Correlation between copy number variations of arm-level result and selected clinical features
Rectum Adenocarcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1Q81BD7
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1Q81BD7
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 77 arm-level events and 11 clinical features across 162 patients, 2 significant findings detected with Q value < 0.25.

  • 4P GAIN MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 2Q LOSS MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 77 arm-level events and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 2 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 		COMPLETENESS
OF
RESECTION 		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 Fisher's exact test Fisher's exact test Fisher's exact test t-test
4P GAIN MUTATION ANALYSIS 8 (5%) 154 0.701
(1.00) 		0.538
(1.00) 		0.258
(1.00) 		0.606
(1.00) 		0.304
(1.00) 		0.287
(1.00) 		0.292
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		2.96e-05
(0.025)
2Q LOSS MUTATION ANALYSIS 6 (4%) 156 0.515
(1.00) 		0.0182
(1.00) 		0.249
(1.00) 		1
(1.00) 		0.0467
(1.00) 		0.776
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1.39e-08
(1.17e-05)
1P GAIN MUTATION ANALYSIS 11 (7%) 151 0.0118
(1.00) 		0.829
(1.00) 		0.268
(1.00) 		0.0176
(1.00) 		0.378
(1.00) 		0.106
(1.00) 		1
(1.00) 		0.0388
(1.00) 		1
(1.00) 		0.216
(1.00) 		0.451
(1.00)
1Q GAIN MUTATION ANALYSIS 32 (20%) 130 0.983
(1.00) 		0.282
(1.00) 		0.273
(1.00) 		0.0025
(1.00) 		0.182
(1.00) 		0.615
(1.00) 		0.429
(1.00) 		0.277
(1.00) 		1
(1.00) 		0.532
(1.00) 		0.0533
(1.00)
2P GAIN MUTATION ANALYSIS 33 (20%) 129 0.535
(1.00) 		0.544
(1.00) 		0.263
(1.00) 		0.416
(1.00) 		0.0937
(1.00) 		0.216
(1.00) 		0.0303
(1.00) 		0.0716
(1.00) 		1
(1.00) 		0.151
(1.00) 		0.845
(1.00)
2Q GAIN MUTATION ANALYSIS 35 (22%) 127 0.94
(1.00) 		0.606
(1.00) 		0.194
(1.00) 		0.248
(1.00) 		0.0568
(1.00) 		0.292
(1.00) 		0.0341
(1.00) 		0.0415
(1.00) 		0.611
(1.00) 		0.266
(1.00) 		0.402
(1.00)
3P GAIN MUTATION ANALYSIS 26 (16%) 136 0.55
(1.00) 		0.851
(1.00) 		0.182
(1.00) 		0.846
(1.00) 		0.319
(1.00) 		0.0317
(1.00) 		0.671
(1.00) 		0.697
(1.00) 		0.247
(1.00) 		0.861
(1.00) 		0.606
(1.00)
3Q GAIN MUTATION ANALYSIS 33 (20%) 129 0.914
(1.00) 		0.95
(1.00) 		0.309
(1.00) 		0.741
(1.00) 		0.374
(1.00) 		0.0459
(1.00) 		0.557
(1.00) 		0.303
(1.00) 		0.603
(1.00) 		0.636
(1.00) 		0.924
(1.00)
4Q GAIN MUTATION ANALYSIS 4 (2%) 158 0.442
(1.00) 		0.921
