Mutation Analysis (MutSig v2.0 and MutSigCV v0.9 merged result)
Skin Cutaneous Melanoma (Metastatic)
Due to issues with GAF 3.0, we strongly advise caution in the use of these results.
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1H993K3
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Mutation Analysis (MutSig v2.0 and MutSigCV v0.9 merged result). Broad Institute of MIT and Harvard. doi:10.7908/C1H993K3
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: SKCM-TM

  • Number of patients in set: 228

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:SKCM-TM.final_analysis_set.maf

  • Significantly mutated genes (q ≤ 0.1): 69

  • Mutations seen in COSMIC: 641

  • Significantly mutated genes in COSMIC territory: 42

  • Significantly mutated genesets: 2

Mutation Preprocessing

  • Read 228 MAFs of type "Broad"

  • Total number of mutations in input MAFs: 199529

  • After removing 4 mutations outside chr1-24: 199525

  • After removing 3914 noncoding mutations: 195611

Mutation Filtering

  • Number of mutations before filtering: 195611

  • After removing 2649 mutations outside gene set: 192962

  • After removing 179 mutations outside category set: 192783

  • After removing 7 "impossible" mutations in

  • gene-patient-category bins of zero coverage: 189948

Results
Breakdown of Mutations by Type

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

type count
Frame_Shift_Del 961
Frame_Shift_Ins 282
In_Frame_Del 413
In_Frame_Ins 57
Missense_Mutation 117592
Nonsense_Mutation 7173
Nonstop_Mutation 49
Silent 64333
Splice_Site 1861
Translation_Start_Site 62
Total 192783
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
(C/T)p*C->T 88967 1812910184 0.000049 49 2.5 1.6
(A/G)p*C->T 9833 1521271502 6.5e-06 6.5 0.33 1.9
A->G 5085 3220290978 1.6e-06 1.6 0.081 2.3
transver 13754 6554472664 2.1e-06 2.1 0.11 5
indel+null 10648 6554472664 1.6e-06 1.6 0.083 NaN
double_null 159 6554472664 2.4e-08 0.024 0.0012 NaN
Total 128446 6554472664 2e-05 20 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: SKCM-TM.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: (C/T)p*C->T

