Correlation between copy number variations of arm-level result and selected clinical features
Breast Invasive Carcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1RB73JD
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1RB73JD
Overview
Introduction

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

Summary

Testing the association between copy number variation 82 arm-level events and 12 clinical features across 1062 patients, 188 significant findings detected with Q value < 0.25.

  • 1p gain cnv correlated to 'YEARS_TO_BIRTH',  'HISTOLOGICAL_TYPE',  'RADIATIONS_RADIATION_REGIMENINDICATION', and 'RACE'.

  • 1q gain cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE', and 'HISTOLOGICAL_TYPE'.

  • 2p gain cnv correlated to 'HISTOLOGICAL_TYPE',  'RACE', and 'ETHNICITY'.

  • 2q gain cnv correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.

  • 3p gain cnv correlated to 'PATHOLOGY_T_STAGE' and 'HISTOLOGICAL_TYPE'.

  • 3q gain cnv correlated to 'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE',  'NUMBER_OF_LYMPH_NODES', and 'RACE'.

  • 4p gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 4q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 5p gain cnv correlated to 'PATHOLOGY_N_STAGE'.

  • 5q gain cnv correlated to 'YEARS_TO_BIRTH' and 'RACE'.

  • 6p gain cnv correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.

  • 6q gain cnv correlated to 'HISTOLOGICAL_TYPE' and 'NUMBER_OF_LYMPH_NODES'.

  • 7p gain cnv correlated to 'GENDER' and 'HISTOLOGICAL_TYPE'.

  • 8q gain cnv correlated to 'HISTOLOGICAL_TYPE',  'RADIATIONS_RADIATION_REGIMENINDICATION', and 'RACE'.

  • 9q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 10p gain cnv correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.

  • 10q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 11p gain cnv correlated to 'HISTOLOGICAL_TYPE' and 'NUMBER_OF_LYMPH_NODES'.

  • 11q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 12p gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 12q gain cnv correlated to 'PATHOLOGY_N_STAGE',  'GENDER', and 'NUMBER_OF_LYMPH_NODES'.

  • 13q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 14q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 15q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 16p gain cnv correlated to 'YEARS_TO_BIRTH',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • 16q gain cnv correlated to 'GENDER' and 'HISTOLOGICAL_TYPE'.

  • 17p gain cnv correlated to 'GENDER' and 'RADIATIONS_RADIATION_REGIMENINDICATION'.

  • 17q gain cnv correlated to 'Time to Death',  'GENDER', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.

  • 18p gain cnv correlated to 'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE',  'NUMBER_OF_LYMPH_NODES', and 'RACE'.

  • 18q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 19p gain cnv correlated to 'NUMBER_OF_LYMPH_NODES'.

  • 19q gain cnv correlated to 'NUMBER_OF_LYMPH_NODES'.

  • 20p gain cnv correlated to 'PATHOLOGY_N_STAGE',  'GENDER',  'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.

  • 20q gain cnv correlated to 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'HISTOLOGICAL_TYPE'.

  • 21q gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'HISTOLOGICAL_TYPE',  'RADIATIONS_RADIATION_REGIMENINDICATION', and 'RACE'.

  • 22q gain cnv correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.

  • xp gain cnv correlated to 'YEARS_TO_BIRTH',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • xq gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 1p loss cnv correlated to 'YEARS_TO_BIRTH',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • 2p loss cnv correlated to 'PATHOLOGY_M_STAGE' and 'RADIATIONS_RADIATION_REGIMENINDICATION'.

  • 2q loss cnv correlated to 'PATHOLOGY_M_STAGE'.

  • 3p loss cnv correlated to 'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE',  'RADIATIONS_RADIATION_REGIMENINDICATION', and 'ETHNICITY'.

  • 3q loss cnv correlated to 'PATHOLOGY_T_STAGE',  'RADIATIONS_RADIATION_REGIMENINDICATION', and 'ETHNICITY'.

  • 4p loss cnv correlated to 'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • 4q loss cnv correlated to 'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • 5p loss cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE', and 'HISTOLOGICAL_TYPE'.

  • 5q loss cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • 6q loss cnv correlated to 'YEARS_TO_BIRTH' and 'RADIATIONS_RADIATION_REGIMENINDICATION'.

  • 7p loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 7q loss cnv correlated to 'ETHNICITY'.

  • 8p loss cnv correlated to 'Time to Death',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • 8q loss cnv correlated to 'RACE'.

  • 9p loss cnv correlated to 'Time to Death',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE', and 'HISTOLOGICAL_TYPE'.

  • 9q loss cnv correlated to 'PATHOLOGY_T_STAGE',  'GENDER',  'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.

  • 10p loss cnv correlated to 'Time to Death',  'PATHOLOGY_T_STAGE', and 'HISTOLOGICAL_TYPE'.

  • 10q loss cnv correlated to 'Time to Death',  'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'ETHNICITY'.

  • 11p loss cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE', and 'RACE'.

  • 11q loss cnv correlated to 'PATHOLOGY_N_STAGE' and 'RACE'.

  • 12p loss cnv correlated to 'PATHOLOGY_T_STAGE' and 'HISTOLOGICAL_TYPE'.

  • 12q loss cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • 13q loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 14q loss cnv correlated to 'Time to Death',  'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • 15q loss cnv correlated to 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'HISTOLOGICAL_TYPE'.

  • 16p loss cnv correlated to 'NUMBER_OF_LYMPH_NODES' and 'RACE'.

  • 16q loss cnv correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.

  • 17p loss cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE', and 'HISTOLOGICAL_TYPE'.

  • 17q loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.

  • 18p loss cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • 18q loss cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE', and 'HISTOLOGICAL_TYPE'.

  • 19p loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.

  • 19q loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.

  • 20p loss cnv correlated to 'PATHOLOGY_M_STAGE'.

  • 20q loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.

  • 21q loss cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • 22q loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'RADIATIONS_RADIATION_REGIMENINDICATION'.

