Correlation between copy number variations of arm-level result and molecular subtypes
Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1JQ10CK
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1JQ10CK
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.

Summary

Testing the association between copy number variation 52 arm-level events and 10 molecular subtypes across 48 patients, no significant finding detected with P value < 0.05 and Q value < 0.25.

  • No arm-level cnvs related to molecular subtypes.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 52 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, no significant finding detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type 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 Fisher's exact test Fisher's exact test
1q gain 6 (12%) 42 0.283
(0.924) 		0.681
(1.00) 		0.391
(0.95) 		0.274
(0.924) 		0.339
(0.926) 		0.55
(1.00) 		0.861
(1.00) 		0.314
(0.926) 		1
(1.00) 		0.841
(1.00)
2p gain 6 (12%) 42 0.597
(1.00) 		0.683
(1.00) 		0.341
(0.926) 		0.826
(1.00) 		0.908
(1.00) 		1
(1.00) 		1
(1.00) 		0.606
(1.00) 		0.498
(1.00) 		0.248
(0.924)
2q gain 6 (12%) 42 0.594
(1.00) 		0.682
(1.00) 		0.341
(0.926) 		0.824
(1.00) 		0.908
(1.00) 		1
(1.00) 		1
(1.00) 		0.604
(1.00) 		0.497
(1.00) 		0.249
(0.924)
3p gain 10 (21%) 38 0.0257
(0.634) 		0.619
(1.00) 		0.451
(1.00) 		0.248
(0.924) 		0.367
(0.943) 		0.127
(0.849) 		0.203
(0.905) 		0.403
(0.965) 		0.761
(1.00) 		0.703
(1.00)
3q gain 13 (27%) 35 0.00231
(0.256) 		0.341
(0.926) 		0.239
(0.924) 		0.0369
(0.634) 		0.0658
(0.788) 		0.013
(0.582) 		0.222
(0.924) 		0.563
(1.00) 		0.876
(1.00) 		0.859
(1.00)
5p gain 7 (15%) 41 0.279
(0.924) 		0.067
(0.788) 		0.774
(1.00) 		0.687
(1.00) 		0.0439
(0.634) 		0.874
(1.00) 		1
(1.00) 		0.638
(1.00) 		0.66
(1.00) 		0.316
(0.926)
5q gain 6 (12%) 42 0.503
(1.00) 		0.256
(0.924) 		0.772
(1.00) 		0.687
(1.00) 		0.104
(0.821) 		0.665
(1.00) 		1
(1.00) 		0.8
(1.00) 		0.587
(1.00) 		0.511
(1.00)
6p gain 6 (12%) 42 0.598
(1.00) 		0.867
(1.00) 		0.875
(1.00) 		0.826
(1.00) 		0.363
(0.943) 		1
(1.00) 		0.672
(1.00) 		0.861
(1.00) 		0.914
(1.00) 		0.909
(1.00)
6q gain 4 (8%) 44 0.105
(0.821) 		0.601
(1.00) 		0.96
(1.00) 		0.77
(1.00) 		0.619
(1.00) 		0.895
(1.00) 		0.441
(1.00) 		1
(1.00) 		0.78
(1.00) 		0.328
(0.926)
7p gain 14 (29%) 34 0.00251
(0.256) 		0.465
(1.00) 		0.815
(1.00) 		0.76
(1.00) 		0.133
(0.864) 		0.0412
