Mutation Analysis (MutSig v1.5)
Adrenocortical Carcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1FT8JRW
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/C1FT8JRW
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: 91

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): 174

  • Mutations seen in COSMIC: 61

  • Significantly mutated genes in COSMIC territory: 4

  • Significantly mutated genesets: 19

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

Mutation Preprocessing

  • Read 91 MAFs of type "Baylor-Illumina"

  • Total number of mutations in input MAFs: 22072

  • After removing 127 mutations outside chr1-24: 21945

  • After removing 1384 blacklisted mutations: 20561

  • After removing 1399 noncoding mutations: 19162

  • After collapsing adjacent/redundant mutations: 19152

Mutation Filtering

  • Number of mutations before filtering: 19152

  • After removing 1118 mutations outside gene set: 18034

  • After removing 67 mutations outside category set: 17967

  • After removing 1 "impossible" mutations in

  • gene-patient-category bins of zero coverage: 16781

Results
Breakdown of Mutations by Type

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

type count
Frame_Shift_Del 514
Frame_Shift_Ins 186
In_Frame_Del 265
In_Frame_Ins 88
Missense_Mutation 10304
Nonsense_Mutation 581
Silent 5784
Splice_Site 244
Translation_Start_Site 1
Total 17967
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 2031 161241575 0.000013 13 2.9 2.1
*CpG->(G/A) 717 161241575 4.4e-06 4.4 1 2.7
*Cp(A/C/T)->mut 4997 1299803062 3.8e-06 3.8 0.9 3.3
A->mut 2560 1387389109 1.8e-06 1.8 0.43 3.9
indel+null 1814 2848433746 6.4e-07 0.64 0.15 NaN
double_null 64 2848433746 2.2e-08 0.022 0.0053 NaN
Total 12183 2848433746 4.3e-06 4.3 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: 174. 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 LACTB lactamase, beta 117609 27 27 3 0 0 0 1 25 1 0 0.0012 <1.00e-15 <4.20e-12
2 C1orf106 chromosome 1 open reading frame 106 160861 16 16 2 0 15 0 0 1 0 0 0.0062 <1.00e-15 <4.20e-12
3 ERCC2 excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D) 198357 19 19 1 0 19 0 0 0 0 0 0.0012 1.55e-15 4.20e-12
4 ZNF517 zinc finger protein 517 113936 34 33 2 0 0 0 0 34 0 0 0.0076 2.11e-15 4.20e-12
5 LRIG1 leucine-rich repeats and immunoglobulin-like domains 1 285347 56 32 2 0 0 0 56 0 0 0 3.2e-08 2.11e-15 4.20e-12
6 ZFPM1 zinc finger protein, multitype 1 134629 92 48 5 0 1 0 5 0 65 21 0.11 2.22e-15 4.20e-12
7 CCDC102A coiled-coil domain containing 102A 84493 26 26 1 0 26 0 0 0 0 0 0.00033 2.22e-15 4.20e-12
8 SYT8 synaptotagmin VIII 100867 14 14 3 0 14 0 0 0 0 0 0.0034 2.44e-15 4.20e-12
9 SARM1 sterile alpha and TIR motif containing 1 138834 14 14 2 1 0 10 0 0 4 0 0.14 3.44e-15 4.20e-12
10 CLDN23 claudin 23 31563 13 13 1 0 0 0 13 0 0 0 0.0052 3.89e-15 4.20e-12
11 OPRD1 opioid receptor, delta 1 71003 26 26 1 1 0 0 26 0 0 0 0.000065 4.11e-15 4.20e-12
12 GLTPD2 glycolipid transfer protein domain containing 2 42681 19 19 1 2 0 19 0 0 0 0 0.017 4.66e-15 4.20e-12
