Correlation between copy number variations of arm-level result and selected clinical features
Breast Invasive Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1J102HX
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1J102HX
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 1079 patients, 179 significant findings detected with Q value < 0.25.

  • 1p gain cnv correlated to 'PATHOLOGY_T_STAGE' and 'HISTOLOGICAL_TYPE'.

  • 1q gain cnv correlated to 'PATHOLOGIC_STAGE',  '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 'HISTOLOGICAL_TYPE'.

  • 3q gain cnv correlated to '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 'Time to Death',  'PATHOLOGY_N_STAGE', and 'HISTOLOGICAL_TYPE'.

  • 5q gain cnv correlated to 'YEARS_TO_BIRTH',  'HISTOLOGICAL_TYPE', 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 'HISTOLOGICAL_TYPE'.

  • 7q gain cnv correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.

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

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

  • 10q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 11p gain cnv correlated to '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',  'HISTOLOGICAL_TYPE', 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 'HISTOLOGICAL_TYPE'.

  • 16q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

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

  • 17q gain cnv correlated to 'GENDER'.

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

  • 18q gain cnv correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.

  • 19p gain cnv correlated to 'PATHOLOGY_M_STAGE' and 'NUMBER_OF_LYMPH_NODES'.

  • 19q gain cnv correlated to 'NUMBER_OF_LYMPH_NODES'.

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

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

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

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

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

  • xq gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 1p loss cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • 1q loss cnv correlated to 'PATHOLOGY_N_STAGE'.

  • 2p loss cnv correlated to 'PATHOLOGY_M_STAGE'.

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

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

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

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

  • 7p loss cnv correlated to 'PATHOLOGY_N_STAGE' and 'HISTOLOGICAL_TYPE'.

  • 7q loss cnv correlated to 'HISTOLOGICAL_TYPE'.

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

  • 9p loss cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'HISTOLOGICAL_TYPE'.

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

  • 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 'RACE'.

  • 11p loss cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE',  'RACE', and 'ETHNICITY'.

  • 11q loss cnv correlated to 'RACE'.

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

  • 12q loss cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'RADIATION_THERAPY',  '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'.

