Mutation Assessor
Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
Maintained by David Heiman (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Mutation Assessor. Broad Institute of MIT and Harvard. doi:10.7908/C1T43RX7
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: 1147

  • Medium Functional Impact Missense Mutations: 7209

  • Low Functional Impact Missense Mutations: 8030

  • Neutral Functional Impact Mutations: 5427

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
KRAS 1 1 9 1 0 3.245 medium medium
HLA-A 2 2 1 0 0 3.915 high high
FBXW7 3 2 8 3 2 2.270 medium medium
HLA-B 4 1 2 0 0 2.235 medium medium
PTEN 5 3 2 1 0 3.330 medium high
ARID1A 6 0 1 4 0 1.700 low low
MAPK1 7 8 0 0 1 4.220 high high
EP300 8 6 4 2 1 3.285 medium high
PIK3CA 9 0 11 43 4 1.620 low low
NFE2L2 10 0 14 0 0 2.865 medium medium
Methods & Data
Input
  1. CESC-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 CESC-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)