Correlation between copy number variation genes (focal events) and selected clinical features
Prostate Adenocarcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1J38R6W
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/C1J38R6W
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 55 focal events and 14 clinical features across 205 patients, 20 significant findings detected with Q value < 0.25.

  • amp_5q35.3 cnv correlated to 'PSA_VALUE'.

  • amp_8q24.21 cnv correlated to 'GLEASON_SCORE_COMBINED',  'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.

  • amp_9q34.3 cnv correlated to 'GLEASON_SCORE_PRIMARY'.

  • amp_20q13.31 cnv correlated to 'PATHOLOGY.T.STAGE' and 'GLEASON_SCORE_PRIMARY'.

  • amp_xp22.11 cnv correlated to 'PSA_VALUE' and 'DAYS_TO_PSA'.

  • 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_1q23.1 cnv correlated to 'DAYS_TO_PSA'.

  • del_4q28.2 cnv correlated to 'PSA_VALUE'.

  • del_6q14.3 cnv correlated to 'GLEASON_SCORE_PRIMARY'.

  • del_8p21.3 cnv correlated to 'GLEASON_SCORE_PRIMARY'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 55 focal events and 14 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 20 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 51 (25%) 154 100
(1.00) 		0.136
(1.00) 		0.0194
(1.00) 		0.0818
(1.00) 		0.935
(1.00) 		0.251
(1.00) 		1.98e-05
(0.0151) 		6.97e-06
(0.00534) 		0.122
(1.00) 		6.67e-05
(0.0509) 		0.0386
(1.00) 		0.416
(1.00) 		0.357
(1.00) 		0.651
(1.00)
amp 20q13 31 11 (5%) 194 100
(1.00) 		0.0139
(1.00) 		0.000192
(0.146) 		0.604
(1.00) 		0.429
(1.00) 		0.000789
(0.582) 		0.0656
(1.00) 		9.53e-06
(0.00729) 		0.871
(1.00) 		0.0316
(1.00) 		0.194
(1.00) 		0.895
(1.00) 		0.66
(1.00) 		0.177
(1.00)
amp xp22 11 8 (4%) 197 100
(1.00) 		0.962
(1.00) 		0.42
(1.00) 		0.573
(1.00) 		1
(1.00) 		0.771
(1.00) 		0.342
(1.00) 		0.276
(1.00) 		0.902
(1.00) 		0.434
(1.00) 		0.393
(1.00) 		0.725
(1.00) 		0.00022
(0.166) 		0.000253
(0.191)
amp 5q35 3 7 (3%) 198 100
(1.00) 		0.00111
(0.811) 		0.0145
(1.00) 		0.524
(1.00) 		0.691
(1.00) 		0.824
(1.00) 		0.289
(1.00) 		0.214
(1.00) 		0.803
(1.00) 		0.0531
(1.00) 		0.673
(1.00) 		0.495
(1.00) 		0.000327
(0.245) 		0.62
(1.00)
amp 9q34 3 20 (10%) 185 100
(1.00) 		0.321
(1.00) 		0.00846
(1.00) 		0.000429
(0.32) 		0.729
(1.00) 		0.0557
(1.00) 		0.000433
(0.323) 		0.000158
(0.12) 		0.0915
(1.00) 		0.000439
(0.327) 		0.0649
(1.00) 		0.241
(1.00) 		0.181
(1.00) 		0.861
(1.00)
amp xp22 11 8 (4%) 197 100
(1.00) 		0.308
(1.00) 		0.42
(1.00) 		0.573
(1.00) 		1
(1.00) 		0.771
(1.00) 		0.342
(1.00) 		0.103
(1.00) 		0.444
(1.00) 		0.779
(1.00) 		0.289
(1.00) 		0.437
(1.00) 		0.000214
(0.162) 		0.0679
(1.00)
amp xp21 1 7 (3%) 198 100
(1.00) 		0.223
(1.00) 		0.267
(1.00) 		0.524
(1.00) 		1
(1.00) 		0.824
(1.00) 		0.529
(1.00) 		0.401
(1.00) 		0.767
