Correlation between copy number variations of arm-level result and selected clinical features
Rectum Adenocarcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C10Z71ZB
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/C10Z71ZB
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 78 arm-level events and 11 clinical features across 162 patients, 3 significant findings detected with Q value < 0.25.

  • 4p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 2q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 7q loss 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 78 arm-level events and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 3 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 9 (6%) 153 0.77
(1.00) 		0.759
(1.00) 		0.308
(1.00) 		0.658
(1.00) 		0.243
(1.00) 		0.345
(1.00) 		0.182
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		7.54e-06
(0.00645)
2q loss 6 (4%) 156 0.323
(1.00) 		0.0183
(1.00) 		0.242
(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
(1.19e-05)
7q loss 3 (2%) 159 0.258
(1.00) 		0.928
(1.00) 		0.692
(1.00) 		0.43
(1.00) 		1
(1.00) 		0.593
(1.00) 		0.231
(1.00) 		1
(1.00) 		1
(1.00) 		1.44e-08
(1.23e-05)
1p gain 12 (7%) 150 0.105
(1.00) 		0.804
(1.00) 		0.285
(1.00) 		0.0291
(1.00) 		0.403
(1.00) 		0.118
(1.00) 		0.772
(1.00) 		0.0507
(1.00) 		1
(1.00) 		0.201
(1.00) 		0.507
(1.00)
1q gain 32 (20%) 130 0.679
(1.00) 		0.379
(1.00) 		0.586
(1.00) 		0.0025
(1.00) 		0.384
(1.00) 		0.387
(1.00) 		0.429
(1.00) 		0.277
(1.00) 		0.338
(1.00) 		0.515
(1.00) 		0.116
(1.00)
2p gain 39 (24%) 123 0.789
(1.00) 		0.351
(1.00) 		0.557
(1.00) 		0.378
(1.00) 		0.29
(1.00) 		0.456
(1.00) 		0.0272
(1.00) 		0.0392
(1.00) 		0.631
(1.00) 		0.2
(1.00) 		0.745
(1.00)
2q gain 41 (25%) 121 0.588
(1.00) 		0.395
(1.00) 		0.423
(1.00) 		0.258
(1.00) 		0.202
(1.00) 		0.568
(1.00) 		0.0294
(1.00) 		0.0213
(1.00) 		0.171
(1.00) 		0.327
(1.00) 		0.711
(1.00)
3p gain 27 (17%) 135 0.484
(1.00) 		0.864
(1.00) 		0.169
(1.00) 		0.765
(1.00) 		0.377
(1.00) 		0.0428
(1.00) 		0.53
(1.00) 		0.469
(1.00) 		0.262
(1.00) 		0.866
(1.00) 		0.699
(1.00)
3q gain 34 (21%) 128 0.808
(1.00) 		0.938
(1.00) 		0.258
(1.00) 		0.655
(1.00) 		0.47
(1.00) 		0.0548
(1.00) 		0.439
(1.00) 		0.3
(1.00) 		0.607
(1.00) 		0.557
(1.00) 		0.979
(1.00)
4q gain 5 (3%) 157 0.936
(1.00) 		0.781
(1.00) 		0.927
(1.00) 		1
(1.00) 		0.707
(1.00) 		0.737
(1.00) 		0.0633
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.00265
(1.00)
5p gain 34 (21%) 128 0.137
(1.00) 		0.482
(1.00) 		0.772
(1.00) 		0.113
(1.00) 		0.658
(1.00) 		0.588
(1.00) 		0.0854
(1.00) 		0.0726
(1.00) 		0.107
(1.00) 		0.346
(1.00) 		0.654
(1.00)
5q gain 22 (14%) 140 0.858
(1.00) 		0.543
(1.00) 		0.384
(1.00) 		0.734
(1.00) 		0.67
(1.00) 		0.783
(1.00) 		0.369
(1.00) 		0.217
(1.00) 		1
(1.00) 		0.724
(1.00) 		0.264
(1.00)
6p gain 40 (25%) 122 0.396
(1.00) 		0.911
(1.00) 		0.273
(1.00) 		0.274
(1.00) 		0.0463
(1.00) 		0.042
