Mutation Analysis (MutSig v2.0 and MutSigCV v0.9 merged result)
Brain Lower Grade Glioma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1707ZGR
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/C1707ZGR
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: LGG-TP

  • Number of patients in set: 217

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:LGG-TP.final_analysis_set.maf

  • Significantly mutated genes (q ≤ 0.1): 16

  • Mutations seen in COSMIC: 425

  • Significantly mutated genes in COSMIC territory: 13

  • Significantly mutated genesets: 100

Mutation Preprocessing

  • Read 217 MAFs of type "Broad"

  • Total number of mutations in input MAFs: 27275

  • After removing 13 mutations outside chr1-24: 27262

  • After removing 590 blacklisted mutations: 26672

  • After removing 573 noncoding mutations: 26099

Mutation Filtering

  • Number of mutations before filtering: 26099

  • After removing 361 mutations outside gene set: 25738

  • After removing 101 mutations outside category set: 25637

  • After removing 3 "impossible" mutations in

  • gene-patient-category bins of zero coverage: 25172

Results
Breakdown of Mutations by Type

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

type count
Frame_Shift_Del 584
Frame_Shift_Ins 291
In_Frame_Del 299
In_Frame_Ins 13
Missense_Mutation 16460
Nonsense_Mutation 1024
Nonstop_Mutation 13
Silent 6454
Splice_Site 453
Translation_Start_Site 46
Total 25637
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 5399 352259750 0.000015 15 5.1 2.1
*Cp(A/C/T)->T 3600 2893376300 1.2e-06 1.2 0.41 1.7
A->G 2256 3122700650 7.2e-07 0.72 0.24 2.3
transver 5250 6368336700 8.2e-07 0.82 0.27 5
indel+null 2587 6368336700 4.1e-07 0.41 0.13 NaN
double_null 89 6368336700 1.4e-08 0.014 0.0046 NaN
Total 19181 6368336700 3e-06 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).

Figure 1. 