(1.00) 		0.359
(1.00) 		0.453
(1.00) 		0.717
(1.00) 		0.000267
(0.201) 		0.172
(1.00)
amp xq21 1 7 (3%) 198 100
(1.00) 		0.669
(1.00) 		0.542
(1.00) 		0.524
(1.00) 		0.458
(1.00) 		0.708
(1.00) 		0.529
(1.00) 		0.606
(1.00) 		0.746
(1.00) 		0.453
(1.00) 		0.987
(1.00) 		0.373
(1.00) 		0.000204
(0.154) 		0.658
(1.00)
amp xq21 1 5 (2%) 200 100
(1.00) 		0.307
(1.00) 		0.449
(1.00) 		0.0772
(1.00) 		0.636
(1.00) 		0.333
(1.00) 		0.404
(1.00) 		0.601
(1.00) 		0.501
(1.00) 		0.465
(1.00) 		0.408
(1.00) 		0.178
(1.00) 		0.000283
(0.213) 		0.436
(1.00)
amp xq21 31 5 (2%) 200 100
(1.00) 		0.219
(1.00) 		1
(1.00) 		1
(1.00) 		0.636
(1.00) 		0.000794
(0.583) 		0.303
(1.00) 		4.35e-30
(3.34e-27) 		0.954
(1.00) 		0.618
(1.00) 		0.461
(1.00) 		0.359
(1.00) 		0.545
(1.00) 		0.782
(1.00)
amp xq25 3 (1%) 202 100
(1.00) 		1.62e-08
(1.24e-05) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.000796
(0.583) 		0.578
(1.00) 		0.6
(1.00) 		0.726
(1.00) 		0.619
(1.00) 		0.708
(1.00) 		0.437
(1.00)
amp xq25 6 (3%) 199 100
(1.00) 		0.77
(1.00) 		0.731
(1.00) 		0.47
(1.00) 		0.66
(1.00) 		0.956
(1.00) 		0.341
(1.00) 		0.874
(1.00) 		0.244
(1.00) 		0.545
(1.00) 		0.843
(1.00) 		0.533
(1.00) 		0.000205
(0.155) 		0.521
(1.00)
del 1q23 1 9 (4%) 196 100
(1.00) 		0.706
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.000792
(0.583) 		0.538
(1.00) 		0.247
(1.00) 		0.98
(1.00) 		0.88
(1.00) 		0.218
(1.00) 		0.0721
(1.00) 		0.0732
(1.00) 		0.000303
(0.227)
del 4q28 2 17 (8%) 188 100
(1.00) 		0.0325
(1.00) 		0.0588
(1.00) 		0.646
(1.00) 		0.561
(1.00) 		0.661
(1.00) 		0.188
(1.00) 		0.0911
(1.00) 		0.755
(1.00) 		0.127
(1.00) 		0.849
(1.00) 		0.193
(1.00) 		0.000183
(0.139) 		0.653
(1.00)
del 6q14 3 64 (31%) 141 100
(1.00) 		0.0433
(1.00) 		0.497
(1.00) 		0.00667
(1.00) 		0.0241
(1.00) 		0.0145
(1.00) 		0.000816
(0.596) 		0.000257
(0.194) 		0.386
(1.00) 		0.000998
(0.728) 		0.00512
(1.00) 		0.277
(1.00) 		0.0781
(1.00) 		0.782
(1.00)
del 8p21 3 115 (56%) 90 100
(1.00) 		0.372
(1.00) 		0.000452
(0.336) 		0.0661
(1.00) 		0.704
(1.00) 		0.0127
(1.00) 		0.138
(1.00) 		0.000196
(0.149) 		0.118
(1.00) 		0.253
(1.00) 		0.00153
(1.00) 		0.211
(1.00) 		0.632
(1.00) 		0.359
(1.00)
amp 1q21 3 13 (6%) 192 100
(1.00) 		0.511
(1.00) 		0.158
(1.00) 		0.337
(1.00) 		0.612
(1.00) 		0.531
(1.00) 		0.0235
(1.00) 		0.0226
(1.00) 		0.308
(1.00) 		0.0347
(1.00) 		0.186
(1.00) 		0.554
(1.00) 		0.591
(1.00) 		0.921
(1.00)
amp 3q22 1 25 (12%) 180 100
(1.00) 		0.0314
(1.00) 		0.0033
(1.00) 		0.705
(1.00) 		0.1
(1.00) 		0.466
(1.00) 		0.101
(1.00) 		0.00834
(1.00) 		0.71
(1.00) 		0.00631
(1.00) 		0.0573
(1.00) 		0.219
(1.00) 		0.0168
(1.00) 		0.18
(1.00)
amp 3q26 2 33 (16%) 172 100
(1.00) 		0.0682
(1.00) 		0.0241
(1.00) 		0.503
(1.00) 		1
(1.00) 		0.315
(1.00) 		0.168
(1.00) 		0.0236
(1.00) 		0.683
(1.00) 		0.0263
