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

Research output: Contribution to journalArticle

477 Citations (Scopus)

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
Pages (from-to)1279-1283
Number of pages5
JournalNature Genetics
Volume48
Issue number10
DOIs
Publication statusPublished - Oct 1 2016

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Haplotypes
Single Nucleotide Polymorphism
Genotype
Gene Frequency
Research Personnel
Genome

ASJC Scopus subject areas

  • Genetics

Cite this

McCarthy, S., Das, S., Kretzschmar, W., Delaneau, O., Wood, A. R., Teumer, 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

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; Abecasis, Gonçalo; Marchini, Jonathan.

In: Nature Genetics, Vol. 48, No. 10, 01.10.2016, p. 1279-1283.

Research output: Contribution to journalArticle

McCarthy, S, Das, S, Kretzschmar, W, Delaneau, O, Wood, AR, Teumer, A, Kang, HM, Fuchsberger, C, Danecek, P, Sharp, K, Luo, Y, Sidore, C, Kwong, A, Timpson, N, Koskinen, S, Vrieze, S, Scott, LJ, Zhang, H, Mahajan, A, Veldink, J, Peters, U, Pato, C, Van Duijn, CM, Gillies, CE, Gandin, I, Mezzavilla, M, Gilly, A, Cocca, M, Traglia, M, Angius, A, Barrett, JC, Boomsma, D, Branham, K, Breen, G, Brummett, CM, Busonero, F, Campbell, H, Chan, A, Chen, S, Chew, E, Collins, FS, Corbin, LJ, Smith, GD, Dedoussis, G, Dorr, M, Farmaki, AE, Ferrucci, L, Forer, L, Fraser, RM, Gabriel, S, Levy, S, Groop, L, Harrison, T, Hattersley, A, Holmen, OL, Hveem, K, Kretzler, M, Lee, JC, McGue, M, Meitinger, T, Melzer, D, Min, JL, Mohlke, KL, Vincent, JB, Nauck, M, Nickerson, D, Palotie, A, Pato, M, Pirastu, N, McInnis, M, Richards, JB, Sala, C, Salomaa, V, Schlessinger, D, Schoenherr, S, Slagboom, PE, Small, K, Spector, T, Stambolian, D, Tuke, M, Tuomilehto, J, Van Den Berg, LH, Van Rheenen, W, Volker, U, Wijmenga, C, Toniolo, D, Zeggini, E, Gasparini, P, Sampson, MG, Wilson, JF, Frayling, T, De Bakker, PIW, Swertz, MA, McCarroll, S, Kooperberg, C, Dekker, A, Altshuler, D, Willer, C, Iacono, W, Ripatti, S, Soranzo, N, Walter, K, Swaroop, A, Cucca, F, Anderson, CA, Myers, RM, Boehnke, M, McCarthy, MI, Durbin, R, Abecasis, G & Marchini, J 2016, 'A reference panel of 64,976 haplotypes for genotype imputation', Nature Genetics, vol. 48, no. 10, pp. 1279-1283. https://doi.org/10.1038/ng.3643
McCarthy S, Das S, Kretzschmar W, Delaneau O, Wood AR, Teumer A et al. A reference panel of 64,976 haplotypes for genotype imputation. Nature Genetics. 2016 Oct 1;48(10):1279-1283. https://doi.org/10.1038/ng.3643
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 ; Abecasis, Gonçalo ; Marchini, Jonathan. / A reference panel of 64,976 haplotypes for genotype imputation. In: Nature Genetics. 2016 ; Vol. 48, No. 10. pp. 1279-1283.
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AU - Kretzschmar, Warren

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AU - Wood, Andrew R.

AU - Teumer, Alexander

AU - Kang, Hyun Min

AU - Fuchsberger, Christian

AU - Danecek, Petr

AU - Sharp, Kevin

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AU - Sidore, Carlo

AU - Kwong, Alan

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AU - Koskinen, Seppo

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AU - Mahajan, Anubha

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AU - Gillies, Christopher E.

AU - Gandin, Ilaria

AU - Mezzavilla, Massimo

AU - Gilly, Arthur

AU - Cocca, Massimiliano

AU - Traglia, Michela

AU - Angius, Andrea

AU - Barrett, Jeffrey C.

AU - Boomsma, Dorrett

AU - Branham, Kari

AU - Breen, Gerome

AU - Brummett, Chad M.

AU - Busonero, Fabio

AU - Campbell, Harry

AU - Chan, Andrew

AU - Chen, Sai

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AU - Melzer, David

AU - Min, Josine L.

AU - Mohlke, Karen L.

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AU - Nauck, Matthias

AU - Nickerson, Deborah

AU - Palotie, Aarno

AU - Pato, Michele

AU - Pirastu, Nicola

AU - McInnis, Melvin

AU - Richards, J. Brent

AU - Sala, Cinzia

AU - Salomaa, Veikko

AU - Schlessinger, David

AU - Schoenherr, Sebastian

AU - Slagboom, P. Eline

AU - Small, Kerrin

AU - Spector, Timothy

AU - Stambolian, Dwight

AU - Tuke, Marcus

AU - Tuomilehto, Jaakko

AU - Van Den Berg, Leonard H.

AU - Van Rheenen, Wouter

AU - Volker, Uwe

AU - Wijmenga, Cisca

AU - Toniolo, Daniela

AU - Zeggini, Eleftheria

AU - Gasparini, Paolo

AU - Sampson, Matthew G.

AU - Wilson, James F.

AU - Frayling, Timothy

AU - De Bakker, Paul I W

AU - Swertz, Morris A.

AU - McCarroll, Steven

AU - Kooperberg, Charles

AU - Dekker, Annelot

AU - Altshuler, David

AU - Willer, Cristen

AU - Iacono, William

AU - Ripatti, Samuli

AU - Soranzo, Nicole

AU - Walter, Klaudia

AU - Swaroop, Anand

AU - Cucca, Francesco

AU - Anderson, Carl A.

AU - Myers, Richard M.

AU - Boehnke, Michael

AU - McCarthy, Mark I.

AU - Durbin, Richard

AU - Abecasis, Gonçalo

AU - Marchini, Jonathan

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