Correlation between copy number variation genes (focal events) and selected clinical features
Prostate Adenocarcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1513WNC
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 variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1513WNC
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 54 focal events and 14 clinical features across 184 patients, 12 significant findings detected with Q value < 0.25.

  • amp_8q24.21 cnv correlated to 'GLEASON_SCORE_COMBINED'.

  • amp_20q13.33 cnv correlated to 'PATHOLOGY.T.STAGE'.

  • amp_xp22.11 cnv correlated to 'PSA_VALUE'.

  • amp_xp22.11 cnv correlated to 'PSA_VALUE'.

  • amp_xp21.1 cnv correlated to 'PSA_VALUE'.

  • amp_xq21.1 cnv correlated to 'PSA_VALUE'.

  • amp_xq21.1 cnv correlated to 'PSA_VALUE'.

  • amp_xq21.31 cnv correlated to 'GLEASON_SCORE_PRIMARY'.

  • amp_xq25 cnv correlated to 'AGE'.

  • amp_xq25 cnv correlated to 'PSA_VALUE'.

  • del_4q27 cnv correlated to 'PSA_VALUE'.

  • del_7q36.1 cnv correlated to 'PSA_VALUE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 54 focal events and 14 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 12 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		COMPLETENESS
OF
RESECTION 		NUMBER
OF
LYMPH
NODES 		GLEASON
SCORE
COMBINED 		GLEASON
SCORE
PRIMARY 		GLEASON
SCORE
SECONDARY 		GLEASON
SCORE 		PSA
RESULT
PREOP 		DAYS
TO
PREOP
PSA 		PSA
VALUE 		DAYS
TO
PSA
nCNV (%) nWild-Type logrank test t-test Fisher's exact test Fisher's exact test Fisher's exact test t-test t-test t-test t-test t-test t-test t-test t-test t-test
amp 8q24 21 47 (26%) 137 100
(1.00) 		0.243
(1.00) 		0.0524
(1.00) 		0.0852
(1.00) 		0.929
(1.00) 		0.27
(1.00) 		0.000278
(0.207) 		0.000461
(0.34) 		0.0963
(1.00) 		0.000593
(0.436) 		0.0598
(1.00) 		0.697
(1.00) 		0.402
(1.00) 		0.162
(1.00)
amp 20q13 33 12 (7%) 172 100
(1.00) 		0.00378
(1.00) 		0.000272
(0.202) 		0.367
(1.00) 		0.054
(1.00) 		0.000779
(0.57) 		0.0487
(1.00) 		0.000717
(0.526) 		0.879
(1.00) 		0.0222
(1.00) 		0.211
(1.00) 		0.47
(1.00) 		0.452
(1.00) 		0.122
(1.00)
amp xp22 11 7 (4%) 177 100
(1.00) 		0.446
(1.00) 		0.557
(1.00) 		0.549
(1.00) 		1
(1.00) 		0.738
(1.00) 		0.596
(1.00) 		0.417
(1.00) 		0.678
(1.00) 		0.697
(1.00) 		0.356
(1.00) 		0.533
(1.00) 		0.000219
(0.163) 		0.00602
(1.00)
amp xp22 11 7 (4%) 177 100
(1.00) 		0.0584
