Skin Cutaneous Melanoma: Mutation Analysis (MutSig v1.5)
(WT cohort)
Maintained by Dan DiCara (Broad Institute)
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: SKCM-WT

  • Number of patients in set: 34

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-WT.final_analysis_set.maf

  • Significantly mutated genes (q ≤ 0.1): 2

  • Mutations seen in COSMIC: 53

  • Significantly mutated genes in COSMIC territory: 5

  • Genes with clustered mutations (≤ 3 aa apart): 156

  • Significantly mutated genesets: 0

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

Mutation Preprocessing

  • Read 34 MAFs of type "Broad"

  • Total number of mutations in input MAFs: 19965

  • After removing 101 blacklisted mutations: 19864

  • After removing 334 noncoding mutations: 19530

Mutation Filtering

  • Number of mutations before filtering: 19530

  • After removing 261 mutations outside gene set: 19269

  • After removing 23 mutations outside category set: 19246

  • After removing 4 "impossible" mutations in

  • gene-patient-category bins of zero coverage: 18958

Results
Breakdown of Mutations by Type

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

type count
Frame_Shift_Del 104
Frame_Shift_Ins 31
In_Frame_Del 22
In_Frame_Ins 9
Missense_Mutation 11627
Nonsense_Mutation 695
Nonstop_Mutation 5
Silent 6564
Splice_Site 182
Translation_Start_Site 7
Total 19246
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 8682 266510991 0.000033 33 2.5 1.6
(A/G)p*C->T 995 223586921 4.5e-06 4.5 0.34 1.9
A->G 532 473016329 1.1e-06 1.1 0.085 2.3
transver 1422 963114241 1.5e-06 1.5 0.11 5
indel+null 1030 963114241 1.1e-06 1.1 0.081 NaN
double_null 18 963114241 1.9e-08 0.019 0.0014 NaN
Total 12679 963114241 0.000013 13 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-WT.patients.counts_and_rates.txt

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:

