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-TP

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-TP.final_analysis_set.maf

- Significantly mutated genes (q ≤ 0.1): 93

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: 93. 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 | 46851 | 0 | 0 | 93 | 43 | 0 | 0
RB1 | 141717 | 0 | 1 | 24 | 23 | 0 | 0
PIK3R1 | 85845 | 0 | 0 | 34 | 20 | 1.1e-205 | 7.2e-202
TP53 | 36666 | 0 | 1 | 100 | 19 | 1.9e-194 | 9.1e-191
RPL5 | 33756 | 0 | 0 | 8 | 6 | 3.5e-169 | 1.3e-165
IDH1 | 46560 | 0 | 0 | 15 | 0 | 1.3e-126 | 4e-123
PIK3CA | 122511 | 0 | 0 | 35 | 7 | 5.6e-111 | 1.5e-107
STAG2 | 144627 | 0 | 0 | 12 | 10 | 1.3e-95 | 3.1e-92
CDC27 | 87009 | 0 | 0 | 7 | 6 | 4.3e-66 | 9e-63
C3orf67 | 59073 | 0 | 0 | 6 | 0 | 1.5e-55 | 2.9e-52
NF1 | 434463 | 0 | 1 | 34 | 28 | 1.8e-46 | 3.2e-43
PRB2 | 19788 | 0 | 0 | 6 | 6 | 1.1e-45 | 1.7e-42
SLC22A9 | 59364 | 0 | 0 | 5 | 0 | 2.3e-34 | 3.3e-31
LZTR1 | 74787 | 0 | 0 | 10 | 1 | 1.3e-33 | 1.8e-30
PDGFRA | 120183 | 0 | 1 | 13 | 2 | 3.7e-33 | 4.6e-30
EGFR | 132987 | 0 | 7 | 95 | 5 | 4e-25 | 4.7e-22
CHD8 | 213012 | 0 | 0 | 10 | 7 | 7.6e-23 | 8e-20
SEMA3C | 82644 | 0 | 1 | 11 | 1 | 7.7e-23 | 8e-20
SEMG1 | 48597 | 0 | 0 | 8 | 1 | 6.7e-22 | 6.7e-19
DYNC1I1 | 63729 | 0 | 0 | 7 | 1 | 3.9e-19 | 3.7e-16
KDR | 145500 | 0 | 0 | 9 | 3 | 1.4e-14 | 1.2e-11
ADAM29 | 88173 | 0 | 1 | 9 | 1 | 3.7e-14 | 3.2e-11
ATRX | 279942 | 0 | 2 | 17 | 12 | 1.7e-12 | 1.4e-09
RBM47 | 48888 | 0 | 3 | 9 | 0 | 3.1e-12 | 2.5e-09
CARD6 | 104760 | 0 | 0 | 7 | 1 | 6.3e-12 | 4.8e-09
CALCR | 54999 | 0 | 0 | 8 | 0 | 8.4e-12 | 6.1e-09
SULT1B1 | 35793 | 0 | 1 | 7 | 1 | 1.1e-11 | 7.6e-09
COL4A4 | 107670 | 0 | 1 | 7 | 0 | 1.3e-11 | 8.6e-09
KIAA1751 | 72168 | 0 | 1 | 6 | 0 | 1.8e-11 | 1.2e-08
QKI | 37248 | 0 | 0 | 5 | 3 | 1.9e-11 | 1.2e-08
MYO1B | 131532 | 0 | 0 | 7 | 0 | 8.2e-11 | 5e-08
KEL | 78570 | 0 | 2 | 15 | 3 | 8e-10 | 4.7e-07
PROKR2 | 42486 | 0 | 0 | 7 | 0 | 8.4e-10 | 4.8e-07
BRAF | 75951 | 0 | 1 | 6 | 0 | 1.3e-09 | 7.2e-07
F5 | 239784 | 0 | 0 | 9 | 3 | 3.9e-09 | 2.1e-06

PTEN

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

RB1

Figure S2. This figure depicts the distribution of mutations and mutation types across the RB1 significant gene.

PIK3R1

Figure S3. This figure depicts the distribution of mutations and mutation types across the PIK3R1 significant gene.

TP53

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

RPL5

Figure S5. This figure depicts the distribution of mutations and mutation types across the RPL5 significant gene.

IDH1

Figure S6. This figure depicts the distribution of mutations and mutation types across the IDH1 significant gene.

PIK3CA

Figure S7. This figure depicts the distribution of mutations and mutation types across the PIK3CA significant gene.

STAG2

Figure S8. This figure depicts the distribution of mutations and mutation types across the STAG2 significant gene.

CDC27

Figure S9. This figure depicts the distribution of mutations and mutation types across the CDC27 significant gene.

C3orf67

Figure S10. This figure depicts the distribution of mutations and mutation types across the C3orf67 significant gene.

NF1

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

SLC22A9

Figure S12. This figure depicts the distribution of mutations and mutation types across the SLC22A9 significant gene.

LZTR1

Figure S13. This figure depicts the distribution of mutations and mutation types across the LZTR1 significant gene.

PDGFRA

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

EGFR

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

CHD8

Figure S16. This figure depicts the distribution of mutations and mutation types across the CHD8 significant gene.

SEMA3C

Figure S17. This figure depicts the distribution of mutations and mutation types across the SEMA3C significant gene.

SEMG1

Figure S18. This figure depicts the distribution of mutations and mutation types across the SEMG1 significant gene.

DYNC1I1

Figure S19. This figure depicts the distribution of mutations and mutation types across the DYNC1I1 significant gene.

KDR

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

ADAM29

Figure S21. This figure depicts the distribution of mutations and mutation types across the ADAM29 significant gene.

ATRX

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

RBM47

Figure S23. This figure depicts the distribution of mutations and mutation types across the RBM47 significant gene.

CARD6

Figure S24. This figure depicts the distribution of mutations and mutation types across the CARD6 significant gene.

CALCR

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

SULT1B1

Figure S26. This figure depicts the distribution of mutations and mutation types across the SULT1B1 significant gene.

COL4A4

Figure S27. This figure depicts the distribution of mutations and mutation types across the COL4A4 significant gene.

KIAA1751

Figure S28. This figure depicts the distribution of mutations and mutation types across the KIAA1751 significant gene.

QKI

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

MYO1B

Figure S30. This figure depicts the distribution of mutations and mutation types across the MYO1B significant gene.

KEL

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

PROKR2

Figure S32. This figure depicts the distribution of mutations and mutation types across the PROKR2 significant gene.

BRAF

Figure S33. This figure depicts the distribution of mutations and mutation types across the BRAF 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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