) 		0.772
(1.00) 		0.47
(1.00) 		2.13e-05
(0.0144) 		0.441
(1.00) 		0.25
(1.00)
AMP PEAK 12(8Q24 21) MUTATION ANALYSIS 604 (64%) 345 0.0665
(1.00) 		0.0354
(1.00) 		0.151
(1.00) 		0.00752
(1.00) 		0.498
(1.00) 		0.0228
(1.00) 		0.343
(1.00) 		2.3e-13
(1.6e-10) 		0.387
(1.00) 		0.336
(1.00)
AMP PEAK 13(10P15 1) MUTATION ANALYSIS 269 (28%) 680 0.147
(1.00) 		0.705
(1.00) 		0.201
(1.00) 		0.388
(1.00) 		0.688
(1.00) 		0.889
(1.00) 		0.298
(1.00) 		6.94e-09
(4.81e-06) 		0.276
(1.00) 		0.91
(1.00)
AMP PEAK 15(11P13) MUTATION ANALYSIS 197 (21%) 752 0.361
(1.00) 		0.397
(1.00) 		0.861
(1.00) 		0.708
(1.00) 		0.803
(1.00) 		0.769
(1.00) 		1
(1.00) 		1.03e-05
(0.00699) 		0.352
(1.00) 		0.254
(1.00)
AMP PEAK 18(12P13 33) MUTATION ANALYSIS 246 (26%) 703 0.95
(1.00) 		0.307
(1.00) 		0.235
(1.00) 		0.0053
(1.00) 		0.704
(1.00) 		0.467
(1.00) 		0.468
(1.00) 		7.17e-05
(0.0479) 		0.121
(1.00) 		0.868
(1.00)
AMP PEAK 23(15Q26 3) MUTATION ANALYSIS 172 (18%) 777 0.234
(1.00) 		0.00946
(1.00) 		0.475
(1.00) 		0.484
(1.00) 		0.942
(1.00) 		0.0464
(1.00) 		0.0891
(1.00) 		6.12e-05
(0.041) 		0.492
(1.00) 		0.941
(1.00)
AMP PEAK 27(19Q12) MUTATION ANALYSIS 238 (25%) 711 0.148
(1.00) 		0.205
(1.00) 		0.283
(1.00) 		0.644
(1.00) 		0.245
(1.00) 		0.0737
(1.00) 		0.28
(1.00) 		2.67e-05
(0.018) 		0.117
(1.00) 		0.27
(1.00)
AMP PEAK 29(20Q13 2) MUTATION ANALYSIS 476 (50%) 473 0.614
(1.00) 		0.224
(1.00) 		0.183
(1.00) 		0.0253
(1.00) 		0.00604
(1.00) 		0.0395
(1.00) 		0.108
(1.00) 		1.04e-13
(7.25e-11) 		0.0101
(1.00) 		0.909
(1.00)
DEL PEAK 1(1P36 13) MUTATION ANALYSIS 392 (41%) 557 0.146
(1.00) 		0.384
(1.00) 		0.0139
(1.00) 		1.22e-06
(0.000836) 		0.004
(1.00) 		0.212
(1.00) 		0.102
(1.00) 		0.0106
(1.00) 		0.701
(1.00) 		0.0726
(1.00)
DEL PEAK 2(1P22 1) MUTATION ANALYSIS 314 (33%) 635 0.00107
(0.699) 		0.162
(1.00) 		0.0107
(1.00) 		6.57e-06
(0.00448) 		0.00384
(1.00) 		0.438
(1.00) 		0.738
(1.00) 		0.0594
(1.00) 		0.335
(1.00) 		0.0608
(1.00)
DEL PEAK 3(2Q37 3) MUTATION ANALYSIS 276 (29%) 673 0.989
(1.00) 		0.668
(1.00) 		0.371
(1.00) 		0.00783
(1.00) 		0.255
(1.00) 		0.566
(1.00) 		0.732
(1.00) 		0.000233
(0.154) 		0.56
(1.00) 		0.204
(1.00)
DEL PEAK 4(3P14 3) MUTATION ANALYSIS 291 (31%) 658 0.0187
(1.00) 		0.000509
(0.336) 		0.674
(1.00) 		0.00287
(1.00) 		0.503
(1.00) 		0.375
(1.00) 		1
(1.00) 		5.79e-06
(0.00396) 		0.412
(1.00) 		0.699
(1.00)
DEL PEAK 5(4P16 3) MUTATION ANALYSIS 292 (31%) 657 0.876
(1.00) 		0.115
(1.00) 		0.249
(1.00) 		0.00127
(0.825) 		0.63
(1.00) 		0.591
(1.00) 		0.732
(1.00) 		3.05e-06
(0.00209) 		0.624
(1.00) 		0.793
(1.00)
DEL PEAK 6(4Q35 2) MUTATION ANALYSIS 295 (31%) 654 0.079
(1.00) 		0.856
(1.00) 		0.434
(1.00) 		0.00671
(1.00) 		0.797
(1.00) 		0.0298
(1.00) 		0.187
(1.00) 		1.3e-06
(0.000894) 		0.744
(1.00) 		0.689
(1.00)
DEL PEAK 7(5Q11 2) MUTATION ANALYSIS 245 (26%) 704 0.25
(1.00) 		0.0034
(1.00) 		0.301
(1.00) 		0.00644
(1.00) 		0.38
(1.00) 		0.284
(1.00) 		0.467
(1.00) 		1.26e-10
(8.76e-08) 		0.667
(1.00) 		0.205
(1.00)
DEL PEAK 8(5Q21 3) MUTATION ANALYSIS 235 (25%) 714 0.315
(1.00) 		0.00995
(1.00) 		0.111
(1.00) 		0.00272
(1.00) 		0.05
(1.00) 		0.443
(1.00) 		0.132
(1.00) 		4.71e-14
(3.29e-11) 		0.793
(1.00) 		0.0012
(0.782)
DEL PEAK 11(6Q27) MUTATION ANALYSIS 319 (34%) 630 0.105
