Mutation Analysis (MutSig v2.0 and MutSigCV v0.9 merged result)
Prostate Adenocarcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C16T0K3K
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Mutation Analysis (MutSig v2.0 and MutSigCV v0.9 merged result). Broad Institute of MIT and Harvard. doi:10.7908/C16T0K3K
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 v2.0 and MutSigCV v0.9 merged result was used to generate the results found in this report.

  • Working with individual set: PRAD-TP

  • Number of patients in set: 251

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

  • Significantly mutated genes (q ≤ 0.1): 7

  • Mutations seen in COSMIC: 92

  • Significantly mutated genes in COSMIC territory: 7

  • Significantly mutated genesets: 26

Mutation Preprocessing

  • Read 251 MAFs of type "Broad"

  • Total number of mutations in input MAFs: 17449

  • After removing 155 mutations outside chr1-24: 17294

  • After removing 1347 blacklisted mutations: 15947

  • After removing 277 noncoding mutations: 15670

Mutation Filtering

  • Number of mutations before filtering: 15670

  • After removing 636 mutations outside gene set: 15034

  • After removing 12 mutations outside category set: 15022

Results
Breakdown of Mutations by Type

Table 1.  Get Full Table Table representing breakdown of mutations by type.

type count
Frame_Shift_Del 579
Frame_Shift_Ins 166
In_Frame_Del 165
In_Frame_Ins 17
Missense_Mutation 9127
Nonsense_Mutation 541
Nonstop_Mutation 7
Silent 3890
Splice_Site 530
Total 15022
Breakdown of Mutation Rates by Category Type

Table 2.  Get Full Table A breakdown of mutation rates per category discovered for this individual set.

category n N rate rate_per_mb relative_rate exp_ns_s_ratio
*CpG->(A/T) 3535 416115424 8.5e-06 8.5 5.7 2.1
*Cp(A/C/T)->(A/T) 3000 3377759523 8.9e-07 0.89 0.59 2.7
A->(C/G) 1501 3631611686 4.1e-07 0.41 0.28 3.4
flip 1091 7425486633 1.5e-07 0.15 0.098 5.3
indel+null 1995 7425486633 2.7e-07 0.27 0.18 NaN
double_null 10 7425486633 1.3e-09 0.0013 0.0009 NaN
Total 11132 7425486633 1.5e-06 1.5 1 3.5
Target Coverage for Each Individual

The x axis represents the samples. The y axis represents the exons, one row per exon, and they are sorted by average coverage across samples. For exons with exactly the same average coverage, they are sorted next by the %GC of the exon. (The secondary sort is especially useful for the zero-coverage exons at the bottom).

Figure 1. 

Distribution of Mutation Counts, Coverage, and Mutation Rates Across Samples

Figure 2.  Patients counts and rates file used to generate this plot: PRAD-TP.patients.counts_and_rates.txt

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 3.  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 4.  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 5.  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:

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

  • n = 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

  • n1 = number of nonsilent mutations of type: *CpG->(A/T)

  • n2 = number of nonsilent mutations of type: *Cp(A/C/T)->(A/T)

  • n3 = number of nonsilent mutations of type: A->(C/G)

  • n4 = number of nonsilent mutations of type: flip

  • n5 = number of nonsilent mutations of type: indel+null

  • n6 = number of nonsilent mutations of type: double_null

  • p_cons = p-value for enrichment of mutations at evolutionarily most-conserved sites in gene

  • p_joint = p-value for clustering + conservation

  • p = p-value (overall)