(1.00) 		0.557
(1.00) 		0.549
(1.00) 		1
(1.00) 		0.738
(1.00) 		0.596
(1.00) 		0.179
(1.00) 		0.304
(1.00) 		0.947
(1.00) 		0.257
(1.00) 		0.152
(1.00) 		0.000207
(0.154) 		0.253
(1.00)
amp xp21 1 6 (3%) 178 100
(1.00) 		0.479
(1.00) 		0.345
(1.00) 		0.494
(1.00) 		0.65
(1.00) 		0.901
(1.00) 		0.845
(1.00) 		0.576
(1.00) 		0.568
(1.00) 		0.594
(1.00) 		0.414
(1.00) 		0.283
(1.00) 		0.000266
(0.198) 		0.564
(1.00)
amp xq21 1 7 (4%) 177 100
(1.00) 		0.67
(1.00) 		0.557
(1.00) 		0.549
(1.00) 		0.425
(1.00) 		0.738
(1.00) 		0.596
(1.00) 		0.636
(1.00) 		0.811
(1.00) 		0.493
(1.00) 		0.961
(1.00) 		0.348
(1.00) 		0.000193
(0.145) 		0.869
(1.00)
amp xq21 1 5 (3%) 179 100
(1.00) 		0.307
(1.00) 		0.461
(1.00) 		0.087
(1.00) 		0.621
(1.00) 		0.341
(1.00) 		0.442
(1.00) 		0.625
(1.00) 		0.541
(1.00) 		0.5
(1.00) 		0.422
(1.00) 		0.169
(1.00) 		0.000261
(0.195) 		0.361
(1.00)
amp xq21 31 5 (3%) 179 100
(1.00) 		0.218
(1.00) 		1
(1.00) 		1
(1.00) 		0.621
(1.00) 		0.000785
(0.572) 		0.327
(1.00) 		1.37e-26
(1.03e-23) 		0.99
(1.00) 		0.646
(1.00) 		0.443
(1.00) 		0.341
(1.00) 		0.47
(1.00) 		0.916
(1.00)
amp xq25 3 (2%) 181 100
(1.00) 		7.81e-09
(5.88e-06) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.000787
(0.572) 		0.604
(1.00) 		0.615
(1.00) 		0.751
(1.00) 		0.641
(1.00) 		0.695
(1.00) 		0.427
(1.00)
amp xq25 6 (3%) 178 100
(1.00) 		0.769
(1.00) 		0.739
(1.00) 		0.494
(1.00) 		0.408
(1.00) 		0.901
(1.00) 		0.374
(1.00) 		0.906
(1.00) 		0.267
(1.00) 		0.594
(1.00) 		0.855
(1.00) 		0.504
(1.00) 		0.000194
(0.146) 		0.426
(1.00)
del 4q27 17 (9%) 167 100
(1.00) 		0.0263
(1.00) 		0.114
(1.00) 		0.678
(1.00) 		0.161
(1.00) 		0.504
(1.00) 		0.235
(1.00) 		0.226
(1.00) 		0.583
(1.00) 		0.153
(1.00) 		0.614
(1.00) 		0.236
(1.00) 		0.000162
(0.121) 		0.211
(1.00)
del 7q36 1 9 (5%) 175 100
(1.00) 		0.868
(1.00) 		0.625
(1.00) 		0.161
(1.00) 		1
(1.00) 		0.391
(1.00) 		0.218
(1.00) 		0.642
(1.00) 		0.201
(1.00) 		0.576
(1.00) 		0.658
(1.00) 		0.232
(1.00) 		0.000149
(0.112) 		0.347
(1.00)
amp 1q21 3 11 (6%) 173 100
(1.00) 		0.748
(1.00) 		0.525
(1.00) 		0.327
(1.00) 		0.742
(1.00) 		0.522
(1.00) 		0.0781
(1.00) 		0.0914
(1.00) 		0.241
(1.00) 		0.101
(1.00) 		0.346
(1.00) 		0.923
(1.00) 		0.582
(1.00) 		0.765
(1.00)
amp 3q22 1 22 (12%) 162 100
(1.00) 		0.0703
(1.00) 		0.00407
(1.00) 		0.707
(1.00) 		0.205
(1.00) 		0.475
(1.00) 		0.15
