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A reference panel of 64,976 haplotypes for genotype imputation

2016; Nature Portfolio; Volume: 48; Issue: 10 Linguagem: Inglês

10.1038/ng.3643

1546-1718

Shane McCarthy, Sayantan Das, Warren W. Kretzschmar, Olivier Delaneau, Andrew R. Wood, Alexander Teumer, Hyun Min Kang, Christian Fuchsberger, Petr Danecek, Kevin Sharp, Yang Luo, Carlo Sidore, Alan Kwong, Nicholas J. Timpson, Seppo Koskinen, Scott Vrieze, Laura J. Scott, He Zhang, Anubha Mahajan, Jan H. Veldink, Ulrike Peters, Carlos N. 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 T. Chan, Sai Chen, Emily Y. Chew, Francis S. Collins, Laura J. Corbin, George Davey Smith, George Dedoussis, Marcus Dörr, Aliki-Eleni Farmaki, Luigi Ferrucci, Lukas Forer, Ross M. Fraser, Stacey Gabriel, Shawn Levy, Leif Groop, Tabitha A. Harrison, Andrew T. Hattersley, Oddgeir L. Holmen, Kristian Hveem, Matthias Kretzler, James Lee, Matt McGue, Thomas Meitinger, David Melzer, Josine L. Min, Karen L. Mohlke, John B. Vincent, Matthias Nauck, Deborah A. Nickerson, Aarno Palotie, Michele T. Pato, Nicola Pirastu, Melvin G. McInnis, J. Brent Richards, Cinzia Sala, Veikko Salomaa, David Schlessinger, Sebastian Schoenherr, P. Eline Slagboom, Kerrin S. Small, Timothy D. Spector, Dwight Stambolian, Marcus A. Tuke, Jaakko Tuomilehto, Leonard H. van den Berg, Wouter van Rheenen, Uwe Völker, Cisca Wijmenga, Daniela Toniolo, Eleftheria Zeggini, Paolo Gasparini, Matthew G. Sampson, James F. Wilson, Timothy M. Frayling, Paul I. W. de Bakker, Morris A. Swertz, Steven A. McCarroll, Charles Kooperberg, Annelot M. Dekker, David Altshuler, Cristen J. Willer, William G. Iacono, Samuli Ripatti, Nicole Soranzo, Klaudia Walter, Anand Swaroop, Francesco Cucca, Carl A. Anderson, R Myers, Michael Boehnke, Mark I. McCarthy, Richard Durbin,

Gene expression and cancer classification

Jonathan Marchini, Gonçalo Abecasis, Richard Durbin and colleagues describe the construction of a reference panel of human haplotypes from whole-genome sequencing data. They are able to use this to accurately impute genotypes at low minor allele frequency and present remote server resources for use by the community. 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.