Mutation Analysis (MutSig 2CV v3.1)
Prostate Adenocarcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1W37V3H
Maintained by David Heiman (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Mutation Analysis (MutSig 2CV v3.1). Broad Institute of MIT and Harvard. doi:10.7908/C1W37V3H
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 2CV v3.1 was used to generate the results found in this report.

  • Working with individual set: PRAD-TP

  • Number of patients in set: 261

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:PRAD-TP.final_analysis_set.maf

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

  • Significantly mutated genes (q ≤ 0.1): 24

Results
Lego Plots

The mutation spectrum is depicted in the lego plots below in which the 96 possible mutation types are subdivided into six large blocks, color-coded to reflect the base substitution type. Each large block is further subdivided into the 16 possible pairs of 5' and 3' neighbors, as listed in the 4x4 trinucleotide context legend. The height of each block corresponds to the mutation frequency for that kind of mutation (counts of mutations normalized by the base coverage in a given bin). The shape of the spectrum is a signature for dominant mutational mechanisms in different tumor types.

Figure 1.  Get High-res Image SNV Mutation rate lego plot for entire set. Each bin is normalized by base coverage for that bin. Colors represent the six SNV types on the upper right. The three-base context for each mutation is labeled in the 4x4 legend on the lower right. The fractional breakdown of SNV counts is shown in the pie chart on the upper left. If this figure is blank, not enough information was provided in the MAF to generate it.

Figure 2.  Get High-res Image SNV Mutation rate lego plots for 4 slices of mutation allele fraction (0<=AF<0.1, 0.1<=AF<0.25, 0.25<=AF<0.5, & 0.5<=AF) . The color code and three-base context legends are the same as the previous figure. If this figure is blank, not enough information was provided in the MAF to generate it.

CoMut Plot

Figure 3.  Get High-res Image The matrix in the center of the figure represents individual mutations in patient samples, color-coded by type of mutation, for the significantly mutated genes. The rate of synonymous and non-synonymous mutations is displayed at the top of the matrix. The barplot on the left of the matrix shows the number of mutations in each gene. The percentages represent the fraction of tumors with at least one mutation in the specified gene. The barplot to the right of the matrix displays the q-values for the most significantly mutated genes. The purple boxplots below the matrix (only displayed if required columns are present in the provided MAF) represent the distributions of allelic fractions observed in each sample. The plot at the bottom represents the base substitution distribution of individual samples, using the same categories that were used to calculate significance.

Significantly Mutated Genes

Column Descriptions:

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

  • npat = number of patients (individuals) with at least one nonsilent mutation

  • nsite = number of unique sites having a non-silent mutation

  • 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: 24. 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).