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

  • n3 = number of nonsilent mutations of type: A->G

  • n4 = number of nonsilent mutations of type: transver

  • 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: 69. 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 C15orf23 chromosome 15 open reading frame 23 232193 15 14 7 4 15 0 0 0 0 0 0 1 0 0.0059 0 0
2 POLDIP2 polymerase (DNA-directed), delta interacting protein 2 184098 8 8 3 0 0 0 0 0 8 0 0 1 0 0.69 0 0
3 NUDT11 nudix (nucleoside diphosphate linked moiety X)-type motif 11 79804 8 8 1 0 0 0 0 0 8 0 0 1 0 1 0 0
4 CDKN2A cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4) 209713 34 34 16 1 10 0 0 2 22 0 6e-05 0 0 8.3e-15 0 0
5 NRAS neuroblastoma RAS viral (v-ras) oncogene homolog 133556 67 67 9 1 2 1 23 41 0 0 0 0 0 0 0 0
6 BRAF v-raf murine sarcoma viral oncogene homolog B1 505506 123 117 17 3 13 1 5 103 1 0 0 0 0 1e-15 0 0
7 OXA1L oxidase (cytochrome c) assembly 1-like 347630 7 7 3 3 7 0 0 0 0 0 0 1 0 0.56 0 0
8 TTN titin 23403499 1051 177 965 371 810 69 33 97 33 9 0 1 0 0.26 0 0
9 UGT2B15 UDP glucuronosyltransferase 2 family, polypeptide B15 692010 25 21 24 13 14 2 1 2 6 0 0 0.7 0 0.067 0 0
10 TP53 tumor protein p53 276551 39 35 33 1 17 0 4 4 14 0 3.2e-06 0.014 4.2e-06 1.4e-13 0 0
11 STK19 serine/threonine kinase 19 246849 13 11 8 0 11 1 0 1 0 0 2e-07 0.94 0 1 0 0
12 PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 257977 18 18 16 0 1 0 3 3 11 0 0.064 0.67 0.13 7.1e-15 3.4e-14 5e-11
13 DSG1 desmoglein 1 725270 56 39 49 10 45 2 0 3 6 0 0.032 0.52 0.048 4.6e-09 5.1e-09 7.1e-06
14 PPP6C protein phosphatase 6, catalytic subunit 228898 19 18 14 2 13 0 0 2 4 0 0.062 0.3 0.11 7e-09 1.6e-08 0.000021
15 AOAH acyloxyacyl hydrolase (neutrophil) 439824 22 21 20 9 12 0 0 5 5 0 0.005 0.12 0.0081 3.1e-06 4.6e-07 0.00055
16 RAC1 ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) 140096 17 17 8 1 15 0 0 2 0 0 0.000055 0.13 0.000017 0.0016 5e-07 0.00056
17 OR51S1 olfactory receptor, family 51, subfamily S, member 1 221261 30 27 21 8 23 3 0 2 2 0 0.0031 0.97 0.0089 8e-06 1.2e-06 0.0013
18 IDH1 isocitrate dehydrogenase 1 (NADP+), soluble 287241 12 12 4 1 10 0 0 2 0 0 4e-07 0.97 3.4e-06 0.029 1.7e-06 0.0017
19 IL32 interleukin 32 113333 9 9 6 3 2 1 0 1 5 0 0.0091 0.87 0.025 6.7e-06 2.8e-06 0.0027
20 PPIAL4G peptidylprolyl isomerase A (cyclophilin A)-like 4G 113772 12 12 9 7 7 0 0 3 2 0 0.07 0.98 0.13 1.6e-06 3.5e-06 0.0031
21 THEMIS thymocyte selection associated 425802 33 27 25 14 27 1 1 2 2 0 0.00013 0.54 0.00034 0.0011 5.9e-06 0.005
22 LRTM1 leucine-rich repeats and transmembrane domains 1 237820 28 23 27 14 17 4 2 3 2 0 0.041 0.96 0.11 0.000012 0.000018 0.015
23 TCEB3C transcription elongation factor B polypeptide 3C (elongin A3) 230241 31 26 23 9 23 2 0 2 4 0 0.05 0.99 0.1 0.000014 0.000021 0.016
24 GPR141 G protein-coupled receptor 141 210024 14 14 10 5 11 0 1 1 1 0 0.18 0.093 0.091 0.000021 0.000028 0.021
25 CHGB chromogranin B (secretogranin 1) 426128 28 25 28 9 23 1 0 0 4 0 0.074 0.044 0.0093 0.00021 0.000028 0.021
26 ELF5 E74-like factor 5 (ets domain transcription factor) 185836 6 6 6 2 4 0 0 0 2 0 0.000034 0.1 0.000046 0.051 0.000032 0.022
27 NMNAT3 nicotinamide nucleotide adenylyltransferase 3 148123 8 8 8 8 3 1 0 1 3 0 0.0039 0.0008 0.0012 0.0027 0.000046 0.031
28 C6orf223 chromosome 6 open reading frame 223 131963 6 6 3 0 1 0 0 0 5 0 0.0029 0.024 0.0016 0.0022 0.000049 0.031
29 EIF2B1 eukaryotic translation initiation factor 2B, subunit 1 alpha, 26kDa 216804 9 9 3 3 1 0 0 1 7 0 0.36 0.96 1 4.2e-06 0.000056 0.035
30 DNAH7 dynein, axonemal, heavy chain 7 2773342 164 83 150 60 122 11 6 3 19 3 0.13 0.96 0.22 2e-05 0.000058 0.035
31 COPG2 coatomer protein complex, subunit gamma 2 280429 11 9 8 1 1 1 0 4 5 0 0.014 0.0077 0.0029 0.0017 0.000066 0.038
32 RAPGEF5 Rap guanine nucleotide exchange factor (GEF) 5 370075 13 12 11 3 10 1 0 0 2 0 8e-06 0.69 0.000036 0.16 0.000076 0.043
33 C1QTNF9 C1q and tumor necrosis factor related protein 9 188774 14 14 12 3 10 1 0 2 1 0 0.057 0.94 0.11 0.000061 0.000085 0.046
34 MS4A2 membrane-spanning 4-domains, subfamily A, member 2 (Fc fragment of IgE, high affinity I, receptor for; beta polypeptide) 180888 10 10 10 1 8 0 0 0 2 0 0.37 0.83 0.59 0.000012 0.000089 0.047
35 SCN5A sodium channel, voltage-gated, type V, alpha subunit 1272711 83 57 80 43 59 8 4 4 8 0 0.18 0.8 0.33 0.000022 0.000091 0.047
C15orf23

Figure S1.  This figure depicts the distribution of mutations and mutation types across the C15orf23 significant gene.