(1.00) 		5.93e-06
(0.00405) 		0.381
(1.00) 		0.755
(1.00) 		0.0392
(1.00) 		0.0452
(1.00) 		0.509
(1.00) 		0.445
(1.00) 		0.423
(1.00) 		0.46
(1.00)
DEL PEAK 12(7P22 3) MUTATION ANALYSIS 122 (13%) 827 0.695
(1.00) 		0.306
(1.00) 		0.117
(1.00) 		0.317
(1.00) 		0.0512
(1.00) 		0.443
(1.00) 		0.626
(1.00) 		0.000285
(0.188) 		0.498
(1.00) 		0.0154
(1.00)
DEL PEAK 14(8P23 2) MUTATION ANALYSIS 495 (52%) 454 0.128
(1.00) 		0.774
(1.00) 		0.965
(1.00) 		0.0149
(1.00) 		0.102
(1.00) 		0.359
(1.00) 		0.346
(1.00) 		8.1e-09
(5.61e-06) 		0.449
(1.00) 		0.854
(1.00)
DEL PEAK 16(9P23) MUTATION ANALYSIS 288 (30%) 661 0.00104
(0.678) 		0.618
(1.00) 		0.0057
(1.00) 		0.00063
(0.414) 		0.00685
(1.00) 		0.0238
(1.00) 		0.181
(1.00) 		3.35e-05
(0.0225) 		0.412
(1.00) 		0.3
(1.00)
DEL PEAK 17(9P21 3) MUTATION ANALYSIS 320 (34%) 629 0.045
(1.00) 		0.867
(1.00) 		0.00776
(1.00) 		0.000739
(0.485) 		0.0115
(1.00) 		0.0982
(1.00) 		0.0955
(1.00) 		1.82e-08
(1.25e-05) 		0.472
(1.00) 		0.712
(1.00)
DEL PEAK 19(9Q34 2) MUTATION ANALYSIS 255 (27%) 694 0.835
(1.00) 		0.841
(1.00) 		0.0866
(1.00) 		0.054
(1.00) 		0.0503
(1.00) 		0.732
(1.00) 		0.0274
(1.00) 		1.13e-06
(0.000781) 		0.496
(1.00) 		0.0687
(1.00)
DEL PEAK 21(10Q26 3) MUTATION ANALYSIS 276 (29%) 673 0.0825
(1.00) 		0.808
(1.00) 		0.312
(1.00) 		0.258
(1.00) 		0.242
(1.00) 		0.319
(1.00) 		0.732
(1.00) 		0.000161
(0.107) 		0.56
(1.00) 		0.68
(1.00)
DEL PEAK 28(13Q11) MUTATION ANALYSIS 376 (40%) 573 0.478
(1.00) 		0.925
(1.00) 		0.775
(1.00) 		0.277
(1.00) 		0.267
(1.00) 		0.679
(1.00) 		0.748
(1.00) 		5.7e-05
(0.0382) 		0.589
(1.00) 		0.154
(1.00)
DEL PEAK 29(13Q14 2) MUTATION ANALYSIS 430 (45%) 519 0.0686
(1.00) 		0.436
(1.00) 		0.572
(1.00) 		0.0613
(1.00) 		0.383
(1.00) 		0.89
(1.00) 		0.362
(1.00) 		2.87e-05
(0.0194) 		0.94
(1.00) 		0.0513
(1.00)
DEL PEAK 30(14Q24 1) MUTATION ANALYSIS 302 (32%) 647 0.101
(1.00) 		0.232
(1.00) 		0.199
(1.00) 		0.00148
(0.96) 		0.142
(1.00) 		0.933
(1.00) 		0.734
(1.00) 		9.53e-09
(6.59e-06) 		0.466
(1.00) 		0.14
(1.00)
DEL PEAK 31(15Q13 1) MUTATION ANALYSIS 325 (34%) 624 0.269
(1.00) 		0.125
(1.00) 		0.215
(1.00) 		0.0267
(1.00) 		0.0613
(1.00) 		0.166
(1.00) 		0.743
(1.00) 		1.17e-05
(0.00798) 		0.0941
(1.00) 		0.754
(1.00)
DEL PEAK 32(16Q24 3) MUTATION ANALYSIS 606 (64%) 343 0.0846
(1.00) 		0.000607
(0.4) 		0.24
(1.00) 		0.262
(1.00) 		0.616
(1.00) 		0.183
(1.00) 		0.754
(1.00) 		2.62e-15
(1.84e-12) 		0.814
(1.00) 		0.566
(1.00)
DEL PEAK 36(19P13 3) MUTATION ANALYSIS 317 (33%) 632 0.184
(1.00) 		0.0154
(1.00) 		0.675
(1.00) 		0.288
(1.00) 		0.743
(1.00) 		0.489
(1.00) 		0.178
(1.00) 		3.37e-09
(2.34e-06) 		0.873
(1.00) 		0.0339
(1.00)
DEL PEAK 37(19Q13 32) MUTATION ANALYSIS 187 (20%) 762 0.612
(1.00) 		0.487
(1.00) 		0.432
(1.00) 		0.513
(1.00) 		0.0475
(1.00) 		0.323
(1.00) 		0.696
(1.00) 		6.92e-07
(0.000477) 		0.107
(1.00) 		0.5
(1.00)
DEL PEAK 38(20P13) MUTATION ANALYSIS 139 (15%) 810 0.0851
(1.00) 		0.156
(1.00) 		0.419
(1.00) 		0.614
(1.00) 		0.777
(1.00) 		0.429
(1.00) 		0.647
(1.00) 		0.000117
(0.0779) 		1
(1.00) 		0.67
(1.00)
AMP PEAK 1(1P22 3) MUTATION ANALYSIS 209 (22%) 740 0.889
(1.00) 		0.526
(1.00) 		0.412
(1.00) 		0.0154
(1.00) 		0.0821
(1.00) 		0.646
(1.00) 		1
(1.00) 		0.222
(1.00) 		0.855
(1.00) 		0.0494