  • xp loss cnv correlated to 'YEARS_TO_BIRTH' and 'RACE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 188 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		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
9p loss 306 (29%) 756 0.0175
(0.14) 		0.615
(0.865) 		0.00139
(0.0253) 		0.00025
(0.00794) 		0.0076
(0.0822) 		0.0281
(0.191) 		0.0878
(0.353) 		1e-05
(0.000615) 		0.0566
(0.281) 		0.126
(0.427) 		0.451
(0.783) 		0.585
(0.859)
18p loss 314 (30%) 748 1.34e-05
(0.000778) 		0.00256
(0.0401) 		0.0465
(0.243) 		0.00258
(0.0401) 		0.387
(0.725) 		1
(1.00) 		1
(1.00) 		0.00371
(0.0493) 		1
(1.00) 		0.202
(0.564) 		0.0434
(0.235) 		1
(1.00)
21q gain 195 (18%) 867 0.0148
(0.13) 		0.043
(0.234) 		0.623
(0.868) 		0.548
(0.843) 		0.63
(0.873) 		1
(1.00) 		1
(1.00) 		3e-05
(0.00155) 		0.0327
(0.205) 		0.566
(0.853) 		0.0212
(0.161) 		0.384
(0.725)
1p loss 239 (23%) 823 0.0606
(0.288) 		0.000115
(0.00453) 		8e-05
(0.00328) 		4e-05
(0.00197) 		0.00642
(0.0743) 		0.291
(0.659) 		1
(1.00) 		0.565
(0.853) 		1
(1.00) 		0.000884
(0.0181) 		0.905
(1.00) 		0.543
(0.839)
21q loss 178 (17%) 884 0.953
(1.00) 		0.404
(0.741) 		0.00873
(0.0924) 		0.207
(0.573) 		0.0151
(0.13) 		0.0176
(0.14) 		0.228
(0.599) 		0.00261
(0.0401) 		0.644
(0.883) 		0.165
(0.502) 		0.0204
(0.158) 		0.499
(0.816)
1p gain 201 (19%) 861 0.305
(0.671) 		0.0374
(0.217) 		0.636
(0.877) 		0.0723
(0.323) 		0.645
(0.883) 		0.781
(0.953) 		1
(1.00) 		0.00244
(0.0394) 		0.0342
(0.209) 		0.253
(0.615) 		0.0275
(0.191) 		0.405
(0.741)
3q gain 211 (20%) 851 0.652
(0.888) 		0.617
(0.865) 		0.284
(0.65) 		0.0367
(0.217) 		0.413
(0.749) 		0.787
(0.957) 		0.703
(0.911) 		1e-05
(0.000615) 		0.341
(0.694) 		0.0138
(0.128) 		0.00498
(0.0636) 		0.678
(0.9)
18p gain 174 (16%) 888 0.455
(0.786) 		0.371
(0.721) 		0.0902
(0.358) 		0.429
(0.755) 		0.0296
(0.193) 		0.769
(0.95) 		0.699
(0.911) 		0.00084
(0.0176) 		0.401
(0.741) 		0.0106
(0.109) 		0.00021
(0.00689) 		0.253
(0.615)
20p gain 411 (39%) 651 0.519
(0.833) 		0.233
(0.605) 		0.333
(0.693) 		0.294
(0.663) 		0.0119
(0.114) 		0.509
(0.829) 		0.0275
(0.191) 		1e-05
(0.000615) 		0.00703
(0.0786) 		0.611
(0.865) 		0.746
(0.942) 		0.238
(0.607)
3p loss 183 (17%) 879 0.469
(0.791) 		0.112
(0.394) 		0.685
(0.907) 		0.00046
(0.0128) 		0.962
(1.00) 		1
(1.00) 		0.228
(0.599) 		0.0331
(0.206) 		0.0281
(0.191) 		0.515
(0.833) 		0.0509
(0.262) 		0.0316
(0.203)
5q loss 222 (21%) 840 0.725
(0.927) 		0.000313
(0.00961) 		0.219
(0.589) 		0.00081
(0.0175) 		0.58
(0.859) 		1
(1.00) 		0.133
(0.438) 		1e-05
(0.000615) 		0.552
(0.845) 		0.111
(0.392) 		1e-05
(0.000615) 		0.309
(0.671)
9q loss 278 (26%) 784 0.421
(0.753) 		0.689
(0.911) 		0.13
(0.429) 		0.00611
(0.0716) 		0.0971
(0.367) 		0.218
(0.589) 		0.0417
(0.231) 		2e-05
(0.00109) 		0.0151
(0.13) 		0.964
(1.00) 		0.0852
(0.346) 		0.572
(0.857)
10q loss 225 (21%) 837 0.0362
(0.217) 		0.597
(0.865) 		0.315
(0.676) 		0.00542
(0.0667) 		0.149
(0.471) 		1
(1.00) 		0.474
(0.795) 		0.00526
(0.0655) 		1
(1.00) 		0.406
(0.741) 		0.072
(0.323) 		0.0419
(0.231)
12q loss 126 (12%) 936 0.713
(0.917) 		0.0115
(0.113) 		0.254
(0.615) 		0.00558
(0.0678) 		0.669
(0.894) 		1
(1.00) 		0.38
(0.723) 		7e-05
(0.00299) 		0.455
(0.786) 		0.114
(0.398) 		0.00521
(0.0655) 		0.613
(0.865)
14q loss 261 (25%) 801 0.0286
(0.191) 		0.574
(0.858) 		0.889
(1.00) 		0.0234
(0.172) 		0.172
(0.516) 		0.611
(0.865) 		0.311
(0.674) 		1e-05
(0.000615) 		0.336
(0.694) 		0.118
(0.407) 		7e-05
(0.00299) 		0.563
(0.853)
18q loss 316 (30%) 746 0.012
(0.114) 		0.0112
(0.112) 		0.0612
(0.288) 		0.017
(0.139) 		0.091
(0.36) 		1
(1.00) 		1
(1.00) 		0.00756
(0.0822) 		0.546
(0.841) 		0.41
(0.746) 		0.188
(0.541) 		0.857
(0.989)
1q gain 694 (65%) 368 0.343
(0.694) 		0.534
(0.835) 		0.0376
(0.217) 		0.00035
(0.0104) 		0.43
(0.755) 		0.819
(0.967) 		0.528
(0.834) 		0.00153
(0.0274) 		1
(1.00) 		0.522
(0.834) 		0.154
(0.476) 		0.12
(0.41)
2p gain 122 (11%) 940 0.475
(0.795) 		0.355
(0.708) 		0.877
(1.00) 		0.374
(0.722) 		0.964
(1.00) 		1
(1.00) 		0.626
(0.869) 		1e-05
(0.000615) 		0.518
(0.833) 		0.841
(0.979) 		0.00055
(0.0139) 		0.0165
(0.138)
8q gain 520 (49%) 542 0.67
(0.894) 		0.882
(1.00) 		0.511
(0.83) 		0.564
(0.853) 		0.402
(0.741) 		0.66
(0.892) 		0.376
(0.723) 		1e-05
(0.000615) 		0.0226
(0.169) 		0.461
(0.791) 		0.0171
(0.139) 		0.0976
(0.367)
12q gain 190 (18%) 872 0.298
(0.666) 		0.129
(0.429) 		0.228
(0.599) 		0.0591
(0.285) 		0.0165
(0.138) 		0.567
(0.853) 		0.0318
(0.203) 		0.059
(0.285) 		0.178
(0.528) 		0.0146
(0.13) 		0.732
(0.933) 		0.379
(0.723)
16p gain 458 (43%) 604 0.359
(0.709) 		0.0397
(0.222) 		0.528
(0.834) 		0.892
(1.00) 		0.383
(0.725) 		1
(1.00) 		0.545
(0.841) 		0.029
(0.193) 		0.781
(0.953) 		0.488
(0.808) 		0.021
(0.161) 		0.0637
(0.297)
17q gain 213 (20%) 849 0.034
(0.209) 		0.83
(0.973) 		0.876
(1.00) 		0.324
(0.681) 		0.694
(0.911) 		1
(1.00) 		0.00189
(0.032) 		0.0542
(0.273) 		0.0386
(0.22) 		0.452
(0.785) 		0.939
(1.00) 		0.679
(0.9)
20q gain 445 (42%) 617 0.577
(0.859) 		0.755
(0.943) 		0.48
(0.8) 		0.0174
(0.14) 		0.0423
(0.231) 		0.825
(0.971) 		0.218
(0.589) 		1e-05
(0.000615) 		0.0501
(0.26) 		0.285
(0.652) 		0.362
(0.713) 		0.13
(0.429)
xp gain 150 (14%) 912 0.581
(0.859) 		0.0199
(0.155) 		0.533
(0.835) 		0.166
(0.502) 		0.707
(0.913) 		0.224
(0.594) 		1
(1.00) 		0.0002
(0.00689) 		0.165
(0.502) 		0.699
(0.911) 		0.0267
(0.191) 		0.464
(0.791)
3q loss 100 (9%) 962 0.198
(0.558) 		0.691
(0.911) 		0.426
(0.755) 		0.00082
(0.0175) 		0.966
(1.00) 		1
(1.00) 		0.613
(0.865) 		0.386
(0.725) 		0.044
(0.236) 		0.621
(0.868) 		0.348
(0.699) 		0.0261
(0.189)
4p loss 347 (33%) 715 0.499
(0.816) 		0.213
(0.585) 		0.563
(0.853) 		0.0151
(0.13) 		0.632
(0.874) 		1
(1.00) 		0.756
(0.943) 		1e-05
(0.000615) 		0.607
(0.865) 		0.938
(1.00) 		0.00468
(0.0606) 		0.481
(0.801)
4q loss 307 (29%) 755 0.939
(1.00) 		0.817
(0.967) 		0.608
(0.865) 		0.0374
(0.217) 		0.701
(0.911) 		0.809
(0.966) 		0.739
(0.935) 		1e-05
(0.000615) 		0.322
(0.681) 		0.846
(0.981) 		0.012
(0.114) 		0.585
(0.859)
5p loss 138 (13%) 924 0.378
(0.723) 		0.00409
(0.0537) 		0.815
(0.967) 		0.0127
(0.119) 		0.912
(1.00) 		1
(1.00) 		1
(1.00) 		1e-05
(0.000615) 		0.26
(0.623) 		0.371
(0.721) 		0.0738
(0.324) 		0.463
(0.791)
8p loss 393 (37%) 669 0.0327
(0.205) 		0.136
(0.443) 		0.995
(1.00) 		0.321
(0.681) 		0.582
(0.859) 		0.821
(0.969) 		0.755
(0.943) 		0.00055
(0.0139) 		0.567
(0.853) 		0.893
(1.00) 		0.0261
(0.189) 		0.307
(0.671)
10p loss 168 (16%) 894 0.037
(0.217) 		0.973
(1.00) 		0.0712
(0.322) 		0.00304
(0.0453) 		0.157
(0.482) 		1
(1.00) 		0.23
(0.601) 		0.0373
(0.217) 		1
(1.00) 		0.266
(0.628) 		0.42
(0.753) 		0.252
(0.615)
11p loss 269 (25%) 793 0.147
(0.468) 		0.582
(0.859) 		0.014
(0.128) 		0.011
(0.111) 		0.0741
(0.324) 		0.801
(0.964) 		0.739
(0.935) 		0.0681
(0.312) 		0.526
(0.834) 		0.0595
(0.286) 		0.00184
(0.0318) 		0.0515
(0.262)
15q loss 314 (30%) 748 0.276
(0.64) 		0.911
(1.00) 		0.441
(0.77) 		0.00298
(0.0451) 		0.0365
(0.217) 		1
(1.00) 		1
(1.00) 		0.00041
(0.0119) 		0.0586
(0.285) 		0.0856
(0.346) 		0.54
(0.839) 		0.28
(0.646)
17p loss 569 (54%) 493 0.462
(0.791) 		0.0355
(0.215) 		0.294
(0.663) 		0.00603
(0.0715) 		0.797
(0.961) 		0.828
(0.971) 		0.364
(0.714) 		0.0293
(0.193) 		0.782
(0.954) 		0.977
(1.00) 		0.106
(0.381) 		0.869
(1)
2q gain 73 (7%) 989 0.793
(0.959) 		0.609
(0.865) 		0.717
(0.92) 		0.396
(0.733) 		0.93
(1.00) 		1
(1.00) 		1
(1.00) 		0.0007
(0.0166) 		0.785
(0.956) 		0.574
(0.858) 		0.0335
(0.207) 		0.103
(0.374)
3p gain 134 (13%) 928 0.474
(0.795) 		0.303
(0.671) 		0.173
(0.516) 		0.0443
(0.236) 		0.386
(0.725) 		0.524
(0.834) 		1
(1.00) 		0.00059
(0.0145) 		0.467
(0.791) 		0.288
(0.655) 		0.542
(0.839) 		0.796
(0.961)
5q gain 209 (20%) 853 0.889
(1.00) 		0.014
(0.128) 		0.703
(0.911) 		0.163
(0.499) 		0.201
(0.563) 		0.0968
(0.367) 		1
(1.00) 		0.127
(0.429) 		0.298
(0.666) 		0.845
(0.981) 		0.00318
(0.046) 		1
(1.00)
6p gain 205 (19%) 857 0.34
(0.694) 		0.942
(1.00) 		0.586
(0.859) 		0.0763
(0.331) 		0.527
(0.834) 		1
(1.00) 		0.701
(0.911) 		0.00021
(0.00689) 		0.221
(0.592) 		0.14
(0.455) 		0.0228
(0.169) 		0.406
(0.741)
6q gain 147 (14%) 915 0.234
(0.605) 		0.889
(1.00) 		0.611
(0.865) 		0.0966
(0.367) 		0.0982
(0.367) 		0.755
(0.943) 		1
(1.00) 		0.00108
(0.0213) 		0.424
(0.755) 		0.0224
(0.168) 		0.296
(0.665) 		0.336
(0.694)
7p gain 307 (29%) 755 0.808
(0.966) 		0.188
(0.542) 		0.776
(0.953) 		0.742
(0.937) 		0.761
(0.947) 		0.623
(0.868) 		0.017
(0.139) 		0.0421
(0.231) 		0.254
(0.615) 		0.961
(1.00) 		0.281
(0.649) 		0.585
(0.859)
10p gain 212 (20%) 850 0.806
(0.966) 		0.789
(0.957) 		0.268
(0.629) 		0.142
(0.455) 		0.196
(0.558) 		0.0576
(0.285) 		1
(1.00) 		1e-05
(0.000615) 		0.0839
(0.346) 		0.372
(0.721) 		0.00071
(0.0166) 		1
(1.00)
11p gain 135 (13%) 927 0.871
(1.00) 		0.818
(0.967) 		0.589
(0.861) 		0.918
