Mutation Assessor - Prostate Adenocarcinoma (Primary solid tumor)

Mutation Assessor

Prostate Adenocarcinoma (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/C1JS9PW9

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: 1246
Medium Functional Impact Missense Mutations: 6689
Low Functional Impact Missense Mutations: 6366
Neutral Functional Impact Mutations: 4925

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	SPOP	9	38	8	1	2.6875	medium	medium
2	TP53	0	40	0	2	2.9925	medium	medium
3	PTEN	2	3	0	0	3.4350	medium	medium
5	MLL2	2	2	4	9	0.6900	neutral	neutral
6	CTNNB1	0	12	1	0	2.4600	medium	medium
7	PIK3CA	0	8	6	2	1.7625	low	medium
9	FOXA1	3	7	4	0	2.6325	medium	medium
10	MLL3	1	6	5	4	1.5000	low	medium
12	TNRC18	0	1	4	0	1.7350	low	low
13	AGAP6	0	3	0	0	2.3050	medium	medium

Methods & Data

Input

PRAD-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 PRAD-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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