Mutation Analysis (MutSig v2.0)
Kidney Renal Papillary 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). Broad Institute of MIT and Harvard. doi:10.7908/C1T1523X
- Overview
+ Introduction
- Summary
  • MAF used for this analysis:KIRP-TP.final_analysis_set.maf

  • Significantly mutated genes (q ≤ 0.1): 4

  • Mutations seen in COSMIC: 42

  • Significantly mutated genes in COSMIC territory: 11

  • Significantly mutated genesets: 0

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

Mutation Preprocessing
  • Read 112 MAFs of type "Broad"

  • Total number of mutations in input MAFs: 10029

  • After removing 78 mutations outside chr1-24: 9951

  • After removing 587 blacklisted mutations: 9364

  • After removing 147 noncoding mutations: 9217

  • After collapsing adjacent/redundant mutations: 7780

Mutation Filtering
  • Number of mutations before filtering: 7780

  • After removing 311 mutations outside gene set: 7469

  • After removing 9 mutations outside category set: 7460

- 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