(1.00) 		0.0201
(1.00) 		0.889
(1.00) 		0.0158
(1.00) 		0.165
(1.00) 		0.152
(1.00) 		0.0142
(1.00) 		0.209
(1.00)
amp 3q26 2 29 (16%) 155 100
(1.00) 		0.2
(1.00) 		0.0363
(1.00) 		0.501
(1.00) 		1
(1.00) 		0.313
(1.00) 		0.334
(1.00) 		0.0855
(1.00) 		0.764
(1.00) 		0.0867
(1.00) 		0.113
(1.00) 		0.438
(1.00) 		0.624
(1.00) 		0.937
(1.00)
amp 4q13 3 4 (2%) 180 100
(1.00) 		0.0778
(1.00) 		0.142
(1.00) 		0.363
(1.00) 		0.259
(1.00) 		0.821
(1.00) 		0.145
(1.00) 		0.279
(1.00) 		0.0859
(1.00) 		0.156
(1.00) 		0.296
(1.00) 		0.539
(1.00) 		0.72
(1.00) 		0.507
(1.00)
amp 7p15 3 35 (19%) 149 100
(1.00) 		0.309
(1.00) 		0.0136
(1.00) 		0.326
(1.00) 		0.0186
(1.00) 		0.272
(1.00) 		0.0246
(1.00) 		0.0473
(1.00) 		0.186
(1.00) 		0.031
(1.00) 		0.0328
(1.00) 		0.472
(1.00) 		0.469
(1.00) 		0.151
(1.00)
amp 8p12 13 (7%) 171 100
(1.00) 		0.666
(1.00) 		0.413
(1.00) 		0.618
(1.00) 		1
(1.00) 		0.853
(1.00) 		0.0307
(1.00) 		0.0604
(1.00) 		0.111
(1.00) 		0.0212
(1.00) 		0.0678
(1.00) 		0.399
(1.00) 		0.0464
(1.00) 		0.255
(1.00)
amp 8p11 22 17 (9%) 167 100
(1.00) 		0.396
(1.00) 		0.389
(1.00) 		0.0562
(1.00) 		1
(1.00) 		0.278
(1.00) 		0.0579
(1.00) 		0.0263
(1.00) 		0.439
(1.00) 		0.0485
(1.00) 		0.141
(1.00) 		0.43
(1.00) 		0.12
(1.00) 		0.462
(1.00)
amp 8q21 3 48 (26%) 136 100
(1.00) 		0.0782
(1.00) 		0.0425
(1.00) 		0.259
(1.00) 		0.731
(1.00) 		0.554
(1.00) 		0.000661
(0.486) 		0.000796
(0.577) 		0.146
(1.00) 		0.000712
(0.523) 		0.0315
(1.00) 		0.278
(1.00) 		0.411
(1.00) 		0.0827
(1.00)
amp 9q34 3 18 (10%) 166 100
(1.00) 		0.71
(1.00) 		0.025
(1.00) 		0.000427
(0.316) 		0.421
(1.00) 		0.055
(1.00) 		0.00183
(1.00) 		0.000828
(0.6) 		0.0713
(1.00) 		0.00178
(1.00) 		0.122
(1.00) 		0.456
(1.00) 		0.169
(1.00) 		0.755
(1.00)
amp 11q13 3 9 (5%) 175 100
(1.00) 		0.743
(1.00) 		0.0445
(1.00) 		0.0554
(1.00) 		0.496
(1.00) 		0.291
(1.00) 		0.12
(1.00) 		0.00996
(1.00) 		0.756
(1.00) 		0.0826
(1.00) 		0.829
(1.00) 		0.225
(1.00) 		0.08
(1.00) 		0.471
(1.00)
amp 12q24 32 7 (4%) 177 100
(1.00) 		0.943
(1.00) 		0.167
(1.00) 		0.161
(1.00) 		0.27
(1.00) 		0.389
(1.00) 		0.095
(1.00) 		0.0252
(1.00) 		0.811
(1.00) 		0.0348
(1.00) 		0.282
(1.00) 		0.148
(1.00) 		0.952
(1.00) 		0.142
(1.00)
amp 14q21 1 8 (4%) 176 100
(1.00) 		0.00129
(0.926) 		0.439
(1.00) 		0.549
(1.00) 		0.456
(1.00) 		0.763
(1.00) 		0.154
(1.00) 		0.568
(1.00) 		0.174
(1.00) 		0.0233
