Correlation between copy number variation genes (focal events) and selected clinical features
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.

Summary

Testing the association between copy number variation 69 focal events and 12 clinical features across 1062 patients, 229 significant findings detected with Q value < 0.25.

  • amp_1p22.3 cnv correlated to 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'NUMBER_OF_LYMPH_NODES', and 'RACE'.

  • amp_1q21.3 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • amp_1q44 cnv correlated to 'Time to Death',  'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • amp_3p25.1 cnv correlated to 'Time to Death',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'HISTOLOGICAL_TYPE'.

  • amp_3q26.32 cnv correlated to 'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • amp_4q13.3 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • amp_5p15.33 cnv correlated to 'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.

  • amp_6p23 cnv correlated to 'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • amp_6q21 cnv correlated to 'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • amp_8p11.23 cnv correlated to 'Time to Death',  'NEOPLASM_DISEASESTAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • amp_8p11.21 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • amp_8q24.21 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • amp_10p15.1 cnv correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.

  • amp_10q22.3 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • amp_11p13 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • amp_11q13.3 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • amp_11q14.1 cnv correlated to 'PATHOLOGY_T_STAGE' and 'HISTOLOGICAL_TYPE'.

  • amp_12p13.33 cnv correlated to 'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE',  'RACE', and 'ETHNICITY'.

  • amp_12q15 cnv correlated to 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'GENDER',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • amp_13q34 cnv correlated to 'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • amp_14q21.1 cnv correlated to 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • amp_15q26.3 cnv correlated to 'YEARS_TO_BIRTH',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • amp_17p11.2 cnv correlated to 'RADIATIONS_RADIATION_REGIMENINDICATION'.

  • amp_17q12 cnv correlated to 'GENDER',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • amp_17q23.1 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'GENDER', and 'HISTOLOGICAL_TYPE'.

  • amp_19p13.12 cnv correlated to 'PATHOLOGY_M_STAGE',  'GENDER',  'HISTOLOGICAL_TYPE',  'RADIATIONS_RADIATION_REGIMENINDICATION', and 'NUMBER_OF_LYMPH_NODES'.

  • amp_19q12 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • amp_19q13.42 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • amp_20q13.2 cnv correlated to 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'GENDER',  'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.

  • del_1p36.13 cnv correlated to 'YEARS_TO_BIRTH',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'GENDER',  'HISTOLOGICAL_TYPE',  'RADIATIONS_RADIATION_REGIMENINDICATION', and 'NUMBER_OF_LYMPH_NODES'.

  • del_1p22.1 cnv correlated to 'Time to Death',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • del_2q37.3 cnv correlated to 'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE',  'RADIATIONS_RADIATION_REGIMENINDICATION', and 'RACE'.

  • del_3p21.31 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • del_4p16.3 cnv correlated to 'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • del_4q35.1 cnv correlated to 'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • del_5q11.2 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • del_5q21.3 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE',  'NUMBER_OF_LYMPH_NODES', and 'RACE'.

  • del_6p25.3 cnv correlated to 'YEARS_TO_BIRTH' and 'PATHOLOGY_T_STAGE'.

  • del_6q15 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_N_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • del_6q27 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_N_STAGE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.

  • del_7p22.3 cnv correlated to 'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • del_7q36.1 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_8p23.2 cnv correlated to 'Time to Death',  'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • del_8p11.21 cnv correlated to 'Time to Death' and 'HISTOLOGICAL_TYPE'.

  • del_9p23 cnv correlated to 'Time to Death',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • del_9p21.3 cnv correlated to 'Time to Death',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'GENDER',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • del_9q21.11 cnv correlated to 'HISTOLOGICAL_TYPE' and 'RADIATIONS_RADIATION_REGIMENINDICATION'.

  • del_9q34.2 cnv correlated to 'PATHOLOGY_T_STAGE',  'GENDER',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • del_10q23.31 cnv correlated to 'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'ETHNICITY'.

  • del_10q26.3 cnv correlated to 'Time to Death',  'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'ETHNICITY'.

  • del_11p15.5 cnv correlated to 'Time to Death',  'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • del_11q13.1 cnv correlated to 'RACE'.

  • del_11q23.3 cnv correlated to 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'GENDER', and 'RACE'.

  • del_11q25 cnv correlated to 'YEARS_TO_BIRTH',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'GENDER',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • del_12p13.1 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_12q23.1 cnv correlated to 'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • del_13q14.2 cnv correlated to 'PATHOLOGY_T_STAGE' and 'HISTOLOGICAL_TYPE'.

  • del_14q24.1 cnv correlated to 'Time to Death',  'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE',  'RADIATIONS_RADIATION_REGIMENINDICATION', and 'RACE'.

  • del_15q13.1 cnv correlated to 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE',  'RADIATIONS_RADIATION_REGIMENINDICATION',  'NUMBER_OF_LYMPH_NODES', and 'RACE'.

  • del_16q24.3 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • del_17p12 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • del_17q21.31 cnv correlated to 'YEARS_TO_BIRTH',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • del_18q23 cnv correlated to 'Time to Death',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE', and 'HISTOLOGICAL_TYPE'.

  • del_19p13.3 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • del_19q13.32 cnv correlated to 'HISTOLOGICAL_TYPE' and 'RADIATIONS_RADIATION_REGIMENINDICATION'.

  • del_20p13 cnv correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.

  • del_21q11.2 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE', and 'HISTOLOGICAL_TYPE'.

