Mutation Analysis (MutSig v1.5)
Colorectal Adenocarcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_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/C1222S2J
- Overview
+ Introduction
- Summary
  • MAF used for this analysis:COADREAD-TP.final_analysis_set.maf

  • Significantly mutated genes (q ≤ 0.1): 51

  • Mutations seen in COSMIC: 738

  • Significantly mutated genes in COSMIC territory: 29

  • Genes with clustered mutations (≤ 3 aa apart): 1744

  • Significantly mutated genesets: 35

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

Mutation Preprocessing
  • Read 140 MAFs of type "Broad"

  • Read 87 MAFs of type "Baylor-SOLiD"

  • Total number of mutations in input MAFs: 91943

  • After removing 1369 invalidated mutations: 90574

  • After removing 1176 noncoding mutations: 89398

  • After collapsing adjacent/redundant mutations: 82119

Mutation Filtering
  • Number of mutations before filtering: 82119

  • After removing 847 mutations outside gene set: 81272

  • After removing 343 mutations outside category set: 80929

  • After removing 12 "impossible" mutations in

  • gene-patient-category bins of zero coverage: 79727

- 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
+ Clustered Mutations
+ Geneset Analyses
+ Methods & Data