A reference panel of 64,976 haplotypes for genotype imputation

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

doi:10.1038/ng.3643

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.

A reference panel of 64,976 haplotypes for genotype imputation / 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; Soranzo, Nicole; Walter, Klaudia; Swaroop, Anand; Cucca, Francesco; Anderson, Carl A; Myers, Richard M; Boehnke, Michael; Mccarthy, Mark I; Durbin, Richard. - In: NATURE GENETICS. - ISSN 1061-4036. - STAMPA. - 48:10(2016), pp. 1279-1283. [10.1038/ng.3643]