Glioblastoma Multiforme: Mutation Analysis (MutSig vS2N)
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 vS2N was used to generate the results found in this report.

- Working with individual set: GBM

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:GBM.final_analysis_set.maf

- Significantly mutated genes (q ≤ 0.1): 89

Results
Significantly Mutated Genes

Column Descriptions:

- N = number of sequenced bases in this gene across the individual set

- nnon = number of (nonsilent) mutations in this gene across the individual set

- nnull = number of (nonsilent) null mutations in this gene across the individual set

- nflank = number of noncoding mutations from this gene's flanking region, across the individual set

- nsil = number of silent mutations in this gene across the individual set

- p = p-value (overall)

- q = q-value, False Discovery Rate (Benjamini-Hochberg procedure)

Table 1. Get Full Table A Ranked List of Significantly Mutated Genes. Number of significant genes found: 89. 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).

gene | N | nflank | nsil | nnon | nnull | p | q
--- | --- | --- | --- | --- | --- | --- | ---
PTEN | 44436 | 0 | 0 | 80 | 35 | 0 | 0
POTEB | 5244 | 0 | 1 | 9 | 0 | 4.1e-212 | 3.9e-208
TP53 | 34776 | 0 | 1 | 91 | 28 | 2.2e-91 | 1.4e-87
IDH1 | 44160 | 0 | 0 | 15 | 0 | 3.6e-83 | 1.7e-79
KRTAP5-5 | 16008 | 0 | 0 | 18 | 14 | 1.3e-73 | 4.8e-70
RB1 | 134412 | 0 | 1 | 21 | 18 | 7.6e-56 | 2.4e-52
MICALCL | 57408 | 0 | 0 | 13 | 12 | 3.5e-44 | 9.5e-41
PIK3CA | 116196 | 0 | 1 | 19 | 2 | 4.3e-32 | 1e-28
FOXRED1 | 44160 | 0 | 0 | 9 | 0 | 5e-30 | 1e-26
EGFR | 126132 | 0 | 5 | 58 | 0 | 8.6e-29 | 1.6e-25
NF1 | 412068 | 0 | 1 | 34 | 20 | 3.2e-26 | 5.6e-23
IRF5 | 41400 | 0 | 0 | 5 | 5 | 6.9e-22 | 1.1e-18
CALN1 | 24012 | 0 | 1 | 9 | 0 | 4.5e-20 | 6.5e-17
ZNF704 | 36984 | 0 | 0 | 5 | 5 | 4.8e-18 | 6.4e-15
PRMT6 | 24288 | 0 | 0 | 5 | 0 | 1.4e-17 | 1.8e-14
COMMD4 | 16008 | 0 | 0 | 6 | 0 | 4.3e-17 | 5e-14
NKPD1 | 12144 | 0 | 0 | 4 | 4 | 1.2e-16 | 1.3e-13
POTED | 13800 | 0 | 1 | 5 | 1 | 1.3e-16 | 1.3e-13
TGM2 | 59064 | 0 | 2 | 9 | 2 | 6.7e-15 | 6.6e-12
ARHGEF2 | 80592 | 0 | 0 | 6 | 1 | 1.1e-14 | 1e-11
NACA | 134136 | 0 | 0 | 7 | 6 | 2.3e-11 | 2e-08
PIK3R1 | 81420 | 0 | 0 | 17 | 8 | 3e-11 | 2.6e-08
LPHN1 | 114816 | 0 | 2 | 10 | 0 | 1.8e-10 | 1.5e-07
STAG2 | 137172 | 0 | 0 | 11 | 7 | 5.6e-10 | 4.4e-07
PLA2G2A | 14904 | 0 | 0 | 5 | 0 | 2.2e-09 | 1.7e-06
EML2 | 56304 | 0 | 1 | 8 | 8 | 3.3e-09 | 2.4e-06
IGSF9 | 73140 | 0 | 0 | 7 | 2 | 2e-08 | 0.000014
MST1 | 58236 | 0 | 0 | 10 | 7 | 2.3e-08 | 0.000016
PRIM2 | 46644 | 0 | 1 | 5 | 5 | 2.9e-08 | 0.000019
PROKR2 | 40296 | 0 | 1 | 6 | 0 | 3.6e-08 | 0.000022
TMEM45A | 29808 | 0 | 0 | 5 | 0 | 7e-08 | 0.000043
EPX | 64584 | 0 | 2 | 6 | 1 | 2.5e-07 | 0.00015
BBS1 | 52992 | 0 | 0 | 8 | 6 | 2.6e-07 | 0.00015
ZFP42 | 30084 | 0 | 4 | 8 | 0 | 2.7e-07 | 0.00015
SEMG1 | 46092 | 0 | 0 | 8 | 0 | 2.9e-07 | 0.00016

PTEN

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

POTEB

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

TP53

Figure S3. This figure depicts the distribution of mutations and mutation types across the TP53 significant gene.

IDH1

Figure S4. This figure depicts the distribution of mutations and mutation types across the IDH1 significant gene.

KRTAP5-5

Figure S5. This figure depicts the distribution of mutations and mutation types across the KRTAP5-5 significant gene.

RB1

Figure S6. This figure depicts the distribution of mutations and mutation types across the RB1 significant gene.

MICALCL

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

PIK3CA

Figure S8. This figure depicts the distribution of mutations and mutation types across the PIK3CA significant gene.

FOXRED1

Figure S9. This figure depicts the distribution of mutations and mutation types across the FOXRED1 significant gene.

EGFR

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

NF1

Figure S11. This figure depicts the distribution of mutations and mutation types across the NF1 significant gene.

CALN1

Figure S12. This figure depicts the distribution of mutations and mutation types across the CALN1 significant gene.

ZNF704

Figure S13. This figure depicts the distribution of mutations and mutation types across the ZNF704 significant gene.

PRMT6

Figure S14. This figure depicts the distribution of mutations and mutation types across the PRMT6 significant gene.

COMMD4

Figure S15. This figure depicts the distribution of mutations and mutation types across the COMMD4 significant gene.

POTED

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

TGM2

Figure S17. This figure depicts the distribution of mutations and mutation types across the TGM2 significant gene.

ARHGEF2

Figure S18. This figure depicts the distribution of mutations and mutation types across the ARHGEF2 significant gene.

NACA

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

PIK3R1

Figure S20. This figure depicts the distribution of mutations and mutation types across the PIK3R1 significant gene.

LPHN1

Figure S21. This figure depicts the distribution of mutations and mutation types across the LPHN1 significant gene.

STAG2

Figure S22. This figure depicts the distribution of mutations and mutation types across the STAG2 significant gene.

PLA2G2A

Figure S23. This figure depicts the distribution of mutations and mutation types across the PLA2G2A significant gene.

EML2

Figure S24. This figure depicts the distribution of mutations and mutation types across the EML2 significant gene.

IGSF9

Figure S25. This figure depicts the distribution of mutations and mutation types across the IGSF9 significant gene.

MST1

Figure S26. This figure depicts the distribution of mutations and mutation types across the MST1 significant gene.

PROKR2

Figure S27. This figure depicts the distribution of mutations and mutation types across the PROKR2 significant gene.

TMEM45A

Figure S28. This figure depicts the distribution of mutations and mutation types across the TMEM45A significant gene.

ZFP42

Figure S29. This figure depicts the distribution of mutations and mutation types across the ZFP42 significant gene.

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.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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