Mutation Analysis (MutSig v1.5)
Lung Squamous Cell Carcinoma (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 v1.5). Broad Institute of MIT and Harvard. doi:10.7908/C1Z31WQB
- Overview
+ Introduction
- Summary
  • MAF used for this analysis:LUSC-TP.final_analysis_set.maf

  • Significantly mutated genes (q ≤ 0.1): 114

  • Mutations seen in COSMIC: 353

  • Significantly mutated genes in COSMIC territory: 11

  • Genes with clustered mutations (≤ 3 aa apart): 615

  • Significantly mutated genesets: 17

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

Mutation Preprocessing
  • Read 178 MAFs of type "Broad"

  • Total number of mutations in input MAFs: 65305

  • After removing 2 mutations outside chr1-24: 65303

  • After removing 419 blacklisted mutations: 64884

  • After removing 588 noncoding mutations: 64296

Mutation Filtering
  • Number of mutations before filtering: 64296

  • After removing 343 mutations outside gene set: 63953

  • After removing 47 mutations outside category set: 63906

  • After removing 2 "impossible" mutations in

  • gene-patient-category bins of zero coverage: 63514

- 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