Mutation Analysis (MutSig v2.0 and MutSigCV v0.9 merged result)
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1V40S7V
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/C1V40S7V
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: KIRP-TP

  • Number of patients in set: 111

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:KIRP-TP.final_analysis_set.maf

  • Significantly mutated genes (q ≤ 0.1): 5

  • Mutations seen in COSMIC: 43

  • Significantly mutated genes in COSMIC territory: 11

  • Significantly mutated genesets: 0

Mutation Preprocessing

  • Read 111 MAFs of type "Broad"

  • Total number of mutations in input MAFs: 10131

  • After removing 42 mutations outside chr1-24: 10089

  • After removing 348 blacklisted mutations: 9741

  • After removing 259 noncoding mutations: 9482

  • After collapsing adjacent/redundant mutations: 8036

Mutation Filtering

  • Number of mutations before filtering: 8036

  • After removing 124 mutations outside gene set: 7912

  • After removing 5 mutations outside category set: 7907

Results
Breakdown of Mutations by Type

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

type count
Frame_Shift_Del 528
Frame_Shift_Ins 201
In_Frame_Del 131
In_Frame_Ins 29
Missense_Mutation 4829
Nonsense_Mutation 266
Nonstop_Mutation 6
Silent 1725
Splice_Site 178
Translation_Start_Site 14
Total 7907
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 511 184714396 2.8e-06 2.8 1.5 2.1
*Cp(A/C/T)->T 905 1496190153 6e-07 0.6 0.32 1.7
A->G 894 1608163559 5.6e-07 0.56 0.3 2.3
transver 2532 3289068108 7.7e-07 0.77 0.41 5
indel+null 1335 3289068108 4.1e-07 0.41 0.22 NaN
double_null 5 3289068108 1.5e-09 0.0015 0.00081 NaN
Total 6182 3289068108 1.9e-06 1.9 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: KIRP-TP.patients.counts_and_rates.txt

Needs description.

Figure 3.  Needs description.

Figure 4.  Needs description.