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

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

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

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

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

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

  • xp loss cnv correlated to 'YEARS_TO_BIRTH',  'HISTOLOGICAL_TYPE', 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, 179 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		PATHOLOGIC
STAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER RADIATION
THERAPY 		HISTOLOGICAL
TYPE 		NUMBER
OF
LYMPH
NODES 		RACE ETHNICITY
nCNV (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test
1p loss 226 (21%) 853 0.00534
(0.064) 		0.000666
(0.0146) 		0.0105
(0.0977) 		0.00949
(0.0915) 		0.0138
(0.116) 		0.289
(0.66) 		1
(1.00) 		0.577
(0.857) 		0.203
(0.575) 		0.00292
(0.0422) 		0.833
(0.984) 		1
(1.00)
18p loss 320 (30%) 759 1.99e-05
(0.000934) 		0.00104
(0.0202) 		0.0341
(0.208) 		0.00276
(0.0405) 		0.381
(0.749) 		1
(1.00) 		1
(1.00) 		0.778
(0.965) 		0.0023
(0.0359) 		0.171
(0.529) 		0.0455
(0.25) 		1
(1.00)
11p loss 270 (25%) 809 0.291
(0.66) 		0.862
(1) 		0.0358
(0.211) 		0.0215
(0.152) 		0.0619
(0.302) 		0.806
(0.979) 		1
(1.00) 		0.163
(0.517) 		0.00393
(0.053) 		0.102
(0.4) 		0.0007
(0.0147) 		0.0363
(0.213)
12q loss 136 (13%) 943 0.535
(0.826) 		0.00886
(0.0879) 		0.431
(0.772) 		0.00733
(0.081) 		0.864
(1) 		1
(1.00) 		1
(1.00) 		0.00448
(0.0566) 		6e-05
(0.00236) 		0.223
(0.597) 		0.00353
(0.0489) 		1
(1.00)
21q loss 179 (17%) 900 0.795
(0.976) 		0.476
(0.796) 		0.0145
(0.12) 		0.169
(0.527) 		0.02
(0.147) 		0.0378
(0.219) 		0.234
(0.607) 		0.495
(0.808) 		0.0149
(0.122) 		0.166
(0.526) 		0.0216
(0.152) 		0.823
(0.984)
12q gain 186 (17%) 893 0.292
(0.661) 		0.0907
(0.378) 		0.509
(0.818) 		0.0822
(0.357) 		0.031
(0.2) 		0.572
(0.857) 		0.0405
(0.231) 		0.552
(0.839) 		0.0212
(0.152) 		0.0183
(0.14) 		0.831
(0.984) 		0.184
(0.549)
18p gain 177 (16%) 902 0.574
(0.857) 		0.445
(0.781) 		0.0898
(0.376) 		0.348
(0.73) 		0.0292
(0.189) 		0.776
(0.965) 		0.428
(0.772) 		0.388
(0.75) 		0.00084
(0.0172) 		0.0189
(0.141) 		0.00018
(0.00521) 		0.184
(0.549)
3p loss 188 (17%) 891 0.52
(0.824) 		0.0696
(0.326) 		0.616
(0.877) 		0.00129
(0.0226) 		0.983
(1.00) 		1
(1.00) 		0.24
(0.614) 		0.0513
(0.271) 		0.0216
(0.152) 		0.435
(0.776) 		0.0247
(0.167) 		0.0319
(0.202)
5p loss 142 (13%) 937 0.474
(0.796) 		0.0012
(0.0219) 		0.611
(0.875) 		0.0342
(0.208) 		0.952
(1.00) 		0.756
(0.954) 		1
(1.00) 		0.776
(0.965) 		1e-05
(0.000492) 		0.375
(0.749) 		0.00878
(0.0879) 		0.346
(0.73)
5q loss 228 (21%) 851 0.9
(1.00) 		6.56e-05
(0.00248) 		0.214
(0.586) 		0.00406
(0.0533) 		0.509
(0.818) 		1
(1.00) 		0.478
(0.796) 		0.694
(0.924) 		1e-05
(0.000492) 		0.0862
(0.368) 		1e-05
(0.000492) 		0.693
(0.924)
9p loss 313 (29%) 766 0.0607
(0.298) 		0.576
(0.857) 		0.00256
(0.0388) 		0.00041
(0.0103) 		0.00492
(0.0598) 		0.0551
(0.279) 		0.0475
(0.255) 		0.943
(1.00) 		1e-05
(0.000492) 		0.101
(0.397) 		0.249
(0.621) 		0.471
(0.796)
10q loss 231 (21%) 848 0.0181
(0.139) 		0.46
(0.79) 		0.218
(0.592) 		0.0048
(0.059) 		0.135
(0.469) 		0.798
(0.976) 		0.479
(0.796) 		1
(1.00) 		0.00027
(0.00718) 		0.405
(0.759) 		0.045
(0.249) 		0.108
(0.416)
14q loss 269 (25%) 810 0.0279
(0.184) 		0.682
(0.922) 		0.888
(1.00) 		0.0219
(0.153) 		0.181
(0.547) 		0.454
(0.787) 		0.313
(0.694) 		0.416
(0.766) 		1e-05
(0.000492) 		0.0857
(0.368) 		7e-05
(0.00255) 		0.448
(0.783)
18q loss 321 (30%) 758 0.0117
(0.103) 		0.00874
(0.0879) 		0.0549
(0.279) 		0.0189
(0.141) 		0.112
(0.422) 		1
(1.00) 		1
(1.00) 		0.204
(0.575) 		0.00117
(0.0217) 		0.386
(0.749) 		0.223
(0.597) 		0.721
(0.944)
1q gain 707 (66%) 372 0.251
(0.626) 		0.621
(0.879) 		0.0166
(0.132) 		0.0007
(0.0147) 		0.376
(0.749) 		0.366
(0.742) 		0.56
(0.847) 		0.636
(0.888) 		0.00173
(0.0284) 		0.615
(0.877) 		0.0875
(0.369) 		0.0853
(0.368)
2p gain 122 (11%) 957 0.191
(0.556) 		0.355
(0.737) 		0.962
(1.00) 		0.726
(0.944) 		0.862
(1) 		1
(1.00) 		0.38
(0.749) 		0.41
(0.759) 		1e-05
(0.000492) 		0.729
(0.945) 		0.00016
(0.00492) 		0.0168
(0.133)
3q gain 213 (20%) 866 0.513
(0.819) 		0.602
(0.872) 		0.42
(0.767) 		0.0471
(0.255) 		0.275
(0.656) 		0.793
(0.976) 		0.478
(0.796) 		0.525
(0.824) 		1e-05
(0.000492) 		0.0233
(0.16) 		0.0112
(0.103) 		0.679
(0.922)
5p gain 315 (29%) 764 0.0245
(0.166) 		0.182
(0.547) 		0.902
(1.00) 		0.493
(0.806) 		0.0142
(0.119) 		1
(1.00) 		0.348
(0.73) 		0.29
(0.66) 		0.0231
(0.16) 		0.709
(0.934) 		0.124
(0.45) 		1
(1.00)
5q gain 211 (20%) 868 0.535
(0.826) 		0.0102
(0.0954) 		0.869
(1.00) 		0.17
(0.529) 		0.232
(0.607) 		0.0992
(0.394) 		1
(1.00) 		0.224
(0.597) 		0.0367
(0.213) 		0.78
(0.967) 		0.00086
(0.0173) 		1
(1.00)
20p gain 410 (38%) 669 0.315
(0.697) 		0.298
(0.67) 		0.464
(0.792) 		0.103
(0.403) 		0.00819
(0.0858) 		0.662
(0.914) 		0.0132
(0.112) 		0.791
(0.976) 		1e-05
(0.000492) 		0.485
(0.799) 		0.877
(1.00) 		0.403
(0.759)
20q gain 450 (42%) 629 0.552
(0.839) 		0.725
(0.944) 		0.805
(0.979) 		0.00371
(0.0507) 		0.0326
(0.203) 		1
(1.00) 		0.138
(0.475) 		0.746
(0.952) 		1e-05
(0.000492) 		0.389
(0.75) 		0.564
(0.848) 		0.187
(0.552)
21q gain 198 (18%) 881 0.028
(0.184) 		0.0792
(0.348) 		0.683
(0.922) 		0.587
(0.861) 		0.739
(0.95) 		1
(1.00) 		1
(1.00) 		0.0992
(0.394) 		1e-05
(0.000492) 		0.643
(0.892) 		0.0258
(0.173) 		0.393
(0.75)
4p loss 353 (33%) 726 0.479
(0.796) 		0.204
(0.575) 		0.395
(0.75) 		0.0129
(0.111) 		0.527
(0.824) 		1
(1.00) 		1
(1.00) 		0.945
(1.00) 		1e-05
(0.000492) 		0.87
(1.00) 		0.00296
(0.0422) 		0.603
(0.872)
4q loss 311 (29%) 768 0.667
(0.915) 		0.922
(1.00) 		0.749
(0.953) 		0.0323
(0.203) 		0.865
(1) 		0.814
(0.984) 		1
(1.00) 		0.831
(0.984) 		1e-05
(0.000492) 		0.889
(1.00) 		0.00893
(0.0879) 		0.856
(0.999)
9q loss 280 (26%) 799 0.538
(0.826) 		0.702
(0.928) 		0.145
(0.49) 		0.00422
(0.0546) 		0.111
(0.42) 		0.326
(0.709) 		0.017
(0.133) 		0.418
(0.766) 		1e-05
(0.000492) 		0.992
(1.00) 		0.0711
(0.329) 		0.451
(0.783)
10p loss 175 (16%) 904 0.0128
(0.11) 		0.95
(1.00) 		0.0659
(0.316) 		0.0048
(0.059) 		0.202
(0.575) 		0.783
(0.969) 		0.233
(0.607) 		0.93
(1.00) 		0.00059
(0.0135) 		0.241
(0.614) 		0.584
(0.861) 		0.498
(0.81)
15q loss 317 (29%) 762 0.244
(0.617) 		0.81
(0.981) 		0.23
(0.607) 		0.00268
(0.04) 		0.0413
(0.234) 		0.817
(0.984) 		0.755
(0.954) 		0.325
(0.709) 		4e-05
(0.00164) 		0.0968
(0.392) 		0.356
(0.737) 		0.473
(0.796)
17q loss 272 (25%) 807 0.6
(0.872) 		0.288
(0.66) 		0.958
(1.00) 		0.773
(0.965) 		0.219
(0.592) 		1
(1.00) 		0.0444
(0.247) 		0.824
(0.984) 		0.00014
(0.00459) 		0.13
(0.455) 		0.00841
(0.0862) 		1
(1.00)
19p loss 197 (18%) 882 0.228
(0.603) 		0.0092
(0.0896) 		0.759
(0.954) 		0.3
(0.671) 		0.345
(0.73) 		0.159
(0.509) 		0.467
(0.796) 		0.805
(0.979) 		1e-05
(0.000492) 		0.594
(0.869) 		0.00042
(0.0103) 		0.393
(0.75)
20q loss 57 (5%) 1022 0.278
(0.656) 		0.00641
(0.0716) 		0.855
(0.999) 		0.231
(0.607) 		0.928
(1.00) 		0.325
(0.709) 		1
(1.00) 		0.776
(0.965) 		0.0347
(0.209) 		0.38
(0.749) 		0.0179
(0.138) 		0.151
(0.501)
xp loss 192 (18%) 887 0.399
(0.754) 		0.0062
(0.071) 		0.885
(1.00) 		0.0962
(0.391) 		0.874
(1.00) 		0.278
(0.656) 		0.457
(0.789) 		0.803
(0.979) 		0.0424
(0.239) 		0.457
(0.789) 		0.00835
(0.0862) 		1
(1.00)
1p gain 227 (21%) 852 0.339
(0.726) 		0.111
(0.42) 		0.533
(0.826) 		0.00811
(0.0858) 		0.605
(0.872) 		0.283
(0.656) 		0.724
(0.944) 		0.583
(0.861) 		0.00186
(0.03) 		0.483
(0.799) 		0.406
(0.759) 		0.429
(0.772)
2q gain 73 (7%) 1006 0.915
(1.00) 		0.735
(0.947) 		0.825
(0.984) 		0.432
(0.772) 		0.965
(1.00) 		0.394
(0.75) 		1
(1.00) 		0.359
(0.74) 		0.00053
(0.0124) 		0.472
(0.796) 		0.00602
(0.0697) 		0.103
(0.404)
6p gain 208 (19%) 871 0.247
(0.621) 		0.829
(0.984) 		0.525
(0.824) 		0.0756
(0.336) 		0.288
(0.66) 		1
(1.00) 		0.48
(0.796) 		0.0736
(0.333) 		1e-05
(0.000492) 		0.188
(0.553) 		0.00991
(0.0938) 		0.529
(0.825)
6q gain 149 (14%) 930 0.188
(0.553) 		0.956
(1.00) 		0.599
(0.872) 		0.156
(0.506) 		0.0525
(0.277) 		0.757
(0.954) 		1
(1.00) 		0.641
(0.891) 		1e-05
(0.000492) 		0.0356
(0.211) 		0.171
(0.529) 		0.469
(0.796)
7q gain 268 (25%) 811 0.741
(0.951) 		0.973
(1.00) 		0.186
(0.552) 		0.407
(0.759) 		0.439
(0.776) 		0.446
(0.781) 		0.185
(0.552) 		0.557
(0.845) 		0.0189
(0.141) 		0.301
(0.671) 		0.0399
(0.228) 		0.446
(0.781)
8q gain 529 (49%) 550 0.412
(0.761) 		0.916
(1.00) 		0.698
(0.927) 		0.329
(0.709) 		0.205
(0.576) 		0.83
(0.984) 		0.256
(0.629) 		0.0722
(0.329) 		1e-05
(0.000492) 		0.852
(0.997) 		0.00638
(0.0716) 		0.0716
(0.329)
10p gain 208 (19%) 871 0.971
(1.00) 		0.723
(0.944) 		0.507
(0.817) 		0.152
(0.501) 		0.242
(0.614) 		0.0633
(0.305) 		1
(1.00) 		0.685
(0.922) 		1e-05
(0.000492) 		0.357
(0.738) 		0.00124
(0.0222) 		1
(1.00)
17p gain 110 (10%) 969 0.426
(0.772) 		0.952
(1.00) 		0.367
(0.742) 		0.106
(0.411) 		0.234
(0.607) 		0.722
(0.944) 		0.00444
(0.0566) 		0.0157
(0.127) 		0.224
(0.597) 		0.832
(0.984) 		0.0548
(0.279) 		0.789
(0.976)
