Correlation between copy number variation genes and molecular subtypes
Sarcoma (Primary solid tumor)
22 February 2013  |  analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C1BK19KR
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 variation genes and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1BK19KR
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.

Summary

Testing the association between copy number variation of 28 peak regions and 4 molecular subtypes across 29 patients, 3 significant findings detected with Q value < 0.25.

  • Amp Peak 9(12q14.1) cnvs correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 28 regions and 4 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 3 significant findings detected.

Molecular
subtypes 		CN
CNMF 		METHLYATION
CNMF 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
Amp Peak 9(12q14 1) 14 (48%) 15 1.05e-05
(0.00118) 		0.00375
(0.409) 		0.000116
(0.0128) 		0.000202
(0.0223)
Amp Peak 1(1q24 3) 10 (34%) 19 0.694
(1.00) 		0.889
(1.00) 		1
(1.00) 		1
(1.00)
Amp Peak 2(4p15 2) 8 (28%) 21 1
(1.00) 		0.516
(1.00) 		0.697
(1.00) 		1
(1.00)
Amp Peak 3(5p14 2) 8 (28%) 21 0.671
(1.00) 		0.871
(1.00) 		0.697
(1.00) 		1
(1.00)
Amp Peak 4(5p14 1) 9 (31%) 20 0.0959
(1.00) 		0.278
(1.00) 		0.454
(1.00) 		0.784
(1.00)
Amp Peak 5(6p21 1) 7 (24%) 22 1
(1.00) 		0.216
(1.00) 		0.41
(1.00) 		0.743
(1.00)
Amp Peak 6(6q25 1) 9 (31%) 20 0.0478
(1.00) 		0.00954
(1.00) 		0.13
(1.00) 		0.278
(1.00)
Amp Peak 7(7p15 3) 10 (34%) 19 0.432
(1.00) 		0.0424
(1.00) 		0.114
(1.00) 		0.152
(1.00)
Amp Peak 8(12p13 32) 7 (24%) 22 0.375
(1.00) 		0.0833
(1.00) 		0.0927
(1.00) 		0.225
(1.00)
Amp Peak 10(17p11 2) 7 (24%) 22 0.202
(1.00) 		1
(1.00) 		0.192
(1.00) 		0.103
(1.00)
Amp Peak 11(19p13 2) 12 (41%) 17 0.438
(1.00) 		0.13
(1.00) 		0.13
(1.00) 		0.0361
(1.00)
Del Peak 1(1q44) 8 (28%) 21 0.433
(1.00) 		0.0734
(1.00) 		0.697
(1.00) 		1
(1.00)
Del Peak 2(2q37 3) 14 (48%) 15 0.45
(1.00) 		0.583
(1.00) 		0.272
(1.00) 		0.345
(1.00)
Del Peak 3(3q25 1) 9 (31%) 20 0.694
(1.00) 		0.476
(1.00) 		0.13
(1.00) 		0.0388
(1.00)
Del Peak 4(4q35 1) 13 (45%) 16 1
(1.00) 		0.184
(1.00) 		0.264
(1.00) 		0.264
(1.00)
Del Peak 5(5q23 3) 6 (21%) 23 0.164
(1.00) 		0.729
(1.00) 		1
(1.00) 		1
(1.00)
Del Peak 6(9p21 3) 11 (38%) 18 0.696
(1.00) 		0.226
(1.00) 		0.702
(1.00) 		0.24
(1.00)
Del Peak 7(11p15 4) 12 (41%) 17 1
(1.00) 		0.364
(1.00) 		1
(1.00) 		0.438
(1.00)
Del Peak 8(11q22 3) 15 (52%) 14 0.45
(1.00) 		0.723
(1.00) 		0.715
(1.00) 		0.847
(1.00)
Del Peak 9(12p12 3) 9 (31%) 20 0.237
(1.00) 		1
(1.00) 		0.454
(1.00) 		0.784
(1.00)
Del Peak 10(13q14 2) 19 (66%) 10 0.432
(1.00) 		0.201
(1.00) 		0.433
(1.00) 		0.629
(1.00)
Del Peak 11(15q13 3) 10 (34%) 19 0.432
(1.00) 		0.34
(1.00) 		0.114
(1.00) 		0.152
(1.00)
Del Peak 12(17p13 1) 8 (28%) 21 0.11
(1.00) 		0.195
(1.00) 		0.406
(1.00) 		0.443
(1.00)
Del Peak 13(17q25 3) 6 (21%) 23 1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
Del Peak 14(19q13 32) 11 (38%) 18 0.449
(1.00) 		0.282
(1.00) 		0.466
(1.00) 		0.422
(1.00)
Del Peak 15(21q22 3) 11 (38%) 18 1
(1.00) 		0.282
(1.00) 		0.702
(1.00) 		0.817
(1.00)
Del Peak 16(Xq21 1) 15 (52%) 14 1
(1.00) 		0.461
(1.00) 		0.462
(1.00) 		0.579
(1.00)
Del Peak 17(Xq28) 12 (41%) 17 0.273
(1.00) 		0.024
(1.00) 		0.274
(1.00) 		0.251
(1.00)
'Amp Peak 9(12q14.1) mutation analysis' versus 'CN_CNMF'

P value = 1.05e-05 (Fisher's exact test), Q value = 0.0012

Table S1.  Gene #9: 'Amp Peak 9(12q14.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2
ALL 18 11
AMP PEAK 9(12Q14.1) MUTATED 3 11
AMP PEAK 9(12Q14.1) WILD-TYPE 15 0

Figure S1.  Get High-res Image Gene #9: 'Amp Peak 9(12q14.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 9(12q14.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000116 (Fisher's exact test), Q value = 0.013

Table S2.  Gene #9: 'Amp Peak 9(12q14.1) mutation analysis' versus Clinical Feature #3: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2
ALL 16 13
AMP PEAK 9(12Q14.1) MUTATED 13 1
AMP PEAK 9(12Q14.1) WILD-TYPE 3 12

Figure S2.  Get High-res Image Gene #9: 'Amp Peak 9(12q14.1) mutation analysis' versus Clinical Feature #3: 'MIRSEQ_CNMF'

'Amp Peak 9(12q14.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000202 (Fisher's exact test), Q value = 0.022

Table S3.  Gene #9: 'Amp Peak 9(12q14.1) mutation analysis' versus Clinical Feature #4: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 12 16
AMP PEAK 9(12Q14.1) MUTATED 0 1 13
AMP PEAK 9(12Q14.1) WILD-TYPE 1 11 3

Figure S3.  Get High-res Image Gene #9: 'Amp Peak 9(12q14.1) mutation analysis' versus Clinical Feature #4: 'MIRSEQ_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.

  • Molecular subtype file = SARC-TP.transferedmergedcluster.txt

  • Number of patients = 29

  • Number of copy number variation regions = 28

  • Number of molecular subtypes = 4

  • Exclude regions that fewer than K tumors have alterations, 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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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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