Correlation between copy number variations of arm-level result and selected clinical features
Breast Invasive Carcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1862F2N
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1862F2N
Overview
Introduction

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

Summary

Testing the association between copy number variation 80 arm-level events and 10 clinical features across 971 patients, 22 significant findings detected with Q value < 0.25.

  • 2p gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 3q gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 6p gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 6q gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 8q gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 10p gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 20p gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 20q gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 1p loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.

  • 4p loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 4q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 5p loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 5q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 8p loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 9p loss cnv correlated to 'PATHOLOGY.T.STAGE' and 'HISTOLOGICAL.TYPE'.

  • 14q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 16q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 18p loss cnv correlated to 'Time to Death'.

  • 19p loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 19q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 10 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 22 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		NUMBER
OF
LYMPH
NODES
nCNV (%) nWild-Type logrank test t-test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test t-test
1p loss 222 (23%) 749 0.0358
(1.00) 		0.00181
(1.00) 		1.33e-05
(0.0105) 		3.83e-05
(0.0302) 		0.00222
(1.00) 		0.352
(1.00) 		1
(1.00) 		0.423
(1.00) 		0.614
(1.00) 		0.00963
(1.00)
9p loss 289 (30%) 682 0.0221
(1.00) 		0.564
(1.00) 		0.00136
(1.00) 		0.00016
(0.125) 		0.024
(1.00) 		0.0532
(1.00) 		0.174
(1.00) 		8.74e-06
(0.00692) 		0.123
(1.00) 		0.732
(1.00)
2p gain 110 (11%) 861 0.255
(1.00) 		0.794
(1.00) 		0.607
(1.00) 		0.621
(1.00) 		0.977
(1.00) 		0.831
(1.00) 		0.614
(1.00) 		3.76e-05
(0.0296) 		0.373
(1.00) 		0.176
(1.00)
3q gain 191 (20%) 780 0.491
(1.00) 		0.513
(1.00) 		0.794
(1.00) 		0.184
(1.00) 		0.656
(1.00) 		0.0427
(1.00) 		0.697
(1.00) 		1.25e-05
(0.00984) 		0.183
