Whole-genome sequence variation, population structure and demographic history of the Dutch population

Laurent C. Francioli, Androniki Menelaou, Sara L. Pulit, Freerk Van Dijk, Pier Francesco Palamara, Clara C. Elbers, Pieter B.T. Neerincx, Kai Ye, Victor Guryev, Wigard P. Kloosterman, Patrick Deelen, Abdel Abdellaoui, Elisabeth M. Van Leeuwen, Mannis Van Oven, Martijn Vermaat, Mingkun Li, Jeroen F.J. Laros, Lennart C. Karssen, Alexandros Kanterakis, Najaf AminJouke Jan Hottenga, Eric Wubbo Lameijer, Mathijs Kattenberg, Martijn Dijkstra, Heorhiy Byelas, Jessica Van Setten, Barbera D.C. Van Schaik, Jan Bot, Isaäc J. Nijman, Ivo Renkens, Tobias Marschall, Alexander Schönhuth, Jayne Y. Hehir-Kwa, Robert E. Handsaker, Paz Polak, Mashaal Sohail, Dana Vuzman, Fereydoun Hormozdiari, David Van Enckevort, Hailiang Mei, Vyacheslav Koval, Matthijs H. Moed, KJoeri Van Der Velde, Fernando Rivadeneira, Karol Estrada, Carolina Medina-Gomez, Aaron Isaacs, Steven A. McCarroll, Marian Beekman, Anton J. Mde Craen, H. Eka D. Suchiman, Albert Hofman, Ben Oostra, André G. Uitterlinden, Gonneke Willemsen, Mathieu Platteel, Jan H. Veldink, Leonard H. Van Den Berg, Steven J. Pitts, Shobha Potluri, Purnima Sundar, David R. Cox, Shamil R. Sunyaev, Johan T. Den Dunnen, Mark Stoneking, Peter De Knijff, Manfred Kayser, Qibin Li, Yingrui Li, Yuanping Du, Ruoyan Chen, Hongzhi Cao, Ning Li, Sujie Cao, Jun Wang, Jasper A. Bovenberg, Itsik Pe'er, P. Eline Slagboom, Cornelia M. Van Duijn, Dorret I. Boomsma, Gert Jan B. Van Ommen, Paul I.W. De Bakker, Morris A. Swertz, Cisca Wijmenga

Research output: Contribution to journalArticle

362 Citations (Scopus)

Abstract

Whole-genome sequencing enables complete characterization of genetic variation, but geographic clustering of rare alleles demands many diverse populations be studied. Here we describe the Genome of the Netherlands (GoNL) Project, in which we sequenced the whole genomes of 250 Dutch parent-offspring families and constructed a haplotype map of 20.4 million single-nucleotide variants and 1.2 million insertions and deletions. The intermediate coverage (∼13×) and trio design enabled extensive characterization of structural variation, including midsize events (30-500 bp) previously poorly catalogued and de novo mutations. We demonstrate that the quality of the haplotypes boosts imputation accuracy in independent samples, especially for lower frequency alleles. Population genetic analyses demonstrate fine-scale structure across the country and support multiple ancient migrations, consistent with historical changes in sea level and flooding. The GoNL Project illustrates how single-population whole-genome sequencing can provide detailed characterization of genetic variation and may guide the design of future population studies.

Original languageEnglish (US)
Pages (from-to)818-825
Number of pages8
JournalNature Genetics
Volume46
Issue number8
DOIs
StatePublished - Jan 1 2014
Externally publishedYes

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Demography
Genome
Population
Netherlands
Haplotypes
Population Genetics
Gene Frequency
Oceans and Seas
Cluster Analysis
Nucleotides
Alleles
Mutation

ASJC Scopus subject areas

  • Genetics

Cite this

Francioli, L. C., Menelaou, A., Pulit, S. L., Van Dijk, F., Palamara, P. F., Elbers, C. C., ... Wijmenga, C. (2014). Whole-genome sequence variation, population structure and demographic history of the Dutch population. Nature Genetics, 46(8), 818-825. https://doi.org/10.1038/ng.3021

