Mutation Analysis (MutSig v1.5)
Adrenocortical Carcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1PZ57MS
Maintained by David Heiman (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Mutation Analysis (MutSig v1.5). Broad Institute of MIT and Harvard. doi:10.7908/C1PZ57MS
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 v1.5 was used to generate the results found in this report.

  • Working with individual set: ACC-TP

  • Number of patients in set: 90

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:ACC-TP.final_analysis_set.maf

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

  • Significantly mutated genes (q ≤ 0.1): 182

  • Mutations seen in COSMIC: 60

  • Significantly mutated genes in COSMIC territory: 3

  • Significantly mutated genesets: 20

  • Significantly mutated genesets: (excluding sig. mutated genes):0

Mutation Preprocessing

  • Read 90 MAFs of type "Baylor-Illumina"

  • Total number of mutations in input MAFs: 20166

  • After removing 1224 blacklisted mutations: 18942

  • After removing 237 noncoding mutations: 18705

  • After collapsing adjacent/redundant mutations: 18696

Mutation Filtering

  • Number of mutations before filtering: 18696

  • After removing 1079 mutations outside gene set: 17617

  • After removing 65 mutations outside category set: 17552

  • After removing 1 "impossible" mutations in

  • gene-patient-category bins of zero coverage: 16407

Results
Breakdown of Mutations by Type

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

type count
Frame_Shift_Del 506
Frame_Shift_Ins 180
In_Frame_Del 263
In_Frame_Ins 87
Missense_Mutation 10056
Nonsense_Mutation 567
Silent 5668
Splice_Site 224
Translation_Start_Site 1
Total 17552
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->T 1998 159474080 0.000013 13 3 2.1
*CpG->(G/A) 690 159474080 4.3e-06 4.3 1 2.7
*Cp(A/C/T)->mut 4860 1285484037 3.8e-06 3.8 0.9 3.3
A->mut 2509 1372092527 1.8e-06 1.8 0.43 3.9
indel+null 1765 2817050644 6.3e-07 0.63 0.15 NaN
double_null 62 2817050644 2.2e-08 0.022 0.0052 NaN
Total 11884 2817050644 4.2e-06 4.2 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). If the figure is unpopulated, then full coverage is assumed (e.g. MutSig CV doesn't use WIGs and assumes full coverage).

Figure 1. 

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

Figure 2.  Patients counts and rates file used to generate this plot: ACC-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->T

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

  • n3 = number of nonsilent mutations of type: *Cp(A/C/T)->mut

  • n4 = number of nonsilent mutations of type: A->mut

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

  • n6 = number of nonsilent mutations of type: double_null

  • p_ns_s = p-value for the observed nonsilent/silent ratio being elevated in this gene

