Mutation Analysis (MutSig v2.0)
Lung Squamous Cell 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/C11V5DFP
- Overview
+ Introduction
- Summary
  • MAF used for this analysis:LUSC-TP.final_analysis_set.maf

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

  • Significantly mutated genes (q ≤ 0.1): 114

  • Mutations seen in COSMIC: 350

  • Significantly mutated genes in COSMIC territory: 11

  • Significantly mutated genesets: 19

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

Mutation Preprocessing
  • Read 178 MAFs of type "maf1"

  • Total number of mutations in input MAFs: 64361

  • After removing 2 mutations outside chr1-24: 64359

  • After removing 591 blacklisted mutations: 63768

  • After removing 1436 noncoding mutations: 62332

Mutation Filtering
  • Number of mutations before filtering: 62332

  • After removing 3143 mutations outside gene set: 59189

  • After removing 42 mutations outside category set: 59147

  • After removing 2 "impossible" mutations in

  • gene-patient-category bins of zero coverage: 55960

- 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
+ Significantly Mutated Genes
+ COSMIC analyses
+ Geneset Analyses
+ Methods & Data