18q gain 154 (14%) 925 0.382
(0.749) 		0.587
(0.861) 		0.363
(0.742) 		0.167
(0.526) 		0.256
(0.629) 		0.761
(0.956) 		0.395
(0.75) 		1
(1.00) 		0.00553
(0.0656) 		0.318
(0.701) 		0.0239
(0.163) 		0.346
(0.73)
19p gain 187 (17%) 892 0.478
(0.796) 		0.412
(0.761) 		0.149
(0.497) 		0.365
(0.742) 		0.248
(0.621) 		0.0214
(0.152) 		0.139
(0.477) 		0.499
(0.81) 		0.0911
(0.378) 		0.0354
(0.211) 		0.624
(0.881) 		0.832
(0.984)
22q gain 99 (9%) 980 0.634
(0.887) 		0.578
(0.857) 		0.178
(0.544) 		0.0506
(0.269) 		0.428
(0.772) 		0.714
(0.939) 		1
(1.00) 		0.821
(0.984) 		0.00032
(0.00829) 		0.24
(0.614) 		0.0328
(0.203) 		1
(1.00)
xp gain 150 (14%) 929 0.897
(1.00) 		0.0532
(0.278) 		0.518
(0.823) 		0.208
(0.581) 		0.669
(0.916) 		0.353
(0.737) 		1
(1.00) 		0.359
(0.74) 		0.00021
(0.0059) 		0.697
(0.927) 		0.0318
(0.202) 		0.467
(0.796)
3q loss 105 (10%) 974 0.0991
(0.394) 		0.608
(0.872) 		0.325
(0.709) 		0.00252
(0.0387) 		0.791
(0.976) 		1
(1.00) 		0.62
(0.877) 		0.511
(0.818) 		0.181
(0.547) 		0.376
(0.749) 		0.199
(0.575) 		0.0268
(0.178)
6q loss 280 (26%) 799 0.297
(0.67) 		0.00115
(0.0217) 		0.764
(0.958) 		0.534
(0.826) 		0.356
(0.737) 		1
(1.00) 		0.203
(0.575) 		0.00567
(0.0665) 		0.479
(0.796) 		0.34
(0.727) 		0.692
(0.924) 		0.575
(0.857)
7p loss 111 (10%) 968 0.583
(0.861) 		0.751
(0.953) 		0.0922
(0.381) 		0.283
(0.656) 		0.032
(0.202) 		0.159
(0.509) 		1
(1.00) 		0.288
(0.66) 		0.00015
(0.00476) 		0.275
(0.656) 		0.199
(0.575) 		0.418
(0.766)
8p loss 394 (37%) 685 0.172
(0.53) 		0.0981
(0.394) 		0.997
(1.00) 		0.366
(0.742) 		0.76
(0.954) 		0.379
(0.749) 		0.552
(0.839) 		1
(1.00) 		0.00025
(0.00683) 		0.994
(1.00) 		0.0398
(0.228) 		0.404
(0.759)
12p loss 152 (14%) 927 0.873
(1.00) 		0.347
(0.73) 		0.487
(0.801) 		0.00988
(0.0938) 		0.619
(0.877) 		1
(1.00) 		0.681
(0.922) 		0.167
(0.527) 		4e-05
(0.00164) 		0.908
(1.00) 		0.0686
(0.325) 		0.641
(0.891)
16q loss 590 (55%) 489 0.285
(0.66) 		0.00088
(0.0173) 		0.604
(0.872) 		0.435
(0.776) 		0.212
(0.585) 		0.13
(0.455) 		0.154
(0.502) 		0.747
(0.953) 		1e-05
(0.000492) 		0.0755
(0.336) 		0.276
(0.656) 		1
(1.00)
17p loss 579 (54%) 500 0.232
(0.607) 		0.0547
(0.279) 		0.488
(0.801) 		0.0153
(0.124) 		0.887
(1.00) 		1
(1.00) 		0.563
(0.848) 		0.158
(0.508) 		0.0115
(0.103) 		0.882
(1.00) 		0.147
(0.491) 		1
(1.00)
19q loss 164 (15%) 915 0.137
(0.474) 		0.384
(0.749) 		0.441
(0.776) 		0.532
(0.826) 		0.161
(0.512) 		0.125
(0.45) 		0.407
(0.759) 		0.724
(0.944) 		1e-05
(0.000492) 		0.45
(0.783) 		0.0161
(0.129) 		1
(1.00)
22q loss 482 (45%) 597 0.373
(0.749) 		0.463
(0.792) 		0.686
(0.922) 		0.282
(0.656) 		0.396
(0.75) 		0.829
(0.984) 		0.39
(0.75) 		0.0082
(0.0858) 		0.00018
(0.00521) 		0.335
(0.721) 		0.425
(0.772) 		0.744
(0.952)
3p gain 137 (13%) 942 0.259
(0.633) 		0.257
(0.63) 		0.361
(0.741) 		0.071
(0.329) 		0.252
(0.626) 		0.535
(0.826) 		1
(1.00) 		0.511
(0.818) 		8e-05
(0.00281) 		0.347
(0.73) 		0.329
(0.709) 		0.799
(0.976)
4p gain 75 (7%) 1004 0.248
(0.621) 		0.754
(0.954) 		0.144
(0.49) 		0.0925
(0.381) 		0.701
(0.928) 		0.677
(0.922) 		0.201
(0.575) 		0.526
(0.824) 		0.0021
(0.0333) 		0.84
(0.988) 		0.516
(0.823) 		0.74
(0.951)
4q gain 71 (7%) 1008 0.0569
(0.285) 		0.943
(1.00) 		0.388
(0.75) 		0.209
(0.582) 		0.735
(0.947) 		0.667
(0.915) 		0.56
(0.847) 		0.896
(1.00) 		0.00345
(0.0485) 		0.837
(0.986) 		0.438
(0.776) 		0.732
(0.947)
7p gain 313 (29%) 766 0.687
(0.922) 		0.0864
(0.368) 		0.492
(0.806) 		0.671
(0.919) 		0.677
(0.922) 		0.636
(0.888) 		0.0475
(0.255) 		0.29
(0.66) 		0.0125
(0.109) 		0.729
(0.945) 		0.238
(0.612) 		0.587
(0.861)
10q gain 114 (11%) 965 0.881
(1.00) 		0.91
(1.00) 		0.913
(1.00) 		0.378
(0.749) 		0.499
(0.81) 		0.73
(0.945) 		1
(1.00) 		1
(1.00) 		0.0117
(0.103) 		0.319
(0.702) 		0.116
(0.429) 		0.585
(0.861)
11p gain 141 (13%) 938 0.945
(1.00) 		0.865
(1) 		0.5
(0.81) 		0.778
(0.965) 		0.193
(0.559) 		0.52
(0.824) 		0.663
(0.914) 		0.391
(0.75) 		0.0694
(0.326) 		0.0113
(0.103) 		0.691
(0.924) 		0.336
(0.721)
11q gain 96 (9%) 983 0.288
(0.66) 		0.819
(0.984) 		0.597
(0.872) 		0.441
(0.776) 		0.568
(0.854) 		1
(1.00) 		1
(1.00) 		0.129
(0.455) 		0.00165
(0.0275) 		0.187
(0.552) 		0.146
(0.491) 		0.386
(0.749)
12p gain 225 (21%) 854 0.548
(0.839) 		0.641
(0.891) 		0.678
(0.922) 		0.0823
(0.357) 		0.153
(0.501) 		0.796
(0.976) 		0.143
(0.489) 		0.751
(0.953) 		0.00131
(0.0226) 		0.606
(0.872) 		0.628
(0.885) 		0.31
(0.688)
13q gain 93 (9%) 986 0.884
(1.00) 		0.477
(0.796) 		0.63
(0.886) 		0.19
(0.555) 		0.542
(0.83) 		1
(1.00) 		1
(1.00) 		0.254
(0.626) 		0.00048
(0.0115) 		0.862
(1) 		0.837
(0.986) 		0.143
(0.49)
14q gain 143 (13%) 936 0.56
(0.847) 		0.114
(0.425) 		0.179
(0.544) 		0.273
(0.656) 		0.121
(0.442) 		0.343
(0.73) 		1
(1.00) 		0.35
(0.732) 		0.0197
(0.146) 		0.0681
(0.324) 		0.693
(0.924) 		0.219
(0.592)
15q gain 88 (8%) 991 0.604
(0.872) 		0.961
(1.00) 		0.689
(0.924) 		0.974
(1.00) 		0.936
(1.00) 		0.429
(0.772) 		1
(1.00) 		0.817
(0.984) 		0.00158
(0.0268) 		0.974
(1.00) 		0.213
(0.585) 		1
(1.00)
16p gain 462 (43%) 617 0.534
(0.826) 		0.126
(0.451) 		0.549
(0.839) 		0.914
(1.00) 		0.537
(0.826) 		1
(1.00) 		0.38
(0.749) 		0.746
(0.952) 		0.00791
(0.0855) 		0.674
(0.921) 		0.0599
(0.296) 		0.0974
(0.393)
16q gain 142 (13%) 937 0.107
(0.415) 		0.843
(0.99) 		0.502
(0.812) 		0.409
(0.759) 		0.0886
(0.372) 		0.522
(0.824) 		0.061
(0.298) 		0.772
(0.965) 		0.00773
(0.0845) 		0.277
(0.656) 		0.439
(0.776) 		0.153
(0.501)
17q gain 221 (20%) 858 0.153
(0.501) 		0.868
(1.00) 		0.796
(0.976) 		0.438
(0.776) 		0.913
(1.00) 		0.794
(0.976) 		0.000637
(0.0143) 		0.13
(0.455) 		0.076
(0.337) 		0.371
(0.749) 		0.27
(0.655) 		0.31
(0.688)
19q gain 219 (20%) 860 0.579
(0.858) 		0.233
(0.607) 		0.0753
(0.336) 		0.686
(0.922) 		0.115
(0.429) 		0.0625
(0.303) 		0.277
(0.656) 		0.577
(0.857) 		0.122
(0.442) 		0.0117
(0.103) 		0.913
(1.00) 		0.687
(0.922)
xq gain 137 (13%) 942 0.472
(0.796) 		0.145
(0.49) 		0.218
(0.592) 		0.328
(0.709) 		0.7
(0.928) 		0.201
(0.575) 		1
(1.00) 		0.631
(0.886) 		0.0001
(0.00339) 		0.872
(1.00) 		0.0799
(0.35) 		0.613
(0.877)
1q loss 48 (4%) 1031 0.282
(0.656) 		0.39
(0.75) 		0.94
(1.00) 		0.895
(1.00) 		0.0442
(0.247) 		1
(1.00) 		1
(1.00) 		0.517
(0.823) 		0.169
(0.527) 		0.212
(0.585) 		0.364
(0.742) 		0.648
(0.896)
2p loss 184 (17%) 895 0.398
(0.753) 		0.458
(0.789) 		0.283
(0.656) 		0.426
(0.772) 		0.0667
(0.319) 		0.0213
(0.152) 		0.441
(0.776) 		0.734
(0.947) 		0.227
(0.603) 		0.463
(0.792) 		0.328
(0.709) 		0.11
(0.42)
7q loss 120 (11%) 959 0.111
(0.42) 		0.202
(0.575) 		0.526
(0.824) 		0.386
(0.749) 		0.417
(0.766) 		0.501
(0.81) 		0.634
(0.887) 		0.41
(0.759) 		0.0358
(0.211) 		0.956
(1.00) 		0.685
(0.922) 		0.112
(0.422)
11q loss 366 (34%) 713 0.941
(1.00) 		0.916
(1.00) 		0.213
(0.585) 		0.209
(0.582) 		0.0503
(0.269) 		0.819
(0.984) 		0.12
(0.44) 		0.282
(0.656) 		0.46
(0.79) 		0.409
(0.759) 		0.00404
(0.0533) 		0.863
(1)
13q loss 430 (40%) 649 0.0716
(0.329) 		0.22
(0.592) 		0.767
(0.96) 		0.334
(0.719) 		0.618
(0.877) 		1
(1.00) 		1
(1.00) 		0.294
(0.663) 		4e-05
(0.00164) 		0.644
(0.892) 		0.128
(0.455) 		0.239
(0.613)
16p loss 174 (16%) 905 0.281
(0.656) 		0.743
(0.952) 		0.63
(0.886) 		0.936
(1.00) 		0.189
(0.554) 		0.236
(0.61) 		0.703
(0.928) 		0.537
(0.826) 		0.203
(0.575) 		0.0283
(0.185) 		0.0464
(0.254) 		0.824
(0.984)
20p loss 93 (9%) 986 0.157
(0.508) 		0.0534
(0.278) 		0.816
(0.984) 		0.127
(0.455) 		0.963
(1.00) 		0.0334
(0.205) 		1
(1.00) 		0.0867
(0.368) 		0.0586
(0.291) 		0.833
(0.984) 		0.116
(0.429) 		0.368
(0.744)
8p gain 291 (27%) 788 0.431
(0.772) 		0.956
(1.00) 		0.484
(0.799) 		0.864
(1) 		0.752
(0.954) 		0.151
(0.5) 		0.323
(0.709) 		0.384
(0.749) 		0.0577
(0.288) 		0.6
(0.872) 		0.0943
(0.387) 		0.852
(0.997)
9p gain 139 (13%) 940 0.608
(0.872) 		0.946
(1.00) 		0.0783
(0.345) 		0.218
(0.592) 		0.158
(0.508) 		0.757
(0.954) 		0.382
(0.749) 		0.505
(0.814) 		0.254
(0.626) 		0.564
(0.848) 		0.423
(0.772) 		1
(1.00)
9q gain 122 (11%) 957 0.242
(0.614) 		0.571
(0.856) 		0.147
(0.491) 		0.178
(0.544) 		0.529
(0.825) 		1
(1.00) 		0.38
(0.749) 		0.484
(0.799) 		0.0739
(0.333) 		0.965
(1.00) 		0.35
(0.732) 		1
(1.00)
2q loss 210 (19%) 869 0.272
(0.656) 		0.722
(0.944) 		0.254
(0.626) 		0.292
(0.661) 		0.116
(0.429) 		0.0543
(0.279) 		1
(1.00) 		0.809
(0.981) 		0.106
(0.411) 		0.364
(0.742) 		0.488
(0.801) 		0.133
(0.463)
6p loss 190 (18%) 889 0.846
(0.992) 		0.0557
(0.281) 		0.841
(0.989) 		0.6
(0.872) 		0.665
(0.915) 		1
(1.00) 		0.703
(0.928) 		0.273
(0.656) 		0.276
(0.656) 		0.816
(0.984) 		0.526
(0.824) 		0.662
(0.914)
8q loss 93 (9%) 986 0.227
(0.603) 		0.618
(0.877) 		0.432
(0.772) 		0.299
(0.671) 		0.277
(0.656) 		0.247
(0.621) 		0.614
(0.877) 		0.171
(0.529) 		0.805
(0.979) 		0.892
(1.00) 		0.0722
(0.329) 		0.386
(0.749)
xq loss 189 (18%) 890 0.874
(1.00) 		0.12
(0.44) 		0.726
(0.944) 		0.0953
(0.389) 		0.601
(0.872) 		0.265
(0.646) 		0.451
(0.783) 		0.451
(0.783) 		0.129
(0.455) 		0.524
(0.824) 		0.175
(0.535) 		1
(1.00)
'1p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00811 (Fisher's exact test), Q value = 0.086

