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

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, PI; 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; Haplotype Reference Consortium,

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

https://hdl.handle.net/10871/23512
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posted on 2025-07-31, 15:52 authored by S McCarthy, S Das, W Kretzschmar, O Delaneau, AR Wood, A Teumer, HM Kang, C Fuchsberger, P Danecek, K Sharp, Y Luo, C Sidore, A Kwong, N Timpson, S Koskinen, S Vrieze, LJ Scott, H Zhang, A Mahajan, J Veldink, U Peters, C Pato, CM van Duijn, CE Gillies, I Gandin, M Mezzavilla, A Gilly, M Cocca, M Traglia, A Angius, JC Barrett, D Boomsma, K Branham, G Breen, CM Brummett, F Busonero, H Campbell, A Chan, S Chen, E Chew, FS Collins, LJ Corbin, GD Smith, G Dedoussis, M Dorr, AE Farmaki, L Ferrucci, L Forer, RM Fraser, S Gabriel, S Levy, L Groop, T Harrison, A Hattersley, OL Holmen, K Hveem, M Kretzler, JC Lee, M McGue, T Meitinger, D Melzer, JL Min, KL Mohlke, JB Vincent, M Nauck, D Nickerson, A Palotie, M Pato, N Pirastu, M McInnis, JB Richards, C Sala, V Salomaa, D Schlessinger, S Schoenherr, PE Slagboom, K Small, T Spector, D Stambolian, M Tuke, J Tuomilehto, LH Van den Berg, W Van Rheenen, U Volker, C Wijmenga, D Toniolo, E Zeggini, P Gasparini, MG Sampson, JF Wilson, T Frayling, PI de Bakker, MA Swertz, S McCarroll, C Kooperberg, A Dekker, D Altshuler, C Willer, W Iacono, S Ripatti, N Soranzo, K Walter, A Swaroop, F Cucca, CA Anderson, RM Myers, M Boehnke, MI McCarthy, R Durbin, G Abecasis, J Marchini, Haplotype Reference Consortium

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.

Funding

J.M acknowledges support from the ERC (Grant no. 617306). W.K acknowledges support from the Wellcome Trust (Grant no. WT097307). S.M and R.D acknowledge support from Wellcome Trust grant WT090851. We are grateful to all participants of all the studies that have contributed data to the HRC.

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PMID - Is identical to https://pubmed.ncbi.nlm.nih.gov/27548312

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Pre print made available under a CC-BY-NC-ND 4.0 International license.

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This is the author pre print version. The final version is available from the publisher via the DOI in this record.

External DOI

https://doi.org/10.1038/ng.3643

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Nature Genetics

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Nature Publishing Group

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en

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doi:10.1038/ng.3643

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Genome-wide association studies Population genetics

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

Funding

J.M acknowledges support from the ERC (Grant no. 617306). W.K acknowledges support from the Wellcome Trust (Grant no. WT097307). S.M and R.D acknowledge support from Wellcome Trust grant WT090851. We are grateful to all participants of all the studies that have contributed data to the HRC.

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