  • 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_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: 2. 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 SERPINI2 serpin peptidase inhibitor, clade I (pancpin), member 2 41024 5 5 5 0 3 0 1 1 0 0 0.18 4.4e-06 0.042
2 RAC1 ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) 20840 5 5 4 0 4 0 0 1 0 0 0.11 4.6e-06 0.042
3 ESRP1 epithelial splicing regulatory protein 1 71635 6 6 6 0 2 0 0 3 1 0 0.16 0.000023 0.11
4 PLCB4 phospholipase C, beta 4 118270 9 6 8 0 5 0 1 1 2 0 0.046 0.000037 0.11
5 TUBA1B tubulin, alpha 1b 44856 4 4 3 0 1 0 0 3 0 0 0.33 0.000041 0.11
6 MUC7 mucin 7, secreted 38240 6 5 5 0 4 0 2 0 0 0 0.083 0.000042 0.11
7 TAF1A TATA box binding protein (TBP)-associated factor, RNA polymerase I, A, 48kDa 47345 4 4 3 0 1 0 0 3 0 0 0.46 0.000044 0.11
8 KRTAP5-1 keratin associated protein 5-1 28538 4 4 4 0 1 0 0 2 1 0 0.46 0.000049 0.11
9 CYLC1 cylicin, basic protein of sperm head cytoskeleton 1 28932 4 4 4 1 3 1 0 0 0 0 0.59 0.000058 0.12
10 CLCC1 chloride channel CLIC-like 1 57643 4 4 4 0 0 0 0 4 0 0 0.52 0.000064 0.12
11 CTNND2 catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein) 113745 11 8 10 0 7 0 0 3 1 0 0.0098 0.000072 0.12
12 OR6N1 olfactory receptor, family 6, subfamily N, member 1 31310 3 3 3 1 1 0 0 1 0 1 0.39 0.000088 0.13
13 OR51M1 olfactory receptor, family 51, subfamily M, member 1 31569 5 4 5 1 4 1 0 0 0 0 0.14 0.0001 0.14
14 PCDHB5 protocadherin beta 5 81328 6 5 6 1 4 0 0 1 1 0 0.17 0.00011 0.15
15 PSG6 pregnancy specific beta-1-glycoprotein 6 44166 6 4 6 1 4 1 1 0 0 0 0.2 0.00018 0.22
16 COLEC10 collectin sub-family member 10 (C-type lectin) 24585 3 3 3 0 1 1 0 1 0 0 0.37 0.00027 0.31
17 FLG2 filaggrin family member 2 243668 10 8 10 1 7 0 2 1 0 0 0.23 0.00029 0.31
18 KLHL13 kelch-like 13 (Drosophila) 65039 6 5 6 1 5 0 1 0 0 0 0.28 0.00033 0.32
19 UGT3A1 UDP glycosyltransferase 3 family, polypeptide A1 53473 6 4 6 1 3 0 0 2 1 0 0.33 0.00034 0.32
20 PLXDC2 plexin domain containing 2 46175 5 4 5 1 4 0 1 0 0 0 0.35 0.00037 0.33
21 IDH1 isocitrate dehydrogenase 1 (NADP+), soluble 42629 3 3 2 0 2 0 0 1 0 0 0.34 0.00041 0.33
22 CASS4 Cas scaffolding protein family member 4 78974 6 4 6 1 2 0 2 2 0 0 0.31 0.00041 0.33
23 NTRK1 neurotrophic tyrosine kinase, receptor, type 1 67001 4 4 4 1 1 0 1 1 1 0 0.6 0.00043 0.33
24 GNA11 guanine nucleotide binding protein (G protein), alpha 11 (Gq class) 33844 3 3 2 0 1 0 0 2 0 0 0.31 0.00046 0.34
25 ADAMTS9 ADAM metallopeptidase with thrombospondin type 1 motif, 9 202507 9 7 8 0 3 0 2 3 1 0 0.062 0.0005 0.36
26 PTPN14 protein tyrosine phosphatase, non-receptor type 14 122571 6 6 6 0 3 0 1 1 1 0 0.091 0.0006 0.39
27 LIPA lipase A, lysosomal acid, cholesterol esterase (Wolman disease) 41633 3 3 3 0 1 1 0 1 0 0 0.39 0.00067 0.39
28 CDH6 cadherin 6, type 2, K-cadherin (fetal kidney) 79373 7 5 7 1 5 0 1 0 1 0 0.16 0.00068 0.39
29 SI sucrase-isomaltase (alpha-glucosidase) 167528 8 6 7 1 5 3 0 0 0 0 0.34 0.00068 0.39
30 ODF1 outer dense fiber of sperm tails 1 25820 3 3 3 0 1 0 0 0 2 0 0.29 0.0007 0.39
31 USH1C Usher syndrome 1C (autosomal recessive, severe) 85057 4 4 4 0 1 0 0 2 1 0 0.34 0.00071 0.39
32 CHODL chondrolectin 24839 4 4 4 0 3 0 0 1 0 0 0.33 0.00075 0.39
33 NDUFS7 NADH dehydrogenase (ubiquinone) Fe-S protein 7, 20kDa (NADH-coenzyme Q reductase) 13929 2 2 2 0 1 0 0 0 1 0 0.55 0.00076 0.39
34 CCNE2 cyclin E2 42806 3 3 2 1 0 0 0 3 0 0 0.84 0.00077 0.39
35 NPY5R neuropeptide Y receptor Y5 45610 4 4 4 0 2 0 0 2 0 0 0.34 0.00077 0.39
SERPINI2

Figure S1.  This figure depicts the distribution of mutations and mutation types across the SERPINI2 significant gene.

RAC1

Figure S2.  This figure depicts the distribution of mutations and mutation types across the RAC1 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: 5. Number of genes displayed: 10

rank gene description n cos n_cos N_cos cos_ev p q
1 IDH1 isocitrate dehydrogenase 1 (NADP+), soluble 3 5 3 170 4476 1.8e-09 8.3e-06
2 LGR6 leucine-rich repeat-containing G protein-coupled receptor 6 5 4 2 136 2 1.6e-06 0.0028
3 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog 3 52 3 1768 14972 2.1e-06 0.0028
4 EPHA4 EPH receptor A4 3 5 2 170 2 2.5e-06 0.0028
5 KIT v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog 4 240 4 8160 606 5.1e-06 0.0046
6 ARHGDIG Rho GDP dissociation inhibitor (GDI) gamma 1 1 1 34 1 0.00045 0.17
7 ARNT aryl hydrocarbon receptor nuclear translocator 1 1 1 34 1 0.00045 0.17
8 CACNB2 calcium channel, voltage-dependent, beta 2 subunit 2 1 1 34 1 0.00045 0.17
9 LRRC4C leucine rich repeat containing 4C 4 1 1 34 1 0.00045 0.17
10 MSTN myostatin 2 1 1 34 1 0.00045 0.17

