Correlation between copy number variations of arm-level result and selected clinical features
Rectum Adenocarcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1S46R1D
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1S46R1D
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 12 clinical features across 165 patients, no significant finding detected with Q value < 0.25.

  • No arm-level cnvs related to clinical features.

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 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, no significant finding 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 		COMPLETENESS
OF
RESECTION 		NUMBER
OF
LYMPH
NODES 		RACE
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 Fisher's exact test Wilcoxon-test Fisher's exact test
1p gain 12 (7%) 153 0.0451
(0.545) 		0.564
(0.988) 		0.175
(0.801) 		0.0276
(0.54) 		0.444
(0.96) 		1
(1.00) 		0.774
(1.00) 		0.0483
(0.565) 		1
(1.00) 		0.217
(0.842) 		0.601
(0.988) 		1
(1.00)
1q gain 34 (21%) 131 0.806
(1.00) 		0.501
(0.98) 		0.619
(0.988) 		0.00475
(0.486) 		0.281
(0.874) 		1
(1.00) 		0.441
(0.959) 		0.298
(0.874) 		0.604
(0.988) 		0.575
(0.988) 		0.096
(0.673) 		0.484
(0.979)
2p gain 41 (25%) 124 0.748
(1.00) 		0.78
(1.00) 		0.415
(0.959) 		0.373
(0.956) 		0.216
(0.842) 		0.442
(0.959) 		0.0311
(0.54) 		0.0222
(0.54) 		0.639
(0.989) 		0.102
(0.681) 		0.869
(1.00) 		0.11
(0.687)
2q gain 43 (26%) 122 0.969
(1.00) 		0.964
(1.00) 		0.298
(0.874) 		0.26
(0.87) 		0.141
(0.746) 		0.609
(0.988) 		0.0332
(0.54) 		0.0206
(0.54) 		0.183
(0.802) 		0.147
(0.767) 		0.546
(0.988) 		0.0121
(0.486)
3p gain 27 (16%) 138 0.569
(0.988) 		0.819
(1.00) 		0.18
(0.802) 		0.834
(1.00) 		0.394
(0.959) 		0.224
(0.842) 		0.533
(0.988) 		0.698
(1.00) 		0.255
(0.87) 		0.883
(1.00) 		0.209
(0.842) 		1
(1.00)
3q gain 34 (21%) 131 0.983
(1.00) 		0.992
(1.00) 		0.272
(0.874) 		0.686
(1.00) 		0.489
(0.98) 		0.265
(0.87) 		0.441
(0.959) 		0.302
(0.884) 		0.604
(0.988) 		0.726
(1.00) 		0.29
(0.874) 		0.705
(1.00)
4p gain 9 (5%) 156 0.843
(1.00) 		0.914
(1.00) 		0.22
(0.842) 		0.65
(0.989) 		0.243
(0.855) 		1
(1.00) 		0.18
(0.802) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0445
(0.545) 		1
(1.00)
4q gain 5 (3%) 160 0.988
(1.00) 		0.857
(1.00) 		0.896
(1.00) 		1
(1.00) 		0.706
(1.00) 		0.587
(0.988) 		0.0626
(0.653) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.439
(0.959)
5p gain 36 (22%) 129 0.662
(0.999) 		0.699
(1.00) 		0.776
(1.00) 		0.156
(0.788) 		0.715
(1.00) 		0.597
(0.988) 		0.092
(0.673) 		0.0412
