Correlation between copy number variations of arm-level result and selected clinical features
Breast Invasive Carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1T72GK3
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1T72GK3
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 1080 patients, 188 significant findings detected with Q value < 0.25.

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

  • 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 'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE',  'NUMBER_OF_LYMPH_NODES', and 'RACE'.

  • 4p gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 4q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 5p gain cnv correlated to '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 'GENDER' and 'HISTOLOGICAL_TYPE'.

  • 7q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 8p gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 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 'HISTOLOGICAL_TYPE' and 'NUMBER_OF_LYMPH_NODES'.

  • 11q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 12p gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 12q gain cnv correlated to 'PATHOLOGY_N_STAGE',  'GENDER',  '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 'YEARS_TO_BIRTH',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • 16q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 17p gain cnv correlated to 'PATHOLOGY_T_STAGE',  '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 'NUMBER_OF_LYMPH_NODES'.

  • 19q gain cnv correlated to 'PATHOLOGIC_STAGE' and '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 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.

  • 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'.

  • 2p loss cnv correlated to 'PATHOLOGY_M_STAGE'.

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

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

  • 6p loss cnv correlated to 'YEARS_TO_BIRTH'.

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

  • 7p loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 7q loss cnv correlated to 'HISTOLOGICAL_TYPE'.

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

  • 8q loss cnv correlated to 'RACE'.

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

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

  • 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', and 'HISTOLOGICAL_TYPE'.

  • 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' and 'RACE'.