(1.00) 		0.144
(1.00)
6p gain 184 (19%) 787 0.336
(1.00) 		0.748
(1.00) 		0.667
(1.00) 		0.119
(1.00) 		0.586
(1.00) 		0.787
(1.00) 		0.697
(1.00) 		0.000184
(0.144) 		0.0872
(1.00) 		0.851
(1.00)
6q gain 132 (14%) 839 0.32
(1.00) 		0.852
(1.00) 		0.615
(1.00) 		0.112
(1.00) 		0.0837
(1.00) 		0.975
(1.00) 		1
(1.00) 		0.000173
(0.135) 		0.257
(1.00) 		0.964
(1.00)
8q gain 478 (49%) 493 0.659
(1.00) 		0.784
(1.00) 		0.335
(1.00) 		0.83
(1.00) 		0.288
(1.00) 		0.0667
(1.00) 		0.541
(1.00) 		1.13e-06
(0.000901) 		0.0163
(1.00) 		0.763
(1.00)
10p gain 193 (20%) 778 0.869
(1.00) 		0.521
(1.00) 		0.246
(1.00) 		0.3
(1.00) 		0.265
(1.00) 		0.268
(1.00) 		0.696
(1.00) 		0.00028
(0.218) 		0.0414
(1.00) 		0.848
(1.00)
20p gain 371 (38%) 600 0.158
(1.00) 		0.34
(1.00) 		0.262
(1.00) 		0.648
(1.00) 		0.0202
(1.00) 		0.0047
(1.00) 		0.0497
(1.00) 		1.22e-06
(0.000974) 		0.00882
(1.00) 		0.674
(1.00)
20q gain 404 (42%) 567 0.211
(1.00) 		0.893
(1.00) 		0.386
(1.00) 		0.117
(1.00) 		0.0742
(1.00) 		0.0158
(1.00) 		0.335
(1.00) 		1.53e-07
(0.000122) 		0.0732
(1.00) 		0.661
(1.00)
4p loss 314 (32%) 657 0.29
(1.00) 		0.359
(1.00) 		0.533
(1.00) 		0.0293
(1.00) 		0.621
(1.00) 		0.369
(1.00) 		1
(1.00) 		3.43e-06
(0.00272) 		0.706
(1.00) 		0.968
(1.00)
4q loss 279 (29%) 692 0.83
(1.00) 		0.957
(1.00) 		0.694
(1.00) 		0.0676
(1.00) 		0.74
(1.00) 		0.298
(1.00) 		0.297
(1.00) 		6.5e-05
(0.051) 		0.436
(1.00) 		0.855
(1.00)
5p loss 126 (13%) 845 0.306
(1.00) 		0.0195
(1.00) 		0.82
(1.00) 		0.0769
(1.00) 		0.86
(1.00) 		0.854
(1.00) 		1
(1.00) 		4.54e-06
(0.00361) 		0.207
(1.00) 		0.758
(1.00)
5q loss 206 (21%) 765 0.296
(1.00) 		0.00127
(0.977) 		0.206
(1.00) 		0.00684
(1.00) 		0.361
(1.00) 		0.448
(1.00) 		0.132
(1.00) 		1.18e-10
(9.47e-08) 		0.489
(1.00) 		0.216
(1.00)
8p loss 357 (37%) 614 0.0262
(1.00) 		0.254
(1.00) 		0.912
(1.00) 		0.193
(1.00) 		0.752
(1.00) 		0.412
(1.00) 		0.753
(1.00) 		6.43e-05
(0.0505) 		0.558
(1.00) 		0.393
(1.00)
14q loss 236 (24%) 735 0.0256
(1.00) 		0.856
(1.00) 		0.843
(1.00) 		0.0602
(1.00) 		0.0643
(1.00) 		0.887
(1.00) 		0.466
(1.00) 		0.000136
(0.107) 		0.285
(1.00) 		0.511
(1.00)
16q loss 534 (55%) 437 0.0645
(1.00) 		0.00115
(0.884) 		0.691
(1.00) 		0.584
(1.00) 		0.184
(1.00) 		0.194
(1.00) 		0.359
(1.00) 		8.74e-12
(6.99e-09) 		0.0886
(1.00) 		0.442
(1.00)
18p loss 290 (30%) 681 6.78e-06
(0.00538) 		0.00471
(1.00) 		0.0401
(1.00) 		0.0143
(1.00) 		0.39
(1.00) 		0.825
(1.00) 		0.732
(1.00) 		0.0388
(1.00) 		1
(1.00) 		0.142
(1.00)
19p loss 173 (18%) 798 0.0922
(1.00) 		0.0909
(1.00) 		0.905
(1.00) 		0.614
(1.00) 		0.486
(1.00) 		0.303
(1.00) 		1
(1.00) 		1.11e-05