(0.545) 		0.119
(0.715) 		0.4
(0.959) 		0.532
(0.988) 		0.239
(0.855)
5q gain 24 (15%) 141 0.674
(1.00) 		0.936
(1.00) 		0.228
(0.843) 		0.583
(0.988) 		0.282
(0.874) 		0.756
(1.00) 		0.386
(0.959) 		0.22
(0.842) 		1
(1.00) 		0.541
(0.988) 		0.211
(0.842) 		0.335
(0.92)
6p gain 41 (25%) 124 0.331
(0.914) 		0.774
(1.00) 		0.209
(0.842) 		0.279
(0.874) 		0.0239
(0.54) 		0.0328
(0.54) 		0.588
(0.988) 		0.187
(0.807) 		0.034
(0.544) 		0.444
(0.96) 		0.0285
(0.54) 		0.0454
(0.545)
6q gain 36 (22%) 129 0.576
(0.988) 		0.917
(1.00) 		0.0428
(0.545) 		0.294
(0.874) 		0.0528
(0.597) 		0.0111
(0.486) 		0.576
(0.988) 		0.0734
(0.658) 		0.021
(0.54) 		0.258
(0.87) 		0.0709
(0.658) 		0.0327
(0.54)
7p gain 102 (62%) 63 0.332
(0.917) 		0.628
(0.988) 		0.0249
(0.54) 		0.435
(0.959) 		0.152
(0.778) 		0.65
(0.989) 		0.63
(0.988) 		0.00466
(0.486) 		1
(1.00) 		0.385
(0.959) 		0.0454
(0.545) 		0.765
(1.00)
7q gain 85 (52%) 80 0.528
(0.988) 		0.504
(0.98) 		0.00494
(0.486) 		0.546
(0.988) 		0.0674
(0.658) 		0.265
(0.87) 		0.534
(0.988) 		0.00748
(0.486) 		1
(1.00) 		0.175
(0.801) 		0.085
(0.673) 		0.223
(0.842)
8p gain 42 (25%) 123 0.274
(0.874) 		0.786
(1.00) 		0.183
(0.802) 		0.206
(0.842) 		0.698
(1.00) 		0.318
(0.91) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.151
(0.778) 		0.521
(0.988) 		1
(1.00)
8q gain 89 (54%) 76 0.175
(0.801) 		0.702
(1.00) 		0.00773
(0.486) 		0.117
(0.715) 		0.11
(0.687) 		0.126
(0.715) 		1
(1.00) 		0.0896
(0.673) 		0.219
(0.842) 		0.0837
(0.673) 		0.189
(0.808) 		0.519
(0.988)
9p gain 42 (25%) 123 0.175
(0.801) 		0.338
(0.922) 		0.282
(0.874) 		0.843
(1.00) 		0.719
(1.00) 		0.617
(0.988) 		1
(1.00) 		0.322
(0.913) 		1
(1.00) 		0.463
(0.971) 		0.898
(1.00) 		0.731
(1.00)
9q gain 33 (20%) 132 0.147
(0.767) 		0.199
(0.841) 		0.0267
(0.54) 		0.935
(1.00) 		0.931
(1.00) 		0.785
(1.00) 		0.439
(0.959) 		0.298
(0.874) 		1
(1.00) 		0.859
(1.00) 		0.889
(1.00) 		0.683
(1.00)
10p gain 13 (8%) 152 0.675
(1.00) 		0.88
(1.00) 		0.878
(1.00) 		0.421
(0.959) 		0.931
(1.00) 		1
(1.00) 		1
(1.00) 		0.603
(0.988) 		0.394
(0.959) 		1
(1.00) 		0.575
(0.988) 		0.451
(0.965)
10q gain 7 (4%) 158 0.427
(0.959) 		0.51
(0.983) 		0.697
(1.00) 		0.68
(1.00) 		0.876
(1.00) 		1
(1.00) 		0.25
(0.868) 		1
(1.00) 		0.232
(0.851) 		1
(1.00) 		0.981
(1.00) 		0.288
(0.874)
11p gain 32 (19%) 133 0.585
(0.988) 		0.326
(0.914) 		0.869
(1.00) 		0.628
(0.988) 		0.457
(0.97) 		1
(1.00) 		0.845
(1.00) 		0.0724
(0.658) 		0.329
(0.914) 		1
(1.00) 		0.587
(0.988) 		0.0268
(0.54)
11q gain 26 (16%) 139 0.375