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

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

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

Results
Overview of the results

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

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		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 243 (22%) 837 0.0244
(0.175) 		9.17e-05
(0.00291) 		8e-05
(0.00281) 		2e-05
(0.000937) 		0.00258
(0.0353) 		0.308
(0.687) 		1
(1.00) 		0.814
(0.969) 		0.349
(0.731) 		0.000334
(0.00782) 		0.908
(1.00) 		0.841
(0.98)
18p loss 320 (30%) 760 6.39e-06
(0.000518) 		0.00195
(0.03) 		0.0396
(0.227) 		0.00245
(0.0349) 		0.336
(0.723) 		1
(1.00) 		1
(1.00) 		0.668
(0.91) 		0.0023
(0.0333) 		0.152
(0.49) 		0.0432
(0.234) 		1
(1.00)
3p loss 186 (17%) 894 0.79
(0.963) 		0.0864
(0.363) 		0.721
(0.93) 		0.00147
(0.0237) 		0.998
(1.00) 		1
(1.00) 		0.238
(0.631) 		0.0373
(0.218) 		0.0316
(0.207) 		0.398
(0.76) 		0.0329
(0.21) 		0.0317
(0.207)
9p loss 313 (29%) 767 0.0626
(0.296) 		0.534
(0.837) 		0.00255
(0.0353) 		0.00036
(0.00824) 		0.00907
(0.0923) 		0.0551
(0.277) 		0.0474
(0.248) 		0.943
(1.00) 		1e-05
(0.000518) 		0.135
(0.47) 		0.248
(0.635) 		0.47
(0.8)
11p loss 275 (25%) 805 0.358
(0.739) 		0.709
(0.929) 		0.0167
(0.138) 		0.0132
(0.118) 		0.0707
(0.322) 		0.809
(0.969) 		1
(1.00) 		0.236
(0.631) 		0.0415
(0.23) 		0.0494
(0.257) 		0.00039
(0.00872) 		0.0359
(0.216)
12q loss 131 (12%) 949 0.636
(0.897) 		0.00637
(0.0729) 		0.22
(0.617) 		0.00369
(0.0466) 		0.724
(0.932) 		1
(1.00) 		1
(1.00) 		0.0199
(0.152) 		3e-05
(0.00134) 		0.147
(0.482) 		0.0016
(0.025) 		0.808
(0.969)
21q loss 180 (17%) 900 0.785
(0.963) 		0.348
(0.731) 		0.01
(0.0989) 		0.193
(0.564) 		0.0279
(0.192) 		0.0385
(0.223) 		0.235
(0.631) 		0.392
(0.756) 		0.00686
(0.0767) 		0.193
(0.564) 		0.0252
(0.18) 		0.663
(0.91)
3q gain 212 (20%) 868 0.779
(0.962) 		0.59
(0.873) 		0.292
(0.67) 		0.0351
(0.213) 		0.34
(0.73) 		0.793
(0.963) 		0.479
(0.8) 		0.871
(0.988) 		1e-05
(0.000518) 		0.00954
(0.0948) 		0.0091
(0.0923) 		0.679
(0.91)
12q gain 191 (18%) 889 0.332
(0.717) 		0.109
(0.41) 		0.477
(0.8) 		0.0565
(0.279) 		0.034
(0.212) 		0.576
(0.862) 		0.0448
(0.238) 		0.735
(0.941) 		0.0171
(0.139) 		0.022
(0.16) 		0.789
(0.963) 		0.382
(0.754)
18p gain 177 (16%) 903 0.482
(0.8) 		0.454
(0.791) 		0.0645
(0.301) 		0.328
(0.713) 		0.021
(0.158) 		0.778
(0.962) 		0.428
(0.779) 		0.293
(0.671) 		0.00078
(0.014) 		0.0104
(0.1) 		0.00015
(0.0041) 		0.184
(0.553)
5q loss 228 (21%) 852 0.922
(1.00) 		0.000147
(0.0041) 		0.116
(0.428) 		0.00114
(0.019) 		0.523
(0.833) 		1
(1.00) 		0.478
(0.8) 		0.691
(0.915) 		1e-05
(0.000518) 		0.0912
(0.377) 		1e-05
(0.000518) 		0.428
(0.779)
9q loss 283 (26%) 797 0.642
(0.901) 		0.482
(0.8) 		0.136
(0.471) 		0.00889
(0.0921) 		0.0951
(0.39) 		0.328
(0.713) 		0.018
(0.143) 		0.334
(0.719) 		1e-05
(0.000518) 		0.997
(1.00) 		0.0402
(0.227) 		0.453
(0.791)
14q loss 266 (25%) 814 0.0408
(0.228) 		0.688
(0.915) 		0.897
(1.00) 		0.0271
(0.188) 		0.205
(0.588) 		0.452
(0.791) 		0.313
(0.693) 		0.366
(0.744) 		1e-05
(0.000518) 		0.17
(0.525) 		9e-05
(0.00291) 		0.347
(0.731)
18q loss 321 (30%) 759 0.00788
(0.084) 		0.011
(0.101) 		0.0608
(0.295) 		0.0153
(0.13) 		0.0749
(0.337) 		1
(1.00) 		1
(1.00) 		0.252
(0.637) 		0.00107
(0.0185) 		0.291
(0.67) 		0.193
(0.564) 		0.721
(0.93)
20q loss 55 (5%) 1025 0.153
(0.49) 		0.0343
(0.212) 		0.579
(0.865) 		0.0428
(0.234) 		0.946
(1.00) 		0.306
(0.686) 		1
(1.00) 		0.885
(0.998) 		0.0345
(0.212) 		0.429
(0.779) 		0.0218
(0.16) 		0.135
(0.47)
1q gain 706 (65%) 374 0.613
(0.882) 		0.473
(0.8) 		0.0197
(0.152) 		0.00033
(0.00782) 		0.372
(0.746) 		0.653
(0.909) 		0.761
(0.952) 		0.891
(1.00) 		0.00064
(0.0117) 		0.555
(0.852) 		0.099
(0.393) 		0.0862
(0.363)
2p gain 123 (11%) 957 0.459
(0.795) 		0.271
(0.653) 		0.855
(0.983) 		0.399
(0.76) 		0.968
(1.00) 		1
(1.00) 		0.38
(0.754) 		0.347
(0.731) 		1e-05
(0.000518) 		0.759
(0.952) 		0.00061
(0.0115) 		0.0171
(0.139)
5p gain 316 (29%) 764 0.0261
(0.184) 		0.234
(0.631) 		0.856
(0.983) 		0.562
(0.852) 		0.0108
(0.1) 		1
(1.00) 		0.348
(0.731) 		0.39
(0.756) 		0.0281
(0.192) 		0.854
(0.983) 		0.164
(0.511) 		1
(1.00)
5q gain 212 (20%) 868 0.617
(0.882) 		0.013
(0.117) 		0.86
(0.983) 		0.177
(0.54) 		0.186
(0.557) 		0.0996
(0.393) 		1
(1.00) 		0.287
(0.665) 		0.0431
(0.234) 		0.678
(0.91) 		0.00198
(0.03) 		1
(1.00)
16p gain 464 (43%) 616 0.485
(0.801) 		0.0398
(0.227) 		0.45
(0.791) 		0.923
(1.00) 		0.369
(0.744) 		1
(1.00) 		0.381
(0.754) 		0.792
(0.963) 		0.0197
(0.152) 		0.595
(0.875) 		0.0371
(0.218) 		0.0985
(0.393)
17p gain 107 (10%) 973 0.301
(0.678) 		0.895
(1.00) 		0.149
(0.486) 		0.0398
(0.227) 		0.0989
(0.393) 		0.489
(0.804) 		0.000465
(0.0102) 		0.0406
(0.228) 		0.189
(0.563) 		0.858
(0.983) 		0.591
(0.873) 		0.788
(0.963)
20p gain 416 (39%) 664 0.407
(0.761) 		0.319
(0.7) 		0.407
(0.761) 		0.159
(0.504) 		0.00794
(0.084) 		0.663
(0.91) 		0.014
(0.122) 		1
(1.00) 		1e-05
(0.000518) 		0.613
(0.882) 		0.761
(0.952) 		0.401
(0.76)
20q gain 451 (42%) 629 0.61
(0.882) 		0.816
(0.969) 		0.711
(0.929) 		0.00812
(0.085) 		0.0339
(0.212) 		0.832
(0.973) 		0.138
(0.474) 		0.791
(0.963) 		1e-05
(0.000518) 		0.284
(0.661) 		0.408
(0.761) 		0.186
(0.557)
21q gain 196 (18%) 884 0.0349
(0.213) 		0.0632
(0.296) 		0.653
(0.909) 		0.572
(0.861) 		0.661
(0.91) 		1
(1.00) 		1
(1.00) 		0.0926
(0.381) 		1e-05
(0.000518) 		0.524
(0.835) 		0.0328
(0.21) 		0.388
(0.756)
4p loss 353 (33%) 727 0.557
(0.852) 		0.175
(0.537) 		0.56
(0.852) 		0.0107
(0.1) 		0.516
(0.825) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1e-05
(0.000518) 		0.768
(0.955) 		0.00294
(0.0391) 		0.603
(0.882)
4q loss 312 (29%) 768 0.788
(0.963) 		0.857
(0.983) 		0.742
(0.941) 		0.0227
(0.165) 		0.779
(0.962) 		0.815
(0.969) 		1
(1.00) 		1
(1.00) 		2e-05
(0.000937) 		0.811
(0.969) 		0.00945
(0.0948) 		0.856
(0.983)
5p loss 140 (13%) 940 0.696
(0.919) 		0.00326
(0.0422) 		0.763
(0.953) 		0.0217
(0.16) 		0.936
(1.00) 		1
(1.00) 		1
(1.00) 		0.847
(0.983) 		1e-05
(0.000518) 		0.316
(0.696) 		0.0517
(0.263) 		0.466
(0.799)
10p loss 173 (16%) 907 0.0313
(0.207) 		0.915
(1.00) 		0.0854
(0.363) 		0.00508
(0.0602) 		0.197
(0.571) 		1
(1.00) 		0.232
(0.631) 		1
(1.00) 		0.00152
(0.0241) 		0.266
(0.652) 		0.509
(0.82) 		0.498
(0.81)
10q loss 229 (21%) 851 0.0366
(0.217) 		0.529
(0.837) 		0.3
(0.678) 		0.0079
(0.084) 		0.144
(0.481) 		0.798
(0.964) 		0.478
(0.8) 		1
(1.00) 		0.00053
(0.0111) 		0.369
(0.744) 		0.0657
(0.305) 		0.108
(0.408)
15q loss 320 (30%) 760 0.262
(0.649) 		0.761
(0.952) 		0.368
(0.744) 		0.00257
(0.0353) 		0.0259
(0.184) 		1
(1.00) 		0.757
(0.952) 		0.669
(0.91) 		5e-05
(0.00205) 		0.0808
(0.355) 		0.303
(0.682) 		0.473
(0.8)
17p loss 579 (54%) 501 0.23
(0.631) 		0.0297
(0.2) 		0.275
(0.656) 		0.00482
(0.0578) 		0.795
(0.963) 		1
(1.00) 		0.244
(0.631) 		0.395
(0.758) 		0.0155
(0.13) 		0.915
(1.00) 		0.108
(0.408) 		1
(1.00)
17q loss 275 (25%) 805 0.7
(0.923) 		0.129
(0.459) 		0.952
(1.00) 		0.663
(0.91) 		0.152
(0.49) 		1
(1.00) 		0.0441
(0.236) 		0.765
(0.954) 		6e-05
(0.00236) 		0.264
(0.652) 		0.0027
(0.0364) 		1
(1.00)
19p loss 193 (18%) 887 0.35
(0.731) 		0.022
(0.16) 		0.888
(0.999) 		0.438
(0.785) 		0.351
(0.731) 		0.268
(0.652) 		0.458
(0.795) 		0.933
(1.00) 		1e-05
(0.000518) 		0.441
(0.789) 		0.00051
(0.0109) 		0.387
(0.756)
1p gain 206 (19%) 874 0.675
(0.91) 		0.0507
(0.26) 		0.438
(0.785) 		0.103
(0.401) 		0.534
(0.837) 		0.782
(0.962) 		0.709
(0.929) 		0.742
(0.941) 		0.0002
(0.00518) 		0.226
(0.629) 		0.0177
(0.142) 		0.407
(0.761)
2q gain 73 (7%) 1007 0.782
(0.962) 		0.609
(0.882) 		0.492
(0.807) 		0.373
(0.746) 		0.852
(0.983) 		1
(1.00) 		1
(1.00) 		0.294
(0.672) 		0.00057
(0.0112) 		0.552
(0.851) 		0.0436
(0.234) 		0.103
(0.401)
6p gain 209 (19%) 871 0.251
(0.637) 		0.835
(0.976) 		0.672
(0.91) 		0.0819
(0.358) 		0.417
(0.773) 		1
(1.00) 		0.48
(0.8) 		0.0707
(0.322) 		9e-05
(0.00291) 		0.145
(0.481) 		0.0108
(0.1) 		0.531
(0.837)
6q gain 150 (14%) 930 0.179
(0.543) 		0.789
(0.963) 		0.758
(0.952) 		0.119
(0.433) 		0.0726
(0.329) 		0.757
(0.952) 		1
(1.00) 		0.638
(0.899) 		0.00012
(0.00347) 		0.032
(0.207) 		0.189
(0.563) 		0.47
(0.8)
7p gain 309 (29%) 771 0.685
(0.913) 		0.136
(0.47) 		0.672
(0.91) 		0.715
(0.93) 		0.782
(0.962) 		0.634
(0.896) 		0.0463
(0.245) 		0.279
(0.661) 		0.0181
(0.143) 		0.859
(0.983) 		0.388
(0.756) 		0.586
(0.869)
8q gain 529 (49%) 551 0.465
(0.799) 		0.881
(0.995) 		0.535
(0.837) 		0.477
(0.8) 		0.293
(0.671) 		0.83
(0.973) 		0.256
(0.64) 		0.117
(0.43) 		1e-05
(0.000518) 		0.721
(0.93) 		0.0155
(0.13) 		0.142
(0.48)
10p gain 214 (20%) 866 0.892
(1.00) 		0.732
(0.941) 		0.37
(0.744) 		0.134
(0.469) 		0.209
(0.595) 		0.104
(0.402) 		1
(1.00) 		0.745
(0.941) 		1e-05
(0.000518) 		0.365
(0.744) 		0.00062
(0.0115) 		1
(1.00)
11p gain 138 (13%) 942 0.892
(1.00) 		0.692
(0.916) 		0.495
(0.808) 		0.867
(0.986) 		0.224
(0.627) 		0.516
(0.825) 		0.658
(0.91) 		0.433
(0.784) 		0.014
(0.122) 		0.00784
(0.084) 		0.659
(0.91) 		0.329
(0.713)
18q gain 153 (14%) 927 0.46
(0.795) 		0.61
(0.882) 		0.243
(0.631) 		0.142
(0.48) 		0.154
(0.49) 		0.761
(0.952) 		0.393
(0.756) 		0.852
(0.983) 		0.00667
(0.0754) 		0.209
(0.595) 		0.0379
(0.221) 		0.346
(0.731)
19q gain 223 (21%) 857 0.531
(0.837) 		0.255
(0.64) 		0.0473
(0.248) 		0.495
(0.808) 		0.0829
(0.361) 		0.0632
(0.296) 		0.283
(0.661) 		0.809
(0.969) 		0.144
(0.481) 		0.0079
(0.084) 		0.992
(1.00) 		0.69
(0.915)
22q gain 99 (9%) 981 0.612
(0.882) 		0.65
(0.909) 		0.154
(0.49) 		0.0498
(0.258) 		0.329
(0.713) 		0.714
(0.93) 		1
(1.00) 		0.821
(0.969) 		0.00032
(0.00782) 		0.161
(0.504) 		0.033
(0.21) 		1
(1.00)
xp gain 151 (14%) 929 0.867
(0.986) 		0.0141
(0.122) 		0.574
(0.861) 		0.224
(0.627) 		0.866
(0.986) 		0.353
(0.732) 		1
(1.00) 		0.404
(0.76) 		0.0001
(0.00307) 		0.717
(0.93) 		0.0501
(0.258) 		0.466
(0.799)
3q loss 103 (10%) 977 0.275
(0.656) 		0.571
(0.86) 		0.46
(0.795) 		0.00416
(0.0512) 		0.804
(0.967) 		1
(1.00) 		0.618
(0.883) 		0.57
(0.86) 		0.234
(0.631) 		0.435
(0.785) 		0.283
(0.661) 		0.0265
(0.185)
6q loss 276 (26%) 804 0.27
(0.653) 		0.00128
(0.021) 		0.86
(0.983) 		0.404
(0.76) 		0.47
(0.8) 		0.81
(0.969) 		0.315
(0.696) 		0.00379
(0.0472) 		0.405
(0.761) 		0.27
(0.653) 		0.551
(0.851) 		0.575
(0.861)
8p loss 399 (37%) 681 0.103
(0.401) 		0.148
(0.483) 		0.998
(1.00) 		0.243
(0.631) 		0.427
(0.779) 		0.66
(0.91) 		0.551
(0.851) 		1
(1.00) 		8e-05
(0.00281) 		0.922
(1.00) 		0.0151
(0.129) 		0.404
(0.76)
12p loss 151 (14%) 929 0.997
(1.00) 		0.309
(0.688) 		0.272
(0.654) 		0.00523
(0.0613) 		0.769
(0.956) 		1
(1.00) 		0.679
(0.91) 		0.45
(0.791) 		4e-05
(0.00171) 		0.481
(0.8) 		0.0964
(0.392) 		0.64
(0.9)
16p loss 173 (16%) 907 0.192
(0.564) 		0.987
(1.00) 		0.475
(0.8) 		0.988
(1.00) 		0.16
(0.504) 		0.154
(0.49) 		1
(1.00) 		0.476
(0.8) 		0.112
(0.417) 		0.0297
(0.2) 		0.0302
(0.202) 		0.825
(0.972)
16q loss 593 (55%) 487 0.277
(0.658) 		0.00101
(0.0177) 		0.616
(0.882) 		0.47
(0.8) 		0.146
(0.481) 		0.128
(0.456) 		0.393
(0.756) 		0.47
(0.8) 		1e-05
(0.000518) 		0.0689
(0.318) 		0.378
(0.754) 		1
(1.00)
19q loss 161 (15%) 919 0.112
(0.417) 		0.485
(0.801) 		0.49
(0.805) 		0.48
(0.8) 		0.139
(0.475) 		0.121
(0.437) 		0.403
(0.76) 		0.718
(0.93) 		1e-05
(0.000518) 		0.448
(0.791) 		0.0109
(0.1) 		1
(1.00)
22q loss 482 (45%) 598 0.322
(0.705) 		0.454
(0.791) 		0.689
(0.915) 		0.27
(0.653) 		0.352
(0.731) 		0.829
(0.973) 		0.39
(0.756) 		0.0106
(0.1) 		7e-05
(0.00265) 		0.267
(0.652) 		0.427
(0.779) 		0.744
(0.941)
xp loss 190 (18%) 890 0.459
(0.795) 		0.00363
(0.0463) 		0.545
(0.847) 		0.0758
(0.339) 		0.735
(0.941) 		0.275
(0.656) 		0.452
(0.791) 		0.611
(0.882) 		0.0528
(0.268) 		0.366
(0.744) 		0.0106
(0.1) 		1
(1.00)
3p gain 135 (12%) 945 0.556
(0.852) 		0.281
(0.661) 		0.248
(0.635) 		0.0564
(0.279) 		0.342
(0.731) 		0.535
(0.837) 		1
(1.00) 		0.771
(0.957) 		0.00022
(0.00555) 		0.23
(0.631) 		0.584
(0.868) 		0.799
(0.964)
4p gain 76 (7%) 1004 0.275
(0.656) 		0.817
(0.969) 		0.176
(0.539) 		0.0864
(0.363) 		0.671
(0.91) 		0.68
(0.91) 		0.204
(0.588) 		0.528
(0.837) 		0.00208
(0.031) 		0.744
(0.941) 		0.512
(0.823) 		0.743
(0.941)
4q gain 73 (7%) 1007 0.0704
(0.322) 		0.873
(0.989) 		0.497
(0.81) 		0.246
(0.633) 		0.687
(0.915) 		0.673
(0.91) 		0.57
(0.86) 		0.797
(0.964) 		0.00317
(0.0416) 		0.851
(0.983) 		0.389
(0.756) 		0.737
(0.941)
7q gain 266 (25%) 814 0.717
(0.93) 		0.986
(1.00) 		0.298
(0.675) 		0.243
(0.631) 		0.422
(0.779) 		0.445
(0.791) 		0.182
(0.549) 		0.65
(0.909) 		0.0304
(0.202) 		0.499
(0.811) 		0.0624
(0.296) 		0.446
(0.791)
8p gain 290 (27%) 790 0.701
(0.924) 		0.885
(0.998) 		0.526
(0.836) 		0.817
(0.969) 		0.553
(0.851) 		0.334
(0.719) 		0.322
(0.705) 		0.605
(0.882) 		0.0429
(0.234) 		0.629
(0.895) 		0.133
(0.468) 		0.852
(0.983)
10q gain 124 (11%) 956 0.736
(0.941) 		0.549
(0.851) 		0.707
(0.928) 		0.361
(0.74) 		0.615
(0.882) 		0.745
(0.941) 		1
(1.00) 		0.92
(1.00) 		0.0011
(0.0187) 		0.355
(0.733) 		0.0853
(0.363) 		0.609
(0.882)
11q gain 94 (9%) 986 0.219
(0.617) 		0.819
(0.969) 		0.297
(0.673) 		0.558
(0.852) 		0.602
(0.882) 		1
(1.00) 		1
(1.00) 		0.23
(0.631) 		0.00057
(0.0112) 		0.122
(0.439) 		0.176
(0.539) 		0.382
(0.754)
12p gain 229 (21%) 851 0.526
(0.836) 		0.531
(0.837) 		0.66
(0.91) 		0.0766
(0.339) 		0.17
(0.525) 		0.799
(0.964) 		0.145
(0.481) 		0.426
(0.779) 		0.00426
(0.0518) 		0.616
(0.882) 		0.502
(0.812) 		0.234
(0.631)
13q gain 92 (9%) 988 0.821
(0.969) 		0.509
(0.82) 		0.68
(0.91) 		0.26
(0.645) 		0.541
(0.844) 		1
(1.00) 		1
(1.00) 		0.296
(0.673) 		0.0006
(0.0115) 		0.866
(0.986) 		0.742
(0.941) 		0.139
(0.475)
14q gain 143 (13%) 937 0.585
(0.868) 		0.142
(0.48) 		0.25
(0.637) 		0.253
(0.639) 		0.125
(0.449) 		0.343
(0.731) 		1
(1.00) 		0.39
(0.756) 		0.0173
(0.14) 		0.0838
(0.362) 		0.831
(0.973) 		0.219
(0.617)
15q gain 87 (8%) 993 0.666
(0.91) 		0.959
(1.00) 		0.71
(0.929) 		0.948
(1.00) 		0.942
(1.00) 		0.426
(0.779) 		1
(1.00) 		0.64
(0.9) 		0.00211
(0.031) 		0.876
(0.992) 		0.243
(0.631) 		1
(1.00)
16q gain 142 (13%) 938 0.0574
(0.281) 		0.666
(0.91) 		0.284
(0.661) 		0.384
(0.755) 		0.101
(0.397) 		0.516
(0.825) 		0.0608
(0.295) 		0.625
(0.889) 		0.036
(0.216) 		0.225
(0.627) 		0.583
(0.868) 		0.152
(0.49)
17q gain 217 (20%) 863 0.091
(0.377) 		0.836
(0.976) 		0.878
(0.993) 		0.396
(0.758) 		0.767
(0.955) 		0.791
(0.963) 		0.000554
(0.0112) 		0.193
(0.564) 		0.107
(0.408) 		0.346
(0.731) 		0.854
(0.983) 		0.544
(0.847)
19p gain 190 (18%) 890 0.574
(0.861) 		0.373
(0.746) 		0.265
(0.652) 		0.168
(0.522) 		0.227
(0.629) 		0.154
(0.49) 		0.241
(0.631) 		0.442
(0.789) 		0.0974
(0.393) 		0.0137
(0.121) 		0.632
(0.896) 		0.832
(0.973)
xq gain 136 (13%) 944 0.485
(0.801) 		0.057
(0.28) 		0.237
(0.631) 		0.307
(0.686) 		0.804
(0.967) 		0.195
(0.566) 		1
(1.00) 		0.623
(0.888) 		0.00016
(0.00426) 		0.556
(0.852) 		0.192
(0.564) 		0.611
(0.882)
2p loss 182 (17%) 898 0.349
(0.731) 		0.409
(0.761) 		0.316
(0.696) 		0.426
(0.779) 		0.0537
(0.271) 		0.0205
(0.155) 		0.437
(0.785) 		0.666
(0.91) 		0.251
(0.637) 		0.446
(0.791) 		0.266
(0.652) 		0.108
(0.408)
6p loss 187 (17%) 893 0.795
(0.963) 		0.0411
(0.228) 		0.984
(1.00) 		0.39
(0.756) 		0.941
(1.00) 		1
(1.00) 		0.703
(0.925) 		0.146
(0.481) 		0.209
(0.595) 		0.852
(0.983) 		0.368
(0.744) 		0.662
(0.91)
7p loss 112 (10%) 968 0.551
(0.851) 		0.562
(0.852) 		0.18
(0.545) 		0.241
(0.631) 		0.0995
(0.393) 		0.16
(0.504) 		1
(1.00) 		0.392
(0.756) 		0.00011
(0.00328) 		0.241
(0.631) 		0.201
(0.58) 		0.418
(0.773)
7q loss 120 (11%) 960 0.106
(0.406) 		0.145
(0.481) 		0.593
(0.874) 		0.361
(0.74) 		0.415
(0.771) 		0.501
(0.812) 		0.634
(0.896) 		0.255
(0.64) 		0.0367
(0.217) 		0.821
(0.969) 		0.651
(0.909) 		0.113
(0.418)
8q loss 93 (9%) 987 0.434
(0.785) 		0.242
(0.631) 		0.861
(0.983) 		0.615
(0.882) 		0.561
(0.852) 		0.247
(0.635) 		0.614
(0.882) 		0.212
(0.6) 		0.593
(0.874) 		0.716
(0.93) 		0.0189
(0.148) 		0.774
(0.959)
11q loss 365 (34%) 715 0.712
(0.93) 		0.809
(0.969) 		0.256
(0.64) 		0.116
(0.428) 		0.0628
(0.296) 		0.818
(0.969) 		0.12
(0.435) 		0.585
(0.868) 		0.521
(0.832) 		0.283
(0.661) 		0.00532
(0.0616) 		1
(1.00)
13q loss 433 (40%) 647 0.118
(0.43) 		0.281
(0.661) 		0.681
(0.91) 		0.28
(0.661) 		0.613
(0.882) 		1
(1.00) 		1
(1.00) 		0.424
(0.779) 		1e-05
(0.000518) 		0.558
(0.852) 		0.0627
(0.296) 		0.239
(0.631)
20p loss 93 (9%) 987 0.133
(0.468) 		0.0836
(0.362) 		0.676
(0.91) 		0.0761
(0.339) 		0.853
(0.983) 		0.0334
(0.211) 		1
(1.00) 		0.0842
(0.362) 		0.0627
(0.296) 		0.743
(0.941) 		0.0982
(0.393) 		0.365
(0.744)
9p gain 141 (13%) 939 0.656
(0.91) 		0.97
(1.00) 		0.132
(0.467) 		0.123
(0.44) 		0.241
(0.631) 		1
(1.00) 		0.384
(0.755) 		0.504
(0.814) 		0.194
(0.564) 		0.668
(0.91) 		0.447
(0.791) 		1
(1.00)
9q gain 119 (11%) 961 0.242
(0.631) 		0.643
(0.901) 		0.227
(0.629) 		0.235
(0.631) 		0.568
(0.859) 		1
(1.00) 		0.382
(0.754) 		0.54
(0.843) 		0.0894
(0.374) 		0.827
(0.973) 		0.31
(0.69) 		1
(1.00)
1q loss 52 (5%) 1028 0.495
(0.808) 		0.465
(0.799) 		0.972
(1.00) 		0.402
(0.76) 		0.163
(0.508) 		1
(1.00) 		1
(1.00) 		0.438
(0.785) 		0.259
(0.645) 		0.296
(0.673) 		0.74
(0.941) 		0.68
(0.91)
2q loss 211 (20%) 869 0.245
(0.632) 		0.631
(0.896) 		0.291
(0.67) 		0.286
(0.664) 		0.0774
(0.341) 		0.0555
(0.277) 		1
(1.00) 		0.682
(0.911) 		0.0962
(0.392) 		0.359
(0.74) 		0.487
(0.803) 		0.0911
(0.377)
xq loss 190 (18%) 890 0.916
(1.00) 		0.108
(0.408) 		0.345
(0.731) 		0.0744
(0.336) 		0.445
(0.791) 		0.268
(0.652) 		0.452
(0.791) 		0.398
(0.76) 		0.146
(0.481) 		0.351
(0.731) 		0.0999
(0.393) 		1
(1.00)
'1p gain' versus 'HISTOLOGICAL_TYPE'

