A reference panel of 64,976 haplotypes for genotype imputation.

Publication Type:

Journal Article

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; Völker, 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; Soranzo, Nicole; Walter, Klaudia; Swaroop, Anand; Cucca, Francesco; Anderson, Carl A; Myers, Richard M; Boehnke, Michael; McCarthy, Mark I; Durbin, Richard

Source:

Nat Genet, Volume 48, Issue 10, p.1279-83 (2016)

Keywords:

Alleles, Genetic Techniques, Genome-Wide Association Study, Genotype, Haplotypes, Humans, Internet, Polymorphism, Single Nucleotide, Reference Values

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.