Esophageal Carcinoma: Correlation between copy number variation genes and molecular subtypes
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
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 27 peak regions and molecular subtype 'METHLYATION_CNMF' across 20 patients, one significant finding detected with Q value < 0.25.

- Del Peak 5(5q11.2) cnvs correlated to 'METHLYATION_CNMF'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 27 regions and 1 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, one significant finding detected.

|  | Molecular subtypes | METHLYATION CNMF
| nCNV (%) | nWild-Type | Fisher's exact test
Del Peak 5(5q11 2) | 11 (55%) | 9 | 0.00125 (0.0338)
Amp Peak 1(1q42 3) | 9 (45%) | 11 | 0.255 (1.00)
Amp Peak 2(2p15) | 10 (50%) | 10 | 1 (1.00)
Amp Peak 3(3q28) | 17 (85%) | 3 | 0.0228 (0.593)
Amp Peak 4(6p12 3) | 6 (30%) | 14 | 1 (1.00)
Amp Peak 5(7p11 2) | 12 (60%) | 8 | 0.103 (1.00)
Amp Peak 6(7q31 1) | 14 (70%) | 6 | 0.638 (1.00)
Amp Peak 8(10p11 21) | 7 (35%) | 13 | 0.457 (1.00)
Amp Peak 9(11p13) | 6 (30%) | 14 | 0.808 (1.00)
Amp Peak 10(11q13 3) | 13 (65%) | 7 | 0.457 (1.00)
Amp Peak 11(12p13 33) | 13 (65%) | 7 | 0.0716 (1.00)
Amp Peak 12(14q21 3) | 11 (55%) | 9 | 0.31 (1.00)
Amp Peak 13(18p11 31) | 8 (40%) | 12 | 0.811 (1.00)
Amp Peak 14(Xp21 1) | 6 (30%) | 14 | 0.808 (1.00)
Del Peak 1(2q22 1) | 6 (30%) | 14 | 1 (1.00)
Del Peak 2(3p14 2) | 16 (80%) | 4 | 0.773 (1.00)
Del Peak 4(4q21 23) | 9 (45%) | 11 | 0.381 (1.00)
Del Peak 6(6p25 3) | 9 (45%) | 11 | 0.464 (1.00)
Del Peak 7(7q31 1) | 7 (35%) | 13 | 0.553 (1.00)
Del Peak 8(9p21 3) | 17 (85%) | 3 | 0.518 (1.00)
Del Peak 9(10p11 21) | 7 (35%) | 13 | 0.0304 (0.76)
Del Peak 10(10q23 31) | 10 (50%) | 10 | 0.7 (1.00)
Del Peak 11(13q14 2) | 11 (55%) | 9 | 0.0388 (0.932)
Del Peak 12(15q22 2) | 5 (25%) | 15 | 0.628 (1.00)
Del Peak 13(16q23 1) | 7 (35%) | 13 | 0.457 (1.00)
Del Peak 15(19q13 31) | 8 (40%) | 12 | 1 (1.00)
Del Peak 16(Xp11 3) | 9 (45%) | 11 | 0.835 (1.00)

'Del Peak 5(5q11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.00125 (Fisher's exact test), Q value = 0.034

Table S1. Gene #17: 'Del Peak 5(5q11.2) mutation analysis' versus Clinical Feature #1: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 12 | 5 | 3
DEL PEAK 5(5Q11.2) MUTATED | 10 | 0 | 1
DEL PEAK 5(5Q11.2) WILD-TYPE | 2 | 5 | 2

Figure S1. Get High-res Image Gene #17: 'Del Peak 5(5q11.2) mutation analysis' versus Clinical Feature #1: 'METHLYATION_CNMF'

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 = ESCA-TP.transferedmergedcluster.txt

- Number of patients = 20

- Number of copy number variation regions = 27

- Number of molecular subtypes = 1: 'METHLYATION_CNMF'

- 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.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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)
[3] GISTIC_version2
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