(0.00878) 		0.518
(1.00) 		0.591
(1.00)
19q loss 146 (15%) 825 0.237
(1.00) 		0.981
(1.00) 		0.685
(1.00) 		0.519
(1.00) 		0.186
(1.00) 		0.352
(1.00) 		1
(1.00) 		0.000138
(0.108) 		0.0933
(1.00) 		0.569
(1.00)
1p gain 181 (19%) 790 0.411
(1.00) 		0.0529
(1.00) 		0.767
(1.00) 		0.131
(1.00) 		0.418
(1.00) 		1
(1.00) 		1
(1.00) 		0.0192
(1.00) 		0.0291
(1.00) 		0.551
(1.00)
1q gain 627 (65%) 344 0.502
(1.00) 		0.447
(1.00) 		0.0302
(1.00) 		0.000843
(0.65) 		0.508
(1.00) 		0.815
(1.00) 		0.749
(1.00) 		0.0199
(1.00) 		0.941
(1.00) 		0.923
(1.00)
2q gain 69 (7%) 902 0.807
(1.00) 		0.937
(1.00) 		0.746
(1.00) 		0.263
(1.00) 		0.94
(1.00) 		1
(1.00) 		1
(1.00) 		0.0357
(1.00) 		0.784
(1.00) 		0.287
(1.00)
3p gain 129 (13%) 842 0.275
(1.00) 		0.207
(1.00) 		0.132
(1.00) 		0.0434
(1.00) 		0.349
(1.00) 		0.000595
(0.461) 		1
(1.00) 		0.0106
(1.00) 		0.603
(1.00) 		0.924
(1.00)
4p gain 74 (8%) 897 0.0935
(1.00) 		0.556
(1.00) 		0.248
(1.00) 		0.0899
(1.00) 		0.684
(1.00) 		0.322
(1.00) 		0.549
(1.00) 		0.0376
(1.00) 		0.595
(1.00) 		0.685
(1.00)
4q gain 70 (7%) 901 0.0487
(1.00) 		0.755
(1.00) 		0.309
(1.00) 		0.211
(1.00) 		0.494
(1.00) 		0.336
(1.00) 		0.529
(1.00) 		0.00481
(1.00) 		1
(1.00) 		0.728
(1.00)
5p gain 286 (29%) 685 0.103
(1.00) 		0.315
(1.00) 		0.506
(1.00) 		0.66
(1.00) 		0.00213
(1.00) 		0.0163
(1.00) 		0.492
(1.00) 		0.456
(1.00) 		0.354
(1.00) 		0.525
(1.00)
5q gain 189 (19%) 782 0.481
(1.00) 		0.0242
(1.00) 		0.562
(1.00) 		0.295
(1.00) 		0.288
(1.00) 		0.183
(1.00) 		1
(1.00) 		0.805
(1.00) 		0.476
(1.00) 		0.687
(1.00)
7p gain 276 (28%) 695 0.592
(1.00) 		0.111
(1.00) 		0.857
(1.00) 		0.782
(1.00) 		0.828
(1.00) 		0.677
(1.00) 		0.036
(1.00) 		0.18
(1.00) 		0.24
(1.00) 		0.619
(1.00)
7q gain 231 (24%) 740 0.856
(1.00) 		0.657
(1.00) 		0.488
(1.00) 		0.502
(1.00) 		0.513
(1.00) 		0.686
(1.00) 		0.261
(1.00) 		0.268
(1.00) 		1
(1.00) 		0.909
(1.00)
8p gain 259 (27%) 712 0.821
(1.00) 		0.728
(1.00) 		0.703
(1.00) 		0.838
(1.00) 		0.868
(1.00) 		0.392
(1.00) 		0.732
(1.00) 		0.601
(1.00) 		0.811
(1.00) 		0.811
(1.00)
9p gain 127 (13%) 844 0.809
(1.00) 		0.702
(1.00) 		0.283
(1.00) 		0.563
(1.00) 		0.123
(1.00) 		0.735
(1.00) 		0.376
(1.00) 		0.642
(1.00) 		1
(1.00) 		0.39
(1.00)
9q gain 107 (11%) 864 0.178
(1.00) 		0.874
(1.00) 		0.688
(1.00) 		0.532
(1.00) 		0.207
(1.00) 		0.908
(1.00) 		0.613
(1.00) 		0.305
(1.00) 		0.653
(1.00) 		0.643
(1.00)
10q gain 112 (12%) 859 0.81
(1.00) 		0.353
(1.00) 		0.386
(1.00) 		0.294
(1.00) 		0.78
(1.00) 		0.681
(1.00) 		0.616
(1.00) 		0.0467
(1.00) 		0.0761
(1.00) 		0.634
(1.00)
11p gain 127 (13%) 844 0.645
(1.00) 		0.953
(1.00) 		0.967
(1.00) 		0.713
(1.00) 		0.21
(1.00) 		0.949
(1.00) 		1
(1.00) 		0.031
(1.00) 		1
(1.00) 		0.202
(1.00)
11q gain 88 (9%) 883 0.191
(1.00) 		0.917
(1.00) 		0.25
(1.00) 		0.739
(1.00) 		0.414
(1.00) 		0.609
(1.00) 		0.612
(1.00) 		0.00367
(1.00) 		0.622
(1.00) 		0.542
(1.00)
12p gain 209 (22%) 762 0.204
(1.00) 		0.764
(1.00) 		0.64
(1.00) 		0.142
(1.00) 		0.0827
(1.00) 		0.607
(1.00) 		0.0431
(1.00) 		0.0412
(1.00) 		0.302
(1.00) 		0.0889
(1.00)
12q gain 176 (18%) 795 0.127
(1.00) 		0.352
(1.00) 		0.14
(1.00) 		0.0531
(1.00) 		0.00659
(1.00) 		0.273
(1.00) 		0.0213
(1.00) 		0.138
(1.00) 		0.233
(1.00) 		0.0584
(1.00)
13q gain 84 (9%) 887 0.772
(1.00) 		0.27
(1.00) 		0.644
(1.00) 		0.411
(1.00) 		0.633
(1.00) 		0.126
(1.00) 		1
(1.00) 		0.0169
(1.00) 		0.38
(1.00) 		0.322
(1.00)
14q gain 132 (14%) 839 0.501
(1.00) 		0.135
(1.00) 		0.307
(1.00) 		0.154
(1.00) 		0.0935
(1.00) 		0.82
(1.00) 		0.374
(1.00) 		0.236
(1.00) 		0.606
(1.00) 		0.131
(1.00)
15q gain 83 (9%) 888 0.378
(1.00) 		0.718
(1.00) 		0.558
(1.00) 		0.819
(1.00) 		0.905
(1.00) 		0.59
(1.00) 		0.593
(1.00) 		0.0174
(1.00) 		0.255
(1.00) 		0.43
(1.00)
16p gain 431 (44%) 540 0.98
(1.00) 		0.0199
(1.00) 		0.619
(1.00) 		0.884
(1.00) 		0.359
(1.00) 		0.887
(1.00) 		0.758
(1.00) 		0.0752
(1.00) 		0.477
(1.00) 		0.817
(1.00)
16q gain 121 (12%) 850 0.0975
(1.00) 		0.546
(1.00) 		0.149
(1.00) 		0.335
(1.00) 		0.256
(1.00) 		0.258
(1.00) 		0.118
(1.00) 		0.0905
(1.00) 		0.915
(1.00) 		0.46
(1.00)
17p gain 98 (10%) 873 0.109
(1.00) 		0.812
(1.00) 		0.134
(1.00) 		0.0186
(1.00) 		0.0977
(1.00) 		0.345
(1.00) 		0.00158
(1.00) 		0.284
(1.00) 		0.0597
(1.00) 		0.36
(1.00)
17q gain 202 (21%) 769 0.0328
(1.00) 		0.557
(1.00) 		0.811
(1.00) 		0.246
(1.00) 		0.689
(1.00) 		0.199
(1.00) 		0.00104
(0.8) 		0.175
(1.00) 		0.0552
(1.00) 		0.628
(1.00)
18p gain 156 (16%) 815 0.341
(1.00) 		0.204
(1.00) 		0.104
(1.00) 		0.398
(1.00) 		0.0275
(1.00) 		0.146
(1.00) 		0.667
(1.00) 		0.0152
(1.00) 		0.387
(1.00) 		0.531
(1.00)
18q gain 134 (14%) 837 0.918
(1.00) 		0.637
(1.00) 		0.136
(1.00) 		0.237
(1.00) 		0.205
(1.00) 		0.0154
(1.00) 		0.636
(1.00) 		0.0823
(1.00) 		0.413
(1.00) 		0.877
(1.00)
19p gain 162 (17%) 809 0.939
(1.00) 		0.958
(1.00) 		0.327
(1.00) 		0.165
(1.00) 		0.226
(1.00) 		0.0751
(1.00) 		0.0689
(1.00) 		0.162
(1.00) 		0.155
(1.00) 		0.148
(1.00)
19q gain 195 (20%) 776 0.455
(1.00) 		0.0416
(1.00) 		0.372
(1.00) 		0.707
(1.00) 		0.133
(1.00) 		0.00716
(1.00) 		0.121
(1.00) 		0.521
(1.00) 		0.378
(1.00) 		0.0485
(1.00)
21q gain 180 (19%) 791 0.00287
(1.00) 		0.104
(1.00) 		0.664
(1.00) 		0.69
(1.00) 		0.62
(1.00) 		0.302