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

Figure 2.  Patients counts and rates file used to generate this plot: LGG-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: 16. 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 113894 6 6 1 0 0 0 0 0 6 0 0.98 0 4.7e-09 0 0
2 IDH2 isocitrate dehydrogenase 2 (NADP+), mitochondrial 252948 9 9 3 0 0 6 0 3 0 0 1 0 0.000074 0 0
3 IDH1 isocitrate dehydrogenase 1 (NADP+), soluble 275139 165 165 2 0 155 0 0 10 0 0 1 0 3.3e-16 0 0
4 TP53 tumor protein p53 267086 148 113 76 2 58 15 21 31 20 3 0 0 1.1e-16 0 0
5 ATRX alpha thalassemia/mental retardation syndrome X-linked (RAD54 homolog, S. cerevisiae) 1632339 98 93 87 3 2 4 8 6 73 5 0.46 0.23 2.6e-15 2.1e-14 7.5e-11
6 CIC capicua homolog (Drosophila) 909824 46 41 39 0 17 1 1 5 21 1 0.88 0.2 6.2e-15 4.3e-14 1.3e-10
7 FUBP1 far upstream element (FUSE) binding protein 1 428208 22 22 21 2 0 0 1 2 19 0 0.9 0.56 8.5e-15 1.6e-13 4.2e-10
8 NOTCH1 Notch homolog 1, translocation-associated (Drosophila) 1333631 26 19 23 3 4 3 1 6 9 3 0.027 0.000043 1.4e-09 1.9e-12 4.4e-09
9 PIK3R1 phosphoinositide-3-kinase, regulatory subunit 1 (alpha) 512641 15 14 13 1 1 2 3 0 9 0 0.85 0.021 4.7e-09 2.4e-09 4.8e-06
10 PIK3CA phosphoinositide-3-kinase, catalytic, alpha polypeptide 712138 21 19 13 0 0 7 7 3 4 0 0.016 0.02 1.7e-08 7.6e-09 0.000014
11 CREBZF CREB/ATF bZIP transcription factor 224089 4 4 1 0 0 0 0 0 4 0 0.32 6e-06 0.00044 5.4e-08 0.000089
12 PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 263317 12 12 12 0 1 1 1 6 3 0 0.26 0.43 7.1e-08 5.6e-07 0.00084
13 TIMD4 T-cell immunoglobulin and mucin domain containing 4 254458 6 6 3 1 0 1 0 1 4 0 0.58 0.012 0.000036 6.6e-06 0.0091
14 EMG1 EMG1 nucleolar protein homolog (S. cerevisiae) 148063 4 4 2 0 0 0 0 0 4 0 0.74 0.13 0.000015 0.000028 0.036
15 NOX4 NADPH oxidase 4 390044 6 5 3 0 0 1 1 0 4 0 0.54 0.0072 0.00045 0.000044 0.053
16 ZNF57 zinc finger protein 57 363748 7 6 4 0 1 1 1 4 0 0 1 0.00014 0.03 0.000056 0.064
17 SCAF1 SR-related CTD-associated factor 1 428190 4 4 2 1 1 0 0 0 3 0 0.18 0.0031 0.025 0.0008 0.84
18 SMARCA4 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 980041 13 13 11 4 3 0 1 5 4 0 0.37 0.052 0.0015 0.00081 0.84
19 CRIPAK cysteine-rich PAK1 inhibitor 288496 5 5 4 2 1 0 0 1 3 0 0.61 0.48 0.00017 0.00084 0.84
20 TCF12 transcription factor 12 (HTF4, helix-loop-helix transcription factors 4) 492075 10 9 9 0 0 0 0 0 10 0 0.33 0.4 0.00021 0.00085 0.84
21 ZCCHC12 zinc finger, CCHC domain containing 12 263212 3 3 1 0 3 0 0 0 0 0 0.74 0.0058 0.079 0.004 1
22 EGFR epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian) 854034 12 10 9 0 1 4 0 6 1 0 0.044 0.036 0.016 0.0049 1
23 EIF1AX eukaryotic translation initiation factor 1A, X-linked 95665 2 2 2 1 1 0 1 0 0 0 0.35 0.017 0.041 0.0057 1
24 C22orf33 chromosome 22 open reading frame 33 127216 2 2 2 1 0 0 1 0 1 0 0.024 0.0097 0.071 0.0057 1
25 CYCS cytochrome c, somatic 70701 2 2 2 0 0 1 0 1 0 0 0.069 0.012 0.077 0.0075 1
26 ARID1A AT rich interactive domain 1A (SWI-like) 1260450 15 13 15 0 1 0 0 1 12 1 0.64 1 0.0011 0.0083 1
27 TRDN triadin 211891 4 4 4 0 0 1 0 0 3 0 0.25 0.1 0.012 0.0095 1
28 C3orf35 chromosome 3 open reading frame 35 111237 3 3 3 0 0 0 2 0 1 0 0.045 0.092 0.015 0.01 1
29 MYH4 myosin, heavy chain 4, skeletal muscle 1294982 5 5 5 0 3 0 0 2 0 0 0.0038 0.002 0.69 0.011 1
30 ZNRF2 zinc and ring finger 2 62533 3 2 3 0 1 0 0 0 2 0 0.35 1 0.0017 0.013 1
31 SLC44A4 solute carrier family 44, member 4 461047 3 3 2 0 0 1 0 0 2 0 0.59 0.0068 0.27 0.013 1
32 MUC7 mucin 7, secreted 247807 8 5 7 0 1 2 5 0 0 0 0.49 0.35 0.0062 0.015 1
33 C5orf34 chromosome 5 open reading frame 34 423786 2 2 2 1 0 0 0 1 1 0 0.0095 0.0039 0.59 0.016 1
34 FAM64A family with sequence similarity 64, member A 157706 2 2 2 0 1 0 1 0 0 0 0.027 0.015 0.18 0.018 1
35 TRAPPC9 trafficking protein particle complex 9 707047 3 1 3 0 3 0 0 0 0 0 0.78 0.0029 0.99 0.019 1
IL32

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

IDH2

Figure S2.  This figure depicts the distribution of mutations and mutation types across the IDH2 significant gene.

