Head and Neck Squamous Cell Carcinoma: 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: HNSC-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:HNSC-TP.final_analysis_set.maf

- Significantly mutated genes (q ≤ 0.1): 61

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: 61. 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
--- | --- | --- | --- | --- | --- | --- | ---
ZNF737 | 848 | 0 | 2 | 11 | 2 | 0 | 0
POTEC | 764 | 0 | 1 | 15 | 1 | 0 | 0
KRTAP4-11 | 184 | 0 | 2 | 7 | 0 | 0 | 0
PRAMEF11 | 624 | 0 | 0 | 10 | 0 | 0 | 0
ANKRD30B | 964 | 0 | 1 | 10 | 2 | 0 | 0
ZNF844 | 644 | 0 | 0 | 6 | 0 | 0 | 0
CDKN2A | 18272 | 0 | 0 | 62 | 49 | 0 | 0
FAM75C1 | 1340 | 0 | 0 | 10 | 2 | 0 | 0
NBPF9 | 1208 | 0 | 1 | 9 | 2 | 0 | 0
ZNF716 | 724 | 0 | 2 | 7 | 0 | 0 | 0
DCAF8L2 | 424 | 0 | 1 | 5 | 0 | 0 | 0
RGPD4 | 1784 | 0 | 1 | 8 | 3 | 0 | 0
TP53 | 38556 | 0 | 5 | 244 | 95 | 2e-286 | 2.9e-283
ZNF860 | 1532 | 0 | 0 | 5 | 0 | 2.3e-103 | 3.1e-100
JUB | 32738 | 0 | 1 | 18 | 12 | 8.2e-86 | 1e-82
PIK3CA | 128834 | 0 | 0 | 64 | 0 | 8.1e-76 | 9.5e-73
CT47B1 | 284 | 0 | 3 | 4 | 1 | 2.3e-48 | 2.6e-45
UBTFL1 | 400 | 0 | 0 | 4 | 0 | 1.1e-39 | 1.2e-36
FAM75A6 | 1100 | 0 | 4 | 13 | 0 | 4.6e-38 | 4.6e-35
FAT1 | 498120 | 0 | 2 | 88 | 66 | 6.4e-38 | 6e-35
MLL2 | 382710 | 0 | 3 | 59 | 37 | 5.5e-29 | 4.9e-26
TGFBR2 | 65790 | 0 | 1 | 11 | 7 | 4.5e-28 | 3.9e-25
ZNF286B | 696 | 0 | 0 | 4 | 0 | 3.5e-26 | 2.9e-23
NSD1 | 276934 | 0 | 1 | 38 | 24 | 5.4e-25 | 4.2e-22
EYS | 68854 | 0 | 2 | 13 | 0 | 6.2e-23 | 4.7e-20
HLA-A | 33044 | 0 | 2 | 9 | 8 | 1.6e-22 | 1.1e-19
NOTCH1 | 159614 | 0 | 5 | 60 | 23 | 1e-20 | 7.2e-18
TRIP11 | 235306 | 0 | 3 | 20 | 1 | 3.8e-15 | 2.5e-12
CASP8 | 71910 | 0 | 0 | 25 | 13 | 1.2e-13 | 7.6e-11
RGPD3 | 1676 | 0 | 1 | 4 | 1 | 2.6e-12 | 1.6e-09
ZNF845 | 1472 | 0 | 4 | 7 | 0 | 4.8e-12 | 2.9e-09
HRAS | 20820 | 0 | 0 | 11 | 0 | 7e-12 | 4.1e-09
ANKRD36 | 15262 | 0 | 3 | 5 | 1 | 3.9e-11 | 2.2e-08
EPHA2 | 92738 | 0 | 0 | 17 | 10 | 4.6e-11 | 2.5e-08
CD248 | 48054 | 0 | 2 | 14 | 0 | 1.4e-08 | 7.7e-06

POTEC

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

KRTAP4-11

Figure S2. This figure depicts the distribution of mutations and mutation types across the KRTAP4-11 significant gene.

PRAMEF11

Figure S3. This figure depicts the distribution of mutations and mutation types across the PRAMEF11 significant gene.

ANKRD30B

Figure S4. This figure depicts the distribution of mutations and mutation types across the ANKRD30B significant gene.

ZNF844

Figure S5. This figure depicts the distribution of mutations and mutation types across the ZNF844 significant gene.

CDKN2A

Figure S6. This figure depicts the distribution of mutations and mutation types across the CDKN2A significant gene.

NBPF9

Figure S7. This figure depicts the distribution of mutations and mutation types across the NBPF9 significant gene.

RGPD4

Figure S8. This figure depicts the distribution of mutations and mutation types across the RGPD4 significant gene.

TP53

Figure S9. This figure depicts the distribution of mutations and mutation types across the TP53 significant gene.

ZNF860

Figure S10. This figure depicts the distribution of mutations and mutation types across the ZNF860 significant gene.

JUB

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

PIK3CA

Figure S12. This figure depicts the distribution of mutations and mutation types across the PIK3CA significant gene.

CT47B1

Figure S13. This figure depicts the distribution of mutations and mutation types across the CT47B1 significant gene.

UBTFL1

Figure S14. This figure depicts the distribution of mutations and mutation types across the UBTFL1 significant gene.

FAM75A6

Figure S15. This figure depicts the distribution of mutations and mutation types across the FAM75A6 significant gene.

FAT1

Figure S16. This figure depicts the distribution of mutations and mutation types across the FAT1 significant gene.

MLL2

Figure S17. This figure depicts the distribution of mutations and mutation types across the MLL2 significant gene.

TGFBR2

Figure S18. This figure depicts the distribution of mutations and mutation types across the TGFBR2 significant gene.

ZNF286B

Figure S19. This figure depicts the distribution of mutations and mutation types across the ZNF286B significant gene.

NSD1

Figure S20. This figure depicts the distribution of mutations and mutation types across the NSD1 significant gene.

EYS

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

HLA-A

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

NOTCH1

Figure S23. This figure depicts the distribution of mutations and mutation types across the NOTCH1 significant gene.

TRIP11

Figure S24. This figure depicts the distribution of mutations and mutation types across the TRIP11 significant gene.

RGPD3

Figure S25. This figure depicts the distribution of mutations and mutation types across the RGPD3 significant gene.

ZNF845

Figure S26. This figure depicts the distribution of mutations and mutation types across the ZNF845 significant gene.

HRAS

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

ANKRD36

Figure S28. This figure depicts the distribution of mutations and mutation types across the ANKRD36 significant gene.

EPHA2

Figure S29. This figure depicts the distribution of mutations and mutation types across the EPHA2 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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