(1.00) 		0.0441
(1.00) 		0.658
(1.00) 		0.617
(1.00) 		0.991
(1.00)
amp 4p16 3 10 (5%) 195 100
(1.00) 		0.396
(1.00) 		0.0279
(1.00) 		1
(1.00) 		0.126
(1.00) 		0.487
(1.00) 		0.0248
(1.00) 		0.0319
(1.00) 		0.176
(1.00) 		0.0235
(1.00) 		0.622
(1.00) 		0.306
(1.00) 		0.0591
(1.00) 		0.676
(1.00)
amp 4q13 3 4 (2%) 201 100
(1.00) 		0.0788
(1.00) 		0.0956
(1.00) 		0.343
(1.00) 		0.261
(1.00) 		0.786
(1.00) 		0.139
(1.00) 		0.273
(1.00) 		0.0805
(1.00) 		0.15
(1.00) 		0.292
(1.00) 		0.499
(1.00) 		0.79
(1.00) 		0.696
(1.00)
amp 7p15 3 39 (19%) 166 100
(1.00) 		0.315
(1.00) 		0.015
(1.00) 		0.32
(1.00) 		0.0264
(1.00) 		0.26
(1.00) 		0.0278
(1.00) 		0.0499
(1.00) 		0.23
(1.00) 		0.0239
(1.00) 		0.0244
(1.00) 		0.365
(1.00) 		0.459
(1.00) 		0.165
(1.00)
amp 8p11 23 18 (9%) 187 100
(1.00) 		0.132
(1.00) 		0.288
(1.00) 		0.172
(1.00) 		0.705
(1.00) 		0.347
(1.00) 		0.0125
(1.00) 		0.0104
(1.00) 		0.23
(1.00) 		0.0104
(1.00) 		0.0469
(1.00) 		0.454
(1.00) 		0.137
(1.00) 		0.19
(1.00)
amp 11q13 3 11 (5%) 194 100
(1.00) 		0.296
(1.00) 		0.0154
(1.00) 		0.0625
(1.00) 		1
(1.00) 		0.293
(1.00) 		0.0476
(1.00) 		0.00183
(1.00) 		0.855
(1.00) 		0.0325
(1.00) 		0.372
(1.00) 		0.101
(1.00) 		0.0737
(1.00) 		0.768
(1.00)
amp 12q24 32 7 (3%) 198 100
(1.00) 		0.943
(1.00) 		0.158
(1.00) 		0.144
(1.00) 		0.289
(1.00) 		0.376
(1.00) 		0.0868
(1.00) 		0.0244
(1.00) 		0.746
(1.00) 		0.0324
(1.00) 		0.272
(1.00) 		0.126
(1.00) 		0.977
(1.00) 		0.2
(1.00)
amp 14q21 1 10 (5%) 195 100
(1.00) 		0.000393
(0.294) 		0.256
(1.00) 		0.573
(1.00) 		1
(1.00) 		0.7
(1.00) 		0.0424
(1.00) 		0.193
(1.00) 		0.29
(1.00) 		0.00496
(1.00) 		0.449
(1.00) 		0.692
(1.00) 		0.851
(1.00) 		0.115
(1.00)
amp 15q11 2 6 (3%) 199 100
(1.00) 		0.241
(1.00) 		0.501
(1.00) 		1
(1.00) 		0.66
(1.00) 		0.000794
(0.583) 		0.706
(1.00) 		0.371
(1.00) 		0.272
(1.00) 		0.545
(1.00) 		0.00942
(1.00) 		0.549
(1.00) 		0.000568
(0.421) 		0.354
(1.00)
amp 19q13 43 5 (2%) 200 100
(1.00) 		0.273
(1.00) 		0.0189
(1.00) 		1
(1.00) 		1
(1.00) 		0.000794
(0.583) 		0.154
(1.00) 		0.161
(1.00) 		0.306
(1.00) 		0.0451
(1.00) 		0.313
(1.00) 		0.758
(1.00) 		0.637
(1.00) 		0.32
(1.00)
amp xq27 1 9 (4%) 196 100
(1.00) 		0.279
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.000792
(0.583) 		0.958
(1.00) 		0.606
(1.00) 		0.661
(1.00) 		0.788
(1.00) 		0.0793
(1.00) 		0.128
(1.00) 		0.000687
(0.508) 		0.157
(1.00)
del 1p31 3 27 (13%) 178 100
(1.00) 		0.554
(1.00) 		0.115
(1.00) 		0.71
(1.00) 		0.101
(1.00) 		0.8
(1.00) 		0.0106
(1.00) 		0.0976
(1.00) 		0.0272
(1.00) 		0.021
(1.00) 		0.628
(1.00) 		0.627
(1.00) 		0.766
(1.00) 		0.211
(1.00)
del 1q42 2 16 (8%) 189 100
(1.00) 		0.215
(1.00) 		0.3
(1.00) 		0.199
(1.00) 		0.28
(1.00) 		0.474
(1.00) 		0.604
(1.00) 		0.289
(1.00) 		0.489
(1.00) 		0.169
(1.00) 		0.364
(1.00) 		0.627
(1.00) 		0.443