POLDIP2

Figure S2.  This figure depicts the distribution of mutations and mutation types across the POLDIP2 significant gene.

CDKN2A

Figure S3.  This figure depicts the distribution of mutations and mutation types across the CDKN2A significant gene.

NRAS

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

BRAF

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

OXA1L

Figure S6.  This figure depicts the distribution of mutations and mutation types across the OXA1L significant gene.

TTN

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

UGT2B15

Figure S8.  This figure depicts the distribution of mutations and mutation types across the UGT2B15 significant gene.

TP53

Figure S9.  This figure depicts the distribution of mutations and mutation types across the TP53 significant gene.

STK19

Figure S10.  This figure depicts the distribution of mutations and mutation types across the STK19 significant gene.

PTEN

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

DSG1

Figure S12.  This figure depicts the distribution of mutations and mutation types across the DSG1 significant gene.

PPP6C

Figure S13.  This figure depicts the distribution of mutations and mutation types across the PPP6C significant gene.

RAC1

Figure S14.  This figure depicts the distribution of mutations and mutation types across the RAC1 significant gene.

OR51S1

Figure S15.  This figure depicts the distribution of mutations and mutation types across the OR51S1 significant gene.

IDH1

Figure S16.  This figure depicts the distribution of mutations and mutation types across the IDH1 significant gene.

IL32

Figure S17.  This figure depicts the distribution of mutations and mutation types across the IL32 significant gene.

PPIAL4G

Figure S18.  This figure depicts the distribution of mutations and mutation types across the PPIAL4G significant gene.

THEMIS

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

LRTM1

Figure S20.  This figure depicts the distribution of mutations and mutation types across the LRTM1 significant gene.

TCEB3C

Figure S21.  This figure depicts the distribution of mutations and mutation types across the TCEB3C significant gene.

GPR141

Figure S22.  This figure depicts the distribution of mutations and mutation types across the GPR141 significant gene.

CHGB

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

ELF5

Figure S24.  This figure depicts the distribution of mutations and mutation types across the ELF5 significant gene.

NMNAT3

Figure S25.  This figure depicts the distribution of mutations and mutation types across the NMNAT3 significant gene.

C6orf223

Figure S26.  This figure depicts the distribution of mutations and mutation types across the C6orf223 significant gene.

EIF2B1

Figure S27.  This figure depicts the distribution of mutations and mutation types across the EIF2B1 significant gene.

DNAH7

Figure S28.  This figure depicts the distribution of mutations and mutation types across the DNAH7 significant gene.

COPG2

Figure S29.  This figure depicts the distribution of mutations and mutation types across the COPG2 significant gene.

RAPGEF5

Figure S30.  This figure depicts the distribution of mutations and mutation types across the RAPGEF5 significant gene.

C1QTNF9

Figure S31.  This figure depicts the distribution of mutations and mutation types across the C1QTNF9 significant gene.

MS4A2

Figure S32.  This figure depicts the distribution of mutations and mutation types across the MS4A2 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: 42. Number of genes displayed: 10

rank gene description n cos n_cos N_cos cos_ev p q
1 STK19 serine/threonine kinase 19 13 2 6 456 12 1.9e-14 8.7e-11
2 IDH1 isocitrate dehydrogenase 1 (NADP+), soluble 12 5 10 1140 14920 4.5e-14 1e-10
3 NRAS neuroblastoma RAS viral (v-ras) oncogene homolog 67 33 65 7524 80983 2.6e-13 4e-10
4 BRAF v-raf murine sarcoma viral oncogene homolog B1 123 89 116 20292 1494071 5.5e-13 5.3e-10
5 TP53 tumor protein p53 39 356 37 81168 3489 6.7e-13 5.3e-10
6 CDKN2A cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4) 34 332 34 75696 1296 7e-13 5.3e-10
7 EPHA6 EPH receptor A6 60 8 5 1824 5 4.7e-10 3e-07
8 EPHA7 EPH receptor A7 42 13 5 2964 5 5.2e-09 3e-06
9 PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 18 767 18 174876 374 2.6e-08 0.000013
10 NF1 neurofibromin 1 (neurofibromatosis, von Recklinghausen disease, Watson disease) 40 285 11 64980 25 1.1e-07 0.000048