IDH1

Figure S3.  This figure depicts the distribution of mutations and mutation types across the IDH1 significant gene.

TP53

Figure S4.  This figure depicts the distribution of mutations and mutation types across the TP53 significant gene.

ATRX

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

CIC

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

FUBP1

Figure S7.  This figure depicts the distribution of mutations and mutation types across the FUBP1 significant gene.

NOTCH1

Figure S8.  This figure depicts the distribution of mutations and mutation types across the NOTCH1 significant gene.

PIK3R1

Figure S9.  This figure depicts the distribution of mutations and mutation types across the PIK3R1 significant gene.

PIK3CA

Figure S10.  This figure depicts the distribution of mutations and mutation types across the PIK3CA significant gene.

CREBZF

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

PTEN

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

TIMD4

Figure S13.  This figure depicts the distribution of mutations and mutation types across the TIMD4 significant gene.

EMG1

Figure S14.  This figure depicts the distribution of mutations and mutation types across the EMG1 significant gene.

NOX4

Figure S15.  This figure depicts the distribution of mutations and mutation types across the NOX4 significant gene.

ZNF57

Figure S16.  This figure depicts the distribution of mutations and mutation types across the ZNF57 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: 13. 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 165 5 165 1085 246180 4.8e-14 1.3e-10
2 IDH2 isocitrate dehydrogenase 2 (NADP+), mitochondrial 9 6 9 1302 747 5.8e-14 1.3e-10
3 PIK3R1 phosphoinositide-3-kinase, regulatory subunit 1 (alpha) 15 33 7 7161 14 3.1e-13 4.7e-10
4 PIK3CA phosphoinositide-3-kinase, catalytic, alpha polypeptide 21 220 19 47740 2990 1.8e-12 2.1e-09
5 TP53 tumor protein p53 148 356 145 77252 51945 2.7e-12 2.5e-09
6 PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 12 767 11 166439 549 1.2e-11 9.4e-09
7 PTPN11 protein tyrosine phosphatase, non-receptor type 11 (Noonan syndrome 1) 6 32 5 6944 178 3.3e-11 2.1e-08
8 EGFR epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian) 12 293 8 63581 71 4e-11 2.3e-08
9 SMARCA4 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 13 30 4 6510 1 6.1e-09 3e-06
10 NF1 neurofibromin 1 (neurofibromatosis, von Recklinghausen disease, Watson disease) 20 285 6 61845 8 4.9e-08 0.000022

