Mutation Analysis (MutSig v2.0 and MutSigCV v0.9 merged result)
Skin Cutaneous Melanoma (Metastatic)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1668BVC
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/C1668BVC
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: SKCM-TM

  • Number of patients in set: 278

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-TM.final_analysis_set.maf

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

  • Significantly mutated genes (q ≤ 0.1): 116

  • Mutations seen in COSMIC: 754

  • Significantly mutated genes in COSMIC territory: 54

  • Significantly mutated genesets: 2

Mutation Preprocessing

  • Read 278 MAFs of type "Broad"

  • Total number of mutations in input MAFs: 258634

  • After removing 391 mutations outside chr1-24: 258243

  • After removing 1760 blacklisted mutations: 256483

  • After removing 3579 noncoding mutations: 252904

  • After collapsing adjacent/redundant mutations: 228614

Mutation Filtering

  • Number of mutations before filtering: 228614

  • After removing 8250 mutations outside gene set: 220364

  • After removing 345 mutations outside category set: 220019

  • After removing 9 "impossible" mutations in

  • gene-patient-category bins of zero coverage: 211415

Results
Breakdown of Mutations by Type

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

type count
Frame_Shift_Del 955
Frame_Shift_Ins 246
In_Frame_Del 250
In_Frame_Ins 28
Missense_Mutation 132329
Nonsense_Mutation 8213
Nonstop_Mutation 53
Silent 72280
Splice_Site 5664
Translation_Start_Site 1
Total 220019
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 101233 2214670000 0.000046 46 2.5 1.6
(A/G)p*C->T 11192 1859082941 6e-06 6 0.33 1.9
A->G 5621 3929510266 1.4e-06 1.4 0.077 2.3
transver 14279 8003263207 1.8e-06 1.8 0.097 5
indel+null 15113 8003263207 1.9e-06 1.9 0.1 NaN
double_null 296 8003263207 3.7e-08 0.037 0.002 NaN
Total 147734 8003263207 0.000018 18 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: SKCM-TM.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: (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_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: 116. 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 C15orf23 chromosome 15 open reading frame 23 282599 20 19 8 3 20 0 0 0 0 0 0 1 0 0.00063 0 0
2 ANKRD20A4 ankyrin repeat domain 20 family, member A4 330573 7 6 5 3 6 0 0 1 0 0 0 0.84 0 1 0 0
3 CDKN2A cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4) 251438 42 41 19 1 12 1 0 1 28 0 2.4e-06 0 0 6.2e-15 0 0
4 NRAS neuroblastoma RAS viral (v-ras) oncogene homolog 162855 86 86 11 0 2 2 33 48 1 0 0 0 0 0 0 0
5 BRAF v-raf murine sarcoma viral oncogene homolog B1 617006 146 140 18 2 15 1 5 122 3 0 0 0 0 1.6e-15 0 0
6 OXA1L oxidase (cytochrome c) assembly 1-like 423771 8 8 3 2 8 0 0 0 0 0 0 1 0 0.58 0 0
7 TP53 tumor protein p53 336707 51 47 41 0 21 1 4 4 20 1 0 0.0014 0 8.7e-15 0 0
8 STK19 serine/threonine kinase 19 301184 18 13 10 0 15 1 0 1 1 0 0 0.95 0 0.99 0 0
9 PCDHAC2 protocadherin alpha subfamily C, 2 792257 474 156 415 295 384 41 6 32 9 2 0.022 0.36 0.036 1.7e-15 2.3e-15 4.7e-12
10 TMEM216 transmembrane protein 216 87785 8 8 1 0 0 0 0 0 8 0 0 1 6e-06 1.3e-11 3e-15 5.4e-12
