Mutation Analysis (MutSig v2.0)
Liver Hepatocellular Carcinoma (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 Analysis (MutSig v2.0). Broad Institute of MIT and Harvard. doi:10.7908/C1610ZQ8
- Overview
+ Introduction
- Summary
  • MAF used for this analysis:LIHC-TP.final_analysis_set.maf

  • Blacklist used for this analysis: pancan_mutation_blacklist.v14.hg19.txt

  • Significantly mutated genes (q ≤ 0.1): 76

  • Mutations seen in COSMIC: 331

  • Significantly mutated genes in COSMIC territory: 14

  • Significantly mutated genesets: 45

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

Mutation Preprocessing
  • Read 373 MAFs of type "maf1"

  • Total number of mutations in input MAFs: 53406

  • After removing 202 mutations outside chr1-24: 53204

  • After removing 178 blacklisted mutations: 53026

  • After removing 1113 noncoding mutations: 51913

  • After collapsing adjacent/redundant mutations: 51877

Mutation Filtering
  • Number of mutations before filtering: 51877

  • After removing 732 mutations outside patient set: 51145

  • After removing 2751 mutations outside gene set: 48394

  • After removing 190 mutations outside category set: 48204

  • After removing 1 "impossible" mutations in

  • gene-patient-category bins of zero coverage: 44530

- 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
+ Lego Plots
+ CoMut Plot
+ Significantly Mutated Genes
+ COSMIC analyses
+ Geneset Analyses
+ Methods & Data