(1.00) 		0.467
(1.00) 		0.187
(1.00) 		0.0332
(1.00) 		0.38
(1.00) 		0.327
(1.00)
6q gain 35 (22%) 127 0.724
(1.00) 		0.83
(1.00) 		0.0398
(1.00) 		0.289
(1.00) 		0.0836
(1.00) 		0.022
(1.00) 		0.566
(1.00) 		0.0726
(1.00) 		0.0202
(1.00) 		0.279
(1.00) 		0.855
(1.00)
7p gain 100 (62%) 62 0.213
(1.00) 		0.413
(1.00) 		0.0497
(1.00) 		0.433
(1.00) 		0.178
(1.00) 		0.798
(1.00) 		0.628
(1.00) 		0.00465
(1.00) 		1
(1.00) 		0.496
(1.00) 		0.138
(1.00)
7q gain 83 (51%) 79 0.293
(1.00) 		0.288
(1.00) 		0.0138
(1.00) 		0.521
(1.00) 		0.0744
(1.00) 		0.39
(1.00) 		0.636
(1.00) 		0.00764
(1.00) 		1
(1.00) 		0.277
(1.00) 		0.902
(1.00)
8p gain 39 (24%) 123 0.483
(1.00) 		0.524
(1.00) 		0.0965
(1.00) 		0.192
(1.00) 		0.597
(1.00) 		0.467
(1.00) 		0.581
(1.00) 		1
(1.00) 		1
(1.00) 		0.205
(1.00) 		0.0686
(1.00)
8q gain 88 (54%) 74 0.135
(1.00) 		0.518
(1.00) 		0.0309
(1.00) 		0.201
(1.00) 		0.163
(1.00) 		0.219
(1.00) 		0.753
(1.00) 		0.083
(1.00) 		0.221
(1.00) 		0.109
(1.00) 		0.318
(1.00)
9p gain 42 (26%) 120 0.224
(1.00) 		0.397
(1.00) 		0.205
(1.00) 		0.816
(1.00) 		0.697
(1.00) 		0.755
(1.00) 		1
(1.00) 		0.329
(1.00) 		1
(1.00) 		0.524
(1.00) 		0.664
(1.00)
9q gain 33 (20%) 129 0.194
(1.00) 		0.172
(1.00) 		0.0162
(1.00) 		0.936
(1.00) 		0.899
(1.00) 		0.928
(1.00) 		0.441
(1.00) 		0.471
(1.00) 		1
(1.00) 		1
(1.00) 		0.846
(1.00)
10p gain 12 (7%) 150 0.934
(1.00) 		0.736
(1.00) 		0.889
(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 6 (4%) 156 0.839
(1.00) 		0.759
(1.00) 		0.803
(1.00) 		0.641
(1.00) 		0.555
(1.00) 		0.737
(1.00) 		0.0938
(1.00) 		1
(1.00) 		0.206
(1.00) 		1
(1.00) 		0.571
(1.00)
11p gain 30 (19%) 132 0.761
(1.00) 		0.66
(1.00) 		0.782
(1.00) 		0.608
(1.00) 		0.403
(1.00) 		0.307
(1.00) 		0.841
(1.00) 		0.0747
(1.00) 		1
(1.00) 		1
(1.00) 		0.526
(1.00)
11q gain 25 (15%) 137 0.557
(1.00) 		0.245
(1.00) 		0.629
(1.00) 		0.391
(1.00) 		0.206
(1.00) 		0.112
(1.00) 		1
(1.00) 		0.13
(1.00) 		0.591
(1.00) 		1
(1.00) 		0.0224
(1.00)
12p gain 33 (20%) 129 0.936
(1.00) 		0.396
(1.00) 		0.733
(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 23 (14%) 139 0.181
(1.00) 		0.223
(1.00) 		0.87
(1.00) 		0.701
(1.00) 		0.633
(1.00) 		0.942
(1.00) 		0.508
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.698
(1.00)
13q gain 110 (68%) 52 0.356
(1.00) 		0.369
(1.00) 		0.316
(1.00) 		0.321
(1.00) 		0.0311
(1.00) 		0.0369
(1.00) 		0.501
(1.00) 		0.000708
(0.604) 		1
(1.00) 		0.949
(1.00) 		0.88
(1.00)
14q gain 8 (5%) 154 0.223
(1.00) 		0.97
(1.00) 		0.798
(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 3 (2%) 159 0.911
(1.00) 		0.746
(1.00) 		0.199
(1.00) 		0.0527
(1.00) 		0.171
(1.00) 		1
(1.00) 		0.0932
(1.00) 		0.231
(1.00) 		1
(1.00) 		1
(1.00) 		0.443
(1.00)
16p gain 39 (24%) 123 0.935
(1.00) 		0.908
(1.00) 		0.0656
(1.00) 		0.741
(1.00) 		0.338
(1.00) 		0.81
(1.00) 		1
(1.00) 		0.0392
(1.00) 		0.151
(1.00) 		0.697
(1.00) 		0.931
(1.00)
16q gain 39 (24%) 123 0.477