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)

Clustered Mutations

Table 5.  Get Full Table Genes with Clustered Mutations

num gene desc n mindist nmuts0 nmuts3 nmuts12 npairs0 npairs3 npairs12
2750 IDH1 isocitrate dehydrogenase 1 (NADP+), soluble 3 0 3 3 3 3 3 3
6123 TMC5 transmembrane channel-like 5 6 0 3 3 3 3 3 3
3730 MUC16 mucin 16, cell surface associated 73 0 2 2 4 2 2 4
3840 NBPF9 neuroblastoma breakpoint family, member 9 6 0 2 2 4 2 2 4
2273 GABRA6 gamma-aminobutyric acid (GABA) A receptor, alpha 6 5 0 1 3 3 1 3 3
4375 PAPPA2 pappalysin 2 9 0 1 2 2 1 2 2
169 ADH1B alcohol dehydrogenase 1B (class I), beta polypeptide 4 0 1 1 3 1 1 3
704 C15orf2 chromosome 15 open reading frame 2 16 0 1 1 3 1 1 3
1 A1CF APOBEC1 complementation factor 4 0 1 1 2 1 1 2
3874 NEBL nebulette 6 0 1 1 2 1 1 2

Note:

n - number of mutations in this gene in the individual set.

mindist - distance (in aa) between closest pair of mutations in this gene

npairs3 - how many pairs of mutations are within 3 aa of each other.

npairs12 - how many pairs of mutations are within 12 aa of each other.

Geneset Analyses

Table 6.  Get Full Table A Ranked List of Significantly Mutated Genesets. (Source: MSigDB GSEA Cannonical Pathway Set).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 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 CDKN2A(2), E2F1(1), PRB1(5), TP53(2) 422815 10 6 10 3 4 0 1 1 4 0 0.34 0.0015 0.92
2 ACTINYPATHWAY The Arp 2/3 complex localizes to the Y-junction of polymerizing actin fibers that enable lamellipod extension and consequent cell motility. ABI-2, ACTA1, ACTR2, ACTR3, ARPC1A, ARPC1B, ARPC2, ARPC3, ARPC4, NCK1, NCKAP1, NTRK1, PIR, PSMA7, RAC1, WASF1, WASF2, WASF3, WASL 18 ARPC1B(3), NCKAP1(1), NTRK1(4), RAC1(5) 752925 13 12 12 2 7 0 2 3 1 0 0.15 0.0075 1
3 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 CDKN2A(2), E2F1(1), POLR1A(2), POLR1B(1), RAC1(5), RB1(1), TP53(2) 1001094 14 11 13 3 7 0 1 2 4 0 0.16 0.0089 1
4 SALMONELLAPATHWAY Salmonella induces membrane ruffling in infected cells via bacterial proteins including SipA, SipC, and SopE, which alter actin structure. ACTA1, ACTR2, ACTR3, ARPC1A, ARPC1B, ARPC2, ARPC3, ARPC4, CDC42, RAC1, WASF1, WASL 12 ARPC1B(3), RAC1(5) 400383 8 8 7 1 6 0 1 1 0 0 0.15 0.018 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 SP1(2), TP53(2) 351795 4 4 4 1 0 0 2 1 1 0 0.69 0.025 1
6 SELENOAMINO_ACID_METABOLISM AHCY, CBS, CTH, GGT1, MARS, MARS2, MAT1A, MAT2B, PAPSS1, PAPSS2, SCLY, SEPHS1 12 AHCY(1), MARS(3), MAT1A(2), PAPSS1(1), PAPSS2(3), SCLY(1) 615278 11 7 11 2 7 2 0 1 1 0 0.077 0.055 1
7 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 CCNE1(1), CCNE2(3), CDKN2A(2), E2F1(1), PRB1(5) 448780 12 8 11 3 5 0 0 4 3 0 0.27 0.055 1
8 CAPROLACTAM_DEGRADATION AKR1A1, ECHS1, EHHADH, HADHA, SDS 5 AKR1A1(1), EHHADH(2), HADHA(2), SDS(1) 240462 6 5 6 0 5 0 0 0 1 0 0.044 0.065 1
9 ACE_INHIBITOR_PATHWAY_PHARMGKB ACE, AGT, AGTR1, AGTR2, BDKRB2, KNG1, NOS3, REN 8 ACE(2), AGTR1(2), AGTR2(1), BDKRB2(3), KNG1(1), NOS3(3), REN(2) 489373 14 8 14 4 6 0 1 4 3 0 0.13 0.072 1
10 CIRCADIANPATHWAY A heterodimer composed of Bmal1 and Clock acts as a transcription factor for proteins that regulate circadian rhythms, such as Per and Cry. ARNTL, CLOCK, CRY1, CRY2, CSNK1E, PER1 6 CLOCK(2), CRY1(2), PER1(1) 417978 5 4 4 0 1 1 0 1 2 0 0.35 0.082 1