Table S1.  Gene #1: '1p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
1P GAIN MUTATED 42 144 26 14
1P GAIN WILD-TYPE 232 481 111 26

Figure S1.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'1p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00186 (Fisher's exact test), Q value = 0.03

Table S2.  Gene #1: '1p gain' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
1P GAIN MUTATED 0 173 24 3 4 8 2 13
1P GAIN WILD-TYPE 1 595 177 3 5 22 15 33

Figure S2.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'1q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0166 (Fisher's exact test), Q value = 0.13

Table S3.  Gene #2: '1q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
ALL 89 83 6 6 352 253 2 155 27 65 20 13
1Q GAIN MUTATED 48 48 2 6 240 168 1 97 22 49 11 8
1Q GAIN WILD-TYPE 41 35 4 0 112 85 1 58 5 16 9 5

Figure S3.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'1q gain' versus 'PATHOLOGY_T_STAGE'

P value = 7e-04 (Fisher's exact test), Q value = 0.015

Table S4.  Gene #2: '1q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
1Q GAIN MUTATED 155 431 88 32
1Q GAIN WILD-TYPE 119 194 49 8

Figure S4.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'1q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00173 (Fisher's exact test), Q value = 0.028

Table S5.  Gene #2: '1q gain' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
1Q GAIN MUTATED 1 485 156 4 4 18 8 31
1Q GAIN WILD-TYPE 0 283 45 2 5 12 9 15

Figure S5.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'2p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00049

Table S6.  Gene #3: '2p gain' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
2P GAIN MUTATED 1 107 5 2 3 1 0 3
2P GAIN WILD-TYPE 0 661 196 4 6 29 17 43

Figure S6.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'2p gain' versus 'RACE'

P value = 0.00016 (Fisher's exact test), Q value = 0.0049

Table S7.  Gene #3: '2p gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
2P GAIN MUTATED 1 11 32 67
2P GAIN WILD-TYPE 0 49 149 677

Figure S7.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #11: 'RACE'

'2p gain' versus 'ETHNICITY'

P value = 0.0168 (Fisher's exact test), Q value = 0.13

Table S8.  Gene #3: '2p gain' versus Clinical Feature #12: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 39 874
2P GAIN MUTATED 0 104
2P GAIN WILD-TYPE 39 770

Figure S8.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #12: 'ETHNICITY'

'2q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00053 (Fisher's exact test), Q value = 0.012

Table S9.  Gene #4: '2q gain' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
2Q GAIN MUTATED 0 64 3 0 3 0 0 3
2Q GAIN WILD-TYPE 1 704 198 6 6 30 17 43

Figure S9.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'2q gain' versus 'RACE'

P value = 0.00602 (Fisher's exact test), Q value = 0.07

Table S10.  Gene #4: '2q gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
2Q GAIN MUTATED 0 9 18 39
2Q GAIN WILD-TYPE 1 51 163 705

Figure S10.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #11: 'RACE'

'3p gain' versus 'HISTOLOGICAL_TYPE'

P value = 8e-05 (Fisher's exact test), Q value = 0.0028

Table S11.  Gene #5: '3p gain' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
3P GAIN MUTATED 0 116 7 2 2 4 1 5
3P GAIN WILD-TYPE 1 652 194 4 7 26 16 41

Figure S11.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'3q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00049

Table S12.  Gene #6: '3q gain' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
3Q GAIN MUTATED 0 181 10 4 4 6 1 7
3Q GAIN WILD-TYPE 1 587 191 2 5 24 16 39

Figure S12.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'3q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0233 (Wilcoxon-test), Q value = 0.16

Table S13.  Gene #6: '3q gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 913 2.4 (4.7)
3Q GAIN MUTATED 177 2.0 (4.2)
3Q GAIN WILD-TYPE 736 2.5 (4.8)

Figure S13.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'3q gain' versus 'RACE'

P value = 0.0112 (Fisher's exact test), Q value = 0.1

Table S14.  Gene #6: '3q gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
3Q GAIN MUTATED 1 13 47 129
3Q GAIN WILD-TYPE 0 47 134 615

Figure S14.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #11: 'RACE'

'4p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0021 (Fisher's exact test), Q value = 0.033

Table S15.  Gene #7: '4p gain' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
4P GAIN MUTATED 0 58 4 1 3 3 1 5
4P GAIN WILD-TYPE 1 710 197 5 6 27 16 41

Figure S15.  Get High-res Image Gene #7: '4p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'4q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00345 (Fisher's exact test), Q value = 0.048

Table S16.  Gene #8: '4q gain' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
4Q GAIN MUTATED 0 55 4 2 2 2 1 5
4Q GAIN WILD-TYPE 1 713 197 4 7 28 16 41

Figure S16.  Get High-res Image Gene #8: '4q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'5p gain' versus 'Time to Death'

P value = 0.0245 (logrank test), Q value = 0.17

Table S17.  Gene #9: '5p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1065 148 0.0 - 282.9 (28.2)
5P GAIN MUTATED 312 46 0.0 - 233.6 (23.8)
5P GAIN WILD-TYPE 753 102 0.0 - 282.9 (30.2)

Figure S17.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #1: 'Time to Death'

'5p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0142 (Fisher's exact test), Q value = 0.12

Table S18.  Gene #9: '5p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 506 358 119 77
5P GAIN MUTATED 161 87 44 18
5P GAIN WILD-TYPE 345 271 75 59

Figure S18.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'5p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0231 (Fisher's exact test), Q value = 0.16

Table S19.  Gene #9: '5p gain' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
5P GAIN MUTATED 1 228 56 2 7 9 2 10
5P GAIN WILD-TYPE 0 540 145 4 2 21 15 36

Figure S19.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'5q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0102 (Wilcoxon-test), Q value = 0.095

Table S20.  Gene #10: '5q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1064 58.6 (13.2)
5Q GAIN MUTATED 208 60.6 (12.5)
5Q GAIN WILD-TYPE 856 58.2 (13.3)

Figure S20.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0367 (Fisher's exact test), Q value = 0.21

Table S21.  Gene #10: '5q gain' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
5Q GAIN MUTATED 0 140 47 1 6 7 2 8
5Q GAIN WILD-TYPE 1 628 154 5 3 23 15 38

Figure S21.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'5q gain' versus 'RACE'

P value = 0.00086 (Fisher's exact test), Q value = 0.017

Table S22.  Gene #10: '5q gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
5Q GAIN MUTATED 0 7 19 162
5Q GAIN WILD-TYPE 1 53 162 582

Figure S22.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #11: 'RACE'

'6p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00049

Table S23.  Gene #11: '6p gain' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
6P GAIN MUTATED 0 165 21 5 4 4 1 7
6P GAIN WILD-TYPE 1 603 180 1 5 26 16 39

Figure S23.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'6p gain' versus 'RACE'

P value = 0.00991 (Fisher's exact test), Q value = 0.094

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

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
6P GAIN MUTATED 0 8 50 131
6P GAIN WILD-TYPE 1 52 131 613

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

'6q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00049

Table S25.  Gene #12: '6q gain' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
6Q GAIN MUTATED 0 117 15 5 4 4 1 3
6Q GAIN WILD-TYPE 1 651 186 1 5 26 16 43

Figure S25.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'6q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0356 (Wilcoxon-test), Q value = 0.21

Table S26.  Gene #12: '6q gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 913 2.4 (4.7)
6Q GAIN MUTATED 126 2.4 (5.4)
6Q GAIN WILD-TYPE 787 2.4 (4.5)

Figure S26.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'7p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0125 (Fisher's exact test), Q value = 0.11

Table S27.  Gene #13: '7p gain' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
7P GAIN MUTATED 1 241 42 1 5 8 2 13
7P GAIN WILD-TYPE 0 527 159 5 4 22 15 33

Figure S27.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'7q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0189 (Fisher's exact test), Q value = 0.14

Table S28.  Gene #14: '7q gain' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
7Q GAIN MUTATED 1 206 37 2 5 6 2 9
7Q GAIN WILD-TYPE 0 562 164 4 4 24 15 37

Figure S28.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'7q gain' versus 'RACE'

P value = 0.0399 (Fisher's exact test), Q value = 0.23

Table S29.  Gene #14: '7q gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
7Q GAIN MUTATED 0 15 59 170
7Q GAIN WILD-TYPE 1 45 122 574

Figure S29.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #11: 'RACE'

'8q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00049

Table S30.  Gene #16: '8q gain' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
8Q GAIN MUTATED 1 416 59 5 6 14 5 22
8Q GAIN WILD-TYPE 0 352 142 1 3 16 12 24

Figure S30.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'8q gain' versus 'RACE'

P value = 0.00638 (Fisher's exact test), Q value = 0.072

Table S31.  Gene #16: '8q gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
8Q GAIN MUTATED 1 29 106 338
8Q GAIN WILD-TYPE 0 31 75 406

Figure S31.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #11: 'RACE'

'10p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00049

Table S32.  Gene #19: '10p gain' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
10P GAIN MUTATED 0 177 16 4 1 4 0 6
10P GAIN WILD-TYPE 1 591 185 2 8 26 17 40

Figure S32.  Get High-res Image Gene #19: '10p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'10p gain' versus 'RACE'

P value = 0.00124 (Fisher's exact test), Q value = 0.022

Table S33.  Gene #19: '10p gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
10P GAIN MUTATED 1 10 51 126
10P GAIN WILD-TYPE 0 50 130 618

Figure S33.  Get High-res Image Gene #19: '10p gain' versus Clinical Feature #11: 'RACE'

'10q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0117 (Fisher's exact test), Q value = 0.1

Table S34.  Gene #20: '10q gain' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
10Q GAIN MUTATED 0 96 10 2 1 2 0 3
10Q GAIN WILD-TYPE 1 672 191 4 8 28 17 43

Figure S34.  Get High-res Image Gene #20: '10q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'11p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0113 (Wilcoxon-test), Q value = 0.1

Table S35.  Gene #21: '11p gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 913 2.4 (4.7)
11P GAIN MUTATED 120 1.8 (3.7)
11P GAIN WILD-TYPE 793 2.5 (4.8)

Figure S35.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'11q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00165 (Fisher's exact test), Q value = 0.028

Table S36.  Gene #22: '11q gain' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
11Q GAIN MUTATED 0 77 5 2 1 3 1 7
11Q GAIN WILD-TYPE 1 691 196 4 8 27 16 39

Figure S36.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'12p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00131 (Fisher's exact test), Q value = 0.023

Table S37.  Gene #23: '12p gain' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
12P GAIN MUTATED 1 178 27 2 2 9 1 4
12P GAIN WILD-TYPE 0 590 174 4 7 21 16 42

Figure S37.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'12q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.031 (Fisher's exact test), Q value = 0.2

Table S38.  Gene #24: '12q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 506 358 119 77
12Q GAIN MUTATED 74 59 28 19
12Q GAIN WILD-TYPE 432 299 91 58

Figure S38.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'12q gain' versus 'GENDER'

P value = 0.0405 (Fisher's exact test), Q value = 0.23

Table S39.  Gene #24: '12q gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1067 12
12Q GAIN MUTATED 181 5
12Q GAIN WILD-TYPE 886 7

Figure S39.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #7: 'GENDER'

'12q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0212 (Fisher's exact test), Q value = 0.15

Table S40.  Gene #24: '12q gain' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
12Q GAIN MUTATED 0 146 25 1 0 9 1 3
12Q GAIN WILD-TYPE 1 622 176 5 9 21 16 43

Figure S40.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'12q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0183 (Wilcoxon-test), Q value = 0.14

Table S41.  Gene #24: '12q gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 913 2.4 (4.7)
12Q GAIN MUTATED 149 3.1 (5.3)
12Q GAIN WILD-TYPE 764 2.2 (4.5)

Figure S41.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'13q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00048 (Fisher's exact test), Q value = 0.012

Table S42.  Gene #25: '13q gain' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
13Q GAIN MUTATED 0 75 4 1 3 2 2 6
13Q GAIN WILD-TYPE 1 693 197 5 6 28 15 40

Figure S42.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'14q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0197 (Fisher's exact test), Q value = 0.15

Table S43.  Gene #26: '14q gain' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
14Q GAIN MUTATED 0 110 15 0 3 8 2 5
14Q GAIN WILD-TYPE 1 658 186 6 6 22 15 41

Figure S43.  Get High-res Image Gene #26: '14q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'15q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00158 (Fisher's exact test), Q value = 0.027

Table S44.  Gene #27: '15q gain' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
15Q GAIN MUTATED 0 76 3 0 1 1 2 4
15Q GAIN WILD-TYPE 1 692 198 6 8 29 15 42

Figure S44.  Get High-res Image Gene #27: '15q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'16p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00791 (Fisher's exact test), Q value = 0.086

Table S45.  Gene #28: '16p gain' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
16P GAIN MUTATED 1 340 86 2 3 16 2 11
16P GAIN WILD-TYPE 0 428 115 4 6 14 15 35

Figure S45.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'16q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00773 (Fisher's exact test), Q value = 0.085

Table S46.  Gene #29: '16q gain' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
16Q GAIN MUTATED 1 112 14 1 3 5 1 5
16Q GAIN WILD-TYPE 0 656 187 5 6 25 16 41

Figure S46.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'17p gain' versus 'GENDER'

P value = 0.00444 (Fisher's exact test), Q value = 0.057

Table S47.  Gene #30: '17p gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1067 12
17P GAIN MUTATED 105 5
17P GAIN WILD-TYPE 962 7

Figure S47.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #7: 'GENDER'

'17p gain' versus 'RADIATION_THERAPY'

P value = 0.0157 (Fisher's exact test), Q value = 0.13

Table S48.  Gene #30: '17p gain' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients NO YES
ALL 437 547
17P GAIN MUTATED 34 69
17P GAIN WILD-TYPE 403 478

Figure S48.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #8: 'RADIATION_THERAPY'

'17q gain' versus 'GENDER'

P value = 0.000637 (Fisher's exact test), Q value = 0.014

Table S49.  Gene #31: '17q gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1067 12
17Q GAIN MUTATED 213 8
17Q GAIN WILD-TYPE 854 4

Figure S49.  Get High-res Image Gene #31: '17q gain' versus Clinical Feature #7: 'GENDER'

'18p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0292 (Fisher's exact test), Q value = 0.19

Table S50.  Gene #32: '18p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 506 358 119 77
18P GAIN MUTATED 100 44 17 13
18P GAIN WILD-TYPE 406 314 102 64

Figure S50.  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 = 0.017

Table S51.  Gene #32: '18p gain' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
18P GAIN MUTATED 0 145 15 2 2 5 0 7
18P GAIN WILD-TYPE 1 623 186 4 7 25 17 39

Figure S51.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'18p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0189 (Wilcoxon-test), Q value = 0.14

Table S52.  Gene #32: '18p gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 913 2.4 (4.7)
18P GAIN MUTATED 145 2.1 (4.4)
18P GAIN WILD-TYPE 768 2.4 (4.7)

Figure S52.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'18p gain' versus 'RACE'

P value = 0.00018 (Fisher's exact test), Q value = 0.0052

Table S53.  Gene #32: '18p gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
18P GAIN MUTATED 0 7 49 101
18P GAIN WILD-TYPE 1 53 132 643

Figure S53.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #11: 'RACE'

'18q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00553 (Fisher's exact test), Q value = 0.066

Table S54.  Gene #33: '18q gain' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
18Q GAIN MUTATED 0 127 13 1 1 5 0 6
18Q GAIN WILD-TYPE 1 641 188 5 8 25 17 40

Figure S54.  Get High-res Image Gene #33: '18q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'18q gain' versus 'RACE'

P value = 0.0239 (Fisher's exact test), Q value = 0.16

Table S55.  Gene #33: '18q gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
18Q GAIN MUTATED 0 8 38 92
18Q GAIN WILD-TYPE 1 52 143 652

Figure S55.  Get High-res Image Gene #33: '18q gain' versus Clinical Feature #11: 'RACE'

'19p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0214 (Fisher's exact test), Q value = 0.15

Table S56.  Gene #34: '19p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 889 22
19P GAIN MUTATED 162 0
19P GAIN WILD-TYPE 727 22

Figure S56.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'19p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0354 (Wilcoxon-test), Q value = 0.21

Table S57.  Gene #34: '19p gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 913 2.4 (4.7)
19P GAIN MUTATED 170 2.1 (4.8)
19P GAIN WILD-TYPE 743 2.5 (4.6)

Figure S57.  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 = 0.0117 (Wilcoxon-test), Q value = 0.1

Table S58.  Gene #35: '19q gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 913 2.4 (4.7)
19Q GAIN MUTATED 193 1.9 (4.3)
19Q GAIN WILD-TYPE 720 2.5 (4.8)

Figure S58.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'20p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00819 (Fisher's exact test), Q value = 0.086

Table S59.  Gene #36: '20p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 506 358 119 77
20P GAIN MUTATED 191 125 61 24
20P GAIN WILD-TYPE 315 233 58 53

Figure S59.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'20p gain' versus 'GENDER'

P value = 0.0132 (Fisher's exact test), Q value = 0.11

Table S60.  Gene #36: '20p gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1067 12
20P GAIN MUTATED 401 9
20P GAIN WILD-TYPE 666 3

Figure S60.  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 = 0.00049

Table S61.  Gene #36: '20p gain' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
20P GAIN MUTATED 0 334 45 2 5 10 1 12
20P GAIN WILD-TYPE 1 434 156 4 4 20 16 34

Figure S61.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'20q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00371 (Fisher's exact test), Q value = 0.051

Table S62.  Gene #37: '20q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
20Q GAIN MUTATED 101 281 44 22
20Q GAIN WILD-TYPE 173 344 93 18

Figure S62.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'20q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0326 (Fisher's exact test), Q value = 0.2

Table S63.  Gene #37: '20q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 506 358 119 77
20Q GAIN MUTATED 208 139 64 29
20Q GAIN WILD-TYPE 298 219 55 48

Figure S63.  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 = 0.00049

Table S64.  Gene #37: '20q gain' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
20Q GAIN MUTATED 0 368 49 1 6 10 1 15
20Q GAIN WILD-TYPE 1 400 152 5 3 20 16 31

Figure S64.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'21q gain' versus 'Time to Death'

P value = 0.028 (logrank test), Q value = 0.18

Table S65.  Gene #38: '21q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1065 148 0.0 - 282.9 (28.2)
21Q GAIN MUTATED 197 37 0.0 - 282.9 (28.0)
21Q GAIN WILD-TYPE 868 111 0.0 - 281.3 (28.2)

Figure S65.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #1: 'Time to Death'

'21q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00049

Table S66.  Gene #38: '21q gain' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
21Q GAIN MUTATED 0 169 17 2 4 0 1 5
21Q GAIN WILD-TYPE 1 599 184 4 5 30 16 41

Figure S66.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'21q gain' versus 'RACE'

P value = 0.0258 (Fisher's exact test), Q value = 0.17

Table S67.  Gene #38: '21q gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
21Q GAIN MUTATED 1 10 43 122
21Q GAIN WILD-TYPE 0 50 138 622

Figure S67.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #11: 'RACE'

'22q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00032 (Fisher's exact test), Q value = 0.0083

Table S68.  Gene #39: '22q gain' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
22Q GAIN MUTATED 0 81 4 1 2 2 1 8
22Q GAIN WILD-TYPE 1 687 197 5 7 28 16 38

Figure S68.  Get High-res Image Gene #39: '22q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'22q gain' versus 'RACE'

P value = 0.0328 (Fisher's exact test), Q value = 0.2

Table S69.  Gene #39: '22q gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
22Q GAIN MUTATED 1 7 21 59
22Q GAIN WILD-TYPE 0 53 160 685

Figure S69.  Get High-res Image Gene #39: '22q gain' versus Clinical Feature #11: 'RACE'

'xp gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00021 (Fisher's exact test), Q value = 0.0059

Table S70.  Gene #40: 'xp gain' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
XP GAIN MUTATED 1 122 11 3 2 4 2 5
XP GAIN WILD-TYPE 0 646 190 3 7 26 15 41

Figure S70.  Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'xp gain' versus 'RACE'

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

Table S71.  Gene #40: 'xp gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
XP GAIN MUTATED 1 6 32 91
XP GAIN WILD-TYPE 0 54 149 653

Figure S71.  Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #11: 'RACE'

'xq gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-04 (Fisher's exact test), Q value = 0.0034

Table S72.  Gene #41: 'xq gain' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
XQ GAIN MUTATED 1 113 9 3 1 2 2 5
XQ GAIN WILD-TYPE 0 655 192 3 8 28 15 41

Figure S72.  Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'1p loss' versus 'Time to Death'

P value = 0.00534 (logrank test), Q value = 0.064

Table S73.  Gene #42: '1p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1065 148 0.0 - 282.9 (28.2)
1P LOSS MUTATED 223 45 0.2 - 233.6 (26.7)
1P LOSS WILD-TYPE 842 103 0.0 - 282.9 (28.5)

Figure S73.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #1: 'Time to Death'

'1p loss' versus 'YEARS_TO_BIRTH'

P value = 0.000666 (Wilcoxon-test), Q value = 0.015

Table S74.  Gene #42: '1p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1064 58.6 (13.2)
1P LOSS MUTATED 221 61.2 (13.1)
1P LOSS WILD-TYPE 843 58.0 (13.2)

Figure S74.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'1p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0105 (Fisher's exact test), Q value = 0.098

Table S75.  Gene #42: '1p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
ALL 89 83 6 6 352 253 2 155 27 65 20 13
1P LOSS MUTATED 13 15 0 1 69 46 1 40 13 18 7 3
1P LOSS WILD-TYPE 76 68 6 5 283 207 1 115 14 47 13 10

Figure S75.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'1p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00949 (Fisher's exact test), Q value = 0.092

Table S76.  Gene #42: '1p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
1P LOSS MUTATED 49 130 30 17
1P LOSS WILD-TYPE 225 495 107 23

Figure S76.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'1p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0138 (Fisher's exact test), Q value = 0.12

Table S77.  Gene #42: '1p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 506 358 119 77
1P LOSS MUTATED 86 80 32 22
1P LOSS WILD-TYPE 420 278 87 55

Figure S77.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'1p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00292 (Wilcoxon-test), Q value = 0.042

Table S78.  Gene #42: '1p loss' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 913 2.4 (4.7)
1P LOSS MUTATED 178 3.1 (5.2)
1P LOSS WILD-TYPE 735 2.2 (4.5)

Figure S78.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'1q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0442 (Fisher's exact test), Q value = 0.25

Table S79.  Gene #43: '1q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 506 358 119 77
1Q LOSS MUTATED 14 22 8 4
1Q LOSS WILD-TYPE 492 336 111 73

Figure S79.  Get High-res Image Gene #43: '1q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'2p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0213 (Fisher's exact test), Q value = 0.15

Table S80.  Gene #44: '2p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 889 22
2P LOSS MUTATED 146 8
2P LOSS WILD-TYPE 743 14

Figure S80.  Get High-res Image Gene #44: '2p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'3p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00129 (Fisher's exact test), Q value = 0.023

Table S81.  Gene #46: '3p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
3P LOSS MUTATED 32 132 20 3
3P LOSS WILD-TYPE 242 493 117 37

Figure S81.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'3p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0216 (Fisher's exact test), Q value = 0.15

Table S82.  Gene #46: '3p loss' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
3P LOSS MUTATED 0 154 20 1 2 3 1 7
3P LOSS WILD-TYPE 1 614 181 5 7 27 16 39

Figure S82.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'3p loss' versus 'RACE'

P value = 0.0247 (Fisher's exact test), Q value = 0.17

Table S83.  Gene #46: '3p loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
3P LOSS MUTATED 0 16 42 119
3P LOSS WILD-TYPE 1 44 139 625

Figure S83.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #11: 'RACE'

'3p loss' versus 'ETHNICITY'

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

Table S84.  Gene #46: '3p loss' versus Clinical Feature #12: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 39 874
3P LOSS MUTATED 2 165
3P LOSS WILD-TYPE 37 709

Figure S84.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #12: 'ETHNICITY'

'3q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00252 (Fisher's exact test), Q value = 0.039

Table S85.  Gene #47: '3q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
3Q LOSS MUTATED 16 78 9 1
3Q LOSS WILD-TYPE 258 547 128 39

Figure S85.  Get High-res Image Gene #47: '3q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'3q loss' versus 'ETHNICITY'

P value = 0.0268 (Fisher's exact test), Q value = 0.18

Table S86.  Gene #47: '3q loss' versus Clinical Feature #12: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 39 874
3Q LOSS MUTATED 0 94
3Q LOSS WILD-TYPE 39 780

Figure S86.  Get High-res Image Gene #47: '3q loss' versus Clinical Feature #12: 'ETHNICITY'

'4p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0129 (Fisher's exact test), Q value = 0.11

Table S87.  Gene #48: '4p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
4P LOSS MUTATED 71 226 39 15
4P LOSS WILD-TYPE 203 399 98 25

Figure S87.  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 = 0.00049

Table S88.  Gene #48: '4p loss' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
4P LOSS MUTATED 1 291 34 3 4 6 0 13
4P LOSS WILD-TYPE 0 477 167 3 5 24 17 33

Figure S88.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'4p loss' versus 'RACE'

P value = 0.00296 (Fisher's exact test), Q value = 0.042

Table S89.  Gene #48: '4p loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
4P LOSS MUTATED 1 20 79 228
4P LOSS WILD-TYPE 0 40 102 516

Figure S89.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #11: 'RACE'

'4q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0323 (Fisher's exact test), Q value = 0.2

Table S90.  Gene #49: '4q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
4Q LOSS MUTATED 61 193 40 15
4Q LOSS WILD-TYPE 213 432 97 25

Figure S90.  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 = 0.00049

Table S91.  Gene #49: '4q loss' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
4Q LOSS MUTATED 0 253 32 2 4 6 0 13
4Q LOSS WILD-TYPE 1 515 169 4 5 24 17 33

Figure S91.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'4q loss' versus 'RACE'

P value = 0.00893 (Fisher's exact test), Q value = 0.088

Table S92.  Gene #49: '4q loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
4Q LOSS MUTATED 1 18 68 198
4Q LOSS WILD-TYPE 0 42 113 546

Figure S92.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #11: 'RACE'

'5p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0012 (Wilcoxon-test), Q value = 0.022

Table S93.  Gene #50: '5p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1064 58.6 (13.2)
5P LOSS MUTATED 139 55.3 (13.8)
5P LOSS WILD-TYPE 925 59.1 (13.1)

Figure S93.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5p loss' versus 'PATHOLOGY_T_STAGE'

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

Table S94.  Gene #50: '5p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
5P LOSS MUTATED 28 98 11 5
5P LOSS WILD-TYPE 246 527 126 35

Figure S94.  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 = 0.00049

Table S95.  Gene #50: '5p loss' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
5P LOSS MUTATED 0 121 3 4 0 5 0 8
5P LOSS WILD-TYPE 1 647 198 2 9 25 17 38

Figure S95.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'5p loss' versus 'RACE'

P value = 0.00878 (Fisher's exact test), Q value = 0.088

Table S96.  Gene #50: '5p loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
5P LOSS MUTATED 1 12 32 88
5P LOSS WILD-TYPE 0 48 149 656

Figure S96.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #11: 'RACE'

'5q loss' versus 'YEARS_TO_BIRTH'

P value = 6.56e-05 (Wilcoxon-test), Q value = 0.0025

Table S97.  Gene #51: '5q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1064 58.6 (13.2)
5Q LOSS MUTATED 225 55.7 (13.2)
5Q LOSS WILD-TYPE 839 59.4 (13.1)

Figure S97.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00406 (Fisher's exact test), Q value = 0.053

Table S98.  Gene #51: '5q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
5Q LOSS MUTATED 45 155 19 8
5Q LOSS WILD-TYPE 229 470 118 32

Figure S98.  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 = 0.00049

Table S99.  Gene #51: '5q loss' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
5Q LOSS MUTATED 1 201 5 5 0 5 0 10
5Q LOSS WILD-TYPE 0 567 196 1 9 25 17 36

Figure S99.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'5q loss' versus 'RACE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00049

Table S100.  Gene #51: '5q loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
5Q LOSS MUTATED 1 18 63 130
5Q LOSS WILD-TYPE 0 42 118 614

Figure S100.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #11: 'RACE'

'6q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00115 (Wilcoxon-test), Q value = 0.022

Table S101.  Gene #53: '6q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1064 58.6 (13.2)
6Q LOSS MUTATED 278 56.3 (13.4)
6Q LOSS WILD-TYPE 786 59.5 (13.0)

Figure S101.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'6q loss' versus 'RADIATION_THERAPY'

P value = 0.00567 (Fisher's exact test), Q value = 0.066

Table S102.  Gene #53: '6q loss' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients NO YES
ALL 437 547
6Q LOSS MUTATED 96 163
6Q LOSS WILD-TYPE 341 384

Figure S102.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #8: 'RADIATION_THERAPY'

'7p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.032 (Fisher's exact test), Q value = 0.2

Table S103.  Gene #54: '7p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 506 358 119 77
7P LOSS MUTATED 60 28 18 4
7P LOSS WILD-TYPE 446 330 101 73

Figure S103.  Get High-res Image Gene #54: '7p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'7p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00015 (Fisher's exact test), Q value = 0.0048

Table S104.  Gene #54: '7p loss' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
7P LOSS MUTATED 0 95 5 2 2 3 0 4
7P LOSS WILD-TYPE 1 673 196 4 7 27 17 42

Figure S104.  Get High-res Image Gene #54: '7p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'7q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0358 (Fisher's exact test), Q value = 0.21

Table S105.  Gene #55: '7q loss' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
7Q LOSS MUTATED 0 99 11 0 2 4 0 4
7Q LOSS WILD-TYPE 1 669 190 6 7 26 17 42

Figure S105.  Get High-res Image Gene #55: '7q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'8p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00025 (Fisher's exact test), Q value = 0.0068

Table S106.  Gene #56: '8p loss' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
8P LOSS MUTATED 1 313 50 2 1 8 3 16
8P LOSS WILD-TYPE 0 455 151 4 8 22 14 30

Figure S106.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'8p loss' versus 'RACE'

P value = 0.0398 (Fisher's exact test), Q value = 0.23

Table S107.  Gene #56: '8p loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
8P LOSS MUTATED 1 30 71 261
8P LOSS WILD-TYPE 0 30 110 483

Figure S107.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #11: 'RACE'

'9p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00256 (Fisher's exact test), Q value = 0.039

Table S108.  Gene #58: '9p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
ALL 89 83 6 6 352 253 2 155 27 65 20 13
9P LOSS MUTATED 21 15 0 2 104 64 1 55 15 19 10 5
9P LOSS WILD-TYPE 68 68 6 4 248 189 1 100 12 46 10 8

Figure S108.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'9p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00041 (Fisher's exact test), Q value = 0.01

Table S109.  Gene #58: '9p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
9P LOSS MUTATED 57 203 34 18
9P LOSS WILD-TYPE 217 422 103 22

Figure S109.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'9p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00492 (Fisher's exact test), Q value = 0.06

Table S110.  Gene #58: '9p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 506 358 119 77
9P LOSS MUTATED 141 92 51 24
9P LOSS WILD-TYPE 365 266 68 53

Figure S110.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'9p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00049

Table S111.  Gene #58: '9p loss' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
9P LOSS MUTATED 0 262 25 3 5 9 3 6
9P LOSS WILD-TYPE 1 506 176 3 4 21 14 40

Figure S111.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'9q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00422 (Fisher's exact test), Q value = 0.055

Table S112.  Gene #59: '9q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
9Q LOSS MUTATED 53 174 34 17
9Q LOSS WILD-TYPE 221 451 103 23

Figure S112.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'9q loss' versus 'GENDER'

P value = 0.017 (Fisher's exact test), Q value = 0.13

Table S113.  Gene #59: '9q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1067 12
9Q LOSS MUTATED 273 7
9Q LOSS WILD-TYPE 794 5

Figure S113.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #7: 'GENDER'