(1.00)
AMP PEAK 2(1Q21 3) MUTATION ANALYSIS 679 (72%) 270 0.813
(1.00) 		0.752
(1.00) 		0.326
(1.00) 		0.0121
(1.00) 		0.794
(1.00) 		0.458
(1.00) 		0.482
(1.00) 		0.18
(1.00) 		0.209
(1.00) 		0.856
(1.00)
AMP PEAK 3(1Q44) MUTATION ANALYSIS 677 (71%) 272 0.0534
(1.00) 		0.567
(1.00) 		0.242
(1.00) 		0.00544
(1.00) 		0.572
(1.00) 		0.653
(1.00) 		1
(1.00) 		0.0243
(1.00) 		0.504
(1.00) 		0.874
(1.00)
AMP PEAK 7(5P15 33) MUTATION ANALYSIS 340 (36%) 609 0.0993
(1.00) 		0.203
(1.00) 		0.658
(1.00) 		0.357
(1.00) 		0.00416
(1.00) 		0.0706
(1.00) 		0.752
(1.00) 		0.139
(1.00) 		0.207
(1.00) 		0.88
(1.00)
AMP PEAK 10(8P11 23) MUTATION ANALYSIS 360 (38%) 589 0.0376
(1.00) 		0.131
(1.00) 		0.0595
(1.00) 		0.545
(1.00) 		0.21
(1.00) 		0.0384
(1.00) 		0.334
(1.00) 		0.638
(1.00) 		0.64
(1.00) 		0.0224
(1.00)
AMP PEAK 11(8P11 21) MUTATION ANALYSIS 367 (39%) 582 0.713
(1.00) 		0.117
(1.00) 		0.736
(1.00) 		0.886
(1.00) 		0.906
(1.00) 		0.432
(1.00) 		0.332
(1.00) 		0.0373
(1.00) 		0.0524
(1.00) 		0.759
(1.00)
AMP PEAK 14(10Q22 3) MUTATION ANALYSIS 135 (14%) 814 0.0833
(1.00) 		0.684
(1.00) 		0.203
(1.00) 		0.069
(1.00) 		0.479
(1.00) 		0.0975
(1.00) 		1
(1.00) 		0.0157
(1.00) 		0.194
(1.00) 		0.317
(1.00)
AMP PEAK 16(11Q13 3) MUTATION ANALYSIS 352 (37%) 597 0.453
(1.00) 		0.261
(1.00) 		0.681
(1.00) 		0.163
(1.00) 		0.816
(1.00) 		0.41
(1.00) 		0.186
(1.00) 		0.128
(1.00) 		0.876
(1.00) 		0.979
(1.00)
AMP PEAK 17(11Q14 1) MUTATION ANALYSIS 234 (25%) 715 0.353
(1.00) 		0.358
(1.00) 		0.319
(1.00) 		0.137
(1.00) 		0.195
(1.00) 		0.0454
(1.00) 		0.273
(1.00) 		0.0024
(1.00) 		0.792
(1.00) 		0.55
(1.00)
AMP PEAK 19(12Q15) MUTATION ANALYSIS 242 (26%) 707 0.146
(1.00) 		0.475
(1.00) 		0.1
(1.00) 		0.0205
(1.00) 		0.00523
(1.00) 		0.139
(1.00) 		0.00378
(1.00) 		0.0466
(1.00) 		0.795
(1.00) 		0.187
(1.00)
AMP PEAK 20(13Q12 3) MUTATION ANALYSIS 129 (14%) 820 0.0769
(1.00) 		0.287
(1.00) 		0.571
(1.00) 		0.138
(1.00) 		0.253
(1.00) 		0.0754
(1.00) 		0.634
(1.00) 		0.0236
(1.00) 		0.44
(1.00) 		0.954
(1.00)
AMP PEAK 21(13Q34) MUTATION ANALYSIS 160 (17%) 789 0.769
(1.00) 		0.0898
(1.00) 		0.237
(1.00) 		0.00886
(1.00) 		0.366
(1.00) 		0.0928
(1.00) 		0.228
(1.00) 		0.0172
(1.00) 		1
(1.00) 		0.49
(1.00)
AMP PEAK 22(14Q21 1) MUTATION ANALYSIS 188 (20%) 761 0.46
(1.00) 		0.0418
(1.00) 		0.0546
(1.00) 		0.00765
(1.00) 		0.0127
(1.00) 		0.313
(1.00) 		0.696
(1.00) 		0.17
(1.00) 		0.925
(1.00) 		0.0597
(1.00)
AMP PEAK 24(17Q12) MUTATION ANALYSIS 301 (32%) 648 0.159
(1.00) 		0.87
(1.00) 		0.485
(1.00) 		0.0578
(1.00) 		0.127
(1.00) 		0.302
(1.00) 		0.00226
(1.00) 		0.0063
(1.00) 		0.685
(1.00) 		0.9
(1.00)
AMP PEAK 26(19P13 12) MUTATION ANALYSIS 196 (21%) 753 0.831
(1.00) 		0.85
(1.00) 		0.76
(1.00) 		0.343
(1.00) 		0.65
(1.00) 		0.185
(1.00) 		0.0365
(1.00) 		0.00737
(1.00) 		0.0249
(1.00) 		0.325
(1.00)
AMP PEAK 28(19Q13 42) MUTATION ANALYSIS 241 (25%) 708 0.396
(1.00) 		0.099
(1.00) 		0.988
(1.00) 		0.485
(1.00) 		0.995
(1.00) 		0.00442
(1.00) 		0.134
(1.00) 		0.0241
(1.00) 		0.297
(1.00) 		0.838
(1.00)
DEL PEAK 9(6P25 3) MUTATION ANALYSIS 180 (19%) 769 0.536
(1.00) 		0.0119
(1.00) 		0.454
(1.00) 		0.125
(1.00) 		0.355
(1.00) 		0.286
(1.00) 		0.411
(1.00) 		0.115
(1.00) 		0.335
(1.00) 		0.17
(1.00)