(1.00) 		0.284
(0.65) 		0.339
(0.694) 		0.64
(0.88) 		0.0031
(0.0455) 		0.606
(0.865) 		0.0115
(0.113) 		0.662
(0.892) 		0.618
(0.865)
16q gain 140 (13%) 922 0.0741
(0.324) 		0.658
(0.892) 		0.252
(0.615) 		0.268
(0.629) 		0.234
(0.605) 		0.339
(0.694) 		0.0454
(0.24) 		0.0445
(0.236) 		0.61
(0.865) 		0.315
(0.676) 		0.665
(0.892) 		0.15
(0.471)
17p gain 104 (10%) 958 0.124
(0.421) 		0.933
(1.00) 		0.224
(0.594) 		0.0561
(0.28) 		0.0897
(0.357) 		1
(1.00) 		0.00234
(0.0389) 		0.0685
(0.312) 		0.0272
(0.191) 		0.95
(1.00) 		0.752
(0.943) 		0.78
(0.953)
22q gain 98 (9%) 964 0.351
(0.703) 		0.808
(0.966) 		0.128
(0.429) 		0.0648
(0.301) 		0.36
(0.709) 		0.712
(0.917) 		1
(1.00) 		0.00047
(0.0128) 		0.34
(0.694) 		0.13
(0.429) 		0.0308
(0.199) 		1
(1.00)
2p loss 179 (17%) 883 0.75
(0.943) 		0.392
(0.733) 		0.299
(0.667) 		0.394
(0.733) 		0.0553
(0.277) 		0.0151
(0.13) 		1
(1.00) 		0.241
(0.608) 		0.0097
(0.1) 		0.516
(0.833) 		0.209
(0.578) 		0.066
(0.305)
6q loss 271 (26%) 791 0.307
(0.671) 		0.00237
(0.0389) 		0.929
(1.00) 		0.309
(0.671) 		0.604
(0.865) 		0.801
(0.964) 		0.307
(0.671) 		0.322
(0.681) 		0.0394
(0.221) 		0.215
(0.587) 		0.566
(0.853) 		0.445
(0.775)
11q loss 360 (34%) 702 0.874
(1.00) 		0.853
(0.988) 		0.239
(0.607) 		0.118
(0.407) 		0.0389
(0.22) 		0.641
(0.88) 		0.198
(0.558) 		0.527
(0.834) 		0.466
(0.791) 		0.197
(0.558) 		0.00361
(0.0487) 		1
(1.00)
12p loss 146 (14%) 916 0.901
(1.00) 		0.429
(0.755) 		0.314
(0.676) 		0.0069
(0.078) 		0.815
(0.967) 		1
(1.00) 		1
(1.00) 		0.00019
(0.00689) 		0.369
(0.721) 		0.418
(0.753) 		0.223
(0.594) 		0.344
(0.694)
16p loss 171 (16%) 891 0.255
(0.616) 		0.932
(1.00) 		0.533
(0.835) 		0.984
(1.00) 		0.111
(0.392) 		0.23
(0.602) 		0.694
(0.911) 		0.0924
(0.362) 		0.348
(0.699) 		0.0383
(0.219) 		0.00881
(0.0924) 		0.661
(0.892)
16q loss 580 (55%) 482 0.145
(0.461) 		0.00159
(0.0279) 		0.599
(0.865) 		0.533
(0.835) 		0.184
(0.539) 		0.183
(0.539) 		0.24
(0.608) 		1e-05
(0.000615) 		0.212
(0.585) 		0.0831
(0.345) 		0.404
(0.741) 		1
(1.00)
17q loss 270 (25%) 792 0.926
(1.00) 		0.218
(0.589) 		0.978
(1.00) 		0.698
(0.911) 		0.12
(0.41) 		0.805
(0.966) 		0.0753
(0.328) 		0.00114
(0.022) 		0.937
(1.00) 		0.234
(0.605) 		0.00357
(0.0487) 		1
(1.00)
19p loss 187 (18%) 875 0.305
(0.671) 		0.0518
(0.263) 		0.916
(1.00) 		0.423
(0.755) 		0.306
(0.671) 		0.244
(0.612) 		1
(1.00) 		1e-05
(0.000615) 		0.469
(0.791) 		0.696
(0.911) 		0.00347
(0.0481) 		0.511
(0.83)
19q loss 157 (15%) 905 0.142
(0.455) 		0.555
(0.846) 		0.598
(0.865) 		0.582
(0.859) 		0.236
(0.607) 		0.108
(0.385) 		0.671
(0.895) 		1e-05
(0.000615) 		0.0797
(0.337) 		0.662
(0.892) 		0.0319
(0.203) 		1
(1.00)
20q loss 54 (5%) 1008 0.323
(0.681) 		0.0511
(0.262) 		0.478
(0.799) 		0.0578
(0.285) 		0.961
(1.00) 		0.283
(0.65) 		1
(1.00) 		0.0372
(0.217) 		0.641
(0.88) 		0.341
(0.694) 		0.0279
(0.191) 		0.125
(0.424)
22q loss 470 (44%) 592 0.0738
(0.324) 		0.497
(0.816) 		0.496
(0.816) 		0.316
(0.676) 		0.261
(0.624) 		0.659
(0.892) 		0.551
(0.845) 		0.001
(0.0201) 		0.00137
(0.0253) 		0.237
(0.607) 		0.522
(0.834) 		0.739
(0.935)
xp loss 186 (18%) 876 0.951
(1.00) 		0.00347
(0.0481) 		0.483
(0.803) 		0.08
(0.337) 		0.777
(0.953) 		0.253
(0.615) 		0.419
(0.753) 		0.0696
(0.315) 		0.65
(0.886) 		0.437
(0.764) 		0.0142
(0.128) 		1
(1.00)
4p gain 75 (7%) 987 0.245
(0.613) 		0.818
(0.967) 		0.193
(0.552) 		0.0855
(0.346) 		0.698
(0.911) 		0.672
(0.895) 		0.555
(0.846) 		0.00749
(0.0822) 		0.789
(0.957) 		0.77
(0.95) 		0.488
(0.808) 		0.739
(0.935)
4q gain 72 (7%) 990 0.148
(0.468) 		0.997
(1.00) 		0.296
(0.665) 		0.242
(0.609) 		0.457
(0.787) 		0.662
(0.892) 		0.54
(0.839) 		0.00592
(0.071) 		0.891
(1.00) 		0.725
(0.927) 		0.393
(0.733) 		0.734
(0.934)
5p gain 311 (29%) 751 0.184
(0.539) 		0.185
(0.54) 		0.845
(0.981) 		0.578
(0.859) 		0.00681
(0.0779) 		1
(1.00) 		0.315
(0.676) 		0.219
(0.589) 		0.198
(0.558) 		0.666
(0.893) 		0.165
(0.502) 		0.855
(0.989)
9q gain 118 (11%) 944 0.393
(0.733) 		0.601
(0.865) 		0.358
(0.708) 		0.225
(0.594) 		0.541
(0.839) 		1
(1.00) 		0.622
(0.868) 		0.0285
(0.191) 		0.827
(0.971) 		0.715
(0.918) 		0.332
(0.693) 		1
(1.00)
10q gain 123 (12%) 939 0.771
(0.95) 		0.632
(0.874) 		0.728
(0.93) 		0.312
(0.674) 		0.69
(0.911) 		0.736
(0.935) 		1
(1.00) 		0.00117
(0.0221) 		0.067
(0.308) 		0.3
(0.667) 		0.084
(0.346) 		0.603
(0.865)
11q gain 92 (9%) 970 0.0881
(0.353) 		0.935
(1.00) 		0.357
(0.708) 		0.678
(0.9) 		0.664
(0.892) 		1
(1.00) 		1
(1.00) 		0.00079
(0.0175) 		0.903
(1.00) 		0.133
(0.437) 		0.187
(0.541) 		0.767
(0.95)
12p gain 226 (21%) 836 0.607
(0.865) 		0.534
(0.835) 		0.609
(0.865) 		0.0989
(0.367) 		0.152
(0.473) 		0.79
(0.957) 		0.0628
(0.294) 		0.0162
(0.138) 		0.152
(0.473) 		0.531
(0.835) 		0.52
(0.833) 		0.308
(0.671)
13q gain 90 (8%) 972 0.395
(0.733) 		0.42
(0.753) 		0.751
(0.943) 		0.243
(0.609) 		0.529
(0.835) 		1
(1.00) 		0.613
(0.865) 		0.00079
(0.0175) 		0.265
(0.628) 		0.986
(1.00) 		0.553
(0.846) 		0.13
(0.429)
14q gain 141 (13%) 921 0.646
(0.883) 		0.114
(0.397) 		0.612
(0.865) 		0.344
(0.694) 		0.101
(0.369) 		0.341
(0.694) 		0.377
(0.723) 		0.0213
(0.161) 		0.611
(0.865) 		0.0782
(0.333) 		0.814
(0.967) 		0.215
(0.587)
15q gain 86 (8%) 976 0.351
(0.703) 		0.918
(1.00) 		0.726
(0.927) 		0.899
(1.00) 		0.957
(1.00) 		0.414
(0.749) 		0.607
(0.865) 		0.00346
(0.0481) 		0.1
(0.369) 		0.968
(1.00) 		0.264
(0.626) 		1
(1.00)
18q gain 149 (14%) 913 0.947
(1.00) 		0.618
(0.865) 		0.286
(0.653) 		0.195
(0.556) 		0.186
(0.541) 		0.543
(0.839) 		0.659
(0.892) 		0.0119
(0.114) 		0.372
(0.721) 		0.247
(0.614) 		0.116
(0.402) 		0.463
(0.791)
19p gain 188 (18%) 874 0.832
(0.973) 		0.429
(0.755) 		0.339
(0.694) 		0.199
(0.558) 		0.252
(0.615) 		0.151
(0.472) 		0.113
(0.396) 		0.0938
(0.363) 		0.279
(0.646) 		0.0181
(0.142) 		0.57
(0.855) 		0.832
(0.973)
19q gain 220 (21%) 842 0.713
(0.917) 		0.263
(0.625) 		0.0927
(0.362) 		0.6
(0.865) 		0.095
(0.367) 		0.0608
(0.288) 		0.253
(0.615) 		0.136
(0.443) 		0.496
(0.816) 		0.00882
(0.0924) 		0.992
(1.00) 		1
(1.00)
xq gain 135 (13%) 927 0.271
(0.634) 		0.0774
(0.333) 		0.257
(0.62) 		0.267
(0.629) 		0.67
(0.894) 		0.184
(0.539) 		1
(1.00) 		0.00018
(0.00681) 		0.213
(0.585) 		0.541
(0.839) 		0.0937
(0.363) 		0.61
(0.865)
2q loss 209 (20%) 853 0.454
(0.786) 		0.577
(0.859) 		0.223
(0.594) 		0.262
(0.625) 		0.0812
(0.34) 		0.0461
(0.243) 		1
(1.00) 		0.078
(0.333) 		0.0824
(0.344) 		0.412
(0.749) 		0.517
(0.833) 		0.0848
(0.346)
7p loss 109 (10%) 953 0.328
(0.687) 		0.465
(0.791) 		0.425
(0.755) 		0.367
(0.72) 		0.108
(0.386) 		0.155
(0.479) 		0.616
(0.865) 		0.00054
(0.0139) 		0.428
(0.755) 		0.263
(0.625) 		0.319
(0.679) 		0.166
(0.502)
7q loss 118 (11%) 944 0.0495
(0.258) 		0.1
(0.369) 		0.636
(0.877) 		0.466
(0.791) 		0.387
(0.725) 		0.498
(0.816) 		1
(1.00) 		0.105
(0.38) 		0.274
(0.638) 		0.791
(0.957) 		0.77
(0.95) 		0.0264
(0.19)
8q loss 91 (9%) 971 0.187
(0.541) 		0.143
(0.458) 		0.965
(1.00) 		0.649
(0.886) 		0.587
(0.859) 		0.407
(0.741) 		0.613
(0.865) 		0.629
(0.873) 		0.176
(0.524) 		0.805
(0.966) 		0.0297
(0.193) 		0.77
(0.95)
13q loss 427 (40%) 635 0.0979
(0.367) 		0.237
(0.607) 		0.859
(0.989) 		0.171
(0.515) 		0.703
(0.911) 		1
(1.00) 		0.763
(0.948) 		7e-05
(0.00299) 		0.325
(0.681) 		0.505
(0.825) 		0.0801
(0.337) 		0.237
(0.607)
20p loss 92 (9%) 970 0.205
(0.571) 		0.111
(0.392) 		0.512
(0.83) 		0.103
(0.374) 		0.839
(0.979) 		0.0275
(0.191) 		1
(1.00) 		0.092
(0.362) 		0.463
(0.791) 		0.822
(0.969) 		0.0986
(0.367) 		0.239
(0.607)
7q gain 262 (25%) 800 0.431
(0.755) 		0.905
(1.00) 		0.386
(0.725) 		0.248
(0.615) 		0.383
(0.725) 		0.303
(0.671) 		0.152
(0.473) 		0.102
(0.372) 		0.81
(0.966) 		0.551
(0.845) 		0.0606
(0.288) 		0.561
(0.853)
8p gain 285 (27%) 777 0.766
(0.95) 		0.774
(0.952) 		0.372
(0.721) 		0.828
(0.971) 		0.501
(0.818) 		0.318
(0.679) 		0.498
(0.816) 		0.0961
(0.367) 		0.815
(0.967) 		0.437
(0.764) 		0.0777
(0.333) 		0.851
(0.987)
9p gain 141 (13%) 921 0.954
(1.00) 		0.98
(1.00) 		0.198
(0.558) 		0.142
(0.455) 		0.33
(0.689) 		0.752
(0.943) 		0.377
(0.723) 		0.0739
(0.324) 		0.839
(0.979) 		0.704
(0.911) 		0.343
(0.694) 		1
(1.00)
1q loss 51 (5%) 1011 0.356
(0.708) 		0.324
(0.681) 		0.959
(1.00) 		0.403
(0.741) 		0.173
(0.516) 		1
(1.00) 		1
(1.00) 		0.354
(0.706) 		0.519
(0.833) 		0.334
(0.693) 		0.759
(0.945) 		1
(1.00)
6p loss 184 (17%) 878 0.705
(0.911) 		0.0584
(0.285) 		0.994
(1.00) 		0.47
(0.791) 		0.987
(1.00) 		0.779
(0.953) 		0.7
(0.911) 		0.259
(0.622) 		0.274
(0.638) 		0.893
(1.00) 		0.427
(0.755) 		0.378
(0.723)
xq loss 187 (18%) 875 0.756
(0.943) 		0.105
(0.38) 		0.474
(0.795) 		0.0867
(0.35) 		0.525
(0.834) 		0.249
(0.615) 		0.421
(0.753) 		0.14
(0.455) 		0.856
(0.989) 		0.375
(0.723) 		0.0988
(0.367) 		1
(1.00)
'1p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0374 (Wilcoxon-test), Q value = 0.22

