Breast Invasive Carcinoma: Mutation Analysis (MutSig vS2N)
Maintained by Dan DiCara (Broad Institute)
Overview
Introduction

This report serves to describe the mutational landscape and properties of a given individual set, as well as rank genes and genesets according to mutational significance. MutSig vS2N was used to generate the results found in this report.

  • Working with individual set: BRCA

Input

The input for this pipeline is a set of individuals with the following files associated for each:

  1. An annotated .maf file describing the mutations called for the respective individual, and their properties.

  2. A .wig file that contains information about the coverage of the sample.

Summary
Results
Significantly Mutated Genes

Column Descriptions:

  • N = number of sequenced bases in this gene across the individual set

  • nnon = number of (nonsilent) mutations in this gene across the individual set

  • nnull = number of (nonsilent) null mutations in this gene across the individual set

  • nflank = number of noncoding mutations from this gene's flanking region, across the individual set

  • nsil = number of silent mutations in this gene across the individual set

  • p = p-value (overall)

  • q = q-value, False Discovery Rate (Benjamini-Hochberg procedure)

Table 1.  Get Full Table A Ranked List of Significantly Mutated Genes. Number of significant genes found: 75. Number of genes displayed: 35. Click on a gene name to display its stick figure depicting the distribution of mutations and mutation types across the chosen gene (this feature may not be available for all significant genes).

gene N nflank nsil nnon nnull p q
PIK3CA 214718 0 3 196 8 0 0
ZNF841 1064 0 0 7 2 0 0
ANKRD30B 964 0 3 6 1 0 0
GATA3 58646 0 1 58 53 0 0
TP53 64260 0 3 190 74 0 0
PTEN 82086 0 0 18 13 0 0
CDH1 148920 0 1 33 29 3e-168 8e-165
RUNX1 52534 0 1 18 12 4.4e-141 1e-137
TBL1XR1 79548 0 0 10 8 2.7e-119 5.6e-116
MAP3K1 236648 0 3 64 55 2.2e-117 4.1e-114
MAP2K4 71404 0 0 20 12 5.5e-81 9.3e-78
ZNF90 832 0 0 4 1 3.9e-67 6.1e-64
DNAH6 82146 0 3 11 1 1.3e-47 1.9e-44
FAM75C1 1340 0 2 4 0 4.8e-44 6.5e-41
RGPD3 1676 0 2 4 1 6.6e-36 8.3e-33
MLL3 824694 0 2 37 23 6.9e-32 8.1e-29
EYS 114754 0 0 11 1 2e-31 2.3e-28
CDKN1B 30604 0 0 5 5 7.9e-30 8.3e-27
NCOR1 402398 0 1 18 15 4e-28 4e-25
TBX3 73938 0 0 13 10 1.9e-27 1.8e-24
CBFB 28568 0 1 8 3 3.9e-21 3.5e-18
SF3B1 231544 0 0 10 1 4.1e-19 3.5e-16
RTL1 27250 0 0 5 0 1.9e-18 1.6e-15
PTPN22 160144 0 0 8 0 5.4e-18 4.3e-15
DNAH12 88748 0 0 7 0 1e-16 7.5e-14
PIK3R1 150454 0 1 14 9 1.9e-16 1.4e-13
CTCF 129540 0 2 13 7 6.1e-13 4.2e-10
GPS2 58140 0 1 6 6 2.8e-09 1.9e-06
ANK3 804278 0 0 12 0 4.4e-09 2.9e-06
WNK3 310052 0 1 8 0 9.8e-09 6.2e-06
RB1 248390 0 0 10 8 2.2e-08 0.000013
SRGAP1 205522 0 0 8 0 3.5e-08 2e-05
FAM47C 144310 0 1 10 0 1.1e-07 0.000063
ATN1 122898 0 1 8 4 1.9e-07 0.0001
AKT1 84664 0 1 12 0 2.6e-07 0.00014
Methods & Data
Methods

In brief, we tabulate the number of mutations and the number of covered bases for each gene. The counts are broken down by mutation context category: four context categories that are discovered by MutSig, and one for indel and 'null' mutations, which include indels, nonsense mutations, splice-site mutations, and non-stop (read-through) mutations. For each gene, we calculate the probability of seeing the observed constellation of mutations, i.e. the product P1 x P2 x ... x Pm, or a more extreme one, given the background mutation rates calculated across the dataset. [1]

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References
[1] TCGA, Integrated genomic analyses of ovarian carcinoma, Nature 474:609 - 615 (2011)
Copyright © 2012 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle