Mutation Analysis (MutSig v2.0)
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
Maintained by David Heiman (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Mutation Analysis (MutSig v2.0). Broad Institute of MIT and Harvard. doi:10.7908/C1QR4WBX
- Overview
+ Introduction
- Summary
  • MAF used for this analysis:KIRC-TP.final_analysis_set.maf

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

  • Significantly mutated genes (q ≤ 0.1): 212

  • Mutations seen in COSMIC: 432

  • Significantly mutated genes in COSMIC territory: 58

  • Significantly mutated genesets: 11

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

Mutation Preprocessing
  • Read 451 MAFs of type "maf1"

  • Total number of mutations in input MAFs: 46768

  • After removing 23 mutations outside chr1-24: 46745

  • After removing 7797 blacklisted mutations: 38948

  • After removing 2073 noncoding mutations: 36875

  • After collapsing adjacent/redundant mutations: 33030

Mutation Filtering
  • Number of mutations before filtering: 33030

  • After removing 1948 mutations outside gene set: 31082

  • After removing 124 mutations outside category set: 30958

  • After removing 7 "impossible" mutations in

  • gene-patient-category bins of zero coverage: 28879

- 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