Table S1.  Gene #1: '1p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1047 58.6 (13.2)
1P GAIN MUTATED 201 56.9 (12.3)
1P GAIN WILD-TYPE 846 59.0 (13.3)

Figure S1.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'1p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00244 (Fisher's exact test), Q value = 0.039

Table S2.  Gene #1: '1p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
1P GAIN MUTATED 0 157 20 3 2 7 1 11
1P GAIN WILD-TYPE 1 606 172 3 2 23 16 37

Figure S2.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'1p gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0342 (Fisher's exact test), Q value = 0.21

Table S3.  Gene #1: '1p gain' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 288 774
1P GAIN MUTATED 67 134
1P GAIN WILD-TYPE 221 640

Figure S3.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'1p gain' versus 'RACE'

P value = 0.0275 (Fisher's exact test), Q value = 0.19

Table S4.  Gene #1: '1p gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
1P GAIN MUTATED 1 7 42 140
1P GAIN WILD-TYPE 0 53 128 596

Figure S4.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #11: 'RACE'

'1q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0376 (Fisher's exact test), Q value = 0.22

Table S5.  Gene #2: '1q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
ALL 89 81 8 3 353 245 2 150 29 63 20 1 13
1Q GAIN MUTATED 48 43 4 3 244 163 1 93 23 46 13 1 8
1Q GAIN WILD-TYPE 41 38 4 0 109 82 1 57 6 17 7 0 5

Figure S5.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'1q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00035 (Fisher's exact test), Q value = 0.01

Table S6.  Gene #2: '1q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
1Q GAIN MUTATED 151 428 83 30
1Q GAIN WILD-TYPE 121 188 47 10

Figure S6.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'1q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00153 (Fisher's exact test), Q value = 0.027

Table S7.  Gene #2: '1q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
1Q GAIN MUTATED 1 482 150 4 2 17 8 30
1Q GAIN WILD-TYPE 0 281 42 2 2 13 9 18

Figure S7.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'2p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00061

Table S8.  Gene #3: '2p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
2P GAIN MUTATED 1 108 4 2 2 0 0 5
2P GAIN WILD-TYPE 0 655 188 4 2 30 17 43

Figure S8.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'2p gain' versus 'RACE'

P value = 0.00055 (Fisher's exact test), Q value = 0.014

Table S9.  Gene #3: '2p gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
2P GAIN MUTATED 1 10 31 69
2P GAIN WILD-TYPE 0 50 139 667

Figure S9.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #11: 'RACE'

'2p gain' versus 'ETHNICITY'

P value = 0.0165 (Fisher's exact test), Q value = 0.14

Table S10.  Gene #3: '2p gain' versus Clinical Feature #12: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 38 858
2P GAIN MUTATED 0 104
2P GAIN WILD-TYPE 38 754

Figure S10.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #12: 'ETHNICITY'

'2q gain' versus 'HISTOLOGICAL_TYPE'

P value = 7e-04 (Fisher's exact test), Q value = 0.017

Table S11.  Gene #4: '2q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
2Q GAIN MUTATED 0 64 3 0 2 0 0 4
2Q GAIN WILD-TYPE 1 699 189 6 2 30 17 44

Figure S11.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'2q gain' versus 'RACE'

P value = 0.0335 (Fisher's exact test), Q value = 0.21

Table S12.  Gene #4: '2q gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
2Q GAIN MUTATED 0 8 17 42
2Q GAIN WILD-TYPE 1 52 153 694

Figure S12.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #11: 'RACE'

'3p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0443 (Fisher's exact test), Q value = 0.24

Table S13.  Gene #5: '3p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
3P GAIN MUTATED 32 83 9 9
3P GAIN WILD-TYPE 240 533 121 31

Figure S13.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'3p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00059 (Fisher's exact test), Q value = 0.015

Table S14.  Gene #5: '3p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
3P GAIN MUTATED 0 113 7 2 0 4 1 7
3P GAIN WILD-TYPE 1 650 185 4 4 26 16 41

Figure S14.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'3q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0367 (Fisher's exact test), Q value = 0.22

Table S15.  Gene #6: '3q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
3Q GAIN MUTATED 45 133 20 13
3Q GAIN WILD-TYPE 227 483 110 27

Figure S15.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'3q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00061

Table S16.  Gene #6: '3q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
3Q GAIN MUTATED 0 179 9 4 2 6 1 10
3Q GAIN WILD-TYPE 1 584 183 2 2 24 16 38

Figure S16.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'3q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0138 (Wilcoxon-test), Q value = 0.13

Table S17.  Gene #6: '3q gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 897 2.4 (4.7)
3Q GAIN MUTATED 175 1.9 (4.1)
3Q GAIN WILD-TYPE 722 2.5 (4.8)

Figure S17.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'3q gain' versus 'RACE'

P value = 0.00498 (Fisher's exact test), Q value = 0.064

Table S18.  Gene #6: '3q gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
3Q GAIN MUTATED 1 13 46 127
3Q GAIN WILD-TYPE 0 47 124 609

Figure S18.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #11: 'RACE'

'4p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00749 (Fisher's exact test), Q value = 0.082

Table S19.  Gene #7: '4p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
4P GAIN MUTATED 0 58 4 1 0 3 1 8
4P GAIN WILD-TYPE 1 705 188 5 4 27 16 40

Figure S19.  Get High-res Image Gene #7: '4p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'4q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00592 (Fisher's exact test), Q value = 0.071

Table S20.  Gene #8: '4q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
4Q GAIN MUTATED 0 56 4 2 0 2 1 7
4Q GAIN WILD-TYPE 1 707 188 4 4 28 16 41

Figure S20.  Get High-res Image Gene #8: '4q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'5p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00681 (Fisher's exact test), Q value = 0.078

Table S21.  Gene #9: '5p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 501 350 117 75
5P GAIN MUTATED 161 84 44 17
5P GAIN WILD-TYPE 340 266 73 58

Figure S21.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'5q gain' versus 'YEARS_TO_BIRTH'

P value = 0.014 (Wilcoxon-test), Q value = 0.13

Table S22.  Gene #10: '5q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1047 58.6 (13.2)
5Q GAIN MUTATED 206 60.5 (12.4)
5Q GAIN WILD-TYPE 841 58.2 (13.3)

Figure S22.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5q gain' versus 'RACE'

P value = 0.00318 (Fisher's exact test), Q value = 0.046

Table S23.  Gene #10: '5q gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
5Q GAIN MUTATED 0 7 19 159
5Q GAIN WILD-TYPE 1 53 151 577

Figure S23.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #11: 'RACE'

'6p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00021 (Fisher's exact test), Q value = 0.0069

Table S24.  Gene #11: '6p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
6P GAIN MUTATED 0 164 19 4 1 3 1 12
6P GAIN WILD-TYPE 1 599 173 2 3 27 16 36

Figure S24.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'6p gain' versus 'RACE'

P value = 0.0228 (Fisher's exact test), Q value = 0.17

Table S25.  Gene #11: '6p gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
6P GAIN MUTATED 0 8 46 132
6P GAIN WILD-TYPE 1 52 124 604

Figure S25.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #11: 'RACE'

'6q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00108 (Fisher's exact test), Q value = 0.021

Table S26.  Gene #12: '6q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
6Q GAIN MUTATED 0 117 13 4 1 3 1 8
6Q GAIN WILD-TYPE 1 646 179 2 3 27 16 40

Figure S26.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'6q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0224 (Wilcoxon-test), Q value = 0.17

Table S27.  Gene #12: '6q gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 897 2.4 (4.7)
6Q GAIN MUTATED 125 2.4 (5.4)
6Q GAIN WILD-TYPE 772 2.4 (4.5)

Figure S27.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'7p gain' versus 'GENDER'

P value = 0.017 (Fisher's exact test), Q value = 0.14

Table S28.  Gene #13: '7p gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1051 11
7P GAIN MUTATED 300 7
7P GAIN WILD-TYPE 751 4

Figure S28.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #7: 'GENDER'

'7p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0421 (Fisher's exact test), Q value = 0.23

Table S29.  Gene #13: '7p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
7P GAIN MUTATED 1 236 41 1 2 8 2 16
7P GAIN WILD-TYPE 0 527 151 5 2 22 15 32

Figure S29.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'8q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00061

Table S30.  Gene #16: '8q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
8Q GAIN MUTATED 1 412 55 5 1 13 4 28
8Q GAIN WILD-TYPE 0 351 137 1 3 17 13 20

Figure S30.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'8q gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0226 (Fisher's exact test), Q value = 0.17

Table S31.  Gene #16: '8q gain' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 288 774
8Q GAIN MUTATED 158 362
8Q GAIN WILD-TYPE 130 412

Figure S31.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'8q gain' versus 'RACE'

P value = 0.0171 (Fisher's exact test), Q value = 0.14

Table S32.  Gene #16: '8q gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
8Q GAIN MUTATED 1 28 98 336
8Q GAIN WILD-TYPE 0 32 72 400

Figure S32.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #11: 'RACE'

'9q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0285 (Fisher's exact test), Q value = 0.19

Table S33.  Gene #18: '9q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
9Q GAIN MUTATED 0 89 18 3 2 1 1 4
9Q GAIN WILD-TYPE 1 674 174 3 2 29 16 44

Figure S33.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'10p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00061

Table S34.  Gene #19: '10p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
10P GAIN MUTATED 0 181 16 4 1 4 0 6
10P GAIN WILD-TYPE 1 582 176 2 3 26 17 42

Figure S34.  Get High-res Image Gene #19: '10p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'10p gain' versus 'RACE'

P value = 0.00071 (Fisher's exact test), Q value = 0.017

Table S35.  Gene #19: '10p gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
10P GAIN MUTATED 1 11 51 129
10P GAIN WILD-TYPE 0 49 119 607

Figure S35.  Get High-res Image Gene #19: '10p gain' versus Clinical Feature #11: 'RACE'

'10q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00117 (Fisher's exact test), Q value = 0.022

Table S36.  Gene #20: '10q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
10Q GAIN MUTATED 0 103 10 3 1 3 0 3
10Q GAIN WILD-TYPE 1 660 182 3 3 27 17 45

Figure S36.  Get High-res Image Gene #20: '10q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'11p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0031 (Fisher's exact test), Q value = 0.046