(1.00) 		1
(1.00) 		0.000675
(0.521) 		0.0365
(1.00) 		0.241
(1.00)
22q gain 89 (9%) 882 0.199
(1.00) 		0.908
(1.00) 		0.196
(1.00) 		0.124
(1.00) 		0.403
(1.00) 		0.383
(1.00) 		0.612
(1.00) 		0.0102
(1.00) 		0.271
(1.00) 		0.362
(1.00)
xq gain 127 (13%) 844 0.3
(1.00) 		0.239
(1.00) 		0.442
(1.00) 		0.462
(1.00) 		0.774
(1.00) 		0.0597
(1.00) 		1
(1.00) 		0.000372
(0.289) 		0.0596
(1.00) 		0.734
(1.00)
1q loss 51 (5%) 920 0.378
(1.00) 		0.375
(1.00) 		0.816
(1.00) 		0.377
(1.00) 		0.0493
(1.00) 		0.38
(1.00) 		1
(1.00) 		0.23
(1.00) 		1
(1.00) 		0.944
(1.00)
2p loss 164 (17%) 807 0.749
(1.00) 		0.359
(1.00) 		0.37
(1.00) 		0.429
(1.00) 		0.036
(1.00) 		0.139
(1.00) 		1
(1.00) 		0.413
(1.00) 		0.0377
(1.00) 		0.484
(1.00)
2q loss 184 (19%) 787 0.307
(1.00) 		0.445
(1.00) 		0.149
(1.00) 		0.426
(1.00) 		0.0359
(1.00) 		0.108
(1.00) 		0.697
(1.00) 		0.318
(1.00) 		0.126
(1.00) 		0.233
(1.00)
3p loss 169 (17%) 802 0.358
(1.00) 		0.0455
(1.00) 		0.833
(1.00) 		0.00154
(1.00) 		0.898
(1.00) 		0.601
(1.00) 		0.225
(1.00) 		0.0175
(1.00) 		0.0196
(1.00) 		0.691
(1.00)
3q loss 93 (10%) 878 0.142
(1.00) 		0.215
(1.00) 		0.316
(1.00) 		0.000592
(0.459) 		0.719
(1.00) 		0.698
(1.00) 		0.611
(1.00) 		0.0802
(1.00) 		0.0405
(1.00) 		0.136
(1.00)
6p loss 166 (17%) 805 0.572
(1.00) 		0.0692
(1.00) 		0.849
(1.00) 		0.485
(1.00) 		0.818
(1.00) 		0.016
(1.00) 		1
(1.00) 		0.67
(1.00) 		0.159
(1.00) 		0.0862
(1.00)
6q loss 245 (25%) 726 0.862
(1.00) 		0.000634
(0.49) 		0.69
(1.00) 		0.292
(1.00) 		0.495
(1.00) 		0.295
(1.00) 		0.466
(1.00) 		0.737
(1.00) 		0.0182
(1.00) 		0.288
(1.00)
7p loss 102 (11%) 869 0.604
(1.00) 		0.881
(1.00) 		0.445
(1.00) 		0.435
(1.00) 		0.0394
(1.00) 		0.167
(1.00) 		0.611
(1.00) 		0.0254
(1.00) 		0.356
(1.00) 		0.0678
(1.00)
7q loss 111 (11%) 860 0.171
(1.00) 		0.197
(1.00) 		0.531
(1.00) 		0.551
(1.00) 		0.226
(1.00) 		0.0814
(1.00) 		0.615
(1.00) 		0.247
(1.00) 		0.437
(1.00) 		0.0524
(1.00)
8q loss 81 (8%) 890 0.0172
(1.00) 		0.13
(1.00) 		0.885
(1.00) 		0.505
(1.00) 		0.391
(1.00) 		0.555
(1.00) 		1
(1.00) 		0.763
(1.00) 		0.0983
(1.00) 		0.672
(1.00)
9q loss 261 (27%) 710 0.296
(1.00) 		0.605
(1.00) 		0.145
(1.00) 		0.00209
(1.00) 		0.0738
(1.00) 		0.584
(1.00) 		0.144
(1.00) 		0.000349
(0.272) 		0.0558
(1.00) 		0.871
(1.00)
10p loss 157 (16%) 814 0.0218
(1.00) 		0.893
(1.00) 		0.0703
(1.00) 		0.0195
(1.00) 		0.141
(1.00) 		0.00491
(1.00) 		0.38
(1.00) 		0.107
(1.00) 		0.848
(1.00) 		0.376
(1.00)
10q loss 208 (21%) 763 0.022
(1.00) 		0.927
(1.00) 		0.186
(1.00) 		0.0162
(1.00) 		0.163
(1.00) 		0.0186
(1.00) 		0.698
(1.00) 		0.038
(1.00) 		1
(1.00) 		0.266
(1.00)
