Mutation Analysis (MutSig v2.0)
Stomach Adenocarcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Mutation Analysis (MutSig v2.0). Broad Institute of MIT and Harvard. doi:10.7908/C10R9MGS
- Overview
+ Introduction
- Summary
  • MAF used for this analysis:STAD-TP.final_analysis_set.maf

  • Significantly mutated genes (q ≤ 0.1): 42

  • Mutations seen in COSMIC: 499

  • Significantly mutated genes in COSMIC territory: 30

  • Genes with clustered mutations (≤ 3 aa apart): 886

  • Significantly mutated genesets: 18

  • Significantly mutated genesets: (excluding sig. mutated genes):0

Mutation Preprocessing
  • Read 221 MAFs of type "Broad"

  • Total number of mutations in input MAFs: 112521

  • After removing 38 mutations outside chr1-24: 112483

  • After removing 711 blacklisted mutations: 111772

  • After removing 1912 noncoding mutations: 109860

Mutation Filtering
  • Number of mutations before filtering: 109860

  • After removing 1339 mutations outside gene set: 108521

  • After removing 114 mutations outside category set: 108407

  • After removing 3 "impossible" mutations in

  • gene-patient-category bins of zero coverage: 106951

- Results
+ Breakdown of Mutations by Type
+ Breakdown of Mutation Rates by Category Type
+ Target Coverage for Each Individual
+ Distribution of Mutation Counts, Coverage, and Mutation Rates Across Samples
+ Needs description.
+ CoMut Plot
+ Significantly Mutated Genes
+ COSMIC analyses
+ Clustered Mutations
+ Geneset Analyses
+ Methods & Data