(0.956) 		0.13
(0.715) 		0.837
(1.00) 		0.441
(0.959) 		0.26
(0.87) 		0.375
(0.956) 		1
(1.00) 		0.129
(0.715) 		0.591
(0.988) 		0.792
(1.00) 		0.297
(0.874) 		0.011
(0.486)
12p gain 33 (20%) 132 0.718
(1.00) 		0.421
(0.959) 		0.799
(1.00) 		0.438
(0.959) 		0.394
(0.959) 		0.572
(0.988) 		0.699
(1.00) 		0.298
(0.874) 		0.0951
(0.673) 		0.395
(0.959) 		0.503
(0.98) 		0.166
(0.797)
12q gain 24 (15%) 141 0.139
(0.746) 		0.21
(0.842) 		0.865
(1.00) 		0.706
(1.00) 		0.559
(0.988) 		1
(1.00) 		0.507
(0.98) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.265
(0.87) 		0.645
(0.989)
13q gain 113 (68%) 52 0.563
(0.988) 		0.67
(1.00) 		0.368
(0.956) 		0.325
(0.914) 		0.0327
(0.54) 		1
(1.00) 		0.506
(0.98) 		0.000593
(0.285) 		1
(1.00) 		0.955
(1.00) 		0.0199
(0.54) 		0.0997
(0.681)
14q gain 8 (5%) 157 0.269
(0.874) 		0.894
(1.00) 		0.686
(1.00) 		1
(1.00) 		0.393
(0.959) 		1
(1.00) 		0.472
(0.971) 		1
(1.00) 		0.261
(0.87) 		1
(1.00) 		0.642
(0.989) 		1
(1.00)
15q gain 3 (2%) 162 0.811
(1.00) 		0.922
(1.00) 		0.0873
(0.673) 		0.0505
(0.577) 		0.172
(0.801) 		1
(1.00) 		0.0956
(0.673) 		0.227
(0.842) 		1
(1.00) 		1
(1.00) 		0.218
(0.842)
16p gain 41 (25%) 124 0.476
(0.975) 		0.777
(1.00) 		0.12
(0.715) 		0.784
(1.00) 		0.322
(0.913) 		1
(1.00) 		1
(1.00) 		0.0222
(0.54) 		0.163
(0.797) 		0.395
(0.959) 		0.294
(0.874) 		0.402
(0.959)
16q gain 41 (25%) 124 0.988
(1.00) 		0.853
(1.00) 		0.464
(0.971) 		0.934
(1.00) 		0.159
(0.795) 		0.297
(0.874) 		0.857
(1.00) 		0.0222
(0.54) 		0.163
(0.797) 		0.623
(0.988) 		0.215
(0.842) 		0.0951
(0.673)
17p gain 8 (5%) 157 0.337
(0.922) 		0.544
(0.988) 		0.638
(0.989) 		0.0395
(0.545) 		0.705
(1.00) 		1
(1.00) 		1
(1.00) 		0.503
(0.98) 		1
(1.00) 		1
(1.00) 		0.859
(1.00) 		1
(1.00)
17q gain 32 (19%) 133 0.217
(0.842) 		0.581
(0.988) 		0.812
(1.00) 		0.951
(1.00) 		0.609
(0.988) 		0.397
(0.959) 		0.556
(0.988) 		0.469
(0.971) 		0.598
(0.988) 		0.461
(0.971) 		0.748
(1.00) 		0.692
(1.00)
18p gain 8 (5%) 157 0.536
(0.988) 		0.425
(0.959) 		0.0404
(0.545) 		0.373
(0.956) 		0.495
(0.98) 		1
(1.00) 		0.727
(1.00) 		0.131
(0.715) 		0.261
(0.87) 		0.152
(0.778) 		0.104
(0.685) 		0.068
(0.658)
18q gain 6 (4%) 159 0.00934
(0.486) 		0.391
(0.959) 		0.0288
(0.54) 		0.164
(0.797) 		0.0842
(0.673) 		0.506
(0.98) 		0.219
(0.842) 		0.406
(0.959) 		0.202
(0.842) 		0.0483
(0.565) 		0.00409
(0.486) 		0.0668
(0.658)
19p gain 33 (20%) 132 0.619
(0.988) 		0.441
(0.959) 		0.849
(1.00) 		0.262
(0.87) 		1
(1.00) 		0.292
(0.874) 		0.559
(0.988) 		0.0718
(0.658) 		0.601