Table S37.  Gene #21: '11p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
11P GAIN MUTATED 0 111 10 1 1 1 2 9
11P GAIN WILD-TYPE 1 652 182 5 3 29 15 39

Figure S37.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'11p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0115 (Wilcoxon-test), Q value = 0.11

Table S38.  Gene #21: '11p gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 897 2.4 (4.7)
11P GAIN MUTATED 116 1.7 (3.6)
11P GAIN WILD-TYPE 781 2.5 (4.8)

Figure S38.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'11q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00079 (Fisher's exact test), Q value = 0.018

Table S39.  Gene #22: '11q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
11Q GAIN MUTATED 0 75 4 2 1 2 1 7
11Q GAIN WILD-TYPE 1 688 188 4 3 28 16 41

Figure S39.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'12p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0162 (Fisher's exact test), Q value = 0.14

Table S40.  Gene #23: '12p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
12P GAIN MUTATED 1 178 27 2 0 8 1 8
12P GAIN WILD-TYPE 0 585 165 4 4 22 16 40

Figure S40.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'12q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0165 (Fisher's exact test), Q value = 0.14

Table S41.  Gene #24: '12q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 501 350 117 75
12Q GAIN MUTATED 76 59 31 18
12Q GAIN WILD-TYPE 425 291 86 57

Figure S41.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'12q gain' versus 'GENDER'

P value = 0.0318 (Fisher's exact test), Q value = 0.2

Table S42.  Gene #24: '12q gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1051 11
12Q GAIN MUTATED 185 5
12Q GAIN WILD-TYPE 866 6

Figure S42.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #7: 'GENDER'

'12q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0146 (Wilcoxon-test), Q value = 0.13

Table S43.  Gene #24: '12q gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 897 2.4 (4.7)
12Q GAIN MUTATED 153 3.1 (5.2)
12Q GAIN WILD-TYPE 744 2.2 (4.5)

Figure S43.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'13q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00079 (Fisher's exact test), Q value = 0.018

Table S44.  Gene #25: '13q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
13Q GAIN MUTATED 0 73 4 0 2 2 2 7
13Q GAIN WILD-TYPE 1 690 188 6 2 28 15 41

Figure S44.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'14q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0213 (Fisher's exact test), Q value = 0.16

Table S45.  Gene #26: '14q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
14Q GAIN MUTATED 0 109 15 0 2 8 2 5
14Q GAIN WILD-TYPE 1 654 177 6 2 22 15 43

Figure S45.  Get High-res Image Gene #26: '14q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'15q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00346 (Fisher's exact test), Q value = 0.048

Table S46.  Gene #27: '15q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
15Q GAIN MUTATED 0 74 3 0 0 1 2 5
15Q GAIN WILD-TYPE 1 689 189 6 4 29 15 43

Figure S46.  Get High-res Image Gene #27: '15q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'16p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0397 (Wilcoxon-test), Q value = 0.22

Table S47.  Gene #28: '16p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1047 58.6 (13.2)
16P GAIN MUTATED 452 59.6 (13.2)
16P GAIN WILD-TYPE 595 57.9 (13.1)

Figure S47.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.029 (Fisher's exact test), Q value = 0.19

Table S48.  Gene #28: '16p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
16P GAIN MUTATED 1 334 86 2 2 16 2 14
16P GAIN WILD-TYPE 0 429 106 4 2 14 15 34

Figure S48.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'16p gain' versus 'RACE'

P value = 0.021 (Fisher's exact test), Q value = 0.16

Table S49.  Gene #28: '16p gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
16P GAIN MUTATED 1 23 56 324
16P GAIN WILD-TYPE 0 37 114 412

Figure S49.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #11: 'RACE'

'16q gain' versus 'GENDER'

P value = 0.0454 (Fisher's exact test), Q value = 0.24

Table S50.  Gene #29: '16q gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1051 11
16Q GAIN MUTATED 136 4
16Q GAIN WILD-TYPE 915 7

Figure S50.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #7: 'GENDER'

'16q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0445 (Fisher's exact test), Q value = 0.24

Table S51.  Gene #29: '16q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
16Q GAIN MUTATED 1 109 17 1 2 4 1 5
16Q GAIN WILD-TYPE 0 654 175 5 2 26 16 43

Figure S51.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'17p gain' versus 'GENDER'

P value = 0.00234 (Fisher's exact test), Q value = 0.039

Table S52.  Gene #30: '17p gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1051 11
17P GAIN MUTATED 99 5
17P GAIN WILD-TYPE 952 6

Figure S52.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #7: 'GENDER'

'17p gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0272 (Fisher's exact test), Q value = 0.19

Table S53.  Gene #30: '17p gain' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 288 774
17P GAIN MUTATED 38 66
17P GAIN WILD-TYPE 250 708

Figure S53.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'17q gain' versus 'Time to Death'

P value = 0.034 (logrank test), Q value = 0.21

Table S54.  Gene #31: '17q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1044 128 0.0 - 234.3 (24.5)
17Q GAIN MUTATED 210 32 0.2 - 186.5 (26.6)
17Q GAIN WILD-TYPE 834 96 0.0 - 234.3 (23.7)

Figure S54.  Get High-res Image Gene #31: '17q gain' versus Clinical Feature #1: 'Time to Death'

'17q gain' versus 'GENDER'

P value = 0.00189 (Fisher's exact test), Q value = 0.032

Table S55.  Gene #31: '17q gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1051 11
17Q GAIN MUTATED 206 7
17Q GAIN WILD-TYPE 845 4

Figure S55.  Get High-res Image Gene #31: '17q gain' versus Clinical Feature #7: 'GENDER'

'17q gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0386 (Fisher's exact test), Q value = 0.22

Table S56.  Gene #31: '17q gain' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 288 774
17Q GAIN MUTATED 70 143
17Q GAIN WILD-TYPE 218 631

Figure S56.  Get High-res Image Gene #31: '17q gain' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'18p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0296 (Fisher's exact test), Q value = 0.19

Table S57.  Gene #32: '18p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 501 350 117 75
18P GAIN MUTATED 99 44 15 13
18P GAIN WILD-TYPE 402 306 102 62

Figure S57.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'18p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00084 (Fisher's exact test), Q value = 0.018

Table S58.  Gene #32: '18p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
18P GAIN MUTATED 0 142 14 2 1 5 0 9
18P GAIN WILD-TYPE 1 621 178 4 3 25 17 39

Figure S58.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'18p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0106 (Wilcoxon-test), Q value = 0.11

Table S59.  Gene #32: '18p gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 897 2.4 (4.7)
18P GAIN MUTATED 143 2.0 (4.4)
18P GAIN WILD-TYPE 754 2.4 (4.7)

Figure S59.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'18p gain' versus 'RACE'

P value = 0.00021 (Fisher's exact test), Q value = 0.0069

Table S60.  Gene #32: '18p gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
18P GAIN MUTATED 0 7 46 101
18P GAIN WILD-TYPE 1 53 124 635

Figure S60.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #11: 'RACE'

'18q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0119 (Fisher's exact test), Q value = 0.11

Table S61.  Gene #33: '18q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
18Q GAIN MUTATED 0 122 13 1 1 5 0 6
18Q GAIN WILD-TYPE 1 641 179 5 3 25 17 42

Figure S61.  Get High-res Image Gene #33: '18q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'19p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0181 (Wilcoxon-test), Q value = 0.14

Table S62.  Gene #34: '19p gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 897 2.4 (4.7)
19P GAIN MUTATED 168 2.0 (4.7)
19P GAIN WILD-TYPE 729 2.5 (4.6)

Figure S62.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'19q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00882 (Wilcoxon-test), Q value = 0.092

Table S63.  Gene #35: '19q gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 897 2.4 (4.7)
19Q GAIN MUTATED 192 1.9 (4.3)
19Q GAIN WILD-TYPE 705 2.5 (4.8)

Figure S63.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'20p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0119 (Fisher's exact test), Q value = 0.11

Table S64.  Gene #36: '20p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 501 350 117 75
20P GAIN MUTATED 195 125 60 23
20P GAIN WILD-TYPE 306 225 57 52

Figure S64.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'20p gain' versus 'GENDER'

P value = 0.0275 (Fisher's exact test), Q value = 0.19

Table S65.  Gene #36: '20p gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1051 11
20P GAIN MUTATED 403 8
20P GAIN WILD-TYPE 648 3

Figure S65.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #7: 'GENDER'

'20p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00061

Table S66.  Gene #36: '20p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
20P GAIN MUTATED 0 335 44 2 2 10 1 16
20P GAIN WILD-TYPE 1 428 148 4 2 20 16 32

Figure S66.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'20p gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.00703 (Fisher's exact test), Q value = 0.079

Table S67.  Gene #36: '20p gain' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 288 774
20P GAIN MUTATED 131 280
20P GAIN WILD-TYPE 157 494

Figure S67.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'20q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0174 (Fisher's exact test), Q value = 0.14

Table S68.  Gene #37: '20q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
20Q GAIN MUTATED 102 274 44 22
20Q GAIN WILD-TYPE 170 342 86 18

Figure S68.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'20q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0423 (Fisher's exact test), Q value = 0.23

Table S69.  Gene #37: '20q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 501 350 117 75
20Q GAIN MUTATED 206 139 63 28
20Q GAIN WILD-TYPE 295 211 54 47

Figure S69.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'20q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00061

Table S70.  Gene #37: '20q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
20Q GAIN MUTATED 0 364 48 1 2 10 1 19
20Q GAIN WILD-TYPE 1 399 144 5 2 20 16 29

Figure S70.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'21q gain' versus 'Time to Death'

P value = 0.0148 (logrank test), Q value = 0.13

Table S71.  Gene #38: '21q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1044 128 0.0 - 234.3 (24.5)
21Q GAIN MUTATED 194 33 0.0 - 211.6 (25.0)
21Q GAIN WILD-TYPE 850 95 0.0 - 234.3 (24.4)

Figure S71.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #1: 'Time to Death'

'21q gain' versus 'YEARS_TO_BIRTH'

P value = 0.043 (Wilcoxon-test), Q value = 0.23

Table S72.  Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1047 58.6 (13.2)
21Q GAIN MUTATED 195 60.3 (12.7)
21Q GAIN WILD-TYPE 852 58.2 (13.2)

Figure S72.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'21q gain' versus 'HISTOLOGICAL_TYPE'

P value = 3e-05 (Fisher's exact test), Q value = 0.0016

Table S73.  Gene #38: '21q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
21Q GAIN MUTATED 0 167 16 2 0 0 1 9
21Q GAIN WILD-TYPE 1 596 176 4 4 30 16 39

Figure S73.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'21q gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0327 (Fisher's exact test), Q value = 0.2

Table S74.  Gene #38: '21q gain' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 288 774
21Q GAIN MUTATED 65 130
21Q GAIN WILD-TYPE 223 644

Figure S74.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'21q gain' versus 'RACE'

P value = 0.0212 (Fisher's exact test), Q value = 0.16

Table S75.  Gene #38: '21q gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
21Q GAIN MUTATED 1 10 41 120
21Q GAIN WILD-TYPE 0 50 129 616

Figure S75.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #11: 'RACE'

'22q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00047 (Fisher's exact test), Q value = 0.013

Table S76.  Gene #39: '22q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
22Q GAIN MUTATED 0 80 4 1 0 2 1 10
22Q GAIN WILD-TYPE 1 683 188 5 4 28 16 38

Figure S76.  Get High-res Image Gene #39: '22q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'22q gain' versus 'RACE'