(1.00) 		0.914
(1.00) 		0.525
(1.00) 		0.894
(1.00) 		0.36
(1.00)
amp 15q11 2 5 (3%) 179 100
(1.00) 		0.00539
(1.00) 		0.704
(1.00) 		1
(1.00) 		0.621
(1.00) 		0.000785
(0.572) 		0.758
(1.00) 		0.625
(1.00) 		0.467
(1.00) 		0.5
(1.00) 		0.0111
(1.00) 		0.826
(1.00) 		0.000484
(0.357) 		0.521
(1.00)
amp xq27 1 9 (5%) 175 100
(1.00) 		0.277
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.000783
(0.571) 		0.845
(1.00) 		0.642
(1.00) 		0.593
(1.00) 		0.699
(1.00) 		0.0739
(1.00) 		0.121
(1.00) 		0.000577
(0.425) 		0.23
(1.00)
del 1p31 3 24 (13%) 160 100
(1.00) 		0.995
(1.00) 		0.236
(1.00) 		0.468
(1.00) 		0.197
(1.00) 		0.731
(1.00) 		0.0236
(1.00) 		0.148
(1.00) 		0.0444
(1.00) 		0.0401
(1.00) 		0.442
(1.00) 		0.623
(1.00) 		0.78
(1.00) 		0.141
(1.00)
del 1p13 3 19 (10%) 165 100
(1.00) 		0.428
(1.00) 		0.186
(1.00) 		1
(1.00) 		0.647
(1.00) 		0.942
(1.00) 		0.12
(1.00) 		0.108
(1.00) 		0.527
(1.00) 		0.179
(1.00) 		0.964
(1.00) 		0.489
(1.00) 		0.553
(1.00) 		0.875
(1.00)
del 1q23 1 8 (4%) 176 100
(1.00) 		0.52
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.000783
(0.571) 		0.542
(1.00) 		0.423
(1.00) 		0.783
(1.00) 		0.862
(1.00) 		0.286
(1.00) 		0.101
(1.00) 		0.0897
(1.00) 		0.00045
(0.333)
del 1q42 2 15 (8%) 169 100
(1.00) 		0.323
(1.00) 		0.245
(1.00) 		0.199
(1.00) 		0.59
(1.00) 		0.475
(1.00) 		0.674
(1.00) 		0.425
(1.00) 		0.614
(1.00) 		0.174
(1.00) 		0.275
(1.00) 		0.657
(1.00) 		0.442
(1.00) 		0.949
(1.00)
del 2p22 1 11 (6%) 173 100
(1.00) 		0.832
(1.00) 		0.237
(1.00) 		0.018
(1.00) 		0.496
(1.00) 		0.209
(1.00) 		0.0289
(1.00) 		0.0747
(1.00) 		0.0589
(1.00) 		0.0366
(1.00) 		0.836
(1.00) 		0.608
(1.00) 		0.643
(1.00) 		0.375
(1.00)
del 2q22 1 23 (12%) 161 100
(1.00) 		0.019
(1.00) 		0.615
(1.00) 		1
(1.00) 		0.596
(1.00) 		0.595
(1.00) 		0.179
(1.00) 		0.00105
(0.759) 		0.31
(1.00) 		0.129
(1.00) 		0.786
(1.00) 		0.0516
(1.00) 		0.0373
(1.00) 		0.652
(1.00)
del 3p13 28 (15%) 156 100
(1.00) 		0.273
(1.00) 		0.347
(1.00) 		1
(1.00) 		0.389
(1.00) 		0.76
(1.00) 		0.911
(1.00) 		0.788
(1.00) 		0.698
(1.00) 		0.707
(1.00) 		0.664
(1.00) 		0.852
(1.00) 		0.398
(1.00) 		0.642
(1.00)
del 3q29 10 (5%) 174 100
(1.00) 		0.121
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.955
(1.00) 		0.851
(1.00) 		0.782
(1.00) 		0.974
(1.00) 		0.976
(1.00) 		0.561
(1.00) 		0.863
(1.00) 		0.000357
(0.265) 		0.622
(1.00)
