Mutation Analysis (MutSig vS2N)
Brain Lower Grade Glioma (Primary solid tumor)
22 February 2013 | analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C1J964M4
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Mutation Analysis (MutSig vS2N). Broad Institute of MIT and Harvard. doi:10.7908/C1J964M4
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): 47

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: 47. 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
--- | --- | --- | --- | --- | --- | --- | ---
IDH1 | 27200 | 0 | 0 | 131 | 0 | 0 | 0
ZNF860 | 340 | 0 | 0 | 6 | 0 | 0 | 0
TP53 | 21420 | 0 | 2 | 116 | 19 | 1e-194 | 6.4e-191
ATRX | 163540 | 0 | 2 | 82 | 65 | 2.8e-187 | 1.3e-183
FUBP1 | 32640 | 0 | 2 | 19 | 16 | 7.6e-175 | 2.9e-171
ARID1A | 98940 | 0 | 0 | 14 | 12 | 5.1e-109 | 1.6e-105
CIC | 58310 | 0 | 0 | 40 | 18 | 3.4e-64 | 9.1e-61
NOTCH1 | 88570 | 0 | 2 | 25 | 11 | 1.2e-33 | 2.9e-30
MUC7 | 17340 | 0 | 0 | 8 | 0 | 2.8e-27 | 5.8e-24
NF1 | 253810 | 0 | 1 | 21 | 15 | 8.4e-25 | 1.6e-21
TCF12 | 41480 | 0 | 0 | 6 | 6 | 1.8e-24 | 3.1e-21
PIK3R1 | 50150 | 0 | 1 | 13 | 7 | 4.8e-22 | 7.5e-19
ARID2 | 103020 | 0 | 0 | 12 | 2 | 3.6e-18 | 5.3e-15
IL32 | 10030 | 0 | 0 | 4 | 4 | 4.5e-16 | 6e-13
AHNAK | 342210 | 0 | 4 | 17 | 0 | 2.6e-14 | 3.2e-11
PTEN | 27370 | 0 | 0 | 8 | 3 | 4.5e-12 | 5.3e-09
FERMT3 | 40290 | 0 | 0 | 5 | 0 | 3.3e-11 | 3.6e-08
DOCK5 | 107610 | 0 | 0 | 8 | 1 | 1.3e-10 | 1.4e-07
TPM1 | 22440 | 0 | 0 | 5 | 1 | 3.3e-10 | 3.3e-07
NIPBL | 176630 | 0 | 0 | 10 | 7 | 2.7e-09 | 2.6e-06
MLL3 | 274890 | 0 | 1 | 12 | 1 | 1.2e-08 | 0.000011
HEATR5B | 116280 | 0 | 0 | 8 | 2 | 5.2e-08 | 0.000045
DMXL1 | 184960 | 0 | 0 | 12 | 5 | 6.6e-08 | 0.000054
ZNF318 | 120530 | 0 | 0 | 8 | 2 | 9.4e-08 | 0.000074
MCCC2 | 31450 | 0 | 0 | 5 | 1 | 1.7e-07 | 0.00013
C2orf71 | 63240 | 0 | 0 | 6 | 0 | 2.9e-07 | 0.00021
SLTM | 59670 | 0 | 0 | 7 | 3 | 2.9e-07 | 0.00021
IQGAP1 | 105230 | 0 | 1 | 9 | 1 | 3.1e-07 | 0.00021
ZNF57 | 34510 | 0 | 0 | 7 | 0 | 9.9e-07 | 0.00064
EGFR | 77690 | 0 | 0 | 10 | 1 | 1.3e-06 | 0.0008
CELSR2 | 136340 | 0 | 2 | 9 | 0 | 4.4e-06 | 0.0027
NLRP1 | 77690 | 0 | 1 | 6 | 1 | 4.8e-06 | 0.0028
PIK3CA | 71570 | 0 | 0 | 15 | 3 | 7.8e-06 | 0.0045
PTPRH | 60520 | 0 | 1 | 6 | 1 | 0.000013 | 0.0067
PRKDC | 219810 | 0 | 2 | 9 | 2 | 0.000013 | 0.0067

IDH1

Figure S1. This figure depicts the distribution of mutations and mutation types across the IDH1 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.

ATRX

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

FUBP1

Figure S5. This figure depicts the distribution of mutations and mutation types across the FUBP1 significant gene.

ARID1A

Figure S6. This figure depicts the distribution of mutations and mutation types across the ARID1A significant gene.

CIC

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

NOTCH1

Figure S8. This figure depicts the distribution of mutations and mutation types across the NOTCH1 significant gene.

MUC7

Figure S9. This figure depicts the distribution of mutations and mutation types across the MUC7 significant gene.

NF1

Figure S10. This figure depicts the distribution of mutations and mutation types across the NF1 significant gene.

TCF12

Figure S11. This figure depicts the distribution of mutations and mutation types across the TCF12 significant gene.

PIK3R1

Figure S12. This figure depicts the distribution of mutations and mutation types across the PIK3R1 significant gene.

ARID2

Figure S13. This figure depicts the distribution of mutations and mutation types across the ARID2 significant gene.

IL32

Figure S14. This figure depicts the distribution of mutations and mutation types across the IL32 significant gene.

AHNAK

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

PTEN

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

FERMT3

Figure S17. This figure depicts the distribution of mutations and mutation types across the FERMT3 significant gene.

DOCK5

Figure S18. This figure depicts the distribution of mutations and mutation types across the DOCK5 significant gene.

TPM1

Figure S19. This figure depicts the distribution of mutations and mutation types across the TPM1 significant gene.

NIPBL

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

MLL3

Figure S21. This figure depicts the distribution of mutations and mutation types across the MLL3 significant gene.

HEATR5B

Figure S22. This figure depicts the distribution of mutations and mutation types across the HEATR5B significant gene.

DMXL1

Figure S23. This figure depicts the distribution of mutations and mutation types across the DMXL1 significant gene.

ZNF318

Figure S24. This figure depicts the distribution of mutations and mutation types across the ZNF318 significant gene.

MCCC2

Figure S25. This figure depicts the distribution of mutations and mutation types across the MCCC2 significant gene.

C2orf71

Figure S26. This figure depicts the distribution of mutations and mutation types across the C2orf71 significant gene.

SLTM

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

IQGAP1

Figure S28. This figure depicts the distribution of mutations and mutation types across the IQGAP1 significant gene.

ZNF57

Figure S29. This figure depicts the distribution of mutations and mutation types across the ZNF57 significant gene.

EGFR

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

CELSR2

Figure S31. This figure depicts the distribution of mutations and mutation types across the CELSR2 significant gene.

NLRP1

Figure S32. This figure depicts the distribution of mutations and mutation types across the NLRP1 significant gene.

PIK3CA

Figure S33. This figure depicts the distribution of mutations and mutation types across the PIK3CA significant gene.

PTPRH

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