GWAS Explorer: an open-source tool to explore, visualize, and access GWAS summary statistics in the PLCO Atlas.

Female Humans Male Genome-Wide Association Study Lung Ovarian Neoplasms Polymorphism, Single Nucleotide Prospective Studies Prostate

Journal

Scientific data

ISSN: 2052-4463

Titre abrégé: Sci Data

Pays: England

ID NLM: 101640192

Informations de publication

Date de publication:
12 01 2023

Historique:

received: 14 05 2022

accepted: 21 12 2022

entrez: 12 1 2023

pubmed: 13 1 2023

medline: 17 1 2023

Statut: epublish

Résumé

The Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial is a prospective cohort study of nearly 155,000 U.S. volunteers aged 55-74 at enrollment in 1993-2001. We developed the PLCO Atlas Project, a large resource for multi-trait genome-wide association studies (GWAS), by genotyping participants with available DNA and genomic consent. Genotyping on high-density arrays and imputation was performed, and GWAS were conducted using a custom semi-automated pipeline. Association summary statistics were generated from a total of 110,562 participants of European, African and Asian ancestry. Application programming interfaces (APIs) and open-source software development kits (SKDs) enable exploring, visualizing and open data access through the PLCO Atlas GWAS Explorer website, promoting Findable, Accessible, Interoperable, and Re-usable (FAIR) principles. Currently the GWAS Explorer hosts association data for 90 traits and >78,000,000 genomic markers, focusing on cancer and cancer-related phenotypes. New traits will be posted as association data becomes available. The PLCO Atlas is a FAIR resource of high-quality genetic and phenotypic data with many potential reuse opportunities for cancer research and genetic epidemiology.

Identifiants

DOI: 10.1038/s41597-022-01921-2 PMID: 36635305 PMC: PMC9837135

pubmed: 36635305

doi: 10.1038/s41597-022-01921-2

pii: 10.1038/s41597-022-01921-2

pmc: PMC9837135

doi:

Types de publication

Dataset Journal Article

Langues

eng

Sous-ensembles de citation

Pagination

Subventions

Organisme : U.S. Department of Health & Human Services | NIH | NCI | Division of Cancer Epidemiology and Genetics, National Cancer Institute (National Cancer Institute Division of Cancer Epidemiology and Genetics)

ID : Intramural Research Program

Informations de copyright

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