Lung Adenocarcinoma: Mutation Analysis (MutSig)
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

- MAF used for this analysis:LUAD.final_analysis_set.maf

- Significantly mutated genes (q ≤ 0.1): 36

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: 36. 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 | 31248 | 3 | 2 | 151 | 59 | 1.1e-162 | 2.1e-158
KRAS | 25787 | 1 | 0 | 71 | 0 | 4.1e-40 | 3.8e-36
STK11 | 21045 | 3 | 0 | 24 | 14 | 1.2e-38 | 7.4e-35
PPP2R2A | 45136 | 4 | 0 | 8 | 0 | 2.6e-17 | 1.2e-13
RBM10 | 49888 | 4 | 1 | 14 | 11 | 1e-15 | 3.8e-12
LOC440563 | 25272 | 2 | 1 | 9 | 1 | 1.1e-14 | 3.4e-11
FAM55B | 18225 | 0 | 3 | 7 | 0 | 5.5e-12 | 1.5e-08
U2AF1 | 21829 | 2 | 0 | 7 | 0 | 2.2e-10 | 5.1e-07
MAP2K1 | 33480 | 2 | 0 | 8 | 1 | 2.1e-09 | 4.4e-06
KEAP1 | 46361 | 2 | 0 | 45 | 5 | 5.1e-09 | 9.6e-06
DCAF8L2 | 25758 | 0 | 2 | 7 | 0 | 1.1e-08 | 0.000018
CDKN2A | 9534 | 4 | 1 | 16 | 5 | 9.9e-08 | 0.00016
BRAF | 64728 | 11 | 1 | 21 | 2 | 1.4e-07 | 0.0002
NFATC3 | 88764 | 4 | 2 | 11 | 0 | 1.5e-07 | 0.0002
KRTAP4-11 | 11178 | 1 | 0 | 5 | 0 | 5.7e-07 | 0.00072
CRIPAK | 26030 | 0 | 5 | 17 | 11 | 6.5e-07 | 0.00076
FAM75C1 | 81405 | 1 | 5 | 23 | 1 | 1.2e-06 | 0.0014
ARID1A | 144336 | 5 | 2 | 19 | 13 | 2.3e-06 | 0.0024
PIK3CA | 104894 | 4 | 1 | 15 | 0 | 6.6e-06 | 0.0064
CENPF | 295854 | 17 | 7 | 33 | 3 | 6.8e-06 | 0.0064
OR2T27 | 24810 | 0 | 2 | 16 | 0 | 7.6e-06 | 0.0068
SMARCA4 | 117477 | 9 | 2 | 21 | 13 | 7.9e-06 | 0.0068
AMY1A | 13893 | 1 | 1 | 5 | 2 | 9.5e-06 | 0.0078
BRE | 42403 | 7 | 0 | 10 | 6 | 0.000027 | 0.022
MAGEC1 | 90024 | 6 | 3 | 42 | 3 | 0.000044 | 0.033
AGAP6 | 56619 | 3 | 2 | 7 | 1 | 0.000066 | 0.048
C9orf64 | 30509 | 2 | 0 | 8 | 6 | 8e-05 | 0.055
RUFY1 | 56787 | 10 | 2 | 8 | 0 | 0.000081 | 0.055
RIT1 | 19592 | 2 | 1 | 12 | 3 | 0.000085 | 0.056
SPRR3 | 12643 | 1 | 0 | 8 | 5 | 0.000091 | 0.057
MGA | 242113 | 6 | 3 | 25 | 14 | 0.000099 | 0.061
SETD2 | 185697 | 2 | 1 | 23 | 12 | 0.0001 | 0.062
ZNF681 | 62496 | 8 | 1 | 8 | 1 | 0.00011 | 0.064
OR14I1 | 29264 | 0 | 2 | 15 | 0 | 0.00013 | 0.072
RIF1 | 234588 | 12 | 3 | 16 | 2 | 0.00017 | 0.089

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.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] TCGA, Integrated genomic analyses of ovarian carcinoma, Nature 474:609 - 615 (2011)
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