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GWAS Explorer: an open-source tool to explore, visualize, and access GWAS summary statistics in the PLCO Atlas.
Mitchell J Machiela1, Wen-Yi Huang2, Wendy Wong2
1Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, USA. mitchell.machiela@nih.gov.
Scientific Data
|January 12, 2023
Summary
The PLCO Atlas Project provides a comprehensive resource for genome-wide association studies (GWAS) on cancer and related traits. This FAIR data resource enables researchers to explore genetic associations, advancing cancer research and genetic epidemiology.
Area of Science:
- Genomic Epidemiology
- Cancer Research
- Bioinformatics
Background:
- The Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial enrolled nearly 155,000 U.S. volunteers.
- A significant portion of participants provided DNA and genomic consent for further research.
- Previous genetic studies were limited in scope and accessibility.
Purpose of the Study:
- To develop the PLCO Atlas Project, a large-scale resource for multi-trait genome-wide association studies (GWAS).
- To generate and provide open access to association summary statistics for cancer and related phenotypes.
- To promote FAIR data principles for enhanced reusability in genetic epidemiology.
Main Methods:
- Genotyping of participants using high-density arrays and imputation.
- Conducting genome-wide association studies (GWAS) via a custom semi-automated pipeline.
- Generating association summary statistics for diverse ancestral populations.
Main Results:
- Developed the PLCO Atlas, hosting association data for 90 traits and over 78,000,000 genomic markers.
- Generated summary statistics from 110,562 participants across European, African, and Asian ancestries.
- Established an online GWAS Explorer with APIs and SDKs for data access and visualization.
Conclusions:
- The PLCO Atlas is a FAIR resource offering high-quality genetic and phenotypic data.
- The resource facilitates exploration and reuse for cancer research and genetic epidemiology.
- Ongoing updates will expand the data available for new traits as they become available.
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