del 5q11 2 26 (14%) 158 100
(1.00) 		0.279
(1.00) 		0.00367
(1.00) 		0.000779
(0.57) 		1
(1.00) 		0.0503
(1.00) 		0.00502
(1.00) 		0.0156
(1.00) 		0.0472
(1.00) 		0.00938
(1.00) 		0.0875
(1.00) 		0.766
(1.00) 		0.5
(1.00) 		0.212
(1.00)
del 5q21 1 32 (17%) 152 100
(1.00) 		0.0456
(1.00) 		0.935
(1.00) 		0.101
(1.00) 		1
(1.00) 		0.251
(1.00) 		0.0614
(1.00) 		0.00388
(1.00) 		0.912
(1.00) 		0.0851
(1.00) 		0.535
(1.00) 		0.71
(1.00) 		0.403
(1.00) 		0.79
(1.00)
del 6q14 3 55 (30%) 129 100
(1.00) 		0.0921
(1.00) 		0.67
(1.00) 		0.00541
(1.00) 		0.0654
(1.00) 		0.0136
(1.00) 		0.00272
(1.00) 		0.000931
(0.673) 		0.396
(1.00) 		0.00378
(1.00) 		0.0146
(1.00) 		0.208
(1.00) 		0.0766
(1.00) 		0.99
(1.00)
del 8p21 3 106 (58%) 78 100
(1.00) 		0.434
(1.00) 		0.00109
(0.786) 		0.0658
(1.00) 		0.879
(1.00) 		0.0137
(1.00) 		0.46
(1.00) 		0.00148
(1.00) 		0.0401
(1.00) 		0.553
(1.00) 		0.00114
(0.82) 		0.278
(1.00) 		0.731
(1.00) 		0.0848
(1.00)
del 8p11 21 61 (33%) 123 100
(1.00) 		0.0811
(1.00) 		0.125
(1.00) 		1
(1.00) 		0.00362
(1.00) 		0.765
(1.00) 		0.37
(1.00) 		0.168
(1.00) 		0.0139
(1.00) 		0.246
(1.00) 		0.218
(1.00) 		0.147
(1.00) 		0.147
(1.00) 		0.046
(1.00)
del 9p23 17 (9%) 167 100
(1.00) 		0.471
(1.00) 		0.389
(1.00) 		0.0201
(1.00) 		0.647
(1.00) 		0.167
(1.00) 		0.0644
(1.00) 		0.0366
(1.00) 		0.396
(1.00) 		0.13
(1.00) 		0.469
(1.00) 		0.438
(1.00) 		0.804
(1.00) 		0.994
(1.00)
del 10q23 31 66 (36%) 118 100
(1.00) 		0.931
(1.00) 		0.0545
(1.00) 		0.00649
(1.00) 		0.446
(1.00) 		0.191
(1.00) 		0.117
(1.00) 		0.205
(1.00) 		0.38
(1.00) 		0.0282
(1.00) 		0.928
(1.00) 		0.339
(1.00) 		0.192
(1.00) 		0.152
(1.00)
del 11q23 2 17 (9%) 167 100
(1.00) 		0.697
(1.00) 		0.00988
(1.00) 		1
(1.00) 		0.483
(1.00) 		0.114
(1.00) 		0.504
(1.00) 		0.484
(1.00) 		0.84
(1.00) 		0.349
(1.00) 		0.452
(1.00) 		0.512
(1.00) 		0.371
(1.00) 		0.704
(1.00)
del 12p13 1 38 (21%) 146 100
(1.00) 		0.781
(1.00) 		0.326
(1.00) 		0.0713
(1.00) 		0.422
(1.00) 		0.398
(1.00) 		0.152
(1.00) 		0.0411
(1.00) 		0.966
(1.00) 		0.147
(1.00) 		0.709
(1.00) 		0.258
(1.00) 		0.909
(1.00) 		0.711
(1.00)
del 13q14 13 81 (44%) 103 100
(1.00) 		0.0315
(1.00) 		0.657
(1.00) 		0.303
(1.00) 		0.302
(1.00) 		0.239
(1.00) 		0.156
(1.00) 		0.338
(1.00) 		0.368
(1.00) 		0.0477
(1.00) 		0.0208
(1.00) 		0.601
(1.00) 		0.751
(1.00) 		0.827
(1.00)
del 13q22 1 68 (37%) 116 100
