Mutation Analysis (MutSig v2.0)
Pan-kidney cohort (KICH+KIRC+KIRP) (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
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/C10G3J6B
- Overview
+ Introduction
- Summary
  • MAF used for this analysis:KIPAN-TP.final_analysis_set.maf

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

  • Significantly mutated genes (q ≤ 0.1): 179

  • Mutations seen in COSMIC: 581

  • Significantly mutated genes in COSMIC territory: 86

  • Significantly mutated genesets: 9

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

Mutation Preprocessing
  • Read 217 MAFs of type "Broad"

  • Read 557 MAFs of type "Baylor-Illumina"

  • Read 120 MAFs of type "Baylor-SOLiD"

  • Total number of mutations in input MAFs: 84875

  • After removing 57 mutations outside chr1-24: 84818

  • After removing 9840 blacklisted mutations: 74978

  • After removing 1773 noncoding mutations: 73205

  • After collapsing adjacent/redundant mutations: 57929

Mutation Filtering
  • Number of mutations before filtering: 57929

  • After removing 2067 mutations outside gene set: 55862

  • After removing 256 mutations outside category set: 55606

  • After removing 9 "impossible" mutations in

  • gene-patient-category bins of zero coverage: 53274

- 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