  • 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: 182. 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_ns_s p q
1 ZFPM1 zinc finger protein, multitype 1 133160 91 47 5 0 1 0 4 0 65 21 0.16 <1.00e-15 <4.58e-12
2 ERCC2 excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D) 196253 19 19 1 0 19 0 0 0 0 0 0.0012 1.89e-15 4.58e-12
3 LACTB lactamase, beta 116298 27 27 3 0 0 0 1 25 1 0 0.0012 2.00e-15 4.58e-12
4 PANK2 pantothenate kinase 2 (Hallervorden-Spatz syndrome) 122370 15 15 2 0 0 0 15 0 0 0 0.024 2.00e-15 4.58e-12
5 MAL2 mal, T-cell differentiation protein 2 37122 23 22 2 1 0 0 1 0 22 0 0.95 2.11e-15 4.58e-12
6 TOR3A torsin family 3, member A 96841 25 25 1 0 0 0 0 25 0 0 0.03 2.33e-15 4.58e-12
7 USP42 ubiquitin specific peptidase 42 231118 26 25 4 2 1 20 0 5 0 0 0.0058 2.44e-15 4.58e-12
8 SYT8 synaptotagmin VIII 99744 14 14 3 0 14 0 0 0 0 0 0.0034 2.89e-15 4.58e-12
9 ASPDH aspartate dehydrogenase domain containing 74718 19 19 2 0 0 0 1 18 0 0 0.0084 3.11e-15 4.58e-12
10 IRX3 iroquois homeobox 3 75820 21 21 1 0 0 0 0 21 0 0 0.056 3.66e-15 4.58e-12
11 TP53 tumor protein p53 117148 18 17 18 1 2 0 4 1 10 1 0.14 4.00e-15 4.58e-12
12 KCNK17 potassium channel, subfamily K, member 17 88332 19 19 2 0 0 0 1 18 0 0 0.044 4.11e-15 4.58e-12
13 ZNF598 zinc finger protein 598 183308 20 19 5 2 0 1 3 16 0 0 0.23 4.33e-15 4.58e-12
14 TPO thyroid peroxidase 229899 22 21 3 0 1 0 21 0 0 0 0.001 4.44e-15 4.58e-12
15 CLDN23 claudin 23 31307 13 13 1 0 0 0 13 0 0 0 0.0052 4.44e-15 4.58e-12
16 C2orf81 chromosome 2 open reading frame 81 152558 15 14 3 0 0 0 0 15 0 0 0.029 4.55e-15 4.58e-12
17 C4orf32 chromosome 4 open reading frame 32 22500 9 9 1 0 0 0 9 0 0 0 0.19 4.66e-15 4.58e-12
18 CCDC102A coiled-coil domain containing 102A 83550 26 26 1 0 26 0 0 0 0 0 0.00033 5.22e-15 4.58e-12
19 ZNF517 zinc finger protein 517 112718 34 33 2 0 0 0 0 34 0 0 0.0076 5.66e-15 4.58e-12
20 TMEM189 transmembrane protein 189 64080 12 12 1 0 0 0 0 12 0 0 0.18 5.66e-15 4.58e-12
21 ZAR1 zygote arrest 1 31893 19 19 2 1 0 0 15 4 0 0 0.056 5.88e-15 4.58e-12
22 OPRD1 opioid receptor, delta 1 70226 26 26 1 1 0 0 26 0 0 0 0.000065 6.00e-15 4.58e-12
23 SEMA5B sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B 275306 17 16 2 0 0 0 1 16 0 0 0.043 6.11e-15 4.58e-12
24 GLTPD2 glycolipid transfer protein domain containing 2 42201 19 19 1 2 0 19 0 0 0 0 0.017 6.77e-15 4.58e-12
25 ATXN1 ataxin 1 201752 15 14 9 1 0 1 4 0 10 0 0.4 7.11e-15 4.58e-12
26 HHIPL1 HHIP-like 1 138992 13 13 1 1 0 0 0 13 0 0 0.4 7.11e-15 4.58e-12
27 BHLHE22 basic helix-loop-helix family, member e22 29589 11 10 3 0 0 0 0 10 1 0 0.46 7.22e-15 4.58e-12
28 FPGS folylpolyglutamate synthase 136084 14 14 2 0 0 0 1 13 0 0 0.086 7.33e-15 4.58e-12
29 C19orf10 chromosome 19 open reading frame 10 40771 10 10 1 0 0 10 0 0 0 0 0.017 7.77e-15 4.58e-12
30 C1orf106 chromosome 1 open reading frame 106 159139 16 16 2 0 15 0 0 1 0 0 0.0062 8.33e-15 4.58e-12
31 RGS9BP regulator of G protein signaling 9 binding protein 18934 11 11 1 0 0 11 0 0 0 0 0.0058 8.33e-15 4.58e-12
32 IDUA iduronidase, alpha-L- 116170 14 14 4 1 2 0 0 12 0 0 0.27 8.99e-15 4.58e-12
33 FAM184B family with sequence similarity 184, member B 276441 18 18 3 1 17 0 1 0 0 0 0.0074 9.10e-15 4.58e-12
34 THEM4 thioesterase superfamily member 4 57800 14 14 1 0 0 0 0 14 0 0 0.032 9.21e-15 4.58e-12
35 RINL Ras and Rab interactor-like 102936 19 19 1 0 0 0 19 0 0 0 0.003 9.33e-15 4.58e-12
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: 3. 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 14 138 14 12420 6397 0 0
2 TP53 tumor protein p53 18 356 17 32040 1628 0 0
3 MEN1 multiple endocrine neoplasia I 8 208 5 18720 25 2.4e-08 0.000036
4 ABCA12 ATP-binding cassette, sub-family A (ABC1), member 12 3 1 1 90 1 0.00038 0.22
5 ANKRD30A ankyrin repeat domain 30A 6 1 1 90 1 0.00038 0.22
6 CCND2 cyclin D2 1 1 1 90 1 0.00038 0.22
7 KRTAP5-5 keratin associated protein 5-5 6 1 1 90 0 0.00038 0.22
8 LACE1 lactation elevated 1 1 1 1 90 1 0.00038 0.22
9 GRM3 glutamate receptor, metabotropic 3 3 2 1 180 1 0.00076 0.34
10 IGFBP3 insulin-like growth factor binding protein 3 1 2 1 180 1 0.00076 0.34