11p loss 247 (25%) 724 0.181
(1.00) 		0.745
(1.00) 		0.108
(1.00) 		0.0858
(1.00) 		0.0269
(1.00) 		0.893
(1.00) 		1
(1.00) 		0.132
(1.00) 		0.516
(1.00) 		0.143
(1.00)
11q loss 330 (34%) 641 0.732
(1.00) 		0.73
(1.00) 		0.235
(1.00) 		0.311
(1.00) 		0.014
(1.00) 		0.449
(1.00) 		0.0977
(1.00) 		0.399
(1.00) 		0.551
(1.00) 		0.504
(1.00)
12p loss 137 (14%) 834 0.465
(1.00) 		0.616
(1.00) 		0.144
(1.00) 		0.0281
(1.00) 		0.54
(1.00) 		0.0827
(1.00) 		1
(1.00) 		0.0156
(1.00) 		0.31
(1.00) 		0.153
(1.00)
12q loss 114 (12%) 857 0.693
(1.00) 		0.0456
(1.00) 		0.191
(1.00) 		0.0104
(1.00) 		0.668
(1.00) 		0.226
(1.00) 		0.617
(1.00) 		0.00457
(1.00) 		0.382
(1.00) 		0.472
(1.00)
13q loss 400 (41%) 571 0.0333
(1.00) 		0.512
(1.00) 		0.776
(1.00) 		0.0973
(1.00) 		0.852
(1.00) 		0.962
(1.00) 		0.749
(1.00) 		0.000572
(0.444) 		0.518
(1.00) 		0.189
(1.00)
15q loss 288 (30%) 683 0.0818
(1.00) 		0.545
(1.00) 		0.437
(1.00) 		0.00791
(1.00) 		0.0711
(1.00) 		0.3
(1.00) 		1
(1.00) 		0.00122
(0.939) 		0.0886
(1.00) 		0.702
(1.00)
16p loss 149 (15%) 822 0.675
(1.00) 		0.577
(1.00) 		0.149
(1.00) 		0.982
(1.00) 		0.0565
(1.00) 		0.581
(1.00) 		0.656
(1.00) 		0.251
(1.00) 		0.434
(1.00) 		0.512
(1.00)
17p loss 523 (54%) 448 0.256
(1.00) 		0.026
(1.00) 		0.0963
(1.00) 		0.00432
(1.00) 		0.792
(1.00) 		0.862
(1.00) 		0.527
(1.00) 		0.0129
(1.00) 		1
(1.00) 		0.775
(1.00)
17q loss 251 (26%) 720 0.976
(1.00) 		0.0905
(1.00) 		0.868
(1.00) 		0.434
(1.00) 		0.226
(1.00) 		0.417
(1.00) 		0.0721
(1.00) 		0.00308
(1.00) 		0.936
(1.00) 		0.879
(1.00)
18q loss 289 (30%) 682 0.00198
(1.00) 		0.00971
(1.00) 		0.0521
(1.00) 		0.0641
(1.00) 		0.117
(1.00) 		0.623
(1.00) 		0.732
(1.00) 		0.0241
(1.00) 		0.44
(1.00) 		0.388
(1.00)
20p loss 84 (9%) 887 0.181
(1.00) 		0.156
(1.00) 		0.464
(1.00) 		0.091
(1.00) 		0.641
(1.00) 		0.336
(1.00) 		0.597
(1.00) 		0.0506
(1.00) 		0.38
(1.00) 		0.447
(1.00)
20q loss 48 (5%) 923 0.416
(1.00) 		0.0625
(1.00) 		0.151
(1.00) 		0.0246
(1.00) 		0.994
(1.00) 		0.329
(1.00) 		1
(1.00) 		0.0222
(1.00) 		0.516
(1.00) 		0.789
(1.00)
21q loss 163 (17%) 808 0.669
(1.00) 		0.434
(1.00) 		0.04
(1.00) 		0.447
(1.00) 		0.0275
(1.00) 		0.337
(1.00) 		0.385
(1.00) 		0.0692
(1.00) 		0.508
(1.00) 		0.762
(1.00)
22q loss 432 (44%) 539 0.14
(1.00) 		0.517
(1.00) 		0.823
(1.00) 		0.464
(1.00) 		0.391
(1.00) 		0.712
(1.00) 		0.354
(1.00) 		0.00398
(1.00) 		0.00172
(1.00) 		0.243
(1.00)
xq loss 162 (17%) 809 0.584
(1.00) 		0.104
(1.00) 		0.363
(1.00) 		0.0392
(1.00) 		0.71
(1.00) 		0.113
(1.00) 		0.225
(1.00) 		0.0936
(1.00) 		0.85
(1.00) 		0.082
(1.00)
'2p gain' versus 'HISTOLOGICAL.TYPE'

