Mutation Analysis (MutSig vS2N)
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
22 February 2013 | analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C11J97ZR
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/C11J97ZR
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: KIRP-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:KIRP-TP.final_analysis_set.maf

- Significantly mutated genes (q ≤ 0.1): 29

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: 29. 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
--- | --- | --- | --- | --- | --- | --- | ---
NF2 | 20909 | 0 | 0 | 5 | 5 | 4.7e-93 | 8.9e-89
KDM6A | 47174 | 0 | 0 | 6 | 6 | 1.1e-78 | 1.1e-74
PCF11 | 48410 | 0 | 1 | 8 | 0 | 1e-51 | 6.4e-48
IL32 | 6077 | 0 | 0 | 4 | 4 | 2.9e-41 | 1.4e-37
STAG2 | 51191 | 0 | 1 | 5 | 5 | 1.9e-38 | 7e-35
MET | 54796 | 0 | 0 | 8 | 0 | 2e-29 | 6.4e-26
SETD2 | 76014 | 0 | 0 | 6 | 5 | 3.9e-26 | 1e-22
FGFR3 | 17407 | 0 | 2 | 5 | 0 | 2.1e-23 | 5e-20
FLJ46321 | 53766 | 0 | 1 | 7 | 3 | 2.5e-22 | 5.3e-19
SRCAP | 85799 | 0 | 1 | 7 | 2 | 2.9e-14 | 5.5e-11
SRRM2 | 74469 | 0 | 1 | 6 | 1 | 5e-11 | 8.2e-08
ATP1A1 | 38419 | 0 | 0 | 5 | 0 | 5.2e-11 | 8.2e-08
RERE | 40582 | 0 | 1 | 5 | 1 | 1.8e-10 | 2.7e-07
QRICH2 | 48307 | 0 | 0 | 5 | 1 | 6.7e-09 | 9e-06
SLC5A12 | 22454 | 0 | 1 | 4 | 0 | 7.5e-09 | 9.3e-06
CDC27 | 30797 | 0 | 0 | 4 | 4 | 7.9e-09 | 9.3e-06
LGI4 | 6592 | 0 | 0 | 4 | 0 | 2.2e-08 | 0.000025
MLL2 | 128853 | 0 | 3 | 12 | 7 | 2.5e-08 | 0.000026
LRBA | 120098 | 0 | 1 | 6 | 4 | 2.1e-06 | 0.002
CMYA5 | 139668 | 0 | 0 | 6 | 1 | 3.2e-06 | 0.003
MUC16 | 475757 | 0 | 0 | 10 | 1 | 7.7e-06 | 0.0068
SFRS2IP | 55105 | 0 | 1 | 5 | 4 | 7.9e-06 | 0.0068
SYNE1 | 337943 | 0 | 0 | 8 | 1 | 0.000022 | 0.018
MLL3 | 166551 | 0 | 0 | 6 | 3 | 0.000025 | 0.019
FAT1 | 167684 | 0 | 1 | 6 | 2 | 0.000026 | 0.02
EP400 | 87653 | 0 | 0 | 5 | 1 | 0.000031 | 0.023
BOD1L | 94554 | 0 | 0 | 5 | 0 | 0.000066 | 0.046
MACF1 | 315386 | 0 | 2 | 9 | 0 | 0.000068 | 0.046
POLQ | 98468 | 0 | 0 | 5 | 1 | 0.000097 | 0.063
PARD6B | 13390 | 0 | 0 | 4 | 2 | 0.00016 | 0.1
SVEP1 | 111137 | 0 | 0 | 5 | 2 | 0.00028 | 0.17
FLG | 112270 | 0 | 1 | 5 | 1 | 0.0003 | 0.18
HERC1 | 148320 | 0 | 0 | 5 | 1 | 0.0022 | 1
SON | 82194 | 0 | 0 | 5 | 1 | 0.0045 | 1
BAP1 | 23072 | 0 | 1 | 4 | 1 | 0.0062 | 1

NF2

Figure S1. This figure depicts the distribution of mutations and mutation types across the NF2 significant gene.

KDM6A

Figure S2. This figure depicts the distribution of mutations and mutation types across the KDM6A significant gene.

PCF11

Figure S3. This figure depicts the distribution of mutations and mutation types across the PCF11 significant gene.

IL32

Figure S4. This figure depicts the distribution of mutations and mutation types across the IL32 significant gene.

STAG2

Figure S5. This figure depicts the distribution of mutations and mutation types across the STAG2 significant gene.

MET

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

SETD2

Figure S7. This figure depicts the distribution of mutations and mutation types across the SETD2 significant gene.

FGFR3

Figure S8. This figure depicts the distribution of mutations and mutation types across the FGFR3 significant gene.

FLJ46321

Figure S9. This figure depicts the distribution of mutations and mutation types across the FLJ46321 significant gene.

SRCAP

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

SRRM2

Figure S11. This figure depicts the distribution of mutations and mutation types across the SRRM2 significant gene.

ATP1A1

Figure S12. This figure depicts the distribution of mutations and mutation types across the ATP1A1 significant gene.

RERE

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

QRICH2

Figure S14. This figure depicts the distribution of mutations and mutation types across the QRICH2 significant gene.

SLC5A12

Figure S15. This figure depicts the distribution of mutations and mutation types across the SLC5A12 significant gene.

CDC27

Figure S16. This figure depicts the distribution of mutations and mutation types across the CDC27 significant gene.

LGI4

Figure S17. This figure depicts the distribution of mutations and mutation types across the LGI4 significant gene.

MLL2

Figure S18. This figure depicts the distribution of mutations and mutation types across the MLL2 significant gene.

LRBA

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

CMYA5

Figure S20. This figure depicts the distribution of mutations and mutation types across the CMYA5 significant gene.

MUC16

Figure S21. This figure depicts the distribution of mutations and mutation types across the MUC16 significant gene.

SYNE1

Figure S22. This figure depicts the distribution of mutations and mutation types across the SYNE1 significant gene.

MLL3

Figure S23. This figure depicts the distribution of mutations and mutation types across the MLL3 significant gene.

FAT1

Figure S24. This figure depicts the distribution of mutations and mutation types across the FAT1 significant gene.

EP400

Figure S25. This figure depicts the distribution of mutations and mutation types across the EP400 significant gene.

BOD1L

Figure S26. This figure depicts the distribution of mutations and mutation types across the BOD1L significant gene.

MACF1

Figure S27. This figure depicts the distribution of mutations and mutation types across the MACF1 significant gene.

POLQ

Figure S28. This figure depicts the distribution of mutations and mutation types across the POLQ 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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