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PMID: 27571263 Published · ppublish English Journal Article Research Support, N.I.H., Intramural Research Support, Non-U.S. Gov't Research Support, N.I.H., Extramural

Next-generation genotype imputation service and methods.

Nature genetics ·Vol. 48 ·No. 10 ·2016-00-00 ·Pages 1284-1287

Das S, Forer L, Schönherr S, Sidore C, Locke AE, Kwong A, Vrieze SI, Chew EY, Levy S, McGue M, Schlessinger D, Stambolian D, Loh PR, Iacono WG, Swaroop A, Scott LJ, Cucca F, Kronenberg F, Boehnke M, Abecasis GR, Fuchsberger C

Abstract

Genotype imputation is a key component of genetic association studies, where it increases power, facilitates meta-analysis, and aids interpretation of signals. Genotype imputation is computationally demanding and, with current tools, typically requires access to a high-performance computing cluster and to a reference panel of sequenced genomes. Here we describe improvements to imputation machinery that reduce computational requirements by more than an order of magnitude with no loss of accuracy in comparison to standard imputation tools. We also describe a new web-based service for imputation that facilitates access to new reference panels and greatly improves user experience and productivity.

MeSH Terms
Algorithms Computer Simulation Genome-Wide Association Study Genotype Haplotypes Humans Internet
Authors & Affiliations
21 authors, click to expand affiliations / ORCID
Das Sayantan
Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA.
Forer Lukas
Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria.
Schönherr Sebastian
Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria.
Sidore Carlo
Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA. | Istituto di Ricerca Genetica e Biomedica, CNR, Monserrato, Cagliari, Italy. | Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy.
Locke Adam E
Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA.
Kwong Alan
Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA.
Vrieze Scott I
Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado, USA.
Chew Emily Y
Clinical Trials Branch, Division of Epidemiology and Clinical Applications, National Eye Institute, US National Institutes of Health, Bethesda, Maryland, USA.
Levy Shawn
HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA.
McGue Matt
Department of Psychology, University of Minnesota, Minneapolis, Minnesota, USA.
Schlessinger David
Laboratory of Genetics, National Institute on Aging, US National Institutes of Health, Baltimore, Maryland, USA.
Stambolian Dwight
Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
Loh Po-Ru
Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA. | Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.
Iacono William G
Department of Psychology, University of Minnesota, Minneapolis, Minnesota, USA.
Swaroop Anand
Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, US National Institutes of Health, Bethesda, Maryland, USA.
Scott Laura J
Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA.
Cucca Francesco
Istituto di Ricerca Genetica e Biomedica, CNR, Monserrato, Cagliari, Italy. | Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy.
Kronenberg Florian
Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria.
Boehnke Michael
Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA.
Abecasis Gonçalo R
Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA.
Fuchsberger Christian
Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA. | Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria. | Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC), affiliated with the University of Lübeck, Bolzano, Italy.
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Article Info
Journal
Nature genetics
Abbr.
Nat Genet
ISSN
1546-1718
DOI
10.1038/ng.3656
Published
2016-00-00
Epub
2016-00-29
Pages
1284-1287
Language
English
Region
United States
NLM ID
9216904
PMCID
PMC5157836
Subset
IM
Grants
NIAAA NIH HHS · R37 AA009367 · United States
NIAAA NIH HHS · R01 AA009367 · United States
NHGRI NIH HHS · R01 HG000376 · United States
NIDA NIH HHS · R01 DA024417 · United States
NIDA NIH HHS · R01 DA037904 · United States
NHLBI NIH HHS · R01 HL117626 · United States
NIDA NIH HHS · R37 DA005147 · United States
NIDA NIH HHS · R01 DA005147 · United States
NIDA NIH HHS · R01 DA036216 · United States
NIDA NIH HHS · U01 DA024417 · United States
NHGRI NIH HHS · R56 HG000376 · United States
NHGRI NIH HHS · R01 HG007022 · United States
NHLBI NIH HHS · U01 HL117626 · United States
External Links
PubMed source DOI: 10.1038/ng.3656 PMC Full Text View journal details
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