Mutation Analysis (MutSig v2.0 and MutSigCV v0.9 merged result)
Acute Myeloid Leukemia (Primary blood derived cancer - Peripheral blood)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1T15285
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Mutation Analysis (MutSig v2.0 and MutSigCV v0.9 merged result). Broad Institute of MIT and Harvard. doi:10.7908/C1T15285
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: LAML-TB

  • Number of patients in set: 197

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:LAML-TB.final_analysis_set.maf

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

  • Significantly mutated genes (q ≤ 0.1): 6

  • Mutations seen in COSMIC: 238

  • Significantly mutated genes in COSMIC territory: 19

  • Significantly mutated genesets: 64

Mutation Preprocessing

  • Read 197 MAFs of type "WashU"

  • Total number of mutations in input MAFs: 2585

  • After removing 41 mutations outside chr1-24: 2544

  • After removing 1 blacklisted mutations: 2543

  • After removing 104 noncoding mutations: 2439

Mutation Filtering

  • Number of mutations before filtering: 2439

  • After removing 204 mutations outside gene set: 2235

  • After removing 14 mutations outside category set: 2221

  • After removing 1 "impossible" mutations in

  • gene-patient-category bins of zero coverage: 2002

Results
Breakdown of Mutations by Type

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

type count
Frame_Shift_Del 51
Frame_Shift_Ins 110
In_Frame_Del 8
In_Frame_Ins 43
Missense_Mutation 1400
Nonsense_Mutation 108
Silent 451
Splice_Site 50
Total 2221
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 508 272168305 1.9e-06 1.9 5.8 2.2
*Cp(A/C/T)->T 312 2466260336 1.3e-07 0.13 0.39 1.7
A->G 182 2743656430 6.6e-08 0.066 0.21 2.3
transver 398 5482085071 7.3e-08 0.073 0.22 5.1
indel+null 357 5482085071 6.5e-08 0.065 0.2 NaN
double_null 13 5482085071 2.4e-09 0.0024 0.0073 NaN
Total 1770 5482085071 3.2e-07 0.32 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: LAML-TB.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: *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: 6. 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_clust p_cons p_joint p_cv p q
1 DNMT3A DNA (cytosine-5-)-methyltransferase 3 alpha 512791 57 51 29 0 34 2 3 4 14 0 0 0 0 1 0 0
2 U2AF1 U2 small nuclear RNA auxiliary factor 1 153266 8 8 2 0 0 5 0 3 0 0 1e-05 0.000096 0 1 0 0
3 FLT3 fms-related tyrosine kinase 3 597107 56 56 30 0 0 0 1 16 39 0 0 1.2e-06 0 1 0 0
4 IDH2 isocitrate dehydrogenase 2 (NADP+), mitochondrial 230293 20 20 2 0 16 3 0 1 0 0 0 0.66 0 1 0 0
5 IDH1 isocitrate dehydrogenase 1 (NADP+), soluble 251569 19 19 2 0 17 0 0 2 0 0 0 0.97 0 1 0 0
6 NPM1 nucleophosmin (nucleolar phosphoprotein B23, numatrin) 183407 54 54 7 0 0 0 1 0 52 1 0 0 0 1 0 0
7 NRAS neuroblastoma RAS viral (v-ras) oncogene homolog 115442 15 15 6 0 0 8 1 6 0 0 6e-07 0.24 4.2e-06 1 0.000056 0.14