(1.00) 		1
(1.00) 		0.656
(1.00) 		0.655
(1.00) 		0.126
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0153
(1.00)
5P GAIN MUTATION ANALYSIS 31 (19%) 131 0.47
(1.00) 		0.702
(1.00) 		0.552
(1.00) 		0.071
(1.00) 		0.552
(1.00) 		0.464
(1.00) 		0.111
(1.00) 		0.0727
(1.00) 		0.323
(1.00) 		0.519
(1.00) 		0.926
(1.00)
5Q GAIN MUTATION ANALYSIS 21 (13%) 141 0.365
(1.00) 		0.665
(1.00) 		0.325
(1.00) 		0.432
(1.00) 		0.486
(1.00) 		0.768
(1.00) 		0.249
(1.00) 		0.218
(1.00) 		1
(1.00) 		0.629
(1.00) 		0.342
(1.00)
6P GAIN MUTATION ANALYSIS 39 (24%) 123 0.942
(1.00) 		0.716
(1.00) 		0.613
(1.00) 		0.25
(1.00) 		0.156
(1.00) 		0.0967
(1.00) 		0.854
(1.00) 		0.19
(1.00) 		0.0302
(1.00) 		0.365
(1.00) 		0.444
(1.00)
6Q GAIN MUTATION ANALYSIS 35 (22%) 127 0.733
(1.00) 		0.649
(1.00) 		0.117
(1.00) 		0.289
(1.00) 		0.202
(1.00) 		0.022
(1.00) 		0.848
(1.00) 		0.0726
(1.00) 		0.0202
(1.00) 		0.279
(1.00) 		0.923
(1.00)
7P GAIN MUTATION ANALYSIS 101 (62%) 61 0.287
(1.00) 		0.583
(1.00) 		0.0617
(1.00) 		0.442
(1.00) 		0.236
(1.00) 		0.827
(1.00) 		0.332
(1.00) 		0.0154
(1.00) 		0.411
(1.00) 		0.492
(1.00) 		0.16
(1.00)
7Q GAIN MUTATION ANALYSIS 90 (56%) 72 0.373
(1.00) 		0.476
(1.00) 		0.00452
(1.00) 		0.782
(1.00) 		0.0543
(1.00) 		0.533
(1.00) 		0.207
(1.00) 		0.0172
(1.00) 		0.228
(1.00) 		0.448
(1.00) 		0.144
(1.00)
8P GAIN MUTATION ANALYSIS 41 (25%) 121 0.979
(1.00) 		0.639
(1.00) 		0.13
(1.00) 		0.134
(1.00) 		0.779
(1.00) 		0.575
(1.00) 		0.589
(1.00) 		1
(1.00) 		0.643
(1.00) 		0.228
(1.00) 		0.0993
(1.00)
8Q GAIN MUTATION ANALYSIS 88 (54%) 74 0.0928
(1.00) 		0.598
(1.00) 		0.0188
(1.00) 		0.109
(1.00) 		0.163
(1.00) 		0.219
(1.00) 		1
(1.00) 		0.0867
(1.00) 		0.221
(1.00) 		0.109
(1.00) 		0.318
(1.00)
9P GAIN MUTATION ANALYSIS 41 (25%) 121 0.637
(1.00) 		0.413
(1.00) 		0.189
(1.00) 		0.841
(1.00) 		0.634
(1.00) 		0.807
(1.00) 		0.857
(1.00) 		0.32
(1.00) 		1
(1.00) 		0.583
(1.00) 		0.609
(1.00)
9Q GAIN MUTATION ANALYSIS 32 (20%) 130 0.648
(1.00) 		0.176
(1.00) 		0.0166
(1.00) 		0.935
(1.00) 		0.929
(1.00) 		1
(1.00) 		0.328
(1.00) 		0.291
(1.00) 		1
(1.00) 		1
(1.00) 		0.923
(1.00)
10P GAIN MUTATION ANALYSIS 12 (7%) 150 0.939
(1.00) 		0.733
(1.00) 		0.884
(1.00) 		0.529
(1.00) 		0.852
(1.00) 		0.672
(1.00) 		0.772
(1.00) 		0.601
(1.00) 		0.375
(1.00) 		1
(1.00) 		0.184
(1.00)
10Q GAIN MUTATION ANALYSIS 6 (4%) 156 0.968
(1.00) 		0.475
(1.00) 		0.337
(1.00) 		0.641
(1.00) 		0.0846
(1.00) 		0.737
(1.00) 		0.0938
(1.00) 		1