13 ASPDH aspartate dehydrogenase domain containing 75573 19 19 2 0 0 0 1 18 0 0 0.0084 5.22e-15 4.20e-12
14 CTNNB1 catenin (cadherin-associated protein), beta 1, 88kDa 218493 14 14 9 0 0 0 4 6 4 0 0.063 5.22e-15 4.20e-12
15 TRIOBP TRIO and F-actin binding protein 627845 25 24 5 0 0 0 3 21 1 0 0.0015 5.33e-15 4.20e-12
16 THEM4 thioesterase superfamily member 4 58444 14 14 1 0 0 0 0 14 0 0 0.032 5.44e-15 4.20e-12
17 TMEM189 transmembrane protein 189 64792 12 12 1 0 0 0 0 12 0 0 0.18 5.55e-15 4.20e-12
18 C4orf32 chromosome 4 open reading frame 32 22750 9 9 1 0 0 0 9 0 0 0 0.19 5.66e-15 4.20e-12
19 ATXN1 ataxin 1 203979 15 14 9 1 0 1 4 0 10 0 0.4 5.77e-15 4.20e-12
20 TOR3A torsin family 3, member A 97918 25 25 1 0 0 0 0 25 0 0 0.03 6.11e-15 4.20e-12
21 C2orf81 chromosome 2 open reading frame 81 154302 15 14 3 0 0 0 0 15 0 0 0.029 6.11e-15 4.20e-12
22 GARS glycyl-tRNA synthetase 186668 36 35 3 6 1 0 34 1 0 0 0.25 6.33e-15 4.20e-12
23 TP53 tumor protein p53 118459 18 17 18 1 2 0 4 1 10 1 0.14 6.33e-15 4.20e-12
24 IRX3 iroquois homeobox 3 76649 21 21 1 0 0 0 0 21 0 0 0.055 6.44e-15 4.20e-12
25 USP42 ubiquitin specific peptidase 42 233660 26 25 4 2 1 20 0 5 0 0 0.0058 6.55e-15 4.20e-12
26 MAL2 mal, T-cell differentiation protein 2 37533 24 23 2 1 0 0 1 0 23 0 0.95 6.77e-15 4.20e-12
27 ZNF598 zinc finger protein 598 185362 20 19 5 2 0 1 3 16 0 0 0.23 6.88e-15 4.20e-12
28 SEMA5B sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B 278346 17 16 2 0 0 0 1 16 0 0 0.043 6.88e-15 4.20e-12
29 ADAD2 adenosine deaminase domain containing 2 154788 15 15 1 0 0 0 15 0 0 0 0.005 7.22e-15 4.20e-12
30 TPO thyroid peroxidase 232451 22 21 3 0 1 0 21 0 0 0 0.001 7.55e-15 4.20e-12
31 C19orf10 chromosome 19 open reading frame 10 41209 10 10 1 0 0 10 0 0 0 0 0.018 7.66e-15 4.20e-12
32 KCNK17 potassium channel, subfamily K, member 17 89242 19 19 2 0 0 0 1 18 0 0 0.044 7.77e-15 4.20e-12
33 PANK2 pantothenate kinase 2 (Hallervorden-Spatz syndrome) 123734 15 15 2 0 0 0 15 0 0 0 0.024 7.99e-15 4.20e-12
34 RINL Ras and Rab interactor-like 104087 19 19 1 0 0 0 19 0 0 0 0.003 8.10e-15 4.20e-12
35 RGS9BP regulator of G protein signaling 9 binding protein 19133 11 11 1 0 0 11 0 0 0 0 0.0058 8.33e-15 4.20e-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: 4. 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 12558 6397 3.4e-13 1.5e-09
2 TP53 tumor protein p53 18 356 17 32396 1628 8e-13 1.8e-09
3 MEN1 multiple endocrine neoplasia I 8 208 5 18928 25 2.7e-08 0.000041
4 KRTAP5-5 keratin associated protein 5-5 7 1 2 91 0 7.5e-08 0.000085
5 ABCA12 ATP-binding cassette, sub-family A (ABC1), member 12 3 1 1 91 1 0.00039 0.22
6 ANKRD30A ankyrin repeat domain 30A 7 1 1 91 1 0.00039 0.22
7 CCND2 cyclin D2 1 1 1 91 1 0.00039 0.22
8 LACE1 lactation elevated 1 1 1 1 91 1 0.00039 0.22
9 GRM3 glutamate receptor, metabotropic 3 4 2 1 182 1 0.00078 0.35
10 IGFBP3 insulin-like growth factor binding protein 3 1 2 1 182 1 0.00078 0.35

