A reference panel of 64,976 haplotypes for genotype imputation

Shane McCarthy, Sayantan Das, Warren Kretzschmar, Olivier Delaneau, Andrew R. Wood, Alexander Teumer, Hyun Min Kang, Christian Fuchsberger, Petr Danecek, Kevin Sharp, Yang Luo, Carlo Sidore, Alan Kwong, Nicholas Timpson, Seppo Koskinen, Scott Vrieze, Laura J. Scott, He Zhang, Anubha Mahajan, Jan VeldinkUlrike Peters, Carlos Pato, Cornelia M. Van Duijn, Christopher E. Gillies, Ilaria Gandin, Massimo Mezzavilla, Arthur Gilly, Massimiliano Cocca, Michela Traglia, Andrea Angius, Jeffrey C. Barrett, Dorrett Boomsma, Kari Branham, Gerome Breen, Chad M. Brummett, Fabio Busonero, Harry Campbell, Andrew Chan, Sai Chen, Emily Chew, Francis S. Collins, Laura J. Corbin, George Davey Smith, George Dedoussis, Marcus Dorr, Aliki Eleni Farmaki, Luigi Ferrucci, Lukas Forer, Ross M. Fraser, Stacey Gabriel, Shawn Levy, Leif Groop, Tabitha Harrison, Andrew Hattersley, Oddgeir L. Holmen, Kristian Hveem, Matthias Kretzler, James C. Lee, Matt McGue, Thomas Meitinger, David Melzer, Josine L. Min, Karen L. Mohlke, John B. Vincent, Matthias Nauck, Deborah Nickerson, Aarno Palotie, Michele Pato, Nicola Pirastu, Melvin McInnis, J. Brent Richards, Cinzia Sala, Veikko Salomaa, David Schlessinger, Sebastian Schoenherr, P. Eline Slagboom, Kerrin Small, Timothy Spector, Dwight Stambolian, Marcus Tuke, Jaakko Tuomilehto, Leonard H. Van Den Berg, Wouter Van Rheenen, Uwe Volker, Cisca Wijmenga, Daniela Toniolo, Eleftheria Zeggini, Paolo Gasparini, Matthew G. Sampson, James F. Wilson, Timothy Frayling, Paul I W De Bakker, Morris A. Swertz, Steven McCarroll, Charles Kooperberg, Annelot Dekker, David Altshuler, Cristen Willer, William Iacono, Samuli Ripatti, Nicole Soranzo, Klaudia Walter, Anand Swaroop, Francesco Cucca, Carl A. Anderson, Richard M. Myers, Michael Boehnke, Mark I. McCarthy, Richard Durbin, Gonçalo Abecasis, Jonathan Marchini

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Abstract

We describe a reference panel of 64,976 human haplotypes at 39,235,157 SNPs constructed using whole-genome sequence data from 20 studies of predominantly European ancestry. Using this resource leads to accurate genotype imputation at minor allele frequencies as low as 0.1% and a large increase in the number of SNPs tested in association studies, and it can help to discover and refine causal loci. We describe remote server resources that allow researchers to carry out imputation and phasing consistently and efficiently.

Original languageEnglish (US)
Pages (from-to)1279-1283
Number of pages5
JournalNature Genetics
Volume48
Issue number10
DOIs
StatePublished - Oct 1 2016

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    McCarthy, S., Das, S., Kretzschmar, W., Delaneau, O., Wood, A. R., Teumer, A., Kang, H. M., Fuchsberger, C., Danecek, P., Sharp, K., Luo, Y., Sidore, C., Kwong, A., Timpson, N., Koskinen, S., Vrieze, S., Scott, L. J., Zhang, H., Mahajan, A., ... Marchini, J. (2016). A reference panel of 64,976 haplotypes for genotype imputation. Nature Genetics, 48(10), 1279-1283. https://doi.org/10.1038/ng.3643