(1.00) 		0.833
(1.00)
del 2p22 1 12 (6%) 193 100
(1.00) 		0.997
(1.00) 		0.134
(1.00) 		0.02
(1.00) 		0.557
(1.00) 		0.216
(1.00) 		0.0304
(1.00) 		0.0404
(1.00) 		0.112
(1.00) 		0.0404
(1.00) 		0.936
(1.00) 		0.532
(1.00) 		0.618
(1.00) 		0.191
(1.00)
del 2q22 1 27 (13%) 178 100
(1.00) 		0.00559
(1.00) 		0.589
(1.00) 		1
(1.00) 		0.489
(1.00) 		0.604
(1.00) 		0.109
(1.00) 		0.00125
(0.91) 		0.424
(1.00) 		0.047
(1.00) 		0.813
(1.00) 		0.0483
(1.00) 		0.0439
(1.00) 		0.498
(1.00)
del 2q22 3 23 (11%) 182 100
(1.00) 		0.0826
(1.00) 		0.596
(1.00) 		1
(1.00) 		0.67
(1.00) 		0.445
(1.00) 		0.489
(1.00) 		0.105
(1.00) 		0.586
(1.00) 		0.0844
(1.00) 		0.861
(1.00) 		0.605
(1.00) 		0.0697
(1.00) 		0.162
(1.00)
del 3p13 32 (16%) 173 100
(1.00) 		0.157
(1.00) 		0.492
(1.00) 		1
(1.00) 		0.164
(1.00) 		0.751
(1.00) 		0.726
(1.00) 		0.779
(1.00) 		0.838
(1.00) 		0.648
(1.00) 		0.657
(1.00) 		0.793
(1.00) 		0.409
(1.00) 		0.88
(1.00)
del 3q29 11 (5%) 194 100
(1.00) 		0.274
(1.00) 		0.66
(1.00) 		1
(1.00) 		1
(1.00) 		0.976
(1.00) 		0.906
(1.00) 		0.971
(1.00) 		0.794
(1.00) 		0.792
(1.00) 		0.687
(1.00) 		0.817
(1.00) 		0.000371
(0.278) 		0.992
(1.00)
del 5q11 2 28 (14%) 177 100
(1.00) 		0.161
(1.00) 		0.000724
(0.534) 		0.000674
(0.499) 		1
(1.00) 		0.0484
(1.00) 		0.0026
(1.00) 		0.00374
(1.00) 		0.115
(1.00) 		0.00297
(1.00) 		0.0208
(1.00) 		0.983
(1.00) 		0.456
(1.00) 		0.196
(1.00)
del 5q21 1 36 (18%) 169 100
(1.00) 		0.0235
(1.00) 		0.881
(1.00) 		0.101
(1.00) 		1
(1.00) 		0.25
(1.00) 		0.0725
(1.00) 		0.00253
(1.00) 		0.641
(1.00) 		0.0415
(1.00) 		0.649
(1.00) 		0.899
(1.00) 		0.396
(1.00) 		0.652
(1.00)
del 8p11 21 66 (32%) 139 100
(1.00) 		0.112
(1.00) 		0.143
(1.00) 		1
(1.00) 		0.0114
(1.00) 		0.735
(1.00) 		0.771
(1.00) 		0.165
(1.00) 		0.0889
(1.00) 		0.489
(1.00) 		0.351
(1.00) 		0.114
(1.00) 		0.135
(1.00) 		0.132
(1.00)
del 9p23 18 (9%) 187 100
(1.00) 		0.782
(1.00) 		0.288
(1.00) 		0.0152
(1.00) 		0.705
(1.00) 		0.152
(1.00) 		0.0327
(1.00) 		0.0145
(1.00) 		0.49
(1.00) 		0.079
(1.00) 		0.19
(1.00) 		0.281
(1.00) 		0.901
(1.00) 		0.777
(1.00)
del 10q23 31 67 (33%) 138 100
(1.00) 		0.894
(1.00) 		0.0192
(1.00) 		0.00286
(1.00) 		0.757
(1.00) 		0.149
(1.00) 		0.0647
(1.00) 		0.205
(1.00) 		0.211
(1.00) 		0.0184
(1.00) 		0.956
(1.00) 		0.547
(1.00) 		0.155
(1.00) 		0.285
(1.00)
del 11q23 2 18 (9%) 187 100
(1.00) 		0.487
(1.00) 		0.00867
(1.00) 		1
(1.00) 		0.561
(1.00) 		0.142
(1.00) 		0.317
(1.00) 		0.244
(1.00) 		0.962
(1.00) 		0.226
(1.00) 		0.244
(1.00) 		0.709
(1.00) 		0.314
(1.00) 		0.951
(1.00)
del 12p13 1 43 (21%) 162 100
(1.00) 		0.951
(1.00) 		0.131
(1.00) 		0.129
(1.00) 		0.54
(1.00) 		0.441
(1.00) 		0.0777
(1.00) 		0.0112
(1.00) 		0.971
(1.00) 		0.0604
(1.00) 		0.83
(1.00) 		0.279
(1.00) 		0.968
(1.00) 		0.568
(1.00)
del 12q24 31 18 (9%) 187 100
