Brain Lower Grade Glioma: 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: LGG-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:LGG-TP.final_analysis_set.maf

- Significantly mutated genes (q ≤ 0.1): 159

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: 159. 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
--- | --- | --- | --- | --- | --- | --- | ---
KRAS | 3502 | 0 | 0 | 24 | 0 | 0 | 0
ZNF860 | 68 | 0 | 0 | 6 | 0 | 0 | 0
TP53 | 4284 | 0 | 0 | 22 | 12 | 0 | 0
VAMP3 | 1326 | 0 | 0 | 7 | 7 | 0 | 0
SPDYE5 | 3298 | 0 | 0 | 8 | 0 | 0 | 0
ZNF479 | 6834 | 0 | 0 | 9 | 0 | 0 | 0
ZNF57 | 6902 | 0 | 2 | 11 | 0 | 0 | 0
LNP1 | 2380 | 0 | 1 | 7 | 7 | 0 | 0
CRIPAK | 3502 | 0 | 0 | 8 | 8 | 0 | 0
OR10A7 | 4216 | 0 | 0 | 8 | 8 | 6.4e-305 | 1.2e-301
CD300A | 3264 | 0 | 0 | 7 | 7 | 1.1e-290 | 1.9e-287
HMGB2 | 2652 | 0 | 0 | 6 | 6 | 3.2e-236 | 5e-233
GIGYF1 | 9180 | 0 | 0 | 10 | 10 | 3.1e-217 | 4.5e-214
HOXB2 | 2924 | 0 | 0 | 6 | 6 | 2.1e-214 | 2.8e-211
DMRT3 | 4080 | 0 | 0 | 9 | 1 | 3.3e-214 | 4.1e-211
FUZ | 3366 | 0 | 0 | 6 | 6 | 1.9e-186 | 2.2e-183
TREML2 | 3434 | 0 | 0 | 6 | 6 | 8.8e-183 | 9.8e-180
PTTG1IP | 1836 | 0 | 0 | 5 | 5 | 5.9e-175 | 6.2e-172
TTBK2 | 14246 | 0 | 0 | 11 | 11 | 6.8e-166 | 6.7e-163
F5 | 28016 | 0 | 1 | 8 | 0 | 1.7e-159 | 1.6e-156
HFE2 | 3978 | 0 | 0 | 6 | 6 | 5.8e-158 | 5.2e-155
CDKN2A | 2040 | 0 | 0 | 6 | 5 | 1.1e-157 | 9.4e-155
LRP10 | 6222 | 0 | 1 | 7 | 7 | 4.6e-153 | 3.8e-150
CHRD | 7446 | 0 | 0 | 5 | 0 | 4e-118 | 3.1e-115
TCF20 | 20434 | 0 | 0 | 11 | 11 | 6.8e-116 | 5.1e-113
UTP3 | 5474 | 0 | 0 | 6 | 6 | 4.4e-115 | 3.2e-112
TSPAN4 | 2822 | 0 | 0 | 6 | 4 | 1.1e-111 | 7.5e-109
SMAD4 | 6188 | 0 | 0 | 8 | 4 | 1.1e-104 | 7.3e-102
LYPD3 | 3162 | 0 | 0 | 5 | 5 | 2.6e-102 | 1.7e-99
FTSJ3 | 10200 | 0 | 0 | 7 | 7 | 1e-93 | 6.6e-91
TMCC1 | 7446 | 0 | 0 | 8 | 6 | 3.8e-87 | 2.3e-84
ADAD1 | 7514 | 0 | 0 | 6 | 6 | 4.4e-84 | 2.6e-81
OR10A2 | 3944 | 0 | 0 | 5 | 5 | 3e-82 | 1.7e-79
MAGEA10 | 4250 | 0 | 0 | 5 | 5 | 2.1e-76 | 1.1e-73
AADACL3 | 4318 | 0 | 0 | 5 | 5 | 3.2e-75 | 1.7e-72

KRAS

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

ZNF860

Figure S2. This figure depicts the distribution of mutations and mutation types across the ZNF860 significant gene.

TP53

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

VAMP3

Figure S4. This figure depicts the distribution of mutations and mutation types across the VAMP3 significant gene.

SPDYE5

Figure S5. This figure depicts the distribution of mutations and mutation types across the SPDYE5 significant gene.

ZNF479

Figure S6. This figure depicts the distribution of mutations and mutation types across the ZNF479 significant gene.

ZNF57

Figure S7. This figure depicts the distribution of mutations and mutation types across the ZNF57 significant gene.

LNP1

Figure S8. This figure depicts the distribution of mutations and mutation types across the LNP1 significant gene.

CRIPAK

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

OR10A7

Figure S10. This figure depicts the distribution of mutations and mutation types across the OR10A7 significant gene.

CD300A

Figure S11. This figure depicts the distribution of mutations and mutation types across the CD300A significant gene.

HMGB2

Figure S12. This figure depicts the distribution of mutations and mutation types across the HMGB2 significant gene.

GIGYF1

Figure S13. This figure depicts the distribution of mutations and mutation types across the GIGYF1 significant gene.

HOXB2

Figure S14. This figure depicts the distribution of mutations and mutation types across the HOXB2 significant gene.

DMRT3

Figure S15. This figure depicts the distribution of mutations and mutation types across the DMRT3 significant gene.

FUZ

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

TREML2

Figure S17. This figure depicts the distribution of mutations and mutation types across the TREML2 significant gene.

PTTG1IP

Figure S18. This figure depicts the distribution of mutations and mutation types across the PTTG1IP significant gene.

TTBK2

Figure S19. This figure depicts the distribution of mutations and mutation types across the TTBK2 significant gene.

F5

Figure S20. This figure depicts the distribution of mutations and mutation types across the F5 significant gene.

HFE2

Figure S21. This figure depicts the distribution of mutations and mutation types across the HFE2 significant gene.

CDKN2A

Figure S22. This figure depicts the distribution of mutations and mutation types across the CDKN2A significant gene.

LRP10

Figure S23. This figure depicts the distribution of mutations and mutation types across the LRP10 significant gene.

CHRD

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

TCF20

Figure S25. This figure depicts the distribution of mutations and mutation types across the TCF20 significant gene.

UTP3

Figure S26. This figure depicts the distribution of mutations and mutation types across the UTP3 significant gene.

TSPAN4

Figure S27. This figure depicts the distribution of mutations and mutation types across the TSPAN4 significant gene.

SMAD4

Figure S28. This figure depicts the distribution of mutations and mutation types across the SMAD4 significant gene.

LYPD3

Figure S29. This figure depicts the distribution of mutations and mutation types across the LYPD3 significant gene.

FTSJ3

Figure S30. This figure depicts the distribution of mutations and mutation types across the FTSJ3 significant gene.

TMCC1

Figure S31. This figure depicts the distribution of mutations and mutation types across the TMCC1 significant gene.

ADAD1

Figure S32. This figure depicts the distribution of mutations and mutation types across the ADAD1 significant gene.

OR10A2

Figure S33. This figure depicts the distribution of mutations and mutation types across the OR10A2 significant gene.

MAGEA10

Figure S34. This figure depicts the distribution of mutations and mutation types across the MAGEA10 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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