rank gene longname codelen nnei nncd nsil nmis nstp nspl nind nnon npat nsite pCV pCL pFN p q
1 SPOP speckle-type POZ protein 1161 137 0 0 26 0 0 1 27 26 11 9.5e-16 1e-05 0.44 1e-16 9.1e-13
2 TP53 tumor protein p53 1889 141 0 0 19 0 1 4 24 23 19 1.7e-15 0.0035 2e-05 1e-16 9.1e-13
3 PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 1244 60 0 0 3 1 1 8 13 13 13 1e-16 0.24 0.92 1.2e-15 7.4e-12
4 CTNNB1 catenin (cadherin-associated protein), beta 1, 88kDa 2406 175 0 0 9 0 0 0 9 9 7 5.8e-10 1e-05 0.047 1.9e-13 8.9e-10
5 TCEB3 transcription elongation factor B (SIII), polypeptide 3 (110kDa, elongin A) 2439 28 0 0 1 1 1 1 4 4 4 1.2e-06 1 0.035 1.4e-06 0.0043
6 FOXA1 forkhead box A1 1423 7 0 2 8 1 0 4 13 12 11 0.00015 0.0025 0.065 1.4e-06 0.0043
7 BRAF v-raf murine sarcoma viral oncogene homolog B1 2371 100 0 0 5 0 0 1 6 6 5 0.000035 0.023 0.044 2e-06 0.0045
8 PIK3CA phosphoinositide-3-kinase, catalytic, alpha polypeptide 3287 45 0 2 10 0 0 0 10 9 10 4.9e-06 0.083 0.13 2e-06 0.0045
9 IDH1 isocitrate dehydrogenase 1 (NADP+), soluble 1277 543 0 0 4 0 0 0 4 4 2 0.00031 0.00045 0.83 2.3e-06 0.0047
10 FAM47C family with sequence similarity 47, member C 3110 53 0 2 10 0 0 0 10 8 5 0.054 1e-05 0.66 8.3e-06 0.014
11 TP53BP1 tumor protein p53 binding protein 1 6042 23 0 0 1 2 0 3 6 5 6 5.1e-06 1 0.096 8.6e-06 0.014
12 CNTNAP1 contactin associated protein 1 4779 143 0 2 4 0 0 1 5 5 3 0.0074 3e-05 0.82 9.1e-06 0.014
13 MLLT10 myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10 3174 11 0 0 3 0 0 1 4 4 2 0.0066 0.0001 0.31 1e-05 0.014
14 ZMYM3 zinc finger, MYM-type 3 4227 7 0 0 3 1 1 2 7 6 7 0.000018 0.033 0.56 0.000012 0.015
15 SMG7 Smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans) 3879 9 0 0 2 0 0 2 4 4 3 0.0019 0.0054 0.01 0.000014 0.017
16 EDC4 enhancer of mRNA decapping 4 4332 23 0 0 1 0 0 2 3 3 2 0.00045 0.0022 1 0.000015 0.017
17 ZNF709 zinc finger protein 709 1938 10 0 1 4 0 0 0 4 4 2 0.015 0.0001 0.9 0.000025 0.027
18 CDK12 cyclin-dependent kinase 12 4525 86 0 0 5 2 1 2 10 7 10 1.8e-06 1 0.93 0.000026 0.027
19 RPTN repetin 2363 80 0 0 3 1 0 2 6 6 5 0.000022 0.067 0.6 0.000028 0.027
20 TNRC18 trinucleotide repeat containing 18 9019 0 0 0 2 0 0 3 5 4 4 0.00052 0.022 0.056 3e-05 0.028
21 MED15 mediator complex subunit 15 2437 36 0 0 3 0 0 2 5 5 5 4e-06 1 0.41 0.000054 0.045
22 NKX3-1 NK3 homeobox 1 711 312 0 0 4 0 0 1 5 5 5 0.000042 1 0.017 0.000055 0.045
23 KDM6A lysine (K)-specific demethylase 6A 4318 5 0 0 2 0 1 3 6 6 6 0.00011 1 0.021 0.000063 0.05
24 RNF31 ring finger protein 31 3596 39 0 0 2 0 0 2 4 4 4 0.0007 0.0083 0.75 0.000087 0.066
25 ESCO1 establishment of cohesion 1 homolog 1 (S. cerevisiae) 2555 19 0 0 1 2 0 1 4 4 4 0.000011 1 0.94 0.00014 0.1
26 LMOD2 leiomodin 2 (cardiac) 1652 174 0 0 0 0 0 3 3 3 1 0.012 0.001 0.38 0.00014 0.1
27 FAM120B family with sequence similarity 120B 2773 59 0 0 2 1 1 0 4 3 4 0.0062 0.0079 0.26 0.00015 0.1
28 CLEC1A C-type lectin domain family 1, member A 865 116 0 0 4 0 0 0 4 4 4 0.000025 1 0.34 0.00017 0.11
29 ITGA2B integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41) 3238 10 0 1 2 0 0 1 3 3 3 0.014 1 0.001 0.00018 0.11
30 RNF17 ring finger protein 17 5014 11 0 0 1 0 2 0 3 3 2 0.0042 0.0061 0.22 0.00018 0.11
31 RP1L1 retinitis pigmentosa 1-like 1 7215 33 0 1 6 0 1 0 7 7 7 0.000026 1 0.54 0.00018 0.11
32 EOMES eomesodermin homolog (Xenopus laevis) 2081 238 0 0 2 0 0 2 4 4 4 0.001 0.017 0.74 0.00021 0.12
33 MTF1 metal-regulatory transcription factor 1 2410 216 0 0 4 0 0 0 4 3 4 0.004 0.0055 0.53 0.00026 0.15
34 NTM neurotrimin 1195 41 0 0 3 0 2 0 5 5 5 0.00056 0.042 0.098 0.00027 0.15
35 OR2AE1 olfactory receptor, family 2, subfamily AE, member 1 972 15 0 1 1 1 0 0 2 2 2 0.0024 1 0.01 0.00028 0.15
SPOP

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

TP53

Figure S2.  This figure depicts the distribution of mutations and mutation types across the TP53 significant gene.

PTEN

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

CTNNB1

Figure S4.  This figure depicts the distribution of mutations and mutation types across the CTNNB1 significant gene.

TCEB3

Figure S5.  This figure depicts the distribution of mutations and mutation types across the TCEB3 significant gene.

FOXA1

Figure S6.  This figure depicts the distribution of mutations and mutation types across the FOXA1 significant gene.

BRAF

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

PIK3CA

Figure S8.  This figure depicts the distribution of mutations and mutation types across the PIK3CA significant gene.

IDH1

Figure S9.  This figure depicts the distribution of mutations and mutation types across the IDH1 significant gene.

FAM47C

Figure S10.  This figure depicts the distribution of mutations and mutation types across the FAM47C significant gene.

TP53BP1

Figure S11.  This figure depicts the distribution of mutations and mutation types across the TP53BP1 significant gene.

CNTNAP1

Figure S12.  This figure depicts the distribution of mutations and mutation types across the CNTNAP1 significant gene.

MLLT10

Figure S13.  This figure depicts the distribution of mutations and mutation types across the MLLT10 significant gene.

ZMYM3

Figure S14.  This figure depicts the distribution of mutations and mutation types across the ZMYM3 significant gene.

SMG7

Figure S15.  This figure depicts the distribution of mutations and mutation types across the SMG7 significant gene.

EDC4

Figure S16.  This figure depicts the distribution of mutations and mutation types across the EDC4 significant gene.

ZNF709

Figure S17.  This figure depicts the distribution of mutations and mutation types across the ZNF709 significant gene.

CDK12

Figure S18.  This figure depicts the distribution of mutations and mutation types across the CDK12 significant gene.

RPTN

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

TNRC18

Figure S20.  This figure depicts the distribution of mutations and mutation types across the TNRC18 significant gene.

MED15

Figure S21.  This figure depicts the distribution of mutations and mutation types across the MED15 significant gene.

NKX3-1

Figure S22.  This figure depicts the distribution of mutations and mutation types across the NKX3-1 significant gene.

KDM6A

Figure S23.  This figure depicts the distribution of mutations and mutation types across the KDM6A significant gene.

RNF31

Figure S24.  This figure depicts the distribution of mutations and mutation types across the RNF31 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

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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