GWAS Explorer: an open-source tool to explore, visualize, and access GWAS summary statistics in the PLCO Atlas.
Mitchell J MachielaWen-Yi HuangWendy WongSonja I BerndtJoshua SampsonJonas De AlmeidaMustapha AbubakarJada HislopKai-Ling ChenCasey L DagnallNorma Diaz-MayoralMary FerrellMichael FurrAlex GonzalezBelynda HicksAubrey K HubbardAmy HutchinsonKevin JiangKristine JonesJia LiuErikka LoftfieldJennifer LoukissasJerome MabieShannon MerkleEric MillerLori M MinasianEllen NordgrenBrian ParkPaul PinskyThomas RileyLorena SandovalNeeraj SaxenaAurelie VogtJiahui WangCraig WilliamsPatrick WrightMeredith YeagerBin ZhuClaire ZhuStephen J ChanockMontserrat Garcia-ClosasNeal D FreedmanPublished in: Scientific data (2023)
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.
Keyphrases
- genome wide
- papillary thyroid
- high density
- electronic health record
- single cell
- squamous cell
- copy number
- genome wide association study
- prostate cancer
- high throughput
- data analysis
- dna methylation
- genome wide association
- clinical trial
- machine learning
- healthcare
- randomized controlled trial
- gene expression
- wastewater treatment
- deep learning
- minimally invasive
- phase iii
- human health
- risk factors
- single molecule