(1.00) 		0.206
(1.00) 		1
(1.00) 		0.406
(1.00)
11P GAIN MUTATION ANALYSIS 28 (17%) 134 0.273
(1.00) 		0.503
(1.00) 		0.884
(1.00) 		0.481
(1.00) 		0.623
(1.00) 		0.269
(1.00) 		0.836
(1.00) 		0.127
(1.00) 		1
(1.00) 		1
(1.00) 		0.666
(1.00)
11Q GAIN MUTATION ANALYSIS 24 (15%) 138 0.6
(1.00) 		0.162
(1.00) 		0.708
(1.00) 		0.294
(1.00) 		0.311
(1.00) 		0.111
(1.00) 		1
(1.00) 		0.221
(1.00) 		0.593
(1.00) 		1
(1.00) 		0.0323
(1.00)
12P GAIN MUTATION ANALYSIS 33 (20%) 129 0.702
(1.00) 		0.402
(1.00) 		0.732
(1.00) 		0.492
(1.00) 		0.361
(1.00) 		0.626
(1.00) 		0.7
(1.00) 		0.471
(1.00) 		0.0996
(1.00) 		0.265
(1.00) 		0.45
(1.00)
12Q GAIN MUTATION ANALYSIS 22 (14%) 140 0.776
(1.00) 		0.238
(1.00) 		0.886
(1.00) 		0.658
(1.00) 		0.716
(1.00) 		0.941
(1.00) 		0.818
(1.00) 		0.688
(1.00) 		0.59
(1.00) 		0.85
(1.00) 		0.775
(1.00)
13Q GAIN MUTATION ANALYSIS 108 (67%) 54 0.0483
(1.00) 		0.273
(1.00) 		0.359
(1.00) 		0.302
(1.00) 		0.0286
(1.00) 		0.0341
(1.00) 		0.738
(1.00) 		0.00104
(0.875) 		0.401
(1.00) 		0.903
(1.00) 		0.897
(1.00)
14Q GAIN MUTATION ANALYSIS 8 (5%) 154 0.298
(1.00) 		0.968
(1.00) 		0.8
(1.00) 		1
(1.00) 		0.445
(1.00) 		0.825
(1.00) 		0.471
(1.00) 		1
(1.00) 		0.266
(1.00) 		1
(1.00) 		0.746
(1.00)
15Q GAIN MUTATION ANALYSIS 5 (3%) 157 0.34
(1.00) 		0.706
(1.00) 		0.607
(1.00) 		0.107
(1.00) 		0.273
(1.00) 		1
(1.00) 		0.179
(1.00) 		0.0557
(1.00) 		0.174
(1.00) 		1
(1.00) 		0.5
(1.00)
16P GAIN MUTATION ANALYSIS 38 (23%) 124 0.932
(1.00) 		0.628
(1.00) 		0.505
(1.00) 		0.884
(1.00) 		0.431
(1.00) 		0.81
(1.00) 		0.58
(1.00) 		0.0389
(1.00) 		0.626
(1.00) 		0.685
(1.00) 		0.931
(1.00)
16Q GAIN MUTATION ANALYSIS 38 (23%) 124 0.344
(1.00) 		0.56
(1.00) 		0.704
(1.00) 		1
(1.00) 		0.233
(1.00) 		0.31
(1.00) 		0.854
(1.00) 		0.0389
(1.00) 		0.626
(1.00) 		0.929
(1.00) 		0.439
(1.00)
17P GAIN MUTATION ANALYSIS 8 (5%) 154 0.62
(1.00) 		0.548
(1.00) 		0.813
(1.00) 		0.0474
(1.00) 		0.702
(1.00) 		0.825
(1.00) 		1
(1.00) 		0.51
(1.00) 		1
(1.00) 		1
(1.00) 		0.551
(1.00)
17Q GAIN MUTATION ANALYSIS 29 (18%) 133 0.41
(1.00) 		0.66
(1.00) 		0.633
(1.00) 		0.981
(1.00) 		0.444
(1.00) 		0.522
(1.00) 		0.683
(1.00) 		0.464
(1.00) 		0.592
(1.00) 		0.89
(1.00) 		0.298
(1.00)
18P GAIN MUTATION ANALYSIS 9 (6%) 153 0.933
(1.00) 		0.413
(1.00) 		0.132
(1.00) 		0.444
(1.00) 		0.653
(1.00) 		0.345
(1.00) 		1
(1.00) 		0.165
(1.00) 		0.294
(1.00) 		0.126
(1.00) 		0.259
(1.00)
18Q GAIN MUTATION ANALYSIS 6 (4%) 156 0.203
(1.00) 		0.397
(1.00) 		0.0794
