Mutation Assessor - Brain Lower Grade Glioma (Primary solid tumor)

Mutation Assessor

Brain Lower Grade Glioma (Primary solid tumor)

Due to issues with GAF 3.0, we strongly advise caution in the use of these results.

23 September 2013 | analyses__2013_09_23

Maintainer Information

Citation Information

doi:10.7908/C1959FT4

Maintained by David Heiman (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Mutation Assessor. Broad Institute of MIT and Harvard. doi:10.7908/C1959FT4

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: 1087
Medium Functional Impact Missense Mutations: 5409
Low Functional Impact Missense Mutations: 5145
Neutral Functional Impact Mutations: 3848

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
TEAD3	1	0	1	0	0	2.2650	medium	medium
ATRX	3	2	7	5	4	1.8075	low	medium
PRCP	4	0	1	0	0	2.7650	medium	medium
IDH2	5	8	0	0	0	3.9000	high	high
IDH1	6	167	0	0	0	4.5400	high	high
TP53	7	0	126	1	1	3.1450	medium	medium
HEATR3	8	0	0	0	1	0.6900	neutral	neutral
CIC	9	4	10	8	2	2.8125	medium	medium
FUBP1	10	0	0	0	1	0.7050	neutral	neutral
NOTCH1	11	3	6	0	4	2.6950	medium	medium

Methods & Data

Input

LGG-TP.maf.annotated
LGG-TP.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 LGG-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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