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

Autor: Mitchell J. Machiela, Wen-Yi Huang, Wendy Wong, Sonja I. Berndt, Joshua Sampson, Jonas De Almeida, Mustapha Abubakar, Jada Hislop, Kai-Ling Chen, Casey Dagnall, Norma Diaz-Mayoral, Mary Ferrell, Michael Furr, Alex Gonzalez, Belynda Hicks, Aubrey K. Hubbard, Amy Hutchinson, Kevin Jiang, Kristine Jones, Jia Liu, Erikka Loftfield, Jennifer Loukissas, Jerome Mabie, Shannon Merkle, Eric Miller, Lori M. Minasian, Ellen Nordgren, Brian Park, Paul Pinsky, Thomas Riley, Lorena Sandoval, Neeraj Saxena, Aurelie Vogt, Jiahui Wang, Craig Williams, Patrick Wright, Meredith Yeager, Bin Zhu, Claire Zhu, Stephen J. Chanock, Montserrat Garcia-Closas, Neal D. Freedman
Jazyk: angličtina
Rok vydání: 2023
Předmět:
Zdroj: Scientific Data, Vol 10, Iss 1, Pp 1-12 (2023)
Druh dokumentu: article
ISSN: 2052-4463
DOI: 10.1038/s41597-022-01921-2
Popis: Abstract 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.
Databáze: Directory of Open Access Journals