Comprehensive analyses of somatic TP53 mutation in tumors with variable mutant allele frequency

Cole, AJ; Zhu, Y; Dwight, T; Yu, B; Dickson, KA; Gard, GB; Maidens, J; Valmadre, S; Gill, AJ; Clifton-Bligh, R; Marsh, DJ

Comprehensive analyses of somatic TP53 mutation in tumors with variable mutant allele frequency

Cole, AJ Zhu, Y Dwight, T Yu, B Dickson, KA

Gard, GB Maidens, J Valmadre, S Gill, AJ Clifton-Bligh, R Marsh, DJ

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Publication Type:: Journal Article
Citation:: Scientific Data, 2017, 4
Issue Date:: 2017-09-05

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Field	Value	Language
dc.contributor.author	Cole, AJ	en_US
dc.contributor.author	Zhu, Y	en_US
dc.contributor.author	Dwight, T	en_US
dc.contributor.author	Yu, B	en_US
dc.contributor.author	Dickson, KA https://orcid.org/0000-0001-7307-8982	en_US
dc.contributor.author	Gard, GB	en_US
dc.contributor.author	Maidens, J	en_US
dc.contributor.author	Valmadre, S	en_US
dc.contributor.author	Gill, AJ	en_US
dc.contributor.author	Clifton-Bligh, R	en_US
dc.contributor.author	Marsh, DJ https://orcid.org/0000-0001-5899-4931	en_US
dc.date.available	2017-07-10	en_US
dc.date.issued	2017-09-05	en_US
dc.identifier.citation	Scientific Data, 2017, 4	en_US
dc.identifier.uri	http://hdl.handle.net/10453/127578
dc.description.abstract	© The Author(s) 2017. Somatic mutation of the tumor suppressor gene TP53 is reported in at least 50% of human malignancies. Most high-grade serous ovarian cancers (HGSC) have a mutant TP53 allele. Accurate detection of these mutants in heterogeneous tumor tissue is paramount as therapies emerge to target mutant p53. We used a Fluidigm Access Array™ System with Massively Parallel Sequencing (MPS) to analyze DNA extracted from 76 serous ovarian tumors. This dataset has been made available to researchers through the European Genome-phenome Archive (EGA; EGAS00001002200). Herein, we present analyses of this dataset using HaplotypeCaller and MuTect2 through the Broad Institute's Genome Analysis Toolkit (GATK). We anticipate that this TP53 mutation dataset will be useful to researchers developing and testing new software to accurately determine high and low frequency variant alleles in heterogeneous aneuploid tumor tissue. Furthermore, the analysis pipeline we present provides a valuable framework for determining somatic variants more broadly in tumor tissue.	en_US
dc.relation.ispartof	Scientific Data	en_US
dc.relation.isbasedon	10.1038/sdata.2017.120	en_US
dc.subject.mesh	Humans	en_US
dc.subject.mesh	Ovarian Neoplasms	en_US
dc.subject.mesh	Gene Frequency	en_US
dc.subject.mesh	Mutation	en_US
dc.subject.mesh	Genes, p53	en_US
dc.subject.mesh	Female	en_US
dc.subject.mesh	High-Throughput Nucleotide Sequencing	en_US
dc.title	Comprehensive analyses of somatic TP53 mutation in tumors with variable mutant allele frequency	en_US
dc.type	Journal Article
utslib.citation.volume	4	en_US
utslib.for	1108 Medical Microbiology	en_US
utslib.for	1112 Oncology and Carcinogenesis	en_US
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Faculty of Science/School of Life Sciences
pubs.organisational-group	/University of Technology Sydney/Strength - CHT - Health Technologies
utslib.copyright.status	open_access
pubs.publication-status	Published	en_US
pubs.volume	4	en_US

Abstract:

© The Author(s) 2017. Somatic mutation of the tumor suppressor gene TP53 is reported in at least 50% of human malignancies. Most high-grade serous ovarian cancers (HGSC) have a mutant TP53 allele. Accurate detection of these mutants in heterogeneous tumor tissue is paramount as therapies emerge to target mutant p53. We used a Fluidigm Access Array™ System with Massively Parallel Sequencing (MPS) to analyze DNA extracted from 76 serous ovarian tumors. This dataset has been made available to researchers through the European Genome-phenome Archive (EGA; EGAS00001002200). Herein, we present analyses of this dataset using HaplotypeCaller and MuTect2 through the Broad Institute's Genome Analysis Toolkit (GATK). We anticipate that this TP53 mutation dataset will be useful to researchers developing and testing new software to accurately determine high and low frequency variant alleles in heterogeneous aneuploid tumor tissue. Furthermore, the analysis pipeline we present provides a valuable framework for determining somatic variants more broadly in tumor tissue.

Please use this identifier to cite or link to this item:

http://hdl.handle.net/10453/127578