(1.00) 		0.767
(1.00) 		0.451
(1.00) 		0.382
(1.00) 		1
(1.00) 		1
(1.00) 		0.108
(1.00) 		0.291
(1.00) 		0.294
(1.00) 		0.138
(1.00) 		0.179
(1.00) 		0.391
(1.00) 		0.0231
(1.00) 		0.829
(1.00)
del 13q14 12 88 (43%) 117 100
(1.00) 		0.0308
(1.00) 		0.575
(1.00) 		0.305
(1.00) 		0.312
(1.00) 		0.24
(1.00) 		0.0891
(1.00) 		0.199
(1.00) 		0.341
(1.00) 		0.0231
(1.00) 		0.0739
(1.00) 		0.539
(1.00) 		0.676
(1.00) 		0.381
(1.00)
del 13q22 1 72 (35%) 133 100
(1.00) 		0.0267
(1.00) 		0.128
(1.00) 		0.0655
(1.00) 		0.804
(1.00) 		0.121
(1.00) 		0.0432
(1.00) 		0.154
(1.00) 		0.2
(1.00) 		0.00424
(1.00) 		0.0188
(1.00) 		0.182
(1.00) 		0.983
(1.00) 		0.406
(1.00)
del 15q21 3 20 (10%) 185 100
(1.00) 		0.696
(1.00) 		0.0999
(1.00) 		0.0152
(1.00) 		0.627
(1.00) 		0.112
(1.00) 		0.00327
(1.00) 		0.000678
(0.502) 		0.399
(1.00) 		0.0041
(1.00) 		0.351
(1.00) 		0.342
(1.00) 		0.921
(1.00) 		0.383
(1.00)
del 16q22 3 71 (35%) 134 100
(1.00) 		0.19
(1.00) 		0.0225
(1.00) 		0.185
(1.00) 		1
(1.00) 		0.123
(1.00) 		0.00467
(1.00) 		0.00129
(0.939) 		0.458
(1.00) 		0.00475
(1.00) 		0.0849
(1.00) 		0.563
(1.00) 		0.0578
(1.00) 		0.352
(1.00)
del 16q23 3 81 (40%) 124 100
(1.00) 		0.284
(1.00) 		0.0361
(1.00) 		0.44
(1.00) 		0.949
(1.00) 		0.2
(1.00) 		0.0019
(1.00) 		0.00269
(1.00) 		0.212
(1.00) 		0.00257
(1.00) 		0.142
(1.00) 		0.776
(1.00) 		0.0407
(1.00) 		0.38
(1.00)
del 17p13 1 52 (25%) 153 100
(1.00) 		0.752
(1.00) 		0.0123
(1.00) 		0.00336
(1.00) 		0.521
(1.00) 		0.0671
(1.00) 		0.00258
(1.00) 		0.00453
(1.00) 		0.15
(1.00) 		0.00244
(1.00) 		0.115
(1.00) 		0.707
(1.00) 		0.102
(1.00) 		0.65
(1.00)
del 17q21 31 39 (19%) 166 100
(1.00) 		0.955
(1.00) 		0.561
(1.00) 		0.748
(1.00) 		0.167
(1.00) 		0.706
(1.00) 		0.587
(1.00) 		0.587
(1.00) 		0.796
(1.00) 		0.588
(1.00) 		0.147
(1.00) 		0.95
(1.00) 		0.963
(1.00) 		0.89
(1.00)
del 18q22 1 51 (25%) 154 100
(1.00) 		0.534
(1.00) 		0.341
(1.00) 		0.375
(1.00) 		0.22
(1.00) 		0.489
(1.00) 		0.0144
(1.00) 		0.111
(1.00) 		0.0485
(1.00) 		0.0114
(1.00) 		0.458
(1.00) 		0.682
(1.00) 		0.412
(1.00) 		0.96
(1.00)
del 19q13 2 17 (8%) 188 100
(1.00) 		0.138
(1.00) 		0.193
(1.00) 		0.0694
(1.00) 		0.233
(1.00) 		0.335
(1.00) 		0.0634
(1.00) 		0.0439
(1.00) 		0.495
(1.00) 		0.0558
(1.00) 		0.303
(1.00) 		0.714
(1.00) 		0.605
(1.00) 		0.414
(1.00)
del 21q22 2 21 (10%) 184 100
(1.00) 		0.181
(1.00) 		0.0567
(1.00) 		0.00241
(1.00) 		0.639
(1.00) 		0.0611
(1.00) 		0.672
(1.00) 		0.927
(1.00) 		0.526
(1.00) 		0.83
(1.00) 		0.283
(1.00) 		0.247
(1.00) 		0.271
(1.00) 		0.932
(1.00)
del 21q22 3 58 (28%) 147 100
(1.00) 		1
(1.00) 		0.0165
(1.00) 		0.00175
(1.00) 		0.291
(1.00) 		0.0461
(1.00) 		0.256
(1.00) 		0.427
(1.00) 		0.411
(1.00) 		0.422
(1.00) 		0.226
(1.00) 		0.0322
(1.00) 		0.274
(1.00) 		0.549
(1.00)
'amp_5q35.3' versus 'PSA_VALUE'