  • del_22q13.32 cnv correlated to 'HISTOLOGICAL_TYPE' and 'RADIATIONS_RADIATION_REGIMENINDICATION'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 69 focal events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 229 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		NUMBER
OF
LYMPH
NODES 		RACE ETHNICITY
nCNV (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test
del 1p36 13 441 (42%) 621 0.0953
(0.3) 		0.0158
(0.0905) 		0.00163
(0.0173) 		1e-05
(0.000244) 		0.00038
(0.00552) 		0.0746
(0.261) 		0.0599
(0.232) 		0.0133
(0.0801) 		0.0498
(0.211) 		0.00136
(0.015) 		0.909
(0.979) 		0.867
(0.953)
del 9p23 321 (30%) 741 0.000376
(0.00552) 		0.305
(0.572) 		0.00267
(0.0246) 		0.00071
(0.00891) 		0.00056
(0.00724) 		0.0541
(0.217) 		0.0984
(0.305) 		1e-05
(0.000244) 		0.549
(0.764) 		0.0244
(0.13) 		0.354
(0.602) 		0.72
(0.867)
del 9p21 3 358 (34%) 704 0.0369
(0.175) 		0.41
(0.651) 		0.0144
(0.084) 		0.0023
(0.0222) 		0.00179
(0.0181) 		0.106
(0.318) 		0.0508
(0.211) 		1e-05
(0.000244) 		0.422
(0.659) 		0.046
(0.199) 		0.217
(0.466) 		0.725
(0.867)
del 11q25 505 (48%) 557 0.329
(0.587) 		0.035
(0.172) 		0.0243
(0.13) 		0.00327
(0.0283) 		0.0341
(0.168) 		0.662
(0.834) 		0.0307
(0.154) 		0.00444
(0.035) 		0.89
(0.967) 		0.222
(0.47) 		0.00037
(0.00552) 		0.869
(0.953)
del 15q13 1 369 (35%) 693 0.634
(0.823) 		0.446
(0.679) 		0.173
(0.411) 		0.00152
(0.0166) 		0.0336
(0.166) 		0.495
(0.719) 		1
(1.00) 		1e-05
(0.000244) 		0.0502
(0.211) 		0.0403
(0.183) 		0.052
(0.213) 		0.73
(0.869)
amp 3p25 1 197 (19%) 865 0.0427
(0.19) 		0.161
(0.394) 		0.0371
(0.175) 		0.0003
(0.00497) 		0.0253
(0.132) 		0.411
(0.651) 		0.7
(0.855) 		1e-05
(0.000244) 		0.535
(0.754) 		0.429
(0.666) 		0.497
(0.721) 		1
(1.00)
amp 12q15 274 (26%) 788 0.289
(0.546) 		0.264
(0.514) 		0.386
(0.632) 		0.0229
(0.125) 		0.00944
(0.0641) 		1
(1.00) 		0.00877
(0.0614) 		0.00579
(0.0436) 		0.875
(0.956) 		0.0115
(0.0747) 		0.39
(0.637) 		0.25
(0.504)
amp 19p13 12 227 (21%) 835 0.554
(0.766) 		0.776
(0.898) 		0.436
(0.672) 		0.46
(0.693) 		0.21
(0.461) 		0.0621
(0.234) 		0.0639
(0.236) 		0.0283
(0.145) 		0.0284
(0.145) 		0.000917
(0.0108) 		0.151
(0.389) 		1
(1.00)
amp 20q13 2 540 (51%) 522 0.672
(0.84) 		0.731
(0.869) 		0.193
(0.437) 		0.0024
(0.0228) 		0.00257
(0.0239) 		0.826
(0.929) 		0.0645
(0.236) 		1e-05
(0.000244) 		0.000252
(0.00427) 		0.167
(0.401) 		0.255
(0.507) 		0.323
(0.587)
del 1p22 1 357 (34%) 705 0.00478
(0.0374) 		0.0738
(0.261) 		0.0165
(0.0935) 		2e-05
(0.000448) 		0.00756
(0.054) 		0.485
(0.712) 		0.522
(0.743) 		0.309
(0.574) 		0.884
(0.964) 		0.00118
(0.0136) 		0.672
(0.84) 		0.156
(0.391)
del 3p21 31 344 (32%) 718 0.0157
(0.0901) 		0.00368
(0.0311) 		0.156
(0.391) 		1e-05
(0.000244) 		0.651
(0.83) 		0.637
(0.823) 		0.754
(0.884) 		3e-05
(0.000637) 		0.338
(0.592) 		0.319
(0.587) 		0.0121
(0.0771) 		0.725
(0.867)
del 5q21 3 265 (25%) 797 0.652
(0.83) 		0.000897
(0.0108) 		0.163
(0.394) 		0.00011
(0.00207) 		0.134
(0.368) 		0.617
(0.814) 		0.0751
(0.261) 		1e-05
(0.000244) 		0.202
(0.451) 		0.00288
(0.0256) 		0.0005
(0.00679) 		0.703
(0.856)
del 14q24 1 346 (33%) 716 0.0402
(0.183) 		0.244
(0.5) 		0.212
(0.463) 		0.00019
(0.00335) 		0.409
(0.651) 		1
(1.00) 		0.755
(0.884) 		1e-05
(0.000244) 		0.0557
(0.219) 		0.331
(0.587) 		0.00077
(0.00952) 		0.725
(0.867)
del 21q11 2 212 (20%) 850 0.405
(0.648) 		0.465
(0.698) 		0.00983
(0.066) 		0.0121
(0.0771) 		0.0142
(0.0836) 		0.0564
(0.22) 		0.703
(0.856) 		0.00042
(0.006) 		0.546
(0.763) 		0.188
(0.431) 		0.244
(0.5) 		0.406
(0.648)
amp 1p22 3 244 (23%) 818 0.938
(0.997) 		0.284
(0.538) 		0.329
(0.587) 		0.00988
(0.066) 		0.0137
(0.0818) 		0.597
(0.801) 		1
(1.00) 		0.329
(0.587) 		0.624
(0.814) 		0.00935
(0.064) 		0.045
(0.197) 		1
(1.00)
amp 1q44 774 (73%) 288 0.0413
(0.187) 		0.374
(0.622) 		0.109
(0.325) 		0.00393
(0.0325) 		0.258
(0.51) 		0.622
(0.814) 		1
(1.00) 		0.0128
(0.08) 		0.938
(0.997) 		0.554
(0.766) 		0.0504
(0.211) 		0.099
(0.305)
amp 8q24 21 668 (63%) 394 0.118
(0.337) 		0.0527
(0.213) 		0.312
(0.577) 		0.0611
(0.233) 		0.322
(0.587) 		0.493
(0.718) 		0.228
(0.477) 		1e-05
(0.000244) 		0.1
(0.308) 		0.622
(0.814) 		0.00243
(0.0229) 		0.172
(0.411)
amp 12p13 33 279 (26%) 783 0.827
(0.929) 		0.439
(0.674) 		0.623
(0.814) 		0.00298
(0.0262) 		0.683
(0.847) 		1
(1.00) 		0.306
(0.572) 		1e-05
(0.000244) 		0.272
(0.525) 		0.35
(0.599) 		0.0235
(0.126) 		0.0613
(0.233)
amp 14q21 1 217 (20%) 845 0.406
(0.648) 		0.201
(0.451) 		0.332
(0.587) 		0.0333
(0.166) 		0.0234
(0.126) 		0.42
(0.659) 		1
(1.00) 		0.009
(0.0621) 		0.732
(0.87) 		0.0104
(0.0691) 		0.568
(0.778) 		0.21
(0.461)
amp 17q23 1 419 (39%) 643 0.12
(0.34) 		0.414
(0.652) 		0.0355
(0.173) 		0.00043
(0.00603) 		0.3
(0.564) 		1
(1.00) 		3.33e-05
(0.000672) 		1e-05
(0.000244) 		0.778
(0.898) 		0.425
(0.663) 		0.157
(0.391) 		0.867
(0.953)
amp 19q12 278 (26%) 784 0.596
(0.801) 		0.58
(0.79) 		0.0177
(0.0991) 		0.619
(0.814) 		0.0376
(0.175) 		0.468
(0.699) 		0.492
(0.718) 		1e-05
(0.000244) 		0.388
(0.635) 		0.00504
(0.0386) 		0.0733
(0.26) 		1
(1.00)
del 2q37 3 313 (29%) 749 0.814
(0.927) 		0.696
(0.855) 		0.337
(0.591) 		0.00185
(0.0185) 		0.333
(0.587) 		0.469
(0.699) 		1
(1.00) 		1e-05
(0.000244) 		0.0493
(0.211) 		0.255
(0.507) 		0.0438
(0.194) 		0.46
(0.693)
del 5q11 2 274 (26%) 788 0.281
(0.537) 		3.32e-05
(0.000672) 		0.26
(0.51) 		0.00051
(0.00681) 		0.348
(0.599) 		0.619
(0.814) 		0.0758
(0.263) 		1e-05
(0.000244) 		0.581
(0.79) 		0.118
(0.337) 		0.00056
(0.00724) 		0.851
(0.946)
del 8p23 2 552 (52%) 510 0.0504
(0.211) 		0.591
(0.799) 		0.901
(0.974) 		0.0132
(0.0801) 		0.0943
(0.3) 		1
(1.00) 		0.55
(0.764) 		1e-05
(0.000244) 		0.836
(0.934) 		0.828
(0.929) 		0.00159
(0.0171) 		0.62
(0.814)
del 9q34 2 293 (28%) 769 0.777
(0.898) 		0.904
(0.975) 		0.104
(0.315) 		0.0253
(0.132) 		0.0926
(0.297) 		0.808
(0.927) 		0.013
(0.0801) 		1e-05
(0.000244) 		0.0763
(0.263) 		0.193
(0.437) 		0.0667
(0.242) 		0.352
(0.601)
del 10q26 3 315 (30%) 747 0.057
(0.222) 		0.557
(0.767) 		0.133
(0.368) 		0.0249
(0.131) 		0.159
(0.393) 		0.233
(0.484) 		0.522
(0.743) 		1e-05
(0.000244) 		0.327
(0.587) 		0.358
(0.603) 		0.142
(0.383) 		0.00623
(0.0465)
del 11p15 5 303 (29%) 759 0.0528
(0.213) 		0.899
(0.974) 		0.205
(0.453) 		0.0041
(0.0334) 		0.394
(0.641) 		0.342
(0.595) 		0.52
(0.742) 		2e-05
(0.000448) 		0.593
(0.799) 		0.869
(0.953) 		0.0173
(0.0972) 		0.265
(0.515)
del 11q23 3 539 (51%) 523 0.508
(0.732) 		0.261
(0.51) 		0.0992
(0.305) 		0.0399
(0.183) 		0.052
(0.213) 		0.278
(0.533) 		0.0644
(0.236) 		0.0764
(0.263) 		1
(1.00) 		0.125
(0.35) 		0.0142
(0.0836) 		1
(1.00)
del 16q24 3 678 (64%) 384 0.711
(0.863) 		0.000601
(0.00766) 		0.234
(0.484) 		0.102
(0.312) 		0.466
(0.698) 		0.0651
(0.238) 		1
(1.00) 		1e-05
(0.000244) 		0.615
(0.814) 		0.314
(0.58) 		0.00412
(0.0334) 		0.231
(0.482)
del 17p12 638 (60%) 424 0.672
(0.84) 		0.0023
(0.0222) 		0.6
(0.802) 		0.0625
(0.234) 		0.803
(0.923) 		0.656
(0.831) 		0.541
(0.761) 		0.00883
(0.0614) 		0.725
(0.867) 		0.865
(0.953) 		0.0551
(0.219) 		0.737
(0.873)
del 18q23 349 (33%) 713 0.0617
(0.233) 		0.259
(0.51) 		0.0673
(0.243) 		0.0194
(0.107) 		0.071
(0.255) 		0.816
(0.927) 		0.355
(0.603) 		0.0011
(0.0128) 		0.142
(0.382) 		0.605
(0.806) 		0.0797
(0.271) 		0.725
(0.867)
del 19p13 3 356 (34%) 706 0.178
(0.416) 		0.00331
(0.0283) 		0.935
(0.997) 		0.0422
(0.19) 		0.967
(1.00) 		0.816
(0.927) 		0.352
(0.601) 		1e-05
(0.000244) 		0.827
(0.929) 		0.162
(0.394) 		0.00134
(0.015) 		0.862
(0.953)
amp 3q26 32 337 (32%) 725 0.871
(0.954) 		0.411
(0.651) 		0.0984
(0.305) 		0.00012
(0.00221) 		0.34
(0.593) 		0.647
(0.828) 		0.75
(0.882) 		1e-05
(0.000244) 		0.0885
(0.288) 		0.115
(0.333) 		0.00192
(0.0189) 		0.106
(0.318)
amp 5p15 33 387 (36%) 675 0.202
(0.451) 		0.153
(0.389) 		0.864
(0.953) 		0.175
(0.411) 		0.0133
(0.0801) 		1
(1.00) 		0.542
(0.761) 		0.0526
(0.213) 		0.0627
(0.234) 		0.958
(1.00) 		0.238
(0.489) 		0.391
(0.637)
amp 6p23 294 (28%) 768 0.828
(0.929) 		0.364
(0.607) 		0.495
(0.719) 		0.00165
(0.0173) 		0.248
(0.504) 		0.808
(0.927) 		0.307
(0.572) 		1e-05
(0.000244) 		0.217
(0.466) 		0.903
(0.974) 		0.00434
(0.0349) 		0.852
(0.946)
amp 6q21 198 (19%) 864 0.128
(0.356) 		0.429
(0.666) 		0.0947
(0.3) 		0.00023
(0.00397) 		0.157
(0.391) 		1
(1.00) 		0.7
(0.855) 		1e-05
(0.000244) 		0.376
(0.623) 		0.037
(0.175) 		0.204
(0.453) 		1
(1.00)
amp 8p11 23 406 (38%) 656 0.0301
(0.153) 		0.173
(0.411) 		0.0553
(0.219) 		0.554
(0.766) 		0.0745
(0.261) 		0.112
(0.329) 		0.546
(0.763) 		0.322
(0.587) 		0.723
(0.867) 		0.00763
(0.054) 		0.625
(0.814) 		0.401
(0.646)
amp 13q34 176 (17%) 886 0.837
(0.934) 		0.0854
(0.283) 		0.225
(0.475) 		0.00724
(0.0526) 		0.248
(0.504) 		0.78
(0.9) 		0.228
(0.477) 		0.00079
(0.00962) 		1
(1.00) 		0.0528
(0.213) 		0.711
(0.863) 		0.826
(0.929)
amp 15q26 3 193 (18%) 869 0.174
(0.411) 		0.00714
(0.0526) 		0.845
(0.941) 		0.31
(0.574) 		0.911
(0.98) 		1
(1.00) 		0.122
(0.344) 		1e-05
(0.000244) 		0.421
(0.659) 		0.751
(0.882) 		0.0449
(0.197) 		0.283
(0.537)
amp 17q12 329 (31%) 733 0.0827
(0.276) 		0.814
(0.927) 		0.399
(0.645) 		0.0916
(0.296) 		0.0948
(0.3) 		0.485
(0.712) 		0.00514
(0.039) 		0.00034
(0.00541) 		0.263
(0.514) 		0.326
(0.587) 		0.00172
(0.0178) 		1
(1.00)
del 4p16 3 333 (31%) 729 0.901
(0.974) 		0.0715
(0.255) 		0.0939
(0.3) 		0.00015
(0.0027) 		0.636
(0.823) 		0.636
(0.823) 		1
(1.00) 		1e-05
(0.000244) 		0.206
(0.455) 		0.687
(0.85) 		0.0307
(0.154) 		0.594
(0.799)
del 4q35 1 340 (32%) 722 0.157
(0.391) 		0.454
(0.687) 		0.436
(0.672) 		0.00273
(0.0248) 		0.689
(0.851) 		0.648
(0.828) 		0.518
(0.742) 		1e-05
(0.000244) 		0.506
(0.729) 		0.745
(0.877) 		0.00762
(0.054) 		0.107
(0.318)
del 6q15 353 (33%) 709 0.588
(0.797) 		0.0616
(0.233) 		0.348
(0.599) 		0.323
(0.587) 		0.0375
(0.175) 		0.356
(0.603) 		1
(1.00) 		0.146
(0.388) 		0.143
(0.383) 		0.0134
(0.0801) 		0.137
(0.372) 		0.481
(0.71)
del 6q27 370 (35%) 692 0.088
(0.288) 		1.2e-05
(0.000284) 		0.526
(0.746) 		0.656
(0.831) 		0.0383
(0.177) 		0.821
(0.929) 		0.347
(0.599) 		0.307
(0.572) 		0.0358
(0.173) 		0.26
(0.51) 		0.642
(0.826) 		0.166
(0.399)
del 7p22 3 135 (13%) 927 0.983
(1.00) 		0.326
(0.587) 		0.473
(0.701) 		0.267
(0.518) 		0.0546
(0.218) 		1
(1.00) 		0.377
(0.624) 		1e-05
(0.000244) 		0.47
(0.7) 		0.0196
(0.108) 		0.759
(0.885) 		1
(1.00)
del 10q23 31 315 (30%) 747 0.647
(0.828) 		0.111
(0.328) 		0.256
(0.507) 		0.0123
(0.078) 		0.147
(0.388) 		1
(1.00) 		0.19
(0.434) 		0.00034
(0.00541) 		0.152
(0.389) 		0.333
(0.587) 		0.324
(0.587) 		0.0189
(0.105)
del 12q23 1 197 (19%) 865 1
(1.00) 		0.136
(0.372) 		0.57
(0.778) 		0.0361
(0.174) 		0.839
(0.935) 		0.399
(0.645) 		0.7
(0.855) 		0.00331
(0.0283) 		0.929
(0.996) 		0.395
(0.641) 		0.00723
(0.0526) 		0.679
(0.844)
del 17q21 31 362 (34%) 700 0.623
(0.814) 		0.000476
(0.00657) 		0.435
(0.672) 		0.0871
(0.287) 		0.117
(0.337) 		0.25
(0.504) 		0.349
(0.599) 		1e-05
(0.000244) 		0.716
(0.867) 		0.759
(0.885) 		0.00035
(0.00547) 		0.862
(0.953)
amp 10p15 1 299 (28%) 763 0.111
(0.328) 		0.69
(0.852) 		0.178
(0.416) 		0.0898
(0.292) 		0.472
(0.701) 		0.34
(0.593) 		0.737
(0.873) 		1e-05
(0.000244) 		0.192
(0.437) 		0.145
(0.388) 		6e-05
(0.00118) 		0.459
(0.693)
amp 11q14 1 262 (25%) 800 0.161
(0.394) 		0.214
(0.463) 		0.322
(0.587) 		0.0636
(0.236) 		0.104
(0.315) 		0.447
(0.679) 		0.152
(0.389) 		0.00383
(0.032) 		0.81
(0.927) 		0.797
(0.917) 		0.118
(0.337) 		0.251
(0.504)
del 6p25 3 202 (19%) 860 0.951
(1.00) 		0.0555
(0.219) 		0.33
(0.587) 		0.0256
(0.133) 		0.122
(0.344) 		1
(1.00) 		0.236
(0.486) 		0.0708
(0.255) 		0.0787
(0.269) 		0.57
(0.778) 		0.485
(0.712) 		0.405
(0.648)
del 8p11 21 198 (19%) 864 0.0495
(0.211) 		0.211
(0.463) 		0.739
(0.873) 		0.152
(0.389) 		0.213
(0.463) 		0.156
(0.391) 		0.233
(0.484) 		0.0128
(0.08) 		0.478
(0.707) 		0.155
(0.391) 		0.136
(0.372) 		0.832
(0.932)
del 9q21 11 292 (27%) 770 0.279
(0.534) 		0.932
(0.997) 		0.359
(0.603) 		0.0877
(0.288) 		0.227
(0.477) 		0.324
(0.587) 		0.0808
(0.271) 		1e-05
(0.000244) 		0.0368
(0.175) 		0.615
(0.814) 		0.162
(0.394) 		0.348
(0.599)
del 13q14 2 489 (46%) 573 0.15
(0.389) 		0.727
(0.868) 		0.854
(0.947) 		0.0456
(0.199) 		0.454
(0.687) 		0.511
(0.734) 		0.763
(0.887) 		1e-05
(0.000244) 		0.166
(0.399) 		0.643
(0.826) 		0.0751
(0.261) 		0.133
(0.368)
del 19q13 32 212 (20%) 850 0.272
(0.525) 		0.492
(0.718) 		0.413
(0.652) 		0.358
(0.603) 		0.0923
(0.297) 		0.274
(0.527) 		1
(1.00) 		1e-05
(0.000244) 		0.0154
(0.0894) 		0.971
(1.00) 		0.152
(0.389) 		0.544
(0.762)
del 20p13 159 (15%) 903 0.187
(0.43) 		0.061
(0.233) 		0.464
(0.698) 		0.503
(0.727) 		0.97
(1.00) 		0.117
(0.337) 		0.22
(0.47) 		3e-05
(0.000637) 		0.146
(0.388) 		0.935
(0.997) 		0.15
(0.389) 		0.639
(0.824)
del 22q13 32 480 (45%) 582 0.498
(0.721) 		0.44
(0.674) 		0.593
(0.799) 		0.185
(0.429) 		0.717
(0.867) 		0.278
(0.533) 		0.558
(0.767) 		0.00136
(0.015) 		0.00444
(0.035) 		0.936
(0.997) 		0.582
(0.79) 		0.618
(0.814)
amp 1q21 3 771 (73%) 291 0.7
(0.855) 		0.887
(0.966) 		0.147
(0.388) 		0.0109
(0.0715) 		0.441
(0.674) 		0.809
(0.927) 		0.185
(0.428) 		0.212
(0.463) 		0.486
(0.713) 		0.674
(0.84) 		0.181
(0.42) 		0.137
(0.372)
amp 4q13 3 161 (15%) 901 0.0835
(0.278) 		0.378
(0.625) 		0.816
(0.927) 		0.193
(0.438) 		0.635
(0.823) 		0.761
(0.887) 		0.225
(0.475) 		1e-05
(0.000244) 		0.336
(0.59) 		0.875
(0.956) 		0.163
(0.394) 		0.246
(0.502)
amp 8p11 21 412 (39%) 650 0.929
(0.996) 		0.158
(0.392) 		0.644
(0.826) 		0.888
(0.966) 		0.822
(0.929) 		0.37
(0.616) 		0.544
(0.762) 		0.00176
(0.018) 		0.202
(0.451) 		0.652
(0.83) 		0.194
(0.438) 		0.4
(0.646)
amp 10q22 3 150 (14%) 912 0.0958
(0.301) 		0.944
(1.00) 		0.35
(0.599) 		0.16
(0.394) 		0.221
(0.47) 		1
(1.00) 		0.66
(0.833) 		0.00038
(0.00552) 		0.113
(0.329) 		0.215
(0.464) 		0.151
(0.389) 		1
(1.00)
amp 11p13 219 (21%) 843 0.55
(0.764) 		0.359
(0.603) 		0.769
(0.892) 		0.476
(0.705) 		0.967
(1.00) 		0.419
(0.658) 		0.252
(0.504) 		1e-05
(0.000244) 		0.148
(0.388) 		0.527
(0.746) 		0.33
(0.587) 		0.679
(0.844)
amp 11q13 3 390 (37%) 672 0.152
(0.389) 		0.223
(0.473) 		0.382
(0.628) 		0.0427
(0.19) 		0.519
(0.742) 		0.175
(0.411) 		0.111
(0.328) 		0.253
(0.505) 		0.668
(0.839) 		0.567
(0.778) 		0.382
(0.628) 		0.73
(0.869)
amp 17p11 2 147 (14%) 915 0.175
(0.411) 		0.347
(0.599) 		0.6
(0.802) 		0.126
(0.352) 		0.614
(0.814) 		0.756
(0.884) 		0.186
(0.429) 		0.696
(0.855) 		0.0459
(0.199) 		0.289
(0.546) 		0.555
(0.766) 		1
(1.00)
amp 19q13 42 271 (26%) 791 0.514
(0.738) 		0.599
(0.802) 		0.963
(1.00) 		0.362
(0.606) 		0.633
(0.823) 		0.22
(0.47) 		0.16
(0.394) 		0.011
(0.0715) 		0.133
(0.368) 		0.115
(0.333) 		0.738
(0.873) 		0.569
(0.778)
del 7q36 1 197 (19%) 865 0.0982
(0.305) 		0.929
(0.996) 		0.656
(0.831) 		0.216
(0.465) 		0.307
(0.572) 		0.153
(0.389) 		1
(1.00) 		9e-05
(0.00173) 		0.658
(0.831) 		0.836
(0.934) 		0.684
(0.848) 		0.283
(0.537)
del 11q13 1 238 (22%) 824 0.33
(0.587) 		0.768
(0.892) 		0.434
(0.672) 		0.104
(0.315) 		0.381
(0.628) 		1
(1.00) 		0.717
(0.867) 		0.534
(0.754) 		0.741
(0.874) 		0.44
(0.674) 		0.0028
(0.0252) 		0.692
(0.853)
del 12p13 1 183 (17%) 879 0.442
(0.674) 		0.439
(0.674) 		0.252
(0.504) 		0.195
(0.439) 		0.955
(1.00) 		1
(1.00) 		0.415
(0.653) 		0.0049
(0.0379) 		0.361
(0.605) 		0.524
(0.745) 		0.673
(0.84) 		0.826
(0.929)
del 12q24 31 205 (19%) 857 0.249
(0.504) 		0.122
(0.344) 		0.892
(0.968) 		0.0804
(0.271) 		0.668
(0.839) 		1
(1.00) 		0.136
(0.372) 		0.0808
(0.271) 		1
(1.00) 		0.235
(0.485) 		0.0805
(0.271) 		0.405
(0.648)
'amp_1p22.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00988 (Fisher's exact test), Q value = 0.066

Table S1.  Gene #1: 'amp_1p22.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
AMP PEAK 1(1P22.3) MUTATED 43 153 35 11
AMP PEAK 1(1P22.3) WILD-TYPE 229 463 95 29

