Thyroid Adenocarcinoma: Mutation Analysis (MutSig vS2N)
(other cohort)
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: THCA-other

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:THCA-other.final_analysis_set.maf

- Significantly mutated genes (q ≤ 0.1): 1

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: 1. 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
--- | --- | --- | --- | --- | --- | --- | ---
BRAF | 4959 | 0 | 0 | 4 | 0 | 3.2e-149 | 6e-145
DNAH2 | 30667 | 0 | 0 | 2 | 0 | 1 | 1
DNAH9 | 30381 | 0 | 0 | 2 | 0 | 1 | 1
EHBP1 | 8370 | 0 | 0 | 2 | 0 | 1 | 1
EIF1AX | 1064 | 0 | 0 | 2 | 1 | 1 | 1
FREM1 | 13571 | 0 | 0 | 2 | 0 | 1 | 1
HRAS | 1319 | 0 | 0 | 2 | 0 | 1 | 1
IRS1 | 6402 | 0 | 0 | 2 | 0 | 1 | 1
NRAS | 1396 | 0 | 0 | 2 | 0 | 1 | 1
TRIM46 | 4198 | 0 | 0 | 2 | 0 | 1 | 1
ABHD4 | 2119 | 0 | 0 | 1 | 0 | 1 | 1
ABP1 | 4540 | 0 | 0 | 1 | 1 | 1 | 1
ACAD10 | 6744 | 0 | 0 | 1 | 0 | 1 | 1
ADH4 | 2603 | 0 | 0 | 1 | 0 | 1 | 1
ADRB1 | 1591 | 0 | 0 | 1 | 0 | 1 | 1
AKAP11 | 13299 | 0 | 0 | 1 | 1 | 1 | 1
AKAP8L | 3371 | 0 | 0 | 1 | 1 | 1 | 1
ALG3 | 2982 | 0 | 0 | 1 | 0 | 1 | 1
ALPK1 | 8398 | 0 | 0 | 1 | 0 | 1 | 1
AMAC1 | 1824 | 0 | 0 | 1 | 0 | 1 | 1
AMY2A | 1806 | 0 | 0 | 1 | 0 | 1 | 1
ANK1 | 12371 | 0 | 0 | 1 | 0 | 1 | 1
ANTXR2 | 2198 | 0 | 0 | 1 | 0 | 1 | 1
AP3B1 | 7883 | 0 | 0 | 1 | 0 | 1 | 1
APOB | 33372 | 0 | 0 | 1 | 0 | 1 | 1
ARHGAP29 | 9119 | 0 | 0 | 1 | 1 | 1 | 1
ARID2 | 11505 | 0 | 0 | 1 | 1 | 1 | 1
ATM | 22860 | 0 | 0 | 1 | 0 | 1 | 1
ATRNL1 | 9384 | 0 | 0 | 1 | 1 | 1 | 1
BAT2 | 9441 | 0 | 0 | 1 | 0 | 1 | 1
BCAR3 | 5187 | 0 | 0 | 1 | 0 | 1 | 1
BCAT1 | 2566 | 0 | 0 | 1 | 1 | 1 | 1
BDP1 | 18135 | 0 | 0 | 1 | 0 | 1 | 1
BLMH | 3391 | 0 | 0 | 1 | 0 | 1 | 1
BMS1 | 8743 | 0 | 0 | 1 | 0 | 1 | 1

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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