P value = 0.0308 (Fisher's exact test), Q value = 0.2

Table S77.  Gene #39: '22q gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
22Q GAIN MUTATED 1 7 20 58
22Q GAIN WILD-TYPE 0 53 150 678

Figure S77.  Get High-res Image Gene #39: '22q gain' versus Clinical Feature #11: 'RACE'

'xp gain' versus 'YEARS_TO_BIRTH'

P value = 0.0199 (Wilcoxon-test), Q value = 0.16

Table S78.  Gene #40: 'xp gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1047 58.6 (13.2)
XP GAIN MUTATED 149 60.8 (12.6)
XP GAIN WILD-TYPE 898 58.3 (13.2)

Figure S78.  Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'xp gain' versus 'HISTOLOGICAL_TYPE'

P value = 2e-04 (Fisher's exact test), Q value = 0.0069

Table S79.  Gene #40: 'xp gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
XP GAIN MUTATED 1 122 11 3 1 3 3 6
XP GAIN WILD-TYPE 0 641 181 3 3 27 14 42

Figure S79.  Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'xp gain' versus 'RACE'

P value = 0.0267 (Fisher's exact test), Q value = 0.19

Table S80.  Gene #40: 'xp gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
XP GAIN MUTATED 1 6 31 91
XP GAIN WILD-TYPE 0 54 139 645

Figure S80.  Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #11: 'RACE'

'xq gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00018 (Fisher's exact test), Q value = 0.0068

Table S81.  Gene #41: 'xq gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
XQ GAIN MUTATED 1 112 9 2 1 1 3 5
XQ GAIN WILD-TYPE 0 651 183 4 3 29 14 43

Figure S81.  Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'1p loss' versus 'YEARS_TO_BIRTH'

P value = 0.000115 (Wilcoxon-test), Q value = 0.0045

Table S82.  Gene #42: '1p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1047 58.6 (13.2)
1P LOSS MUTATED 233 61.4 (13.0)
1P LOSS WILD-TYPE 814 57.8 (13.1)

Figure S82.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'1p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 8e-05 (Fisher's exact test), Q value = 0.0033

Table S83.  Gene #42: '1p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
ALL 89 81 8 3 353 245 2 150 29 63 20 1 13
1P LOSS MUTATED 13 13 1 1 77 43 1 42 17 19 7 0 5
1P LOSS WILD-TYPE 76 68 7 2 276 202 1 108 12 44 13 1 8

Figure S83.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'1p loss' versus 'PATHOLOGY_T_STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.002

Table S84.  Gene #42: '1p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
1P LOSS MUTATED 50 139 27 22
1P LOSS WILD-TYPE 222 477 103 18

Figure S84.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'1p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00642 (Fisher's exact test), Q value = 0.074

Table S85.  Gene #42: '1p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 501 350 117 75
1P LOSS MUTATED 94 79 36 24
1P LOSS WILD-TYPE 407 271 81 51

Figure S85.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'1p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000884 (Wilcoxon-test), Q value = 0.018

Table S86.  Gene #42: '1p loss' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 897 2.4 (4.7)
1P LOSS MUTATED 185 3.3 (5.4)
1P LOSS WILD-TYPE 712 2.1 (4.4)

Figure S86.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'2p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0151 (Fisher's exact test), Q value = 0.13

Table S87.  Gene #44: '2p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 879 21
2P LOSS MUTATED 143 8
2P LOSS WILD-TYPE 736 13

Figure S87.  Get High-res Image Gene #44: '2p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'2p loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0097 (Fisher's exact test), Q value = 0.1

Table S88.  Gene #44: '2p loss' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 288 774
2P LOSS MUTATED 63 116
2P LOSS WILD-TYPE 225 658

Figure S88.  Get High-res Image Gene #44: '2p loss' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'2q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0461 (Fisher's exact test), Q value = 0.24

Table S89.  Gene #45: '2q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 879 21
2Q LOSS MUTATED 168 8
2Q LOSS WILD-TYPE 711 13

Figure S89.  Get High-res Image Gene #45: '2q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'3p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00046 (Fisher's exact test), Q value = 0.013

Table S90.  Gene #46: '3p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
3P LOSS MUTATED 29 130 20 3
3P LOSS WILD-TYPE 243 486 110 37

Figure S90.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'3p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0331 (Fisher's exact test), Q value = 0.21

Table S91.  Gene #46: '3p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
3P LOSS MUTATED 0 149 19 1 1 3 1 9
3P LOSS WILD-TYPE 1 614 173 5 3 27 16 39

Figure S91.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'3p loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0281 (Fisher's exact test), Q value = 0.19

Table S92.  Gene #46: '3p loss' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 288 774
3P LOSS MUTATED 62 121
3P LOSS WILD-TYPE 226 653

Figure S92.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'3p loss' versus 'ETHNICITY'

P value = 0.0316 (Fisher's exact test), Q value = 0.2

Table S93.  Gene #46: '3p loss' versus Clinical Feature #12: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 38 858
3P LOSS MUTATED 2 160
3P LOSS WILD-TYPE 36 698

Figure S93.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #12: 'ETHNICITY'

'3q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00082 (Fisher's exact test), Q value = 0.018

Table S94.  Gene #47: '3q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
3Q LOSS MUTATED 13 76 9 1
3Q LOSS WILD-TYPE 259 540 121 39

Figure S94.  Get High-res Image Gene #47: '3q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'3q loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.044 (Fisher's exact test), Q value = 0.24

Table S95.  Gene #47: '3q loss' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 288 774
3Q LOSS MUTATED 36 64
3Q LOSS WILD-TYPE 252 710

Figure S95.  Get High-res Image Gene #47: '3q loss' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'3q loss' versus 'ETHNICITY'

P value = 0.0261 (Fisher's exact test), Q value = 0.19

Table S96.  Gene #47: '3q loss' versus Clinical Feature #12: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 38 858
3Q LOSS MUTATED 0 90
3Q LOSS WILD-TYPE 38 768

Figure S96.  Get High-res Image Gene #47: '3q loss' versus Clinical Feature #12: 'ETHNICITY'

'4p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0151 (Fisher's exact test), Q value = 0.13

Table S97.  Gene #48: '4p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
4P LOSS MUTATED 70 222 38 15
4P LOSS WILD-TYPE 202 394 92 25

Figure S97.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'4p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00061

Table S98.  Gene #48: '4p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
4P LOSS MUTATED 1 286 32 3 3 6 0 15
4P LOSS WILD-TYPE 0 477 160 3 1 24 17 33

Figure S98.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'4p loss' versus 'RACE'

P value = 0.00468 (Fisher's exact test), Q value = 0.061

Table S99.  Gene #48: '4p loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
4P LOSS MUTATED 1 20 74 227
4P LOSS WILD-TYPE 0 40 96 509

Figure S99.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #11: 'RACE'

'4q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0374 (Fisher's exact test), Q value = 0.22

Table S100.  Gene #49: '4q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
4Q LOSS MUTATED 61 190 39 15
4Q LOSS WILD-TYPE 211 426 91 25

Figure S100.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'4q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00061

Table S101.  Gene #49: '4q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
4Q LOSS MUTATED 0 250 30 2 3 6 0 15
4Q LOSS WILD-TYPE 1 513 162 4 1 24 17 33

Figure S101.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'4q loss' versus 'RACE'

P value = 0.012 (Fisher's exact test), Q value = 0.11

Table S102.  Gene #49: '4q loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
4Q LOSS MUTATED 1 18 64 198
4Q LOSS WILD-TYPE 0 42 106 538

Figure S102.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #11: 'RACE'

'5p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00409 (Wilcoxon-test), Q value = 0.054

Table S103.  Gene #50: '5p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1047 58.6 (13.2)
5P LOSS MUTATED 135 55.7 (13.6)
5P LOSS WILD-TYPE 912 59.1 (13.0)

Figure S103.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0127 (Fisher's exact test), Q value = 0.12

Table S104.  Gene #50: '5p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
5P LOSS MUTATED 27 97 9 5
5P LOSS WILD-TYPE 245 519 121 35

Figure S104.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'5p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00061

Table S105.  Gene #50: '5p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
5P LOSS MUTATED 0 118 2 4 0 5 0 8
5P LOSS WILD-TYPE 1 645 190 2 4 25 17 40

Figure S105.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'5q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000313 (Wilcoxon-test), Q value = 0.0096

Table S106.  Gene #51: '5q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1047 58.6 (13.2)
5Q LOSS MUTATED 219 56.0 (13.1)
5Q LOSS WILD-TYPE 828 59.3 (13.1)

Figure S106.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00081 (Fisher's exact test), Q value = 0.018

Table S107.  Gene #51: '5q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
5Q LOSS MUTATED 44 153 15 8
5Q LOSS WILD-TYPE 228 463 115 32

Figure S107.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'5q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00061

Table S108.  Gene #51: '5q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
5Q LOSS MUTATED 1 197 4 4 0 5 0 10
5Q LOSS WILD-TYPE 0 566 188 2 4 25 17 38

Figure S108.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'5q loss' versus 'RACE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00061

Table S109.  Gene #51: '5q loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
5Q LOSS MUTATED 0 18 57 130
5Q LOSS WILD-TYPE 1 42 113 606

Figure S109.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #11: 'RACE'

'6q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00237 (Wilcoxon-test), Q value = 0.039

Table S110.  Gene #53: '6q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1047 58.6 (13.2)
6Q LOSS MUTATED 269 56.4 (13.3)
6Q LOSS WILD-TYPE 778 59.4 (13.1)

Figure S110.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'6q loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0394 (Fisher's exact test), Q value = 0.22

Table S111.  Gene #53: '6q loss' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 288 774
6Q LOSS MUTATED 87 184
6Q LOSS WILD-TYPE 201 590

Figure S111.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'7p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00054 (Fisher's exact test), Q value = 0.014

Table S112.  Gene #54: '7p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
7P LOSS MUTATED 0 93 5 2 0 3 0 6
7P LOSS WILD-TYPE 1 670 187 4 4 27 17 42

Figure S112.  Get High-res Image Gene #54: '7p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'7q loss' versus 'ETHNICITY'

P value = 0.0264 (Fisher's exact test), Q value = 0.19

Table S113.  Gene #55: '7q loss' versus Clinical Feature #12: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 38 858
7Q LOSS MUTATED 0 94
7Q LOSS WILD-TYPE 38 764

Figure S113.  Get High-res Image Gene #55: '7q loss' versus Clinical Feature #12: 'ETHNICITY'

'8p loss' versus 'Time to Death'

P value = 0.0327 (logrank test), Q value = 0.2

Table S114.  Gene #56: '8p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1044 128 0.0 - 234.3 (24.5)
8P LOSS MUTATED 388 59 0.2 - 216.8 (24.7)
8P LOSS WILD-TYPE 656 69 0.0 - 234.3 (24.5)

Figure S114.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #1: 'Time to Death'

'8p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00055 (Fisher's exact test), Q value = 0.014

Table S115.  Gene #56: '8p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
8P LOSS MUTATED 1 311 50 2 0 7 3 18
8P LOSS WILD-TYPE 0 452 142 4 4 23 14 30

Figure S115.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'8p loss' versus 'RACE'

P value = 0.0261 (Fisher's exact test), Q value = 0.19

Table S116.  Gene #56: '8p loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
8P LOSS MUTATED 1 31 67 260
8P LOSS WILD-TYPE 0 29 103 476

Figure S116.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #11: 'RACE'

'8q loss' versus 'RACE'