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

Table 3.  Get Full Table A Ranked List of Significantly Mutated Genes. Number of significant genes found: 7. 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 description N n npat nsite nsil n1 n2 n3 n4 n5 n6 p_clust p_cons p_joint p_cv p q
1 CTNNB1 catenin (cadherin-associated protein), beta 1, 88kDa 601492 9 9 7 0 0 2 5 2 0 0 1.4e-06 0.026 0 0.0075 0 0
2 SPOP speckle-type POZ protein 291266 24 24 10 0 0 2 16 5 1 0 0 0.61 0 1.2e-14 0 0
3 PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 289090 13 13 13 0 0 2 1 0 10 0 0.2 0.92 0.35 1e-14 1.2e-13 7.5e-10
4 PCDHAC2 protocadherin alpha subfamily C, 2 740909 27 26 27 19 20 6 0 1 0 0 NaN NaN NaN 1e-12 1e-12 4.6e-09
5 FOXA1 forkhead box A1 269759 11 11 9 2 1 0 4 2 3 1 0.000027 0.064 6.4e-06 2.9e-07 5.3e-11 1.9e-07
6 TP53 tumor protein p53 310636 20 20 17 1 8 2 5 0 5 0 0.000093 0.00047 0.000044 3.2e-06 3.3e-09 1e-05
7 TMEM216 transmembrane protein 216 80630 4 4 1 0 0 0 0 0 4 0 0.0051 1 0.014 1.3e-06 3.4e-07 0.00088
8 LMOD2 leiomodin 2 (cardiac) 261451 3 3 1 1 0 0 0 0 3 0 0.00017 0.3 0.0011 0.0076 0.00011 0.25
9 IDH1 isocitrate dehydrogenase 1 (NADP+), soluble 317204 4 4 2 0 3 0 0 1 0 0 4e-05 0.58 0.000076 0.21 0.00019 0.39
10 CDKN1B cyclin-dependent kinase inhibitor 1B (p27, Kip1) 151716 4 4 4 0 0 0 0 0 4 0 0.31 0.37 0.4 0.000062 0.00029 0.52
11 MED12 mediator complex subunit 12 1403740 5 5 4 0 0 3 0 2 0 0 0.000052 0.1 0.000054 0.89 0.00053 0.87
12 SLC10A2 solute carrier family 10 (sodium/bile acid cotransporter family), member 2 267554 5 5 5 0 1 3 0 0 1 0 0.51 0.72 0.89 0.000067 0.00064 0.96
13 BRAF v-raf murine sarcoma viral oncogene homolog B1 559308 6 6 5 0 0 1 2 2 1 0 0.06 0.017 0.013 0.0094 0.0013 1
14 ITGA2B integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41) 694879 3 3 3 1 1 1 0 0 1 0 0.12 0.00014 0.00024 0.57 0.0014 1
15 SMG7 Smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans) 869240 4 4 3 0 0 0 1 1 2 0 0.06 0.0035 0.0023 0.092 0.002 1
16 RBPMS2 RNA binding protein with multiple splicing 2 129790 3 3 3 1 0 0 0 0 3 0 0.024 1 0.43 0.00053 0.0021 1
17 SETD5 SET domain containing 5 1014560 4 1 4 2 0 3 0 1 0 0 0.0002 0.45 0.00047 0.96 0.0039 1
18 LCE1F late cornified envelope 1F 90360 3 2 3 0 1 1 0 1 0 0 0.01 0.57 0.025 0.021 0.0045 1
19 LCE2D late cornified envelope 2D 84587 3 3 3 0 1 1 0 0 1 0 0.84 0.71 1 0.0006 0.0051 1
20 IL10RA interleukin 10 receptor, alpha 425072 3 3 3 0 1 0 1 0 1 0 0.023 0.0026 0.0022 0.3 0.0057 1
21 ETV3 ets variant gene 3 110772 3 3 3 0 0 0 1 0 2 0 0.02 0.49 0.05 0.014 0.0057 1
22 RYBP RING1 and YY1 binding protein 164700 4 4 4 0 0 1 2 0 1 0 0.46 0.23 0.45 0.0017 0.0062 1
23 NKX3-1 NK3 homeobox 1 138283 4 4 4 0 0 0 3 0 1 0 0.23 0.029 0.17 0.0048 0.0065 1
24 HBG1 hemoglobin, gamma A 59723 2 2 2 0 0 1 0 0 1 0 NaN NaN NaN 0.0074 0.0074 1
25 GPS2 G protein pathway suppressor 2 240753 4 4 4 2 0 1 1 1 1 0 0.24 0.026 0.054 0.024 0.0097 1
26 C1QTNF9 C1q and tumor necrosis factor related protein 9 217157 2 2 2 0 1 1 0 0 0 0 0.013 0.059 0.0047 0.27 0.0098 1
27 FAM53B family with sequence similarity 53, member B 283735 2 2 2 0 1 0 0 1 0 0 0.52 0.0022 0.0033 0.43 0.011 1
28 ZMYM3 zinc finger, MYM-type 3 788350 8 7 8 0 0 1 1 1 5 0 0.63 0.48 0.81 0.0019 0.011 1
29 RYR1 ryanodine receptor 1 (skeletal) 3474949 7 7 7 3 5 1 0 0 1 0 0.00081 0.92 0.0021 0.98 0.015 1
30 OR2AE1 olfactory receptor, family 2, subfamily AE, member 1 244976 2 2 2 1 1 0 0 0 1 0 0.17 0.018 0.046 0.049 0.016 1
31 OR52D1 olfactory receptor, family 52, subfamily D, member 1 241152 3 3 3 1 0 1 1 0 1 0 0.012 0.63 0.082 0.028 0.016 1
32 WDR69 WD repeat domain 69 324778 2 2 2 0 0 1 1 0 0 0 0.051 0.0019 0.0057 0.4 0.016 1
33 ARID1B AT rich interactive domain 1B (SWI1-like) 1347281 5 3 5 1 2 2 0 0 1 0 0.0013 0.61 0.0029 1 0.02 1
34 C1orf95 chromosome 1 open reading frame 95 82811 2 2 2 0 0 0 0 0 2 0 0.71 0.5 1 0.003 0.02 1
35 MT4 metallothionein 4 50451 1 1 1 0 0 0 0 0 1 0 NaN NaN NaN 0.021 0.021 1
CTNNB1

Figure S1.  This figure depicts the distribution of mutations and mutation types across the CTNNB1 significant gene.

