Mutation Analysis (MutSig v2.0)
Skin Cutaneous Melanoma (Metastatic)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Skin Cutaneous Melanoma (Metastatic cohort) - 21 April 2013: Mutation Analysis (MutSig v2.0). Broad Institute of MIT and Harvard. doi:10.7908/C1JW8BVC
- Overview
+ Introduction
- Summary
  • MAF used for this analysis:SKCM-TM.final_analysis_set.maf

  • Significantly mutated genes (q ≤ 0.1): 98

  • Mutations seen in COSMIC: 595

  • Significantly mutated genes in COSMIC territory: 41

  • Genes with clustered mutations (≤ 3 aa apart): 1213

  • Significantly mutated genesets: 2

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

Mutation Preprocessing
  • Read 225 MAFs of type "Broad"

  • Total number of mutations in input MAFs: 172938

  • After removing 4 mutations outside chr1-24: 172934

  • After removing 790 blacklisted mutations: 172144

  • After removing 3204 noncoding mutations: 168940

Mutation Filtering
  • Number of mutations before filtering: 168940

  • After removing 2144 mutations outside gene set: 166796

  • After removing 110 mutations outside category set: 166686

  • After removing 7 "impossible" mutations in

  • gene-patient-category bins of zero coverage: 164425

- 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
+ CoMut Plot
+ Significantly Mutated Genes
+ COSMIC analyses
+ Clustered Mutations
+ Geneset Analyses
+ Methods & Data