(0.988) 		0.497
(0.98) 		0.788
(1.00) 		0.183
(0.802)
19q gain 32 (19%) 133 0.165
(0.797) 		0.491
(0.98) 		0.93
(1.00) 		0.179
(0.802) 		1
(1.00) 		0.277
(0.874) 		0.694
(1.00) 		0.0724
(0.658) 		0.598
(0.988) 		0.248
(0.868) 		0.639
(0.989) 		0.0942
(0.673)
20p gain 109 (66%) 56 0.428
(0.959) 		0.183
(0.802) 		0.0106
(0.486) 		0.774
(1.00) 		0.33
(0.914) 		0.643
(0.989) 		0.1
(0.681) 		0.0328
(0.54) 		1
(1.00) 		0.303
(0.884) 		0.335
(0.92) 		0.416
(0.959)
20q gain 145 (88%) 20 0.128
(0.715) 		0.14
(0.746) 		0.12
(0.715) 		0.563
(0.988) 		0.0303
(0.54) 		0.312
(0.906) 		0.812
(1.00) 		0.000953
(0.305) 		0.545
(0.988) 		0.184
(0.802) 		0.108
(0.687) 		0.0992
(0.681)
21q gain 10 (6%) 155 0.428
(0.959) 		0.482
(0.979) 		0.532
(0.988) 		0.742
(1.00) 		0.906
(1.00) 		0.637
(0.989) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.675
(1.00) 		0.899
(1.00) 		1
(1.00)
22q gain 9 (5%) 156 0.0614
(0.647) 		0.858
(1.00) 		0.612
(0.988) 		0.7
(1.00) 		0.394
(0.959) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.625
(0.988) 		0.357
(0.949) 		1
(1.00)
xp gain 34 (21%) 131 0.446
(0.961) 		0.452
(0.965) 		0.437
(0.959) 		0.379
(0.959) 		0.172
(0.801) 		0.265
(0.87) 		0.441
(0.959) 		0.0718
(0.658) 		0.347
(0.936) 		0.318
(0.91) 		0.57
(0.988) 		0.706
(1.00)
xq gain 34 (21%) 131 0.823
(1.00) 		0.284
(0.874) 		0.775
(1.00) 		0.207
(0.842) 		0.436
(0.959) 		0.586
(0.988) 		0.441
(0.959) 		0.469
(0.971) 		0.347
(0.936) 		0.927
(1.00) 		0.613
(0.988) 		0.693
(1.00)
1p loss 46 (28%) 119 0.482
(0.979) 		0.549
(0.988) 		0.901
(1.00) 		0.724
(1.00) 		0.554
(0.988) 		0.807
(1.00) 		0.489
(0.98) 		0.0203
(0.54) 		0.35
(0.941) 		0.885
(1.00) 		0.282
(0.874) 		0.102
(0.681)
1q loss 26 (16%) 139 0.628
(0.988) 		0.658
(0.994) 		0.653
(0.991) 		0.731
(1.00) 		0.577
(0.988) 		0.352
(0.942) 		0.284
(0.874) 		0.224
(0.842) 		0.24
(0.855) 		0.578
(0.988) 		0.504
(0.98) 		0.00661
(0.486)
2p loss 11 (7%) 154 0.638
(0.989) 		0.00649
(0.486) 		0.648
(0.989) 		0.607
(0.988) 		0.493
(0.98) 		1
(1.00) 		0.756
(1.00) 		0.585
(0.988) 		0.343
(0.931) 		0.717
(1.00) 		0.255
(0.87) 		1
(1.00)
2q loss 6 (4%) 159 0.32
(0.913) 		0.0267
(0.54) 		0.529
(0.988) 		1
(1.00) 		0.0661
(0.658) 		0.59
(0.988) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0279
(0.54)
3p loss 15 (9%) 150 0.000293
(0.282) 		0.673
(1.00) 		0.0449
(0.545) 		0.153
(0.778) 		0.207
(0.842) 		0.00725
(0.486) 		0.0544
(0.6) 		0.0758
(0.664) 		0.0936
(0.673) 		0.0125
(0.486) 		0.0537
(0.599) 		0.115
(0.715)
3q loss 10 (6%) 155 0.0305
(0.54) 		0.516
