Thyroid Adenocarcinoma: Mutation Analysis (MutSig vS2N)
(tall-cell 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-tall-cell

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-tall-cell.final_analysis_set.maf

- Significantly mutated genes (q ≤ 0.1): 0

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: 0. 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 | 6003 | 0 | 0 | 21 | 0 | 0 | 0
TG | 22627 | 0 | 1 | 3 | 2 | 1 | 1
TTN | 293246 | 0 | 1 | 3 | 1 | 1 | 1
ZNF28 | 5917 | 0 | 0 | 3 | 0 | 1 | 1
ARID1B | 12532 | 0 | 0 | 2 | 1 | 1 | 1
COL6A2 | 6244 | 0 | 0 | 2 | 0 | 1 | 1
CT45A5 | 940 | 0 | 0 | 2 | 0 | 1 | 1
DBN1 | 4163 | 0 | 0 | 2 | 0 | 1 | 1
FANCD2 | 13188 | 0 | 0 | 2 | 0 | 1 | 1
KIF2C | 6121 | 0 | 0 | 2 | 0 | 1 | 1
MYOM2 | 11902 | 0 | 0 | 2 | 0 | 1 | 1
NAV3 | 18567 | 0 | 0 | 2 | 0 | 1 | 1
SETX | 23144 | 0 | 0 | 2 | 0 | 1 | 1
TOPBP1 | 12069 | 0 | 0 | 2 | 0 | 1 | 1
TRPM4 | 7130 | 0 | 0 | 2 | 0 | 1 | 1
A2M | 11211 | 0 | 0 | 1 | 0 | 1 | 1
ABCA3 | 12117 | 0 | 0 | 1 | 0 | 1 | 1
ABCB11 | 10470 | 0 | 0 | 1 | 0 | 1 | 1
ABCB7 | 5856 | 0 | 0 | 1 | 1 | 1 | 1
ABCD1 | 3387 | 0 | 0 | 1 | 0 | 1 | 1
ACAD10 | 8148 | 0 | 0 | 1 | 1 | 1 | 1
ACOT12 | 4442 | 0 | 0 | 1 | 0 | 1 | 1
ACVR2A | 4353 | 0 | 0 | 1 | 0 | 1 | 1
ADAM33 | 3304 | 0 | 0 | 1 | 1 | 1 | 1
ADAMTS18 | 9266 | 0 | 0 | 1 | 0 | 1 | 1
ADAMTSL3 | 13041 | 0 | 0 | 1 | 0 | 1 | 1
ADAMTSL4 | 6038 | 0 | 0 | 1 | 0 | 1 | 1
ADC | 3631 | 0 | 0 | 1 | 0 | 1 | 1
ADH7 | 3200 | 0 | 0 | 1 | 0 | 1 | 1
AIM1 | 12839 | 0 | 0 | 1 | 0 | 1 | 1
AMOTL2 | 4571 | 0 | 0 | 1 | 0 | 1 | 1
ANAPC5 | 6348 | 0 | 0 | 1 | 0 | 1 | 1
ANK2 | 30498 | 0 | 0 | 1 | 0 | 1 | 1
AP2B1 | 8122 | 0 | 0 | 1 | 0 | 1 | 1
AP3B1 | 9511 | 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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