(1.00) 		0.0239
(1.00) 		0.147
(1.00) 		0.0691
(1.00) 		0.804
(1.00) 		0.128
(1.00) 		0.0874
(1.00) 		0.201
(1.00) 		0.32
(1.00) 		0.0121
(1.00) 		0.00674
(1.00) 		0.165
(1.00) 		0.874
(1.00) 		0.109
(1.00)
del 15q21 3 18 (10%) 166 100
(1.00) 		0.71
(1.00) 		0.0756
(1.00) 		0.0201
(1.00) 		0.539
(1.00) 		0.122
(1.00) 		0.00579
(1.00) 		0.00329
(1.00) 		0.189
(1.00) 		0.00633
(1.00) 		0.839
(1.00) 		0.352
(1.00) 		0.784
(1.00) 		0.557
(1.00)
del 16q22 3 63 (34%) 121 100
(1.00) 		0.239
(1.00) 		0.0228
(1.00) 		0.184
(1.00) 		0.93
(1.00) 		0.123
(1.00) 		0.0172
(1.00) 		0.00323
(1.00) 		0.631
(1.00) 		0.0121
(1.00) 		0.155
(1.00) 		0.599
(1.00) 		0.0621
(1.00) 		0.697
(1.00)
del 16q23 3 74 (40%) 110 100
(1.00) 		0.276
(1.00) 		0.0334
(1.00) 		0.446
(1.00) 		1
(1.00) 		0.218
(1.00) 		0.00977
(1.00) 		0.00483
(1.00) 		0.439
(1.00) 		0.00863
(1.00) 		0.302
(1.00) 		0.73
(1.00) 		0.0493
(1.00) 		0.962
(1.00)
del 17p13 1 47 (26%) 137 100
(1.00) 		0.754
(1.00) 		0.0217
(1.00) 		0.00704
(1.00) 		0.928
(1.00) 		0.0721
(1.00) 		0.0113
(1.00) 		0.00585
(1.00) 		0.343
(1.00) 		0.00818
(1.00) 		0.163
(1.00) 		0.828
(1.00) 		0.109
(1.00) 		0.585
(1.00)
del 17q21 31 36 (20%) 148 100
(1.00) 		0.885
(1.00) 		0.549
(1.00) 		0.748
(1.00) 		0.224
(1.00) 		0.695
(1.00) 		0.505
(1.00) 		0.387
(1.00) 		0.902
(1.00) 		0.468
(1.00) 		0.193
(1.00) 		0.621
(1.00) 		0.923
(1.00) 		0.522
(1.00)
del 18q22 1 49 (27%) 135 100
(1.00) 		0.773
(1.00) 		0.269
(1.00) 		0.396
(1.00) 		0.345
(1.00) 		0.579
(1.00) 		0.0203
(1.00) 		0.0774
(1.00) 		0.108
(1.00) 		0.0132
(1.00) 		0.399
(1.00) 		0.596
(1.00) 		0.466
(1.00) 		0.601
(1.00)
del 18q23 56 (30%) 128 100
(1.00) 		0.352
(1.00) 		0.154
(1.00) 		0.0523
(1.00) 		0.19
(1.00) 		0.174
(1.00) 		0.0104
(1.00) 		0.103
(1.00) 		0.0355
(1.00) 		0.00463
(1.00) 		0.361
(1.00) 		0.681
(1.00) 		0.557
(1.00) 		0.476
(1.00)
del 21q22 2 19 (10%) 165 100
(1.00) 		0.234
(1.00) 		0.0556
(1.00) 		0.00237
(1.00) 		1
(1.00) 		0.0602
(1.00) 		0.536
(1.00) 		0.722
(1.00) 		0.483
(1.00) 		0.657
(1.00) 		0.377
(1.00) 		0.351
(1.00) 		0.241
(1.00) 		0.622
(1.00)
del 21q22 3 55 (30%) 129 100
(1.00) 		0.959
(1.00) 		0.0146
(1.00) 		0.00358
(1.00) 		0.307
(1.00) 		0.0507
(1.00) 		0.242
(1.00) 		0.293
(1.00) 		0.543
(1.00) 		0.368
(1.00) 		0.253
(1.00) 		0.0643
(1.00) 		0.306
(1.00) 		0.461
(1.00)
'amp_8q24.21' versus 'GLEASON_SCORE_COMBINED'