(0.988) 		0.0433
(0.545) 		0.392
(0.959) 		0.165
(0.797) 		0.0231
(0.54) 		0.11
(0.687) 		0.00277
(0.486) 		0.0437
(0.545) 		0.0202
(0.54) 		0.0808
(0.673) 		0.116
(0.715)
4p loss 59 (36%) 106 0.148
(0.77) 		0.6
(0.988) 		0.622
(0.988) 		0.518
(0.988) 		0.459
(0.97) 		0.821
(1.00) 		0.517
(0.988) 		0.381
(0.959) 		0.0225
(0.54) 		0.399
(0.959) 		0.286
(0.874) 		0.783
(1.00)
4q loss 66 (40%) 99 0.0666
(0.658) 		0.918
(1.00) 		0.562
(0.988) 		0.554
(0.988) 		0.738
(1.00) 		0.65
(0.989) 		0.339
(0.922) 		0.253
(0.87) 		0.0382
(0.545) 		0.25
(0.868) 		0.535
(0.988) 		1
(1.00)
5p loss 26 (16%) 139 0.224
(0.842) 		0.93
(1.00) 		0.709
(1.00) 		0.843
(1.00) 		0.472
(0.971) 		1
(1.00) 		0.0916
(0.673) 		0.696
(1.00) 		0.24
(0.855) 		1
(1.00) 		0.241
(0.855) 		1
(1.00)
5q loss 40 (24%) 125 0.992
(1.00) 		0.145
(0.763) 		0.779
(1.00) 		0.672
(1.00) 		1
(1.00) 		0.609
(0.988) 		0.589
(0.988) 		0.189
(0.808) 		0.0311
(0.54) 		0.571
(0.988) 		0.729
(1.00) 		0.705
(1.00)
6p loss 13 (8%) 152 0.0432
(0.545) 		0.732
(1.00) 		0.141
(0.746) 		0.42
(0.959) 		0.0326
(0.54) 		0.694
(1.00) 		1
(1.00) 		0.0613
(0.647) 		0.394
(0.959) 		0.463
(0.971) 		0.236
(0.855) 		0.0833
(0.673)
6q loss 22 (13%) 143 0.384
(0.959) 		0.838
(1.00) 		0.035
(0.545) 		0.426
(0.959) 		0.0814
(0.673) 		1
(1.00) 		0.173
(0.801) 		0.0127
(0.486) 		0.582
(0.988) 		0.759
(1.00) 		0.803
(1.00) 		0.131
(0.715)
7q loss 3 (2%) 162 0.227
(0.842) 		0.96
(1.00) 		0.682
(1.00) 		0.429
(0.959) 		1
(1.00) 		0.595
(0.988) 		0.227
(0.842) 		1
(1.00) 		1
(1.00) 		0.125
(0.715)
8p loss 73 (44%) 92 0.0371
(0.545) 		0.0897
(0.673) 		0.907
(1.00) 		0.577
(0.988) 		0.277
(0.874) 		0.825
(1.00) 		0.435
(0.959) 		0.776
(1.00) 		0.407
(0.959) 		0.957
(1.00) 		0.0718
(0.658) 		0.636
(0.989)
8q loss 11 (7%) 154 0.755
(1.00) 		0.468
(0.971) 		0.943
(1.00) 		0.373
(0.956) 		0.593
(0.988) 		0.689
(1.00) 		0.0117
(0.486) 		0.602
(0.988) 		1
(1.00) 		1
(1.00) 		0.943
(1.00) 		0.285
(0.874)
9p loss 23 (14%) 142 0.167
(0.798) 		0.643
(0.989) 		0.187
(0.807) 		0.108
(0.687) 		1
(1.00) 		0.0596
(0.643) 		0.507
(0.98) 		1
(1.00) 		1
(1.00) 		0.00596
(0.486) 		0.505
(0.98) 		0.623
(0.988)
9q loss 23 (14%) 142 0.131
(0.715) 		0.6
(0.988) 		0.645
(0.989) 		0.056
(0.611) 		0.695
(1.00) 		0.211
(0.842) 		0.507
(0.98) 		1
(1.00) 		1
(1.00) 		0.00815
(0.486) 		0.821
(1.00) 		0.624
(0.988)
10p loss 33 (20%) 132 0.0795
(0.673) 		0.0017
(0.408) 		0.469
(0.971) 		0.691
(1.00) 		0.869
(1.00) 		0.411
(0.959) 		0.699
(1.00) 		0.0252
(0.54) 		0.0951
(0.673) 		0.2
