GWAS Explorer: an open-source tool to explore, visualize, and access GWAS summary statistics in the PLCO Atlas.
| Title: | GWAS Explorer: an open-source tool to explore, visualize, and access GWAS summary statistics in the PLCO Atlas. |
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| Authors: | Machiela MJ; Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, USA. mitchell.machiela@nih.gov.; Huang WY; Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, USA.; Wong W; Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, USA.; Berndt SI; Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, USA.; Sampson J; Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, USA.; De Almeida J; Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, USA.; Abubakar M; Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, USA.; Hislop J; Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, USA.; Chen KL; Essential Software Inc., Center for Biomedical Informatics and Information Technology, NCI, Rockville, USA.; Dagnall C; Cancer Genomics Research Laboratory, DCEG, NCI, Frederick National Laboratory for Cancer Research (FNLCR), Leidos Biomedical Research, Inc., Rockville, USA.; Diaz-Mayoral N; BioProcessing and Trial Logistics Laboratory, FNLCR, Leidos Biomedical Research, Inc. Division of Cancer Prevention, NCI, NIH, Rockville, USA.; Ferrell M; NCI at Frederick Central Repository, American Type Culture Collection, Rockville, USA.; Furr M; Information Management Services, Inc., Danbury, USA.; Gonzalez A; NCI at Frederick Central Repository, American Type Culture Collection, Rockville, USA.; Hicks B; Cancer Genomics Research Laboratory, DCEG, NCI, Frederick National Laboratory for Cancer Research (FNLCR), Leidos Biomedical Research, Inc., Rockville, USA.; Hubbard AK; Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, USA.; Hutchinson A; Cancer Genomics Research Laboratory, DCEG, NCI, Frederick National Laboratory for Cancer Research (FNLCR), Leidos Biomedical Research, Inc., Rockville, USA.; Jiang K; Essential Software Inc., Center for Biomedical Informatics and Information Technology, NCI, Rockville, USA.; Jones K; Cancer Genomics Research Laboratory, DCEG, NCI, Frederick National Laboratory for Cancer Research (FNLCR), Leidos Biomedical Research, Inc., Rockville, USA.; Liu J; Cancer Genomics Research Laboratory, DCEG, NCI, Frederick National Laboratory for Cancer Research (FNLCR), Leidos Biomedical Research, Inc., Rockville, USA.; Loftfield E; Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, USA.; Loukissas J; Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, USA.; Mabie J; Information Management Services, Inc., Danbury, USA.; Merkle S; Information Management Services, Inc., Danbury, USA.; Miller E; Division of Cancer Prevention, NCI, NIH, Rockville, USA.; Minasian LM; Division of Cancer Prevention, NCI, NIH, Rockville, USA.; Nordgren E; NCI at Frederick Central Repository, American Type Culture Collection, Rockville, USA.; Park B; Essential Software Inc., Center for Biomedical Informatics and Information Technology, NCI, Rockville, USA.; Pinsky P; Division of Cancer Prevention, NCI, NIH, Rockville, USA.; Riley T; Information Management Services, Inc., Danbury, USA.; Sandoval L; Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, USA.; Saxena N; Division of Cancer Prevention, NCI, NIH, Rockville, USA.; Vogt A; Cancer Genomics Research Laboratory, DCEG, NCI, Frederick National Laboratory for Cancer Research (FNLCR), Leidos Biomedical Research, Inc., Rockville, USA.; Wang J; Cancer Genomics Research Laboratory, DCEG, NCI, Frederick National Laboratory for Cancer Research (FNLCR), Leidos Biomedical Research, Inc., Rockville, USA.; Williams C; Information Management Services, Inc., Danbury, USA.; Wright P; Information Management Services, Inc., Danbury, USA.; Yeager M; Cancer Genomics Research Laboratory, DCEG, NCI, Frederick National Laboratory for Cancer Research (FNLCR), Leidos Biomedical Research, Inc., Rockville, USA.; Zhu B; Cancer Genomics Research Laboratory, DCEG, NCI, Frederick National Laboratory for Cancer Research (FNLCR), Leidos Biomedical Research, Inc., Rockville, USA.; Zhu C; Division of Cancer Prevention, NCI, NIH, Rockville, USA.; Chanock SJ; Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, USA.; Garcia-Closas M; Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, USA.; Freedman ND; Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, USA. |
| Source: | Scientific data [Sci Data] 2023 Jan 12; Vol. 10 (1), pp. 25. Date of Electronic Publication: 2023 Jan 12. |
| Publication Type: | Dataset; Journal Article |
| Language: | English |
| Journal Info: | Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101640192 Publication Model: Electronic Cited Medium: Internet ISSN: 2052-4463 (Electronic) Linking ISSN: 20524463 NLM ISO Abbreviation: Sci Data Subsets: MEDLINE |
| Imprint Name(s): | Original Publication: London : Nature Publishing Group, 2014- |
| MeSH Terms: | Genome-Wide Association Study* ; Ovarian Neoplasms*; Female ; Humans ; Male ; Lung ; Polymorphism, Single Nucleotide ; Prospective Studies ; Prostate |
| 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.; (© 2023. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.) |
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| Grant Information: | Intramural Research Program U.S. Department of Health & Human Services | NIH | NCI | Division of Cancer Epidemiology and Genetics, National Cancer Institute (National Cancer Institute Division of Cancer Epidemiology and Genetics) |
| Entry Date(s): | Date Created: 20230112 Date Completed: 20230117 Latest Revision: 20240910 |
| Update Code: | 20260130 |
| PubMed Central ID: | PMC9837135 |
| DOI: | 10.1038/s41597-022-01921-2 |
| PMID: | 36635305 |
| Database: | MEDLINE |
Dataset; Journal Article