8 WT1 Wilms tumor 1 164692 12 12 10 0 1 1 0 0 9 1 0.00012 0.99 0.00022 1 0.002 1
9 RUNX1 runt-related transcription factor 1 (acute myeloid leukemia 1; aml1 oncogene) 145189 20 18 16 0 2 3 2 2 10 1 0.026 0.01 0.0032 1 0.021 1
10 SMG1 smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans) 2065151 3 3 3 0 0 1 1 1 0 0 0.0053 0.1 0.0033 1 0.022 1
11 KIT v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog 585287 9 8 5 0 1 0 0 6 1 1 0.011 0.084 0.015 1 0.079 1
12 EZH2 enhancer of zeste homolog 2 (Drosophila) 459010 3 3 3 0 1 0 0 0 1 1 0.018 0.81 0.028 1 0.13 1
13 TP53 tumor protein p53 258267 18 15 18 1 3 2 3 2 8 0 0.015 0.25 0.028 1 0.13 1
14 GSTK1 glutathione S-transferase kappa 1 172769 2 2 2 0 1 0 0 1 0 0 0.024 0.22 0.031 1 0.14 1
15 GATA2 GATA binding protein 2 159964 2 2 2 0 0 1 0 1 0 0 0.46 0.025 0.035 1 0.15 1
16 FCGBP Fc fragment of IgG binding protein 2259984 3 3 3 2 1 1 0 1 0 0 0.047 0.075 0.038 1 0.16 1
17 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog 139279 8 8 6 0 0 4 1 3 0 0 0.023 0.64 0.039 1 0.16 1
18 DOCK2 dedicator of cytokinesis 2 1113838 2 2 2 0 0 0 1 0 1 0 0.077 0.0046 0.043 1 0.18 1
19 PTPN11 protein tyrosine phosphatase, non-receptor type 11 (Noonan syndrome 1) 359328 9 9 9 0 0 3 2 4 0 0 0.045 0.26 0.06 1 0.23 1
20 PKD1L2 polycystic kidney disease 1-like 2 1191259 2 2 2 2 1 1 0 0 0 0 0.28 0.066 0.064 1 0.24 1
21 TRPM3 transient receptor potential cation channel, subfamily M, member 3 1053359 2 2 2 0 1 1 0 0 0 0 0.022 0.44 0.068 1 0.25 1
22 CBL Cas-Br-M (murine) ecotropic retroviral transforming sequence 509442 2 2 2 1 0 0 1 0 1 0 0.014 0.39 0.084 1 0.29 1
23 COL12A1 collagen, type XII, alpha 1 1846875 3 3 3 1 1 1 0 1 0 0 0.95 0.01 0.093 1 0.31 1
24 NR2E1 nuclear receptor subfamily 2, group E, member 1 182225 2 2 2 0 0 1 0 1 0 0 0.3 0.091 0.1 1 0.33 1
25 PDCD2L programmed cell death 2-like 161934 2 2 2 0 0 0 2 0 0 0 0.35 0.075 0.1 1 0.34 1
26 HNRNPK heterogeneous nuclear ribonucleoprotein K 293530 2 2 2 0 0 0 0 0 1 1 0.025 0.79 0.11 1 0.34 1
27 CSMD3 CUB and Sushi multiple domains 3 2259590 2 2 2 0 1 1 0 0 0 0 0.12 0.13 0.11 1 0.36 1
28 SMC1A structural maintenance of chromosomes 1A 744857 7 7 7 0 3 0 1 2 1 0 0.47 0.032 0.11 1 0.36 1
29 KIAA1683 KIAA1683 543523 2 2 2 1 0 0 1 0 1 0 0.48 0.072 0.12 1 0.37 1
30 PHACTR1 phosphatase and actin regulator 1 323868 3 3 2 0 0 0 0 1 2 0 0.04 0.7 0.12 1 0.38 1
31 PLCE1 phospholipase C, epsilon 1 1441843 4 4 4 0 0 0 1 3 0 0 0.068 0.92 0.12 1 0.38 1
32 SI sucrase-isomaltase (alpha-glucosidase) 1117384 2 2 2 0 0 0 1 1 0 0 0.064 0.24 0.13 1 0.39 1
33 THRAP3 thyroid hormone receptor associated protein 3 572876 2 2 2 0 1 0 0 0 1 0 0.24 0.12 0.13 1 0.39 1
34 NF1 neurofibromin 1 (neurofibromatosis, von Recklinghausen disease, Watson disease) 1721977 2 2 2 0 1 0 0 0 1 0 0.031 0.52 0.14 1 0.42 1
35 ZBTB33 zinc finger and BTB domain containing 33 398531 2 2 2 0 0 0 0 2 0 0 0.2 0.13 0.15 1 0.43 1
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: 19. Number of genes displayed: 10

