Thyroid Adenocarcinoma: 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: THCA

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.final_analysis_set.maf

- Significantly mutated genes (q ≤ 0.1): 27

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: 27. 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 | 84303 | 0 | 1 | 183 | 0 | 0 | 0
NRAS | 23793 | 0 | 0 | 26 | 0 | 0 | 0
HRAS | 22606 | 0 | 0 | 12 | 0 | 0 | 0
EMG1 | 30471 | 0 | 0 | 6 | 6 | 0 | 0
TG | 318793 | 0 | 3 | 16 | 10 | 1.5e-153 | 5.5e-150
EIF1AX | 18088 | 0 | 0 | 6 | 1 | 1.3e-64 | 4.2e-61
MUC7 | 33160 | 0 | 1 | 5 | 1 | 2.6e-43 | 7.1e-40
ZNF845 | 78752 | 0 | 0 | 6 | 0 | 1.5e-35 | 3.4e-32
RPTN | 83871 | 0 | 0 | 8 | 7 | 3.5e-35 | 7.3e-32
PPM1D | 56848 | 0 | 0 | 5 | 4 | 1.4e-25 | 2.7e-22
TROAP | 68476 | 0 | 0 | 5 | 0 | 2.4e-21 | 4.1e-18
GPR44 | 14753 | 0 | 0 | 4 | 4 | 1.5e-18 | 2.4e-15
PRG4 | 148467 | 0 | 1 | 7 | 3 | 8.3e-17 | 1.2e-13
FAM47C | 90339 | 0 | 3 | 5 | 0 | 2.3e-16 | 3.1e-13
ARID1B | 175821 | 0 | 0 | 6 | 2 | 2.5e-16 | 3.1e-13
DNMT3A | 91623 | 0 | 0 | 5 | 4 | 3.8e-16 | 4.5e-13
ZNF799 | 73430 | 0 | 1 | 5 | 0 | 1.2e-14 | 1.3e-11
CCDC15 | 86277 | 0 | 1 | 5 | 0 | 2.2e-12 | 2.3e-09
MLL3 | 523575 | 0 | 0 | 8 | 4 | 1.8e-11 | 1.8e-08
ZNF780A | 77399 | 0 | 1 | 4 | 0 | 4.1e-11 | 3.9e-08
ZFHX3 | 379957 | 0 | 2 | 8 | 2 | 3.4e-07 | 0.00031
DICER1 | 232455 | 0 | 0 | 5 | 2 | 8.4e-07 | 0.00072
COL5A3 | 116809 | 0 | 0 | 6 | 2 | 1.1e-06 | 0.00093
LRP1 | 476861 | 0 | 1 | 6 | 2 | 1.8e-06 | 0.0014
ZNF208 | 161113 | 1 | 0 | 4 | 0 | 4.4e-06 | 0.0033
CHD2 | 219636 | 0 | 0 | 4 | 4 | 0.000022 | 0.016
CD209 | 45543 | 0 | 1 | 4 | 0 | 0.000097 | 0.068
ANK1 | 210063 | 0 | 0 | 4 | 0 | 0.00019 | 0.13
ATM | 388254 | 0 | 0 | 5 | 2 | 0.00023 | 0.15
PKHD1L1 | 454465 | 0 | 0 | 5 | 4 | 0.00078 | 0.49
PRDM9 | 98838 | 0 | 3 | 6 | 1 | 0.0014 | 0.84
ACRC | 65795 | 0 | 0 | 4 | 0 | 0.0017 | 0.98
DNAH2 | 521217 | 0 | 0 | 5 | 0 | 0.0019 | 1
APOB | 567507 | 0 | 0 | 5 | 1 | 0.0032 | 1
MAP3K3 | 74181 | 0 | 0 | 4 | 1 | 0.0034 | 1

BRAF

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

NRAS

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

HRAS

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

EMG1

Figure S4. This figure depicts the distribution of mutations and mutation types across the EMG1 significant gene.

TG

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

EIF1AX

Figure S6. This figure depicts the distribution of mutations and mutation types across the EIF1AX significant gene.

MUC7

Figure S7. This figure depicts the distribution of mutations and mutation types across the MUC7 significant gene.

ZNF845

Figure S8. This figure depicts the distribution of mutations and mutation types across the ZNF845 significant gene.

RPTN

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

PPM1D

Figure S10. This figure depicts the distribution of mutations and mutation types across the PPM1D significant gene.

TROAP

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

GPR44

Figure S12. This figure depicts the distribution of mutations and mutation types across the GPR44 significant gene.

PRG4

Figure S13. This figure depicts the distribution of mutations and mutation types across the PRG4 significant gene.

FAM47C

Figure S14. This figure depicts the distribution of mutations and mutation types across the FAM47C significant gene.

ARID1B

Figure S15. This figure depicts the distribution of mutations and mutation types across the ARID1B significant gene.

DNMT3A

Figure S16. This figure depicts the distribution of mutations and mutation types across the DNMT3A significant gene.

ZNF799

Figure S17. This figure depicts the distribution of mutations and mutation types across the ZNF799 significant gene.

CCDC15

Figure S18. This figure depicts the distribution of mutations and mutation types across the CCDC15 significant gene.

MLL3

Figure S19. This figure depicts the distribution of mutations and mutation types across the MLL3 significant gene.

ZNF780A

Figure S20. This figure depicts the distribution of mutations and mutation types across the ZNF780A significant gene.

ZFHX3

Figure S21. This figure depicts the distribution of mutations and mutation types across the ZFHX3 significant gene.

DICER1

Figure S22. This figure depicts the distribution of mutations and mutation types across the DICER1 significant gene.

COL5A3

Figure S23. This figure depicts the distribution of mutations and mutation types across the COL5A3 significant gene.

CHD2

Figure S24. This figure depicts the distribution of mutations and mutation types across the CHD2 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)
Copyright © 2012 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
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