P value = 2e-04 (Fisher's exact test), Q value = 0.0052

Table S1.  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 1 770 200 6 9 29 17 47
1P GAIN MUTATED 0 161 19 3 4 6 1 12
1P GAIN WILD-TYPE 1 609 181 3 5 23 16 35

Figure S1.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'1p gain' versus 'RACE'

P value = 0.0177 (Fisher's exact test), Q value = 0.14

Table S2.  Gene #1: '1p gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
1P GAIN MUTATED 1 7 46 142
1P GAIN WILD-TYPE 0 53 135 603

Figure S2.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #11: 'RACE'

'1q gain' versus 'PATHOLOGIC_STAGE'

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

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 TIS STAGE X
ALL 89 85 6 6 353 252 2 154 29 65 20 1 13
1Q GAIN MUTATED 48 47 2 6 242 168 1 96 23 48 12 1 8
1Q GAIN WILD-TYPE 41 38 4 0 111 84 1 58 6 17 8 0 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 = 0.00033 (Fisher's exact test), Q value = 0.0078

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

nPatients T1 T2 T3 T4
ALL 276 624 136 40
1Q GAIN MUTATED 153 433 88 30
1Q GAIN WILD-TYPE 123 191 48 10

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

'1q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00064 (Fisher's exact test), Q value = 0.012

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 1 770 200 6 9 29 17 47
1Q GAIN MUTATED 1 485 156 4 4 16 8 32
1Q GAIN WILD-TYPE 0 285 44 2 5 13 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 = 0.00052

