Mutation Analysis (MutSig v2.0)
Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
Maintained by David Heiman (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/C1B27T47
- Overview
+ Introduction
- Summary
  • MAF used for this analysis:CESC-TP.final_analysis_set.maf

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

  • Significantly mutated genes (q ≤ 0.1): 17

  • Mutations seen in COSMIC: 191

  • Significantly mutated genes in COSMIC territory: 10

  • Significantly mutated genesets: 32

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

Mutation Preprocessing
  • Read 194 MAFs of type "WashU"

  • Total number of mutations in input MAFs: 46547

  • After removing 120 mutations outside chr1-24: 46427

  • After removing 302 blacklisted mutations: 46125

  • After removing 6065 noncoding mutations: 40060

  • After collapsing adjacent/redundant mutations: 39450

Mutation Filtering
  • Number of mutations before filtering: 39450

  • After removing 2753 mutations outside gene set: 36697

  • After removing 56 mutations outside category set: 36641

  • After removing 6 "impossible" mutations in

  • gene-patient-category bins of zero coverage: 33826

- 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