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: 20. 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 FOLATE_BIOSYNTHESIS ALPI, ALPL, ALPP, ALPP, ALPPL2, ALPPL2, DHFR, FPGS, GCH1, GGH, SPR 9 ALPI(1), ALPP(1), ALPPL2(8), FPGS(14), SPR(1) 921600 25 23 7 2 0 9 3 13 0 0 0.041 1.4e-13 8.4e-11
2 STILBENE_COUMARINE_AND_LIGNIN_BIOSYNTHESIS EPX, GBA3, LPO, MPO, PRDX1, PRDX2, PRDX5, PRDX6, TPO, TYR 10 EPX(1), PRDX1(1), PRDX2(2), TPO(22) 1336570 26 25 7 2 3 0 21 0 2 0 0.016 2.9e-09 8.9e-07
3 HSA00940_PHENYLPROPANOID_BIOSYNTHESIS Genes involved in phenylpropanoid biosynthesis EPX, GBA, GBA3, LPO, MPO, PRDX6, TPO 7 EPX(1), TPO(22) 1154920 23 22 4 2 2 0 21 0 0 0 0.018 3.8e-08 7.8e-06
4 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 ARF3(1), CDKN2A(2), MDM2(2), TP53(18) 1124314 23 18 23 2 2 0 7 1 12 1 0.1 3.2e-07 5e-05
5 METHANE_METABOLISM ADH5, ATP6V0C, SHMT1, CAT, EPX, LPO, MPO, PRDX1, PRDX2, PRDX5, PRDX6, SHMT1, SHMT2, TPO 13 ATP6V0C(1), EPX(1), PRDX1(1), PRDX2(2), SHMT2(1), TPO(22) 1628686 28 27 9 3 4 0 22 0 2 0 0.025 4.2e-07 0.000051
6 PMLPATHWAY Ring-shaped PML nuclear bodies regulate transcription and are required co-activators in p53- and DAXX-mediated apoptosis. CREBBP, DAXX, HRAS, PAX3, PML, PRAM-1, RARA, RB1, SIRT1, SP100, TNF, TNFRSF1A, TNFRSF1B, TNFRSF6, TNFSF6, TP53, UBL1 13 CREBBP(1), DAXX(4), PML(2), RARA(1), RB1(2), SIRT1(1), TNFRSF1A(1), TP53(18) 2553179 30 24 30 2 3 1 7 1 17 1 0.046 6.2e-07 0.000063
7 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(1), TP53(18) 1391271 19 17 19 1 2 0 5 1 10 1 0.12 2.3e-06 0.0002
8 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(5), ATR(3), CHEK2(2), TP53(18) 2105624 28 24 28 4 3 0 6 3 15 1 0.48 3e-06 0.00022
9 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(5), MDM2(2), RB1(2), TIMP3(1), TP53(18) 2416850 29 23 29 3 2 0 6 1 19 1 0.21 3.2e-06 0.00022
10 GSPATHWAY Activated G-protein coupled receptors stimulate cAMP production and thus activate protein kinase A, involved in a number of signal transduction pathways. ADCY1, GNAS, GNB1, GNGT1, PRKACA, PRKAR1A 6 ADCY1(1), GNAS(5), GNB1(2), PRKACA(1), PRKAR1A(7) 921215 16 15 15 2 1 0 3 2 10 0 0.51 0.000047 0.0027

