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

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...

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Autores principales: Machiela, Mitchell J., Huang, Wen-Yi, Wong, Wendy, Berndt, Sonja I., Sampson, Joshua, De Almeida, Jonas, Abubakar, Mustapha, Hislop, Jada, Chen, Kai-Ling, Dagnall, Casey, Diaz-Mayoral, Norma, Ferrell, Mary, Furr, Michael, Gonzalez, Alex, Hicks, Belynda, Hubbard, Aubrey K., Hutchinson, Amy, Jiang, Kevin, Jones, Kristine, Liu, Jia, Loftfield, Erikka, Loukissas, Jennifer, Mabie, Jerome, Merkle, Shannon, Miller, Eric, Minasian, Lori M., Nordgren, Ellen, Park, Brian, Pinsky, Paul, Riley, Thomas, Sandoval, Lorena, Saxena, Neeraj, Vogt, Aurelie, Wang, Jiahui, Williams, Craig, Wright, Patrick, Yeager, Meredith, Zhu, Bin, Zhu, Claire, Chanock, Stephen J., Garcia-Closas, Montserrat, Freedman, Neal D.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Data Descriptor
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9837135/
https://www.ncbi.nlm.nih.gov/pubmed/36635305
http://dx.doi.org/10.1038/s41597-022-01921-2
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author Machiela, Mitchell J.
Huang, Wen-Yi
Wong, Wendy
Berndt, Sonja I.
Sampson, Joshua
De Almeida, Jonas
Abubakar, Mustapha
Hislop, Jada
Chen, Kai-Ling
Dagnall, Casey
Diaz-Mayoral, Norma
Ferrell, Mary
Furr, Michael
Gonzalez, Alex
Hicks, Belynda
Hubbard, Aubrey K.
Hutchinson, Amy
Jiang, Kevin
Jones, Kristine
Liu, Jia
Loftfield, Erikka
Loukissas, Jennifer
Mabie, Jerome
Merkle, Shannon
Miller, Eric
Minasian, Lori M.
Nordgren, Ellen
Park, Brian
Pinsky, Paul
Riley, Thomas
Sandoval, Lorena
Saxena, Neeraj
Vogt, Aurelie
Wang, Jiahui
Williams, Craig
Wright, Patrick
Yeager, Meredith
Zhu, Bin
Zhu, Claire
Chanock, Stephen J.
Garcia-Closas, Montserrat
Freedman, Neal D.
author_facet Machiela, Mitchell J.
Huang, Wen-Yi
Wong, Wendy
Berndt, Sonja I.
Sampson, Joshua
De Almeida, Jonas
Abubakar, Mustapha
Hislop, Jada
Chen, Kai-Ling
Dagnall, Casey
Diaz-Mayoral, Norma
Ferrell, Mary
Furr, Michael
Gonzalez, Alex
Hicks, Belynda
Hubbard, Aubrey K.
Hutchinson, Amy
Jiang, Kevin
Jones, Kristine
Liu, Jia
Loftfield, Erikka
Loukissas, Jennifer
Mabie, Jerome
Merkle, Shannon
Miller, Eric
Minasian, Lori M.
Nordgren, Ellen
Park, Brian
Pinsky, Paul
Riley, Thomas
Sandoval, Lorena
Saxena, Neeraj
Vogt, Aurelie
Wang, Jiahui
Williams, Craig
Wright, Patrick
Yeager, Meredith
Zhu, Bin
Zhu, Claire
Chanock, Stephen J.
Garcia-Closas, Montserrat
Freedman, Neal D.
author_sort Machiela, Mitchell J.
collection PubMed
description 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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spelling pubmed-98371352023-01-14 GWAS Explorer: an open-source tool to explore, visualize, and access GWAS summary statistics in the PLCO Atlas Machiela, Mitchell J. Huang, Wen-Yi Wong, Wendy Berndt, Sonja I. Sampson, Joshua De Almeida, Jonas Abubakar, Mustapha Hislop, Jada Chen, Kai-Ling Dagnall, Casey Diaz-Mayoral, Norma Ferrell, Mary Furr, Michael Gonzalez, Alex Hicks, Belynda Hubbard, Aubrey K. Hutchinson, Amy Jiang, Kevin Jones, Kristine Liu, Jia Loftfield, Erikka Loukissas, Jennifer Mabie, Jerome Merkle, Shannon Miller, Eric Minasian, Lori M. Nordgren, Ellen Park, Brian Pinsky, Paul Riley, Thomas Sandoval, Lorena Saxena, Neeraj Vogt, Aurelie Wang, Jiahui Williams, Craig Wright, Patrick Yeager, Meredith Zhu, Bin Zhu, Claire Chanock, Stephen J. Garcia-Closas, Montserrat Freedman, Neal D. Sci Data Data Descriptor 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. Nature Publishing Group UK 2023-01-12 /pmc/articles/PMC9837135/ /pubmed/36635305 http://dx.doi.org/10.1038/s41597-022-01921-2 Text en © This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Data Descriptor
Machiela, Mitchell J.
Huang, Wen-Yi
Wong, Wendy
Berndt, Sonja I.
Sampson, Joshua
De Almeida, Jonas
Abubakar, Mustapha
Hislop, Jada
Chen, Kai-Ling
Dagnall, Casey
Diaz-Mayoral, Norma
Ferrell, Mary
Furr, Michael
Gonzalez, Alex
Hicks, Belynda
Hubbard, Aubrey K.
Hutchinson, Amy
Jiang, Kevin
Jones, Kristine
Liu, Jia
Loftfield, Erikka
Loukissas, Jennifer
Mabie, Jerome
Merkle, Shannon
Miller, Eric
Minasian, Lori M.
Nordgren, Ellen
Park, Brian
Pinsky, Paul
Riley, Thomas
Sandoval, Lorena
Saxena, Neeraj
Vogt, Aurelie
Wang, Jiahui
Williams, Craig
Wright, Patrick
Yeager, Meredith
Zhu, Bin
Zhu, Claire
Chanock, Stephen J.
Garcia-Closas, Montserrat
Freedman, Neal D.
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
title_full GWAS Explorer: an open-source tool to explore, visualize, and access GWAS summary statistics in the PLCO Atlas
title_fullStr GWAS Explorer: an open-source tool to explore, visualize, and access GWAS summary statistics in the PLCO Atlas
title_full_unstemmed GWAS Explorer: an open-source tool to explore, visualize, and access GWAS summary statistics in the PLCO Atlas
title_short GWAS Explorer: an open-source tool to explore, visualize, and access GWAS summary statistics in the PLCO Atlas
title_sort gwas explorer: an open-source tool to explore, visualize, and access gwas summary statistics in the plco atlas
topic Data Descriptor
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9837135/
https://www.ncbi.nlm.nih.gov/pubmed/36635305
http://dx.doi.org/10.1038/s41597-022-01921-2
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