(1.00) 		0.17
(1.00) 		0.0846
(1.00) 		0.145
(1.00) 		0.221
(1.00) 		0.412
(1.00) 		0.206
(1.00) 		0.041
(1.00) 		0.175
(1.00)
19P GAIN MUTATION ANALYSIS 29 (18%) 133 0.855
(1.00) 		0.951
(1.00) 		0.62
(1.00) 		0.149
(1.00) 		0.858
(1.00) 		0.299
(1.00) 		0.539
(1.00) 		0.129
(1.00) 		0.592
(1.00) 		0.455
(1.00) 		0.967
(1.00)
19Q GAIN MUTATION ANALYSIS 30 (19%) 132 0.523
(1.00) 		0.93
(1.00) 		0.551
(1.00) 		0.118
(1.00) 		0.742
(1.00) 		0.311
(1.00) 		0.418
(1.00) 		0.0747
(1.00) 		0.594
(1.00) 		0.239
(1.00) 		0.044
(1.00)
20P GAIN MUTATION ANALYSIS 103 (64%) 59 0.384
(1.00) 		0.58
(1.00) 		0.0492
(1.00) 		0.824
(1.00) 		0.297
(1.00) 		0.825
(1.00) 		0.194
(1.00) 		0.0139
(1.00) 		1
(1.00) 		0.141
(1.00) 		0.97
(1.00)
20Q GAIN MUTATION ANALYSIS 142 (88%) 20 0.0364
(1.00) 		0.142
(1.00) 		0.0845
(1.00) 		0.53
(1.00) 		0.023
(1.00) 		0.634
(1.00) 		0.811
(1.00) 		0.00106
(0.893) 		0.552
(1.00) 		0.11
(1.00) 		0.557
(1.00)
21Q GAIN MUTATION ANALYSIS 10 (6%) 152 0.75
(1.00) 		0.617
(1.00) 		0.306
(1.00) 		0.752
(1.00) 		0.905
(1.00) 		0.639
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.661
(1.00) 		0.125
(1.00)
22Q GAIN MUTATION ANALYSIS 9 (6%) 153 0.00296
(1.00) 		0.905
(1.00) 		0.475
(1.00) 		0.707
(1.00) 		0.39
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.61
(1.00) 		0.359
(1.00)
XQ GAIN MUTATION ANALYSIS 34 (21%) 128 0.827
(1.00) 		0.067
(1.00) 		0.613
(1.00) 		0.226
(1.00) 		0.448
(1.00) 		0.637
(1.00) 		0.121
(1.00) 		0.307
(1.00) 		0.345
(1.00) 		0.778
(1.00) 		0.517
(1.00)
1P LOSS MUTATION ANALYSIS 42 (26%) 120 0.462
(1.00) 		0.495
(1.00) 		0.926
(1.00) 		0.841
(1.00) 		0.566
(1.00) 		0.822
(1.00) 		0.284
(1.00) 		0.0223
(1.00) 		0.181
(1.00) 		0.735
(1.00) 		0.365
(1.00)
1Q LOSS MUTATION ANALYSIS 24 (15%) 138 0.78
(1.00) 		0.798
(1.00) 		0.329
(1.00) 		0.76
(1.00) 		0.222
(1.00) 		0.276
(1.00) 		0.119
(1.00) 		0.218
(1.00) 		0.0426
(1.00) 		0.724
(1.00) 		0.522
(1.00)
2P LOSS MUTATION ANALYSIS 11 (7%) 151 0.491
(1.00) 		0.00112
(0.944) 		0.347
(1.00) 		0.614
(1.00) 		0.491
(1.00) 		1
(1.00) 		0.551
(1.00) 		0.592
(1.00) 		0.349
(1.00) 		0.705
(1.00) 		0.878
(1.00)
3P LOSS MUTATION ANALYSIS 15 (9%) 147 0.14
(1.00) 		0.718
(1.00) 		0.0387
(1.00) 		0.145
(1.00) 		0.207
(1.00) 		0.0201
(1.00) 		0.0545
(1.00) 		0.0794
(1.00) 		0.0967
(1.00) 		0.0119
(1.00) 		0.0926
(1.00)
3Q LOSS MUTATION ANALYSIS 10 (6%) 152 0.0961
(1.00) 		0.743
(1.00) 		0.0298
(1.00) 		0.4
(1.00) 		0.166
(1.00) 		0.0422
(1.00) 		0.112