(0.841) 		0.354
(0.944) 		0.73
(1.00)
10q loss 38 (23%) 127 0.226
(0.842) 		0.0428
(0.545) 		0.41
(0.959) 		0.802
(1.00) 		0.969
(1.00) 		0.0673
(0.658) 		0.458
(0.97) 		0.0786
(0.673) 		0.136
(0.736) 		0.159
(0.795) 		0.646
(0.989) 		0.744
(1.00)
11p loss 23 (14%) 142 0.563
(0.988) 		0.865
(1.00) 		0.107
(0.687) 		0.447
(0.961) 		0.285
(0.874) 		0.53
(0.988) 		1
(1.00) 		0.0728
(0.658) 		1
(1.00) 		0.398
(0.959) 		0.0426
(0.545) 		0.164
(0.797)
11q loss 30 (18%) 135 0.328
(0.914) 		0.746
(1.00) 		0.719
(1.00) 		0.531
(0.988) 		0.963
(1.00) 		0.0804
(0.673) 		1
(1.00) 		0.0404
(0.545) 		0.0742
(0.659) 		0.317
(0.91) 		0.713
(1.00) 		0.168
(0.8)
12p loss 22 (13%) 143 0.312
(0.906) 		0.555
(0.988) 		0.745
(1.00) 		0.653
(0.991) 		0.461
(0.971) 		0.53
(0.988) 		0.492
(0.98) 		0.219
(0.842) 		0.582
(0.988) 		1
(1.00) 		0.41
(0.959) 		1
(1.00)
12q loss 19 (12%) 146 0.293
(0.874) 		0.195
(0.83) 		0.67
(1.00) 		1
(1.00) 		0.55
(0.988) 		0.479
(0.976) 		0.809
(1.00) 		0.365
(0.956) 		0.526
(0.988) 		1
(1.00) 		0.394
(0.959) 		0.647
(0.989)
13q loss 8 (5%) 157 0.98
(1.00) 		0.805
(1.00) 		0.324
(0.914) 		0.597
(0.988) 		0.445
(0.96) 		0.615
(0.988) 		1
(1.00) 		0.131
(0.715) 		1
(1.00) 		0.626
(0.988) 		0.605
(0.988)
14q loss 67 (41%) 98 0.898
(1.00) 		0.858
(1.00) 		0.33
(0.914) 		0.55
(0.988) 		0.238
(0.855) 		0.823
(1.00) 		0.427
(0.959) 		0.0155
(0.54) 		0.688
(1.00) 		0.213
(0.842) 		0.76
(1.00) 		0.394
(0.959)
15q loss 73 (44%) 92 0.424
(0.959) 		0.91
(1.00) 		0.316
(0.91) 		0.318
(0.91) 		0.441
(0.959) 		0.827
(1.00) 		0.16
(0.795) 		1
(1.00) 		0.0886
(0.673) 		0.881
(1.00) 		0.0879
(0.673) 		1
(1.00)
16p loss 9 (5%) 156 0.592
(0.988) 		0.373
(0.956) 		0.0907
(0.673) 		0.847
(1.00) 		0.108
(0.687) 		1
(1.00) 		0.734
(1.00) 		0.503
(0.98) 		1
(1.00) 		1
(1.00) 		0.784
(1.00) 		1
(1.00)
16q loss 15 (9%) 150 0.616
(0.988) 		0.738
(1.00) 		0.272
(0.874) 		0.812
(1.00) 		0.0137
(0.507) 		0.47
(0.971) 		0.596
(0.988) 		1
(1.00) 		0.441
(0.959) 		0.756
(1.00) 		0.839
(1.00) 		1
(1.00)
17p loss 107 (65%) 58 0.614
(0.988) 		0.0761
(0.664) 		0.731
(1.00) 		0.036
(0.545) 		0.953
(1.00) 		1
(1.00) 		0.625
(0.988) 		0.223
(0.842) 		1
(1.00) 		0.655
(0.992) 		0.979
(1.00) 		0.611
(0.988)
17q loss 26 (16%) 139 0.292
(0.874) 		0.692
(1.00) 		0.751
(1.00) 		0.485
(0.98) 		0.746
(1.00) 		0.765
(1.00) 		0.831
(1.00) 		1
(1.00) 		0.24
(0.855) 		0.183
(0.802) 		0.393
(0.959) 		0.219
(0.842)
18p loss 128 (78%) 37 0.358
(0.951) 		0.413
(0.959) 		0.428
(0.959) 		0.258
(0.87) 		0.7
(1.00) 		0.108
(0.687) 		1
