Thyroid Adenocarcinoma: Correlation between copy number variations of arm-level result and molecular subtypes<BR>(other cohort)

Thyroid Adenocarcinoma: Correlation between copy number variations of arm-level result and molecular subtypes
(other cohort)

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Overview

Introduction

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

Summary

Testing the association between copy number variation 11 arm-level results and 3 molecular subtypes across 20 patients, no significant finding detected with 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 11 arm-level results and 3 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, no significant finding detected.


		Molecular subtypes	METHLYATION CNMF	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test
5p gain	3 (15%)	17	0.242 (1.00)	0.218 (1.00)	0.484 (1.00)
5q gain	3 (15%)	17	0.242 (1.00)	0.218 (1.00)	0.484 (1.00)
7p gain	3 (15%)	17	0.242 (1.00)	0.218 (1.00)	0.484 (1.00)
7q gain	4 (20%)	16	0.117 (1.00)	0.591 (1.00)	1 (1.00)
12p gain	3 (15%)	17	0.242 (1.00)	0.218 (1.00)	0.484 (1.00)
12q gain	3 (15%)	17	0.242 (1.00)	0.218 (1.00)	0.484 (1.00)
17p gain	3 (15%)	17	0.242 (1.00)	0.218 (1.00)	0.484 (1.00)
17q gain	3 (15%)	17	0.242 (1.00)	0.218 (1.00)	0.484 (1.00)
19p gain	3 (15%)	17	0.242 (1.00)	0.218 (1.00)	0.484 (1.00)
19q gain	3 (15%)	17	0.242 (1.00)	0.218 (1.00)	0.484 (1.00)
22q loss	4 (20%)	16	1 (1.00)	0.591 (1.00)	0.636 (1.00)

Methods & Data

Input

Mutation data file = broad_values_by_arm.mutsig.cluster.txt
Molecular subtypes file = THCA-other.transferedmergedcluster.txt
Number of patients = 20
Number of significantly arm-level cnvs = 11
Number of molecular subtypes = 3
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

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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