(1.00) 		0.00297
(1.00) 		0.0452
(1.00) 		0.0177
(1.00) 		0.158
(1.00)
4P LOSS MUTATION ANALYSIS 57 (35%) 105 0.416
(1.00) 		0.722
(1.00) 		0.534
(1.00) 		0.478
(1.00) 		0.447
(1.00) 		0.98
(1.00) 		0.328
(1.00) 		0.545
(1.00) 		0.0208
(1.00) 		0.202
(1.00) 		0.397
(1.00)
4Q LOSS MUTATION ANALYSIS 65 (40%) 97 0.18
(1.00) 		0.832
(1.00) 		0.485
(1.00) 		0.482
(1.00) 		0.807
(1.00) 		0.8
(1.00) 		0.262
(1.00) 		0.252
(1.00) 		0.0387
(1.00) 		0.137
(1.00) 		0.586
(1.00)
5P LOSS MUTATION ANALYSIS 25 (15%) 137 0.474
(1.00) 		0.494
(1.00) 		0.816
(1.00) 		0.895
(1.00) 		0.706
(1.00) 		0.946
(1.00) 		0.131
(1.00) 		0.694
(1.00) 		0.232
(1.00) 		0.388
(1.00) 		0.209
(1.00)
5Q LOSS MUTATION ANALYSIS 39 (24%) 123 0.542
(1.00) 		0.631
(1.00) 		0.748
(1.00) 		0.805
(1.00) 		1
(1.00) 		0.688
(1.00) 		0.464
(1.00) 		0.19
(1.00) 		0.00324
(1.00) 		0.63
(1.00) 		0.795
(1.00)
6P LOSS MUTATION ANALYSIS 14 (9%) 148 0.0137
(1.00) 		0.701
(1.00) 		0.131
(1.00) 		0.367
(1.00) 		0.0194
(1.00) 		0.81
(1.00) 		1
(1.00) 		0.0794
(1.00) 		0.424
(1.00) 		0.453
(1.00) 		0.951
(1.00)
6Q LOSS MUTATION ANALYSIS 22 (14%) 140 0.0823
(1.00) 		0.837
(1.00) 		0.0108
(1.00) 		0.425
(1.00) 		0.0717
(1.00) 		1
(1.00) 		0.176
(1.00) 		0.0137
(1.00) 		0.59
(1.00) 		0.644
(1.00) 		0.27
(1.00)
8P LOSS MUTATION ANALYSIS 74 (46%) 88 0.226
(1.00) 		0.443
(1.00) 		0.877
(1.00) 		0.866
(1.00) 		0.387
(1.00) 		0.641
(1.00) 		0.636
(1.00) 		0.773
(1.00) 		0.413
(1.00) 		0.868
(1.00) 		0.0377
(1.00)
8Q LOSS MUTATION ANALYSIS 11 (7%) 151 0.959
(1.00) 		0.42
(1.00) 		0.93
(1.00) 		0.381
(1.00) 		0.593
(1.00) 		0.672
(1.00) 		0.0672
(1.00) 		0.601
(1.00) 		1
(1.00) 		1
(1.00) 		0.649
(1.00)
9P LOSS MUTATION ANALYSIS 22 (14%) 140 0.0171
(1.00) 		0.96
(1.00) 		0.188
(1.00) 		0.0921
(1.00) 		1
(1.00) 		0.0475
(1.00) 		0.369
(1.00) 		1
(1.00) 		0.59
(1.00) 		0.00975
(1.00) 		0.635
(1.00)
9Q LOSS MUTATION ANALYSIS 21 (13%) 141 0.0154
(1.00) 		0.716
(1.00) 		0.416
(1.00) 		0.0317
(1.00) 		0.472
(1.00) 		0.113
(1.00) 		0.249
(1.00) 		1
(1.00) 		0.571
(1.00) 		0.00975
(1.00) 		0.126
(1.00)
10P LOSS MUTATION ANALYSIS 32 (20%) 130 0.0943
(1.00) 		0.00151
(1.00) 		0.589
(1.00) 		0.809
(1.00) 		0.677
(1.00) 		0.296
(1.00) 		0.558
(1.00) 		0.0235
(1.00) 		0.0144
(1.00) 		0.252
(1.00) 		0.592
(1.00)
10Q LOSS MUTATION ANALYSIS 37 (23%) 125 0.245
(1.00) 		0.066
(1.00) 		0.434
(1.00) 		0.779
(1.00) 		0.822
(1.00) 		0.351
(1.00) 		0.348
(1.00) 		0.0773
(1.00) 		0.0249
(1.00) 		0.141
(1.00) 		0.894