11 PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 311413 23 23 21 0 2 0 3 5 13 0 0.1 0.58 0.16 4.4e-15 2.5e-14 4.1e-11
12 MRPS31 mitochondrial ribosomal protein S31 322993 20 19 5 0 1 0 0 1 18 0 0.82 0.55 1 9.3e-15 3.1e-13 4.7e-10
13 PCDHGC5 protocadherin gamma subfamily C, 5 796146 354 141 329 248 265 24 15 33 17 0 0.42 0.54 0.73 3.8e-13 8.2e-12 1.1e-08
14 BAGE B melanoma antigen 34978 8 8 6 1 0 0 0 0 8 0 NaN NaN NaN 1.2e-11 1.2e-11 1.6e-08
15 DSG1 desmoglein 1 885454 63 45 55 11 48 4 1 3 7 0 0.068 0.54 0.11 3.6e-09 9.1e-09 0.000011
16 PPP6C protein phosphatase 6, catalytic subunit 279243 21 20 15 3 14 0 0 2 5 0 0.05 0.37 0.098 8.9e-09 1.9e-08 0.000021
17 RAC1 ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) 171147 20 20 9 1 17 0 0 3 0 0 6e-07 0.31 3e-06 0.00033 2.1e-08 0.000022
18 SERPINB3 serpin peptidase inhibitor, clade B (ovalbumin), member 3 315773 57 42 48 17 43 2 1 5 5 1 0.76 0.031 0.15 1.1e-08 3.5e-08 0.000035
19 TSHB thyroid stimulating hormone, beta 118027 6 5 5 3 4 1 0 0 1 0 0.1 0.054 0.03 1e-07 6.5e-08 0.000062
20 NDUFB9 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 9, 22kDa 154566 8 8 1 1 0 0 0 0 8 0 NaN NaN NaN 2.6e-07 2.6e-07 0.00024
21 MS4A2 membrane-spanning 4-domains, subfamily A, member 2 (Fc fragment of IgE, high affinity I, receptor for; beta polypeptide) 220087 13 13 12 1 9 0 0 0 4 0 0.68 0.89 1 2.5e-08 4.6e-07 0.00039
22 RPS27 ribosomal protein S27 (metallopanstimulin 1) 56962 25 24 3 0 1 0 0 0 24 0 NaN NaN NaN 5.3e-07 5.3e-07 0.00043
23 PPIAL4G peptidylprolyl isomerase A (cyclophilin A)-like 4G 138722 15 15 11 8 9 0 0 4 2 0 0.06 0.99 0.1 3.6e-07 6.5e-07 0.00051
24 LUZP2 leucine zipper protein 2 277052 28 27 25 4 19 1 1 2 5 0 0.045 0.32 0.063 6.8e-07 7.7e-07 0.00058
25 FAM113B family with sequence similarity 113, member B 300241 29 28 25 20 23 0 0 2 4 0 0.54 0.29 0.57 8.7e-08 8.8e-07 0.00063
26 IDH1 isocitrate dehydrogenase 1 (NADP+), soluble 349685 16 16 6 2 13 0 0 2 1 0 8e-07 0.98 5.2e-06 0.01 9.4e-07 0.00065
27 OR51S1 olfactory receptor, family 51, subfamily S, member 1 270011 33 30 22 10 27 2 0 2 2 0 0.0016 0.96 0.0034 0.000026 1.6e-06 0.001
28 CYP4X1 cytochrome P450, family 4, subfamily X, polypeptide 1 433239 26 21 24 13 17 1 1 1 5 1 0.0041 0.61 0.012 0.000016 3.1e-06 0.002
29 ARMC4 armadillo repeat containing 4 815288 81 54 64 21 59 4 2 5 11 0 0.41 0.92 0.51 4.3e-07 3.6e-06 0.0022
30 TUBAL3 tubulin, alpha-like 3 375670 11 10 11 5 7 3 0 0 1 0 0.68 0.39 0.78 4.1e-07 5.2e-06 0.0031
31 AOAH acyloxyacyl hydrolase (neutrophil) 536795 27 27 24 11 17 0 0 5 4 1 0.15 0.41 0.25 1.5e-06 6.1e-06 0.0036
32 NMNAT3 nicotinamide nucleotide adenylyltransferase 3 180398 11 11 10 9 4 1 1 2 3 0 0.00096 0.0029 0.00039 0.0011 6.6e-06 0.0037
33 THEMIS thymocyte selection associated 521883 44 34 33 17 37 1 1 3 2 0 0.000098 0.76 0.00032 0.0015 7.5e-06 0.0041
34 CYP4Z1 cytochrome P450, family 4, subfamily Z, polypeptide 1 398973 28 27 22 10 23 1 0 1 3 0 0.093 0.48 0.18 3.3e-06 9.2e-06 0.0049
35 CTAGE6P 184178 8 7 6 3 8 0 0 0 0 0 3.6e-06 0.88 3.6e-06 0.2 0.000011 0.0055
C15orf23

Figure S1.  This figure depicts the distribution of mutations and mutation types across the C15orf23 significant gene.