rank gene description n cos n_cos N_cos cos_ev p q
1 TP53 tumor protein p53 18 824 16 162328 3427 0 0
2 IDH1 isocitrate dehydrogenase 1 (NADP+), soluble 19 5 19 985 28348 3.7e-14 6.4e-11
3 IDH2 isocitrate dehydrogenase 2 (NADP+), mitochondrial 20 6 20 1182 2000 4.4e-14 6.4e-11
4 PTPN11 protein tyrosine phosphatase, non-receptor type 11 (Noonan syndrome 1) 9 32 8 6304 216 2.3e-13 2.1e-10
5 NRAS neuroblastoma RAS viral (v-ras) oncogene homolog 15 33 15 6501 11840 2.4e-13 2.1e-10
6 NPM1 nucleophosmin (nucleolar phosphoprotein B23, numatrin) 54 41 53 8077 112668 3e-13 2.2e-10
7 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog 8 52 7 10244 46308 3.8e-13 2.4e-10
8 FLT3 fms-related tyrosine kinase 3 56 124 52 24428 6301 9e-13 4.9e-10
9 RUNX1 runt-related transcription factor 1 (acute myeloid leukemia 1; aml1 oncogene) 20 178 18 35066 93 1.3e-12 5.9e-10
10 WT1 Wilms tumor 1 12 185 9 36445 444 1.3e-12 5.9e-10

