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

About this Publication
Title
GWAS Explorer: an open-source tool to explore, visualize, and access GWAS summary statistics in the PLCO Atlas.
Pubmed ID
36635305 (View this publication on the PubMed website)
Digital Object Identifier
Publication
Sci Data. 2023 Jan 12; Volume 10 (Issue 1): Pages 25
Authors
Machiela MJ, Huang WY, Wong W, Berndt SI, Sampson J, De Almeida J, Abubakar M, Hislop J, Chen KL, Dagnall C, Diaz-Mayoral N, Ferrell M, Furr M, Gonzalez A, Hicks B, Hubbard AK, Hutchinson A, Jiang K, Jones K, Liu J, ...show more Loftfield E, Loukissas J, Mabie J, Merkle S, Miller E, Minasian LM, Nordgren E, Park B, Pinsky P, Riley T, Sandoval L, Saxena N, Vogt A, Wang J, Williams C, Wright P, Yeager M, Zhu B, Zhu C, Chanock SJ, Garcia-Closas M, Freedman ND
Affiliations
  • Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, USA. mitchell.machiela@nih.gov.
  • Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, USA.
  • Essential Software Inc., Center for Biomedical Informatics and Information Technology, NCI, Rockville, USA.
  • Cancer Genomics Research Laboratory, DCEG, NCI, Frederick National Laboratory for Cancer Research (FNLCR), Leidos Biomedical Research, Inc., Rockville, USA.
  • BioProcessing and Trial Logistics Laboratory, FNLCR, Leidos Biomedical Research, Inc. Division of Cancer Prevention, NCI, NIH, Rockville, USA.
  • NCI at Frederick Central Repository, American Type Culture Collection, Rockville, USA.
  • Information Management Services, Inc., Danbury, USA.
  • Division of Cancer Prevention, NCI, NIH, Rockville, USA.
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.

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