Figure S1.  Get High-res Image Gene #1: 'amp_1p22.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_1p22.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.0137 (Fisher's exact test), Q value = 0.082

Table S2.  Gene #1: 'amp_1p22.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 501 350 117 75
AMP PEAK 1(1P22.3) MUTATED 135 67 19 19
AMP PEAK 1(1P22.3) WILD-TYPE 366 283 98 56

Figure S2.  Get High-res Image Gene #1: 'amp_1p22.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_1p22.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00935 (Wilcoxon-test), Q value = 0.064

Table S3.  Gene #1: 'amp_1p22.3' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 897 2.4 (4.7)
AMP PEAK 1(1P22.3) MUTATED 215 1.9 (4.0)
AMP PEAK 1(1P22.3) WILD-TYPE 682 2.5 (4.8)

Figure S3.  Get High-res Image Gene #1: 'amp_1p22.3' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'amp_1p22.3' versus 'RACE'

P value = 0.045 (Fisher's exact test), Q value = 0.2

Table S4.  Gene #1: 'amp_1p22.3' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
AMP PEAK 1(1P22.3) MUTATED 0 9 51 162
AMP PEAK 1(1P22.3) WILD-TYPE 1 51 119 574

Figure S4.  Get High-res Image Gene #1: 'amp_1p22.3' versus Clinical Feature #11: 'RACE'

'amp_1q21.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.0109 (Fisher's exact test), Q value = 0.071

Table S5.  Gene #2: 'amp_1q21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
AMP PEAK 2(1Q21.3) MUTATED 180 456 97 35
AMP PEAK 2(1Q21.3) WILD-TYPE 92 160 33 5

Figure S5.  Get High-res Image Gene #2: 'amp_1q21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_1q44' versus 'Time to Death'

P value = 0.0413 (logrank test), Q value = 0.19

Table S6.  Gene #3: 'amp_1q44' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1044 128 0.0 - 234.3 (24.5)
AMP PEAK 3(1Q44) MUTATED 763 84 0.0 - 234.3 (23.8)
AMP PEAK 3(1Q44) WILD-TYPE 281 44 0.0 - 160.9 (24.8)

Figure S6.  Get High-res Image Gene #3: 'amp_1q44' versus Clinical Feature #1: 'Time to Death'

'amp_1q44' versus 'PATHOLOGY_T_STAGE'

P value = 0.00393 (Fisher's exact test), Q value = 0.033

Table S7.  Gene #3: 'amp_1q44' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
AMP PEAK 3(1Q44) MUTATED 176 467 95 33
AMP PEAK 3(1Q44) WILD-TYPE 96 149 35 7

Figure S7.  Get High-res Image Gene #3: 'amp_1q44' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_1q44' versus 'HISTOLOGICAL_TYPE'

P value = 0.0128 (Fisher's exact test), Q value = 0.08

Table S8.  Gene #3: 'amp_1q44' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
AMP PEAK 3(1Q44) MUTATED 1 544 159 5 3 21 9 32
AMP PEAK 3(1Q44) WILD-TYPE 0 219 33 1 1 9 8 16

Figure S8.  Get High-res Image Gene #3: 'amp_1q44' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_1q44' versus 'RACE'

P value = 0.0504 (Fisher's exact test), Q value = 0.21

Table S9.  Gene #3: 'amp_1q44' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
AMP PEAK 3(1Q44) MUTATED 1 35 125 546
AMP PEAK 3(1Q44) WILD-TYPE 0 25 45 190

Figure S9.  Get High-res Image Gene #3: 'amp_1q44' versus Clinical Feature #11: 'RACE'

'amp_3p25.1' versus 'Time to Death'

P value = 0.0427 (logrank test), Q value = 0.19

Table S10.  Gene #4: 'amp_3p25.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1044 128 0.0 - 234.3 (24.5)
AMP PEAK 4(3P25.1) MUTATED 195 31 0.3 - 220.9 (24.5)
AMP PEAK 4(3P25.1) WILD-TYPE 849 97 0.0 - 234.3 (24.6)

Figure S10.  Get High-res Image Gene #4: 'amp_3p25.1' versus Clinical Feature #1: 'Time to Death'

'amp_3p25.1' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0371 (Fisher's exact test), Q value = 0.17

Table S11.  Gene #4: 'amp_3p25.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
ALL 89 81 8 3 353 245 2 150 29 63 20 1 13
AMP PEAK 4(3P25.1) MUTATED 12 12 0 1 79 34 0 33 10 8 6 0 2
AMP PEAK 4(3P25.1) WILD-TYPE 77 69 8 2 274 211 2 117 19 55 14 1 11

Figure S11.  Get High-res Image Gene #4: 'amp_3p25.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'amp_3p25.1' versus 'PATHOLOGY_T_STAGE'

P value = 3e-04 (Fisher's exact test), Q value = 0.005

Table S12.  Gene #4: 'amp_3p25.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
AMP PEAK 4(3P25.1) MUTATED 37 132 14 13
AMP PEAK 4(3P25.1) WILD-TYPE 235 484 116 27

Figure S12.  Get High-res Image Gene #4: 'amp_3p25.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_3p25.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0253 (Fisher's exact test), Q value = 0.13

Table S13.  Gene #4: 'amp_3p25.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 501 350 117 75
AMP PEAK 4(3P25.1) MUTATED 94 54 33 12
AMP PEAK 4(3P25.1) WILD-TYPE 407 296 84 63

Figure S13.  Get High-res Image Gene #4: 'amp_3p25.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_3p25.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S14.  Gene #4: 'amp_3p25.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
AMP PEAK 4(3P25.1) MUTATED 1 167 14 1 0 5 1 8
AMP PEAK 4(3P25.1) WILD-TYPE 0 596 178 5 4 25 16 40

Figure S14.  Get High-res Image Gene #4: 'amp_3p25.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_3q26.32' versus 'PATHOLOGY_T_STAGE'

P value = 0.00012 (Fisher's exact test), Q value = 0.0022

Table S15.  Gene #5: 'amp_3q26.32' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
AMP PEAK 5(3Q26.32) MUTATED 65 224 30 17
AMP PEAK 5(3Q26.32) WILD-TYPE 207 392 100 23

Figure S15.  Get High-res Image Gene #5: 'amp_3q26.32' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_3q26.32' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S16.  Gene #5: 'amp_3q26.32' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
AMP PEAK 5(3Q26.32) MUTATED 1 291 15 5 3 6 1 14
AMP PEAK 5(3Q26.32) WILD-TYPE 0 472 177 1 1 24 16 34

Figure S16.  Get High-res Image Gene #5: 'amp_3q26.32' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_3q26.32' versus 'RACE'

P value = 0.00192 (Fisher's exact test), Q value = 0.019

Table S17.  Gene #5: 'amp_3q26.32' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
AMP PEAK 5(3Q26.32) MUTATED 1 27 63 206
AMP PEAK 5(3Q26.32) WILD-TYPE 0 33 107 530

Figure S17.  Get High-res Image Gene #5: 'amp_3q26.32' versus Clinical Feature #11: 'RACE'

'amp_4q13.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S18.  Gene #6: 'amp_4q13.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
AMP PEAK 6(4Q13.3) MUTATED 0 140 7 2 0 2 1 9
AMP PEAK 6(4Q13.3) WILD-TYPE 1 623 185 4 4 28 16 39

Figure S18.  Get High-res Image Gene #6: 'amp_4q13.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_5p15.33' versus 'PATHOLOGY_N_STAGE'

P value = 0.0133 (Fisher's exact test), Q value = 0.08

Table S19.  Gene #7: 'amp_5p15.33' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 501 350 117 75
AMP PEAK 7(5P15.33) MUTATED 196 107 53 26
AMP PEAK 7(5P15.33) WILD-TYPE 305 243 64 49

Figure S19.  Get High-res Image Gene #7: 'amp_5p15.33' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_5p15.33' versus 'HISTOLOGICAL_TYPE'

P value = 0.0526 (Fisher's exact test), Q value = 0.21

Table S20.  Gene #7: 'amp_5p15.33' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
AMP PEAK 7(5P15.33) MUTATED 1 293 60 2 3 9 2 16
AMP PEAK 7(5P15.33) WILD-TYPE 0 470 132 4 1 21 15 32

Figure S20.  Get High-res Image Gene #7: 'amp_5p15.33' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_5p15.33' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0627 (Fisher's exact test), Q value = 0.23

Table S21.  Gene #7: 'amp_5p15.33' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 288 774
AMP PEAK 7(5P15.33) MUTATED 118 269
AMP PEAK 7(5P15.33) WILD-TYPE 170 505

Figure S21.  Get High-res Image Gene #7: 'amp_5p15.33' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'amp_6p23' versus 'PATHOLOGY_T_STAGE'

P value = 0.00165 (Fisher's exact test), Q value = 0.017

Table S22.  Gene #8: 'amp_6p23' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
AMP PEAK 8(6P23) MUTATED 53 195 33 12
AMP PEAK 8(6P23) WILD-TYPE 219 421 97 28

Figure S22.  Get High-res Image Gene #8: 'amp_6p23' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_6p23' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S23.  Gene #8: 'amp_6p23' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
AMP PEAK 8(6P23) MUTATED 0 242 25 4 1 5 2 14
AMP PEAK 8(6P23) WILD-TYPE 1 521 167 2 3 25 15 34

Figure S23.  Get High-res Image Gene #8: 'amp_6p23' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_6p23' versus 'RACE'

P value = 0.00434 (Fisher's exact test), Q value = 0.035

Table S24.  Gene #8: 'amp_6p23' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
AMP PEAK 8(6P23) MUTATED 0 15 65 185
AMP PEAK 8(6P23) WILD-TYPE 1 45 105 551

Figure S24.  Get High-res Image Gene #8: 'amp_6p23' versus Clinical Feature #11: 'RACE'

'amp_6q21' versus 'PATHOLOGY_T_STAGE'

P value = 0.00023 (Fisher's exact test), Q value = 0.004

Table S25.  Gene #9: 'amp_6q21' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
AMP PEAK 9(6Q21) MUTATED 32 141 21 4
AMP PEAK 9(6Q21) WILD-TYPE 240 475 109 36

Figure S25.  Get High-res Image Gene #9: 'amp_6q21' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_6q21' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S26.  Gene #9: 'amp_6q21' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
AMP PEAK 9(6Q21) MUTATED 1 167 14 3 2 1 0 10
AMP PEAK 9(6Q21) WILD-TYPE 0 596 178 3 2 29 17 38

Figure S26.  Get High-res Image Gene #9: 'amp_6q21' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_6q21' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.037 (Wilcoxon-test), Q value = 0.17

Table S27.  Gene #9: 'amp_6q21' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 897 2.4 (4.7)
AMP PEAK 9(6Q21) MUTATED 169 2.0 (4.4)
AMP PEAK 9(6Q21) WILD-TYPE 728 2.5 (4.7)

Figure S27.  Get High-res Image Gene #9: 'amp_6q21' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'amp_8p11.23' versus 'Time to Death'

P value = 0.0301 (logrank test), Q value = 0.15

Table S28.  Gene #10: 'amp_8p11.23' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1044 128 0.0 - 234.3 (24.5)
AMP PEAK 10(8P11.23) MUTATED 400 62 0.0 - 220.9 (24.3)
AMP PEAK 10(8P11.23) WILD-TYPE 644 66 0.0 - 234.3 (24.8)

Figure S28.  Get High-res Image Gene #10: 'amp_8p11.23' versus Clinical Feature #1: 'Time to Death'

'amp_8p11.23' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0553 (Fisher's exact test), Q value = 0.22

Table S29.  Gene #10: 'amp_8p11.23' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
ALL 89 81 8 3 353 245 2 150 29 63 20 1 13
AMP PEAK 10(8P11.23) MUTATED 24 28 4 0 135 92 2 56 16 28 12 0 6
AMP PEAK 10(8P11.23) WILD-TYPE 65 53 4 3 218 153 0 94 13 35 8 1 7

Figure S29.  Get High-res Image Gene #10: 'amp_8p11.23' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'amp_8p11.23' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00763 (Wilcoxon-test), Q value = 0.054

Table S30.  Gene #10: 'amp_8p11.23' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 897 2.4 (4.7)
AMP PEAK 10(8P11.23) MUTATED 341 2.9 (5.3)
AMP PEAK 10(8P11.23) WILD-TYPE 556 2.1 (4.2)

Figure S30.  Get High-res Image Gene #10: 'amp_8p11.23' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'amp_8p11.21' versus 'HISTOLOGICAL_TYPE'

P value = 0.00176 (Fisher's exact test), Q value = 0.018

Table S31.  Gene #11: 'amp_8p11.21' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
AMP PEAK 11(8P11.21) MUTATED 1 316 53 5 1 11 4 20
AMP PEAK 11(8P11.21) WILD-TYPE 0 447 139 1 3 19 13 28

Figure S31.  Get High-res Image Gene #11: 'amp_8p11.21' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_8q24.21' versus 'YEARS_TO_BIRTH'

P value = 0.0527 (Wilcoxon-test), Q value = 0.21

Table S32.  Gene #12: 'amp_8q24.21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1047 58.6 (13.2)
AMP PEAK 12(8Q24.21) MUTATED 660 58.0 (13.1)
AMP PEAK 12(8Q24.21) WILD-TYPE 387 59.8 (13.3)

Figure S32.  Get High-res Image Gene #12: 'amp_8q24.21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_8q24.21' versus 'PATHOLOGY_T_STAGE'

P value = 0.0611 (Fisher's exact test), Q value = 0.23

Table S33.  Gene #12: 'amp_8q24.21' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
AMP PEAK 12(8Q24.21) MUTATED 156 407 76 25
AMP PEAK 12(8Q24.21) WILD-TYPE 116 209 54 15

Figure S33.  Get High-res Image Gene #12: 'amp_8q24.21' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_8q24.21' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S34.  Gene #12: 'amp_8q24.21' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
AMP PEAK 12(8Q24.21) MUTATED 1 539 68 6 2 17 5 29
AMP PEAK 12(8Q24.21) WILD-TYPE 0 224 124 0 2 13 12 19

Figure S34.  Get High-res Image Gene #12: 'amp_8q24.21' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_8q24.21' versus 'RACE'

P value = 0.00243 (Fisher's exact test), Q value = 0.023

Table S35.  Gene #12: 'amp_8q24.21' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
AMP PEAK 12(8Q24.21) MUTATED 1 41 123 432
AMP PEAK 12(8Q24.21) WILD-TYPE 0 19 47 304

Figure S35.  Get High-res Image Gene #12: 'amp_8q24.21' versus Clinical Feature #11: 'RACE'

'amp_10p15.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S36.  Gene #13: 'amp_10p15.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
AMP PEAK 13(10P15.1) MUTATED 1 258 19 5 0 5 0 10
AMP PEAK 13(10P15.1) WILD-TYPE 0 505 173 1 4 25 17 38

Figure S36.  Get High-res Image Gene #13: 'amp_10p15.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_10p15.1' versus 'RACE'

P value = 6e-05 (Fisher's exact test), Q value = 0.0012

Table S37.  Gene #13: 'amp_10p15.1' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
AMP PEAK 13(10P15.1) MUTATED 1 14 71 184
AMP PEAK 13(10P15.1) WILD-TYPE 0 46 99 552

Figure S37.  Get High-res Image Gene #13: 'amp_10p15.1' versus Clinical Feature #11: 'RACE'

'amp_10q22.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.00038 (Fisher's exact test), Q value = 0.0055

Table S38.  Gene #14: 'amp_10q22.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
AMP PEAK 14(10Q22.3) MUTATED 0 125 11 3 1 4 0 6
AMP PEAK 14(10Q22.3) WILD-TYPE 1 638 181 3 3 26 17 42

Figure S38.  Get High-res Image Gene #14: 'amp_10q22.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_11p13' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S39.  Gene #15: 'amp_11p13' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
AMP PEAK 15(11P13) MUTATED 1 184 16 3 1 2 2 10
AMP PEAK 15(11P13) WILD-TYPE 0 579 176 3 3 28 15 38