(0.634) 		0.665
(1.00) 		0.698
(1.00) 		0.434
(1.00) 		0.735
(1.00)
7q gain 12 (25%) 36 0.0035
(0.256) 		0.749
(1.00) 		0.824
(1.00) 		1
(1.00) 		0.198
(0.905) 		0.0678
(0.788) 		0.649
(1.00) 		0.918
(1.00) 		0.0885
(0.793) 		0.473
(1.00)
8p gain 7 (15%) 41 1
(1.00) 		0.117
(0.838) 		0.921
(1.00) 		1
(1.00) 		0.151
(0.875) 		0.705
(1.00) 		0.264
(0.924) 		0.00552
(0.319) 		0.38
(0.943) 		0.15
(0.875)
8q gain 8 (17%) 40 0.875
(1.00) 		0.041
(0.634) 		0.771
(1.00) 		0.824
(1.00) 		0.0485
(0.664) 		0.324
(0.926) 		0.136
(0.866) 		0.0276
(0.634) 		0.376
(0.943) 		0.148
(0.875)
9p gain 7 (15%) 41 1
(1.00) 		0.387
(0.944) 		0.975
(1.00) 		0.438
(1.00) 		0.311
(0.926) 		0.0245
(0.634) 		0.264
(0.924) 		0.639
(1.00) 		0.912
(1.00) 		0.299
(0.924)
9q gain 7 (15%) 41 0.652
(1.00) 		0.384
(0.944) 		0.975
(1.00) 		0.438
(1.00) 		0.874
(1.00) 		0.09
(0.793) 		0.266
(0.924) 		0.293
(0.924) 		0.854
(1.00) 		0.295
(0.924)
10p gain 4 (8%) 44 0.107
(0.821) 		0.897
(1.00) 		0.022
(0.634) 		0.199
(0.905) 		0.676
(1.00) 		1
(1.00) 		0.779
(1.00) 		0.326
(0.926)
10q gain 4 (8%) 44 0.107
(0.821) 		0.6
(1.00) 		0.961
(1.00) 		0.768
(1.00) 		0.182
(0.905) 		0.197
(0.905) 		0.445
(1.00) 		0.778
(1.00) 		0.0817
(0.788) 		0.0125
(0.582)
11p gain 9 (19%) 39 0.47
(1.00) 		0.872
(1.00) 		0.297
(0.924) 		0.378
(0.943) 		0.204
(0.905) 		0.517
(1.00) 		0.197
(0.905) 		0.164
(0.902) 		0.342
(0.926) 		0.377
(0.943)
11q gain 13 (27%) 35 0.822
(1.00) 		0.486
(1.00) 		0.1
(0.821) 		0.359
(0.943) 		0.153
(0.875) 		0.443
(1.00) 		0.913
(1.00) 		0.0748
(0.788) 		0.463
(1.00) 		0.339
(0.926)
12p gain 7 (15%) 41 0.278
(0.924) 		0.533
(1.00) 		0.874
(1.00) 		0.299
(0.924) 		0.761
(1.00) 		0.199
(0.905) 		0.363
(0.943) 		0.275
(0.924) 		0.688
(1.00) 		0.623
(1.00)
12q gain 9 (19%) 39 0.474
(1.00) 		0.233
(0.924) 		1
(1.00) 		0.476
(1.00) 		0.607
(1.00) 		0.302
(0.924) 		0.197
(0.905) 		0.137
(0.866) 		0.262
(0.924) 		0.142
(0.875)
13q gain 5 (10%) 43 0.687
(1.00) 		0.782
(1.00) 		0.269
(0.924) 		1
(1.00) 		0.366
(0.943) 		0.257
(0.924) 		0.0347
(0.634) 		0.661
(1.00) 		0.196
(0.905) 		0.571
(1.00)
16p gain 7 (15%) 41 0.653
(1.00) 		0.194
(0.905) 		0.619
(1.00) 		1
(1.00) 		0.0833
(0.788) 		0.0772
(0.788) 		0.468
(1.00) 		0.0295
(0.634) 		0.243
(0.924) 		0.0432
(0.634)
16q gain 7 (15%) 41 0.558
(1.00) 		0.0979
(0.821) 		0.618
(1.00) 		1
(1.00) 		0.337
(0.926) 		0.318
(0.926) 		0.467
(1.00) 		0.0145
(0.582) 		0.243