'9q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00049

Table S114.  Gene #59: '9q loss' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
9Q LOSS MUTATED 0 232 22 2 4 9 3 8
9Q LOSS WILD-TYPE 1 536 179 4 5 21 14 38

Figure S114.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'10p loss' versus 'Time to Death'

P value = 0.0128 (logrank test), Q value = 0.11

Table S115.  Gene #60: '10p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1065 148 0.0 - 282.9 (28.2)
10P LOSS MUTATED 173 31 0.0 - 282.9 (24.4)
10P LOSS WILD-TYPE 892 117 0.0 - 281.3 (28.9)

Figure S115.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #1: 'Time to Death'

'10p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0048 (Fisher's exact test), Q value = 0.059

Table S116.  Gene #60: '10p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
10P LOSS MUTATED 27 116 22 9
10P LOSS WILD-TYPE 247 509 115 31

Figure S116.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'10p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00059 (Fisher's exact test), Q value = 0.014

Table S117.  Gene #60: '10p loss' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
10P LOSS MUTATED 0 131 22 0 6 9 1 5
10P LOSS WILD-TYPE 1 637 179 6 3 21 16 41

Figure S117.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'10q loss' versus 'Time to Death'

P value = 0.0181 (logrank test), Q value = 0.14

Table S118.  Gene #61: '10q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1065 148 0.0 - 282.9 (28.2)
10Q LOSS MUTATED 230 39 0.0 - 282.9 (24.4)
10Q LOSS WILD-TYPE 835 109 0.0 - 281.3 (29.3)

Figure S118.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #1: 'Time to Death'

'10q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0048 (Fisher's exact test), Q value = 0.059

Table S119.  Gene #61: '10q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
10Q LOSS MUTATED 40 148 28 13
10Q LOSS WILD-TYPE 234 477 109 27

Figure S119.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'10q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00027 (Fisher's exact test), Q value = 0.0072

Table S120.  Gene #61: '10q loss' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
10Q LOSS MUTATED 0 180 25 1 6 9 1 8
10Q LOSS WILD-TYPE 1 588 176 5 3 21 16 38

Figure S120.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'10q loss' versus 'RACE'

P value = 0.045 (Fisher's exact test), Q value = 0.25

Table S121.  Gene #61: '10q loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
10Q LOSS MUTATED 0 19 46 145
10Q LOSS WILD-TYPE 1 41 135 599

Figure S121.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #11: 'RACE'

'11p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0358 (Fisher's exact test), Q value = 0.21

Table S122.  Gene #62: '11p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
ALL 89 83 6 6 352 253 2 155 27 65 20 13
11P LOSS MUTATED 20 13 1 1 85 61 0 51 14 17 4 2
11P LOSS WILD-TYPE 69 70 5 5 267 192 2 104 13 48 16 11

Figure S122.  Get High-res Image Gene #62: '11p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'11p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0215 (Fisher's exact test), Q value = 0.15

Table S123.  Gene #62: '11p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
11P LOSS MUTATED 59 159 34 18
11P LOSS WILD-TYPE 215 466 103 22

Figure S123.  Get High-res Image Gene #62: '11p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'11p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00393 (Fisher's exact test), Q value = 0.053

Table S124.  Gene #62: '11p loss' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
11P LOSS MUTATED 0 206 35 5 2 10 3 9
11P LOSS WILD-TYPE 1 562 166 1 7 20 14 37

Figure S124.  Get High-res Image Gene #62: '11p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'11p loss' versus 'RACE'

P value = 7e-04 (Fisher's exact test), Q value = 0.015

Table S125.  Gene #62: '11p loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
11P LOSS MUTATED 1 18 62 162
11P LOSS WILD-TYPE 0 42 119 582

Figure S125.  Get High-res Image Gene #62: '11p loss' versus Clinical Feature #11: 'RACE'

'11p loss' versus 'ETHNICITY'

P value = 0.0363 (Fisher's exact test), Q value = 0.21

Table S126.  Gene #62: '11p loss' versus Clinical Feature #12: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 39 874
11P LOSS MUTATED 4 216
11P LOSS WILD-TYPE 35 658

Figure S126.  Get High-res Image Gene #62: '11p loss' versus Clinical Feature #12: 'ETHNICITY'

'11q loss' versus 'RACE'

P value = 0.00404 (Fisher's exact test), Q value = 0.053

Table S127.  Gene #63: '11q loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
11Q LOSS MUTATED 1 23 77 227
11Q LOSS WILD-TYPE 0 37 104 517

Figure S127.  Get High-res Image Gene #63: '11q loss' versus Clinical Feature #11: 'RACE'

'12p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00988 (Fisher's exact test), Q value = 0.094

Table S128.  Gene #64: '12p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
12P LOSS MUTATED 32 90 16 13
12P LOSS WILD-TYPE 242 535 121 27

Figure S128.  Get High-res Image Gene #64: '12p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'12p loss' versus 'HISTOLOGICAL_TYPE'

P value = 4e-05 (Fisher's exact test), Q value = 0.0016

Table S129.  Gene #64: '12p loss' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
12P LOSS MUTATED 0 130 11 2 3 3 1 2
12P LOSS WILD-TYPE 1 638 190 4 6 27 16 44

Figure S129.  Get High-res Image Gene #64: '12p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'12q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00886 (Wilcoxon-test), Q value = 0.088

Table S130.  Gene #65: '12q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1064 58.6 (13.2)
12Q LOSS MUTATED 136 56.1 (13.2)
12Q LOSS WILD-TYPE 928 59.0 (13.2)

Figure S130.  Get High-res Image Gene #65: '12q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'12q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00733 (Fisher's exact test), Q value = 0.081

Table S131.  Gene #65: '12q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
12Q LOSS MUTATED 25 86 13 11
12Q LOSS WILD-TYPE 249 539 124 29

Figure S131.  Get High-res Image Gene #65: '12q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'12q loss' versus 'RADIATION_THERAPY'

P value = 0.00448 (Fisher's exact test), Q value = 0.057

Table S132.  Gene #65: '12q loss' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients NO YES
ALL 437 547
12Q LOSS MUTATED 39 82
12Q LOSS WILD-TYPE 398 465

Figure S132.  Get High-res Image Gene #65: '12q loss' versus Clinical Feature #8: 'RADIATION_THERAPY'

'12q loss' versus 'HISTOLOGICAL_TYPE'

P value = 6e-05 (Fisher's exact test), Q value = 0.0024

Table S133.  Gene #65: '12q loss' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
12Q LOSS MUTATED 0 115 10 3 3 2 0 3
12Q LOSS WILD-TYPE 1 653 191 3 6 28 17 43

Figure S133.  Get High-res Image Gene #65: '12q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'12q loss' versus 'RACE'

P value = 0.00353 (Fisher's exact test), Q value = 0.049

Table S134.  Gene #65: '12q loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
12Q LOSS MUTATED 0 6 39 85
12Q LOSS WILD-TYPE 1 54 142 659

Figure S134.  Get High-res Image Gene #65: '12q loss' versus Clinical Feature #11: 'RACE'

'13q loss' versus 'HISTOLOGICAL_TYPE'

P value = 4e-05 (Fisher's exact test), Q value = 0.0016

Table S135.  Gene #66: '13q loss' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
13Q LOSS MUTATED 0 337 59 4 5 11 2 11
13Q LOSS WILD-TYPE 1 431 142 2 4 19 15 35

Figure S135.  Get High-res Image Gene #66: '13q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'14q loss' versus 'Time to Death'

P value = 0.0279 (logrank test), Q value = 0.18

Table S136.  Gene #67: '14q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1065 148 0.0 - 282.9 (28.2)
14Q LOSS MUTATED 265 46 0.0 - 255.7 (24.8)
14Q LOSS WILD-TYPE 800 102 0.0 - 282.9 (29.7)

Figure S136.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #1: 'Time to Death'

'14q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0219 (Fisher's exact test), Q value = 0.15

Table S137.  Gene #67: '14q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
14Q LOSS MUTATED 52 176 31 8
14Q LOSS WILD-TYPE 222 449 106 32

Figure S137.  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 = 0.00049

Table S138.  Gene #67: '14q loss' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
14Q LOSS MUTATED 0 217 30 5 5 4 1 6
14Q LOSS WILD-TYPE 1 551 171 1 4 26 16 40

Figure S138.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'14q loss' versus 'RACE'

P value = 7e-05 (Fisher's exact test), Q value = 0.0026

Table S139.  Gene #67: '14q loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
14Q LOSS MUTATED 0 14 70 162
14Q LOSS WILD-TYPE 1 46 111 582

Figure S139.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #11: 'RACE'

'15q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00268 (Fisher's exact test), Q value = 0.04

Table S140.  Gene #68: '15q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
15Q LOSS MUTATED 60 210 37 9
15Q LOSS WILD-TYPE 214 415 100 31

Figure S140.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'15q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0413 (Fisher's exact test), Q value = 0.23

Table S141.  Gene #68: '15q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 506 358 119 77
15Q LOSS MUTATED 162 89 43 20
15Q LOSS WILD-TYPE 344 269 76 57

Figure S141.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'15q loss' versus 'HISTOLOGICAL_TYPE'

P value = 4e-05 (Fisher's exact test), Q value = 0.0016

Table S142.  Gene #68: '15q loss' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
15Q LOSS MUTATED 0 252 34 3 5 10 2 11
15Q LOSS WILD-TYPE 1 516 167 3 4 20 15 35

Figure S142.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'16p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0283 (Wilcoxon-test), Q value = 0.18

Table S143.  Gene #69: '16p loss' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 913 2.4 (4.7)
16P LOSS MUTATED 150 1.9 (4.2)
16P LOSS WILD-TYPE 763 2.5 (4.8)

Figure S143.  Get High-res Image Gene #69: '16p loss' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'16q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00088 (Wilcoxon-test), Q value = 0.017

Table S144.  Gene #70: '16q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1064 58.6 (13.2)
16Q LOSS MUTATED 582 59.9 (12.9)
16Q LOSS WILD-TYPE 482 57.1 (13.4)

Figure S144.  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 = 0.00049

Table S145.  Gene #70: '16q loss' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
16Q LOSS MUTATED 0 387 161 3 1 18 3 17
16Q LOSS WILD-TYPE 1 381 40 3 8 12 14 29

Figure S145.  Get High-res Image Gene #70: '16q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'17p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0153 (Fisher's exact test), Q value = 0.12

Table S146.  Gene #71: '17p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
17P LOSS MUTATED 126 358 74 19
17P LOSS WILD-TYPE 148 267 63 21

Figure S146.  Get High-res Image Gene #71: '17p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'17p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0115 (Fisher's exact test), Q value = 0.1

Table S147.  Gene #71: '17p loss' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
17P LOSS MUTATED 0 432 93 5 5 19 6 18
17P LOSS WILD-TYPE 1 336 108 1 4 11 11 28