Figure S39.  Get High-res Image Gene #15: 'amp_11p13' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_11q13.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.0427 (Fisher's exact test), Q value = 0.19

Table S40.  Gene #16: 'amp_11q13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
AMP PEAK 16(11Q13.3) MUTATED 85 241 42 19
AMP PEAK 16(11Q13.3) WILD-TYPE 187 375 88 21

Figure S40.  Get High-res Image Gene #16: 'amp_11q13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_11q14.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.0636 (Fisher's exact test), Q value = 0.24

Table S41.  Gene #17: 'amp_11q14.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
AMP PEAK 17(11Q14.1) MUTATED 60 167 22 10
AMP PEAK 17(11Q14.1) WILD-TYPE 212 449 108 30

Figure S41.  Get High-res Image Gene #17: 'amp_11q14.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_11q14.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00383 (Fisher's exact test), Q value = 0.032

Table S42.  Gene #17: 'amp_11q14.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
AMP PEAK 17(11Q14.1) MUTATED 1 209 31 2 1 3 2 13
AMP PEAK 17(11Q14.1) WILD-TYPE 0 554 161 4 3 27 15 35

Figure S42.  Get High-res Image Gene #17: 'amp_11q14.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_12p13.33' versus 'PATHOLOGY_T_STAGE'

P value = 0.00298 (Fisher's exact test), Q value = 0.026

Table S43.  Gene #18: 'amp_12p13.33' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
AMP PEAK 18(12P13.33) MUTATED 49 182 34 12
AMP PEAK 18(12P13.33) WILD-TYPE 223 434 96 28

Figure S43.  Get High-res Image Gene #18: 'amp_12p13.33' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_12p13.33' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S44.  Gene #18: 'amp_12p13.33' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
AMP PEAK 18(12P13.33) MUTATED 1 227 27 4 0 10 1 9
AMP PEAK 18(12P13.33) WILD-TYPE 0 536 165 2 4 20 16 39

Figure S44.  Get High-res Image Gene #18: 'amp_12p13.33' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_12p13.33' versus 'RACE'

P value = 0.0235 (Fisher's exact test), Q value = 0.13

Table S45.  Gene #18: 'amp_12p13.33' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
AMP PEAK 18(12P13.33) MUTATED 0 13 59 178
AMP PEAK 18(12P13.33) WILD-TYPE 1 47 111 558

Figure S45.  Get High-res Image Gene #18: 'amp_12p13.33' versus Clinical Feature #11: 'RACE'

'amp_12p13.33' versus 'ETHNICITY'

P value = 0.0613 (Fisher's exact test), Q value = 0.23

Table S46.  Gene #18: 'amp_12p13.33' versus Clinical Feature #12: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 38 858
AMP PEAK 18(12P13.33) MUTATED 5 231
AMP PEAK 18(12P13.33) WILD-TYPE 33 627

Figure S46.  Get High-res Image Gene #18: 'amp_12p13.33' versus Clinical Feature #12: 'ETHNICITY'

'amp_12q15' versus 'PATHOLOGY_T_STAGE'

P value = 0.0229 (Fisher's exact test), Q value = 0.12

Table S47.  Gene #19: 'amp_12q15' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
AMP PEAK 19(12Q15) MUTATED 55 173 30 15
AMP PEAK 19(12Q15) WILD-TYPE 217 443 100 25

Figure S47.  Get High-res Image Gene #19: 'amp_12q15' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_12q15' versus 'PATHOLOGY_N_STAGE'

P value = 0.00944 (Fisher's exact test), Q value = 0.064

Table S48.  Gene #19: 'amp_12q15' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 501 350 117 75
AMP PEAK 19(12Q15) MUTATED 113 88 44 22
AMP PEAK 19(12Q15) WILD-TYPE 388 262 73 53

Figure S48.  Get High-res Image Gene #19: 'amp_12q15' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_12q15' versus 'GENDER'

P value = 0.00877 (Fisher's exact test), Q value = 0.061

Table S49.  Gene #19: 'amp_12q15' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1051 11
AMP PEAK 19(12Q15) MUTATED 267 7
AMP PEAK 19(12Q15) WILD-TYPE 784 4

Figure S49.  Get High-res Image Gene #19: 'amp_12q15' versus Clinical Feature #7: 'GENDER'

'amp_12q15' versus 'HISTOLOGICAL_TYPE'

P value = 0.00579 (Fisher's exact test), Q value = 0.044

Table S50.  Gene #19: 'amp_12q15' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
AMP PEAK 19(12Q15) MUTATED 0 222 33 1 0 9 2 7
AMP PEAK 19(12Q15) WILD-TYPE 1 541 159 5 4 21 15 41

Figure S50.  Get High-res Image Gene #19: 'amp_12q15' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_12q15' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0115 (Wilcoxon-test), Q value = 0.075

Table S51.  Gene #19: 'amp_12q15' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 897 2.4 (4.7)
AMP PEAK 19(12Q15) MUTATED 217 2.7 (4.6)
AMP PEAK 19(12Q15) WILD-TYPE 680 2.3 (4.7)

Figure S51.  Get High-res Image Gene #19: 'amp_12q15' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'amp_13q34' versus 'PATHOLOGY_T_STAGE'

P value = 0.00724 (Fisher's exact test), Q value = 0.053

Table S52.  Gene #20: 'amp_13q34' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
AMP PEAK 20(13Q34) MUTATED 30 122 17 6
AMP PEAK 20(13Q34) WILD-TYPE 242 494 113 34

Figure S52.  Get High-res Image Gene #20: 'amp_13q34' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_13q34' versus 'HISTOLOGICAL_TYPE'

P value = 0.00079 (Fisher's exact test), Q value = 0.0096

Table S53.  Gene #20: 'amp_13q34' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
AMP PEAK 20(13Q34) MUTATED 0 144 13 1 2 4 2 10
AMP PEAK 20(13Q34) WILD-TYPE 1 619 179 5 2 26 15 38

Figure S53.  Get High-res Image Gene #20: 'amp_13q34' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_13q34' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0528 (Wilcoxon-test), Q value = 0.21

Table S54.  Gene #20: 'amp_13q34' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 897 2.4 (4.7)
AMP PEAK 20(13Q34) MUTATED 152 1.9 (4.4)
AMP PEAK 20(13Q34) WILD-TYPE 745 2.5 (4.7)

Figure S54.  Get High-res Image Gene #20: 'amp_13q34' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'amp_14q21.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.0333 (Fisher's exact test), Q value = 0.17

Table S55.  Gene #21: 'amp_14q21.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
AMP PEAK 21(14Q21.1) MUTATED 43 145 21 8
AMP PEAK 21(14Q21.1) WILD-TYPE 229 471 109 32

Figure S55.  Get High-res Image Gene #21: 'amp_14q21.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_14q21.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0234 (Fisher's exact test), Q value = 0.13

Table S56.  Gene #21: 'amp_14q21.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 501 350 117 75
AMP PEAK 21(14Q21.1) MUTATED 86 73 32 21
AMP PEAK 21(14Q21.1) WILD-TYPE 415 277 85 54

Figure S56.  Get High-res Image Gene #21: 'amp_14q21.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_14q21.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.009 (Fisher's exact test), Q value = 0.062

Table S57.  Gene #21: 'amp_14q21.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
AMP PEAK 21(14Q21.1) MUTATED 0 172 23 0 2 9 2 9
AMP PEAK 21(14Q21.1) WILD-TYPE 1 591 169 6 2 21 15 39

Figure S57.  Get High-res Image Gene #21: 'amp_14q21.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_14q21.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0104 (Wilcoxon-test), Q value = 0.069

Table S58.  Gene #21: 'amp_14q21.1' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 897 2.4 (4.7)
AMP PEAK 21(14Q21.1) MUTATED 175 2.9 (4.8)
AMP PEAK 21(14Q21.1) WILD-TYPE 722 2.3 (4.6)

Figure S58.  Get High-res Image Gene #21: 'amp_14q21.1' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'amp_15q26.3' versus 'YEARS_TO_BIRTH'

P value = 0.00714 (Wilcoxon-test), Q value = 0.053

Table S59.  Gene #22: 'amp_15q26.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1047 58.6 (13.2)
AMP PEAK 22(15Q26.3) MUTATED 189 56.3 (12.9)
AMP PEAK 22(15Q26.3) WILD-TYPE 858 59.1 (13.2)

Figure S59.  Get High-res Image Gene #22: 'amp_15q26.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_15q26.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S60.  Gene #22: 'amp_15q26.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
AMP PEAK 22(15Q26.3) MUTATED 0 166 11 3 0 4 3 5
AMP PEAK 22(15Q26.3) WILD-TYPE 1 597 181 3 4 26 14 43

Figure S60.  Get High-res Image Gene #22: 'amp_15q26.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_15q26.3' versus 'RACE'

P value = 0.0449 (Fisher's exact test), Q value = 0.2

Table S61.  Gene #22: 'amp_15q26.3' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
AMP PEAK 22(15Q26.3) MUTATED 0 16 38 118
AMP PEAK 22(15Q26.3) WILD-TYPE 1 44 132 618

Figure S61.  Get High-res Image Gene #22: 'amp_15q26.3' versus Clinical Feature #11: 'RACE'

'amp_17p11.2' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0459 (Fisher's exact test), Q value = 0.2

Table S62.  Gene #23: 'amp_17p11.2' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 288 774
AMP PEAK 23(17P11.2) MUTATED 50 97
AMP PEAK 23(17P11.2) WILD-TYPE 238 677

Figure S62.  Get High-res Image Gene #23: 'amp_17p11.2' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'amp_17q12' versus 'GENDER'

P value = 0.00514 (Fisher's exact test), Q value = 0.039

Table S63.  Gene #24: 'amp_17q12' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1051 11
AMP PEAK 24(17Q12) MUTATED 321 8
AMP PEAK 24(17Q12) WILD-TYPE 730 3

Figure S63.  Get High-res Image Gene #24: 'amp_17q12' versus Clinical Feature #7: 'GENDER'

'amp_17q12' versus 'HISTOLOGICAL_TYPE'

P value = 0.00034 (Fisher's exact test), Q value = 0.0054

Table S64.  Gene #24: 'amp_17q12' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
AMP PEAK 24(17Q12) MUTATED 0 268 37 1 2 5 4 12
AMP PEAK 24(17Q12) WILD-TYPE 1 495 155 5 2 25 13 36

Figure S64.  Get High-res Image Gene #24: 'amp_17q12' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_17q12' versus 'RACE'

P value = 0.00172 (Fisher's exact test), Q value = 0.018

Table S65.  Gene #24: 'amp_17q12' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
AMP PEAK 24(17Q12) MUTATED 1 30 49 208
AMP PEAK 24(17Q12) WILD-TYPE 0 30 121 528

Figure S65.  Get High-res Image Gene #24: 'amp_17q12' versus Clinical Feature #11: 'RACE'

'amp_17q23.1' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0355 (Fisher's exact test), Q value = 0.17

Table S66.  Gene #25: 'amp_17q23.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
ALL 89 81 8 3 353 245 2 150 29 63 20 1 13
AMP PEAK 25(17Q23.1) MUTATED 27 23 2 1 151 100 1 66 16 20 9 1 2
AMP PEAK 25(17Q23.1) WILD-TYPE 62 58 6 2 202 145 1 84 13 43 11 0 11

Figure S66.  Get High-res Image Gene #25: 'amp_17q23.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'amp_17q23.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00043 (Fisher's exact test), Q value = 0.006

Table S67.  Gene #25: 'amp_17q23.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
AMP PEAK 25(17Q23.1) MUTATED 80 272 47 18
AMP PEAK 25(17Q23.1) WILD-TYPE 192 344 83 22

Figure S67.  Get High-res Image Gene #25: 'amp_17q23.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_17q23.1' versus 'GENDER'

P value = 3.33e-05 (Fisher's exact test), Q value = 0.00067

Table S68.  Gene #25: 'amp_17q23.1' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1051 11
AMP PEAK 25(17Q23.1) MUTATED 408 11
AMP PEAK 25(17Q23.1) WILD-TYPE 643 0

Figure S68.  Get High-res Image Gene #25: 'amp_17q23.1' versus Clinical Feature #7: 'GENDER'

'amp_17q23.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S69.  Gene #25: 'amp_17q23.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
AMP PEAK 25(17Q23.1) MUTATED 1 337 41 3 2 11 5 18
AMP PEAK 25(17Q23.1) WILD-TYPE 0 426 151 3 2 19 12 30

Figure S69.  Get High-res Image Gene #25: 'amp_17q23.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_19p13.12' versus 'PATHOLOGY_M_STAGE'

P value = 0.0621 (Fisher's exact test), Q value = 0.23

Table S70.  Gene #26: 'amp_19p13.12' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 879 21
AMP PEAK 26(19P13.12) MUTATED 191 1
AMP PEAK 26(19P13.12) WILD-TYPE 688 20

Figure S70.  Get High-res Image Gene #26: 'amp_19p13.12' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_19p13.12' versus 'GENDER'

P value = 0.0639 (Fisher's exact test), Q value = 0.24

Table S71.  Gene #26: 'amp_19p13.12' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1051 11
AMP PEAK 26(19P13.12) MUTATED 222 5
AMP PEAK 26(19P13.12) WILD-TYPE 829 6

Figure S71.  Get High-res Image Gene #26: 'amp_19p13.12' versus Clinical Feature #7: 'GENDER'

'amp_19p13.12' versus 'HISTOLOGICAL_TYPE'

P value = 0.0283 (Fisher's exact test), Q value = 0.15

Table S72.  Gene #26: 'amp_19p13.12' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
AMP PEAK 26(19P13.12) MUTATED 1 167 33 4 2 6 2 12
AMP PEAK 26(19P13.12) WILD-TYPE 0 596 159 2 2 24 15 36

Figure S72.  Get High-res Image Gene #26: 'amp_19p13.12' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_19p13.12' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0284 (Fisher's exact test), Q value = 0.15

Table S73.  Gene #26: 'amp_19p13.12' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 288 774
AMP PEAK 26(19P13.12) MUTATED 75 152
AMP PEAK 26(19P13.12) WILD-TYPE 213 622

Figure S73.  Get High-res Image Gene #26: 'amp_19p13.12' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'amp_19p13.12' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000917 (Wilcoxon-test), Q value = 0.011

Table S74.  Gene #26: 'amp_19p13.12' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 897 2.4 (4.7)
AMP PEAK 26(19P13.12) MUTATED 204 1.9 (4.5)
AMP PEAK 26(19P13.12) WILD-TYPE 693 2.5 (4.7)

Figure S74.  Get High-res Image Gene #26: 'amp_19p13.12' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'amp_19q12' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0177 (Fisher's exact test), Q value = 0.099

Table S75.  Gene #27: 'amp_19q12' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
ALL 89 81 8 3 353 245 2 150 29 63 20 1 13
AMP PEAK 27(19Q12) MUTATED 23 17 2 0 120 54 0 35 8 12 4 0 0
AMP PEAK 27(19Q12) WILD-TYPE 66 64 6 3 233 191 2 115 21 51 16 1 13

Figure S75.  Get High-res Image Gene #27: 'amp_19q12' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'amp_19q12' versus 'PATHOLOGY_N_STAGE'

P value = 0.0376 (Fisher's exact test), Q value = 0.18

Table S76.  Gene #27: 'amp_19q12' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 501 350 117 75
AMP PEAK 27(19Q12) MUTATED 153 82 28 14
AMP PEAK 27(19Q12) WILD-TYPE 348 268 89 61

Figure S76.  Get High-res Image Gene #27: 'amp_19q12' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_19q12' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S77.  Gene #27: 'amp_19q12' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
AMP PEAK 27(19Q12) MUTATED 0 221 29 6 2 6 2 12
AMP PEAK 27(19Q12) WILD-TYPE 1 542 163 0 2 24 15 36