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 1 770 200 6 9 29 17 47
2P GAIN MUTATED 1 109 5 2 3 0 0 3
2P GAIN WILD-TYPE 0 661 195 4 6 29 17 44

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

'2p gain' versus 'RACE'

P value = 0.00061 (Fisher's exact test), Q value = 0.012

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 60 181 745
2P GAIN MUTATED 1 10 32 69
2P GAIN WILD-TYPE 0 50 149 676

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

'2p gain' versus 'ETHNICITY'

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

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

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 39 875
2P GAIN MUTATED 0 105
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 = 0.00057 (Fisher's exact test), Q value = 0.011

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 1 770 200 6 9 29 17 47
2Q GAIN MUTATED 0 64 3 0 3 0 0 3
2Q GAIN WILD-TYPE 1 706 197 6 6 29 17 44

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

'2q gain' versus 'RACE'

P value = 0.0436 (Fisher's exact test), Q value = 0.23

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 60 181 745
2Q GAIN MUTATED 0 8 17 42
2Q GAIN WILD-TYPE 1 52 164 703

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

'3p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00022 (Fisher's exact test), Q value = 0.0056

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 1 770 200 6 9 29 17 47
3P GAIN MUTATED 0 114 7 2 2 4 1 5
3P GAIN WILD-TYPE 1 656 193 4 7 25 16 42

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

'3q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0351 (Fisher's exact test), Q value = 0.21

Table S12.  Gene #6: '3q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
3Q GAIN MUTATED 45 133 21 13
3Q GAIN WILD-TYPE 231 491 115 27

Figure S12.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'3q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00052

Table S13.  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 1 770 200 6 9 29 17 47
3Q GAIN MUTATED 0 180 10 4 4 6 1 7
3Q GAIN WILD-TYPE 1 590 190 2 5 23 16 40

Figure S13.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'3q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00954 (Wilcoxon-test), Q value = 0.095

Table S14.  Gene #6: '3q gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 914 2.4 (4.7)
3Q GAIN MUTATED 176 1.9 (4.0)
3Q GAIN WILD-TYPE 738 2.5 (4.8)

Figure S14.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'3q gain' versus 'RACE'

P value = 0.0091 (Fisher's exact test), Q value = 0.092

Table S15.  Gene #6: '3q gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
3Q GAIN MUTATED 1 13 47 128
3Q GAIN WILD-TYPE 0 47 134 617

Figure S15.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #11: 'RACE'

'4p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00208 (Fisher's exact test), Q value = 0.031

Table S16.  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 1 770 200 6 9 29 17 47
4P GAIN MUTATED 0 59 4 1 3 3 1 5
4P GAIN WILD-TYPE 1 711 196 5 6 26 16 42

Figure S16.  Get High-res Image Gene #7: '4p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'4q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00317 (Fisher's exact test), Q value = 0.042

Table S17.  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 1 770 200 6 9 29 17 47
4Q GAIN MUTATED 0 57 4 2 2 2 1 5
4Q GAIN WILD-TYPE 1 713 196 4 7 27 16 42

Figure S17.  Get High-res Image Gene #8: '4q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'5p gain' versus 'Time to Death'

P value = 0.0261 (logrank test), Q value = 0.18

Table S18.  Gene #9: '5p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1064 147 0.0 - 282.9 (27.9)
5P GAIN MUTATED 312 45 0.0 - 233.6 (23.9)
5P GAIN WILD-TYPE 752 102 0.0 - 282.9 (29.8)

Figure S18.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #1: 'Time to Death'

'5p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0108 (Fisher's exact test), Q value = 0.1

Table S19.  Gene #9: '5p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 507 358 119 77
5P GAIN MUTATED 161 87 45 18
5P GAIN WILD-TYPE 346 271 74 59

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

'5p gain' versus 'HISTOLOGICAL_TYPE'

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

Table S20.  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 1 770 200 6 9 29 17 47
5P GAIN MUTATED 1 229 56 2 7 8 2 11
5P GAIN WILD-TYPE 0 541 144 4 2 21 15 36

Figure S20.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'5q gain' versus 'YEARS_TO_BIRTH'

P value = 0.013 (Wilcoxon-test), Q value = 0.12

Table S21.  Gene #10: '5q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1065 58.6 (13.2)
5Q GAIN MUTATED 209 60.6 (12.5)
5Q GAIN WILD-TYPE 856 58.2 (13.3)

Figure S21.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0431 (Fisher's exact test), Q value = 0.23

Table S22.  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 1 770 200 6 9 29 17 47
5Q GAIN MUTATED 0 141 47 1 6 6 2 9
5Q GAIN WILD-TYPE 1 629 153 5 3 23 15 38

Figure S22.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'5q gain' versus 'RACE'

P value = 0.00198 (Fisher's exact test), Q value = 0.03

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

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
5Q GAIN MUTATED 0 7 20 162
5Q GAIN WILD-TYPE 1 53 161 583

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

'6p gain' versus 'HISTOLOGICAL_TYPE'

P value = 9e-05 (Fisher's exact test), Q value = 0.0029

Table S24.  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 1 770 200 6 9 29 17 47
6P GAIN MUTATED 0 168 20 4 4 3 1 8
6P GAIN WILD-TYPE 1 602 180 2 5 26 16 39

Figure S24.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'6p gain' versus 'RACE'

P value = 0.0108 (Fisher's exact test), Q value = 0.1

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

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
6P GAIN MUTATED 0 8 50 132
6P GAIN WILD-TYPE 1 52 131 613

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

'6q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00012 (Fisher's exact test), Q value = 0.0035

Table S26.  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 1 770 200 6 9 29 17 47
6Q GAIN MUTATED 0 120 14 4 4 3 1 4
6Q GAIN WILD-TYPE 1 650 186 2 5 26 16 43

Figure S26.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'6q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.032 (Wilcoxon-test), Q value = 0.21

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

nPatients Mean (Std.Dev)
ALL 914 2.4 (4.7)
6Q GAIN MUTATED 128 2.4 (5.4)
6Q GAIN WILD-TYPE 786 2.4 (4.5)

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

'7p gain' versus 'GENDER'

P value = 0.0463 (Fisher's exact test), Q value = 0.25

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

nPatients FEMALE MALE
ALL 1068 12
7P GAIN MUTATED 302 7
7P GAIN WILD-TYPE 766 5

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

'7p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0181 (Fisher's exact test), Q value = 0.14

Table S29.  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 1 770 200 6 9 29 17 47
7P GAIN MUTATED 1 237 42 1 5 7 2 14
7P GAIN WILD-TYPE 0 533 158 5 4 22 15 33

Figure S29.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'7q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0304 (Fisher's exact test), Q value = 0.2

Table S30.  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 1 770 200 6 9 29 17 47
7Q GAIN MUTATED 1 203 37 2 5 6 2 10
7Q GAIN WILD-TYPE 0 567 163 4 4 23 15 37

Figure S30.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'8p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0429 (Fisher's exact test), Q value = 0.23

Table S31.  Gene #15: '8p 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 1 770 200 6 9 29 17 47
8P GAIN MUTATED 0 221 39 3 5 8 3 11
8P GAIN WILD-TYPE 1 549 161 3 4 21 14 36

Figure S31.  Get High-res Image Gene #15: '8p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'8q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00052

Table S32.  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 1 770 200 6 9 29 17 47
8Q GAIN MUTATED 1 418 58 5 6 12 4 24
8Q GAIN WILD-TYPE 0 352 142 1 3 17 13 23

Figure S32.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'8q gain' versus 'RACE'

P value = 0.0155 (Fisher's exact test), Q value = 0.13

Table S33.  Gene #16: '8q gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
8Q GAIN MUTATED 1 28 104 340
8Q GAIN WILD-TYPE 0 32 77 405

Figure S33.  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 = 0.00052

Table S34.  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 1 770 200 6 9 29 17 47
10P GAIN MUTATED 0 183 16 4 1 4 0 6
10P GAIN WILD-TYPE 1 587 184 2 8 25 17 41

Figure S34.  Get High-res Image Gene #19: '10p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'10p gain' versus 'RACE'

P value = 0.00062 (Fisher's exact test), Q value = 0.012

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

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
10P GAIN MUTATED 1 11 53 129
10P GAIN WILD-TYPE 0 49 128 616

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

'10q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0011 (Fisher's exact test), Q value = 0.019

Table S36.  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 1 770 200 6 9 29 17 47
10Q GAIN MUTATED 0 104 10 3 1 3 0 3
10Q GAIN WILD-TYPE 1 666 190 3 8 26 17 44

Figure S36.  Get High-res Image Gene #20: '10q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'11p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.014 (Fisher's exact test), Q value = 0.12

Table S37.  Gene #21: '11p 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 1 770 200 6 9 29 17 47
11P GAIN MUTATED 0 113 12 1 2 1 2 7
11P GAIN WILD-TYPE 1 657 188 5 7 28 15 40

Figure S37.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'11p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00784 (Wilcoxon-test), Q value = 0.084

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

nPatients Mean (Std.Dev)
ALL 914 2.4 (4.7)
11P GAIN MUTATED 119 1.7 (3.6)
11P GAIN WILD-TYPE 795 2.5 (4.8)

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

'11q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00057 (Fisher's exact test), Q value = 0.011

Table S39.  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 1 770 200 6 9 29 17 47
11Q GAIN MUTATED 0 77 4 2 1 2 1 7
11Q GAIN WILD-TYPE 1 693 196 4 8 27 16 40

Figure S39.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'12p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00426 (Fisher's exact test), Q value = 0.052

Table S40.  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 1 770 200 6 9 29 17 47
12P GAIN MUTATED 1 181 28 2 2 8 1 5
12P GAIN WILD-TYPE 0 589 172 4 7 21 16 42

Figure S40.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'12q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.034 (Fisher's exact test), Q value = 0.21

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

nPatients N0 N1 N2 N3
ALL 507 358 119 77
12Q GAIN MUTATED 77 60 30 18
12Q GAIN WILD-TYPE 430 298 89 59

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

'12q gain' versus 'GENDER'

P value = 0.0448 (Fisher's exact test), Q value = 0.24

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

nPatients FEMALE MALE
ALL 1068 12
12Q GAIN MUTATED 186 5
12Q GAIN WILD-TYPE 882 7

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

'12q gain' versus 'HISTOLOGICAL_TYPE'

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

Table S43.  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 1 770 200 6 9 29 17 47
12Q GAIN MUTATED 0 150 26 1 0 9 1 3
12Q GAIN WILD-TYPE 1 620 174 5 9 20 16 44

Figure S43.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'12q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.022 (Wilcoxon-test), Q value = 0.16

Table S44.  Gene #24: '12q gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 914 2.4 (4.7)
12Q GAIN MUTATED 154 3.1 (5.2)
12Q GAIN WILD-TYPE 760 2.3 (4.5)

Figure S44.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'13q gain' versus 'HISTOLOGICAL_TYPE'