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: 19. 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) 931966 25 23 7 2 0 9 3 13 0 0 0.041 2e-13 1.3e-10
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) 1351480 26 25 7 2 3 0 21 0 2 0 0.016 4.2e-09 1.3e-06
3 HSA00940_PHENYLPROPANOID_BIOSYNTHESIS Genes involved in phenylpropanoid biosynthesis EPX, GBA, GBA3, LPO, MPO, PRDX6, TPO 7 EPX(1), TPO(22) 1167797 23 22 4 2 2 0 21 0 0 0 0.018 5.3e-08 0.000011
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) 1136927 23 18 23 2 2 0 7 1 12 1 0.1 4.3e-07 0.000067
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) 1646854 28 27 9 3 4 0 22 0 2 0 0.025 5.8e-07 0.000072
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) 2581860 30 24 30 2 3 1 7 1 17 1 0.046 8.9e-07 0.000092
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) 1406891 19 17 19 1 2 0 5 1 10 1 0.12 3.1e-06 0.00027
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) 2129466 28 24 28 4 3 0 6 3 15 1 0.48 4.1e-06 0.00031
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) 2444225 29 23 29 3 2 0 6 1 19 1 0.21 4.5e-06 0.00031
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) 931484 16 15 15 2 1 0 3 2 10 0 0.51 0.000059 0.0036

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 HSA00472_D_ARGININE_AND_D_ORNITHINE_METABOLISM Genes involved in D-arginine and D-ornithine metabolism DAO 1 DAO(2) 98644 2 2 2 0 1 0 0 0 1 0 0.51 0.014 1
2 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) 332581 3 3 3 1 0 0 2 1 0 0 0.74 0.065 1
3 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) 411853 6 5 6 2 0 0 4 2 0 0 0.68 0.088 1
4 CAPROLACTAM_DEGRADATION AKR1A1, ECHS1, EHHADH, HADHA, SDS 5 AKR1A1(1), ECHS1(2), EHHADH(1), HADHA(1), SDS(1) 672997 6 5 6 1 1 0 2 1 2 0 0.54 0.095 1
5 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) 817853 5 5 4 0 1 1 0 3 0 0 0.25 0.098 1
6 CYSTEINE_METABOLISM CARS, CTH, GOT1, GOT2, LDHA, LDHB, LDHC, MPST 8 CTH(1), GOT1(1), GOT2(2), LDHA(3) 920795 7 7 7 2 3 0 2 1 1 0 0.65 0.11 1
7 HSA00401_NOVOBIOCIN_BIOSYNTHESIS Genes involved in novobiocin biosynthesis GOT1, GOT2, TAT 3 GOT1(1), GOT2(2) 360688 3 3 3 0 2 0 1 0 0 0 0.4 0.12 1
8 SULFUR_METABOLISM BPNT1, PAPSS1, PAPSS2, SULT1A2, SULT1A3, SULT1A3, SULT1A4, SULT1E1, SULT2A1, SUOX 7 BPNT1(3), PAPSS2(1), SUOX(2) 824400 6 5 6 1 0 0 3 0 2 1 0.78 0.13 1
9 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) 975354 7 6 7 0 1 0 4 0 2 0 0.22 0.14 1
10 BLOOD_GROUP_GLYCOLIPID_BIOSYNTHESIS_LACTOSERIES ABO, FUT1, FUT2, FUT3, FUT5, FUT6, SIAT6, ST3GAL3 7 FUT3(3), FUT6(2) 715421 5 5 5 1 2 0 2 1 0 0 0.44 0.16 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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