Figure S77.  Get High-res Image Gene #27: 'amp_19q12' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_19q12' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00504 (Wilcoxon-test), Q value = 0.039

Table S78.  Gene #27: 'amp_19q12' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 897 2.4 (4.7)
AMP PEAK 27(19Q12) MUTATED 240 2.0 (4.6)
AMP PEAK 27(19Q12) WILD-TYPE 657 2.5 (4.7)

Figure S78.  Get High-res Image Gene #27: 'amp_19q12' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'amp_19q13.42' versus 'HISTOLOGICAL_TYPE'

P value = 0.011 (Fisher's exact test), Q value = 0.072

Table S79.  Gene #28: 'amp_19q13.42' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
AMP PEAK 28(19Q13.42) MUTATED 1 213 33 2 2 5 2 13
AMP PEAK 28(19Q13.42) WILD-TYPE 0 550 159 4 2 25 15 35

Figure S79.  Get High-res Image Gene #28: 'amp_19q13.42' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_20q13.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.0024 (Fisher's exact test), Q value = 0.023

Table S80.  Gene #29: 'amp_20q13.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
AMP PEAK 29(20Q13.2) MUTATED 118 341 56 22
AMP PEAK 29(20Q13.2) WILD-TYPE 154 275 74 18

Figure S80.  Get High-res Image Gene #29: 'amp_20q13.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_20q13.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.00257 (Fisher's exact test), Q value = 0.024

Table S81.  Gene #29: 'amp_20q13.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 501 350 117 75
AMP PEAK 29(20Q13.2) MUTATED 245 176 77 31
AMP PEAK 29(20Q13.2) WILD-TYPE 256 174 40 44

Figure S81.  Get High-res Image Gene #29: 'amp_20q13.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_20q13.2' versus 'GENDER'

P value = 0.0645 (Fisher's exact test), Q value = 0.24

Table S82.  Gene #29: 'amp_20q13.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1051 11
AMP PEAK 29(20Q13.2) MUTATED 531 9
AMP PEAK 29(20Q13.2) WILD-TYPE 520 2

Figure S82.  Get High-res Image Gene #29: 'amp_20q13.2' versus Clinical Feature #7: 'GENDER'

'amp_20q13.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S83.  Gene #29: 'amp_20q13.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
AMP PEAK 29(20Q13.2) MUTATED 1 446 53 1 3 12 1 23
AMP PEAK 29(20Q13.2) WILD-TYPE 0 317 139 5 1 18 16 25

Figure S83.  Get High-res Image Gene #29: 'amp_20q13.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_20q13.2' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.000252 (Fisher's exact test), Q value = 0.0043

Table S84.  Gene #29: 'amp_20q13.2' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 288 774
AMP PEAK 29(20Q13.2) MUTATED 173 367
AMP PEAK 29(20Q13.2) WILD-TYPE 115 407

Figure S84.  Get High-res Image Gene #29: 'amp_20q13.2' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'del_1p36.13' versus 'YEARS_TO_BIRTH'

P value = 0.0158 (Wilcoxon-test), Q value = 0.09

Table S85.  Gene #30: 'del_1p36.13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1047 58.6 (13.2)
DEL PEAK 1(1P36.13) MUTATED 435 59.6 (13.1)
DEL PEAK 1(1P36.13) WILD-TYPE 612 58.0 (13.2)

Figure S85.  Get High-res Image Gene #30: 'del_1p36.13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_1p36.13' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00163 (Fisher's exact test), Q value = 0.017

Table S86.  Gene #30: 'del_1p36.13' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
ALL 89 81 8 3 353 245 2 150 29 63 20 1 13
DEL PEAK 1(1P36.13) MUTATED 28 22 1 1 137 112 1 72 18 31 12 0 5
DEL PEAK 1(1P36.13) WILD-TYPE 61 59 7 2 216 133 1 78 11 32 8 1 8

Figure S86.  Get High-res Image Gene #30: 'del_1p36.13' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_1p36.13' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S87.  Gene #30: 'del_1p36.13' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
DEL PEAK 1(1P36.13) MUTATED 81 282 51 26
DEL PEAK 1(1P36.13) WILD-TYPE 191 334 79 14

Figure S87.  Get High-res Image Gene #30: 'del_1p36.13' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_1p36.13' versus 'PATHOLOGY_N_STAGE'

P value = 0.00038 (Fisher's exact test), Q value = 0.0055

Table S88.  Gene #30: 'del_1p36.13' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 501 350 117 75
DEL PEAK 1(1P36.13) MUTATED 175 164 55 39
DEL PEAK 1(1P36.13) WILD-TYPE 326 186 62 36

Figure S88.  Get High-res Image Gene #30: 'del_1p36.13' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_1p36.13' versus 'GENDER'

P value = 0.0599 (Fisher's exact test), Q value = 0.23

Table S89.  Gene #30: 'del_1p36.13' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1051 11
DEL PEAK 1(1P36.13) MUTATED 433 8
DEL PEAK 1(1P36.13) WILD-TYPE 618 3

Figure S89.  Get High-res Image Gene #30: 'del_1p36.13' versus Clinical Feature #7: 'GENDER'

'del_1p36.13' versus 'HISTOLOGICAL_TYPE'

P value = 0.0133 (Fisher's exact test), Q value = 0.08

Table S90.  Gene #30: 'del_1p36.13' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
DEL PEAK 1(1P36.13) MUTATED 1 341 69 1 0 8 4 17
DEL PEAK 1(1P36.13) WILD-TYPE 0 422 123 5 4 22 13 31

Figure S90.  Get High-res Image Gene #30: 'del_1p36.13' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_1p36.13' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0498 (Fisher's exact test), Q value = 0.21

Table S91.  Gene #30: 'del_1p36.13' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 288 774
DEL PEAK 1(1P36.13) MUTATED 134 307
DEL PEAK 1(1P36.13) WILD-TYPE 154 467

Figure S91.  Get High-res Image Gene #30: 'del_1p36.13' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'del_1p36.13' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00136 (Wilcoxon-test), Q value = 0.015

Table S92.  Gene #30: 'del_1p36.13' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 897 2.4 (4.7)
DEL PEAK 1(1P36.13) MUTATED 362 2.8 (5.1)
DEL PEAK 1(1P36.13) WILD-TYPE 535 2.1 (4.4)

Figure S92.  Get High-res Image Gene #30: 'del_1p36.13' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'del_1p22.1' versus 'Time to Death'

P value = 0.00478 (logrank test), Q value = 0.037

Table S93.  Gene #31: 'del_1p22.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1044 128 0.0 - 234.3 (24.5)
DEL PEAK 2(1P22.1) MUTATED 351 53 0.0 - 162.1 (23.1)
DEL PEAK 2(1P22.1) WILD-TYPE 693 75 0.0 - 234.3 (25.0)

Figure S93.  Get High-res Image Gene #31: 'del_1p22.1' versus Clinical Feature #1: 'Time to Death'

'del_1p22.1' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0165 (Fisher's exact test), Q value = 0.093

Table S94.  Gene #31: 'del_1p22.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
ALL 89 81 8 3 353 245 2 150 29 63 20 1 13
DEL PEAK 2(1P22.1) MUTATED 20 20 1 0 116 81 1 60 16 26 9 0 5
DEL PEAK 2(1P22.1) WILD-TYPE 69 61 7 3 237 164 1 90 13 37 11 1 8

Figure S94.  Get High-res Image Gene #31: 'del_1p22.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_1p22.1' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00045

Table S95.  Gene #31: 'del_1p22.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
DEL PEAK 2(1P22.1) MUTATED 67 224 42 24
DEL PEAK 2(1P22.1) WILD-TYPE 205 392 88 16

Figure S95.  Get High-res Image Gene #31: 'del_1p22.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_1p22.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.00756 (Fisher's exact test), Q value = 0.054

Table S96.  Gene #31: 'del_1p22.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 501 350 117 75
DEL PEAK 2(1P22.1) MUTATED 144 126 50 30
DEL PEAK 2(1P22.1) WILD-TYPE 357 224 67 45

Figure S96.  Get High-res Image Gene #31: 'del_1p22.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_1p22.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00118 (Wilcoxon-test), Q value = 0.014

Table S97.  Gene #31: 'del_1p22.1' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 897 2.4 (4.7)
DEL PEAK 2(1P22.1) MUTATED 287 2.9 (5.3)
DEL PEAK 2(1P22.1) WILD-TYPE 610 2.1 (4.3)

Figure S97.  Get High-res Image Gene #31: 'del_1p22.1' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'del_2q37.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00185 (Fisher's exact test), Q value = 0.018

Table S98.  Gene #32: 'del_2q37.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
DEL PEAK 3(2Q37.3) MUTATED 60 195 37 19
DEL PEAK 3(2Q37.3) WILD-TYPE 212 421 93 21

Figure S98.  Get High-res Image Gene #32: 'del_2q37.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_2q37.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S99.  Gene #32: 'del_2q37.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
DEL PEAK 3(2Q37.3) MUTATED 0 258 25 3 3 9 3 11
DEL PEAK 3(2Q37.3) WILD-TYPE 1 505 167 3 1 21 14 37

Figure S99.  Get High-res Image Gene #32: 'del_2q37.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_2q37.3' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0493 (Fisher's exact test), Q value = 0.21

Table S100.  Gene #32: 'del_2q37.3' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 288 774
DEL PEAK 3(2Q37.3) MUTATED 98 215
DEL PEAK 3(2Q37.3) WILD-TYPE 190 559

Figure S100.  Get High-res Image Gene #32: 'del_2q37.3' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'del_2q37.3' versus 'RACE'

P value = 0.0438 (Fisher's exact test), Q value = 0.19

Table S101.  Gene #32: 'del_2q37.3' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
DEL PEAK 3(2Q37.3) MUTATED 0 25 54 197
DEL PEAK 3(2Q37.3) WILD-TYPE 1 35 116 539

Figure S101.  Get High-res Image Gene #32: 'del_2q37.3' versus Clinical Feature #11: 'RACE'

'del_3p21.31' versus 'Time to Death'

P value = 0.0157 (logrank test), Q value = 0.09

Table S102.  Gene #33: 'del_3p21.31' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1044 128 0.0 - 234.3 (24.5)
DEL PEAK 4(3P21.31) MUTATED 339 52 0.2 - 177.0 (23.3)
DEL PEAK 4(3P21.31) WILD-TYPE 705 76 0.0 - 234.3 (24.9)

Figure S102.  Get High-res Image Gene #33: 'del_3p21.31' versus Clinical Feature #1: 'Time to Death'

'del_3p21.31' versus 'YEARS_TO_BIRTH'

P value = 0.00368 (Wilcoxon-test), Q value = 0.031

Table S103.  Gene #33: 'del_3p21.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1047 58.6 (13.2)
DEL PEAK 4(3P21.31) MUTATED 338 56.8 (13.0)
DEL PEAK 4(3P21.31) WILD-TYPE 709 59.5 (13.1)

Figure S103.  Get High-res Image Gene #33: 'del_3p21.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_3p21.31' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S104.  Gene #33: 'del_3p21.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
DEL PEAK 4(3P21.31) MUTATED 57 236 39 10
DEL PEAK 4(3P21.31) WILD-TYPE 215 380 91 30

Figure S104.  Get High-res Image Gene #33: 'del_3p21.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_3p21.31' versus 'HISTOLOGICAL_TYPE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00064

Table S105.  Gene #33: 'del_3p21.31' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
DEL PEAK 4(3P21.31) MUTATED 1 282 40 1 1 6 1 12
DEL PEAK 4(3P21.31) WILD-TYPE 0 481 152 5 3 24 16 36

Figure S105.  Get High-res Image Gene #33: 'del_3p21.31' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_3p21.31' versus 'RACE'

P value = 0.0121 (Fisher's exact test), Q value = 0.077

Table S106.  Gene #33: 'del_3p21.31' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
DEL PEAK 4(3P21.31) MUTATED 0 26 69 224
DEL PEAK 4(3P21.31) WILD-TYPE 1 34 101 512

Figure S106.  Get High-res Image Gene #33: 'del_3p21.31' versus Clinical Feature #11: 'RACE'

'del_4p16.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00015 (Fisher's exact test), Q value = 0.0027

Table S107.  Gene #34: 'del_4p16.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
DEL PEAK 5(4P16.3) MUTATED 58 222 38 13
DEL PEAK 5(4P16.3) WILD-TYPE 214 394 92 27

Figure S107.  Get High-res Image Gene #34: 'del_4p16.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_4p16.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S108.  Gene #34: 'del_4p16.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
DEL PEAK 5(4P16.3) MUTATED 1 276 31 4 2 6 0 13
DEL PEAK 5(4P16.3) WILD-TYPE 0 487 161 2 2 24 17 35

Figure S108.  Get High-res Image Gene #34: 'del_4p16.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_4p16.3' versus 'RACE'

P value = 0.0307 (Fisher's exact test), Q value = 0.15

Table S109.  Gene #34: 'del_4p16.3' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
DEL PEAK 5(4P16.3) MUTATED 1 17 68 224
DEL PEAK 5(4P16.3) WILD-TYPE 0 43 102 512

Figure S109.  Get High-res Image Gene #34: 'del_4p16.3' versus Clinical Feature #11: 'RACE'

'del_4q35.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00273 (Fisher's exact test), Q value = 0.025

Table S110.  Gene #35: 'del_4q35.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
DEL PEAK 6(4Q35.1) MUTATED 66 220 36 16
DEL PEAK 6(4Q35.1) WILD-TYPE 206 396 94 24

Figure S110.  Get High-res Image Gene #35: 'del_4q35.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_4q35.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S111.  Gene #35: 'del_4q35.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
DEL PEAK 6(4Q35.1) MUTATED 1 284 34 4 3 3 0 10
DEL PEAK 6(4Q35.1) WILD-TYPE 0 479 158 2 1 27 17 38

Figure S111.  Get High-res Image Gene #35: 'del_4q35.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_4q35.1' versus 'RACE'

P value = 0.00762 (Fisher's exact test), Q value = 0.054

Table S112.  Gene #35: 'del_4q35.1' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
DEL PEAK 6(4Q35.1) MUTATED 1 23 69 217
DEL PEAK 6(4Q35.1) WILD-TYPE 0 37 101 519

Figure S112.  Get High-res Image Gene #35: 'del_4q35.1' versus Clinical Feature #11: 'RACE'

'del_5q11.2' versus 'YEARS_TO_BIRTH'

P value = 3.32e-05 (Wilcoxon-test), Q value = 0.00067

Table S113.  Gene #36: 'del_5q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1047 58.6 (13.2)
DEL PEAK 7(5Q11.2) MUTATED 271 55.9 (13.2)
DEL PEAK 7(5Q11.2) WILD-TYPE 776 59.6 (13.0)

Figure S113.  Get High-res Image Gene #36: 'del_5q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_5q11.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00051 (Fisher's exact test), Q value = 0.0068

Table S114.  Gene #36: 'del_5q11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
DEL PEAK 7(5Q11.2) MUTATED 58 184 19 12
DEL PEAK 7(5Q11.2) WILD-TYPE 214 432 111 28

Figure S114.  Get High-res Image Gene #36: 'del_5q11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_5q11.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S115.  Gene #36: 'del_5q11.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
DEL PEAK 7(5Q11.2) MUTATED 1 239 11 5 0 5 1 11
DEL PEAK 7(5Q11.2) WILD-TYPE 0 524 181 1 4 25 16 37

Figure S115.  Get High-res Image Gene #36: 'del_5q11.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_5q11.2' versus 'RACE'

P value = 0.00056 (Fisher's exact test), Q value = 0.0072

Table S116.  Gene #36: 'del_5q11.2' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
DEL PEAK 7(5Q11.2) MUTATED 1 20 62 170
DEL PEAK 7(5Q11.2) WILD-TYPE 0 40 108 566