Figure S147.  Get High-res Image Gene #71: '17p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'17q loss' versus 'GENDER'

P value = 0.0444 (Fisher's exact test), Q value = 0.25

Table S148.  Gene #72: '17q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1067 12
17Q LOSS MUTATED 272 0
17Q LOSS WILD-TYPE 795 12

Figure S148.  Get High-res Image Gene #72: '17q loss' versus Clinical Feature #7: 'GENDER'

'17q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00014 (Fisher's exact test), Q value = 0.0046

Table S149.  Gene #72: '17q loss' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
17Q LOSS MUTATED 0 214 36 4 5 5 0 8
17Q LOSS WILD-TYPE 1 554 165 2 4 25 17 38

Figure S149.  Get High-res Image Gene #72: '17q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'17q loss' versus 'RACE'

P value = 0.00841 (Fisher's exact test), Q value = 0.086

Table S150.  Gene #72: '17q loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
17Q LOSS MUTATED 0 21 59 170
17Q LOSS WILD-TYPE 1 39 122 574

Figure S150.  Get High-res Image Gene #72: '17q loss' versus Clinical Feature #11: 'RACE'

'18p loss' versus 'Time to Death'

P value = 1.99e-05 (logrank test), Q value = 0.00093

Table S151.  Gene #73: '18p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1065 148 0.0 - 282.9 (28.2)
18P LOSS MUTATED 314 59 0.0 - 233.6 (24.4)
18P LOSS WILD-TYPE 751 89 0.0 - 282.9 (31.0)

Figure S151.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #1: 'Time to Death'

'18p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00104 (Wilcoxon-test), Q value = 0.02

Table S152.  Gene #73: '18p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1064 58.6 (13.2)
18P LOSS MUTATED 311 60.7 (13.7)
18P LOSS WILD-TYPE 753 57.8 (12.9)

Figure S152.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'18p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0341 (Fisher's exact test), Q value = 0.21

Table S153.  Gene #73: '18p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
ALL 89 83 6 6 352 253 2 155 27 65 20 13
18P LOSS MUTATED 25 23 0 0 98 75 0 48 15 26 6 1
18P LOSS WILD-TYPE 64 60 6 6 254 178 2 107 12 39 14 12

Figure S153.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'18p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00276 (Fisher's exact test), Q value = 0.041

Table S154.  Gene #73: '18p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
18P LOSS MUTATED 69 188 41 22
18P LOSS WILD-TYPE 205 437 96 18

Figure S154.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'18p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0023 (Fisher's exact test), Q value = 0.036

Table S155.  Gene #73: '18p loss' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
18P LOSS MUTATED 0 249 48 3 4 7 0 9
18P LOSS WILD-TYPE 1 519 153 3 5 23 17 37

Figure S155.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'18p loss' versus 'RACE'

P value = 0.0455 (Fisher's exact test), Q value = 0.25

Table S156.  Gene #73: '18p loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
18P LOSS MUTATED 0 27 53 213
18P LOSS WILD-TYPE 1 33 128 531

Figure S156.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #11: 'RACE'

'18q loss' versus 'Time to Death'

P value = 0.0117 (logrank test), Q value = 0.1

Table S157.  Gene #74: '18q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1065 148 0.0 - 282.9 (28.2)
18Q LOSS MUTATED 315 52 0.0 - 255.7 (23.5)
18Q LOSS WILD-TYPE 750 96 0.2 - 282.9 (31.0)

Figure S157.  Get High-res Image Gene #74: '18q loss' versus Clinical Feature #1: 'Time to Death'

'18q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00874 (Wilcoxon-test), Q value = 0.088

Table S158.  Gene #74: '18q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1064 58.6 (13.2)
18Q LOSS MUTATED 313 60.3 (13.5)
18Q LOSS WILD-TYPE 751 57.9 (13.0)

Figure S158.  Get High-res Image Gene #74: '18q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'18q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0189 (Fisher's exact test), Q value = 0.14

Table S159.  Gene #74: '18q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 274 625 137 40
18Q LOSS MUTATED 70 191 39 20
18Q LOSS WILD-TYPE 204 434 98 20

Figure S159.  Get High-res Image Gene #74: '18q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'18q loss' versus 'HISTOLOGICAL_TYPE'

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

Table S160.  Gene #74: '18q loss' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
18Q LOSS MUTATED 1 246 53 2 5 7 0 7
18Q LOSS WILD-TYPE 0 522 148 4 4 23 17 39

Figure S160.  Get High-res Image Gene #74: '18q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'19p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0092 (Wilcoxon-test), Q value = 0.09

Table S161.  Gene #75: '19p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1064 58.6 (13.2)
19P LOSS MUTATED 192 56.3 (13.2)
19P LOSS WILD-TYPE 872 59.2 (13.2)

Figure S161.  Get High-res Image Gene #75: '19p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00049

Table S162.  Gene #75: '19p loss' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
19P LOSS MUTATED 0 171 8 1 3 5 4 4
19P LOSS WILD-TYPE 1 597 193 5 6 25 13 42

Figure S162.  Get High-res Image Gene #75: '19p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'19p loss' versus 'RACE'

P value = 0.00042 (Fisher's exact test), Q value = 0.01

Table S163.  Gene #75: '19p loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
19P LOSS MUTATED 0 16 48 111
19P LOSS WILD-TYPE 1 44 133 633

Figure S163.  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 = 0.00049

Table S164.  Gene #76: '19q loss' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
19Q LOSS MUTATED 0 144 5 1 0 4 4 5
19Q LOSS WILD-TYPE 1 624 196 5 9 26 13 41

Figure S164.  Get High-res Image Gene #76: '19q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'19q loss' versus 'RACE'

P value = 0.0161 (Fisher's exact test), Q value = 0.13

Table S165.  Gene #76: '19q loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
19Q LOSS MUTATED 0 13 37 95
19Q LOSS WILD-TYPE 1 47 144 649

Figure S165.  Get High-res Image Gene #76: '19q loss' versus Clinical Feature #11: 'RACE'

'20p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0334 (Fisher's exact test), Q value = 0.21

Table S166.  Gene #77: '20p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 889 22
20P LOSS MUTATED 73 5
20P LOSS WILD-TYPE 816 17

Figure S166.  Get High-res Image Gene #77: '20p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'20q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00641 (Wilcoxon-test), Q value = 0.072

Table S167.  Gene #78: '20q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1064 58.6 (13.2)
20Q LOSS MUTATED 55 54.1 (11.7)
20Q LOSS WILD-TYPE 1009 58.9 (13.2)

Figure S167.  Get High-res Image Gene #78: '20q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0347 (Fisher's exact test), Q value = 0.21

Table S168.  Gene #78: '20q loss' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
20Q LOSS MUTATED 0 42 7 3 0 1 1 3
20Q LOSS WILD-TYPE 1 726 194 3 9 29 16 43

Figure S168.  Get High-res Image Gene #78: '20q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'20q loss' versus 'RACE'

P value = 0.0179 (Fisher's exact test), Q value = 0.14

Table S169.  Gene #78: '20q loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
20Q LOSS MUTATED 0 5 17 30
20Q LOSS WILD-TYPE 1 55 164 714

Figure S169.  Get High-res Image Gene #78: '20q loss' versus Clinical Feature #11: 'RACE'

'21q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0145 (Fisher's exact test), Q value = 0.12

Table S170.  Gene #79: '21q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
ALL 89 83 6 6 352 253 2 155 27 65 20 13
21Q LOSS MUTATED 10 12 0 0 50 51 1 31 9 5 6 3
21Q LOSS WILD-TYPE 79 71 6 6 302 202 1 124 18 60 14 10

Figure S170.  Get High-res Image Gene #79: '21q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'21q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.02 (Fisher's exact test), Q value = 0.15

Table S171.  Gene #79: '21q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 506 358 119 77
21Q LOSS MUTATED 72 65 30 9
21Q LOSS WILD-TYPE 434 293 89 68

Figure S171.  Get High-res Image Gene #79: '21q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'21q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0378 (Fisher's exact test), Q value = 0.22

Table S172.  Gene #79: '21q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 889 22
21Q LOSS MUTATED 147 8
21Q LOSS WILD-TYPE 742 14

Figure S172.  Get High-res Image Gene #79: '21q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'21q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0149 (Fisher's exact test), Q value = 0.12

Table S173.  Gene #79: '21q loss' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
21Q LOSS MUTATED 0 143 21 2 2 7 1 3
21Q LOSS WILD-TYPE 1 625 180 4 7 23 16 43

Figure S173.  Get High-res Image Gene #79: '21q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'21q loss' versus 'RACE'

P value = 0.0216 (Fisher's exact test), Q value = 0.15

Table S174.  Gene #79: '21q loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
21Q LOSS MUTATED 0 17 35 109
21Q LOSS WILD-TYPE 1 43 146 635

Figure S174.  Get High-res Image Gene #79: '21q loss' versus Clinical Feature #11: 'RACE'

'22q loss' versus 'RADIATION_THERAPY'

P value = 0.0082 (Fisher's exact test), Q value = 0.086

Table S175.  Gene #80: '22q loss' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients NO YES
ALL 437 547
22Q LOSS MUTATED 176 267
22Q LOSS WILD-TYPE 261 280

Figure S175.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #8: 'RADIATION_THERAPY'

'22q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00018 (Fisher's exact test), Q value = 0.0052

Table S176.  Gene #80: '22q loss' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
22Q LOSS MUTATED 0 357 88 2 3 19 1 11
22Q LOSS WILD-TYPE 1 411 113 4 6 11 16 35

Figure S176.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'xp loss' versus 'YEARS_TO_BIRTH'

P value = 0.0062 (Wilcoxon-test), Q value = 0.071

Table S177.  Gene #81: 'xp loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1064 58.6 (13.2)
XP LOSS MUTATED 188 56.1 (13.2)
XP LOSS WILD-TYPE 876 59.2 (13.1)

Figure S177.  Get High-res Image Gene #81: 'xp loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'xp loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0424 (Fisher's exact test), Q value = 0.24

Table S178.  Gene #81: 'xp loss' versus Clinical Feature #9: '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 1 768 201 6 9 30 17 46
XP LOSS MUTATED 0 154 21 0 0 6 3 7
XP LOSS WILD-TYPE 1 614 180 6 9 24 14 39

Figure S178.  Get High-res Image Gene #81: 'xp loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'xp loss' versus 'RACE'

P value = 0.00835 (Fisher's exact test), Q value = 0.086

Table S179.  Gene #81: 'xp loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 744
XP LOSS MUTATED 0 17 42 116
XP LOSS WILD-TYPE 1 43 139 628

Figure S179.  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/22531238/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BRCA-TP/22506573/BRCA-TP.merged_data.txt

  • Number of patients = 1079

  • 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)
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