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: 64. 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 GLUTATHIONE_METABOLISM ANPEP, G6PD, GCLC, GCLM, GGT1, GPX1, GPX2, GPX3, GPX4, GPX5, GSS, GSTA1, GSTA2, GSTA3, GSTA4, GSTM1, GSTM2, GSTM3, GSTM4, GSTM5, GSTO2, GSTP1, GSTT1, GSTT2, GSTZ1, IDH1, IDH2, MGST1, MGST2, MGST3, PGD 29 GCLM(1), GPX2(1), GSTM3(1), IDH1(19), IDH2(20) 5170462 42 40 7 0 33 4 0 5 0 0 1.7e-07 2e-15 3.1e-13
2 ERYTHPATHWAY Erythropoietin selectively stimulates erythrocyte differentiation from CFU-GEMM cells in bone marrow. CCL3, CSF2, CSF3, EPO, FLT3, IGF1, IL11, IL1A, IL3, IL6, IL9, KITLG, TGFB1, TGFB2, TGFB3 14 FLT3(56) 2377790 56 56 30 0 0 0 1 16 39 0 0.048 2.2e-15 3.1e-13
3 HSA00271_METHIONINE_METABOLISM Genes involved in methionine metabolism AHCY, AMD1, BHMT, CBS, CTH, DNMT1, DNMT3A, DNMT3B, KIAA0828, MARS, MARS2, MAT1A, MAT2B, MTAP, MTFMT, MTR, SRM, TAT 17 DNMT1(1), DNMT3A(57), DNMT3B(1), MAT1A(1) 5703150 60 53 32 0 36 2 3 5 14 0 1.2e-09 2.8e-15 3.1e-13
4 HSA04640_HEMATOPOIETIC_CELL_LINEAGE Genes involved in hematopoietic cell lineage ANPEP, CD14, CD19, CD1A, CD1B, CD1C, CD1D, CD1E, CD2, CD22, CD24, CD33, CD34, CD36, CD37, CD38, CD3D, CD3E, CD3G, CD4, CD44, CD5, CD55, CD59, CD7, CD8A, CD8B, CD9, CR1, CR2, CSF1, CSF1R, CSF2, CSF2RA, CSF3, CSF3R, DNTT, EPO, EPOR, FCER2, FCGR1A, FLT3, FLT3LG, GP1BA, GP1BB, GP5, GP9, GYPA, HLA-DRA, HLA-DRB1, HLA-DRB3, HLA-DRB4, HLA-DRB5, IL11, IL11RA, IL1A, IL1B, IL1R1, IL1R2, IL2RA, IL3, IL3RA, IL4, IL4R, IL5, IL5RA, IL6, IL6R, IL7, IL7R, IL9R, ITGA1, ITGA2, ITGA2B, ITGA3, ITGA4, ITGA5, ITGA6, ITGAM, ITGB3, KIT, KITLG, MME, MS4A1, TFRC, THPO, TNF, TPO 82 CR1(1), CSF3R(1), FLT3(56), HLA-DRB1(1), IL1R1(1), KIT(9), TPO(1) 23610450 70 68 40 1 2 2 1 24 40 1 0.0088 3.8e-15 3.1e-13
5 HSA00480_GLUTATHIONE_METABOLISM Genes involved in glutathione metabolism ANPEP, G6PD, GCLC, GCLM, GGT1, GGTL3, GGTL4, GPX1, GPX2, GPX3, GPX4, GPX5, GPX6, GPX7, GSR, GSS, GSTA1, GSTA2, GSTA3, GSTA4, GSTA5, GSTK1, GSTM1, GSTM2, GSTM3, GSTM4, GSTM5, GSTO2, GSTP1, GSTT1, GSTT2, GSTZ1, IDH1, IDH2, MGST1, MGST2, MGST3, OPLAH, TXNDC12 34 GCLM(1), GPX2(1), GSTK1(2), GSTM3(1), IDH1(19), IDH2(20) 5770918 44 42 9 0 34 4 0 6 0 0 1e-07 3.9e-15 3.1e-13
6 NUCLEAR_RECEPTORS ALK, AR, ESR1, ESR2, ESRRA, HNF4A, NPM1, NR0B1, NR1D2, NR1H2, NR1H3, NR1I2, NR1I3, NR2C2, NR2E1, NR2F1, NR2F2, NR2F6, NR3C1, NR4A1, NR4A2, NR5A1, NR5A2, PGR, PPARA, PPARD, PPARG, RARA, RARB, RARG, ROR1, RORA, RORC, RXRA, RXRB, RXRG, THRA, THRA, NR1D1, THRB, VDR 38 NPM1(54), NR2E1(2), THRB(1) 11589707 57 56 10 0 1 1 1 1 52 1 0.25 4.1e-15 3.1e-13
7 HSA00020_CITRATE_CYCLE Genes involved in citrate cycle (TCA cycle) ACLY, ACO1, ACO2, CLYBL, CS, DLD, DLST, FH, IDH1, IDH2, IDH3A, IDH3B, IDH3G, LOC283398, LOC441996, MDH1, MDH2, OGDH, OGDHL, PC, PCK1, PCK2, SDHA, SDHB, SDHC, SDHD, SUCLA2, SUCLG1, SUCLG2 27 DLD(1), IDH1(19), IDH2(20) 8626236 40 39 5 2 33 4 0 3 0 0 0.000017 4.7e-15 3.1e-13
8 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 DLD(1), IDH1(19), IDH2(20) 5929109 40 39 5 1 33 4 0 3 0 0 1.5e-06 5.3e-15 3.1e-13
9 REDUCTIVE_CARBOXYLATE_CYCLE_CO2_FIXATION ACO1, ACO2, FH, IDH1, IDH2, MDH1, MDH2, SDHB, SUCLA2 9 IDH1(19), IDH2(20) 2582079 39 38 4 0 33 3 0 3 0 0 2.8e-07 5.3e-15 3.1e-13
10 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 IDH2(20) 2741649 20 20 2 0 16 3 0 1 0 0 0.00031 6.1e-15 3.1e-13
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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