DEL PEAK 10(6Q15) MUTATION ANALYSIS 305 (32%) 644 0.577
(1.00) 		0.0336
(1.00) 		0.221
(1.00) 		0.221
(1.00) 		0.0717
(1.00) 		0.405
(1.00) 		1
(1.00) 		0.44
(1.00) 		0.686
(1.00) 		0.159
(1.00)
DEL PEAK 13(7Q36 1) MUTATION ANALYSIS 182 (19%) 767 0.0757
(1.00) 		0.935
(1.00) 		0.775
(1.00) 		0.335
(1.00) 		0.341
(1.00) 		0.373
(1.00) 		1
(1.00) 		0.0137
(1.00) 		0.701
(1.00) 		0.893
(1.00)
DEL PEAK 15(8P11 21) MUTATION ANALYSIS 180 (19%) 769 0.0369
(1.00) 		0.302
(1.00) 		0.609
(1.00) 		0.133
(1.00) 		0.32
(1.00) 		0.398
(1.00) 		0.223
(1.00) 		0.0167
(1.00) 		1
(1.00) 		0.359
(1.00)
DEL PEAK 18(9Q21 11) MUTATION ANALYSIS 258 (27%) 691 0.441
(1.00) 		0.944
(1.00) 		0.287
(1.00) 		0.0794
(1.00) 		0.36
(1.00) 		0.331
(1.00) 		0.146
(1.00) 		0.000936
(0.613) 		0.61
(1.00) 		0.235
(1.00)
DEL PEAK 20(10Q23 31) MUTATION ANALYSIS 271 (29%) 678 0.746
(1.00) 		0.259
(1.00) 		0.321
(1.00) 		0.0721
(1.00) 		0.525
(1.00) 		0.3
(1.00) 		0.297
(1.00) 		0.000801
(0.525) 		0.316
(1.00) 		0.926
(1.00)
DEL PEAK 22(11P15 5) MUTATION ANALYSIS 270 (28%) 679 0.0909
(1.00) 		0.736
(1.00) 		0.33
(1.00) 		0.00757
(1.00) 		0.33
(1.00) 		0.89
(1.00) 		0.482
(1.00) 		0.00556
(1.00) 		1
(1.00) 		0.221
(1.00)
DEL PEAK 23(11Q13 1) MUTATION ANALYSIS 201 (21%) 748 0.219
(1.00) 		0.506
(1.00) 		0.304
(1.00) 		0.327
(1.00) 		0.211
(1.00) 		0.709
(1.00) 		0.449
(1.00) 		0.807
(1.00) 		0.517
(1.00) 		0.896
(1.00)
DEL PEAK 24(11Q23 2) MUTATION ANALYSIS 473 (50%) 476 0.36
(1.00) 		0.302
(1.00) 		0.2
(1.00) 		0.0729
(1.00) 		0.085
(1.00) 		0.427
(1.00) 		0.0634
(1.00) 		0.21
(1.00) 		1
(1.00) 		0.69
(1.00)
DEL PEAK 25(11Q25) MUTATION ANALYSIS 441 (46%) 508 0.261
(1.00) 		0.0226
(1.00) 		0.132
(1.00) 		0.0064
(1.00) 		0.12
(1.00) 		0.606
(1.00) 		0.0514
(1.00) 		0.0609
(1.00) 		0.82
(1.00) 		0.759
(1.00)
DEL PEAK 26(12P13 1) MUTATION ANALYSIS 162 (17%) 787 0.831
(1.00) 		0.465
(1.00) 		0.311
(1.00) 		0.48
(1.00) 		0.786
(1.00) 		0.0294
(1.00) 		0.388
(1.00) 		0.00564
(1.00) 		0.841
(1.00) 		0.21
(1.00)
DEL PEAK 27(12Q24 31) MUTATION ANALYSIS 169 (18%) 780 0.242
(1.00) 		0.33
(1.00) 		0.674
(1.00) 		0.0829
(1.00) 		0.718
(1.00) 		0.803
(1.00) 		0.224
(1.00) 		0.0622
(1.00) 		0.555
(1.00) 		0.276
(1.00)
DEL PEAK 33(17P12) MUTATION ANALYSIS 570 (60%) 379 0.393
(1.00) 		0.00208
(1.00) 		0.648
(1.00) 		0.0971
(1.00) 		0.684
(1.00) 		0.897
(1.00) 		0.331
(1.00) 		0.00501
(1.00) 		0.877
(1.00) 		0.824
(1.00)
DEL PEAK 35(18Q23) MUTATION ANALYSIS 307 (32%) 642 0.0796
(1.00) 		0.46
(1.00) 		0.242
(1.00) 		0.0707
(1.00) 		0.181
(1.00) 		0.625
(1.00) 		0.735
(1.00) 		0.0113
(1.00) 		0.419
(1.00) 		0.513
(1.00)
DEL PEAK 39(21Q11 2) MUTATION ANALYSIS 185 (19%) 764 0.333
(1.00) 		0.386
(1.00) 		0.0134
(1.00) 		0.103
(1.00) 		0.00732
(1.00) 		0.464
(1.00) 		0.697
(1.00) 		0.00835
(1.00) 		0.39
(1.00) 		0.319
(1.00)
DEL PEAK 40(22Q11 1) MUTATION ANALYSIS 400 (42%) 549 0.524
(1.00) 		0.798
(1.00) 		0.822
(1.00) 		0.694
(1.00) 		0.462
(1.00) 		0.283
(1.00) 		0.532
(1.00) 		0.0386
(1.00) 		0.0265
(1.00) 		0.574
(1.00)
DEL PEAK 41(22Q13 31) MUTATION ANALYSIS 434 (46%) 515 0.446
(1.00) 		0.417
(1.00) 		0.835
(1.00) 		0.318
(1.00) 		0.631
(1.00) 		0.44
(1.00) 		0.526
(1.00) 		0.0372
(1.00) 		0.0483
(1.00) 		0.808
(1.00)
'AMP PEAK 4(3P26.1) MUTATION STATUS' versus 'PATHOLOGY.T.STAGE'