P value = 3.76e-05 (Chi-square test), Q value = 0.03

Table S1.  Gene #3: '2p gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 719 158 5 29 14 44
2P GAIN MUTATED 1 99 4 1 0 0 5
2P GAIN WILD-TYPE 0 620 154 4 29 14 39

Figure S1.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'3q gain' versus 'HISTOLOGICAL.TYPE'

P value = 1.25e-05 (Chi-square test), Q value = 0.0098

Table S2.  Gene #6: '3q gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 719 158 5 29 14 44
3Q GAIN MUTATED 0 164 8 3 6 1 9
3Q GAIN WILD-TYPE 1 555 150 2 23 13 35

Figure S2.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'6p gain' versus 'HISTOLOGICAL.TYPE'

P value = 0.000184 (Chi-square test), Q value = 0.14

Table S3.  Gene #11: '6p gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 719 158 5 29 14 44
6P GAIN MUTATED 0 150 15 4 3 1 10
6P GAIN WILD-TYPE 1 569 143 1 26 13 34

Figure S3.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'6q gain' versus 'HISTOLOGICAL.TYPE'

P value = 0.000173 (Chi-square test), Q value = 0.14

Table S4.  Gene #12: '6q gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 719 158 5 29 14 44
6Q GAIN MUTATED 0 106 11 4 3 1 7
6Q GAIN WILD-TYPE 1 613 147 1 26 13 37

Figure S4.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'8q gain' versus 'HISTOLOGICAL.TYPE'

P value = 1.13e-06 (Chi-square test), Q value = 9e-04

Table S5.  Gene #16: '8q gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 719 158 5 29 14 44
8Q GAIN MUTATED 1 385 46 4 12 4 25
8Q GAIN WILD-TYPE 0 334 112 1 17 10 19

Figure S5.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'10p gain' versus 'HISTOLOGICAL.TYPE'

P value = 0.00028 (Chi-square test), Q value = 0.22

Table S6.  Gene #19: '10p gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 719 158 5 29 14 44
10P GAIN MUTATED 0 165 15 3 4 0 6
10P GAIN WILD-TYPE 1 554 143 2 25 14 38

Figure S6.  Get High-res Image Gene #19: '10p gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'20p gain' versus 'HISTOLOGICAL.TYPE'

P value = 1.22e-06 (Chi-square test), Q value = 0.00097

Table S7.  Gene #36: '20p gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 719 158 5 29 14 44
20P GAIN MUTATED 0 313 33 1 9 1 13
20P GAIN WILD-TYPE 1 406 125 4 20 13 31

Figure S7.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'20q gain' versus 'HISTOLOGICAL.TYPE'

P value = 1.53e-07 (Chi-square test), Q value = 0.00012

Table S8.  Gene #37: '20q gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 719 158 5 29 14 44
20Q GAIN MUTATED 0 341 37 1 9 1 15
20Q GAIN WILD-TYPE 1 378 121 4 20 13 29

Figure S8.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'1p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.33e-05 (Chi-square test), Q value = 0.011

Table S9.  Gene #41: '1p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
ALL 77 74 9 9 327 221 2 136 27 56 15 1 16
1P LOSS MUTATED 10 10 1 3 72 39 1 42 16 18 6 0 4
1P LOSS WILD-TYPE 67 64 8 6 255 182 1 94 11 38 9 1 12

Figure S9.  Get High-res Image Gene #41: '1p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'1p loss' versus 'PATHOLOGY.T.STAGE'

P value = 3.83e-05 (Fisher's exact test), Q value = 0.03

Table S10.  Gene #41: '1p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 249 568 115 36
1P LOSS MUTATED 43 132 27 20
1P LOSS WILD-TYPE 206 436 88 16

Figure S10.  Get High-res Image Gene #41: '1p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'4p loss' versus 'HISTOLOGICAL.TYPE'

P value = 3.43e-06 (Chi-square test), Q value = 0.0027

Table S11.  Gene #47: '4p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 719 158 5 29 14 44
4P LOSS MUTATED 1 263 25 2 7 0 15
4P LOSS WILD-TYPE 0 456 133 3 22 14 29

Figure S11.  Get High-res Image Gene #47: '4p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'4q loss' versus 'HISTOLOGICAL.TYPE'

P value = 6.5e-05 (Chi-square test), Q value = 0.051

Table S12.  Gene #48: '4q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 719 158 5 29 14 44
4Q LOSS MUTATED 0 233 22 1 7 0 15
4Q LOSS WILD-TYPE 1 486 136 4 22 14 29