(1.00) 		0.842
(1.00) 		0.454
(1.00) 		0.944
(1.00) 		0.146
(1.00) 		0.31
(1.00) 		0.854
(1.00) 		0.0392
(1.00) 		0.151
(1.00) 		0.933
(1.00) 		0.439
(1.00)
17p gain 8 (5%) 154 0.281
(1.00) 		0.546
(1.00) 		0.806
(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 30 (19%) 132 0.317
(1.00) 		0.78
(1.00) 		0.758
(1.00) 		1
(1.00) 		0.594
(1.00) 		0.33
(1.00) 		0.546
(1.00) 		0.465
(1.00) 		0.594
(1.00) 		0.455
(1.00) 		0.263
(1.00)
18p gain 8 (5%) 154 0.646
(1.00) 		0.395
(1.00) 		0.069
(1.00) 		0.384
(1.00) 		0.496
(1.00) 		0.287
(1.00) 		0.728
(1.00) 		0.135
(1.00) 		0.266
(1.00) 		0.0941
(1.00) 		0.23
(1.00)
18q gain 6 (4%) 156 0.0301
(1.00) 		0.396
(1.00) 		0.0846
(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 31 (19%) 131 0.744
(1.00) 		0.923
(1.00) 		0.756
(1.00) 		0.335
(1.00) 		0.834
(1.00) 		0.311
(1.00) 		0.549
(1.00) 		0.0727
(1.00) 		1
(1.00) 		0.492
(1.00) 		0.821
(1.00)
19q gain 30 (19%) 132 0.419
(1.00) 		0.743
(1.00) 		0.731
(1.00) 		0.229
(1.00) 		0.742
(1.00) 		0.299
(1.00) 		0.686
(1.00) 		0.0747
(1.00) 		1
(1.00) 		0.239
(1.00) 		0.0382
(1.00)
20p gain 104 (64%) 58 0.332
(1.00) 		0.175
(1.00) 		0.0355
(1.00) 		0.816
(1.00) 		0.342
(1.00) 		0.855
(1.00) 		0.255
(1.00) 		0.0127
(1.00) 		1
(1.00) 		0.12
(1.00) 		0.823
(1.00)
20q gain 142 (88%) 20 0.0872
(1.00) 		0.141
(1.00) 		0.0795
(1.00) 		0.53
(1.00) 		0.023
(1.00) 		0.634
(1.00) 		0.811
(1.00) 		0.00106
(0.904) 		0.552
(1.00) 		0.11
(1.00) 		0.557
(1.00)
21q gain 10 (6%) 152 0.385
(1.00) 		0.619
(1.00) 		0.314
(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 9 (6%) 153 0.0355
(1.00) 		0.902
(1.00) 		0.47
(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 32 (20%) 130 0.603
(1.00) 		0.234
(1.00) 		0.514
(1.00) 		0.135
(1.00) 		0.246
(1.00) 		0.544
(1.00) 		0.235
(1.00) 		0.465
(1.00) 		0.599
(1.00) 		0.756
(1.00) 		0.677
(1.00)
1p loss 44 (27%) 118 0.641
(1.00) 		0.778
(1.00) 		0.904
(1.00) 		0.723
(1.00) 		0.542
(1.00) 		0.896
(1.00) 		0.293
(1.00) 		0.0206
(1.00) 		0.346
(1.00) 		0.759
(1.00) 		0.424
(1.00)
1q loss 25 (15%) 137 0.344
(1.00) 		0.915
(1.00) 		0.526
(1.00) 		0.588
(1.00) 		0.559
(1.00) 		0.583
(1.00) 		0.0794
(1.00) 		0.221
(1.00) 		0.232
(1.00) 		0.759
(1.00) 		0.647
(1.00)
2p loss 11 (7%) 151 0.723
(1.00) 		0.00114
(0.967) 		0.34
(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 15 (9%) 147 0.00314
(1.00) 		0.721
(1.00) 		0.0498
(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 10 (6%) 152 0.071
(1.00) 		0.745
(1.00) 		0.0373
(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 58 (36%) 104 0.171
(1.00) 		0.518
(1.00) 		0.557
(1.00) 		0.516
(1.00) 		0.537
(1.00) 		0.941
(1.00) 		0.511
(1.00) 		0.38
(1.00) 		0.0226
(1.00) 		0.208
(1.00) 		0.441
(1.00)
4q loss 65 (40%) 97 0.0803
(1.00) 		0.944
(1.00) 		0.519
(1.00) 		0.525
(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 26 (16%) 136 0.152
(1.00) 		0.805
(1.00) 		0.81
(1.00) 		0.846
(1.00) 		0.491
(1.00) 		0.949