Table 7.  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 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 CDKN2A(2), E2F1(1), PRB1(5), TP53(2) 422815 10 6 10 3 4 0 1 1 4 0 0.34 0.0015 0.92
2 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(2), TP53(2) 351795 4 4 4 1 0 0 2 1 1 0 0.69 0.025 1
3 SELENOAMINO_ACID_METABOLISM AHCY, CBS, CTH, GGT1, MARS, MARS2, MAT1A, MAT2B, PAPSS1, PAPSS2, SCLY, SEPHS1 12 AHCY(1), MARS(3), MAT1A(2), PAPSS1(1), PAPSS2(3), SCLY(1) 615278 11 7 11 2 7 2 0 1 1 0 0.077 0.055 1
4 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 CCNE1(1), CCNE2(3), CDKN2A(2), E2F1(1), PRB1(5) 448780 12 8 11 3 5 0 0 4 3 0 0.27 0.055 1
5 CAPROLACTAM_DEGRADATION AKR1A1, ECHS1, EHHADH, HADHA, SDS 5 AKR1A1(1), EHHADH(2), HADHA(2), SDS(1) 240462 6 5 6 0 5 0 0 0 1 0 0.044 0.065 1
6 ACE_INHIBITOR_PATHWAY_PHARMGKB ACE, AGT, AGTR1, AGTR2, BDKRB2, KNG1, NOS3, REN 8 ACE(2), AGTR1(2), AGTR2(1), BDKRB2(3), KNG1(1), NOS3(3), REN(2) 489373 14 8 14 4 6 0 1 4 3 0 0.13 0.072 1
7 CIRCADIANPATHWAY A heterodimer composed of Bmal1 and Clock acts as a transcription factor for proteins that regulate circadian rhythms, such as Per and Cry. ARNTL, CLOCK, CRY1, CRY2, CSNK1E, PER1 6 CLOCK(2), CRY1(2), PER1(1) 417978 5 4 4 0 1 1 0 1 2 0 0.35 0.082 1
8 NICOTINATE_AND_NICOTINAMIDE_METABOLISM AOX1, CD38, ENPP1, ENPP3, NADSYN1, NMNAT1, NMNAT2, NNMT, NNT, NP, NT5C, NT5E, NT5M, QPRT 13 AOX1(3), CD38(2), ENPP1(1), ENPP3(1), NADSYN1(2), NNMT(1), NT5E(1), QPRT(1) 714118 12 7 12 2 7 1 0 2 2 0 0.13 0.084 1
9 FXRPATHWAY The nuclear receptor transcription factors FXR and LXR are activated by cholesterol metabolites and regulate cholesterol homeostasis. FABP6, LDLR, NR0B2, NR1H3, NR1H4, RXRA 6 LDLR(3), NR1H4(2), RXRA(1) 270174 6 4 6 1 3 2 1 0 0 0 0.17 0.087 1
10 HSA00643_STYRENE_DEGRADATION Genes involved in styrene degradation FAH, GSTZ1, HGD 3 FAH(1), HGD(2) 111602 3 3 3 2 1 1 1 0 0 0 0.75 0.093 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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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