P value = 5.03e-05 (Fisher's exact test), Q value = 0.034

Table S1.  Gene #4: 'AMP PEAK 4(3P26.1) MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 247 551 113 35
AMP PEAK 4(3P26.1) MUTATED 31 131 16 13
AMP PEAK 4(3P26.1) WILD-TYPE 216 420 97 22

Figure S1.  Get High-res Image Gene #4: 'AMP PEAK 4(3P26.1) MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'AMP PEAK 5(3Q26.32) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 1.61e-11 (Chi-square test), Q value = 1.1e-08

Table S2.  Gene #5: 'AMP PEAK 5(3Q26.32) MUTATION STATUS' 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 1 706 151 5 28 14 43
AMP PEAK 5(3Q26.32) MUTATED 1 259 12 4 5 1 12
AMP PEAK 5(3Q26.32) WILD-TYPE 0 447 139 1 23 13 31

Figure S2.  Get High-res Image Gene #5: 'AMP PEAK 5(3Q26.32) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'AMP PEAK 6(4Q13.3) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 2.48e-05 (Chi-square test), Q value = 0.017

Table S3.  Gene #6: 'AMP PEAK 6(4Q13.3) MUTATION STATUS' 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 1 706 151 5 28 14 43
AMP PEAK 6(4Q13.3) MUTATED 0 132 4 2 1 1 6
AMP PEAK 6(4Q13.3) WILD-TYPE 1 574 147 3 27 13 37

Figure S3.  Get High-res Image Gene #6: 'AMP PEAK 6(4Q13.3) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'AMP PEAK 8(6P23) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 2.13e-05 (Chi-square test), Q value = 0.014

Table S4.  Gene #8: 'AMP PEAK 8(6P23) MUTATION STATUS' 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 1 706 151 5 28 14 43
AMP PEAK 8(6P23) MUTATED 0 214 16 3 4 2 12
AMP PEAK 8(6P23) WILD-TYPE 1 492 135 2 24 12 31

Figure S4.  Get High-res Image Gene #8: 'AMP PEAK 8(6P23) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'AMP PEAK 9(6Q21) MUTATION STATUS' versus 'PATHOLOGY.T.STAGE'

P value = 9.41e-05 (Fisher's exact test), Q value = 0.063

Table S5.  Gene #9: 'AMP PEAK 9(6Q21) MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 247 551 113 35
AMP PEAK 9(6Q21) MUTATED 27 129 19 3
AMP PEAK 9(6Q21) WILD-TYPE 220 422 94 32

Figure S5.  Get High-res Image Gene #9: 'AMP PEAK 9(6Q21) MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'AMP PEAK 9(6Q21) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 1.24e-05 (Chi-square test), Q value = 0.0084

Table S6.  Gene #9: 'AMP PEAK 9(6Q21) MUTATION STATUS' 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 1 706 151 5 28 14 43
AMP PEAK 9(6Q21) MUTATED 1 152 12 3 1 0 9
AMP PEAK 9(6Q21) WILD-TYPE 0 554 139 2 27 14 34

Figure S6.  Get High-res Image Gene #9: 'AMP PEAK 9(6Q21) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'AMP PEAK 12(8Q24.21) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 2.3e-13 (Chi-square test), Q value = 1.6e-10

Table S7.  Gene #12: 'AMP PEAK 12(8Q24.21) MUTATION STATUS' 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 1 706 151 5 28 14 43
AMP PEAK 12(8Q24.21) MUTATED 1 496 55 5 15 5 26
AMP PEAK 12(8Q24.21) WILD-TYPE 0 210 96 0 13 9 17

Figure S7.  Get High-res Image Gene #12: 'AMP PEAK 12(8Q24.21) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'AMP PEAK 13(10P15.1) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 6.94e-09 (Chi-square test), Q value = 4.8e-06

Table S8.  Gene #13: 'AMP PEAK 13(10P15.1) MUTATION STATUS' 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 1 706 151 5 28 14 43
AMP PEAK 13(10P15.1) MUTATED 1 234 17 4 4 0 8
AMP PEAK 13(10P15.1) WILD-TYPE 0 472 134 1 24 14 35

Figure S8.  Get High-res Image Gene #13: 'AMP PEAK 13(10P15.1) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'AMP PEAK 15(11P13) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 1.03e-05 (Chi-square test), Q value = 0.007

Table S9.  Gene #15: 'AMP PEAK 15(11P13) MUTATION STATUS' 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 1 706 151 5 28 14 43
AMP PEAK 15(11P13) MUTATED 1 168 12 3 1 2 10
AMP PEAK 15(11P13) WILD-TYPE 0 538 139 2 27 12 33