(1.00) 		0.0884
(1.00) 		0.697
(1.00) 		0.247
(1.00) 		1
(1.00) 		0.0928
(1.00)
5q loss 40 (25%) 122 0.953
(1.00) 		0.39
(1.00) 		0.858
(1.00) 		0.868
(1.00) 		0.886
(1.00) 		0.751
(1.00) 		0.585
(1.00) 		0.187
(1.00) 		0.00368
(1.00) 		0.641
(1.00) 		0.573
(1.00)
6p loss 13 (8%) 149 0.114
(1.00) 		0.713
(1.00) 		0.0954
(1.00) 		0.429
(1.00) 		0.0266
(1.00) 		0.715
(1.00) 		1
(1.00) 		0.0643
(1.00) 		0.4
(1.00) 		0.419
(1.00) 		0.87
(1.00)
6q loss 22 (14%) 140 0.602
(1.00) 		0.832
(1.00) 		0.0102
(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 75 (46%) 87 0.115
(1.00) 		0.464
(1.00) 		0.831
(1.00) 		0.894
(1.00) 		0.321
(1.00) 		0.663
(1.00) 		0.753
(1.00) 		0.773
(1.00) 		0.417
(1.00) 		0.91
(1.00) 		0.0405
(1.00)
8q loss 11 (7%) 151 0.716
(1.00) 		0.675
(1.00) 		0.985
(1.00) 		0.831
(1.00) 		0.593
(1.00) 		0.672
(1.00) 		0.0672
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.649
(1.00)
9p loss 22 (14%) 140 0.0671
(1.00) 		0.965
(1.00) 		0.227
(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 22 (14%) 140 0.0353
(1.00) 		0.895
(1.00) 		0.564
(1.00) 		0.0472
(1.00) 		0.419
(1.00) 		0.121
(1.00) 		0.369
(1.00) 		1
(1.00) 		0.59
(1.00) 		0.014
(1.00) 		0.0891
(1.00)
10p loss 32 (20%) 130 0.0929
(1.00) 		0.00445
(1.00) 		0.578
(1.00) 		0.668
(1.00) 		0.932
(1.00) 		0.278
(1.00) 		0.558
(1.00) 		0.0235
(1.00) 		0.092
(1.00) 		0.228
(1.00) 		0.639
(1.00)
10q loss 37 (23%) 125 0.261
(1.00) 		0.0676
(1.00) 		0.474
(1.00) 		0.8
(1.00) 		1
(1.00) 		0.281
(1.00) 		0.348
(1.00) 		0.0773
(1.00) 		0.133
(1.00) 		0.141
(1.00) 		0.817
(1.00)
11p loss 24 (15%) 138 0.418
(1.00) 		0.478
(1.00) 		0.336
(1.00) 		0.242
(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 30 (19%) 132 0.616
(1.00) 		0.916
(1.00) 		0.701
(1.00) 		0.608
(1.00) 		0.963
(1.00) 		0.172
(1.00) 		1
(1.00) 		0.0436
(1.00) 		0.0778
(1.00) 		0.238
(1.00) 		0.352
(1.00)
12p loss 22 (14%) 140 0.379
(1.00) 		0.796
(1.00) 		0.722
(1.00) 		0.58
(1.00) 		0.509
(1.00) 		0.736
(1.00) 		0.491
(1.00) 		0.218
(1.00) 		0.59
(1.00) 		1
(1.00) 		0.993
(1.00)
12q loss 20 (12%) 142 0.456
(1.00) 		0.314
(1.00) 		0.559
(1.00) 		0.942
(1.00) 		0.698
(1.00) 		0.708
(1.00) 		1
(1.00) 		0.37
(1.00) 		0.552
(1.00) 		1
(1.00) 		0.96
(1.00)
13q loss 8 (5%) 154 0.892
(1.00) 		0.584
(1.00) 		0.49
(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 65 (40%) 97 0.898
(1.00) 		0.852
(1.00) 		0.302
(1.00) 		0.614
(1.00) 		0.191
(1.00) 		0.874
(1.00) 		0.262
(1.00) 		0.0155
(1.00) 		0.685
(1.00) 		0.288
(1.00) 		0.903
(1.00)
15q loss 72 (44%) 90 0.363
(1.00) 		0.968
(1.00) 		0.293
(1.00) 		0.306
(1.00) 		0.547
(1.00) 		0.804
(1.00) 		0.153
(1.00) 		1
(1.00) 		0.0892
(1.00) 		0.868
(1.00) 		0.0391
(1.00)
16p loss 9 (6%) 153 0.594
(1.00) 		0.256
(1.00) 		0.0316
(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 14 (9%) 148 0.966
(1.00) 		0.546
(1.00) 		0.249
(1.00) 		0.8
(1.00) 		0.014
(1.00) 		0.899
(1.00) 		0.784
(1.00) 		1
(1.00) 		0.424