(0.924) 		0.227
(0.924)
17q gain 3 (6%) 45 0.756
(1.00) 		0.643
(1.00) 		0.96
(1.00) 		0.77
(1.00) 		0.166
(0.902) 		0.538
(1.00) 		0.763
(1.00) 		0.0355
(0.634) 		0.781
(1.00) 		1
(1.00)
18p gain 13 (27%) 35 0.00209
(0.256) 		0.537
(1.00) 		0.0037
(0.256) 		0.779
(1.00) 		0.498
(1.00) 		0.311
(0.926) 		0.221
(0.924) 		0.123
(0.849) 		0.664
(1.00) 		0.371
(0.943)
18q gain 13 (27%) 35 0.00217
(0.256) 		0.537
(1.00) 		0.00394
(0.256) 		0.778
(1.00) 		0.495
(1.00) 		0.311
(0.926) 		0.219
(0.924) 		0.12
(0.843) 		0.665
(1.00) 		0.372
(0.943)
19p gain 3 (6%) 45 0.27
(0.924) 		1
(1.00) 		0.881
(1.00) 		0.634
(1.00) 		1
(1.00) 		0.69
(1.00)
19q gain 3 (6%) 45 0.269
(0.924) 		1
(1.00) 		0.882
(1.00) 		0.635
(1.00) 		1
(1.00) 		0.692
(1.00)
20p gain 5 (10%) 43 0.836
(1.00) 		1
(1.00) 		0.63
(1.00) 		0.155
(0.875) 		0.0722
(0.788) 		0.431
(1.00) 		0.596
(1.00) 		0.378
(0.943) 		0.898
(1.00) 		1
(1.00)
20q gain 4 (8%) 44 1
(1.00) 		1
(1.00) 		0.96
(1.00) 		0.118
(0.838) 		0.226
(0.924) 		0.514
(1.00) 		1
(1.00) 		0.818
(1.00) 		1
(1.00) 		0.515
(1.00)
21q gain 10 (21%) 38 0.627
(1.00) 		0.0575
(0.766) 		0.353
(0.943) 		0.034
(0.634) 		0.0452
(0.635) 		0.267
(0.924) 		0.111
(0.821) 		0.183
(0.905) 		0.296
(0.924) 		0.431
(1.00)
xp gain 6 (12%) 42 0.594
(1.00) 		0.685
(1.00) 		0.921
(1.00) 		0.816
(1.00) 		0.908
(1.00) 		1
(1.00) 		0.336
(0.926) 		0.177
(0.905) 		0.0648
(0.788) 		0.042
(0.634)
xq gain 7 (15%) 41 0.329
(0.926) 		0.762
(1.00) 		0.921
(1.00) 		0.815
(1.00) 		0.557
(1.00) 		0.747
(1.00) 		1
(1.00) 		0.273
(0.924) 		0.399
(0.961) 		0.0855
(0.793)
1p loss 3 (6%) 45 1
(1.00) 		0.556
(1.00) 		0.663
(1.00) 		0.57
(1.00) 		0.708
(1.00) 		1
(1.00) 		1
(1.00) 		0.847
(1.00)
3p loss 4 (8%) 44 1
(1.00) 		1
(1.00) 		0.293
(0.924) 		0.717
(1.00) 		0.11
(0.821) 		0.778
(1.00) 		0.462
(1.00) 		0.379
(0.943)
3q loss 3 (6%) 45 0.756
(1.00) 		0.642
(1.00) 		0.0693
(0.788) 		0.354
(0.943) 		0.304
(0.924) 		0.921
(1.00)
4p loss 3 (6%) 45 0.275
(0.924) 		0.553
(1.00) 		0.129
(0.849) 		0.0891
(0.793) 		0.0281
(0.634) 		0.687
(1.00)
4q loss 4 (8%) 44 0.106
(0.821) 		0.895
(1.00) 		0.662
(1.00) 		0.57
(1.00) 		0.492
(1.00) 		0.896
(1.00) 		0.445
(1.00) 		0.235
(0.924) 		0.896
(1.00) 		0.573
(1.00)
6q loss 7 (15%) 41 0.278
(0.924) 		0.24
(0.924) 		0.0221
(0.634) 		1
(1.00) 		0.883
(1.00) 		0.937
(1.00) 		0.598
(1.00) 		0.727
(1.00) 		0.77
(1.00) 		0.804
(1.00)
8p loss 8 (17%) 40 0.224