(1.00) 		0.0294
(0.54) 		1
(1.00) 		0.734
(1.00) 		0.548
(0.988) 		0.123
(0.715)
18q loss 138 (84%) 27 0.371
(0.956) 		0.263
(0.87) 		0.251
(0.868) 		0.0498
(0.576) 		0.755
(1.00) 		0.127
(0.715) 		0.674
(1.00) 		0.432
(0.959) 		1
(1.00) 		0.721
(1.00) 		0.646
(0.989) 		0.122
(0.715)
19p loss 21 (13%) 144 0.275
(0.874) 		0.769
(1.00) 		0.0302
(0.54) 		0.52
(0.988) 		0.285
(0.874) 		0.53
(0.988) 		1
(1.00) 		0.368
(0.956) 		0.564
(0.988) 		1
(1.00) 		0.0916
(0.673) 		1
(1.00)
19q loss 20 (12%) 145 0.626
(0.988) 		0.498
(0.98) 		0.0359
(0.545) 		0.258
(0.87) 		0.488
(0.98) 		0.739
(1.00) 		0.475
(0.975) 		0.365
(0.956) 		0.545
(0.988) 		0.615
(0.988) 		0.37
(0.956) 		1
(1.00)
20p loss 23 (14%) 142 0.853
(1.00) 		0.361
(0.955) 		0.0889
(0.673) 		0.599
(0.988) 		0.63
(0.988) 		1
(1.00) 		0.368
(0.956) 		1
(1.00) 		0.597
(0.988) 		0.242
(0.855) 		0.522
(0.988) 		0.174
(0.801)
21q loss 68 (41%) 97 0.586
(0.988) 		0.491
(0.98) 		0.679
(1.00) 		0.13
(0.715) 		0.278
(0.874) 		0.183
(0.802) 		0.636
(0.989) 		0.242
(0.855) 		0.691
(1.00) 		0.237
(0.855) 		0.186
(0.807) 		1
(1.00)
22q loss 58 (35%) 107 0.103
(0.683) 		0.102
(0.681) 		0.456
(0.97) 		0.417
(0.959) 		0.0113
(0.486) 		0.815
(1.00) 		0.871
(1.00) 		1
(1.00) 		0.425
(0.959) 		0.877
(1.00) 		0.125
(0.715) 		1
(1.00)
xp loss 25 (15%) 140 0.53
(0.988) 		0.973
(1.00) 		0.373
(0.956) 		0.216
(0.842) 		0.127
(0.715) 		0.765
(1.00) 		0.287
(0.874) 		0.0974
(0.678) 		1
(1.00) 		0.693
(1.00) 		0.23
(0.847) 		0.0734
(0.658)
xq loss 24 (15%) 141 0.478
(0.976) 		0.694
(1.00) 		0.47
(0.971) 		0.126
(0.715) 		0.411
(0.959) 		0.352
(0.942) 		0.268
(0.874) 		0.404
(0.959) 		1
(1.00) 		0.426
(0.959) 		0.451
(0.965) 		0.0868
(0.673)
Methods & Data
Input

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

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/READ-TP/15096456/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/READ-TP/15087528/READ-TP.merged_data.txt

  • Number of patients = 165

  • Number of significantly arm-level cnvs = 80

  • Number of selected clinical features = 12

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

Survival analysis

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

Fisher's exact test

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

Q value calculation

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

Download Results

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

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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