Mutation Assessor - Testicular Germ Cell Tumors (Primary solid tumor)

Mutation Assessor

Testicular Germ Cell Tumors (Primary solid tumor)

21 August 2015 | analyses__2015_08_21

Maintainer Information

Citation Information

Maintained by David Heiman (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Mutation Assessor. Broad Institute of MIT and Harvard. doi:10.7908/C1WS8SJS

Overview

Introduction

This report serves to summarize the functional impact of missense mutations in each gene as determined by Mutation Assessor[1].

Summary

High Functional Impact Missense Mutations: 356
Medium Functional Impact Missense Mutations: 1957
Low Functional Impact Missense Mutations: 2232
Neutral Functional Impact Mutations: 1723

Results

Functional Impact by Gene

Table 1. Get Full Table A gene-level breakdown of missense mutation functional impact, ordered by MutSig rank. Includes missense mutation counts broken down by level of functional impact (high, medium, low, neutral), median functional impact score and level, and most common level(s) of functional impact (mode) per gene.

Gene	MutSig Rank	High Functional Impact Count	Medium Functional Impact Count	Low Functional Impact Count	Neutral Functional Impact Count	Median Functional Impact Score	Median Functional Impact Level	Mode Functional Impact Level
FAM18B2	1	0	0	0	26	-3.335	neutral	neutral
KIT	2	0	6	12	6	1.235	low	low
KRAS	3	5	12	2	0	3.135	medium	medium
CSGALNACT2	5	0	2	0	0	3.005	medium	medium
NRAS	6	1	5	1	0	3.325	medium	medium
DDX11	7	0	1	2	0	1.745	low	low
MUC6	8	0	2	9	3	1.490	low	low
SERINC2	10	0	0	3	0	1.355	low	low
RHPN2	11	0	6	0	0	2.455	medium	medium
HSF4	13	0	3	0	3	1.550	low	medium/neutral

Methods & Data

Input

TGCT-TP.maf.annotated
sig_genes.txt
Mutation Assessor Scores Release 2:

hg18
hg19

A lookup is done against the relevant Mutation Assessor Scores table for each missense mutation in a given MAF file, and available functional impact score and level are appended as two new columns to generate TGCT-TP.maf.annotated. These are summarized in Table 1, sorted by MutSig rank.

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] Boris Reva, Yevgeniy Antipin, and Chris Sander, Predicting the functional impact of protein mutations: application to cancer genomics, Nucl. Acids Res. 39(17):e118 (2011)

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