Lung Adenocarcinoma: 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: LUAD

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: 19. 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
TP53 18396 0 2 73 28 2.3e-144 4.4e-140
KRAS 15183 0 0 38 0 7.9e-51 7.5e-47
STK11 12403 1 0 18 9 2.5e-33 1.6e-29
RBM10 29354 3 0 13 10 9.3e-26 4.4e-22
FAM75C1 48575 0 2 15 0 9.7e-19 3.7e-15
KRTAP4-11 6670 1 0 5 0 1.3e-11 3.9e-08
LOC440563 15080 1 1 6 1 4.1e-10 1.1e-06
DCAF8L2 15370 0 0 6 0 6.2e-10 1.5e-06
AGAP6 33785 1 2 6 0 7.9e-08 0.00016
KEAP1 27299 2 0 27 3 8.6e-08 0.00016
SETD2 109343 1 0 18 12 1.4e-07 0.00024
ZNF679 21170 2 1 6 2 2.1e-07 0.00032
FSCB 33435 0 2 15 2 1.1e-06 0.0015
BRAF 38106 2 1 15 2 1.1e-06 0.0015
ZNF770 39560 0 2 6 0 1.3e-06 0.0016
U2AF1 12849 1 0 5 0 1.6e-06 0.0019
SMARCA4 69189 3 1 14 8 4.6e-06 0.0051
HRNR 79852 1 7 36 10 0.000014 0.014
EGFR 66577 12 5 24 6 0.000016 0.016
ARID1A 84972 3 1 10 8 0.00012 0.12
CDKN2A 5570 2 1 8 3 0.00016 0.15
MGA 142509 4 2 18 9 0.00017 0.15
FAM75A2 19422 0 0 5 1 0.00018 0.15
RGPD4 64670 6 3 14 0 0.00022 0.17
FLG 159865 2 17 102 15 0.00025 0.19
POLR3B 63072 4 0 12 2 0.00033 0.24
NPSR1 23360 7 0 7 0 0.00035 0.24
ANKRD55 30660 4 2 10 1 0.00042 0.28
PKHD1L1 205279 22 12 40 4 0.0006 0.39
MUC17 198266 7 17 56 4 0.00097 0.61
FAM123C 27735 0 1 13 3 0.001 0.63
NEO1 71685 6 1 11 0 0.0013 0.78
RIT1 11534 2 1 8 1 0.0014 0.78
MUC7 15037 0 0 13 2 0.0015 0.83
DLGAP2 25410 4 2 13 0 0.0016 0.84
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.
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