P value = 6e-04 (Fisher's exact test), Q value = 0.012

Table S45.  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 1 770 200 6 9 29 17 47
13Q GAIN MUTATED 0 75 4 0 3 2 2 6
13Q GAIN WILD-TYPE 1 695 196 6 6 27 15 41

Figure S45.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'14q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0173 (Fisher's exact test), Q value = 0.14

Table S46.  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 1 770 200 6 9 29 17 47
14Q GAIN MUTATED 0 110 15 0 3 8 2 5
14Q GAIN WILD-TYPE 1 660 185 6 6 21 15 42

Figure S46.  Get High-res Image Gene #26: '14q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'15q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00211 (Fisher's exact test), Q value = 0.031

Table S47.  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 1 770 200 6 9 29 17 47
15Q GAIN MUTATED 0 75 3 0 1 1 2 4
15Q GAIN WILD-TYPE 1 695 197 6 8 28 15 43

Figure S47.  Get High-res Image Gene #27: '15q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'16p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0398 (Wilcoxon-test), Q value = 0.23

Table S48.  Gene #28: '16p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1065 58.6 (13.2)
16P GAIN MUTATED 458 59.6 (13.2)
16P GAIN WILD-TYPE 607 57.9 (13.2)

Figure S48.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16p gain' versus 'HISTOLOGICAL_TYPE'

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

Table S49.  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 1 770 200 6 9 29 17 47
16P GAIN MUTATED 1 338 88 2 3 16 2 13
16P GAIN WILD-TYPE 0 432 112 4 6 13 15 34

Figure S49.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'16p gain' versus 'RACE'

P value = 0.0371 (Fisher's exact test), Q value = 0.22

Table S50.  Gene #28: '16p gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
16P GAIN MUTATED 1 23 61 325
16P GAIN WILD-TYPE 0 37 120 420

Figure S50.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #11: 'RACE'

'16q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.036 (Fisher's exact test), Q value = 0.22

Table S51.  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 1 770 200 6 9 29 17 47
16Q GAIN MUTATED 1 111 17 1 3 4 1 4
16Q GAIN WILD-TYPE 0 659 183 5 6 25 16 43

Figure S51.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'17p gain' versus 'PATHOLOGY_T_STAGE'

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

Table S52.  Gene #30: '17p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
17P GAIN MUTATED 23 58 17 9
17P GAIN WILD-TYPE 253 566 119 31

Figure S52.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'17p gain' versus 'GENDER'

P value = 0.000465 (Fisher's exact test), Q value = 0.01

Table S53.  Gene #30: '17p gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1068 12
17P GAIN MUTATED 101 6
17P GAIN WILD-TYPE 967 6

Figure S53.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #7: 'GENDER'

'17p gain' versus 'RADIATION_THERAPY'

P value = 0.0406 (Fisher's exact test), Q value = 0.23

Table S54.  Gene #30: '17p gain' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients NO YES
ALL 429 518
17P GAIN MUTATED 34 62
17P GAIN WILD-TYPE 395 456

Figure S54.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #8: 'RADIATION_THERAPY'

'17q gain' versus 'GENDER'

P value = 0.000554 (Fisher's exact test), Q value = 0.011

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

nPatients FEMALE MALE
ALL 1068 12
17Q GAIN MUTATED 209 8
17Q GAIN WILD-TYPE 859 4

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

'18p gain' versus 'PATHOLOGY_N_STAGE'

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

Table S56.  Gene #32: '18p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 507 358 119 77
18P GAIN MUTATED 101 44 16 13
18P GAIN WILD-TYPE 406 314 103 64

Figure S56.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'18p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00078 (Fisher's exact test), Q value = 0.014

Table S57.  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 1 770 200 6 9 29 17 47
18P GAIN MUTATED 0 145 15 2 2 5 0 7
18P GAIN WILD-TYPE 1 625 185 4 7 24 17 40

Figure S57.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'18p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0104 (Wilcoxon-test), Q value = 0.1

Table S58.  Gene #32: '18p gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 914 2.4 (4.7)
18P GAIN MUTATED 145 2.0 (4.4)
18P GAIN WILD-TYPE 769 2.5 (4.7)

Figure S58.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'18p gain' versus 'RACE'

P value = 0.00015 (Fisher's exact test), Q value = 0.0041

Table S59.  Gene #32: '18p gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
18P GAIN MUTATED 0 7 49 101
18P GAIN WILD-TYPE 1 53 132 644

Figure S59.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #11: 'RACE'

'18q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00667 (Fisher's exact test), Q value = 0.075

Table S60.  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 1 770 200 6 9 29 17 47
18Q GAIN MUTATED 0 126 13 1 1 5 0 6
18Q GAIN WILD-TYPE 1 644 187 5 8 24 17 41

Figure S60.  Get High-res Image Gene #33: '18q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'18q gain' versus 'RACE'

P value = 0.0379 (Fisher's exact test), Q value = 0.22

Table S61.  Gene #33: '18q gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
18Q GAIN MUTATED 0 8 37 92
18Q GAIN WILD-TYPE 1 52 144 653

Figure S61.  Get High-res Image Gene #33: '18q gain' versus Clinical Feature #11: 'RACE'

'19p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0137 (Wilcoxon-test), Q value = 0.12

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

nPatients Mean (Std.Dev)
ALL 914 2.4 (4.7)
19P GAIN MUTATED 170 2.0 (4.7)
19P GAIN WILD-TYPE 744 2.5 (4.7)

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

'19q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0473 (Fisher's exact test), Q value = 0.25

Table S63.  Gene #35: '19q 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 TIS STAGE X
ALL 89 85 6 6 353 252 2 154 29 65 20 1 13
19Q GAIN MUTATED 18 15 2 2 93 44 0 28 8 10 1 0 0
19Q GAIN WILD-TYPE 71 70 4 4 260 208 2 126 21 55 19 1 13

Figure S63.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'19q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0079 (Wilcoxon-test), Q value = 0.084

Table S64.  Gene #35: '19q gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 914 2.4 (4.7)
19Q GAIN MUTATED 195 1.9 (4.2)
19Q GAIN WILD-TYPE 719 2.5 (4.8)

Figure S64.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'20p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00794 (Fisher's exact test), Q value = 0.084

Table S65.  Gene #36: '20p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 507 358 119 77
20P GAIN MUTATED 197 127 61 23
20P GAIN WILD-TYPE 310 231 58 54

Figure S65.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'20p gain' versus 'GENDER'

P value = 0.014 (Fisher's exact test), Q value = 0.12

Table S66.  Gene #36: '20p gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1068 12
20P GAIN MUTATED 407 9
20P GAIN WILD-TYPE 661 3

Figure S66.  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 = 0.00052

Table S67.  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 1 770 200 6 9 29 17 47
20P GAIN MUTATED 0 339 46 2 5 9 1 13
20P GAIN WILD-TYPE 1 431 154 4 4 20 16 34

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

'20q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00812 (Fisher's exact test), Q value = 0.085

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

nPatients T1 T2 T3 T4
ALL 276 624 136 40
20Q GAIN MUTATED 104 278 44 22
20Q GAIN WILD-TYPE 172 346 92 18

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

'20q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0339 (Fisher's exact test), Q value = 0.21

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

nPatients N0 N1 N2 N3
ALL 507 358 119 77
20Q GAIN MUTATED 208 142 64 28
20Q GAIN WILD-TYPE 299 216 55 49

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

'20q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00052

Table S70.  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 1 770 200 6 9 29 17 47
20Q GAIN MUTATED 0 368 50 1 6 9 1 16
20Q GAIN WILD-TYPE 1 402 150 5 3 20 16 31

Figure S70.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'21q gain' versus 'Time to Death'

P value = 0.0349 (logrank test), Q value = 0.21

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

nPatients nDeath Duration Range (Median), Month
ALL 1064 147 0.0 - 282.9 (27.9)
21Q GAIN MUTATED 195 36 0.0 - 282.9 (27.1)
21Q GAIN WILD-TYPE 869 111 0.0 - 281.3 (27.9)

Figure S71.  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 = 0.00052

Table S72.  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 1 770 200 6 9 29 17 47
21Q GAIN MUTATED 0 168 16 2 4 0 1 5
21Q GAIN WILD-TYPE 1 602 184 4 5 29 16 42

Figure S72.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'21q gain' versus 'RACE'

P value = 0.0328 (Fisher's exact test), Q value = 0.21

Table S73.  Gene #38: '21q gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
21Q GAIN MUTATED 1 10 42 121
21Q GAIN WILD-TYPE 0 50 139 624

Figure S73.  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 = 0.0078

Table S74.  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 1 770 200 6 9 29 17 47
22Q GAIN MUTATED 0 81 4 1 2 2 1 8
22Q GAIN WILD-TYPE 1 689 196 5 7 27 16 39

Figure S74.  Get High-res Image Gene #39: '22q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'22q gain' versus 'RACE'

P value = 0.033 (Fisher's exact test), Q value = 0.21

Table S75.  Gene #39: '22q gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
22Q GAIN MUTATED 1 7 21 59
22Q GAIN WILD-TYPE 0 53 160 686

Figure S75.  Get High-res Image Gene #39: '22q gain' versus Clinical Feature #11: 'RACE'

'xp gain' versus 'YEARS_TO_BIRTH'

P value = 0.0141 (Wilcoxon-test), Q value = 0.12

Table S76.  Gene #40: 'xp gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1065 58.6 (13.2)
XP GAIN MUTATED 150 61.0 (12.7)
XP GAIN WILD-TYPE 915 58.2 (13.3)

Figure S76.  Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'xp gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-04 (Fisher's exact test), Q value = 0.0031

Table S77.  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 1 770 200 6 9 29 17 47
XP GAIN MUTATED 1 122 11 3 2 3 3 6
XP GAIN WILD-TYPE 0 648 189 3 7 26 14 41

Figure S77.  Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'xq gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00016 (Fisher's exact test), Q value = 0.0043

Table S78.  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 1 770 200 6 9 29 17 47
XQ GAIN MUTATED 1 112 9 2 1 1 3 6
XQ GAIN WILD-TYPE 0 658 191 4 8 28 14 41

Figure S78.  Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'1p loss' versus 'Time to Death'

P value = 0.0244 (logrank test), Q value = 0.17

Table S79.  Gene #42: '1p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1064 147 0.0 - 282.9 (27.9)
1P LOSS MUTATED 240 44 0.2 - 255.7 (26.0)
1P LOSS WILD-TYPE 824 103 0.0 - 282.9 (28.9)

Figure S79.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #1: 'Time to Death'

'1p loss' versus 'YEARS_TO_BIRTH'

P value = 9.17e-05 (Wilcoxon-test), Q value = 0.0029

Table S80.  Gene #42: '1p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1065 58.6 (13.2)
1P LOSS MUTATED 237 61.4 (13.1)
1P LOSS WILD-TYPE 828 57.8 (13.1)

Figure S80.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'1p loss' versus 'PATHOLOGIC_STAGE'

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

Table S81.  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 TIS STAGE X
ALL 89 85 6 6 353 252 2 154 29 65 20 1 13
1P LOSS MUTATED 13 14 0 1 77 45 1 42 17 21 7 0 5
1P LOSS WILD-TYPE 76 71 6 5 276 207 1 112 12 44 13 1 8

Figure S81.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'1p loss' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00094

Table S82.  Gene #42: '1p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
1P LOSS MUTATED 50 141 29 22
1P LOSS WILD-TYPE 226 483 107 18

Figure S82.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'1p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00258 (Fisher's exact test), Q value = 0.035

Table S83.  Gene #42: '1p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 507 358 119 77
1P LOSS MUTATED 94 81 36 26
1P LOSS WILD-TYPE 413 277 83 51

Figure S83.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'1p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000334 (Wilcoxon-test), Q value = 0.0078

Table S84.  Gene #42: '1p loss' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 914 2.4 (4.7)
1P LOSS MUTATED 189 3.4 (5.5)
1P LOSS WILD-TYPE 725 2.1 (4.4)

Figure S84.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'2p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0205 (Fisher's exact test), Q value = 0.16

Table S85.  Gene #44: '2p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 889 22
2P LOSS MUTATED 145 8
2P LOSS WILD-TYPE 744 14

Figure S85.  Get High-res Image Gene #44: '2p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'3p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00147 (Fisher's exact test), Q value = 0.024

Table S86.  Gene #46: '3p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
3P LOSS MUTATED 32 130 20 3
3P LOSS WILD-TYPE 244 494 116 37

Figure S86.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'3p loss' versus 'RADIATION_THERAPY'

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

Table S87.  Gene #46: '3p loss' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients NO YES
ALL 429 518
3P LOSS MUTATED 61 101
3P LOSS WILD-TYPE 368 417

Figure S87.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #8: 'RADIATION_THERAPY'

'3p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0316 (Fisher's exact test), Q value = 0.21

Table S88.  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 1 770 200 6 9 29 17 47
3P LOSS MUTATED 0 152 20 1 2 3 1 7
3P LOSS WILD-TYPE 1 618 180 5 7 26 16 40

Figure S88.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'3p loss' versus 'RACE'

P value = 0.0329 (Fisher's exact test), Q value = 0.21

Table S89.  Gene #46: '3p loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
3P LOSS MUTATED 0 16 41 119
3P LOSS WILD-TYPE 1 44 140 626

Figure S89.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #11: 'RACE'

'3p loss' versus 'ETHNICITY'

P value = 0.0317 (Fisher's exact test), Q value = 0.21

Table S90.  Gene #46: '3p loss' versus Clinical Feature #12: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 39 875
3P LOSS MUTATED 2 163
3P LOSS WILD-TYPE 37 712

Figure S90.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #12: 'ETHNICITY'

'3q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00416 (Fisher's exact test), Q value = 0.051

Table S91.  Gene #47: '3q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
3Q LOSS MUTATED 16 76 9 1
3Q LOSS WILD-TYPE 260 548 127 39

Figure S91.  Get High-res Image Gene #47: '3q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'3q loss' versus 'ETHNICITY'

P value = 0.0265 (Fisher's exact test), Q value = 0.19

Table S92.  Gene #47: '3q loss' versus Clinical Feature #12: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 39 875
3Q LOSS MUTATED 0 93
3Q LOSS WILD-TYPE 39 782

Figure S92.  Get High-res Image Gene #47: '3q loss' versus Clinical Feature #12: 'ETHNICITY'

'4p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0107 (Fisher's exact test), Q value = 0.1

Table S93.  Gene #48: '4p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
4P LOSS MUTATED 71 226 39 15
4P LOSS WILD-TYPE 205 398 97 25

Figure S93.  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 = 0.00052

Table S94.  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 1 770 200 6 9 29 17 47
4P LOSS MUTATED 1 291 34 3 4 6 0 13
4P LOSS WILD-TYPE 0 479 166 3 5 23 17 34

Figure S94.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'4p loss' versus 'RACE'

P value = 0.00294 (Fisher's exact test), Q value = 0.039

Table S95.  Gene #48: '4p loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
4P LOSS MUTATED 1 20 79 228
4P LOSS WILD-TYPE 0 40 102 517

Figure S95.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #11: 'RACE'

'4q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0227 (Fisher's exact test), Q value = 0.16

Table S96.  Gene #49: '4q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
4Q LOSS MUTATED 61 194 40 15
4Q LOSS WILD-TYPE 215 430 96 25

Figure S96.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'4q loss' versus 'HISTOLOGICAL_TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00094

Table S97.  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 1 770 200 6 9 29 17 47
4Q LOSS MUTATED 0 254 32 2 4 6 0 13
4Q LOSS WILD-TYPE 1 516 168 4 5 23 17 34

Figure S97.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'4q loss' versus 'RACE'

P value = 0.00945 (Fisher's exact test), Q value = 0.095

Table S98.  Gene #49: '4q loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
4Q LOSS MUTATED 1 18 68 199
4Q LOSS WILD-TYPE 0 42 113 546

Figure S98.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #11: 'RACE'

'5p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00326 (Wilcoxon-test), Q value = 0.042

Table S99.  Gene #50: '5p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1065 58.6 (13.2)
5P LOSS MUTATED 137 55.6 (13.8)
5P LOSS WILD-TYPE 928 59.1 (13.1)

Figure S99.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0217 (Fisher's exact test), Q value = 0.16

Table S100.  Gene #50: '5p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
5P LOSS MUTATED 28 97 10 5
5P LOSS WILD-TYPE 248 527 126 35

Figure S100.  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 = 0.00052

Table S101.  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 1 770 200 6 9 29 17 47
5P LOSS MUTATED 0 120 3 4 0 4 0 8
5P LOSS WILD-TYPE 1 650 197 2 9 25 17 39

Figure S101.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'5q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000147 (Wilcoxon-test), Q value = 0.0041

Table S102.  Gene #51: '5q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1065 58.6 (13.2)
5Q LOSS MUTATED 225 55.8 (13.2)
5Q LOSS WILD-TYPE 840 59.4 (13.1)

Figure S102.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00114 (Fisher's exact test), Q value = 0.019

Table S103.  Gene #51: '5q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
5Q LOSS MUTATED 45 156 17 8
5Q LOSS WILD-TYPE 231 468 119 32

Figure S103.  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 = 0.00052

Table S104.  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 1 770 200 6 9 29 17 47
5Q LOSS MUTATED 1 202 5 4 0 5 0 10
5Q LOSS WILD-TYPE 0 568 195 2 9 24 17 37

Figure S104.  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 = 0.00052

Table S105.  Gene #51: '5q loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
5Q LOSS MUTATED 0 18 63 130
5Q LOSS WILD-TYPE 1 42 118 615

Figure S105.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #11: 'RACE'

'6p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0411 (Wilcoxon-test), Q value = 0.23

Table S106.  Gene #52: '6p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1065 58.6 (13.2)
6P LOSS MUTATED 186 56.8 (13.8)
6P LOSS WILD-TYPE 879 59.0 (13.1)

Figure S106.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'6q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00128 (Wilcoxon-test), Q value = 0.021

Table S107.  Gene #53: '6q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1065 58.6 (13.2)
6Q LOSS MUTATED 274 56.3 (13.4)
6Q LOSS WILD-TYPE 791 59.4 (13.1)

Figure S107.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'6q loss' versus 'RADIATION_THERAPY'

P value = 0.00379 (Fisher's exact test), Q value = 0.047

Table S108.  Gene #53: '6q loss' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients NO YES
ALL 429 518
6Q LOSS MUTATED 93 156
6Q LOSS WILD-TYPE 336 362

Figure S108.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #8: 'RADIATION_THERAPY'

'7p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00011 (Fisher's exact test), Q value = 0.0033

Table S109.  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 1 770 200 6 9 29 17 47
7P LOSS MUTATED 0 96 5 2 2 3 0 4
7P LOSS WILD-TYPE 1 674 195 4 7 26 17 43

Figure S109.  Get High-res Image Gene #54: '7p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'7q loss' versus 'HISTOLOGICAL_TYPE'

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

Table S110.  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 1 770 200 6 9 29 17 47
7Q LOSS MUTATED 0 100 11 0 2 3 0 4
7Q LOSS WILD-TYPE 1 670 189 6 7 26 17 43

Figure S110.  Get High-res Image Gene #55: '7q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'8p loss' versus 'HISTOLOGICAL_TYPE'

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

Table S111.  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 1 770 200 6 9 29 17 47
8P LOSS MUTATED 1 316 50 2 1 7 3 18
8P LOSS WILD-TYPE 0 454 150 4 8 22 14 29

Figure S111.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'8p loss' versus 'RACE'

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

Table S112.  Gene #56: '8p loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
8P LOSS MUTATED 1 31 73 260
8P LOSS WILD-TYPE 0 29 108 485

Figure S112.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #11: 'RACE'

'8q loss' versus 'RACE'

P value = 0.0189 (Fisher's exact test), Q value = 0.15

Table S113.  Gene #57: '8q loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
8Q LOSS MUTATED 0 10 23 56
8Q LOSS WILD-TYPE 1 50 158 689

Figure S113.  Get High-res Image Gene #57: '8q loss' versus Clinical Feature #11: 'RACE'

'9p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00255 (Fisher's exact test), Q value = 0.035

Table S114.  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 TIS STAGE X
ALL 89 85 6 6 353 252 2 154 29 65 20 1 13
9P LOSS MUTATED 21 15 0 2 105 64 1 54 16 19 10 0 5
9P LOSS WILD-TYPE 68 70 6 4 248 188 1 100 13 46 10 1 8

Figure S114.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'9p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00036 (Fisher's exact test), Q value = 0.0082

Table S115.  Gene #58: '9p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
9P LOSS MUTATED 57 202 35 18
9P LOSS WILD-TYPE 219 422 101 22

Figure S115.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'9p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00907 (Fisher's exact test), Q value = 0.092

Table S116.  Gene #58: '9p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 507 358 119 77
9P LOSS MUTATED 142 92 50 24
9P LOSS WILD-TYPE 365 266 69 53

Figure S116.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'9p loss' versus 'GENDER'

P value = 0.0474 (Fisher's exact test), Q value = 0.25

Table S117.  Gene #58: '9p loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1068 12
9P LOSS MUTATED 306 7
9P LOSS WILD-TYPE 762 5

Figure S117.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #7: 'GENDER'

'9p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00052

Table S118.  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 1 770 200 6 9 29 17 47
9P LOSS MUTATED 0 263 25 3 4 9 3 6
9P LOSS WILD-TYPE 1 507 175 3 5 20 14 41

Figure S118.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'9q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00889 (Fisher's exact test), Q value = 0.092

Table S119.  Gene #59: '9q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
9Q LOSS MUTATED 54 176 35 16
9Q LOSS WILD-TYPE 222 448 101 24

Figure S119.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'9q loss' versus 'GENDER'

