Mutation Analysis (MutSig vS2N)
Lung Squamous Cell Carcinoma (Primary solid tumor)
22 February 2013  |  analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C1X34VP9
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Mutation Analysis (MutSig vS2N). Broad Institute of MIT and Harvard. doi:10.7908/C1X34VP9
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: LUSC-TP

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: 29. 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
PTEN 28658 0 0 16 8 4.1e-57 7.7e-53
CDKN2A 10680 0 1 26 12 1.7e-56 1.6e-52
TP53 22428 0 7 147 47 1.8e-50 1.2e-46
PIK3CA 74938 0 1 29 0 7.8e-39 3.7e-35
EYS 40050 0 1 14 4 1e-22 3.9e-19
NFE2L2 38270 0 0 28 1 2.1e-16 6.6e-13
HLA-A 19224 0 0 7 6 6.4e-16 1.7e-12
KEAP1 32752 0 0 24 2 6.8e-15 1.6e-11
WHSC1L1 93628 0 1 16 2 3.9e-14 8.1e-11
MLL2 222678 0 6 41 18 1.2e-11 2.3e-08
RB1 86686 0 0 12 8 1.5e-09 2.5e-06
CPS1 99680 0 3 29 2 2.2e-07 0.00035
ZNF221 41296 0 0 5 0 2.8e-07 0.00041
NOTUM 16732 0 1 6 1 1.5e-06 0.0021
EBF1 33464 0 1 8 1 3.8e-06 0.0048
PRR23B 9612 0 2 9 0 9.8e-06 0.012
AKAP13 169812 0 4 19 0 0.000014 0.015
KIAA0319 65148 0 0 8 0 0.000026 0.027
DCAF5 54112 0 0 7 2 0.000037 0.037
DPP8 61054 0 0 8 0 0.000039 0.037
COL22A1 61054 0 5 35 6 0.000041 0.037
COL19A1 56604 0 5 19 2 0.000058 0.05
CD109 98968 0 1 8 0 0.000082 0.067
REG3A 10858 0 2 14 1 0.000085 0.067
TRIOBP 96298 0 1 20 1 0.000094 0.071
SPHKAP 103062 0 3 36 1 0.0001 0.076
FAM58B 14596 0 1 5 3 0.00011 0.076
FAM47C 50374 0 5 21 1 0.00014 0.091
PDGFRA 73514 0 3 10 0 0.00014 0.094
FSCB 40940 0 2 19 1 0.00017 0.11
NNT 65326 0 1 10 1 0.00023 0.14
SCN1A 140798 0 9 33 3 0.00023 0.14
PI16 21894 0 1 7 1 0.00025 0.15
PIK3CG 71556 0 4 18 1 0.0003 0.17
ASCL4 3204 0 0 6 2 0.00036 0.19
PTEN

Figure S1.  This figure depicts the distribution of mutations and mutation types across the PTEN significant gene.

CDKN2A

Figure S2.  This figure depicts the distribution of mutations and mutation types across the CDKN2A significant gene.

TP53

Figure S3.  This figure depicts the distribution of mutations and mutation types across the TP53 significant gene.

PIK3CA

Figure S4.  This figure depicts the distribution of mutations and mutation types across the PIK3CA significant gene.

EYS

Figure S5.  This figure depicts the distribution of mutations and mutation types across the EYS significant gene.

NFE2L2

Figure S6.  This figure depicts the distribution of mutations and mutation types across the NFE2L2 significant gene.

HLA-A

Figure S7.  This figure depicts the distribution of mutations and mutation types across the HLA-A significant gene.

KEAP1

Figure S8.  This figure depicts the distribution of mutations and mutation types across the KEAP1 significant gene.

WHSC1L1

Figure S9.  This figure depicts the distribution of mutations and mutation types across the WHSC1L1 significant gene.

MLL2

Figure S10.  This figure depicts the distribution of mutations and mutation types across the MLL2 significant gene.

RB1

Figure S11.  This figure depicts the distribution of mutations and mutation types across the RB1 significant gene.

CPS1

Figure S12.  This figure depicts the distribution of mutations and mutation types across the CPS1 significant gene.

ZNF221

Figure S13.  This figure depicts the distribution of mutations and mutation types across the ZNF221 significant gene.

NOTUM

Figure S14.  This figure depicts the distribution of mutations and mutation types across the NOTUM significant gene.

EBF1

Figure S15.  This figure depicts the distribution of mutations and mutation types across the EBF1 significant gene.

PRR23B

Figure S16.  This figure depicts the distribution of mutations and mutation types across the PRR23B significant gene.

AKAP13

Figure S17.  This figure depicts the distribution of mutations and mutation types across the AKAP13 significant gene.

KIAA0319

Figure S18.  This figure depicts the distribution of mutations and mutation types across the KIAA0319 significant gene.

DCAF5

Figure S19.  This figure depicts the distribution of mutations and mutation types across the DCAF5 significant gene.

DPP8

Figure S20.  This figure depicts the distribution of mutations and mutation types across the DPP8 significant gene.

COL22A1

Figure S21.  This figure depicts the distribution of mutations and mutation types across the COL22A1 significant gene.

COL19A1

Figure S22.  This figure depicts the distribution of mutations and mutation types across the COL19A1 significant gene.

CD109

Figure S23.  This figure depicts the distribution of mutations and mutation types across the CD109 significant gene.

REG3A

Figure S24.  This figure depicts the distribution of mutations and mutation types across the REG3A significant gene.

TRIOBP

Figure S25.  This figure depicts the distribution of mutations and mutation types across the TRIOBP significant gene.

SPHKAP

Figure S26.  This figure depicts the distribution of mutations and mutation types across the SPHKAP significant gene.

FAM58B

Figure S27.  This figure depicts the distribution of mutations and mutation types across the FAM58B significant gene.

FAM47C

Figure S28.  This figure depicts the distribution of mutations and mutation types across the FAM47C significant gene.

PDGFRA

Figure S29.  This figure depicts the distribution of mutations and mutation types across the PDGFRA significant gene.

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)
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