Figure S116.  Get High-res Image Gene #36: 'del_5q11.2' versus Clinical Feature #11: 'RACE'

'del_5q21.3' versus 'YEARS_TO_BIRTH'

P value = 0.000897 (Wilcoxon-test), Q value = 0.011

Table S117.  Gene #37: 'del_5q21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1047 58.6 (13.2)
DEL PEAK 8(5Q21.3) MUTATED 262 56.4 (13.3)
DEL PEAK 8(5Q21.3) WILD-TYPE 785 59.4 (13.0)

Figure S117.  Get High-res Image Gene #37: 'del_5q21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_5q21.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00011 (Fisher's exact test), Q value = 0.0021

Table S118.  Gene #37: 'del_5q21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
DEL PEAK 8(5Q21.3) MUTATED 52 181 18 12
DEL PEAK 8(5Q21.3) WILD-TYPE 220 435 112 28

Figure S118.  Get High-res Image Gene #37: 'del_5q21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_5q21.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S119.  Gene #37: 'del_5q21.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
DEL PEAK 8(5Q21.3) MUTATED 1 237 5 6 1 5 0 9
DEL PEAK 8(5Q21.3) WILD-TYPE 0 526 187 0 3 25 17 39

Figure S119.  Get High-res Image Gene #37: 'del_5q21.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_5q21.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00288 (Wilcoxon-test), Q value = 0.026

Table S120.  Gene #37: 'del_5q21.3' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 897 2.4 (4.7)
DEL PEAK 8(5Q21.3) MUTATED 226 1.7 (3.7)
DEL PEAK 8(5Q21.3) WILD-TYPE 671 2.6 (4.9)

Figure S120.  Get High-res Image Gene #37: 'del_5q21.3' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'del_5q21.3' versus 'RACE'

P value = 5e-04 (Fisher's exact test), Q value = 0.0068

Table S121.  Gene #37: 'del_5q21.3' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
DEL PEAK 8(5Q21.3) MUTATED 0 18 63 163
DEL PEAK 8(5Q21.3) WILD-TYPE 1 42 107 573

Figure S121.  Get High-res Image Gene #37: 'del_5q21.3' versus Clinical Feature #11: 'RACE'

'del_6p25.3' versus 'YEARS_TO_BIRTH'

P value = 0.0555 (Wilcoxon-test), Q value = 0.22

Table S122.  Gene #38: 'del_6p25.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1047 58.6 (13.2)
DEL PEAK 9(6P25.3) MUTATED 199 56.9 (12.9)
DEL PEAK 9(6P25.3) WILD-TYPE 848 59.0 (13.2)

Figure S122.  Get High-res Image Gene #38: 'del_6p25.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_6p25.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.0256 (Fisher's exact test), Q value = 0.13

Table S123.  Gene #38: 'del_6p25.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
DEL PEAK 9(6P25.3) MUTATED 46 135 15 6
DEL PEAK 9(6P25.3) WILD-TYPE 226 481 115 34

Figure S123.  Get High-res Image Gene #38: 'del_6p25.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_6q15' versus 'YEARS_TO_BIRTH'

P value = 0.0616 (Wilcoxon-test), Q value = 0.23

Table S124.  Gene #39: 'del_6q15' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1047 58.6 (13.2)
DEL PEAK 10(6Q15) MUTATED 350 57.5 (13.1)
DEL PEAK 10(6Q15) WILD-TYPE 697 59.2 (13.2)

Figure S124.  Get High-res Image Gene #39: 'del_6q15' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_6q15' versus 'PATHOLOGY_N_STAGE'

P value = 0.0375 (Fisher's exact test), Q value = 0.18

Table S125.  Gene #39: 'del_6q15' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 501 350 117 75
DEL PEAK 10(6Q15) MUTATED 148 126 49 23
DEL PEAK 10(6Q15) WILD-TYPE 353 224 68 52

Figure S125.  Get High-res Image Gene #39: 'del_6q15' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_6q15' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0134 (Wilcoxon-test), Q value = 0.08

Table S126.  Gene #39: 'del_6q15' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 897 2.4 (4.7)
DEL PEAK 10(6Q15) MUTATED 288 2.6 (4.6)
DEL PEAK 10(6Q15) WILD-TYPE 609 2.3 (4.7)

Figure S126.  Get High-res Image Gene #39: 'del_6q15' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'del_6q27' versus 'YEARS_TO_BIRTH'

P value = 1.2e-05 (Wilcoxon-test), Q value = 0.00028

Table S127.  Gene #40: 'del_6q27' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1047 58.6 (13.2)
DEL PEAK 11(6Q27) MUTATED 366 56.1 (12.6)
DEL PEAK 11(6Q27) WILD-TYPE 681 60.0 (13.3)

Figure S127.  Get High-res Image Gene #40: 'del_6q27' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_6q27' versus 'PATHOLOGY_N_STAGE'

P value = 0.0383 (Fisher's exact test), Q value = 0.18

Table S128.  Gene #40: 'del_6q27' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 501 350 117 75
DEL PEAK 11(6Q27) MUTATED 167 134 46 17
DEL PEAK 11(6Q27) WILD-TYPE 334 216 71 58

Figure S128.  Get High-res Image Gene #40: 'del_6q27' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_6q27' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0358 (Fisher's exact test), Q value = 0.17

Table S129.  Gene #40: 'del_6q27' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 288 774
DEL PEAK 11(6Q27) MUTATED 115 255
DEL PEAK 11(6Q27) WILD-TYPE 173 519

Figure S129.  Get High-res Image Gene #40: 'del_6q27' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'del_7p22.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.0546 (Fisher's exact test), Q value = 0.22

Table S130.  Gene #41: 'del_7p22.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 501 350 117 75
DEL PEAK 12(7P22.3) MUTATED 74 35 18 5
DEL PEAK 12(7P22.3) WILD-TYPE 427 315 99 70

Figure S130.  Get High-res Image Gene #41: 'del_7p22.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_7p22.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S131.  Gene #41: 'del_7p22.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
DEL PEAK 12(7P22.3) MUTATED 0 119 4 1 1 4 0 6
DEL PEAK 12(7P22.3) WILD-TYPE 1 644 188 5 3 26 17 42

Figure S131.  Get High-res Image Gene #41: 'del_7p22.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_7p22.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0196 (Wilcoxon-test), Q value = 0.11

Table S132.  Gene #41: 'del_7p22.3' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 897 2.4 (4.7)
DEL PEAK 12(7P22.3) MUTATED 108 1.6 (3.5)
DEL PEAK 12(7P22.3) WILD-TYPE 789 2.5 (4.8)

Figure S132.  Get High-res Image Gene #41: 'del_7p22.3' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'del_7q36.1' versus 'HISTOLOGICAL_TYPE'

P value = 9e-05 (Fisher's exact test), Q value = 0.0017

Table S133.  Gene #42: 'del_7q36.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
DEL PEAK 13(7Q36.1) MUTATED 0 164 15 0 0 7 0 11
DEL PEAK 13(7Q36.1) WILD-TYPE 1 599 177 6 4 23 17 37

Figure S133.  Get High-res Image Gene #42: 'del_7q36.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_8p23.2' versus 'Time to Death'

P value = 0.0504 (logrank test), Q value = 0.21

Table S134.  Gene #43: 'del_8p23.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1044 128 0.0 - 234.3 (24.5)
DEL PEAK 14(8P23.2) MUTATED 545 81 0.2 - 220.9 (24.4)
DEL PEAK 14(8P23.2) WILD-TYPE 499 47 0.0 - 234.3 (24.8)

Figure S134.  Get High-res Image Gene #43: 'del_8p23.2' versus Clinical Feature #1: 'Time to Death'

'del_8p23.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.0132 (Fisher's exact test), Q value = 0.08

Table S135.  Gene #43: 'del_8p23.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
DEL PEAK 14(8P23.2) MUTATED 155 320 52 23
DEL PEAK 14(8P23.2) WILD-TYPE 117 296 78 17

Figure S135.  Get High-res Image Gene #43: 'del_8p23.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_8p23.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S136.  Gene #43: 'del_8p23.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
DEL PEAK 14(8P23.2) MUTATED 1 441 64 3 1 11 4 26
DEL PEAK 14(8P23.2) WILD-TYPE 0 322 128 3 3 19 13 22

Figure S136.  Get High-res Image Gene #43: 'del_8p23.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_8p23.2' versus 'RACE'

P value = 0.00159 (Fisher's exact test), Q value = 0.017

Table S137.  Gene #43: 'del_8p23.2' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
DEL PEAK 14(8P23.2) MUTATED 1 41 99 356
DEL PEAK 14(8P23.2) WILD-TYPE 0 19 71 380

Figure S137.  Get High-res Image Gene #43: 'del_8p23.2' versus Clinical Feature #11: 'RACE'

'del_8p11.21' versus 'Time to Death'

P value = 0.0495 (logrank test), Q value = 0.21

Table S138.  Gene #44: 'del_8p11.21' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1044 128 0.0 - 234.3 (24.5)
DEL PEAK 15(8P11.21) MUTATED 195 26 0.2 - 189.0 (22.8)
DEL PEAK 15(8P11.21) WILD-TYPE 849 102 0.0 - 234.3 (24.9)

Figure S138.  Get High-res Image Gene #44: 'del_8p11.21' versus Clinical Feature #1: 'Time to Death'

'del_8p11.21' versus 'HISTOLOGICAL_TYPE'

P value = 0.0128 (Fisher's exact test), Q value = 0.08

Table S139.  Gene #44: 'del_8p11.21' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
DEL PEAK 15(8P11.21) MUTATED 0 164 20 0 0 5 1 8
DEL PEAK 15(8P11.21) WILD-TYPE 1 599 172 6 4 25 16 40

Figure S139.  Get High-res Image Gene #44: 'del_8p11.21' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_9p23' versus 'Time to Death'

P value = 0.000376 (logrank test), Q value = 0.0055

Table S140.  Gene #45: 'del_9p23' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1044 128 0.0 - 234.3 (24.5)
DEL PEAK 16(9P23) MUTATED 316 48 0.0 - 162.1 (22.3)
DEL PEAK 16(9P23) WILD-TYPE 728 80 0.0 - 234.3 (25.1)

Figure S140.  Get High-res Image Gene #45: 'del_9p23' versus Clinical Feature #1: 'Time to Death'

'del_9p23' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00267 (Fisher's exact test), Q value = 0.025

Table S141.  Gene #45: 'del_9p23' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
ALL 89 81 8 3 353 245 2 150 29 63 20 1 13
DEL PEAK 16(9P23) MUTATED 21 19 1 0 98 68 1 62 16 19 10 0 4
DEL PEAK 16(9P23) WILD-TYPE 68 62 7 3 255 177 1 88 13 44 10 1 9

Figure S141.  Get High-res Image Gene #45: 'del_9p23' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_9p23' versus 'PATHOLOGY_T_STAGE'

P value = 0.00071 (Fisher's exact test), Q value = 0.0089

Table S142.  Gene #45: 'del_9p23' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
DEL PEAK 16(9P23) MUTATED 60 204 37 19
DEL PEAK 16(9P23) WILD-TYPE 212 412 93 21

Figure S142.  Get High-res Image Gene #45: 'del_9p23' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_9p23' versus 'PATHOLOGY_N_STAGE'

P value = 0.00056 (Fisher's exact test), Q value = 0.0072

Table S143.  Gene #45: 'del_9p23' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 501 350 117 75
DEL PEAK 16(9P23) MUTATED 135 101 55 24
DEL PEAK 16(9P23) WILD-TYPE 366 249 62 51

Figure S143.  Get High-res Image Gene #45: 'del_9p23' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_9p23' versus 'PATHOLOGY_M_STAGE'

P value = 0.0541 (Fisher's exact test), Q value = 0.22

Table S144.  Gene #45: 'del_9p23' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 879 21
DEL PEAK 16(9P23) MUTATED 272 11
DEL PEAK 16(9P23) WILD-TYPE 607 10

Figure S144.  Get High-res Image Gene #45: 'del_9p23' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_9p23' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S145.  Gene #45: 'del_9p23' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
DEL PEAK 16(9P23) MUTATED 0 265 25 3 3 9 5 11
DEL PEAK 16(9P23) WILD-TYPE 1 498 167 3 1 21 12 37

Figure S145.  Get High-res Image Gene #45: 'del_9p23' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_9p23' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0244 (Wilcoxon-test), Q value = 0.13

Table S146.  Gene #45: 'del_9p23' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 897 2.4 (4.7)
DEL PEAK 16(9P23) MUTATED 259 2.8 (5.0)
DEL PEAK 16(9P23) WILD-TYPE 638 2.2 (4.5)

Figure S146.  Get High-res Image Gene #45: 'del_9p23' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'del_9p21.3' versus 'Time to Death'

P value = 0.0369 (logrank test), Q value = 0.17

Table S147.  Gene #46: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1044 128 0.0 - 234.3 (24.5)
DEL PEAK 17(9P21.3) MUTATED 354 47 0.0 - 177.0 (23.1)
DEL PEAK 17(9P21.3) WILD-TYPE 690 81 0.0 - 234.3 (25.1)

Figure S147.  Get High-res Image Gene #46: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

'del_9p21.3' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0144 (Fisher's exact test), Q value = 0.084

Table S148.  Gene #46: 'del_9p21.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
ALL 89 81 8 3 353 245 2 150 29 63 20 1 13
DEL PEAK 17(9P21.3) MUTATED 24 22 2 0 113 75 1 64 17 23 10 0 6
DEL PEAK 17(9P21.3) WILD-TYPE 65 59 6 3 240 170 1 86 12 40 10 1 7

Figure S148.  Get High-res Image Gene #46: 'del_9p21.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_9p21.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.0023 (Fisher's exact test), Q value = 0.022

Table S149.  Gene #46: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
DEL PEAK 17(9P21.3) MUTATED 71 225 41 20
DEL PEAK 17(9P21.3) WILD-TYPE 201 391 89 20

Figure S149.  Get High-res Image Gene #46: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_9p21.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.00179 (Fisher's exact test), Q value = 0.018

Table S150.  Gene #46: 'del_9p21.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 501 350 117 75
DEL PEAK 17(9P21.3) MUTATED 159 107 57 30
DEL PEAK 17(9P21.3) WILD-TYPE 342 243 60 45

Figure S150.  Get High-res Image Gene #46: 'del_9p21.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_9p21.3' versus 'GENDER'

P value = 0.0508 (Fisher's exact test), Q value = 0.21

Table S151.  Gene #46: 'del_9p21.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1051 11
DEL PEAK 17(9P21.3) MUTATED 351 7
DEL PEAK 17(9P21.3) WILD-TYPE 700 4

Figure S151.  Get High-res Image Gene #46: 'del_9p21.3' versus Clinical Feature #7: 'GENDER'

'del_9p21.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S152.  Gene #46: 'del_9p21.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
DEL PEAK 17(9P21.3) MUTATED 1 297 23 4 3 12 5 13
DEL PEAK 17(9P21.3) WILD-TYPE 0 466 169 2 1 18 12 35

Figure S152.  Get High-res Image Gene #46: 'del_9p21.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_9p21.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.046 (Wilcoxon-test), Q value = 0.2

Table S153.  Gene #46: 'del_9p21.3' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 897 2.4 (4.7)
DEL PEAK 17(9P21.3) MUTATED 289 2.6 (4.5)
DEL PEAK 17(9P21.3) WILD-TYPE 608 2.3 (4.7)

Figure S153.  Get High-res Image Gene #46: 'del_9p21.3' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'del_9q21.11' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S154.  Gene #47: 'del_9q21.11' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
DEL PEAK 18(9Q21.11) MUTATED 0 243 23 2 1 10 3 10
DEL PEAK 18(9Q21.11) WILD-TYPE 1 520 169 4 3 20 14 38