Figure S9.  Get High-res Image Gene #15: 'AMP PEAK 15(11P13) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'AMP PEAK 18(12P13.33) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 7.17e-05 (Chi-square test), Q value = 0.048

Table S10.  Gene #18: 'AMP PEAK 18(12P13.33) MUTATION STATUS' 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 1 706 151 5 28 14 43
AMP PEAK 18(12P13.33) MUTATED 1 203 21 4 8 1 8
AMP PEAK 18(12P13.33) WILD-TYPE 0 503 130 1 20 13 35

Figure S10.  Get High-res Image Gene #18: 'AMP PEAK 18(12P13.33) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'AMP PEAK 23(15Q26.3) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 6.12e-05 (Chi-square test), Q value = 0.041

Table S11.  Gene #23: 'AMP PEAK 23(15Q26.3) MUTATION STATUS' 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 1 706 151 5 28 14 43
AMP PEAK 23(15Q26.3) MUTATED 0 151 6 2 4 3 5
AMP PEAK 23(15Q26.3) WILD-TYPE 1 555 145 3 24 11 38

Figure S11.  Get High-res Image Gene #23: 'AMP PEAK 23(15Q26.3) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'AMP PEAK 25(17Q23.1) MUTATION STATUS' versus 'PATHOLOGY.T.STAGE'

P value = 0.000156 (Fisher's exact test), Q value = 0.1

Table S12.  Gene #25: 'AMP PEAK 25(17Q23.1) MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 247 551 113 35
AMP PEAK 25(17Q23.1) MUTATED 71 249 45 16
AMP PEAK 25(17Q23.1) WILD-TYPE 176 302 68 19

Figure S12.  Get High-res Image Gene #25: 'AMP PEAK 25(17Q23.1) MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'AMP PEAK 25(17Q23.1) MUTATION STATUS' versus 'GENDER'

P value = 0.000107 (Fisher's exact test), Q value = 0.071

Table S13.  Gene #25: 'AMP PEAK 25(17Q23.1) MUTATION STATUS' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 939 10
AMP PEAK 25(17Q23.1) MUTATED 373 10
AMP PEAK 25(17Q23.1) WILD-TYPE 566 0

Figure S13.  Get High-res Image Gene #25: 'AMP PEAK 25(17Q23.1) MUTATION STATUS' versus Clinical Feature #7: 'GENDER'

'AMP PEAK 27(19Q12) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 2.67e-05 (Chi-square test), Q value = 0.018

Table S14.  Gene #27: 'AMP PEAK 27(19Q12) MUTATION STATUS' 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 1 706 151 5 28 14 43
AMP PEAK 27(19Q12) MUTATED 0 197 21 5 5 2 8
AMP PEAK 27(19Q12) WILD-TYPE 1 509 130 0 23 12 35

Figure S14.  Get High-res Image Gene #27: 'AMP PEAK 27(19Q12) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'AMP PEAK 29(20Q13.2) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 1.04e-13 (Chi-square test), Q value = 7.2e-11

Table S15.  Gene #29: 'AMP PEAK 29(20Q13.2) MUTATION STATUS' 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 1 706 151 5 28 14 43
AMP PEAK 29(20Q13.2) MUTATED 1 408 37 1 10 1 18
AMP PEAK 29(20Q13.2) WILD-TYPE 0 298 114 4 18 13 25

Figure S15.  Get High-res Image Gene #29: 'AMP PEAK 29(20Q13.2) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'DEL PEAK 1(1P36.13) MUTATION STATUS' versus 'PATHOLOGY.T.STAGE'

P value = 1.22e-06 (Fisher's exact test), Q value = 0.00084

Table S16.  Gene #30: 'DEL PEAK 1(1P36.13) MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 247 551 113 35
DEL PEAK 1(1P36.13) MUTATED 73 255 40 23
DEL PEAK 1(1P36.13) WILD-TYPE 174 296 73 12

Figure S16.  Get High-res Image Gene #30: 'DEL PEAK 1(1P36.13) MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'DEL PEAK 2(1P22.1) MUTATION STATUS' versus 'PATHOLOGY.T.STAGE'

P value = 6.57e-06 (Fisher's exact test), Q value = 0.0045

Table S17.  Gene #31: 'DEL PEAK 2(1P22.1) MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 247 551 113 35
DEL PEAK 2(1P22.1) MUTATED 57 203 33 21
DEL PEAK 2(1P22.1) WILD-TYPE 190 348 80 14

Figure S17.  Get High-res Image Gene #31: 'DEL PEAK 2(1P22.1) MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'DEL PEAK 3(2Q37.3) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 0.000233 (Chi-square test), Q value = 0.15

Table S18.  Gene #32: 'DEL PEAK 3(2Q37.3) MUTATION STATUS' 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 1 706 151 5 28 14 43
DEL PEAK 3(2Q37.3) MUTATED 0 232 20 2 9 3 9
DEL PEAK 3(2Q37.3) WILD-TYPE 1 474 131 3 19 11 34

Figure S18.  Get High-res Image Gene #32: 'DEL PEAK 3(2Q37.3) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'DEL PEAK 4(3P14.3) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 5.79e-06 (Chi-square test), Q value = 0.004

Table S19.  Gene #33: 'DEL PEAK 4(3P14.3) MUTATION STATUS' 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 1 706 151 5 28 14 43
DEL PEAK 4(3P14.3) MUTATED 0 251 25 2 4 0 9
DEL PEAK 4(3P14.3) WILD-TYPE 1 455 126 3 24 14 34

Figure S19.  Get High-res Image Gene #33: 'DEL PEAK 4(3P14.3) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'DEL PEAK 5(4P16.3) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 3.05e-06 (Chi-square test), Q value = 0.0021

Table S20.  Gene #34: 'DEL PEAK 5(4P16.3) MUTATION STATUS' 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 1 706 151 5 28 14 43
DEL PEAK 5(4P16.3) MUTATED 1 246 22 3 6 0 14
DEL PEAK 5(4P16.3) WILD-TYPE 0 460 129 2 22 14 29

Figure S20.  Get High-res Image Gene #34: 'DEL PEAK 5(4P16.3) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'DEL PEAK 6(4Q35.2) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 1.3e-06 (Chi-square test), Q value = 0.00089

Table S21.  Gene #35: 'DEL PEAK 6(4Q35.2) MUTATION STATUS' 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 1 706 151 5 28 14 43
DEL PEAK 6(4Q35.2) MUTATED 1 251 24 3 4 0 11
DEL PEAK 6(4Q35.2) WILD-TYPE 0 455 127 2 24 14 32

Figure S21.  Get High-res Image Gene #35: 'DEL PEAK 6(4Q35.2) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'DEL PEAK 7(5Q11.2) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 1.26e-10 (Chi-square test), Q value = 8.8e-08

Table S22.  Gene #36: 'DEL PEAK 7(5Q11.2) MUTATION STATUS' 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 1 706 151 5 28 14 43
DEL PEAK 7(5Q11.2) MUTATED 1 217 8 4 4 1 9
DEL PEAK 7(5Q11.2) WILD-TYPE 0 489 143 1 24 13 34

Figure S22.  Get High-res Image Gene #36: 'DEL PEAK 7(5Q11.2) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'DEL PEAK 8(5Q21.3) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 4.71e-14 (Chi-square test), Q value = 3.3e-11

Table S23.  Gene #37: 'DEL PEAK 8(5Q21.3) MUTATION STATUS' 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 1 706 151 5 28 14 43
DEL PEAK 8(5Q21.3) MUTATED 1 211 4 5 4 0 9
DEL PEAK 8(5Q21.3) WILD-TYPE 0 495 147 0 24 14 34

Figure S23.  Get High-res Image Gene #37: 'DEL PEAK 8(5Q21.3) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'DEL PEAK 11(6Q27) MUTATION STATUS' versus 'AGE'

P value = 5.93e-06 (t-test), Q value = 0.004

Table S24.  Gene #40: 'DEL PEAK 11(6Q27) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 946 58.5 (13.2)
DEL PEAK 11(6Q27) MUTATED 318 55.9 (12.5)
DEL PEAK 11(6Q27) WILD-TYPE 628 59.9 (13.3)

Figure S24.  Get High-res Image Gene #40: 'DEL PEAK 11(6Q27) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'DEL PEAK 12(7P22.3) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 0.000285 (Chi-square test), Q value = 0.19

Table S25.  Gene #41: 'DEL PEAK 12(7P22.3) MUTATION STATUS' 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 1 706 151 5 28 14 43
DEL PEAK 12(7P22.3) MUTATED 0 112 3 0 2 0 5
DEL PEAK 12(7P22.3) WILD-TYPE 1 594 148 5 26 14 38

Figure S25.  Get High-res Image Gene #41: 'DEL PEAK 12(7P22.3) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'DEL PEAK 14(8P23.2) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 8.1e-09 (Chi-square test), Q value = 5.6e-06

Table S26.  Gene #43: 'DEL PEAK 14(8P23.2) MUTATION STATUS' 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 1 706 151 5 28 14 43
DEL PEAK 14(8P23.2) MUTATED 1 408 45 3 10 3 24
DEL PEAK 14(8P23.2) WILD-TYPE 0 298 106 2 18 11 19

Figure S26.  Get High-res Image Gene #43: 'DEL PEAK 14(8P23.2) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'DEL PEAK 16(9P23) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 3.35e-05 (Chi-square test), Q value = 0.023

Table S27.  Gene #45: 'DEL PEAK 16(9P23) MUTATION STATUS' 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 1 706 151 5 28 14 43
DEL PEAK 16(9P23) MUTATED 0 244 19 2 8 5 10
DEL PEAK 16(9P23) WILD-TYPE 1 462 132 3 20 9 33

Figure S27.  Get High-res Image Gene #45: 'DEL PEAK 16(9P23) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'DEL PEAK 17(9P21.3) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 1.82e-08 (Chi-square test), Q value = 1.3e-05

Table S28.  Gene #46: 'DEL PEAK 17(9P21.3) MUTATION STATUS' 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 1 706 151 5 28 14 43
DEL PEAK 17(9P21.3) MUTATED 1 271 18 4 10 5 11
DEL PEAK 17(9P21.3) WILD-TYPE 0 435 133 1 18 9 32

Figure S28.  Get High-res Image Gene #46: 'DEL PEAK 17(9P21.3) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'DEL PEAK 19(9Q34.2) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 1.13e-06 (Chi-square test), Q value = 0.00078

Table S29.  Gene #48: 'DEL PEAK 19(9Q34.2) MUTATION STATUS' 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 1 706 151 5 28 14 43
DEL PEAK 19(9Q34.2) MUTATED 0 219 16 4 5 3 7
DEL PEAK 19(9Q34.2) WILD-TYPE 1 487 135 1 23 11 36

Figure S29.  Get High-res Image Gene #48: 'DEL PEAK 19(9Q34.2) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'DEL PEAK 21(10Q26.3) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 0.000161 (Chi-square test), Q value = 0.11

Table S30.  Gene #50: 'DEL PEAK 21(10Q26.3) MUTATION STATUS' 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 1 706 151 5 28 14 43
DEL PEAK 21(10Q26.3) MUTATED 0 228 25 4 5 1 12
DEL PEAK 21(10Q26.3) WILD-TYPE 1 478 126 1 23 13 31

Figure S30.  Get High-res Image Gene #50: 'DEL PEAK 21(10Q26.3) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'DEL PEAK 28(13Q11) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 5.7e-05 (Chi-square test), Q value = 0.038