P value = 0.018 (Fisher's exact test), Q value = 0.14

Table S120.  Gene #59: '9q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1068 12
9Q LOSS MUTATED 276 7
9Q LOSS WILD-TYPE 792 5

Figure S120.  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 = 0.00052

Table S121.  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 1 770 200 6 9 29 17 47
9Q LOSS MUTATED 0 235 22 2 4 9 3 8
9Q LOSS WILD-TYPE 1 535 178 4 5 20 14 39

Figure S121.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'9q loss' versus 'RACE'

P value = 0.0402 (Fisher's exact test), Q value = 0.23

Table S122.  Gene #59: '9q loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
9Q LOSS MUTATED 0 18 59 174
9Q LOSS WILD-TYPE 1 42 122 571

Figure S122.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #11: 'RACE'

'10p loss' versus 'Time to Death'

P value = 0.0313 (logrank test), Q value = 0.21

Table S123.  Gene #60: '10p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1064 147 0.0 - 282.9 (27.9)
10P LOSS MUTATED 171 29 0.0 - 282.9 (24.4)
10P LOSS WILD-TYPE 893 118 0.0 - 281.3 (28.5)

Figure S123.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #1: 'Time to Death'

'10p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00508 (Fisher's exact test), Q value = 0.06

Table S124.  Gene #60: '10p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
10P LOSS MUTATED 27 115 21 9
10P LOSS WILD-TYPE 249 509 115 31

Figure S124.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'10p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00152 (Fisher's exact test), Q value = 0.024

Table S125.  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 1 770 200 6 9 29 17 47
10P LOSS MUTATED 0 129 22 0 6 8 1 6
10P LOSS WILD-TYPE 1 641 178 6 3 21 16 41

Figure S125.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'10q loss' versus 'Time to Death'

P value = 0.0366 (logrank test), Q value = 0.22

Table S126.  Gene #61: '10q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1064 147 0.0 - 282.9 (27.9)
10Q LOSS MUTATED 228 37 0.0 - 282.9 (24.4)
10Q LOSS WILD-TYPE 836 110 0.0 - 281.3 (28.9)

Figure S126.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #1: 'Time to Death'

'10q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0079 (Fisher's exact test), Q value = 0.084

Table S127.  Gene #61: '10q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
10Q LOSS MUTATED 41 146 27 13
10Q LOSS WILD-TYPE 235 478 109 27

Figure S127.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'10q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00053 (Fisher's exact test), Q value = 0.011

Table S128.  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 1 770 200 6 9 29 17 47
10Q LOSS MUTATED 0 178 25 1 6 8 1 9
10Q LOSS WILD-TYPE 1 592 175 5 3 21 16 38

Figure S128.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'11p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0167 (Fisher's exact test), Q value = 0.14

Table S129.  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 TIS STAGE X
ALL 89 85 6 6 353 252 2 154 29 65 20 1 13
11P LOSS MUTATED 20 11 1 1 90 62 0 50 14 18 4 1 2
11P LOSS WILD-TYPE 69 74 5 5 263 190 2 104 15 47 16 0 11

Figure S129.  Get High-res Image Gene #62: '11p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'11p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0132 (Fisher's exact test), Q value = 0.12

Table S130.  Gene #62: '11p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
11P LOSS MUTATED 58 165 33 18
11P LOSS WILD-TYPE 218 459 103 22

Figure S130.  Get High-res Image Gene #62: '11p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'11p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0415 (Fisher's exact test), Q value = 0.23

Table S131.  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 1 770 200 6 9 29 17 47
11P LOSS MUTATED 0 209 37 4 2 10 3 10
11P LOSS WILD-TYPE 1 561 163 2 7 19 14 37

Figure S131.  Get High-res Image Gene #62: '11p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'11p loss' versus 'RACE'

P value = 0.00039 (Fisher's exact test), Q value = 0.0087

Table S132.  Gene #62: '11p loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
11P LOSS MUTATED 1 19 63 163
11P LOSS WILD-TYPE 0 41 118 582

Figure S132.  Get High-res Image Gene #62: '11p loss' versus Clinical Feature #11: 'RACE'

'11p loss' versus 'ETHNICITY'

P value = 0.0359 (Fisher's exact test), Q value = 0.22

Table S133.  Gene #62: '11p loss' versus Clinical Feature #12: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 39 875
11P LOSS MUTATED 4 218
11P LOSS WILD-TYPE 35 657

Figure S133.  Get High-res Image Gene #62: '11p loss' versus Clinical Feature #12: 'ETHNICITY'

'11q loss' versus 'RACE'

P value = 0.00532 (Fisher's exact test), Q value = 0.062

Table S134.  Gene #63: '11q loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
11Q LOSS MUTATED 1 23 76 226
11Q LOSS WILD-TYPE 0 37 105 519

Figure S134.  Get High-res Image Gene #63: '11q loss' versus Clinical Feature #11: 'RACE'

'12p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00523 (Fisher's exact test), Q value = 0.061

Table S135.  Gene #64: '12p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
12P LOSS MUTATED 33 91 13 13
12P LOSS WILD-TYPE 243 533 123 27

Figure S135.  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 = 0.0017

Table S136.  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 1 770 200 6 9 29 17 47
12P LOSS MUTATED 0 130 10 2 3 3 1 2
12P LOSS WILD-TYPE 1 640 190 4 6 26 16 45

Figure S136.  Get High-res Image Gene #64: '12p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'12q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00637 (Wilcoxon-test), Q value = 0.073

Table S137.  Gene #65: '12q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1065 58.6 (13.2)
12Q LOSS MUTATED 131 56.0 (13.4)
12Q LOSS WILD-TYPE 934 59.0 (13.2)

Figure S137.  Get High-res Image Gene #65: '12q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'12q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00369 (Fisher's exact test), Q value = 0.047

Table S138.  Gene #65: '12q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
12Q LOSS MUTATED 26 83 10 11
12Q LOSS WILD-TYPE 250 541 126 29

Figure S138.  Get High-res Image Gene #65: '12q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'12q loss' versus 'RADIATION_THERAPY'

P value = 0.0199 (Fisher's exact test), Q value = 0.15

Table S139.  Gene #65: '12q loss' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients NO YES
ALL 429 518
12Q LOSS MUTATED 39 73
12Q LOSS WILD-TYPE 390 445

Figure S139.  Get High-res Image Gene #65: '12q loss' versus Clinical Feature #8: 'RADIATION_THERAPY'

'12q loss' versus 'HISTOLOGICAL_TYPE'

P value = 3e-05 (Fisher's exact test), Q value = 0.0013

Table S140.  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 1 770 200 6 9 29 17 47
12Q LOSS MUTATED 0 111 9 3 3 1 0 4
12Q LOSS WILD-TYPE 1 659 191 3 6 28 17 43

Figure S140.  Get High-res Image Gene #65: '12q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'12q loss' versus 'RACE'

P value = 0.0016 (Fisher's exact test), Q value = 0.025

Table S141.  Gene #65: '12q loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
12Q LOSS MUTATED 0 6 39 81
12Q LOSS WILD-TYPE 1 54 142 664

Figure S141.  Get High-res Image Gene #65: '12q loss' versus Clinical Feature #11: 'RACE'

'13q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00052

Table S142.  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 1 770 200 6 9 29 17 47
13Q LOSS MUTATED 0 340 58 5 5 11 2 11
13Q LOSS WILD-TYPE 1 430 142 1 4 18 15 36

Figure S142.  Get High-res Image Gene #66: '13q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'14q loss' versus 'Time to Death'

P value = 0.0408 (logrank test), Q value = 0.23

Table S143.  Gene #67: '14q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1064 147 0.0 - 282.9 (27.9)
14Q LOSS MUTATED 261 45 0.0 - 255.7 (24.8)
14Q LOSS WILD-TYPE 803 102 0.0 - 282.9 (29.0)

Figure S143.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #1: 'Time to Death'

'14q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0271 (Fisher's exact test), Q value = 0.19

Table S144.  Gene #67: '14q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
14Q LOSS MUTATED 53 174 29 8
14Q LOSS WILD-TYPE 223 450 107 32

Figure S144.  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 = 0.00052

Table S145.  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 1 770 200 6 9 29 17 47
14Q LOSS MUTATED 0 215 29 5 5 4 1 6
14Q LOSS WILD-TYPE 1 555 171 1 4 25 16 41

Figure S145.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'14q loss' versus 'RACE'

P value = 9e-05 (Fisher's exact test), Q value = 0.0029

Table S146.  Gene #67: '14q loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
14Q LOSS MUTATED 0 14 69 161
14Q LOSS WILD-TYPE 1 46 112 584

Figure S146.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #11: 'RACE'

'15q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00257 (Fisher's exact test), Q value = 0.035

Table S147.  Gene #68: '15q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
15Q LOSS MUTATED 62 212 36 9
15Q LOSS WILD-TYPE 214 412 100 31

Figure S147.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'15q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0259 (Fisher's exact test), Q value = 0.18

Table S148.  Gene #68: '15q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 507 358 119 77
15Q LOSS MUTATED 164 89 44 20
15Q LOSS WILD-TYPE 343 269 75 57

Figure S148.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'15q loss' versus 'HISTOLOGICAL_TYPE'

P value = 5e-05 (Fisher's exact test), Q value = 0.002

Table S149.  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 1 770 200 6 9 29 17 47
15Q LOSS MUTATED 0 254 34 3 5 10 2 12
15Q LOSS WILD-TYPE 1 516 166 3 4 19 15 35

Figure S149.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'16p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0297 (Wilcoxon-test), Q value = 0.2

Table S150.  Gene #69: '16p loss' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 914 2.4 (4.7)
16P LOSS MUTATED 152 1.9 (4.3)
16P LOSS WILD-TYPE 762 2.5 (4.7)

Figure S150.  Get High-res Image Gene #69: '16p loss' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'16p loss' versus 'RACE'

P value = 0.0302 (Fisher's exact test), Q value = 0.2

Table S151.  Gene #69: '16p loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
16P LOSS MUTATED 0 11 42 108
16P LOSS WILD-TYPE 1 49 139 637

Figure S151.  Get High-res Image Gene #69: '16p loss' versus Clinical Feature #11: 'RACE'

'16q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00101 (Wilcoxon-test), Q value = 0.018

Table S152.  Gene #70: '16q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1065 58.6 (13.2)
16Q LOSS MUTATED 585 59.9 (13.0)
16Q LOSS WILD-TYPE 480 57.1 (13.4)

Figure S152.  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 = 0.00052

Table S153.  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 1 770 200 6 9 29 17 47
16Q LOSS MUTATED 0 390 158 3 1 18 3 19
16Q LOSS WILD-TYPE 1 380 42 3 8 11 14 28

Figure S153.  Get High-res Image Gene #70: '16q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'17p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0297 (Wilcoxon-test), Q value = 0.2