P value = 0.000327 (t-test), Q value = 0.24

Table S1.  Gene #6: 'amp_5q35.3' versus Clinical Feature #13: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 176 1.3 (4.3)
AMP PEAK 6(5Q35.3) MUTATED 6 0.1 (0.1)
AMP PEAK 6(5Q35.3) WILD-TYPE 170 1.4 (4.4)

Figure S1.  Get High-res Image Gene #6: 'amp_5q35.3' versus Clinical Feature #13: 'PSA_VALUE'

'amp_8q24.21' versus 'GLEASON_SCORE_COMBINED'

P value = 1.98e-05 (t-test), Q value = 0.015

Table S2.  Gene #9: 'amp_8q24.21' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 205 7.2 (0.8)
AMP PEAK 9(8Q24.21) MUTATED 51 7.7 (0.9)
AMP PEAK 9(8Q24.21) WILD-TYPE 154 7.1 (0.7)

Figure S2.  Get High-res Image Gene #9: 'amp_8q24.21' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

'amp_8q24.21' versus 'GLEASON_SCORE_PRIMARY'

P value = 6.97e-06 (t-test), Q value = 0.0053

Table S3.  Gene #9: 'amp_8q24.21' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 205 3.5 (0.6)
AMP PEAK 9(8Q24.21) MUTATED 51 3.8 (0.6)
AMP PEAK 9(8Q24.21) WILD-TYPE 154 3.4 (0.5)

Figure S3.  Get High-res Image Gene #9: 'amp_8q24.21' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

'amp_8q24.21' versus 'GLEASON_SCORE'

P value = 6.67e-05 (t-test), Q value = 0.051

Table S4.  Gene #9: 'amp_8q24.21' versus Clinical Feature #10: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 205 7.3 (0.8)
AMP PEAK 9(8Q24.21) MUTATED 51 7.7 (1.0)
AMP PEAK 9(8Q24.21) WILD-TYPE 154 7.1 (0.7)

Figure S4.  Get High-res Image Gene #9: 'amp_8q24.21' versus Clinical Feature #10: 'GLEASON_SCORE'