P value = 0.0297 (Fisher's exact test), Q value = 0.19

Table S117.  Gene #57: '8q loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
8Q LOSS MUTATED 0 10 21 56
8Q LOSS WILD-TYPE 1 50 149 680

Figure S117.  Get High-res Image Gene #57: '8q loss' versus Clinical Feature #11: 'RACE'

'9p loss' versus 'Time to Death'

P value = 0.0175 (logrank test), Q value = 0.14

Table S118.  Gene #58: '9p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1044 128 0.0 - 234.3 (24.5)
9P LOSS MUTATED 302 44 0.0 - 162.1 (23.6)
9P LOSS WILD-TYPE 742 84 0.0 - 234.3 (24.8)

Figure S118.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #1: 'Time to Death'

'9p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00139 (Fisher's exact test), Q value = 0.025

Table S119.  Gene #58: '9p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
ALL 89 81 8 3 353 245 2 150 29 63 20 1 13
9P LOSS MUTATED 21 15 0 0 104 61 1 53 16 19 10 0 5
9P LOSS WILD-TYPE 68 66 8 3 249 184 1 97 13 44 10 1 8

Figure S119.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'9p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00025 (Fisher's exact test), Q value = 0.0079

Table S120.  Gene #58: '9p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
9P LOSS MUTATED 55 198 34 18
9P LOSS WILD-TYPE 217 418 96 22

Figure S120.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'9p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0076 (Fisher's exact test), Q value = 0.082

Table S121.  Gene #58: '9p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 501 350 117 75
9P LOSS MUTATED 139 89 49 24
9P LOSS WILD-TYPE 362 261 68 51

Figure S121.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'9p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0281 (Fisher's exact test), Q value = 0.19

Table S122.  Gene #58: '9p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 879 21
9P LOSS MUTATED 255 11
9P LOSS WILD-TYPE 624 10

Figure S122.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'9p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00061

Table S123.  Gene #58: '9p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
9P LOSS MUTATED 0 256 24 3 1 9 3 10
9P LOSS WILD-TYPE 1 507 168 3 3 21 14 38

Figure S123.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'9q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00611 (Fisher's exact test), Q value = 0.072

Table S124.  Gene #59: '9q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
9Q LOSS MUTATED 52 173 35 16
9Q LOSS WILD-TYPE 220 443 95 24

Figure S124.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'9q loss' versus 'GENDER'

P value = 0.0417 (Fisher's exact test), Q value = 0.23

Table S125.  Gene #59: '9q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1051 11
9Q LOSS MUTATED 272 6
9Q LOSS WILD-TYPE 779 5

Figure S125.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #7: 'GENDER'

'9q loss' versus 'HISTOLOGICAL_TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.0011

Table S126.  Gene #59: '9q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
9Q LOSS MUTATED 0 230 21 2 1 9 3 12
9Q LOSS WILD-TYPE 1 533 171 4 3 21 14 36

Figure S126.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'9q loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0151 (Fisher's exact test), Q value = 0.13

Table S127.  Gene #59: '9q loss' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 288 774
9Q LOSS MUTATED 91 187
9Q LOSS WILD-TYPE 197 587

Figure S127.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'10p loss' versus 'Time to Death'

P value = 0.037 (logrank test), Q value = 0.22

Table S128.  Gene #60: '10p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1044 128 0.0 - 234.3 (24.5)
10P LOSS MUTATED 166 25 0.0 - 139.2 (22.0)
10P LOSS WILD-TYPE 878 103 0.0 - 234.3 (25.0)

Figure S128.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #1: 'Time to Death'

'10p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00304 (Fisher's exact test), Q value = 0.045

Table S129.  Gene #60: '10p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
10P LOSS MUTATED 26 114 18 9
10P LOSS WILD-TYPE 246 502 112 31

Figure S129.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'10p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0373 (Fisher's exact test), Q value = 0.22

Table S130.  Gene #60: '10p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
10P LOSS MUTATED 0 126 19 0 1 8 1 12
10P LOSS WILD-TYPE 1 637 173 6 3 22 16 36

Figure S130.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'10q loss' versus 'Time to Death'

P value = 0.0362 (logrank test), Q value = 0.22

Table S131.  Gene #61: '10q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1044 128 0.0 - 234.3 (24.5)
10Q LOSS MUTATED 224 33 0.0 - 211.6 (22.2)
10Q LOSS WILD-TYPE 820 95 0.0 - 234.3 (25.0)

Figure S131.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #1: 'Time to Death'

'10q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00542 (Fisher's exact test), Q value = 0.067

Table S132.  Gene #61: '10q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
10Q LOSS MUTATED 40 145 25 13
10Q LOSS WILD-TYPE 232 471 105 27

Figure S132.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'10q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00526 (Fisher's exact test), Q value = 0.066

Table S133.  Gene #61: '10q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
10Q LOSS MUTATED 0 175 23 1 1 8 1 15
10Q LOSS WILD-TYPE 1 588 169 5 3 22 16 33

Figure S133.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'10q loss' versus 'ETHNICITY'

P value = 0.0419 (Fisher's exact test), Q value = 0.23

Table S134.  Gene #61: '10q loss' versus Clinical Feature #12: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 38 858
10Q LOSS MUTATED 3 186
10Q LOSS WILD-TYPE 35 672

Figure S134.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #12: 'ETHNICITY'

'11p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.014 (Fisher's exact test), Q value = 0.13

Table S135.  Gene #62: '11p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
ALL 89 81 8 3 353 245 2 150 29 63 20 1 13
11P LOSS MUTATED 20 10 2 0 90 58 0 48 14 18 5 1 2
11P LOSS WILD-TYPE 69 71 6 3 263 187 2 102 15 45 15 0 11

Figure S135.  Get High-res Image Gene #62: '11p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'11p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.011 (Fisher's exact test), Q value = 0.11

Table S136.  Gene #62: '11p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
11P LOSS MUTATED 56 162 32 18
11P LOSS WILD-TYPE 216 454 98 22

Figure S136.  Get High-res Image Gene #62: '11p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'11p loss' versus 'RACE'

P value = 0.00184 (Fisher's exact test), Q value = 0.032

Table S137.  Gene #62: '11p loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
11P LOSS MUTATED 1 19 57 163
11P LOSS WILD-TYPE 0 41 113 573

Figure S137.  Get High-res Image Gene #62: '11p loss' versus Clinical Feature #11: 'RACE'

'11q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0389 (Fisher's exact test), Q value = 0.22

Table S138.  Gene #63: '11q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 501 350 117 75
11Q LOSS MUTATED 156 119 53 24
11Q LOSS WILD-TYPE 345 231 64 51

Figure S138.  Get High-res Image Gene #63: '11q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'11q loss' versus 'RACE'

P value = 0.00361 (Fisher's exact test), Q value = 0.049

Table S139.  Gene #63: '11q loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
11Q LOSS MUTATED 1 23 73 224
11Q LOSS WILD-TYPE 0 37 97 512

Figure S139.  Get High-res Image Gene #63: '11q loss' versus Clinical Feature #11: 'RACE'

'12p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0069 (Fisher's exact test), Q value = 0.078

Table S140.  Gene #64: '12p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
12P LOSS MUTATED 32 87 13 13
12P LOSS WILD-TYPE 240 529 117 27

Figure S140.  Get High-res Image Gene #64: '12p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'12p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00019 (Fisher's exact test), Q value = 0.0069

Table S141.  Gene #64: '12p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
12P LOSS MUTATED 0 127 8 2 0 3 1 5
12P LOSS WILD-TYPE 1 636 184 4 4 27 16 43

Figure S141.  Get High-res Image Gene #64: '12p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'12q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0115 (Wilcoxon-test), Q value = 0.11

Table S142.  Gene #65: '12q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1047 58.6 (13.2)
12Q LOSS MUTATED 126 56.2 (13.3)
12Q LOSS WILD-TYPE 921 59.0 (13.1)

Figure S142.  Get High-res Image Gene #65: '12q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'12q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00558 (Fisher's exact test), Q value = 0.068

Table S143.  Gene #65: '12q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
12Q LOSS MUTATED 25 79 10 11
12Q LOSS WILD-TYPE 247 537 120 29

Figure S143.  Get High-res Image Gene #65: '12q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'12q loss' versus 'HISTOLOGICAL_TYPE'

P value = 7e-05 (Fisher's exact test), Q value = 0.003

Table S144.  Gene #65: '12q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
12Q LOSS MUTATED 0 108 7 3 0 1 0 7
12Q LOSS WILD-TYPE 1 655 185 3 4 29 17 41

Figure S144.  Get High-res Image Gene #65: '12q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'12q loss' versus 'RACE'

P value = 0.00521 (Fisher's exact test), Q value = 0.066

Table S145.  Gene #65: '12q loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
12Q LOSS MUTATED 0 6 35 79
12Q LOSS WILD-TYPE 1 54 135 657

Figure S145.  Get High-res Image Gene #65: '12q loss' versus Clinical Feature #11: 'RACE'

'13q loss' versus 'HISTOLOGICAL_TYPE'

P value = 7e-05 (Fisher's exact test), Q value = 0.003

Table S146.  Gene #66: '13q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
13Q LOSS MUTATED 0 337 56 5 1 10 2 15
13Q LOSS WILD-TYPE 1 426 136 1 3 20 15 33

Figure S146.  Get High-res Image Gene #66: '13q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'14q loss' versus 'Time to Death'

P value = 0.0286 (logrank test), Q value = 0.19

Table S147.  Gene #67: '14q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1044 128 0.0 - 234.3 (24.5)
14Q LOSS MUTATED 256 39 0.0 - 211.6 (22.8)
14Q LOSS WILD-TYPE 788 89 0.0 - 234.3 (25.0)

Figure S147.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #1: 'Time to Death'

'14q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0234 (Fisher's exact test), Q value = 0.17

Table S148.  Gene #67: '14q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
14Q LOSS MUTATED 52 172 27 8
14Q LOSS WILD-TYPE 220 444 103 32

Figure S148.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'14q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00061

Table S149.  Gene #67: '14q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
14Q LOSS MUTATED 0 212 27 5 2 3 1 10
14Q LOSS WILD-TYPE 1 551 165 1 2 27 16 38

Figure S149.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'14q loss' versus 'RACE'

P value = 7e-05 (Fisher's exact test), Q value = 0.003

Table S150.  Gene #67: '14q loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
14Q LOSS MUTATED 0 14 65 159
14Q LOSS WILD-TYPE 1 46 105 577

Figure S150.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #11: 'RACE'

'15q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00298 (Fisher's exact test), Q value = 0.045

Table S151.  Gene #68: '15q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
15Q LOSS MUTATED 61 209 34 9
15Q LOSS WILD-TYPE 211 407 96 31

Figure S151.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'15q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0365 (Fisher's exact test), Q value = 0.22

Table S152.  Gene #68: '15q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 501 350 117 75
15Q LOSS MUTATED 161 87 43 20
15Q LOSS WILD-TYPE 340 263 74 55

Figure S152.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'15q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00041 (Fisher's exact test), Q value = 0.012

Table S153.  Gene #68: '15q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
15Q LOSS MUTATED 0 249 33 3 2 10 2 15
15Q LOSS WILD-TYPE 1 514 159 3 2 20 15 33

Figure S153.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'16p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0383 (Wilcoxon-test), Q value = 0.22

Table S154.  Gene #69: '16p loss' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 897 2.4 (4.7)
16P LOSS MUTATED 150 2.0 (4.4)
16P LOSS WILD-TYPE 747 2.5 (4.7)