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: 100. 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 HSA00720_REDUCTIVE_CARBOXYLATE_CYCLE Genes involved in reductive carboxylate cycle (CO2 fixation) ACLY, ACO1, ACO2, ACSS1, ACSS2, FH, IDH1, IDH2, LOC441996, MDH1, MDH2, SUCLA2 11 ACLY(3), ACO1(2), ACO2(2), ACSS1(1), ACSS2(3), FH(1), IDH1(165), IDH2(9) 4296350 186 177 17 0 160 8 0 16 2 0 <1.00e-15 <1.00e-15 <8.80e-14
2 CITRATE_CYCLE_TCA_CYCLE ACO1, ACO2, CS, DLD, DLST, DLSTP, FH, IDH1, IDH2, IDH3A, IDH3B, IDH3G, MDH1, MDH2, PC, PCK1, SDHA, SDHA, SDHAL2, SDHB, SUCLA2, SUCLG1, SUCLG2 20 ACO1(2), ACO2(2), FH(1), IDH1(165), IDH2(9), IDH3B(1), PC(1), PCK1(3), SUCLG2(1) 6652756 185 175 16 2 160 10 0 15 0 0 <1.00e-15 <1.00e-15 <8.80e-14
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 ABL1(4), CDKN2A(2), E2F1(1), MDM2(2), PIK3CA(21), PIK3R1(15), POLR1A(4), POLR1B(2), RAC1(1), RB1(4), TBX2(1), TP53(148) 6553032 205 141 123 9 64 26 34 39 39 3 <1.00e-15 <1.00e-15 <8.80e-14
4 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(4), BAX(1), CCND1(1), CDK2(1), CDK4(1), E2F1(1), MDM2(2), RB1(4), TIMP3(2), TP53(148) 5848889 166 117 94 6 61 17 26 35 24 3 1.32e-14 <1.00e-15 <8.80e-14
5 RBPATHWAY The ATM protein kinase recognizes DNA damage and blocks cell cycle progression by phosphorylating chk1 and p53, which normally inhibits Rb to allow G1/S transitions. ATM, CDC2, CDC25A, CDC25B, CDC25C, CDK2, CDK4, CHEK1, MYT1, RB1, TP53, WEE1, YWHAH 12 ATM(4), CDC25A(1), CDK2(1), CDK4(1), CHEK1(3), MYT1(3), RB1(4), TP53(148), WEE1(1), YWHAH(1) 5683263 167 117 95 9 61 17 24 33 29 3 2.39e-11 <1.00e-15 <8.80e-14
6 ATMPATHWAY The tumor-suppressing protein kinase ATM responds to radiation-induced DNA damage by blocking cell-cycle progression and activating DNA repair. ABL1, ATM, BRCA1, CDKN1A, CHEK1, CHEK2, GADD45A, JUN, MAPK8, MDM2, MRE11A, NBS1, NFKB1, NFKBIA, RAD50, RAD51, RBBP8, RELA, TP53, TP73 19 ABL1(4), ATM(4), BRCA1(1), CHEK1(3), CHEK2(3), MAPK8(1), MDM2(2), MRE11A(2), NFKB1(1), RAD50(2), RBBP8(2), RELA(1), TP53(148) 9630116 174 115 102 13 64 22 24 38 23 3 1.64e-10 <1.00e-15 <8.80e-14
7 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 ARF1(1), CCND1(1), CDK2(1), CDK4(1), CDKN1B(1), CDKN2A(2), CFL1(1), E2F1(1), MDM2(2), PRB1(2), TP53(148) 2712441 161 114 89 7 61 17 24 34 22 3 3.65e-14 <1.00e-15 <8.80e-14
8 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 MAX(4), SP3(2), TP53(148), WT1(1) 2279162 155 116 82 2 61 16 21 34 20 3 <1.00e-15 1.22e-15 9.12e-14
9 REDUCTIVE_CARBOXYLATE_CYCLE_CO2_FIXATION ACO1, ACO2, FH, IDH1, IDH2, MDH1, MDH2, SDHB, SUCLA2 9 ACO1(2), ACO2(2), FH(1), IDH1(165), IDH2(9) 2876483 179 175 10 0 158 7 0 14 0 0 1.22e-15 1.33e-15 9.12e-14
10 P53HYPOXIAPATHWAY Hypoxia induces p53 accumulation and consequent apoptosis with p53-mediated cell cycle arrest, which is present under conditions of DNA damage. ABCB1, AKT1, ATM, BAX, CDKN1A, CPB2, CSNK1A1, CSNK1D, FHL2, GADD45A, HIC1, HIF1A, HSPA1A, HSPCA, IGFBP3, MAPK8, MDM2, NFKBIB, NQO1, TP53 19 ABCB1(3), AKT1(1), ATM(4), BAX(1), CPB2(1), CSNK1A1(2), CSNK1D(1), IGFBP3(1), MAPK8(1), MDM2(2), TP53(148) 6705131 165 115 93 9 62 17 24 37 22 3 8.04e-13 1.55e-15 9.40e-14
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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