(1.00)
11P LOSS MUTATION ANALYSIS 24 (15%) 138 0.833
(1.00) 		0.28
(1.00) 		0.513
(1.00) 		0.413
(1.00) 		0.184
(1.00) 		0.156
(1.00) 		1
(1.00) 		0.0898
(1.00) 		0.217
(1.00) 		0.316
(1.00) 		0.0684
(1.00)
11Q LOSS MUTATION ANALYSIS 29 (18%) 133 0.19
(1.00) 		0.653
(1.00) 		0.791
(1.00) 		0.803
(1.00) 		0.858
(1.00) 		0.173
(1.00) 		1
(1.00) 		0.037
(1.00) 		0.0711
(1.00) 		0.278
(1.00) 		0.316
(1.00)
12P LOSS MUTATION ANALYSIS 23 (14%) 139 0.113
(1.00) 		0.746
(1.00) 		0.598
(1.00) 		0.519
(1.00) 		0.603
(1.00) 		0.841
(1.00) 		0.508
(1.00) 		0.217
(1.00) 		1
(1.00) 		0.861
(1.00) 		0.895
(1.00)
12Q LOSS MUTATION ANALYSIS 21 (13%) 141 0.0523
(1.00) 		0.283
(1.00) 		0.529
(1.00) 		0.917
(1.00) 		0.823
(1.00) 		0.721
(1.00) 		0.819
(1.00) 		0.221
(1.00) 		0.571
(1.00) 		1
(1.00) 		0.939
(1.00)
13Q LOSS MUTATION ANALYSIS 8 (5%) 154 0.31
(1.00) 		0.582
(1.00) 		0.494
(1.00) 		0.469
(1.00) 		0.35
(1.00) 		0.171
(1.00) 		1
(1.00) 		0.135
(1.00) 		1
(1.00) 		0.61
(1.00) 		0.445
(1.00)
14Q LOSS MUTATION ANALYSIS 64 (40%) 98 0.24
(1.00) 		0.644
(1.00) 		0.253
(1.00) 		0.483
(1.00) 		0.172
(1.00) 		0.858
(1.00) 		0.198
(1.00) 		0.0159
(1.00) 		0.681
(1.00) 		0.269
(1.00) 		0.841
(1.00)
15Q LOSS MUTATION ANALYSIS 70 (43%) 92 0.137
(1.00) 		0.928
(1.00) 		0.254
(1.00) 		0.213
(1.00) 		0.364
(1.00) 		0.803
(1.00) 		0.152
(1.00) 		0.779
(1.00) 		0.404
(1.00) 		0.907
(1.00) 		0.029
(1.00)
16P LOSS MUTATION ANALYSIS 9 (6%) 153 0.0164
(1.00) 		0.254
(1.00) 		0.0328
(1.00) 		0.776
(1.00) 		0.0918
(1.00) 		1
(1.00) 		0.733
(1.00) 		0.51
(1.00) 		1
(1.00) 		1
(1.00) 		0.58
(1.00)
16Q LOSS MUTATION ANALYSIS 15 (9%) 147 0.974
(1.00) 		0.712
(1.00) 		0.191
(1.00) 		0.845
(1.00) 		0.0117
(1.00) 		0.904
(1.00) 		0.593
(1.00) 		1
(1.00) 		0.447
(1.00) 		0.736
(1.00) 		0.219
(1.00)
17P LOSS MUTATION ANALYSIS 104 (64%) 58 0.785
(1.00) 		0.115
(1.00) 		0.554
(1.00) 		0.0306
(1.00) 		0.928
(1.00) 		0.273
(1.00) 		1
(1.00) 		0.226
(1.00) 		1
(1.00) 		0.753
(1.00) 		0.743
(1.00)
17Q LOSS MUTATION ANALYSIS 25 (15%) 137 0.548
(1.00) 		0.596
(1.00) 		0.639
(1.00) 		0.601
(1.00) 		0.598
(1.00) 		0.655
(1.00) 		0.383
(1.00) 		0.693
(1.00) 		0.232
(1.00) 		0.329
(1.00) 		0.718
(1.00)
18P LOSS MUTATION ANALYSIS 124 (77%) 38 0.775
(1.00) 		0.208
(1.00) 		0.46
(1.00) 		0.351
(1.00) 		0.597
(1.00) 		0.285
(1.00) 		0.854
(1.00) 		0.0373
(1.00) 		1
(1.00) 		0.465
(1.00) 		0.575
(1.00)
18Q LOSS MUTATION ANALYSIS 135 (83%) 27 0.976
(1.00) 		0.148
(1.00) 		0.314
(1.00) 		0.0571