ANKRD20A4

Figure S2.  This figure depicts the distribution of mutations and mutation types across the ANKRD20A4 significant gene.

CDKN2A

Figure S3.  This figure depicts the distribution of mutations and mutation types across the CDKN2A significant gene.

NRAS

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

BRAF

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

OXA1L

Figure S6.  This figure depicts the distribution of mutations and mutation types across the OXA1L significant gene.

TP53

Figure S7.  This figure depicts the distribution of mutations and mutation types across the TP53 significant gene.

STK19

Figure S8.  This figure depicts the distribution of mutations and mutation types across the STK19 significant gene.

PCDHAC2

Figure S9.  This figure depicts the distribution of mutations and mutation types across the PCDHAC2 significant gene.

TMEM216

Figure S10.  This figure depicts the distribution of mutations and mutation types across the TMEM216 significant gene.

PTEN

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

MRPS31

Figure S12.  This figure depicts the distribution of mutations and mutation types across the MRPS31 significant gene.

PCDHGC5

Figure S13.  This figure depicts the distribution of mutations and mutation types across the PCDHGC5 significant gene.

BAGE

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

DSG1

Figure S15.  This figure depicts the distribution of mutations and mutation types across the DSG1 significant gene.

PPP6C

Figure S16.  This figure depicts the distribution of mutations and mutation types across the PPP6C significant gene.

RAC1

Figure S17.  This figure depicts the distribution of mutations and mutation types across the RAC1 significant gene.

SERPINB3

Figure S18.  This figure depicts the distribution of mutations and mutation types across the SERPINB3 significant gene.

TSHB

Figure S19.  This figure depicts the distribution of mutations and mutation types across the TSHB significant gene.

NDUFB9

Figure S20.  This figure depicts the distribution of mutations and mutation types across the NDUFB9 significant gene.

MS4A2

Figure S21.  This figure depicts the distribution of mutations and mutation types across the MS4A2 significant gene.

RPS27

Figure S22.  This figure depicts the distribution of mutations and mutation types across the RPS27 significant gene.

PPIAL4G

Figure S23.  This figure depicts the distribution of mutations and mutation types across the PPIAL4G significant gene.

LUZP2

Figure S24.  This figure depicts the distribution of mutations and mutation types across the LUZP2 significant gene.

FAM113B

Figure S25.  This figure depicts the distribution of mutations and mutation types across the FAM113B significant gene.

IDH1

Figure S26.  This figure depicts the distribution of mutations and mutation types across the IDH1 significant gene.

OR51S1

Figure S27.  This figure depicts the distribution of mutations and mutation types across the OR51S1 significant gene.

CYP4X1

Figure S28.  This figure depicts the distribution of mutations and mutation types across the CYP4X1 significant gene.

ARMC4

Figure S29.  This figure depicts the distribution of mutations and mutation types across the ARMC4 significant gene.

TUBAL3

Figure S30.  This figure depicts the distribution of mutations and mutation types across the TUBAL3 significant gene.

NMNAT3

Figure S31.  This figure depicts the distribution of mutations and mutation types across the NMNAT3 significant gene.

THEMIS

Figure S32.  This figure depicts the distribution of mutations and mutation types across the THEMIS significant gene.