Table 6.  Get Full Table A Ranked List of Significantly Mutated Genesets (Excluding Significantly Mutated Genes). Number of significant genesets found: 0. 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 BBCELLPATHWAY Fas ligand expression by T cells induces apoptosis in Fas-expressing, inactive B cells. CD28, CD4, HLA-DRA, HLA-DRB1, TNFRSF5, TNFRSF6, TNFSF5, TNFSF6 4 HLA-DRB1(3) 328912 3 3 3 1 0 0 2 1 0 0 0.74 0.061 1
2 EOSINOPHILSPATHWAY Recruitment of eosinophils in the inflammatory response observed in asthma occurs via the chemoattractant eotaxin binding to the CCR3 receptor. CCL11, CCL5, CCR3, CSF2, HLA-DRA, HLA-DRB1, IL3, IL5 8 CCL11(1), CCR3(1), HLA-DRB1(3), IL3(1) 407360 6 5 6 2 0 0 4 2 0 0 0.68 0.083 1
3 CAPROLACTAM_DEGRADATION AKR1A1, ECHS1, EHHADH, HADHA, SDS 5 AKR1A1(1), ECHS1(2), EHHADH(1), HADHA(1), SDS(1) 665589 6 5 6 0 1 0 2 1 2 0 0.24 0.089 1
4 ARGININECPATHWAY Related catabolic pathways process arginine, histidine, glutamine, and proline through glutamate to alpha-ketoglutamate, which feeds into the citric acid cycle. ALDH4A1, ARG1, GLS, GLUD1, OAT, PRODH 6 GLUD1(1), PRODH(4) 808834 5 5 4 0 1 1 0 3 0 0 0.25 0.09 1
5 HSA00472_D_ARGININE_AND_D_ORNITHINE_METABOLISM Genes involved in D-arginine and D-ornithine metabolism DAO 1 DAO(1) 97560 1 1 1 0 0 0 0 0 1 0 0.72 0.096 1
6 CYSTEINE_METABOLISM CARS, CTH, GOT1, GOT2, LDHA, LDHB, LDHC, MPST 8 CTH(1), GOT1(1), GOT2(2), LDHA(3) 910674 7 7 7 2 3 0 2 1 1 0 0.65 0.099 1
7 HSA00401_NOVOBIOCIN_BIOSYNTHESIS Genes involved in novobiocin biosynthesis GOT1, GOT2, TAT 3 GOT1(1), GOT2(2) 356738 3 3 3 0 2 0 1 0 0 0 0.4 0.11 1
8 SULFUR_METABOLISM BPNT1, PAPSS1, PAPSS2, SULT1A2, SULT1A3, SULT1A3, SULT1A4, SULT1E1, SULT2A1, SUOX 7 BPNT1(3), PAPSS2(1), SUOX(2) 815298 6 5 6 1 0 0 3 0 2 1 0.78 0.12 1
9 HSA00530_AMINOSUGARS_METABOLISM Genes involved in aminosugars metabolism AMDHD2, CHIA, CHIT1, CMAS, CTBS, CYB5R1, CYB5R3, GFPT1, GFPT2, GNE, GNPDA1, GNPDA2, GNPNAT1, HEXA, HEXB, HK1, HK2, HK3, LHPP, MTMR1, MTMR2, MTMR6, NAGK, NANS, NPL, PGM3, PHPT1, RENBP, UAP1 29 AMDHD2(2), CHIA(2), CHIT1(3), CTBS(1), GNE(1), GNPDA1(1), HEXB(1), HK2(3), HK3(3), LHPP(2), MTMR1(1), MTMR2(1) 3943997 21 19 19 3 1 3 10 2 5 0 0.19 0.13 1
10 UBIQUINONE_BIOSYNTHESIS NDUFA1, NDUFA10, NDUFA11, NDUFA4, NDUFA5, NDUFA8, NDUFB2, NDUFB4, NDUFB5, NDUFB6, NDUFB7, NDUFS1, NDUFS2, NDUFV1, NDUFV2 15 NDUFA1(1), NDUFA10(2), NDUFB5(2), NDUFB7(1), NDUFS2(1) 964591 7 6 7 0 1 0 4 0 2 0 0.22 0.13 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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