Figure S12.  Get High-res Image Gene #48: '4q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'5p loss' versus 'HISTOLOGICAL.TYPE'

P value = 4.54e-06 (Chi-square test), Q value = 0.0036

Table S13.  Gene #49: '5p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 719 158 5 29 14 44
5P LOSS MUTATED 0 110 2 3 4 0 6
5P LOSS WILD-TYPE 1 609 156 2 25 14 38

Figure S13.  Get High-res Image Gene #49: '5p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'5q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1.18e-10 (Chi-square test), Q value = 9.5e-08

Table S14.  Gene #50: '5q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 719 158 5 29 14 44
5Q LOSS MUTATED 1 186 3 3 4 0 8
5Q LOSS WILD-TYPE 0 533 155 2 25 14 36

Figure S14.  Get High-res Image Gene #50: '5q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'8p loss' versus 'HISTOLOGICAL.TYPE'

P value = 6.43e-05 (Chi-square test), Q value = 0.051

Table S15.  Gene #55: '8p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 719 158 5 29 14 44
8P LOSS MUTATED 1 293 34 2 8 1 17
8P LOSS WILD-TYPE 0 426 124 3 21 13 27

Figure S15.  Get High-res Image Gene #55: '8p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'9p loss' versus 'PATHOLOGY.T.STAGE'

P value = 0.00016 (Fisher's exact test), Q value = 0.13

Table S16.  Gene #57: '9p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 249 568 115 36
9P LOSS MUTATED 53 189 29 18
9P LOSS WILD-TYPE 196 379 86 18

Figure S16.  Get High-res Image Gene #57: '9p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'9p loss' versus 'HISTOLOGICAL.TYPE'

P value = 8.74e-06 (Chi-square test), Q value = 0.0069

Table S17.  Gene #57: '9p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 719 158 5 29 14 44
9P LOSS MUTATED 0 245 20 3 9 3 9
9P LOSS WILD-TYPE 1 474 138 2 20 11 35

Figure S17.  Get High-res Image Gene #57: '9p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'14q loss' versus 'HISTOLOGICAL.TYPE'

P value = 0.000136 (Chi-square test), Q value = 0.11

Table S18.  Gene #66: '14q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 719 158 5 29 14 44
14Q LOSS MUTATED 0 196 22 4 3 1 9
14Q LOSS WILD-TYPE 1 523 136 1 26 13 35

Figure S18.  Get High-res Image Gene #66: '14q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'16q loss' versus 'HISTOLOGICAL.TYPE'

P value = 8.74e-12 (Chi-square test), Q value = 7e-09

Table S19.  Gene #69: '16q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 719 158 5 29 14 44
16Q LOSS MUTATED 0 373 124 2 19 1 14
16Q LOSS WILD-TYPE 1 346 34 3 10 13 30

Figure S19.  Get High-res Image Gene #69: '16q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'18p loss' versus 'Time to Death'

P value = 6.78e-06 (logrank test), Q value = 0.0054

Table S20.  Gene #72: '18p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 950 112 0.0 - 234.3 (21.5)
18P LOSS MUTATED 282 49 0.0 - 189.0 (20.4)
18P LOSS WILD-TYPE 668 63 0.0 - 234.3 (22.5)

Figure S20.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #1: 'Time to Death'

'19p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1.11e-05 (Chi-square test), Q value = 0.0088

Table S21.  Gene #74: '19p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 719 158 5 29 14 44
19P LOSS MUTATED 0 155 5 1 3 3 5
19P LOSS WILD-TYPE 1 564 153 4 26 11 39

Figure S21.  Get High-res Image Gene #74: '19p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'19q loss' versus 'HISTOLOGICAL.TYPE'

P value = 0.000138 (Chi-square test), Q value = 0.11

Table S22.  Gene #75: '19q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 719 158 5 29 14 44
19Q LOSS MUTATED 0 130 4 1 3 3 4
19Q LOSS WILD-TYPE 1 589 154 4 26 11 40

Figure S22.  Get High-res Image Gene #75: '19q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

Methods & Data
Input

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

  • Clinical data file = BRCA-TP.merged_data.txt

  • Number of patients = 971

  • Number of significantly arm-level cnvs = 80

  • Number of selected clinical features = 10

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

Survival analysis

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

Student's t-test analysis

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

Chi-square test

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

Fisher's exact test

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

Q value calculation

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

Download Results

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

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