(1.00) 		0.754
(1.00) 		0.291
(1.00) 		0.674
(1.00) 		0.439
(1.00) 		1
(1.00) 		0.615
(1.00) 		0.768
(1.00)
19P LOSS MUTATION ANALYSIS 23 (14%) 139 0.415
(1.00) 		0.897
(1.00) 		0.0118
(1.00) 		0.393
(1.00) 		0.416
(1.00) 		0.794
(1.00) 		0.508
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.305
(1.00)
19Q LOSS MUTATION ANALYSIS 20 (12%) 142 0.613
(1.00) 		0.337
(1.00) 		0.00468
(1.00) 		0.236
(1.00) 		0.437
(1.00) 		0.934
(1.00) 		0.473
(1.00) 		1
(1.00) 		0.552
(1.00) 		0.673
(1.00) 		0.332
(1.00)
20P LOSS MUTATION ANALYSIS 24 (15%) 138 0.665
(1.00) 		0.932
(1.00) 		0.0522
(1.00) 		0.889
(1.00) 		0.612
(1.00) 		1
(1.00) 		0.664
(1.00) 		0.41
(1.00) 		0.593
(1.00) 		0.309
(1.00) 		0.787
(1.00)
21Q LOSS MUTATION ANALYSIS 64 (40%) 98 0.852
(1.00) 		0.38
(1.00) 		0.524
(1.00) 		0.193
(1.00) 		0.164
(1.00) 		0.643
(1.00) 		0.872
(1.00) 		0.252
(1.00) 		0.681
(1.00) 		0.462
(1.00) 		0.0652
(1.00)
22Q LOSS MUTATION ANALYSIS 56 (35%) 106 0.00768
(1.00) 		0.259
(1.00) 		0.261
(1.00) 		0.348
(1.00) 		0.00805
(1.00) 		0.518
(1.00) 		0.623
(1.00) 		1
(1.00) 		0.417
(1.00) 		0.642
(1.00) 		0.429
(1.00)
XQ LOSS MUTATION ANALYSIS 25 (15%) 137 0.276
(1.00) 		0.927
(1.00) 		0.441
(1.00) 		0.0659
(1.00) 		0.322
(1.00) 		0.596
(1.00) 		0.282
(1.00) 		0.424
(1.00) 		1
(1.00) 		0.364
(1.00) 		0.692
(1.00)
'4P GAIN MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2.96e-05 (t-test), Q value = 0.025

Table S1.  Gene #7: '4P GAIN MUTATION STATUS' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 152 2.6 (5.4)
4P GAIN MUTATED 7 0.3 (0.8)
4P GAIN WILD-TYPE 145 2.7 (5.5)

Figure S1.  Get High-res Image Gene #7: '4P GAIN MUTATION STATUS' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'2Q LOSS MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.39e-08 (t-test), Q value = 1.2e-05

Table S2.  Gene #44: '2Q LOSS MUTATION STATUS' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 152 2.6 (5.4)
2Q LOSS MUTATED 6 0.0 (0.0)
2Q LOSS WILD-TYPE 146 2.7 (5.4)

Figure S2.  Get High-res Image Gene #44: '2Q LOSS MUTATION STATUS' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

Methods & Data
Input

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

  • Clinical data file = READ-TP.clin.merged.picked.txt

  • Number of patients = 162

  • Number of significantly arm-level cnvs = 77

  • Number of selected clinical features = 11

  • 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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