'amp_9q34.3' versus 'GLEASON_SCORE_PRIMARY'

P value = 0.000158 (t-test), Q value = 0.12

Table S5.  Gene #10: 'amp_9q34.3' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 205 3.5 (0.6)
AMP PEAK 10(9Q34.3) MUTATED 20 4.0 (0.6)
AMP PEAK 10(9Q34.3) WILD-TYPE 185 3.4 (0.5)

Figure S5.  Get High-res Image Gene #10: 'amp_9q34.3' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

'amp_20q13.31' versus 'PATHOLOGY.T.STAGE'

P value = 0.000192 (Fisher's exact test), Q value = 0.15

Table S6.  Gene #16: 'amp_20q13.31' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

nPatients T2 T3 T4
ALL 92 106 5
AMP PEAK 16(20Q13.31) MUTATED 0 9 2
AMP PEAK 16(20Q13.31) WILD-TYPE 92 97 3

Figure S6.  Get High-res Image Gene #16: 'amp_20q13.31' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

'amp_20q13.31' versus 'GLEASON_SCORE_PRIMARY'

P value = 9.53e-06 (t-test), Q value = 0.0073

Table S7.  Gene #16: 'amp_20q13.31' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 205 3.5 (0.6)
AMP PEAK 16(20Q13.31) MUTATED 11 4.1 (0.3)
AMP PEAK 16(20Q13.31) WILD-TYPE 194 3.4 (0.6)

Figure S7.  Get High-res Image Gene #16: 'amp_20q13.31' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

'amp_xp22.11' versus 'PSA_VALUE'

P value = 0.00022 (t-test), Q value = 0.17

Table S8.  Gene #17: 'amp_xp22.11' versus Clinical Feature #13: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 176 1.3 (4.3)
AMP PEAK 17(XP22.11) MUTATED 5 0.1 (0.1)
AMP PEAK 17(XP22.11) WILD-TYPE 171 1.4 (4.4)

Figure S8.  Get High-res Image Gene #17: 'amp_xp22.11' versus Clinical Feature #13: 'PSA_VALUE'

'amp_xp22.11' versus 'DAYS_TO_PSA'

P value = 0.000253 (t-test), Q value = 0.19

Table S9.  Gene #17: 'amp_xp22.11' versus Clinical Feature #14: 'DAYS_TO_PSA'

nPatients Mean (Std.Dev)
ALL 181 577.6 (545.5)
AMP PEAK 17(XP22.11) MUTATED 5 191.4 (125.9)
AMP PEAK 17(XP22.11) WILD-TYPE 176 588.6 (548.9)

Figure S9.  Get High-res Image Gene #17: 'amp_xp22.11' versus Clinical Feature #14: 'DAYS_TO_PSA'

'amp_xp22.11' versus 'PSA_VALUE'

P value = 0.000214 (t-test), Q value = 0.16

Table S10.  Gene #18: 'amp_xp22.11' versus Clinical Feature #13: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 176 1.3 (4.3)
AMP PEAK 18(XP22.11) MUTATED 6 0.1 (0.1)
AMP PEAK 18(XP22.11) WILD-TYPE 170 1.4 (4.4)

Figure S10.  Get High-res Image Gene #18: 'amp_xp22.11' versus Clinical Feature #13: 'PSA_VALUE'

'amp_xp21.1' versus 'PSA_VALUE'

P value = 0.000267 (t-test), Q value = 0.2

Table S11.  Gene #19: 'amp_xp21.1' versus Clinical Feature #13: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 176 1.3 (4.3)
AMP PEAK 19(XP21.1) MUTATED 5 0.1 (0.0)
AMP PEAK 19(XP21.1) WILD-TYPE 171 1.4 (4.4)

Figure S11.  Get High-res Image Gene #19: 'amp_xp21.1' versus Clinical Feature #13: 'PSA_VALUE'

'amp_xq21.1' versus 'PSA_VALUE'

P value = 0.000204 (t-test), Q value = 0.15

Table S12.  Gene #20: 'amp_xq21.1' versus Clinical Feature #13: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 176 1.3 (4.3)
AMP PEAK 20(XQ21.1) MUTATED 6 0.1 (0.0)
AMP PEAK 20(XQ21.1) WILD-TYPE 170 1.4 (4.4)

Figure S12.  Get High-res Image Gene #20: 'amp_xq21.1' versus Clinical Feature #13: 'PSA_VALUE'