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: *Cp(A/C/T)->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: 5. 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_cons p_joint p_cv p q
1 IL32 interleukin 32 61843 4 4 2 0 0 0 0 0 4 0 0.92 0.0002 1.8e-06 8e-09 0.00014
2 CDC27 cell division cycle 27 homolog (S. cerevisiae) 278169 4 4 1 0 0 0 0 0 4 0 0.083 4.8e-06 0.00055 5.5e-08 0.00049
3 NF2 neurofibromin 2 (merlin) 180272 7 7 7 0 0 0 0 0 7 0 0.97 0.68 1.1e-08 1.5e-07 0.00089
4 PPARGC1B peroxisome proliferator-activated receptor gamma, coactivator 1 beta 317931 3 3 1 0 0 0 0 0 3 0 0.00046 0.000015 0.008 2.1e-06 0.0094
5 SFRS2IP splicing factor, arginine/serine-rich 2, interacting protein 490729 5 5 2 1 0 0 0 1 4 0 0.0012 0.00012 0.0011 2.2e-06 0.0094
6 MET met proto-oncogene (hepatocyte growth factor receptor) 474520 9 9 8 0 0 3 2 4 0 0 0.0016 0.000066 0.92 0.00065 1
7 ELF3 E74-like factor 3 (ets domain transcription factor, epithelial-specific ) 126731 3 3 3 0 0 0 0 1 2 0 0.86 1 0.000097 0.00099 1
8 PCF11 PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae) 472280 8 7 7 3 0 1 4 3 0 0 0.85 0.00066 0.21 0.0014 1
9 LGI4 leucine-rich repeat LGI family, member 4 78183 4 4 4 0 0 1 1 2 0 0 0.018 0.057 0.0029 0.0016 1
10 RAB27B RAB27B, member RAS oncogene family 73617 1 1 1 0 0 0 0 0 1 0 NaN NaN 0.0018 0.0018 1
11 STAG2 stromal antigen 2 432647 5 5 5 1 0 0 0 0 5 0 0.43 0.85 0.00025 0.002 1
12 PIPOX pipecolic acid oxidase 133755 2 2 2 0 0 0 0 0 2 0 0.42 0.6 0.00053 0.0029 1
13 C6orf195 chromosome 6 open reading frame 195 43068 2 2 2 0 0 0 0 0 2 0 0.51 0.51 0.00081 0.0036 1
14 ACSBG2 acyl-CoA synthetase bubblegum family member 2 224342 3 3 1 0 0 0 0 3 0 0 1 0.0011 0.42 0.0041 1
15 BHMT betaine-homocysteine methyltransferase 138466 4 4 4 0 0 0 3 0 1 0 0.1 0.22 0.0025 0.0046 1
16 LYAR Ly1 antibody reactive homolog (mouse) 130092 2 2 2 0 1 0 0 0 1 0 0.12 0.037 0.021 0.0062 1
17 LHFPL4 lipoma HMGIC fusion partner-like 4 83748 1 1 1 0 0 0 0 0 1 0 NaN NaN 0.0063 0.0063 1
18 POMC proopiomelanocortin (adrenocorticotropin/ beta-lipotropin/ alpha-melanocyte stimulating hormone/ beta-melanocyte stimulating hormone/ beta-endorphin) 63547 3 3 3 0 1 0 0 1 1 0 0.54 0.4 0.002 0.0064 1
19 RPTN repetin 262185 3 3 3 0 1 0 1 0 1 0 0.022 0.0034 0.24 0.0066 1
20 SAV1 salvador homolog 1 (Drosophila) 128652 3 3 3 0 0 1 0 0 2 0 0.98 0.18 0.0049 0.0072 1
21 NFE2L2 nuclear factor (erythroid-derived 2)-like 2 197785 3 3 3 0 0 0 1 2 0 0 0.013 0.0048 0.21 0.0079 1
22 IFNA16 interferon, alpha 16 63475 2 2 1 0 0 1 0 1 0 0 0.16 0.048 0.021 0.0079 1
23 PEBP1 phosphatidylethanolamine binding protein 1 48779 2 2 2 0 0 1 0 1 0 0 0.21 0.023 0.045 0.0082 1
24 MCCC2 methylcrotonoyl-Coenzyme A carboxylase 2 (beta) 180567 2 2 2 0 0 0 0 1 1 0 0.035 0.018 0.068 0.0096 1
25 POU4F2 POU class 4 homeobox 2 120647 2 2 1 0 0 0 0 0 2 0 0.99 0.18 0.0074 0.01 1
26 PARD6B par-6 partitioning defective 6 homolog beta (C. elegans) 117771 4 4 4 0 0 0 2 0 2 0 0.74 0.98 0.0015 0.011 1
27 VPS37D vacuolar protein sorting 37 homolog D (S. cerevisiae) 30362 1 1 1 0 0 0 0 0 1 0 NaN NaN 0.011 0.011 1
28 STARD3 StAR-related lipid transfer (START) domain containing 3 152873 2 2 2 0 0 0 0 0 2 0 0.059 0.088 0.019 0.012 1
29 WFDC10A WAP four-disulfide core domain 10A 27441 1 1 1 0 0 0 0 0 1 0 NaN NaN 0.015 0.015 1
30 LRFN4 leucine rich repeat and fibronectin type III domain containing 4 130619 3 3 3 0 1 0 0 0 2 0 0.69 1 0.0022 0.016 1
31 TMEM37 transmembrane protein 37 61716 1 1 1 0 0 0 1 0 0 0 NaN NaN 0.017 0.017 1
32 SEPT7 septin 7 96217 2 2 2 0 0 0 0 0 2 0 0.88 1 0.003 0.02 1
33 C10orf95 chromosome 10 open reading frame 95 29115 1 1 1 0 0 0 0 0 1 0 NaN NaN 0.021 0.021 1
34 C15orf52 chromosome 15 open reading frame 52 156736 1 1 1 0 0 0 0 0 1 0 NaN NaN 0.021 0.021 1
35 KDELR3 KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 3 80347 2 2 2 0 0 0 1 0 1 0 0.14 0.18 0.018 0.022 1
IL32

Figure S1.  This figure depicts the distribution of mutations and mutation types across the IL32 significant gene.

CDC27

Figure S2.  This figure depicts the distribution of mutations and mutation types across the CDC27 significant gene.

NF2

Figure S3.  This figure depicts the distribution of mutations and mutation types across the NF2 significant gene.

PPARGC1B

Figure S4.  This figure depicts the distribution of mutations and mutation types across the PPARGC1B 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: 11. Number of genes displayed: 10

rank gene description n cos n_cos N_cos cos_ev p q
1 MET met proto-oncogene (hepatocyte growth factor receptor) 9 34 4 3774 12 1e-10 4.7e-07
2 FGFR3 fibroblast growth factor receptor 3 (achondroplasia, thanatophoric dwarfism) 5 62 3 6882 1469 3.6e-07 0.00081
3 NF2 neurofibromin 2 (merlin) 7 550 4 61050 29 6.6e-06 0.0099
4 SMARCA4 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 5 30 2 3330 3 0.000019 0.022
5 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog 2 52 2 5772 29208 0.000058 0.053
6 BRAF v-raf murine sarcoma viral oncogene homolog B1 4 89 2 9879 14380 0.00017 0.086
7 CDCA8 cell division cycle associated 8 1 1 1 111 1 0.00021 0.086
8 FLCN folliculin 1 1 1 111 1 0.00021 0.086
9 G6PC glucose-6-phosphatase, catalytic subunit 1 1 1 111 1 0.00021 0.086
10 PLXDC2 plexin domain containing 2 1 1 1 111 1 0.00021 0.086