Table S31.  Gene #57: 'DEL PEAK 28(13Q11) MUTATION STATUS' 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 1 706 151 5 28 14 43
DEL PEAK 28(13Q11) MUTATED 1 310 37 2 11 1 13
DEL PEAK 28(13Q11) WILD-TYPE 0 396 114 3 17 13 30

Figure S31.  Get High-res Image Gene #57: 'DEL PEAK 28(13Q11) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'DEL PEAK 29(13Q14.2) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 2.87e-05 (Chi-square test), Q value = 0.019

Table S32.  Gene #58: 'DEL PEAK 29(13Q14.2) MUTATION STATUS' 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 1 706 151 5 28 14 43
DEL PEAK 29(13Q14.2) MUTATED 0 352 47 4 10 2 14
DEL PEAK 29(13Q14.2) WILD-TYPE 1 354 104 1 18 12 29

Figure S32.  Get High-res Image Gene #58: 'DEL PEAK 29(13Q14.2) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'DEL PEAK 30(14Q24.1) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 9.53e-09 (Chi-square test), Q value = 6.6e-06

Table S33.  Gene #59: 'DEL PEAK 30(14Q24.1) MUTATION STATUS' 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 1 706 151 5 28 14 43
DEL PEAK 30(14Q24.1) MUTATED 1 261 23 4 3 1 8
DEL PEAK 30(14Q24.1) WILD-TYPE 0 445 128 1 25 13 35

Figure S33.  Get High-res Image Gene #59: 'DEL PEAK 30(14Q24.1) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'DEL PEAK 31(15Q13.1) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 1.17e-05 (Chi-square test), Q value = 0.008

Table S34.  Gene #60: 'DEL PEAK 31(15Q13.1) MUTATION STATUS' 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 1 706 151 5 28 14 43
DEL PEAK 31(15Q13.1) MUTATED 1 270 30 4 8 1 10
DEL PEAK 31(15Q13.1) WILD-TYPE 0 436 121 1 20 13 33

Figure S34.  Get High-res Image Gene #60: 'DEL PEAK 31(15Q13.1) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'DEL PEAK 32(16Q24.3) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 2.62e-15 (Chi-square test), Q value = 1.8e-12

Table S35.  Gene #61: 'DEL PEAK 32(16Q24.3) MUTATION STATUS' 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 1 706 151 5 28 14 43
DEL PEAK 32(16Q24.3) MUTATED 0 433 135 2 19 1 16
DEL PEAK 32(16Q24.3) WILD-TYPE 1 273 16 3 9 13 27

Figure S35.  Get High-res Image Gene #61: 'DEL PEAK 32(16Q24.3) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'DEL PEAK 34(17Q21.31) MUTATION STATUS' versus 'AGE'

P value = 0.000368 (t-test), Q value = 0.24

Table S36.  Gene #63: 'DEL PEAK 34(17Q21.31) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 946 58.5 (13.2)
DEL PEAK 34(17Q21.31) MUTATED 326 56.4 (13.4)
DEL PEAK 34(17Q21.31) WILD-TYPE 620 59.7 (12.9)

Figure S36.  Get High-res Image Gene #63: 'DEL PEAK 34(17Q21.31) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'DEL PEAK 34(17Q21.31) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 1.53e-05 (Chi-square test), Q value = 0.01

Table S37.  Gene #63: 'DEL PEAK 34(17Q21.31) MUTATION STATUS' 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 1 706 151 5 28 14 43
DEL PEAK 34(17Q21.31) MUTATED 0 268 27 4 10 1 16
DEL PEAK 34(17Q21.31) WILD-TYPE 1 438 124 1 18 13 27

Figure S37.  Get High-res Image Gene #63: 'DEL PEAK 34(17Q21.31) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'DEL PEAK 36(19P13.3) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 3.37e-09 (Chi-square test), Q value = 2.3e-06

Table S38.  Gene #65: 'DEL PEAK 36(19P13.3) MUTATION STATUS' 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 1 706 151 5 28 14 43
DEL PEAK 36(19P13.3) MUTATED 1 270 16 4 7 4 14
DEL PEAK 36(19P13.3) WILD-TYPE 0 436 135 1 21 10 29

Figure S38.  Get High-res Image Gene #65: 'DEL PEAK 36(19P13.3) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'DEL PEAK 37(19Q13.32) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 6.92e-07 (Chi-square test), Q value = 0.00048

Table S39.  Gene #66: 'DEL PEAK 37(19Q13.32) MUTATION STATUS' 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 1 706 151 5 28 14 43
DEL PEAK 37(19Q13.32) MUTATED 0 166 6 3 4 3 4
DEL PEAK 37(19Q13.32) WILD-TYPE 1 540 145 2 24 11 39

Figure S39.  Get High-res Image Gene #66: 'DEL PEAK 37(19Q13.32) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'DEL PEAK 38(20P13) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 0.000117 (Chi-square test), Q value = 0.078

Table S40.  Gene #67: 'DEL PEAK 38(20P13) MUTATION STATUS' 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 1 706 151 5 28 14 43
DEL PEAK 38(20P13) MUTATED 1 122 8 2 2 0 4
DEL PEAK 38(20P13) WILD-TYPE 0 584 143 3 26 14 39

Figure S40.  Get High-res Image Gene #67: 'DEL PEAK 38(20P13) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

Methods & Data
Input

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

  • Clinical data file = BRCA-TP.clin.merged.picked.txt

  • Number of patients = 949

  • Number of significantly focal cnvs = 70

  • Number of selected clinical features = 10

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

Survival analysis

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

Student's t-test analysis

For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' function in R

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Fisher's exact test

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

Q value calculation

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

Download Results

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

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[4] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[5] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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