Mutation Assessor
Brain Lower Grade Glioma (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/C1736QBQ
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: 1861

  • Medium Functional Impact Missense Mutations: 8248

  • Low Functional Impact Missense Mutations: 7726

  • Neutral Functional Impact Mutations: 5667

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 IDH1 401 0 0 0 4.5400 high high
2 TP53 0 248 2 1 3.1450 medium medium
4 CIC 16 29 17 4 3.3200 medium medium
5 NOTCH1 10 10 0 5 3.1550 medium high/medium
6 IDH2 20 0 0 0 3.9000 high high
7 PIK3R1 0 6 1 0 2.7100 medium medium
8 FUBP1 0 0 0 1 0.7050 neutral neutral
9 NF1 0 7 2 2 2.2500 medium medium
11 PTEN 7 6 2 0 3.4600 medium high
12 ARID1A 0 4 2 2 1.9375 medium medium
Methods & Data
Input
  1. LGG-TP.maf.annotated

  2. sig_genes.txt

  3. Mutation Assessor Scores Release 2:

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)