Whole-genome sequence variation, population structure and demographic history of the Dutch population. / Francioli, Laurent C.; Menelaou, Androniki; Pulit, Sara L.; Van Dijk, Freerk; Palamara, Pier Francesco; Elbers, Clara C.; Neerincx, Pieter B.T.; Ye, Kai; Guryev, Victor; Kloosterman, Wigard P.; Deelen, Patrick; Abdellaoui, Abdel; Van Leeuwen, Elisabeth M.; Van Oven, Mannis; Vermaat, Martijn; Li, Mingkun; Laros, Jeroen F.J.; Karssen, Lennart C.; Kanterakis, Alexandros; Amin, Najaf; Hottenga, Jouke Jan; Lameijer, Eric Wubbo; Kattenberg, Mathijs; Dijkstra, Martijn; Byelas, Heorhiy; Van Setten, Jessica; Van Schaik, Barbera D.C.; Bot, Jan; Nijman, Isaäc J.; Renkens, Ivo; Marschall, Tobias; Schönhuth, Alexander; Hehir-Kwa, Jayne Y.; Handsaker, Robert E.; Polak, Paz; Sohail, Mashaal; Vuzman, Dana; Hormozdiari, Fereydoun; Van Enckevort, David; Mei, Hailiang; Koval, Vyacheslav; Moed, Matthijs H.; Van Der Velde, KJoeri; Rivadeneira, Fernando; Estrada, Karol; Medina-Gomez, Carolina; Isaacs, Aaron; McCarroll, Steven A.; Beekman, Marian; Mde Craen, Anton J.; Suchiman, H. Eka D.; Hofman, Albert; Oostra, Ben; Uitterlinden, André G.; Willemsen, Gonneke; Platteel, Mathieu; Veldink, Jan H.; Van Den Berg, Leonard H.; Pitts, Steven J.; Potluri, Shobha; Sundar, Purnima; Cox, David R.; Sunyaev, Shamil R.; Den Dunnen, Johan T.; Stoneking, Mark; De Knijff, Peter; Kayser, Manfred; Li, Qibin; Li, Yingrui; Du, Yuanping; Chen, Ruoyan; Cao, Hongzhi; Li, Ning; Cao, Sujie; Wang, Jun; Bovenberg, Jasper A.; Pe'er, Itsik; Slagboom, P. Eline; Van Duijn, Cornelia M.; Boomsma, Dorret I.; Van Ommen, Gert Jan B.; De Bakker, Paul I.W.; Swertz, Morris A.; Wijmenga, Cisca.

In: Nature Genetics, Vol. 46, No. 8, 01.01.2014, p. 818-825.

Research output: Contribution to journalArticle

Francioli, LC, Menelaou, A, Pulit, SL, Van Dijk, F, Palamara, PF, Elbers, CC, Neerincx, PBT, Ye, K, Guryev, V, Kloosterman, WP, Deelen, P, Abdellaoui, A, Van Leeuwen, EM, Van Oven, M, Vermaat, M, Li, M, Laros, JFJ, Karssen, LC, Kanterakis, A, Amin, N, Hottenga, JJ, Lameijer, EW, Kattenberg, M, Dijkstra, M, Byelas, H, Van Setten, J, Van Schaik, BDC, Bot, J, Nijman, IJ, Renkens, I, Marschall, T, Schönhuth, A, Hehir-Kwa, JY, Handsaker, RE, Polak, P, Sohail, M, Vuzman, D, Hormozdiari, F, Van Enckevort, D, Mei, H, Koval, V, Moed, MH, Van Der Velde, KJ, Rivadeneira, F, Estrada, K, Medina-Gomez, C, Isaacs, A, McCarroll, SA, Beekman, M, Mde Craen, AJ, Suchiman, HED, Hofman, A, Oostra, B, Uitterlinden, AG, Willemsen, G, Platteel, M, Veldink, JH, Van Den Berg, LH, Pitts, SJ, Potluri, S, Sundar, P, Cox, DR, Sunyaev, SR, Den Dunnen, JT, Stoneking, M, De Knijff, P, Kayser, M, Li, Q, Li, Y, Du, Y, Chen, R, Cao, H, Li, N, Cao, S, Wang, J, Bovenberg, JA, Pe'er, I, Slagboom, PE, Van Duijn, CM, Boomsma, DI, Van Ommen, GJB, De Bakker, PIW, Swertz, MA & Wijmenga, C 2014, 'Whole-genome sequence variation, population structure and demographic history of the Dutch population', Nature Genetics, vol. 46, no. 8, pp. 818-825. https://doi.org/10.1038/ng.3021
Francioli LC, Menelaou A, Pulit SL, Van Dijk F, Palamara PF, Elbers CC et al. Whole-genome sequence variation, population structure and demographic history of the Dutch population. Nature Genetics. 2014 Jan 1;46(8):818-825. https://doi.org/10.1038/ng.3021
Francioli, Laurent C. ; Menelaou, Androniki ; Pulit, Sara L. ; Van Dijk, Freerk ; Palamara, Pier Francesco ; Elbers, Clara C. ; Neerincx, Pieter B.T. ; Ye, Kai ; Guryev, Victor ; Kloosterman, Wigard P. ; Deelen, Patrick ; Abdellaoui, Abdel ; Van Leeuwen, Elisabeth M. ; Van Oven, Mannis ; Vermaat, Martijn ; Li, Mingkun ; Laros, Jeroen F.J. ; Karssen, Lennart C. ; Kanterakis, Alexandros ; Amin, Najaf ; Hottenga, Jouke Jan ; Lameijer, Eric Wubbo ; Kattenberg, Mathijs ; Dijkstra, Martijn ; Byelas, Heorhiy ; Van Setten, Jessica ; Van Schaik, Barbera D.C. ; Bot, Jan ; Nijman, Isaäc J. ; Renkens, Ivo ; Marschall, Tobias ; Schönhuth, Alexander ; Hehir-Kwa, Jayne Y. ; Handsaker, Robert E. ; Polak, Paz ; Sohail, Mashaal ; Vuzman, Dana ; Hormozdiari, Fereydoun ; Van Enckevort, David ; Mei, Hailiang ; Koval, Vyacheslav ; Moed, Matthijs H. ; Van Der Velde, KJoeri ; Rivadeneira, Fernando ; Estrada, Karol ; Medina-Gomez, Carolina ; Isaacs, Aaron ; McCarroll, Steven A. ; Beekman, Marian ; Mde Craen, Anton J. ; Suchiman, H. Eka D. ; Hofman, Albert ; Oostra, Ben ; Uitterlinden, André G. ; Willemsen, Gonneke ; Platteel, Mathieu ; Veldink, Jan H. ; Van Den Berg, Leonard H. ; Pitts, Steven J. ; Potluri, Shobha ; Sundar, Purnima ; Cox, David R. ; Sunyaev, Shamil R. ; Den Dunnen, Johan T. ; Stoneking, Mark ; De Knijff, Peter ; Kayser, Manfred ; Li, Qibin ; Li, Yingrui ; Du, Yuanping ; Chen, Ruoyan ; Cao, Hongzhi ; Li, Ning ; Cao, Sujie ; Wang, Jun ; Bovenberg, Jasper A. ; Pe'er, Itsik ; Slagboom, P. Eline ; Van Duijn, Cornelia M. ; Boomsma, Dorret I. ; Van Ommen, Gert Jan B. ; De Bakker, Paul I.W. ; Swertz, Morris A. ; Wijmenga, Cisca. / Whole-genome sequence variation, population structure and demographic history of the Dutch population. In: Nature Genetics. 2014 ; Vol. 46, No. 8. pp. 818-825.
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T1 - Whole-genome sequence variation, population structure and demographic history of the Dutch population

AU - Francioli, Laurent C.

AU - Menelaou, Androniki

AU - Pulit, Sara L.

AU - Van Dijk, Freerk

AU - Palamara, Pier Francesco

AU - Elbers, Clara C.

AU - Neerincx, Pieter B.T.

AU - Ye, Kai

AU - Guryev, Victor

AU - Kloosterman, Wigard P.

AU - Deelen, Patrick

AU - Abdellaoui, Abdel

AU - Van Leeuwen, Elisabeth M.

AU - Van Oven, Mannis

AU - Vermaat, Martijn

AU - Li, Mingkun

AU - Laros, Jeroen F.J.

AU - Karssen, Lennart C.

AU - Kanterakis, Alexandros

AU - Amin, Najaf

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AU - Dijkstra, Martijn

AU - Byelas, Heorhiy

AU - Van Setten, Jessica

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AU - Bot, Jan

AU - Nijman, Isaäc J.

AU - Renkens, Ivo

AU - Marschall, Tobias

AU - Schönhuth, Alexander

AU - Hehir-Kwa, Jayne Y.

AU - Handsaker, Robert E.

AU - Polak, Paz

AU - Sohail, Mashaal

AU - Vuzman, Dana

AU - Hormozdiari, Fereydoun

AU - Van Enckevort, David

AU - Mei, Hailiang

AU - Koval, Vyacheslav

AU - Moed, Matthijs H.

AU - Van Der Velde, KJoeri

AU - Rivadeneira, Fernando

AU - Estrada, Karol

AU - Medina-Gomez, Carolina

AU - Isaacs, Aaron

AU - McCarroll, Steven A.

AU - Beekman, Marian

AU - Mde Craen, Anton J.

AU - Suchiman, H. Eka D.

AU - Hofman, Albert

AU - Oostra, Ben

AU - Uitterlinden, André G.

AU - Willemsen, Gonneke

AU - Platteel, Mathieu

AU - Veldink, Jan H.

AU - Van Den Berg, Leonard H.

AU - Pitts, Steven J.

AU - Potluri, Shobha

AU - Sundar, Purnima

AU - Cox, David R.

AU - Sunyaev, Shamil R.

AU - Den Dunnen, Johan T.

AU - Stoneking, Mark

AU - De Knijff, Peter

AU - Kayser, Manfred

AU - Li, Qibin

AU - Li, Yingrui

AU - Du, Yuanping

AU - Chen, Ruoyan

AU - Cao, Hongzhi

AU - Li, Ning

AU - Cao, Sujie

AU - Wang, Jun

AU - Bovenberg, Jasper A.

AU - Pe'er, Itsik

AU - Slagboom, P. Eline

AU - Van Duijn, Cornelia M.

AU - Boomsma, Dorret I.

AU - Van Ommen, Gert Jan B.

AU - De Bakker, Paul I.W.

AU - Swertz, Morris A.

AU - Wijmenga, Cisca

PY - 2014/1/1

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