SPOP

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

PTEN

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

PCDHAC2

Figure S4.  This figure depicts the distribution of mutations and mutation types across the PCDHAC2 significant gene.

FOXA1

Figure S5.  This figure depicts the distribution of mutations and mutation types across the FOXA1 significant gene.

TP53

Figure S6.  This figure depicts the distribution of mutations and mutation types across the TP53 significant gene.

TMEM216

Figure S7.  This figure depicts the distribution of mutations and mutation types across the TMEM216 significant gene.

COSMIC analyses

In this analysis, COSMIC is used as a filter to increase power by restricting the territory of each gene. Cosmic version: v48.

Table 4.  Get Full Table Significantly mutated genes (COSMIC territory only). To access the database please go to: COSMIC. Number of significant genes found: 7. Number of genes displayed: 10

rank gene description n cos n_cos N_cos cos_ev p q
1 CTNNB1 catenin (cadherin-associated protein), beta 1, 88kDa 9 138 8 34638 3282 3e-13 8e-10
2 PIK3CA phosphoinositide-3-kinase, catalytic, alpha polypeptide 9 220 9 55220 1953 4.6e-13 8e-10
3 IDH1 isocitrate dehydrogenase 1 (NADP+), soluble 4 5 4 1255 5968 5.3e-13 8e-10
4 TP53 tumor protein p53 20 356 20 89356 6877 7.1e-13 8e-10
5 PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 13 767 13 192517 188 1.3e-12 1.2e-09
6 BRAF v-raf murine sarcoma viral oncogene homolog B1 6 89 4 22339 210 5.1e-08 0.000038
7 SMAD4 SMAD family member 4 4 159 4 39909 19 5.1e-07 0.00033
8 ATAD1 ATPase family, AAA domain containing 1 1 1 1 251 1 0.00038 0.13
9 BRE brain and reproductive organ-expressed (TNFRSF1A modulator) 2 1 1 251 1 0.00038 0.13
10 KCNH1 potassium voltage-gated channel, subfamily H (eag-related), member 1 1 1 1 251 1 0.00038 0.13

Note:

n - number of (nonsilent) mutations in this gene across the individual set.

cos = number of unique mutated sites in this gene in COSMIC

n_cos = overlap between n and cos.

N_cos = number of individuals times cos.

cos_ev = total evidence: number of reports in COSMIC for mutations seen in this gene.

p = p-value for seeing the observed amount of overlap in this gene)

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

Geneset Analyses

Table 5.  Get Full Table A Ranked List of Significantly Mutated Genesets. (Source: MSigDB GSEA Cannonical Pathway Set).Number of significant genesets found: 26. Number of genesets displayed: 10