Figure S154.  Get High-res Image Gene #69: '16p loss' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'16p loss' versus 'RACE'

P value = 0.00881 (Fisher's exact test), Q value = 0.092

Table S155.  Gene #69: '16p loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
16P LOSS MUTATED 0 11 42 106
16P LOSS WILD-TYPE 1 49 128 630

Figure S155.  Get High-res Image Gene #69: '16p loss' versus Clinical Feature #11: 'RACE'

'16q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00159 (Wilcoxon-test), Q value = 0.028

Table S156.  Gene #70: '16q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1047 58.6 (13.2)
16Q LOSS MUTATED 572 59.9 (12.9)
16Q LOSS WILD-TYPE 475 57.1 (13.4)

Figure S156.  Get High-res Image Gene #70: '16q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00061

Table S157.  Gene #70: '16q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
16Q LOSS MUTATED 0 387 150 3 1 18 3 17
16Q LOSS WILD-TYPE 1 376 42 3 3 12 14 31

Figure S157.  Get High-res Image Gene #70: '16q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'17p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0355 (Wilcoxon-test), Q value = 0.22

Table S158.  Gene #71: '17p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1047 58.6 (13.2)
17P LOSS MUTATED 560 57.9 (13.3)
17P LOSS WILD-TYPE 487 59.5 (13.0)

Figure S158.  Get High-res Image Gene #71: '17p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'17p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00603 (Fisher's exact test), Q value = 0.071

Table S159.  Gene #71: '17p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
17P LOSS MUTATED 124 353 72 17
17P LOSS WILD-TYPE 148 263 58 23

Figure S159.  Get High-res Image Gene #71: '17p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'17p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0293 (Fisher's exact test), Q value = 0.19

Table S160.  Gene #71: '17p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
17P LOSS MUTATED 0 428 88 5 2 18 6 21
17P LOSS WILD-TYPE 1 335 104 1 2 12 11 27

Figure S160.  Get High-res Image Gene #71: '17p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'17q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00114 (Fisher's exact test), Q value = 0.022

Table S161.  Gene #72: '17q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
17Q LOSS MUTATED 0 216 34 3 2 5 0 10
17Q LOSS WILD-TYPE 1 547 158 3 2 25 17 38

Figure S161.  Get High-res Image Gene #72: '17q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'17q loss' versus 'RACE'

P value = 0.00357 (Fisher's exact test), Q value = 0.049

Table S162.  Gene #72: '17q loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
17Q LOSS MUTATED 1 22 54 169
17Q LOSS WILD-TYPE 0 38 116 567

Figure S162.  Get High-res Image Gene #72: '17q loss' versus Clinical Feature #11: 'RACE'

'18p loss' versus 'Time to Death'

P value = 1.34e-05 (logrank test), Q value = 0.00078

Table S163.  Gene #73: '18p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1044 128 0.0 - 234.3 (24.5)
18P LOSS MUTATED 306 53 0.0 - 189.0 (21.7)
18P LOSS WILD-TYPE 738 75 0.0 - 234.3 (25.0)

Figure S163.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #1: 'Time to Death'

'18p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00256 (Wilcoxon-test), Q value = 0.04

Table S164.  Gene #73: '18p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1047 58.6 (13.2)
18P LOSS MUTATED 305 60.6 (13.6)
18P LOSS WILD-TYPE 742 57.8 (12.9)

Figure S164.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'18p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0465 (Fisher's exact test), Q value = 0.24

Table S165.  Gene #73: '18p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
ALL 89 81 8 3 353 245 2 150 29 63 20 1 13
18P LOSS MUTATED 25 23 0 0 100 69 0 47 16 25 6 0 1
18P LOSS WILD-TYPE 64 58 8 3 253 176 2 103 13 38 14 1 12

Figure S165.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'18p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00258 (Fisher's exact test), Q value = 0.04

Table S166.  Gene #73: '18p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
18P LOSS MUTATED 68 186 38 22
18P LOSS WILD-TYPE 204 430 92 18

Figure S166.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'18p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00371 (Fisher's exact test), Q value = 0.049

Table S167.  Gene #73: '18p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
18P LOSS MUTATED 0 246 46 3 2 6 0 11
18P LOSS WILD-TYPE 1 517 146 3 2 24 17 37

Figure S167.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'18p loss' versus 'RACE'

P value = 0.0434 (Fisher's exact test), Q value = 0.23

Table S168.  Gene #73: '18p loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
18P LOSS MUTATED 0 27 50 209
18P LOSS WILD-TYPE 1 33 120 527

Figure S168.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #11: 'RACE'

'18q loss' versus 'Time to Death'

P value = 0.012 (logrank test), Q value = 0.11

Table S169.  Gene #74: '18q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1044 128 0.0 - 234.3 (24.5)
18Q LOSS MUTATED 308 46 0.0 - 211.6 (21.2)
18Q LOSS WILD-TYPE 736 82 0.2 - 234.3 (25.6)

Figure S169.  Get High-res Image Gene #74: '18q loss' versus Clinical Feature #1: 'Time to Death'

'18q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0112 (Wilcoxon-test), Q value = 0.11

Table S170.  Gene #74: '18q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1047 58.6 (13.2)
18Q LOSS MUTATED 308 60.3 (13.4)
18Q LOSS WILD-TYPE 739 57.9 (13.0)

Figure S170.  Get High-res Image Gene #74: '18q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'18q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.017 (Fisher's exact test), Q value = 0.14

Table S171.  Gene #74: '18q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
18Q LOSS MUTATED 69 189 37 20
18Q LOSS WILD-TYPE 203 427 93 20

Figure S171.  Get High-res Image Gene #74: '18q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'18q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00756 (Fisher's exact test), Q value = 0.082

Table S172.  Gene #74: '18q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
18Q LOSS MUTATED 1 244 50 2 2 6 0 11
18Q LOSS WILD-TYPE 0 519 142 4 2 24 17 37

Figure S172.  Get High-res Image Gene #74: '18q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'19p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00061

Table S173.  Gene #75: '19p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
19P LOSS MUTATED 0 162 8 1 1 4 4 6
19P LOSS WILD-TYPE 1 601 184 5 3 26 13 42

Figure S173.  Get High-res Image Gene #75: '19p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'19p loss' versus 'RACE'

P value = 0.00347 (Fisher's exact test), Q value = 0.048

Table S174.  Gene #75: '19p loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
19P LOSS MUTATED 0 16 41 109
19P LOSS WILD-TYPE 1 44 129 627

Figure S174.  Get High-res Image Gene #75: '19p loss' versus Clinical Feature #11: 'RACE'

'19q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00061

Table S175.  Gene #76: '19q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
19Q LOSS MUTATED 0 137 5 1 0 4 4 5
19Q LOSS WILD-TYPE 1 626 187 5 4 26 13 43

Figure S175.  Get High-res Image Gene #76: '19q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'19q loss' versus 'RACE'

P value = 0.0319 (Fisher's exact test), Q value = 0.2

Table S176.  Gene #76: '19q loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
19Q LOSS MUTATED 0 13 33 93
19Q LOSS WILD-TYPE 1 47 137 643

Figure S176.  Get High-res Image Gene #76: '19q loss' versus Clinical Feature #11: 'RACE'

'20p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0275 (Fisher's exact test), Q value = 0.19

Table S177.  Gene #77: '20p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 879 21
20P LOSS MUTATED 72 5
20P LOSS WILD-TYPE 807 16

Figure S177.  Get High-res Image Gene #77: '20p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'20q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0372 (Fisher's exact test), Q value = 0.22

Table S178.  Gene #78: '20q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
20Q LOSS MUTATED 0 39 7 3 0 1 1 3
20Q LOSS WILD-TYPE 1 724 185 3 4 29 16 45

Figure S178.  Get High-res Image Gene #78: '20q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'20q loss' versus 'RACE'

P value = 0.0279 (Fisher's exact test), Q value = 0.19

Table S179.  Gene #78: '20q loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
20Q LOSS MUTATED 0 5 15 29
20Q LOSS WILD-TYPE 1 55 155 707

Figure S179.  Get High-res Image Gene #78: '20q loss' versus Clinical Feature #11: 'RACE'

'21q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00873 (Fisher's exact test), Q value = 0.092

Table S180.  Gene #79: '21q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
ALL 89 81 8 3 353 245 2 150 29 63 20 1 13
21Q LOSS MUTATED 11 13 0 0 52 46 1 29 10 5 7 1 3
21Q LOSS WILD-TYPE 78 68 8 3 301 199 1 121 19 58 13 0 10

Figure S180.  Get High-res Image Gene #79: '21q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'21q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0151 (Fisher's exact test), Q value = 0.13

Table S181.  Gene #79: '21q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 501 350 117 75
21Q LOSS MUTATED 73 62 31 9
21Q LOSS WILD-TYPE 428 288 86 66

Figure S181.  Get High-res Image Gene #79: '21q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'21q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0176 (Fisher's exact test), Q value = 0.14

Table S182.  Gene #79: '21q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 879 21
21Q LOSS MUTATED 147 8
21Q LOSS WILD-TYPE 732 13

Figure S182.  Get High-res Image Gene #79: '21q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'21q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00261 (Fisher's exact test), Q value = 0.04

Table S183.  Gene #79: '21q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
21Q LOSS MUTATED 0 144 18 2 2 7 1 4
21Q LOSS WILD-TYPE 1 619 174 4 2 23 16 44

Figure S183.  Get High-res Image Gene #79: '21q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'21q loss' versus 'RACE'

P value = 0.0204 (Fisher's exact test), Q value = 0.16

Table S184.  Gene #79: '21q loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
21Q LOSS MUTATED 0 17 34 109
21Q LOSS WILD-TYPE 1 43 136 627

Figure S184.  Get High-res Image Gene #79: '21q loss' versus Clinical Feature #11: 'RACE'

'22q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.001 (Fisher's exact test), Q value = 0.02

Table S185.  Gene #80: '22q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
22Q LOSS MUTATED 0 349 84 2 2 18 1 13
22Q LOSS WILD-TYPE 1 414 108 4 2 12 16 35

Figure S185.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'22q loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.00137 (Fisher's exact test), Q value = 0.025

Table S186.  Gene #80: '22q loss' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 288 774
22Q LOSS MUTATED 151 319
22Q LOSS WILD-TYPE 137 455

Figure S186.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'xp loss' versus 'YEARS_TO_BIRTH'

P value = 0.00347 (Wilcoxon-test), Q value = 0.048

Table S187.  Gene #81: 'xp loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1047 58.6 (13.2)
XP LOSS MUTATED 182 55.9 (13.1)
XP LOSS WILD-TYPE 865 59.2 (13.1)

Figure S187.  Get High-res Image Gene #81: 'xp loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'xp loss' versus 'RACE'

P value = 0.0142 (Fisher's exact test), Q value = 0.13

Table S188.  Gene #81: 'xp loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
XP LOSS MUTATED 0 17 38 114
XP LOSS WILD-TYPE 1 43 132 622

Figure S188.  Get High-res Image Gene #81: 'xp loss' versus Clinical Feature #11: 'RACE'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BRCA-TP/15086289/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BRCA-TP/15076769/BRCA-TP.merged_data.txt

  • Number of patients = 1062

  • Number of significantly arm-level cnvs = 82

  • Number of selected clinical features = 12

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

Survival analysis

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

Fisher's exact test

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

Q value calculation

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

Download Results

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

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
Copyright © 2015 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle