Scientific Data (Jan 2023)
GWAS Explorer: an open-source tool to explore, visualize, and access GWAS summary statistics in the PLCO Atlas
- 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
Affiliations
- Mitchell J. Machiela
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH)
- Wen-Yi Huang
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH)
- Wendy Wong
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH)
- Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH)
- Joshua Sampson
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH)
- Jonas De Almeida
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH)
- Mustapha Abubakar
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH)
- Jada Hislop
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH)
- Kai-Ling Chen
- Essential Software Inc., Center for Biomedical Informatics and Information Technology, NCI
- Casey Dagnall
- Cancer Genomics Research Laboratory, DCEG, NCI, Frederick National Laboratory for Cancer Research (FNLCR), Leidos Biomedical Research, Inc.
- Norma Diaz-Mayoral
- BioProcessing and Trial Logistics Laboratory, FNLCR, Leidos Biomedical Research, Inc. Division of Cancer Prevention, NCI, NIH
- Mary Ferrell
- NCI at Frederick Central Repository, American Type Culture Collection
- Michael Furr
- Information Management Services, Inc.
- Alex Gonzalez
- NCI at Frederick Central Repository, American Type Culture Collection
- Belynda Hicks
- Cancer Genomics Research Laboratory, DCEG, NCI, Frederick National Laboratory for Cancer Research (FNLCR), Leidos Biomedical Research, Inc.
- Aubrey K. Hubbard
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH)
- Amy Hutchinson
- Cancer Genomics Research Laboratory, DCEG, NCI, Frederick National Laboratory for Cancer Research (FNLCR), Leidos Biomedical Research, Inc.
- Kevin Jiang
- Essential Software Inc., Center for Biomedical Informatics and Information Technology, NCI
- Kristine Jones
- Cancer Genomics Research Laboratory, DCEG, NCI, Frederick National Laboratory for Cancer Research (FNLCR), Leidos Biomedical Research, Inc.
- Jia Liu
- Cancer Genomics Research Laboratory, DCEG, NCI, Frederick National Laboratory for Cancer Research (FNLCR), Leidos Biomedical Research, Inc.
- Erikka Loftfield
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH)
- Jennifer Loukissas
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH)
- Jerome Mabie
- Information Management Services, Inc.
- Shannon Merkle
- Information Management Services, Inc.
- Eric Miller
- Division of Cancer Prevention, NCI, NIH
- Lori M. Minasian
- Division of Cancer Prevention, NCI, NIH
- Ellen Nordgren
- NCI at Frederick Central Repository, American Type Culture Collection
- Brian Park
- Essential Software Inc., Center for Biomedical Informatics and Information Technology, NCI
- Paul Pinsky
- Division of Cancer Prevention, NCI, NIH
- Thomas Riley
- Information Management Services, Inc.
- Lorena Sandoval
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH)
- Neeraj Saxena
- Division of Cancer Prevention, NCI, NIH
- Aurelie Vogt
- Cancer Genomics Research Laboratory, DCEG, NCI, Frederick National Laboratory for Cancer Research (FNLCR), Leidos Biomedical Research, Inc.
- Jiahui Wang
- Cancer Genomics Research Laboratory, DCEG, NCI, Frederick National Laboratory for Cancer Research (FNLCR), Leidos Biomedical Research, Inc.
- Craig Williams
- Information Management Services, Inc.
- Patrick Wright
- Information Management Services, Inc.
- Meredith Yeager
- Cancer Genomics Research Laboratory, DCEG, NCI, Frederick National Laboratory for Cancer Research (FNLCR), Leidos Biomedical Research, Inc.
- Bin Zhu
- Cancer Genomics Research Laboratory, DCEG, NCI, Frederick National Laboratory for Cancer Research (FNLCR), Leidos Biomedical Research, Inc.
- Claire Zhu
- Division of Cancer Prevention, NCI, NIH
- Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH)
- Montserrat Garcia-Closas
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH)
- Neal D. Freedman
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH)
- DOI
- https://doi.org/10.1038/s41597-022-01921-2
- Journal volume & issue
-
Vol. 10,
no. 1
pp. 1 – 12
Abstract
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.
