Mutation Assessor - Uveal Melanoma (Primary solid tumor)

Mutation Assessor

Uveal Melanoma (Primary solid tumor)

02 April 2015 | analyses__2015_04_02

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/C1XS5THX

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: 170
Medium Functional Impact Missense Mutations: 375
Low Functional Impact Missense Mutations: 356
Neutral Functional Impact Mutations: 281

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
GNAQ	1	40	0	0	0	3.9750	high	high
GNA11	2	36	0	0	0	4.5300	high	high
SF3B1	4	18	0	0	0	3.8050	high	high
BAP1	5	1	0	1	2	1.2450	low	neutral
PRMT8	6	0	0	5	0	1.3550	low	low
CYSLTR2	7	3	0	0	0	4.0750	high	high
SELE	10	1	1	0	0	3.7125	high	high/medium
PLCB2	11	0	1	0	0	2.5200	medium	medium
PLCB4	13	2	1	0	0	3.5550	high	high
CSNK1A1L	14	0	1	0	1	1.0150	low	medium/neutral

Methods & Data

Input

UVM-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 UVM-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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