rank geneset description genes N_genes mut_tally N n npat nsite nsil n1 n2 n3 n4 n5 n6 p_ns_s p q
1 TERTPATHWAY hTERC, the RNA subunit of telomerase, and hTERT, the catalytic protein subunit, are required for telomerase activity and are overexpressed in many cancers. HDAC1, MAX, MYC, SP1, SP3, TP53, WT1, ZNF42 7 SP1(1), SP3(2), TP53(20) 2651631 23 22 20 1 8 3 5 1 6 0 0.012 6.5e-12 4e-09
2 P53HYPOXIAPATHWAY Hypoxia induces p53 accumulation and consequent apoptosis with p53-mediated cell cycle arrest, which is present under conditions of DNA damage. ABCB1, AKT1, ATM, BAX, CDKN1A, CPB2, CSNK1A1, CSNK1D, FHL2, GADD45A, HIC1, HIF1A, HSPA1A, HSPCA, IGFBP3, MAPK8, MDM2, NFKBIB, NQO1, TP53 19 ABCB1(4), AKT1(1), ATM(12), CDKN1A(2), CPB2(1), HIC1(1), HSPA1A(1), MDM2(1), NQO1(1), TP53(20) 7808812 44 38 41 2 15 9 8 4 8 0 0.00094 1.4e-11 4e-09
3 SA_G1_AND_S_PHASES Cdk2, 4, and 6 bind cyclin D in G1, while cdk2/cyclin E promotes the G1/S transition. ARF1, ARF3, CCND1, CDK2, CDK4, CDKN1A, CDKN1B, CDKN2A, CFL1, E2F1, E2F2, MDM2, NXT1, PRB1, TP53 15 CDK4(1), CDKN1A(2), CDKN1B(4), CDKN2A(1), CFL1(1), MDM2(1), PRB1(1), TP53(20) 3197612 31 29 28 3 11 3 5 0 12 0 0.063 2e-11 4e-09
4 PLK3PATHWAY Active Plk3 phosphorylates CDC25c, blocking the G2/M transition, and phosphorylates p53 to induce apoptosis. ATM, ATR, CDC25C, CHEK1, CHEK2, CNK, TP53, YWHAH 7 ATM(12), CHEK2(1), TP53(20) 5977834 33 30 30 2 8 8 7 4 6 0 0.022 4.1e-11 6.4e-09
5 P53PATHWAY p53 induces cell cycle arrest or apoptosis under conditions of DNA damage. APAF1, ATM, BAX, BCL2, CCND1, CCNE1, CDK2, CDK4, CDKN1A, E2F1, GADD45A, MDM2, PCNA, RB1, TIMP3, TP53 16 APAF1(1), ATM(12), CDK4(1), CDKN1A(2), MDM2(1), RB1(3), TP53(20) 6785968 40 34 37 3 11 9 8 4 7 1 0.0075 3.5e-10 4.4e-08
6 CHEMICALPATHWAY DNA damage promotes Bid cleavage, which stimulates mitochondrial cytochrome c release and consequent caspase activation, resulting in apoptosis. ADPRT, AKT1, APAF1, ATM, BAD, BAX, BCL2, BCL2L1, BID, CASP3, CASP6, CASP7, CASP9, CYCS, EIF2S1, PRKCA, PRKCB1, PTK2, PXN, STAT1, TLN1, TP53 20 AKT1(1), APAF1(1), ATM(12), BAD(1), CASP7(1), PRKCA(1), PTK2(2), PXN(1), STAT1(1), TLN1(2), TP53(20) 10294761 43 40 40 1 10 13 8 5 7 0 0.00016 8.4e-10 8.7e-08
7 RBPATHWAY The ATM protein kinase recognizes DNA damage and blocks cell cycle progression by phosphorylating chk1 and p53, which normally inhibits Rb to allow G1/S transitions. ATM, CDC2, CDC25A, CDC25B, CDC25C, CDK2, CDK4, CHEK1, MYT1, RB1, TP53, WEE1, YWHAH 12 ATM(12), CDC25A(1), CDC25B(1), CDK4(1), MYT1(1), RB1(3), TP53(20) 6574080 39 35 36 4 11 8 8 5 6 1 0.026 9.9e-10 8.8e-08
8 ARFPATHWAY Cyclin-dependent kinase inhibitor 2A is a tumor suppressor that induces G1 arrest and can activate the p53 pathway, leading to G2/M arrest. ABL1, CDKN2A, E2F1, MDM2, MYC, PIK3CA, PIK3R1, POLR1A, POLR1B, POLR1C, POLR1D, RAC1, RB1, TBX2, TP53, TWIST1 16 ABL1(3), CDKN2A(1), MDM2(1), PIK3CA(9), PIK3R1(2), POLR1A(4), POLR1B(1), POLR1C(2), RAC1(1), RB1(3), TP53(20) 7626178 47 37 44 3 14 9 11 4 8 1 0.00086 2.2e-09 1.7e-07
9 RNAPATHWAY dsRNA-activated protein kinase phosphorylates elF2a, which generally inhibits translation, and activates NF-kB to provoke inflammation. CHUK, DNAJC3, EIF2S1, EIF2S2, MAP3K14, NFKB1, NFKBIA, PRKR, RELA, TP53 9 NFKB1(2), RELA(1), TP53(20) 3678521 23 22 20 1 8 5 5 0 5 0 0.016 4e-09 2.7e-07
10 PTENPATHWAY PTEN suppresses AKT-induced cell proliferation and antagonizes the action of PI3K. AKT1, BCAR1, CDKN1B, FOXO3A, GRB2, ILK, ITGB1, MAPK1, MAPK3, PDK2, PDPK1, PIK3CA, PIK3R1, PTEN, PTK2, SHC1, SOS1, TNFSF6 16 AKT1(1), BCAR1(1), CDKN1B(4), MAPK1(1), PDPK1(1), PIK3CA(9), PIK3R1(2), PTEN(13), PTK2(2), SHC1(2), SOS1(1) 7236178 37 33 37 3 8 8 4 2 15 0 0.05 4.9e-08 3e-06
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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