Table S154.  Gene #71: '17p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1065 58.6 (13.2)
17P LOSS MUTATED 570 57.9 (13.3)
17P LOSS WILD-TYPE 495 59.5 (13.0)

Figure S154.  Get High-res Image Gene #71: '17p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'17p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00482 (Fisher's exact test), Q value = 0.058

Table S155.  Gene #71: '17p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
17P LOSS MUTATED 126 359 74 17
17P LOSS WILD-TYPE 150 265 62 23

Figure S155.  Get High-res Image Gene #71: '17p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'17p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0155 (Fisher's exact test), Q value = 0.13

Table S156.  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 1 770 200 6 9 29 17 47
17P LOSS MUTATED 0 433 92 5 5 18 6 19
17P LOSS WILD-TYPE 1 337 108 1 4 11 11 28

Figure S156.  Get High-res Image Gene #71: '17p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'17q loss' versus 'GENDER'

P value = 0.0441 (Fisher's exact test), Q value = 0.24

Table S157.  Gene #72: '17q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1068 12
17Q LOSS MUTATED 275 0
17Q LOSS WILD-TYPE 793 12

Figure S157.  Get High-res Image Gene #72: '17q loss' versus Clinical Feature #7: 'GENDER'

'17q loss' versus 'HISTOLOGICAL_TYPE'

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

Table S158.  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 1 770 200 6 9 29 17 47
17Q LOSS MUTATED 0 220 34 3 5 5 0 8
17Q LOSS WILD-TYPE 1 550 166 3 4 24 17 39

Figure S158.  Get High-res Image Gene #72: '17q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'17q loss' versus 'RACE'

P value = 0.0027 (Fisher's exact test), Q value = 0.036

Table S159.  Gene #72: '17q loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
17Q LOSS MUTATED 1 22 58 171
17Q LOSS WILD-TYPE 0 38 123 574

Figure S159.  Get High-res Image Gene #72: '17q loss' versus Clinical Feature #11: 'RACE'

'18p loss' versus 'Time to Death'

P value = 6.39e-06 (logrank test), Q value = 0.00052

Table S160.  Gene #73: '18p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1064 147 0.0 - 282.9 (27.9)
18P LOSS MUTATED 313 59 0.0 - 233.6 (23.9)
18P LOSS WILD-TYPE 751 88 0.0 - 282.9 (30.6)

Figure S160.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #1: 'Time to Death'

'18p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00195 (Wilcoxon-test), Q value = 0.03

Table S161.  Gene #73: '18p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1065 58.6 (13.2)
18P LOSS MUTATED 311 60.6 (13.7)
18P LOSS WILD-TYPE 754 57.8 (12.9)

Figure S161.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'18p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0396 (Fisher's exact test), Q value = 0.23

Table S162.  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 TIS STAGE X
ALL 89 85 6 6 353 252 2 154 29 65 20 1 13
18P LOSS MUTATED 25 23 0 0 100 73 0 48 16 26 6 0 1
18P LOSS WILD-TYPE 64 62 6 6 253 179 2 106 13 39 14 1 12

Figure S162.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'18p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00245 (Fisher's exact test), Q value = 0.035

Table S163.  Gene #73: '18p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
18P LOSS MUTATED 69 189 40 22
18P LOSS WILD-TYPE 207 435 96 18

Figure S163.  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 = 0.033

Table S164.  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 1 770 200 6 9 29 17 47
18P LOSS MUTATED 0 250 47 3 4 6 0 10
18P LOSS WILD-TYPE 1 520 153 3 5 23 17 37

Figure S164.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'18p loss' versus 'RACE'

P value = 0.0432 (Fisher's exact test), Q value = 0.23

Table S165.  Gene #73: '18p loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
18P LOSS MUTATED 0 27 54 212
18P LOSS WILD-TYPE 1 33 127 533

Figure S165.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #11: 'RACE'

'18q loss' versus 'Time to Death'

P value = 0.00788 (logrank test), Q value = 0.084

Table S166.  Gene #74: '18q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1064 147 0.0 - 282.9 (27.9)
18Q LOSS MUTATED 314 52 0.0 - 255.7 (23.4)
18Q LOSS WILD-TYPE 750 95 0.2 - 282.9 (30.5)

Figure S166.  Get High-res Image Gene #74: '18q loss' versus Clinical Feature #1: 'Time to Death'

'18q loss' versus 'YEARS_TO_BIRTH'

P value = 0.011 (Wilcoxon-test), Q value = 0.1

Table S167.  Gene #74: '18q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1065 58.6 (13.2)
18Q LOSS MUTATED 313 60.3 (13.5)
18Q LOSS WILD-TYPE 752 57.9 (13.0)

Figure S167.  Get High-res Image Gene #74: '18q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'18q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0153 (Fisher's exact test), Q value = 0.13

Table S168.  Gene #74: '18q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
18Q LOSS MUTATED 70 192 38 20
18Q LOSS WILD-TYPE 206 432 98 20

Figure S168.  Get High-res Image Gene #74: '18q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'18q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00107 (Fisher's exact test), Q value = 0.018

Table S169.  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 1 770 200 6 9 29 17 47
18Q LOSS MUTATED 1 247 52 2 5 6 0 8
18Q LOSS WILD-TYPE 0 523 148 4 4 23 17 39

Figure S169.  Get High-res Image Gene #74: '18q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'19p loss' versus 'YEARS_TO_BIRTH'

P value = 0.022 (Wilcoxon-test), Q value = 0.16

Table S170.  Gene #75: '19p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1065 58.6 (13.2)
19P LOSS MUTATED 188 56.6 (13.2)
19P LOSS WILD-TYPE 877 59.1 (13.2)

Figure S170.  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 = 0.00052

Table S171.  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 1 770 200 6 9 29 17 47
19P LOSS MUTATED 0 168 8 1 3 4 4 4
19P LOSS WILD-TYPE 1 602 192 5 6 25 13 43

Figure S171.  Get High-res Image Gene #75: '19p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'19p loss' versus 'RACE'

P value = 0.00051 (Fisher's exact test), Q value = 0.011

Table S172.  Gene #75: '19p loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
19P LOSS MUTATED 0 16 47 109
19P LOSS WILD-TYPE 1 44 134 636

Figure S172.  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 = 0.00052

Table S173.  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 1 770 200 6 9 29 17 47
19Q LOSS MUTATED 0 141 5 1 0 4 4 5
19Q LOSS WILD-TYPE 1 629 195 5 9 25 13 42

Figure S173.  Get High-res Image Gene #76: '19q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'19q loss' versus 'RACE'

P value = 0.0109 (Fisher's exact test), Q value = 0.1

Table S174.  Gene #76: '19q loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
19Q LOSS MUTATED 0 13 37 93
19Q LOSS WILD-TYPE 1 47 144 652

Figure S174.  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 S175.  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 S175.  Get High-res Image Gene #77: '20p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'20q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0343 (Wilcoxon-test), Q value = 0.21

Table S176.  Gene #78: '20q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1065 58.6 (13.2)
20Q LOSS MUTATED 53 55.2 (12.6)
20Q LOSS WILD-TYPE 1012 58.8 (13.2)

Figure S176.  Get High-res Image Gene #78: '20q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0428 (Fisher's exact test), Q value = 0.23

Table S177.  Gene #78: '20q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 276 624 136 40
20Q LOSS MUTATED 7 42 5 1
20Q LOSS WILD-TYPE 269 582 131 39

Figure S177.  Get High-res Image Gene #78: '20q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'20q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0345 (Fisher's exact test), Q value = 0.21

Table S178.  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 1 770 200 6 9 29 17 47
20Q LOSS MUTATED 0 40 7 3 0 1 1 3
20Q LOSS WILD-TYPE 1 730 193 3 9 28 16 44

Figure S178.  Get High-res Image Gene #78: '20q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'20q loss' versus 'RACE'

P value = 0.0218 (Fisher's exact test), Q value = 0.16

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

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
20Q LOSS MUTATED 0 5 16 29
20Q LOSS WILD-TYPE 1 55 165 716

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

'21q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.01 (Fisher's exact test), Q value = 0.099

Table S180.  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 TIS STAGE X
ALL 89 85 6 6 353 252 2 154 29 65 20 1 13
21Q LOSS MUTATED 11 13 0 0 51 50 1 29 10 5 6 1 3
21Q LOSS WILD-TYPE 78 72 6 6 302 202 1 125 19 60 14 0 10

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

'21q loss' versus 'PATHOLOGY_N_STAGE'

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

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

nPatients N0 N1 N2 N3
ALL 507 358 119 77
21Q LOSS MUTATED 74 64 30 9
21Q LOSS WILD-TYPE 433 294 89 68

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

'21q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0385 (Fisher's exact test), Q value = 0.22

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

nPatients 0 1
ALL 889 22
21Q LOSS MUTATED 149 8
21Q LOSS WILD-TYPE 740 14

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

'21q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00686 (Fisher's exact test), Q value = 0.077

Table S183.  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 1 770 200 6 9 29 17 47
21Q LOSS MUTATED 0 145 20 2 2 7 1 3
21Q LOSS WILD-TYPE 1 625 180 4 7 22 16 44

Figure S183.  Get High-res Image Gene #79: '21q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'21q loss' versus 'RACE'

P value = 0.0252 (Fisher's exact test), Q value = 0.18

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

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
21Q LOSS MUTATED 0 17 35 110
21Q LOSS WILD-TYPE 1 43 146 635

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

'22q loss' versus 'RADIATION_THERAPY'

P value = 0.0106 (Fisher's exact test), Q value = 0.1

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

nPatients NO YES
ALL 429 518
22Q LOSS MUTATED 176 256
22Q LOSS WILD-TYPE 253 262

Figure S185.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #8: 'RADIATION_THERAPY'

'22q loss' versus 'HISTOLOGICAL_TYPE'

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

Table S186.  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 1 770 200 6 9 29 17 47
22Q LOSS MUTATED 0 357 88 2 3 19 1 11
22Q LOSS WILD-TYPE 1 413 112 4 6 10 16 36

Figure S186.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'xp loss' versus 'YEARS_TO_BIRTH'

P value = 0.00363 (Wilcoxon-test), Q value = 0.046

Table S187.  Gene #81: 'xp loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1065 58.6 (13.2)
XP LOSS MUTATED 186 55.9 (13.2)
XP LOSS WILD-TYPE 879 59.2 (13.2)

Figure S187.  Get High-res Image Gene #81: 'xp loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'xp loss' versus 'RACE'

P value = 0.0106 (Fisher's exact test), Q value = 0.1

Table S188.  Gene #81: 'xp loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 181 745
XP LOSS MUTATED 0 17 41 115
XP LOSS WILD-TYPE 1 43 140 630

Figure S188.  Get High-res Image Gene #81: 'xp loss' versus Clinical Feature #11: 'RACE'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BRCA-TP/19785967/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BRCA-TP/19775058/BRCA-TP.merged_data.txt

  • Number of patients = 1080

  • 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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