Mutation Analysis (MutSig v2.0 and MutSigCV v0.9 merged result)
Head and Neck Squamous Cell Carcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Mutation Analysis (MutSig v2.0 and MutSigCV v0.9 merged result). Broad Institute of MIT and Harvard. doi:10.7908/C15Q4TH1
- Overview
+ Introduction
- Summary
  • MAF used for this analysis:HNSC-TP.final_analysis_set.maf

  • Significantly mutated genes (q ≤ 0.1): 30

  • Mutations seen in COSMIC: 472

  • Significantly mutated genes in COSMIC territory: 6

  • Significantly mutated genesets: 68

Mutation Preprocessing
  • Read 306 MAFs of type "Broad"

  • Total number of mutations in input MAFs: 74008

  • After removing 10 mutations outside chr1-24: 73998

  • After removing 3058 blacklisted mutations: 70940

  • After removing 4120 noncoding mutations: 66820

  • After collapsing adjacent/redundant mutations: 56803

Mutation Filtering
  • Number of mutations before filtering: 56803

  • After removing 732 mutations outside gene set: 56071

  • After removing 53 mutations outside category set: 56018

- 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