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: 2. 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 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 CCND1(1), CDK4(5), CDKN1A(4), CDKN1B(1), CDKN2A(34), CFL1(1), E2F1(5), E2F2(4), MDM2(3), NXT1(2), PRB1(29), TP53(39) 2837450 128 80 100 16 62 3 6 17 40 0 2.2e-09 2.7e-06 0.0017
2 ST_G_ALPHA_S_PATHWAY The G-alpha-s protein activates adenylyl cyclases, which catalyze cAMP formation. ASAH1, BF, BFAR, BRAF, CAMP, CREB1, CREB3, CREB5, EPAC, GAS, GRF2, MAPK1, RAF1, SNX13, SRC, TERF2IP 12 BRAF(123), CAMP(1), CREB3(1), CREB5(9), MAPK1(4), RAF1(8), SNX13(1), SRC(1), TERF2IP(1) 3751054 149 130 43 30 28 4 6 107 4 0 0.02 0.00016 0.048
3 SA_REG_CASCADE_OF_CYCLIN_EXPR Expression of cyclins regulates progression through the cell cycle by activating cyclin-dependent kinases. CCNA1, CCNA2, CCND1, CCNE1, CCNE2, CDK2, CDK4, CDKN1B, CDKN2A, E2F1, E2F2, E2F4, PRB1 13 CCNA1(13), CCND1(1), CCNE1(4), CCNE2(12), CDK4(5), CDKN1B(1), CDKN2A(34), E2F1(5), E2F2(4), E2F4(1), PRB1(29) 3023744 109 77 83 17 61 0 4 19 25 0 2.4e-06 0.024 1
4 HSA00472_D_ARGININE_AND_D_ORNITHINE_METABOLISM Genes involved in D-arginine and D-ornithine metabolism DAO 1 DAO(10) 240807 10 10 10 2 7 1 1 1 0 0 0.12 0.11 1
5 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 HDAC1(1), MYC(5), SP1(5), SP3(1), TP53(39), WT1(5) 2379389 56 44 50 8 26 2 7 6 15 0 0.00078 0.24 1
6 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(12), CDKN2A(34), E2F1(5), MDM2(3), MYC(5), PIK3CA(8), PIK3R1(3), POLR1A(11), POLR1B(8), POLR1C(1), RAC1(17), RB1(8), TBX2(6), TP53(39), TWIST1(1) 6784714 161 96 127 24 84 8 6 17 43 3 8.2e-10 0.46 1
7 HSA00627_1,4_DICHLOROBENZENE_DEGRADATION Genes involved in 1,4-dichlorobenzene degradation CMBL 1 CMBL(4) 172740 4 4 4 1 4 0 0 0 0 0 0.48 0.47 1
8 FOSBPATHWAY FOSB gene expression and drug abuse CDK5, FOSB, GRIA2, JUND, PPP1R1B 5 CDK5(4), FOSB(5), GRIA2(34), JUND(1), PPP1R1B(2) 1226014 46 39 43 15 28 3 2 6 7 0 0.069 0.83 1
9 HSA00401_NOVOBIOCIN_BIOSYNTHESIS Genes involved in novobiocin biosynthesis GOT1, GOT2, TAT 3 GOT1(6), GOT2(5), TAT(17) 883649 28 18 27 7 21 2 2 1 2 0 0.015 0.88 1
10 SLRPPATHWAY Small leucine-rich proteoglycans (SLRPs) interact with and reorganize collagen fibers in the extracellular matrix. BGN, DCN, DSPG3, FMOD, KERA, LUM 5 BGN(6), DCN(17), FMOD(4), KERA(14), LUM(11) 1178331 52 38 48 16 41 4 3 1 3 0 0.0018 0.89 1
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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