P value = 0.000278 (t-test), Q value = 0.21

Table S1.  Gene #9: 'amp_8q24.21' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 184 7.3 (0.8)
AMP PEAK 9(8Q24.21) MUTATED 47 7.7 (0.9)
AMP PEAK 9(8Q24.21) WILD-TYPE 137 7.1 (0.7)

Figure S1.  Get High-res Image Gene #9: 'amp_8q24.21' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

'amp_20q13.33' versus 'PATHOLOGY.T.STAGE'

P value = 0.000272 (Fisher's exact test), Q value = 0.2

Table S2.  Gene #15: 'amp_20q13.33' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

nPatients T2 T3 T4
ALL 80 97 5
AMP PEAK 15(20Q13.33) MUTATED 0 10 2
AMP PEAK 15(20Q13.33) WILD-TYPE 80 87 3

Figure S2.  Get High-res Image Gene #15: 'amp_20q13.33' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

'amp_xp22.11' versus 'PSA_VALUE'

P value = 0.000219 (t-test), Q value = 0.16

Table S3.  Gene #16: 'amp_xp22.11' versus Clinical Feature #13: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 162 1.4 (4.5)
AMP PEAK 16(XP22.11) MUTATED 4 0.1 (0.1)
AMP PEAK 16(XP22.11) WILD-TYPE 158 1.5 (4.5)

Figure S3.  Get High-res Image Gene #16: 'amp_xp22.11' versus Clinical Feature #13: 'PSA_VALUE'

'amp_xp22.11' versus 'PSA_VALUE'

P value = 0.000207 (t-test), Q value = 0.15

Table S4.  Gene #17: 'amp_xp22.11' versus Clinical Feature #13: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 162 1.4 (4.5)
AMP PEAK 17(XP22.11) MUTATED 5 0.1 (0.1)
AMP PEAK 17(XP22.11) WILD-TYPE 157 1.5 (4.6)

Figure S4.  Get High-res Image Gene #17: 'amp_xp22.11' versus Clinical Feature #13: 'PSA_VALUE'

'amp_xp21.1' versus 'PSA_VALUE'

P value = 0.000266 (t-test), Q value = 0.2

Table S5.  Gene #18: 'amp_xp21.1' versus Clinical Feature #13: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 162 1.4 (4.5)
AMP PEAK 18(XP21.1) MUTATED 4 0.1 (0.0)
AMP PEAK 18(XP21.1) WILD-TYPE 158 1.5 (4.5)

Figure S5.  Get High-res Image Gene #18: 'amp_xp21.1' versus Clinical Feature #13: 'PSA_VALUE'

'amp_xq21.1' versus 'PSA_VALUE'