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: 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 MTORPATHWAY Mammalian target of rapamycin (mTOR) senses mitogenic factors and nutrients, including ATP, and induces cell proliferation. AKT1, EIF3S10, EIF4A1, EIF4A2, EIF4B, EIF4E, EIF4EBP1, EIF4G1, EIF4G2, EIF4G3, FKBP1A, FRAP1, MKNK1, PDK2, PDPK1, PIK3CA, PIK3R1, PPP2CA, PTEN, RPS6, RPS6KB1, TSC1, TSC2 21 EIF4A1(1), EIF4B(2), EIF4G1(2), EIF4G3(4), PIK3CA(2), PIK3R1(1), PTEN(3), TSC1(2), TSC2(4) 4612682 21 19 21 2 2 6 3 3 7 0 0.047 0.0011 0.66
2 ALANINE_AND_ASPARTATE_METABOLISM AARS, ABAT, ADSL, ADSS, AGXT, AGXT2, ASL, ASNS, ASPA, ASS, CAD, CRAT, DARS, DDO, GAD1, GAD2, GOT1, GOT2, GPT, GPT2, NARS, PC 21 AARS(1), ADSL(1), AGXT(1), AGXT2(1), ASNS(1), CAD(3), CRAT(1), DARS(3), DDO(1), GPT(2), PC(4) 4337938 19 17 19 1 0 3 1 8 7 0 0.078 0.0034 1
3 CBLPATHWAY Activated EGF receptors undergo endocytosis into clathrin-coated vesicles, where they are recycled to the membrane or ubiquitinated by Cbl. CBL, CSF1R, EGF, EGFR, GRB2, MET, PDGFRA, PRKCA, PRKCB1, SH3GLB1, SH3GLB2, SH3KBP1, SRC 12 CSF1R(1), EGF(1), MET(9), PDGFRA(2) 3225375 13 12 12 1 1 3 2 6 1 0 0.11 0.0074 1
4 NEUTROPHILPATHWAY Neutrophils are phagocytotic leukocytes that destroy foreign cells with reactive oxygen species or enzymatic digestion and express CD11 and CD18. CD44, ICAM1, ITGAL, ITGAM, ITGB2, PECAM1, SELE, SELL 8 ITGAL(3), ITGAM(2), ITGB2(1), SELE(1), SELL(1) 1726164 8 8 8 0 1 2 0 3 2 0 0.13 0.01 1
5 KREBPATHWAY The Krebs (citric acid) cycle takes place in mitochondria, where it extracts energy in the form of electron carriers NADH and FADH2, which drive the electron transport chain. ACO2, CS, FH, IDH2, MDH1, OGDH, SDHA, SUCLA2 8 FH(1), IDH2(1), MDH1(1), OGDH(2), SDHA(2) 1558671 7 7 7 0 0 3 0 1 3 0 0.072 0.01 1
6 LYMPHOCYTEPATHWAY B and T cell lymphocytes interact with other cells via transmembrane adhesion proteins such as CD44, which interacts with endothelial cells. CD44, ICAM1, ITGA4, ITGAL, ITGB1, ITGB2, PECAM1, SELE, SELL 9 ITGA4(1), ITGAL(3), ITGB1(1), ITGB2(1), SELE(1), SELL(1) 1999098 8 8 8 0 1 2 1 1 3 0 0.15 0.011 1
7 MONOCYTEPATHWAY Monocytes are a class of immune phagocytes that can develop into macrophages and express LFA-1, CD44, and other surface signaling proteins. CD44, ICAM1, ITGA4, ITGAL, ITGAM, ITGB1, ITGB2, PECAM1, SELE, SELL, SELP 11 ITGA4(1), ITGAL(3), ITGAM(2), ITGB1(1), ITGB2(1), SELE(1), SELL(1) 2640660 10 10 10 0 1 2 1 3 3 0 0.11 0.014 1
8 DNAFRAGMENTPATHWAY DNA fragmentation during apoptosis is effected by DFF, a caspase-activated DNAse, and by endonuclease G. CASP3, CASP7, DFFA, DFFB, ENDOG, GZMB, HMGB1, HMGB2, TOP2A, TOP2B 9 HMGB1(3), HMGB2(2), TOP2B(3) 1504641 8 7 8 0 1 1 1 3 2 0 0.21 0.016 1
9 HSA00830_RETINOL_METABOLISM Genes involved in retinol metabolism ALDH1A1, ALDH1A2, BCMO1, RDH5 4 BCMO1(2), RDH5(2) 643601 4 4 4 1 0 0 3 0 1 0 0.72 0.017 1
10 RABPATHWAY Rab family GTPases regulate vesicle transport, endocytosis and exocytosis, and vesicle docking via interactions with the rabphilins. ACTA1, MEL, RAB11A, RAB1A, RAB2, RAB27A, RAB3A, RAB4A, RAB5A, RAB6A, RAB7, RAB9A 9 ACTA1(1), RAB11A(1), RAB3A(1), RAB6A(1) 705580 4 4 4 1 0 1 0 2 1 0 0.81 0.021 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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