Next-generation genotype imputation service and methods

Sayantan Das; Lukas Forer; Sebastian Schönherr; Carlo Sidore; Adam E. Locke; Alan Kwong; Scott I. Vrieze; Emily Y. Chew; Shawn Levy; Matt McGue; David Schlessinger; Dwight Stambolian; Po Ru Loh; William G. Iacono; Anand Swaroop; Laura J. Scott; Francesco Cucca; Florian Kronenberg; Michael Boehnke; Gonçalo R. Abecasis; Christian Fuchsberger

doi:10.1038/ng.3656

Next-generation genotype imputation service and methods

Sayantan Das, Lukas Forer, Sebastian Schönherr, Carlo Sidore, Adam E. Locke, Alan Kwong, Scott I. Vrieze, Emily Y. Chew, Shawn Levy, Matt McGue, David Schlessinger, Dwight Stambolian, Po Ru Loh, William G. Iacono, Anand Swaroop, Laura J. Scott, Francesco Cucca, Florian Kronenberg, Michael Boehnke, Gonçalo R. AbecasisChristian Fuchsberger

Psychology (Twin Cities)

Research output: Contribution to journal › Article › peer-review

1400 Scopus citations

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.

Original language	English (US)
Pages (from-to)	1284-1287
Number of pages	4
Journal	Nature Genetics
Volume	48
Issue number	10
DOIs	https://doi.org/10.1038/ng.3656
State	Published - Oct 1 2016

Bibliographical note

Funding Information:
Acknowledgments: The authors gratefully acknowledge D. Hinds for assistance with minimac3 code optimizations and A.L. Williams for providing HAPI-UR. We acknowledge support from National Institutes of Health grants HG007022 and HL117626 (G.R.A.), HG000376 (M.B.), and R01DA037904 (S.I.V.), Austrian Science Fund (FWF) grant J-3401 (C.F.), and the European Community's Seventh Framework Programme (FP7/2007-2013) under grant agreement 602133 (L.F. and S.S.). This work was also supported in part by the Intramural Research Program of the National Institute on Aging, National Institutes of Health (D. Schlessinger).

Publisher Copyright:
© 2016 Nature America, Inc. All rights reserved.

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http://europepmc.org/articles/pmc5157836

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Das, S., Forer, L., Schönherr, S., Sidore, C., Locke, A. E., Kwong, A., Vrieze, S. I., Chew, E. Y., Levy, S., McGue, M., Schlessinger, D., Stambolian, D., Loh, P. R., Iacono, W. G., Swaroop, A., Scott, L. J., Cucca, F., Kronenberg, F., Boehnke, M., ... Fuchsberger, C. (2016). Next-generation genotype imputation service and methods. Nature Genetics, 48(10), 1284-1287. https://doi.org/10.1038/ng.3656

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 2016, 'Next-generation genotype imputation service and methods', Nature Genetics, vol. 48, no. 10, pp. 1284-1287. https://doi.org/10.1038/ng.3656

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Next-generation genotype imputation service and methods

Abstract

Bibliographical note

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