Figure S154.  Get High-res Image Gene #47: 'del_9q21.11' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_9q21.11' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0368 (Fisher's exact test), Q value = 0.17

Table S155.  Gene #47: 'del_9q21.11' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 288 774
DEL PEAK 18(9Q21.11) MUTATED 93 199
DEL PEAK 18(9Q21.11) WILD-TYPE 195 575

Figure S155.  Get High-res Image Gene #47: 'del_9q21.11' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'del_9q34.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.0253 (Fisher's exact test), Q value = 0.13

Table S156.  Gene #48: 'del_9q34.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
DEL PEAK 19(9Q34.2) MUTATED 59 185 32 15
DEL PEAK 19(9Q34.2) WILD-TYPE 213 431 98 25

Figure S156.  Get High-res Image Gene #48: 'del_9q34.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_9q34.2' versus 'GENDER'

P value = 0.013 (Fisher's exact test), Q value = 0.08

Table S157.  Gene #48: 'del_9q34.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1051 11
DEL PEAK 19(9Q34.2) MUTATED 286 7
DEL PEAK 19(9Q34.2) WILD-TYPE 765 4

Figure S157.  Get High-res Image Gene #48: 'del_9q34.2' versus Clinical Feature #7: 'GENDER'

'del_9q34.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S158.  Gene #48: 'del_9q34.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
DEL PEAK 19(9Q34.2) MUTATED 0 247 21 4 1 7 3 9
DEL PEAK 19(9Q34.2) WILD-TYPE 1 516 171 2 3 23 14 39

Figure S158.  Get High-res Image Gene #48: 'del_9q34.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_9q34.2' versus 'RACE'

P value = 0.0667 (Fisher's exact test), Q value = 0.24

Table S159.  Gene #48: 'del_9q34.2' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
DEL PEAK 19(9Q34.2) MUTATED 0 17 59 186
DEL PEAK 19(9Q34.2) WILD-TYPE 1 43 111 550

Figure S159.  Get High-res Image Gene #48: 'del_9q34.2' versus Clinical Feature #11: 'RACE'

'del_10q23.31' versus 'PATHOLOGY_T_STAGE'

P value = 0.0123 (Fisher's exact test), Q value = 0.078

Table S160.  Gene #49: 'del_10q23.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
DEL PEAK 20(10Q23.31) MUTATED 68 189 36 20
DEL PEAK 20(10Q23.31) WILD-TYPE 204 427 94 20

Figure S160.  Get High-res Image Gene #49: 'del_10q23.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_10q23.31' versus 'HISTOLOGICAL_TYPE'

P value = 0.00034 (Fisher's exact test), Q value = 0.0054

Table S161.  Gene #49: 'del_10q23.31' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
DEL PEAK 20(10Q23.31) MUTATED 0 242 39 5 2 8 1 17
DEL PEAK 20(10Q23.31) WILD-TYPE 1 521 153 1 2 22 16 31

Figure S161.  Get High-res Image Gene #49: 'del_10q23.31' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_10q23.31' versus 'ETHNICITY'

P value = 0.0189 (Fisher's exact test), Q value = 0.1

Table S162.  Gene #49: 'del_10q23.31' versus Clinical Feature #12: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 38 858
DEL PEAK 20(10Q23.31) MUTATED 5 263
DEL PEAK 20(10Q23.31) WILD-TYPE 33 595

Figure S162.  Get High-res Image Gene #49: 'del_10q23.31' versus Clinical Feature #12: 'ETHNICITY'

'del_10q26.3' versus 'Time to Death'

P value = 0.057 (logrank test), Q value = 0.22

Table S163.  Gene #50: 'del_10q26.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1044 128 0.0 - 234.3 (24.5)
DEL PEAK 21(10Q26.3) MUTATED 312 44 0.0 - 211.6 (23.1)
DEL PEAK 21(10Q26.3) WILD-TYPE 732 84 0.0 - 234.3 (24.8)

Figure S163.  Get High-res Image Gene #50: 'del_10q26.3' versus Clinical Feature #1: 'Time to Death'

'del_10q26.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.0249 (Fisher's exact test), Q value = 0.13

Table S164.  Gene #50: 'del_10q26.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
DEL PEAK 21(10Q26.3) MUTATED 65 191 39 18
DEL PEAK 21(10Q26.3) WILD-TYPE 207 425 91 22

Figure S164.  Get High-res Image Gene #50: 'del_10q26.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_10q26.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S165.  Gene #50: 'del_10q26.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
DEL PEAK 21(10Q26.3) MUTATED 0 251 31 5 2 8 2 15
DEL PEAK 21(10Q26.3) WILD-TYPE 1 512 161 1 2 22 15 33

Figure S165.  Get High-res Image Gene #50: 'del_10q26.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_10q26.3' versus 'ETHNICITY'

P value = 0.00623 (Fisher's exact test), Q value = 0.046

Table S166.  Gene #50: 'del_10q26.3' versus Clinical Feature #12: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 38 858
DEL PEAK 21(10Q26.3) MUTATED 4 262
DEL PEAK 21(10Q26.3) WILD-TYPE 34 596

Figure S166.  Get High-res Image Gene #50: 'del_10q26.3' versus Clinical Feature #12: 'ETHNICITY'

'del_11p15.5' versus 'Time to Death'

P value = 0.0528 (logrank test), Q value = 0.21

Table S167.  Gene #51: 'del_11p15.5' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1044 128 0.0 - 234.3 (24.5)
DEL PEAK 22(11P15.5) MUTATED 300 42 0.0 - 177.0 (23.5)
DEL PEAK 22(11P15.5) WILD-TYPE 744 86 0.0 - 234.3 (24.7)

Figure S167.  Get High-res Image Gene #51: 'del_11p15.5' versus Clinical Feature #1: 'Time to Death'

'del_11p15.5' versus 'PATHOLOGY_T_STAGE'

P value = 0.0041 (Fisher's exact test), Q value = 0.033

Table S168.  Gene #51: 'del_11p15.5' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
DEL PEAK 22(11P15.5) MUTATED 58 197 32 15
DEL PEAK 22(11P15.5) WILD-TYPE 214 419 98 25

Figure S168.  Get High-res Image Gene #51: 'del_11p15.5' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_11p15.5' versus 'HISTOLOGICAL_TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00045

Table S169.  Gene #51: 'del_11p15.5' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
DEL PEAK 22(11P15.5) MUTATED 0 244 30 4 1 12 2 10
DEL PEAK 22(11P15.5) WILD-TYPE 1 519 162 2 3 18 15 38

Figure S169.  Get High-res Image Gene #51: 'del_11p15.5' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_11p15.5' versus 'RACE'

P value = 0.0173 (Fisher's exact test), Q value = 0.097

Table S170.  Gene #51: 'del_11p15.5' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
DEL PEAK 22(11P15.5) MUTATED 0 19 63 190
DEL PEAK 22(11P15.5) WILD-TYPE 1 41 107 546

Figure S170.  Get High-res Image Gene #51: 'del_11p15.5' versus Clinical Feature #11: 'RACE'

'del_11q13.1' versus 'RACE'

P value = 0.0028 (Fisher's exact test), Q value = 0.025

Table S171.  Gene #52: 'del_11q13.1' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
DEL PEAK 23(11Q13.1) MUTATED 0 21 48 142
DEL PEAK 23(11Q13.1) WILD-TYPE 1 39 122 594

Figure S171.  Get High-res Image Gene #52: 'del_11q13.1' versus Clinical Feature #11: 'RACE'

'del_11q23.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.0399 (Fisher's exact test), Q value = 0.18

Table S172.  Gene #53: 'del_11q23.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
DEL PEAK 24(11Q23.3) MUTATED 119 323 74 22
DEL PEAK 24(11Q23.3) WILD-TYPE 153 293 56 18

Figure S172.  Get High-res Image Gene #53: 'del_11q23.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_11q23.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.052 (Fisher's exact test), Q value = 0.21

Table S173.  Gene #53: 'del_11q23.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 501 350 117 75
DEL PEAK 24(11Q23.3) MUTATED 236 190 67 33
DEL PEAK 24(11Q23.3) WILD-TYPE 265 160 50 42

Figure S173.  Get High-res Image Gene #53: 'del_11q23.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_11q23.3' versus 'GENDER'

P value = 0.0644 (Fisher's exact test), Q value = 0.24

Table S174.  Gene #53: 'del_11q23.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1051 11
DEL PEAK 24(11Q23.3) MUTATED 530 9
DEL PEAK 24(11Q23.3) WILD-TYPE 521 2

Figure S174.  Get High-res Image Gene #53: 'del_11q23.3' versus Clinical Feature #7: 'GENDER'

'del_11q23.3' versus 'RACE'

P value = 0.0142 (Fisher's exact test), Q value = 0.084

Table S175.  Gene #53: 'del_11q23.3' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
DEL PEAK 24(11Q23.3) MUTATED 1 33 101 350
DEL PEAK 24(11Q23.3) WILD-TYPE 0 27 69 386

Figure S175.  Get High-res Image Gene #53: 'del_11q23.3' versus Clinical Feature #11: 'RACE'

'del_11q25' versus 'YEARS_TO_BIRTH'

P value = 0.035 (Wilcoxon-test), Q value = 0.17

Table S176.  Gene #54: 'del_11q25' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1047 58.6 (13.2)
DEL PEAK 25(11Q25) MUTATED 498 57.6 (13.5)
DEL PEAK 25(11Q25) WILD-TYPE 549 59.5 (12.8)

Figure S176.  Get High-res Image Gene #54: 'del_11q25' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_11q25' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0243 (Fisher's exact test), Q value = 0.13

Table S177.  Gene #54: 'del_11q25' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
ALL 89 81 8 3 353 245 2 150 29 63 20 1 13
DEL PEAK 25(11Q25) MUTATED 31 31 3 1 163 132 1 85 12 26 10 0 8
DEL PEAK 25(11Q25) WILD-TYPE 58 50 5 2 190 113 1 65 17 37 10 1 5

Figure S177.  Get High-res Image Gene #54: 'del_11q25' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_11q25' versus 'PATHOLOGY_T_STAGE'

P value = 0.00327 (Fisher's exact test), Q value = 0.028

Table S178.  Gene #54: 'del_11q25' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
DEL PEAK 25(11Q25) MUTATED 105 312 70 17
DEL PEAK 25(11Q25) WILD-TYPE 167 304 60 23

Figure S178.  Get High-res Image Gene #54: 'del_11q25' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_11q25' versus 'PATHOLOGY_N_STAGE'

P value = 0.0341 (Fisher's exact test), Q value = 0.17

Table S179.  Gene #54: 'del_11q25' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 501 350 117 75
DEL PEAK 25(11Q25) MUTATED 221 180 64 30
DEL PEAK 25(11Q25) WILD-TYPE 280 170 53 45

Figure S179.  Get High-res Image Gene #54: 'del_11q25' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_11q25' versus 'GENDER'

P value = 0.0307 (Fisher's exact test), Q value = 0.15

Table S180.  Gene #54: 'del_11q25' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 1051 11
DEL PEAK 25(11Q25) MUTATED 496 9
DEL PEAK 25(11Q25) WILD-TYPE 555 2

Figure S180.  Get High-res Image Gene #54: 'del_11q25' versus Clinical Feature #7: 'GENDER'

'del_11q25' versus 'HISTOLOGICAL_TYPE'

P value = 0.00444 (Fisher's exact test), Q value = 0.035

Table S181.  Gene #54: 'del_11q25' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
DEL PEAK 25(11Q25) MUTATED 1 374 88 5 3 16 5 12
DEL PEAK 25(11Q25) WILD-TYPE 0 389 104 1 1 14 12 36

Figure S181.  Get High-res Image Gene #54: 'del_11q25' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_11q25' versus 'RACE'

P value = 0.00037 (Fisher's exact test), Q value = 0.0055

Table S182.  Gene #54: 'del_11q25' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
DEL PEAK 25(11Q25) MUTATED 1 29 102 320
DEL PEAK 25(11Q25) WILD-TYPE 0 31 68 416

Figure S182.  Get High-res Image Gene #54: 'del_11q25' versus Clinical Feature #11: 'RACE'

'del_12p13.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.0049 (Fisher's exact test), Q value = 0.038

Table S183.  Gene #55: 'del_12p13.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
DEL PEAK 26(12P13.1) MUTATED 0 154 17 1 0 3 1 6
DEL PEAK 26(12P13.1) WILD-TYPE 1 609 175 5 4 27 16 42

Figure S183.  Get High-res Image Gene #55: 'del_12p13.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_12q23.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.0361 (Fisher's exact test), Q value = 0.17

Table S184.  Gene #56: 'del_12q23.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
DEL PEAK 27(12Q23.1) MUTATED 36 127 22 10
DEL PEAK 27(12Q23.1) WILD-TYPE 236 489 108 30

Figure S184.  Get High-res Image Gene #56: 'del_12q23.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_12q23.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00331 (Fisher's exact test), Q value = 0.028

Table S185.  Gene #56: 'del_12q23.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
DEL PEAK 27(12Q23.1) MUTATED 0 159 21 3 0 4 0 10
DEL PEAK 27(12Q23.1) WILD-TYPE 1 604 171 3 4 26 17 38

Figure S185.  Get High-res Image Gene #56: 'del_12q23.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_12q23.1' versus 'RACE'

P value = 0.00723 (Fisher's exact test), Q value = 0.053

Table S186.  Gene #56: 'del_12q23.1' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
DEL PEAK 27(12Q23.1) MUTATED 0 13 47 123
DEL PEAK 27(12Q23.1) WILD-TYPE 1 47 123 613

Figure S186.  Get High-res Image Gene #56: 'del_12q23.1' versus Clinical Feature #11: 'RACE'

'del_13q14.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.0456 (Fisher's exact test), Q value = 0.2

Table S187.  Gene #58: 'del_13q14.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
DEL PEAK 29(13Q14.2) MUTATED 106 303 59 18
DEL PEAK 29(13Q14.2) WILD-TYPE 166 313 71 22

Figure S187.  Get High-res Image Gene #58: 'del_13q14.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_13q14.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S188.  Gene #58: 'del_13q14.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
DEL PEAK 29(13Q14.2) MUTATED 0 386 65 5 1 12 2 17
DEL PEAK 29(13Q14.2) WILD-TYPE 1 377 127 1 3 18 15 31

Figure S188.  Get High-res Image Gene #58: 'del_13q14.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_14q24.1' versus 'Time to Death'

P value = 0.0402 (logrank test), Q value = 0.18

Table S189.  Gene #59: 'del_14q24.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1044 128 0.0 - 234.3 (24.5)
DEL PEAK 30(14Q24.1) MUTATED 342 51 0.0 - 211.6 (24.8)
DEL PEAK 30(14Q24.1) WILD-TYPE 702 77 0.0 - 234.3 (24.3)

Figure S189.  Get High-res Image Gene #59: 'del_14q24.1' versus Clinical Feature #1: 'Time to Death'

'del_14q24.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00019 (Fisher's exact test), Q value = 0.0033

Table S190.  Gene #59: 'del_14q24.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
DEL PEAK 30(14Q24.1) MUTATED 65 233 35 11
DEL PEAK 30(14Q24.1) WILD-TYPE 207 383 95 29

Figure S190.  Get High-res Image Gene #59: 'del_14q24.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_14q24.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S191.  Gene #59: 'del_14q24.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
DEL PEAK 30(14Q24.1) MUTATED 1 292 31 4 2 3 1 11
DEL PEAK 30(14Q24.1) WILD-TYPE 0 471 161 2 2 27 16 37

Figure S191.  Get High-res Image Gene #59: 'del_14q24.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_14q24.1' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0557 (Fisher's exact test), Q value = 0.22