CYP4Z1

Figure S33.  This figure depicts the distribution of mutations and mutation types across the CYP4Z1 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: 54. Number of genes displayed: 10

rank gene description n cos n_cos N_cos cos_ev p q
1 NDUFB9 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 9, 22kDa 8 1 8 278 8 5e-15 2.2e-11
2 STK19 serine/threonine kinase 19 18 2 8 556 16 9.7e-15 2.2e-11
3 IDH1 isocitrate dehydrogenase 1 (NADP+), soluble 16 5 12 1390 17904 2.4e-14 3.6e-11
4 NRAS neuroblastoma RAS viral (v-ras) oncogene homolog 86 33 83 9174 102748 1.4e-13 1.5e-10
5 BRAF v-raf murine sarcoma viral oncogene homolog B1 146 89 139 24742 1795885 2.7e-13 1.9e-10
6 TP53 tumor protein p53 51 356 48 98968 5013 2.8e-13 1.9e-10
7 CDKN2A cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4) 42 332 42 92296 1570 2.9e-13 1.9e-10
8 EPHA6 EPH receptor A6 67 8 6 2224 6 6.4e-12 3.6e-09
9 PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 23 767 22 213226 410 2.6e-10 1.3e-07
10 EPHA7 EPH receptor A7 52 13 5 3614 5 1e-08 4.7e-06

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: 2. 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 ST_G_ALPHA_S_PATHWAY The G-alpha-s protein activates adenylyl cyclases, which catalyze cAMP formation. ASAH1, BF, BFAR, BRAF, CAMP, CREB1, CREB3, CREB5, EPAC, GAS, GRF2, MAPK1, RAF1, SNX13, SRC, TERF2IP 12 BFAR(1), BRAF(146), CAMP(2), CREB3(1), CREB5(9), MAPK1(4), RAF1(10), SNX13(5), SRC(2), TERF2IP(1) 4563015 181 157 52 33 38 4 6 127 6 0 0.0023 5.5e-11 3.4e-08
2 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 CCND1(2), CDK4(7), CDKN1A(3), CDKN1B(1), CDKN2A(42), CFL1(2), E2F1(5), E2F2(5), MDM2(1), NXT1(2), PRB1(37), TP53(51) 3459942 158 99 114 17 80 5 6 12 54 1 8.4e-13 2.9e-09 9.1e-07
3 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 HDAC1(2), MYC(5), SP1(5), SP3(1), TP53(51), WT1(8) 2903335 72 58 61 5 31 4 7 6 23 1 1.5e-07 0.00052 0.11
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 CCNA1(14), CCND1(2), CCNE1(4), CCNE2(8), CDK4(7), CDKN1B(1), CDKN2A(42), E2F1(5), E2F2(5), E2F4(3), PRB1(37) 3685602 128 88 93 20 74 2 4 15 33 0 2.9e-07 0.019 1
5 HSA00472_D_ARGININE_AND_D_ORNITHINE_METABOLISM Genes involved in D-arginine and D-ornithine metabolism DAO 1 DAO(11) 293722 11 11 11 2 8 1 1 1 0 0 0.088 0.086 1
6 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(13), CDKN2A(42), E2F1(5), MDM2(1), MYC(5), PIK3CA(10), PIK3R1(2), POLR1A(13), POLR1B(9), POLR1C(1), RAC1(20), RB1(10), TBX2(6), TP53(51), TWIST1(1) 8282634 189 115 143 28 96 9 7 15 58 4 4.7e-11 0.34 1
7 HSA00627_1,4_DICHLOROBENZENE_DEGRADATION Genes involved in 1,4-dichlorobenzene degradation CMBL 1 CMBL(5) 210423 5 5 5 1 5 0 0 0 0 0 0.37 0.36 1
8 HSA00401_NOVOBIOCIN_BIOSYNTHESIS Genes involved in novobiocin biosynthesis GOT1, GOT2, TAT 3 GOT1(6), GOT2(6), TAT(19) 1077313 31 20 30 7 23 3 2 1 2 0 0.0061 0.84 1
9 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 CHUK(2), DNAJC3(3), EIF2S1(1), MAP3K14(6), NFKB1(6), NFKBIA(2), RELA(4), TP53(51) 3955534 75 62 65 13 35 5 5 7 22 1 0.00032 0.95 1
10 BOTULINPATHWAY Blockade of Neurotransmitter Relase by Botulinum Toxin CHRM1, CHRNA1, SNAP25, STX1A, VAMP2 5 CHRM1(5), CHRNA1(7), SNAP25(8) 1337968 20 18 18 3 15 1 0 1 3 0 0.0017 0.95 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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