A reference panel of 64,976 haplotypes for genotype imputation

• Published in: Nature genetics Vol. 48; no. 10; pp. 1279 - 1283
• Main Authors: McCarthy, Shane, Das, Sayantan, Kretzschmar, Warren, Delaneau, Olivier, Wood, Andrew R, Teumer, Alexander, Kang, Hyun Min, Fuchsberger, Christian, Danecek, Petr, Sharp, Kevin, Luo, Yang, Sidore, Carlo, Kwong, Alan, Timpson, Nicholas, Koskinen, Seppo, Vrieze, Scott, Scott, Laura J, Zhang, He, Mahajan, Anubha, Veldink, Jan, Peters, Ulrike, Pato, Carlos, van Duijn, Cornelia M, Gillies, Christopher E, Gandin, Ilaria, Mezzavilla, Massimo, Gilly, Arthur, Cocca, Massimiliano, Traglia, Michela, Angius, Andrea, Barrett, Jeffrey C, Boomsma, Dorrett, Branham, Kari, Breen, Gerome, Brummett, Chad M, Busonero, Fabio, Campbell, Harry, Chan, Andrew, Chen, Sai, Chew, Emily, Collins, Francis S, Corbin, Laura J, Smith, George Davey, Dedoussis, George, Dorr, Marcus, Farmaki, Aliki-Eleni, Ferrucci, Luigi, Forer, Lukas, Fraser, Ross M, Gabriel, Stacey, Levy, Shawn, Groop, Leif, Harrison, Tabitha, Hattersley, Andrew, Holmen, Oddgeir L, Hveem, Kristian, Kretzler, Matthias, Lee, James C, McGue, Matt, Meitinger, Thomas, Melzer, David, Min, Josine L, Mohlke, Karen L, Vincent, John B, Nauck, Matthias, Nickerson, Deborah, Palotie, Aarno, Pato, Michele, Pirastu, Nicola, McInnis, Melvin, Richards, J Brent, Sala, Cinzia, Salomaa, Veikko, Schlessinger, David, Schoenherr, Sebastian, Slagboom, P Eline, Small, Kerrin, Spector, Timothy, Stambolian, Dwight, Tuke, Marcus, Tuomilehto, Jaakko, Van den Berg, Leonard H, Van Rheenen, Wouter, Volker, Uwe, Wijmenga, Cisca, Toniolo, Daniela, Zeggini, Eleftheria, Gasparini, Paolo, Sampson, Matthew G, Wilson, James F, Frayling, Timothy, de Bakker, Paul I W, Swertz, Morris A, McCarroll, Steven, Kooperberg, Charles, Dekker, Annelot, Altshuler, David, Willer, Cristen, Iacono, William, Ripatti, Samuli
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.10.2016; Nature Publishing Group
• Subjects: 45; 45/43; 631/208/205/2138; 631/208/457; Accuracy; Agriculture; Alleles; Animal Genetics and Genomics; Basic Medicine; Biomedicine; Cancer Research; Collaboration; Consortia; Datasets; DNA sequencing; Gene Function; Genealogy; Genetic aspects; Genetic Techniques; Genome-Wide Association Study; Genomes; Genomics; Genotype; Haplotypes; Human Genetics; Humans; Internet; letter; Medical and Health Sciences; Medical Genetics and Genomics (including Gene Therapy); Medicin och hälsovetenskap; Medicinsk genetik och genomik (Här ingår: Genterapi); Medicinska och farmaceutiska grundvetenskaper; Polymorphism, Single Nucleotide; Reference Values; Researchers; Studies
• ISSN: 1061-4036; 1546-1718; 1546-1718
• DOI: 10.1038/ng.3643

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.