Table S192.  Gene #59: 'del_14q24.1' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 288 774
DEL PEAK 30(14Q24.1) MUTATED 107 239
DEL PEAK 30(14Q24.1) WILD-TYPE 181 535

Figure S192.  Get High-res Image Gene #59: 'del_14q24.1' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'del_14q24.1' versus 'RACE'

P value = 0.00077 (Fisher's exact test), Q value = 0.0095

Table S193.  Gene #59: 'del_14q24.1' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
DEL PEAK 30(14Q24.1) MUTATED 0 18 77 218
DEL PEAK 30(14Q24.1) WILD-TYPE 1 42 93 518

Figure S193.  Get High-res Image Gene #59: 'del_14q24.1' versus Clinical Feature #11: 'RACE'

'del_15q13.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00152 (Fisher's exact test), Q value = 0.017

Table S194.  Gene #60: 'del_15q13.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
DEL PEAK 31(15Q13.1) MUTATED 72 243 41 12
DEL PEAK 31(15Q13.1) WILD-TYPE 200 373 89 28

Figure S194.  Get High-res Image Gene #60: 'del_15q13.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_15q13.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0336 (Fisher's exact test), Q value = 0.17

Table S195.  Gene #60: 'del_15q13.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 501 350 117 75
DEL PEAK 31(15Q13.1) MUTATED 190 108 48 20
DEL PEAK 31(15Q13.1) WILD-TYPE 311 242 69 55

Figure S195.  Get High-res Image Gene #60: 'del_15q13.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_15q13.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S196.  Gene #60: 'del_15q13.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
DEL PEAK 31(15Q13.1) MUTATED 1 300 38 4 1 9 1 14
DEL PEAK 31(15Q13.1) WILD-TYPE 0 463 154 2 3 21 16 34

Figure S196.  Get High-res Image Gene #60: 'del_15q13.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_15q13.1' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0502 (Fisher's exact test), Q value = 0.21

Table S197.  Gene #60: 'del_15q13.1' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 288 774
DEL PEAK 31(15Q13.1) MUTATED 114 255
DEL PEAK 31(15Q13.1) WILD-TYPE 174 519

Figure S197.  Get High-res Image Gene #60: 'del_15q13.1' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'del_15q13.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0403 (Wilcoxon-test), Q value = 0.18

Table S198.  Gene #60: 'del_15q13.1' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 897 2.4 (4.7)
DEL PEAK 31(15Q13.1) MUTATED 314 2.2 (4.8)
DEL PEAK 31(15Q13.1) WILD-TYPE 583 2.5 (4.6)

Figure S198.  Get High-res Image Gene #60: 'del_15q13.1' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'del_15q13.1' versus 'RACE'

P value = 0.052 (Fisher's exact test), Q value = 0.21

Table S199.  Gene #60: 'del_15q13.1' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
DEL PEAK 31(15Q13.1) MUTATED 0 23 73 242
DEL PEAK 31(15Q13.1) WILD-TYPE 1 37 97 494

Figure S199.  Get High-res Image Gene #60: 'del_15q13.1' versus Clinical Feature #11: 'RACE'

'del_16q24.3' versus 'YEARS_TO_BIRTH'

P value = 0.000601 (Wilcoxon-test), Q value = 0.0077

Table S200.  Gene #61: 'del_16q24.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1047 58.6 (13.2)
DEL PEAK 32(16Q24.3) MUTATED 669 59.7 (12.9)
DEL PEAK 32(16Q24.3) WILD-TYPE 378 56.7 (13.3)

Figure S200.  Get High-res Image Gene #61: 'del_16q24.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_16q24.3' versus 'PATHOLOGY_M_STAGE'

P value = 0.0651 (Fisher's exact test), Q value = 0.24

Table S201.  Gene #61: 'del_16q24.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 879 21
DEL PEAK 32(16Q24.3) MUTATED 561 9
DEL PEAK 32(16Q24.3) WILD-TYPE 318 12

Figure S201.  Get High-res Image Gene #61: 'del_16q24.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_16q24.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S202.  Gene #61: 'del_16q24.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
DEL PEAK 32(16Q24.3) MUTATED 0 460 172 3 1 20 3 19
DEL PEAK 32(16Q24.3) WILD-TYPE 1 303 20 3 3 10 14 29

Figure S202.  Get High-res Image Gene #61: 'del_16q24.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_16q24.3' versus 'RACE'

P value = 0.00412 (Fisher's exact test), Q value = 0.033

Table S203.  Gene #61: 'del_16q24.3' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
DEL PEAK 32(16Q24.3) MUTATED 1 34 89 483
DEL PEAK 32(16Q24.3) WILD-TYPE 0 26 81 253

Figure S203.  Get High-res Image Gene #61: 'del_16q24.3' versus Clinical Feature #11: 'RACE'

'del_17p12' versus 'YEARS_TO_BIRTH'

P value = 0.0023 (Wilcoxon-test), Q value = 0.022

Table S204.  Gene #62: 'del_17p12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1047 58.6 (13.2)
DEL PEAK 33(17P12) MUTATED 628 57.7 (13.0)
DEL PEAK 33(17P12) WILD-TYPE 419 60.1 (13.3)

Figure S204.  Get High-res Image Gene #62: 'del_17p12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_17p12' versus 'PATHOLOGY_T_STAGE'

P value = 0.0625 (Fisher's exact test), Q value = 0.23

Table S205.  Gene #62: 'del_17p12' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
DEL PEAK 33(17P12) MUTATED 146 388 79 22
DEL PEAK 33(17P12) WILD-TYPE 126 228 51 18

Figure S205.  Get High-res Image Gene #62: 'del_17p12' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_17p12' versus 'HISTOLOGICAL_TYPE'

P value = 0.00883 (Fisher's exact test), Q value = 0.061

Table S206.  Gene #62: 'del_17p12' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
DEL PEAK 33(17P12) MUTATED 0 482 99 5 2 18 6 25
DEL PEAK 33(17P12) WILD-TYPE 1 281 93 1 2 12 11 23

Figure S206.  Get High-res Image Gene #62: 'del_17p12' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_17p12' versus 'RACE'

P value = 0.0551 (Fisher's exact test), Q value = 0.22

Table S207.  Gene #62: 'del_17p12' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
DEL PEAK 33(17P12) MUTATED 1 44 107 428
DEL PEAK 33(17P12) WILD-TYPE 0 16 63 308

Figure S207.  Get High-res Image Gene #62: 'del_17p12' versus Clinical Feature #11: 'RACE'

'del_17q21.31' versus 'YEARS_TO_BIRTH'

P value = 0.000476 (Wilcoxon-test), Q value = 0.0066

Table S208.  Gene #63: 'del_17q21.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1047 58.6 (13.2)
DEL PEAK 34(17Q21.31) MUTATED 354 56.8 (13.3)
DEL PEAK 34(17Q21.31) WILD-TYPE 693 59.5 (13.0)

Figure S208.  Get High-res Image Gene #63: 'del_17q21.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_17q21.31' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S209.  Gene #63: 'del_17q21.31' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
DEL PEAK 34(17Q21.31) MUTATED 0 290 37 4 2 11 1 16
DEL PEAK 34(17Q21.31) WILD-TYPE 1 473 155 2 2 19 16 32

Figure S209.  Get High-res Image Gene #63: 'del_17q21.31' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_17q21.31' versus 'RACE'

P value = 0.00035 (Fisher's exact test), Q value = 0.0055

Table S210.  Gene #63: 'del_17q21.31' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
DEL PEAK 34(17Q21.31) MUTATED 0 34 67 232
DEL PEAK 34(17Q21.31) WILD-TYPE 1 26 103 504

Figure S210.  Get High-res Image Gene #63: 'del_17q21.31' versus Clinical Feature #11: 'RACE'

'del_18q23' versus 'Time to Death'

P value = 0.0617 (logrank test), Q value = 0.23

Table S211.  Gene #64: 'del_18q23' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1044 128 0.0 - 234.3 (24.5)
DEL PEAK 35(18Q23) MUTATED 340 45 0.0 - 211.6 (21.8)
DEL PEAK 35(18Q23) WILD-TYPE 704 83 0.2 - 234.3 (25.8)

Figure S211.  Get High-res Image Gene #64: 'del_18q23' versus Clinical Feature #1: 'Time to Death'

'del_18q23' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0673 (Fisher's exact test), Q value = 0.24

Table S212.  Gene #64: 'del_18q23' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
ALL 89 81 8 3 353 245 2 150 29 63 20 1 13
DEL PEAK 35(18Q23) MUTATED 23 29 0 0 113 74 0 55 15 28 6 0 3
DEL PEAK 35(18Q23) WILD-TYPE 66 52 8 3 240 171 2 95 14 35 14 1 10

Figure S212.  Get High-res Image Gene #64: 'del_18q23' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_18q23' versus 'PATHOLOGY_T_STAGE'

P value = 0.0194 (Fisher's exact test), Q value = 0.11

Table S213.  Gene #64: 'del_18q23' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
DEL PEAK 35(18Q23) MUTATED 74 212 42 20
DEL PEAK 35(18Q23) WILD-TYPE 198 404 88 20

Figure S213.  Get High-res Image Gene #64: 'del_18q23' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_18q23' versus 'HISTOLOGICAL_TYPE'

P value = 0.0011 (Fisher's exact test), Q value = 0.013

Table S214.  Gene #64: 'del_18q23' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
DEL PEAK 35(18Q23) MUTATED 1 271 52 3 2 8 0 11
DEL PEAK 35(18Q23) WILD-TYPE 0 492 140 3 2 22 17 37

Figure S214.  Get High-res Image Gene #64: 'del_18q23' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_19p13.3' versus 'YEARS_TO_BIRTH'

P value = 0.00331 (Wilcoxon-test), Q value = 0.028

Table S215.  Gene #65: 'del_19p13.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1047 58.6 (13.2)
DEL PEAK 36(19P13.3) MUTATED 348 57.0 (13.5)
DEL PEAK 36(19P13.3) WILD-TYPE 699 59.4 (12.9)

Figure S215.  Get High-res Image Gene #65: 'del_19p13.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_19p13.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.0422 (Fisher's exact test), Q value = 0.19

Table S216.  Gene #65: 'del_19p13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
DEL PEAK 36(19P13.3) MUTATED 78 227 36 15
DEL PEAK 36(19P13.3) WILD-TYPE 194 389 94 25

Figure S216.  Get High-res Image Gene #65: 'del_19p13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_19p13.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S217.  Gene #65: 'del_19p13.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
DEL PEAK 36(19P13.3) MUTATED 1 295 24 5 1 9 5 15
DEL PEAK 36(19P13.3) WILD-TYPE 0 468 168 1 3 21 12 33

Figure S217.  Get High-res Image Gene #65: 'del_19p13.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_19p13.3' versus 'RACE'

P value = 0.00134 (Fisher's exact test), Q value = 0.015

Table S218.  Gene #65: 'del_19p13.3' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 60 170 736
DEL PEAK 36(19P13.3) MUTATED 0 28 72 223
DEL PEAK 36(19P13.3) WILD-TYPE 1 32 98 513

Figure S218.  Get High-res Image Gene #65: 'del_19p13.3' versus Clinical Feature #11: 'RACE'

'del_19q13.32' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S219.  Gene #66: 'del_19q13.32' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
DEL PEAK 37(19Q13.32) MUTATED 0 181 9 3 1 6 4 7
DEL PEAK 37(19Q13.32) WILD-TYPE 1 582 183 3 3 24 13 41

Figure S219.  Get High-res Image Gene #66: 'del_19q13.32' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_19q13.32' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0154 (Fisher's exact test), Q value = 0.089

Table S220.  Gene #66: 'del_19q13.32' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 288 774
DEL PEAK 37(19Q13.32) MUTATED 72 140
DEL PEAK 37(19Q13.32) WILD-TYPE 216 634

Figure S220.  Get High-res Image Gene #66: 'del_19q13.32' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'del_20p13' versus 'YEARS_TO_BIRTH'

P value = 0.061 (Wilcoxon-test), Q value = 0.23

Table S221.  Gene #67: 'del_20p13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1047 58.6 (13.2)
DEL PEAK 38(20P13) MUTATED 156 56.8 (12.2)
DEL PEAK 38(20P13) WILD-TYPE 891 59.0 (13.3)

Figure S221.  Get High-res Image Gene #67: 'del_20p13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_20p13' versus 'HISTOLOGICAL_TYPE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00064

Table S222.  Gene #67: 'del_20p13' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
DEL PEAK 38(20P13) MUTATED 1 136 10 2 0 2 1 7
DEL PEAK 38(20P13) WILD-TYPE 0 627 182 4 4 28 16 41

Figure S222.  Get High-res Image Gene #67: 'del_20p13' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_21q11.2' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00983 (Fisher's exact test), Q value = 0.066

Table S223.  Gene #68: 'del_21q11.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
ALL 89 81 8 3 353 245 2 150 29 63 20 1 13
DEL PEAK 39(21Q11.2) MUTATED 12 11 1 0 67 51 1 38 12 8 7 1 3
DEL PEAK 39(21Q11.2) WILD-TYPE 77 70 7 3 286 194 1 112 17 55 13 0 10

Figure S223.  Get High-res Image Gene #68: 'del_21q11.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_21q11.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.0121 (Fisher's exact test), Q value = 0.077

Table S224.  Gene #68: 'del_21q11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 272 616 130 40
DEL PEAK 39(21Q11.2) MUTATED 41 136 21 13
DEL PEAK 39(21Q11.2) WILD-TYPE 231 480 109 27

Figure S224.  Get High-res Image Gene #68: 'del_21q11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_21q11.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.0142 (Fisher's exact test), Q value = 0.084

Table S225.  Gene #68: 'del_21q11.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 501 350 117 75
DEL PEAK 39(21Q11.2) MUTATED 88 73 36 12
DEL PEAK 39(21Q11.2) WILD-TYPE 413 277 81 63

Figure S225.  Get High-res Image Gene #68: 'del_21q11.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_21q11.2' versus 'PATHOLOGY_M_STAGE'

P value = 0.0564 (Fisher's exact test), Q value = 0.22

Table S226.  Gene #68: 'del_21q11.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 879 21
DEL PEAK 39(21Q11.2) MUTATED 178 8
DEL PEAK 39(21Q11.2) WILD-TYPE 701 13

Figure S226.  Get High-res Image Gene #68: 'del_21q11.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_21q11.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.00042 (Fisher's exact test), Q value = 0.006

Table S227.  Gene #68: 'del_21q11.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
DEL PEAK 39(21Q11.2) MUTATED 0 172 19 2 2 9 2 6
DEL PEAK 39(21Q11.2) WILD-TYPE 1 591 173 4 2 21 15 42

Figure S227.  Get High-res Image Gene #68: 'del_21q11.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_22q13.32' versus 'HISTOLOGICAL_TYPE'

P value = 0.00136 (Fisher's exact test), Q value = 0.015

Table S228.  Gene #69: 'del_22q13.32' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 763 192 6 4 30 17 48
DEL PEAK 40(22Q13.32) MUTATED 1 353 87 3 2 18 1 14
DEL PEAK 40(22Q13.32) WILD-TYPE 0 410 105 3 2 12 16 34

Figure S228.  Get High-res Image Gene #69: 'del_22q13.32' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_22q13.32' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.00444 (Fisher's exact test), Q value = 0.035

Table S229.  Gene #69: 'del_22q13.32' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 288 774
DEL PEAK 40(22Q13.32) MUTATED 151 329
DEL PEAK 40(22Q13.32) WILD-TYPE 137 445

Figure S229.  Get High-res Image Gene #69: 'del_22q13.32' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

Methods & Data
Input

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

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BRCA-TP/15086288/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BRCA-TP/15076769/BRCA-TP.merged_data.txt

  • Number of patients = 1062

  • Number of significantly focal cnvs = 69

  • Number of selected clinical features = 12

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

Survival analysis

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

Fisher's exact test

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

Q value calculation

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

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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