Mutation Assessor - Glioma (Primary solid tumor)

Mutation Assessor

Glioma (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/C1125RP1

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: 2636
Medium Functional Impact Missense Mutations: 12012
Low Functional Impact Missense Mutations: 11099
Neutral Functional Impact Mutations: 8352

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
IDH1	1	412	0	0	0	4.540	high	high
TP53	2	0	319	4	1	3.145	medium	medium
PTEN	4	24	31	7	0	3.100	medium	medium
CIC	5	16	29	17	4	3.320	medium	medium
PIK3CA	6	0	31	14	17	1.835	low	medium
NF1	7	0	10	2	3	2.340	medium	medium
PIK3R1	8	1	18	2	0	2.710	medium	medium
NOTCH1	9	10	10	0	5	3.155	medium	high/medium
FUBP1	10	0	0	0	1	0.705	neutral	neutral
RB1	11	0	0	2	0	1.290	low	low

Methods & Data

Input

GBMLGG-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 GBMLGG-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)

Made with Nozzle