'amp_xq21.1' versus 'PSA_VALUE'

P value = 0.000283 (t-test), Q value = 0.21

Table S13.  Gene #21: 'amp_xq21.1' versus Clinical Feature #13: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 176 1.3 (4.3)
AMP PEAK 21(XQ21.1) MUTATED 4 0.1 (0.0)
AMP PEAK 21(XQ21.1) WILD-TYPE 172 1.4 (4.4)

Figure S13.  Get High-res Image Gene #21: 'amp_xq21.1' versus Clinical Feature #13: 'PSA_VALUE'

'amp_xq21.31' versus 'GLEASON_SCORE_PRIMARY'

P value = 4.35e-30 (t-test), Q value = 3.3e-27

Table S14.  Gene #22: 'amp_xq21.31' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 205 3.5 (0.6)
AMP PEAK 22(XQ21.31) MUTATED 5 4.0 (0.0)
AMP PEAK 22(XQ21.31) WILD-TYPE 200 3.5 (0.6)

Figure S14.  Get High-res Image Gene #22: 'amp_xq21.31' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

'amp_xq25' versus 'AGE'

P value = 1.62e-08 (t-test), Q value = 1.2e-05

Table S15.  Gene #23: 'amp_xq25' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 203 60.2 (6.9)
AMP PEAK 23(XQ25) MUTATED 3 65.7 (0.6)
AMP PEAK 23(XQ25) WILD-TYPE 200 60.2 (6.9)

Figure S15.  Get High-res Image Gene #23: 'amp_xq25' versus Clinical Feature #2: 'AGE'

'amp_xq25' versus 'PSA_VALUE'

P value = 0.000205 (t-test), Q value = 0.16

Table S16.  Gene #24: 'amp_xq25' versus Clinical Feature #13: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 176 1.3 (4.3)
AMP PEAK 24(XQ25) MUTATED 5 0.1 (0.0)
AMP PEAK 24(XQ25) WILD-TYPE 171 1.4 (4.4)

Figure S16.  Get High-res Image Gene #24: 'amp_xq25' versus Clinical Feature #13: 'PSA_VALUE'

'del_1q23.1' versus 'DAYS_TO_PSA'

P value = 0.000303 (t-test), Q value = 0.23

Table S17.  Gene #27: 'del_1q23.1' versus Clinical Feature #14: 'DAYS_TO_PSA'

nPatients Mean (Std.Dev)
ALL 181 577.6 (545.5)
DEL PEAK 2(1Q23.1) MUTATED 8 264.5 (163.8)
DEL PEAK 2(1Q23.1) WILD-TYPE 173 592.1 (552.8)

Figure S17.  Get High-res Image Gene #27: 'del_1q23.1' versus Clinical Feature #14: 'DAYS_TO_PSA'

'del_4q28.2' versus 'PSA_VALUE'

P value = 0.000183 (t-test), Q value = 0.14

Table S18.  Gene #34: 'del_4q28.2' versus Clinical Feature #13: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 176 1.3 (4.3)
DEL PEAK 9(4Q28.2) MUTATED 11 0.1 (0.0)
DEL PEAK 9(4Q28.2) WILD-TYPE 165 1.4 (4.5)

Figure S18.  Get High-res Image Gene #34: 'del_4q28.2' versus Clinical Feature #13: 'PSA_VALUE'

'del_6q14.3' versus 'GLEASON_SCORE_PRIMARY'

P value = 0.000257 (t-test), Q value = 0.19

Table S19.  Gene #37: 'del_6q14.3' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 205 3.5 (0.6)
DEL PEAK 12(6Q14.3) MUTATED 64 3.7 (0.6)
DEL PEAK 12(6Q14.3) WILD-TYPE 141 3.4 (0.5)

Figure S19.  Get High-res Image Gene #37: 'del_6q14.3' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

'del_8p21.3' versus 'GLEASON_SCORE_PRIMARY'

P value = 0.000196 (t-test), Q value = 0.15

Table S20.  Gene #38: 'del_8p21.3' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 205 3.5 (0.6)
DEL PEAK 13(8P21.3) MUTATED 115 3.6 (0.6)
DEL PEAK 13(8P21.3) WILD-TYPE 90 3.3 (0.5)

Figure S20.  Get High-res Image Gene #38: 'del_8p21.3' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

Methods & Data
Input

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

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

  • Number of patients = 205

  • Number of significantly focal cnvs = 55

  • 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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