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 Veldink; Ulrike 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; Josine L Min; Nicole Soranzo; Haplotype Reference Consortium

doi:10.1038/ng.3643

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, Josine L Min, Nicole Soranzo, Haplotype Reference Consortium

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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 language	English
Pages (from-to)	1279-1283
Number of pages	5
Journal	Nature Genetics
Volume	48
Issue number	10
Early online date	22 Aug 2016
DOIs	https://doi.org/10.1038/ng.3643
Publication status	Published - Oct 2016

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MRC UoB UNITE Unit - programme 3
Timpson, N. J. & Timpson, N. J.
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Professor Nicholas John Timpson
- N.J.Timpson@bristol.ac.uk
- Bristol Medical School (PHS) - Professor of Genetic Epidemiology
- Bristol Population Health Science Institute
- MRC Integrative Epidemiology Unit
- Cancer
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McCarthy, S., Das, S., Kretzschmar, W., Delaneau, O., Wood, A. R., Teumer, A., Kang, H. M., Fuchsberger, C., Danecek, P., Sharp, K., Luo, Y., Sidore, C., Kwong, A., Timpson, N., Koskinen, S., Vrieze, S., Scott, L. J., Zhang, H., Mahajan, A., ... Haplotype Reference Consortium (2016). A reference panel of 64,976 haplotypes for genotype imputation. Nature Genetics, 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 ; Min, Josine L ; Soranzo, Nicole ; Haplotype Reference Consortium. / 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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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.",

author = "Shane McCarthy and Sayantan Das and Warren Kretzschmar and Olivier Delaneau and Wood, {Andrew R} and Alexander Teumer and Kang, {Hyun Min} and Christian Fuchsberger and Petr Danecek and Kevin Sharp and Yang Luo and Carlo Sidore and Alan Kwong and Nicholas Timpson and Seppo Koskinen and Scott Vrieze and Scott, {Laura J} and He Zhang and Anubha Mahajan and Jan Veldink and Ulrike Peters and Carlos Pato and {van Duijn}, {Cornelia M} and Gillies, {Christopher E} and Ilaria Gandin and Massimo Mezzavilla and Arthur Gilly and Massimiliano Cocca and Michela Traglia and Andrea Angius and Barrett, {Jeffrey C} and Dorrett Boomsma and Kari Branham and Gerome Breen and Brummett, {Chad M} and Fabio Busonero and Harry Campbell and Andrew Chan and Sai Chen and Emily Chew and Collins, {Francis S} and Corbin, {Laura J} and Smith, {George Davey} and George Dedoussis and Marcus Dorr and Aliki-Eleni Farmaki and Luigi Ferrucci and Lukas Forer and Min, {Josine L} and Nicole Soranzo and {Haplotype Reference Consortium}",

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volume = "48",

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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, A-E, Ferrucci, L, Forer, L, Min, JL, Soranzo, N & Haplotype Reference Consortium 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

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; Min, Josine L; Soranzo, Nicole; Haplotype Reference Consortium.

In: Nature Genetics, Vol. 48, No. 10, 10.2016, p. 1279-1283.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

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AU - Das, Sayantan

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AU - Teumer, Alexander

AU - Kang, Hyun Min

AU - Fuchsberger, Christian

AU - Danecek, Petr

AU - Sharp, Kevin

AU - Luo, Yang

AU - Sidore, Carlo

AU - Kwong, Alan

AU - Timpson, Nicholas

AU - Koskinen, Seppo

AU - Vrieze, Scott

AU - Scott, Laura J

AU - Zhang, He

AU - Mahajan, Anubha

AU - Veldink, Jan

AU - Peters, Ulrike

AU - Pato, Carlos

AU - van Duijn, Cornelia M

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

AU - Chew, Emily

AU - Collins, Francis S

AU - Corbin, Laura J

AU - Smith, George Davey

AU - Dedoussis, George

AU - Dorr, Marcus

AU - Farmaki, Aliki-Eleni

AU - Ferrucci, Luigi

AU - Forer, Lukas

AU - Min, Josine L

AU - Soranzo, Nicole

AU - Haplotype Reference Consortium

PY - 2016/10

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AB - 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.

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DO - 10.1038/ng.3643

M3 - Article (Academic Journal)

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VL - 48

SP - 1279

EP - 1283

JO - Nature Genetics

JF - Nature Genetics

SN - 1061-4036

IS - 10

ER -

A reference panel of 64,976 haplotypes for genotype imputation

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