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; Leonard H Van den Berg; Wouter Van Rheenen; Paul I W de Bakker; Annelot Dekker

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, Leonard H Van den Berg, Wouter Van Rheenen, Paul I W de Bakker, Annelot Dekker,

Research output: Contribution to journal › Letter › Academic › peer-review

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
Journal	Nature Genetics
Volume	48
DOIs	https://doi.org/10.1038/ng.3643
Publication status	Published - 22 Aug 2016

Access to Document

10.1038/ng.3643

Cite this

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. (2016). A reference panel of 64,976 haplotypes for genotype imputation. Nature Genetics, 48, 1279–1283. https://doi.org/10.1038/ng.3643

@article{95756da3a79b4e8891190a6d98f04805,

title = "A reference panel of 64,976 haplotypes for genotype imputation",

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 {Van den Berg}, {Leonard H} and {Van Rheenen}, Wouter and {de Bakker}, {Paul I W} and Annelot Dekker",

year = "2016",

month = aug,

day = "22",

doi = "10.1038/ng.3643",

language = "English",

volume = "48",

pages = "1279–1283",

journal = "Nature Genetics",

issn = "1061-4036",

publisher = "Nature Publishing Group",

}

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, Van den Berg, LH , Van Rheenen, W, de Bakker, PIW, Dekker, A 2016, 'A reference panel of 64,976 haplotypes for genotype imputation', Nature Genetics, vol. 48, pp. 1279–1283. https://doi.org/10.1038/ng.3643

TY - JOUR

T1 - A reference panel of 64,976 haplotypes for genotype imputation

AU - McCarthy, Shane

AU - Das, Sayantan

AU - Kretzschmar, Warren

AU - Delaneau, Olivier

AU - Wood, Andrew R

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 - Van den Berg, Leonard H

AU - Van Rheenen, Wouter

AU - de Bakker, Paul I W

AU - Dekker, Annelot

PY - 2016/8/22

Y1 - 2016/8/22

N2 - 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.

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.

U2 - 10.1038/ng.3643

DO - 10.1038/ng.3643

M3 - Letter

C2 - 27548312

SN - 1061-4036

VL - 48

SP - 1279

EP - 1283

JO - Nature Genetics

JF - Nature Genetics

ER -

A reference panel of 64,976 haplotypes for genotype imputation

Abstract

Access to Document

Fingerprint

Cite this