P value = 0.000193 (t-test), Q value = 0.14

Table S6.  Gene #19: 'amp_xq21.1' versus Clinical Feature #13: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 162 1.4 (4.5)
AMP PEAK 19(XQ21.1) MUTATED 6 0.1 (0.0)
AMP PEAK 19(XQ21.1) WILD-TYPE 156 1.5 (4.6)

Figure S6.  Get High-res Image Gene #19: 'amp_xq21.1' versus Clinical Feature #13: 'PSA_VALUE'

'amp_xq21.1' versus 'PSA_VALUE'

P value = 0.000261 (t-test), Q value = 0.19

Table S7.  Gene #20: 'amp_xq21.1' versus Clinical Feature #13: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 162 1.4 (4.5)
AMP PEAK 20(XQ21.1) MUTATED 4 0.1 (0.0)
AMP PEAK 20(XQ21.1) WILD-TYPE 158 1.5 (4.5)

Figure S7.  Get High-res Image Gene #20: 'amp_xq21.1' versus Clinical Feature #13: 'PSA_VALUE'

'amp_xq21.31' versus 'GLEASON_SCORE_PRIMARY'

P value = 1.37e-26 (t-test), Q value = 1e-23

Table S8.  Gene #21: 'amp_xq21.31' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 184 3.5 (0.6)
AMP PEAK 21(XQ21.31) MUTATED 5 4.0 (0.0)
AMP PEAK 21(XQ21.31) WILD-TYPE 179 3.5 (0.6)

Figure S8.  Get High-res Image Gene #21: 'amp_xq21.31' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

'amp_xq25' versus 'AGE'

P value = 7.81e-09 (t-test), Q value = 5.9e-06

Table S9.  Gene #22: 'amp_xq25' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 182 60.2 (7.0)
AMP PEAK 22(XQ25) MUTATED 3 65.7 (0.6)
AMP PEAK 22(XQ25) WILD-TYPE 179 60.2 (7.0)

Figure S9.  Get High-res Image Gene #22: 'amp_xq25' versus Clinical Feature #2: 'AGE'

'amp_xq25' versus 'PSA_VALUE'

P value = 0.000194 (t-test), Q value = 0.15

Table S10.  Gene #23: 'amp_xq25' versus Clinical Feature #13: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 162 1.4 (4.5)
AMP PEAK 23(XQ25) MUTATED 5 0.1 (0.0)
AMP PEAK 23(XQ25) WILD-TYPE 157 1.5 (4.6)

Figure S10.  Get High-res Image Gene #23: 'amp_xq25' versus Clinical Feature #13: 'PSA_VALUE'

'del_4q27' versus 'PSA_VALUE'

P value = 0.000162 (t-test), Q value = 0.12

Table S11.  Gene #33: 'del_4q27' versus Clinical Feature #13: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 162 1.4 (4.5)
DEL PEAK 9(4Q27) MUTATED 10 0.1 (0.0)
DEL PEAK 9(4Q27) WILD-TYPE 152 1.5 (4.6)

Figure S11.  Get High-res Image Gene #33: 'del_4q27' versus Clinical Feature #13: 'PSA_VALUE'

'del_7q36.1' versus 'PSA_VALUE'

P value = 0.000149 (t-test), Q value = 0.11

Table S12.  Gene #37: 'del_7q36.1' versus Clinical Feature #13: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 162 1.4 (4.5)
DEL PEAK 13(7Q36.1) MUTATED 9 0.1 (0.0)
DEL PEAK 13(7Q36.1) WILD-TYPE 153 1.5 (4.6)

Figure S12.  Get High-res Image Gene #37: 'del_7q36.1' versus Clinical Feature #13: 'PSA_VALUE'

Methods & Data
Input

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

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

  • Number of patients = 184

  • Number of significantly focal cnvs = 54

  • Number of selected clinical features = 14

  • 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

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

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] 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)
[4] 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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