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Faucon A, Samaroo J, Ge T, Davis LK, Cox NJ, Tao R, Shuey MM. Improving the computation efficiency of polygenic risk score modeling: faster in Julia. Life Sci Alliance 2022; 5:5/12/e202201382. [PMID: 35851544 PMCID: PMC9297586 DOI: 10.26508/lsa.202201382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 11/24/2022] Open
Abstract
To enable computationally efficient polygenic risk score (PRS) calculations, PRS.jl translates a field standard PRS construction method, PRS-CS, to the Julia programming language. To enable large-scale application of polygenic risk scores (PRSs) in a computationally efficient manner, we translate a widely used PRS construction method, PRS–continuous shrinkage, to the Julia programming language, PRS.jl. On nine different traits with varying genetic architectures, we demonstrate that PRS.jl maintains accuracy of prediction while decreasing the average runtime by 5.5×. Additional programmatic modifications improve usability and robustness. This freely available software substantially improves work flow and democratizes usage of PRSs by lowering the computational burden of the PRS–continuous shrinkage method.
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Affiliation(s)
- Annika Faucon
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Julian Samaroo
- JuliaLab, Massachusetts Institute of Technology, Boston, MA, USA
| | - Tian Ge
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Lea K Davis
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.,Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nancy J Cox
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.,Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ran Tao
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Megan M Shuey
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA .,Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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de Macena Sobreira NL, Repetto GM, Temtamy SA, Alvarez Perez AB. Using Online Mendelian Inheritance in Man in low- and middle-income countries. Am J Med Genet A 2021; 185:3284-3286. [PMID: 34492150 DOI: 10.1002/ajmg.a.62467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 07/27/2021] [Accepted: 08/05/2021] [Indexed: 01/04/2023]
Abstract
Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders, has been used in the low- and middle-income countries largely as a tool for improving clinical care, teaching genetics and genomics, and for clinical and research analysis of next-generation sequencing. By facilitating free access to curated, updated, and comprehensive information in genetics and genomics, OMIM has led to better clinical care and research advancement in countries where clinicians and researchers in private or public hospitals and universities cannot afford to pay for other resources including journal subscriptions.
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Affiliation(s)
- Nara Lygia de Macena Sobreira
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Gabriela M Repetto
- Rare Diseases Program, Institute of Science and Innovation in Medicine, Facultad de Medicina Clinica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Samia A Temtamy
- Department of Clinical Genetics, Division of Human Genetics and Genome Research, National Research Center, Cairo, Egypt
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Kaur M, Hadley DW, Muenke M, Hart PS. An International Summit in Human Genetics and Genomics: Empowering clinical practice and research in developing countries. Mol Genet Genomic Med 2019; 7:e00599. [PMID: 30786327 PMCID: PMC6382448 DOI: 10.1002/mgg3.599] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 01/16/2019] [Accepted: 01/16/2019] [Indexed: 12/30/2022] Open
Abstract
To help fill the knowledge gap in human genetics and genomics, an International Summit (IS) in Human Genetics and Genomics was conceived and organized by the National Human Genome Research Institute (NHGRI) of the National Institutes of Health (NIH) as a 5‐year initiative, from 2016 to 2020. In its first 3 years, 71 professionals from 34 countries received training.![]()
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Affiliation(s)
- Manjit Kaur
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Donald W Hadley
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Maximilian Muenke
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - P Suzanne Hart
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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