Mutation Assessor - Stomach and Esophageal carcinoma (Primary solid tumor)

Mutation Assessor

Stomach and Esophageal carcinoma (Primary solid tumor)

28 January 2016 | analyses__2016_01_28

Maintainer Information

Citation Information

Maintained by David Heiman (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Mutation Assessor. Broad Institute of MIT and Harvard. doi:10.7908/C1DZ07SN

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: 7727
Medium Functional Impact Missense Mutations: 43173
Low Functional Impact Missense Mutations: 42953
Neutral Functional Impact Mutations: 32124

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.

MutSig Rank	Gene	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
1	TP53	0	221	11	3	3.0750	medium	medium
2	ARID1A	0	10	13	4	1.5900	low	low
3	MLL2	4	10	12	39	0.5500	neutral	neutral
4	RNF43	0	1	2	9	0.4475	neutral	neutral
5	SMAD4	12	20	0	0	3.4850	medium	medium
6	KRAS	3	32	5	0	3.2450	medium	medium
7	XYLT2	0	8	4	2	2.0175	medium	medium
8	PTEN	6	8	2	1	2.8900	medium	medium
9	LARP4B	1	1	5	3	1.1475	low	low
10	FBXW7	1	15	5	8	2.1650	medium	medium

Methods & Data

Input

STES-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 STES-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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