(1.00) 		0.736
(1.00) 		0.197
(1.00)
17p loss 104 (64%) 58 0.914
(1.00) 		0.061
(1.00) 		0.801
(1.00) 		0.0415
(1.00) 		0.928
(1.00) 		0.273
(1.00) 		0.742
(1.00) 		0.226
(1.00) 		1
(1.00) 		0.753
(1.00) 		0.743
(1.00)
17q loss 25 (15%) 137 0.1
(1.00) 		0.664
(1.00) 		0.856
(1.00) 		0.459
(1.00) 		0.881
(1.00) 		0.895
(1.00) 		0.663
(1.00) 		1
(1.00) 		0.232
(1.00) 		0.497
(1.00) 		0.672
(1.00)
18p loss 125 (77%) 37 0.569
(1.00) 		0.199
(1.00) 		0.4
(1.00) 		0.288
(1.00) 		0.632
(1.00) 		0.289
(1.00) 		1
(1.00) 		0.0322
(1.00) 		1
(1.00) 		0.53
(1.00) 		0.529
(1.00)
18q loss 135 (83%) 27 0.566
(1.00) 		0.146
(1.00) 		0.302
(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 22 (14%) 140 0.456
(1.00) 		0.918
(1.00) 		0.0336
(1.00) 		0.719
(1.00) 		0.329
(1.00) 		0.783
(1.00) 		1
(1.00) 		0.221
(1.00) 		0.59
(1.00) 		1
(1.00) 		0.281
(1.00)
19q loss 21 (13%) 141 0.829
(1.00) 		0.545
(1.00) 		0.0304
(1.00) 		0.482
(1.00) 		0.449
(1.00) 		0.823
(1.00) 		0.64
(1.00) 		0.37
(1.00) 		0.571
(1.00) 		0.61
(1.00) 		0.376
(1.00)
20p loss 25 (15%) 137 0.789
(1.00) 		0.473
(1.00) 		0.058
(1.00) 		0.86
(1.00) 		0.478
(1.00) 		1
(1.00) 		0.83
(1.00) 		0.424
(1.00) 		0.591
(1.00) 		0.329
(1.00) 		0.692
(1.00)
21q loss 66 (41%) 96 0.601
(1.00) 		0.564
(1.00) 		0.645
(1.00) 		0.132
(1.00) 		0.197
(1.00) 		0.572
(1.00) 		0.631
(1.00) 		0.244
(1.00) 		0.688
(1.00) 		0.385
(1.00) 		0.0619
(1.00)
22q loss 57 (35%) 105 0.0922
(1.00) 		0.159
(1.00) 		0.359
(1.00) 		0.412
(1.00) 		0.0121
(1.00) 		0.563
(1.00) 		0.744
(1.00) 		1
(1.00) 		0.426
(1.00) 		0.675
(1.00) 		0.477
(1.00)
xq loss 25 (15%) 137 0.252
(1.00) 		0.932
(1.00) 		0.457
(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' versus 'NUMBER.OF.LYMPH.NODES'

P value = 7.54e-06 (t-test), Q value = 0.0064

Table S1.  Gene #7: '4p gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 152 2.6 (5.4)
4P GAIN MUTATED 8 0.2 (0.7)
4P GAIN WILD-TYPE 144 2.7 (5.5)

Figure S1.  Get High-res Image Gene #7: '4p gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'2q loss' versus 'NUMBER.OF.LYMPH.NODES'

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

Table S2.  Gene #44: '2q loss' 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' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'7q loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.44e-08 (t-test), Q value = 1.2e-05

Table S3.  Gene #53: '7q loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 152 2.6 (5.4)
7Q LOSS MUTATED 3 0.0 (0.0)
7Q LOSS WILD-TYPE 149 2.7 (5.4)

Figure S3.  Get High-res Image Gene #53: '7q loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

Methods & Data
Input

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

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

  • Number of patients = 162

  • Number of significantly arm-level cnvs = 78

  • 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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