(0.924) 		1
(1.00) 		0.148
(0.875) 		0.0432
(0.634) 		0.517
(1.00) 		0.809
(1.00) 		0.895
(1.00) 		0.0258
(0.634) 		1
(1.00) 		0.659
(1.00)
8q loss 4 (8%) 44 0.106
(0.821) 		0.738
(1.00) 		0.414
(0.988) 		0.0766
(0.788) 		0.784
(1.00) 		0.582
(1.00) 		0.675
(1.00) 		0.158
(0.883)
13q loss 3 (6%) 45 0.757
(1.00) 		0.468
(1.00) 		0.0679
(0.788) 		0.353
(0.943) 		1
(1.00) 		0.848
(1.00)
15q loss 7 (15%) 41 0.0264
(0.634) 		0.129
(0.849) 		0.661
(1.00) 		0.572
(1.00) 		0.0225
(0.634) 		0.222
(0.924) 		0.116
(0.838) 		0.367
(0.943) 		0.322
(0.926) 		0.212
(0.924)
16q loss 4 (8%) 44 0.108
(0.821) 		0.243
(0.924) 		0.172
(0.902) 		0.567
(1.00) 		0.492
(1.00) 		0.895
(1.00) 		0.204
(0.905) 		0.129
(0.849) 		0.178
(0.905) 		0.0825
(0.788)
17p loss 9 (19%) 39 0.285
(0.924) 		0.664
(1.00) 		1
(1.00) 		1
(1.00) 		0.0825
(0.788) 		0.703
(1.00) 		0.737
(1.00) 		0.501
(1.00) 		0.399
(0.961) 		0.174
(0.905)
17q loss 4 (8%) 44 1
(1.00) 		0.381
(0.943) 		0.183
(0.905) 		0.647
(1.00) 		0.445
(1.00) 		0.49
(1.00) 		0.0819
(0.788) 		0.0376
(0.634)
18p loss 5 (10%) 43 0.691
(1.00) 		0.428
(1.00) 		0.96
(1.00) 		0.274
(0.924) 		0.462
(1.00) 		0.0353
(0.634) 		0.859
(1.00) 		0.249
(0.924) 		0.209
(0.919) 		0.386
(0.944)
18q loss 5 (10%) 43 0.837
(1.00) 		0.426
(1.00) 		0.145
(0.875) 		0.168
(0.902) 		1
(1.00) 		0.728
(1.00) 		0.195
(0.905) 		0.152
(0.875)
22q loss 3 (6%) 45 0.271
(0.924) 		0.742
(1.00) 		0.295
(0.924) 		0.768
(1.00) 		0.881
(1.00) 		1
(1.00) 		1
(1.00) 		0.44
(1.00)
xp loss 5 (10%) 43 0.549
(1.00) 		0.342
(0.926) 		0.172
(0.902) 		0.572
(1.00) 		0.297
(0.924) 		0.839
(1.00) 		0.6
(1.00) 		0.0135
(0.582) 		0.662
(1.00) 		0.255
(0.924)
xq loss 4 (8%) 44 0.794
(1.00) 		0.146
(0.875) 		0.171
(0.902) 		0.57
(1.00) 		0.0796
(0.788) 		0.451
(1.00) 		0.304
(0.924) 		0.00223
(0.256) 		0.312
(0.926) 		0.0402
(0.634)
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/DLBC-TP/22516374/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/DLBC-TP/22541055/DLBC-TP.transferedmergedcluster.txt

  • Number of patients = 48

  • Number of significantly arm-level cnvs = 52

  • Number of molecular subtypes = 10

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

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] 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)
[2] 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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