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

L.C. Francioli; A. Menelaou; S.L. Pulit; F. Dijk; P.F. Palamara; C.C. Elbers; P.B.T. Neerincx; K. Ye; V. Guryev; W.P. Kloosterman; P. Deelen; A. Abdellaoui; E. van Leeuwen; M. van Oven; M. Vermaat; M. Li; J.F.J. Laros; L.C. Karssen; A. Kanterakis; N. Amin; E.W. Lameijer; V.M. Kattenberg; M. Dijkstra; H. Byelas; J. van Setten; B.D.C. van Schaik; J. Bot; I.J. Nijman; I. Renkens; T. Marschall; A. Schönhuth; J.Y. Hehir-Kwa; R.E. Handsaker; P. Polak; M. Sohail; D. Vuzman; F. Hormozdiari; D. van Enckevort; H. Mei; V. Koval; M.H. Moed; K.J. van der Velde; F. Rivadeneira; K. Estrada; C. Medina-Gomez; A. Isaacs; S.A. McCarroll; M. Beekman; A.J. de Craen; H.E.D. Suchiman; A. Hofman; B.A. Oostra; A.G. Uitterlinden; G. Willemsen; M. Platteel; J.H. Veldink; L.H. Van den Berg; S.J. Pitts; S. Potluri; P. Sundar; D.R. Cox; S.R. Sunyaev; J.T. den Dunnen; M. Stoneking; P. de Knijff; M. Kayser; Q. Li; Y. Li; Y. Du; R. Chen; H. Cao; N. Li; S. Cao; J. Wang; J.A. Bovenberg; I. Pe'er; P.E. Slagboom; C.M. van Duijn; D.I. Boomsma; G.J.B van Ommen; P.I.W. Bakker; M. Swertz; C. Wijmenga

doi:10.1038/ng.3021

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

L.C. Francioli, A. Menelaou, S.L. Pulit, F. Dijk, P.F. Palamara, C.C. Elbers, P.B.T. Neerincx, K. Ye, V. Guryev, W.P. Kloosterman, P. Deelen, A. Abdellaoui, E. van Leeuwen, M. van Oven, M. Vermaat, M. Li, J.F.J. Laros, L.C. Karssen, A. Kanterakis, N. AminE.W. Lameijer, V.M. Kattenberg, M. Dijkstra, H. Byelas, J. van Setten, B.D.C. van Schaik, J. Bot, I.J. Nijman, I. Renkens, T. Marschall, A. Schönhuth, J.Y. Hehir-Kwa, R.E. Handsaker, P. Polak, M. Sohail, D. Vuzman, F. Hormozdiari, D. van Enckevort, H. Mei, V. Koval, M.H. Moed, K.J. van der Velde, F. Rivadeneira, K. Estrada, C. Medina-Gomez, A. Isaacs, S.A. McCarroll, M. Beekman, A.J. de Craen, H.E.D. Suchiman, A. Hofman, B.A. Oostra, A.G. Uitterlinden, G. Willemsen, M. Platteel, J.H. Veldink, L.H. Van den Berg, S.J. Pitts, S. Potluri, P. Sundar, D.R. Cox, S.R. Sunyaev, J.T. den Dunnen, M. Stoneking, P. de Knijff, M. Kayser, Q. Li, Y. Li, Y. Du, R. Chen, H. Cao, N. Li, S. Cao, J. Wang, J.A. Bovenberg, I. Pe'er, P.E. Slagboom, C.M. van Duijn, D.I. Boomsma, G.J.B van Ommen, P.I.W. Bakker, M. Swertz, C. Wijmenga

Biological Psychology

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

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. © 2014 Nature America, Inc.

Original language	English
Pages (from-to)	818-825
Number of pages	8
Journal	Nature Genetics
Volume	46
Issue number	8
DOIs	https://doi.org/10.1038/ng.3021
Publication status	Published - 2014

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Francioli, L. C., Menelaou, A., Pulit, S. L., Dijk, F., Palamara, P. F., Elbers, C. C., Neerincx, P. B. T., Ye, K., Guryev, V., Kloosterman, W. P., Deelen, P., Abdellaoui, A., van Leeuwen, E., van Oven, M., Vermaat, M., Li, M., Laros, J. F. J., Karssen, L. C., Kanterakis, A., ... 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

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

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. {\textcopyright} 2014 Nature America, Inc.",

author = "L.C. Francioli and A. Menelaou and S.L. Pulit and F. Dijk and P.F. Palamara and C.C. Elbers and P.B.T. Neerincx and K. Ye and V. Guryev and W.P. Kloosterman and P. Deelen and A. Abdellaoui and {van Leeuwen}, E. and {van Oven}, M. and M. Vermaat and M. Li and J.F.J. Laros and L.C. Karssen and A. Kanterakis and N. Amin and E.W. Lameijer and V.M. Kattenberg and M. Dijkstra and H. Byelas and {van Setten}, J. and {van Schaik}, B.D.C. and J. Bot and I.J. Nijman and I. Renkens and T. Marschall and A. Sch{\"o}nhuth and J.Y. Hehir-Kwa and R.E. Handsaker and P. Polak and M. Sohail and D. Vuzman and F. Hormozdiari and {van Enckevort}, D. and H. Mei and V. Koval and M.H. Moed and {van der Velde}, K.J. and F. Rivadeneira and K. Estrada and C. Medina-Gomez and A. Isaacs and S.A. McCarroll and M. Beekman and {de Craen}, A.J. and H.E.D. Suchiman and A. Hofman and B.A. Oostra and A.G. Uitterlinden and G. Willemsen and M. Platteel and J.H. Veldink and {Van den Berg}, L.H. and S.J. Pitts and S. Potluri and P. Sundar and D.R. Cox and S.R. Sunyaev and {den Dunnen}, J.T. and M. Stoneking and {de Knijff}, P. and M. Kayser and Q. Li and Y. Li and Y. Du and R. Chen and H. Cao and N. Li and S. Cao and J. Wang and J.A. Bovenberg and I. Pe'er and P.E. Slagboom and {van Duijn}, C.M. and D.I. Boomsma and {van Ommen}, G.J.B and P.I.W. Bakker and M. Swertz and C. Wijmenga",

year = "2014",

doi = "10.1038/ng.3021",

language = "English",

volume = "46",

pages = "818--825",

journal = "Nature Genetics",

issn = "1061-4036",

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number = "8",

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Francioli, LC, Menelaou, A, Pulit, SL, Dijk, F, Palamara, PF, Elbers, CC, Neerincx, PBT, Ye, K, Guryev, V, Kloosterman, WP, Deelen, P, Abdellaoui, A, van Leeuwen, E, van Oven, M, Vermaat, M, Li, M, Laros, JFJ, Karssen, LC, Kanterakis, A, Amin, N, Lameijer, EW, Kattenberg, VM, 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, de Craen, AJ, Suchiman, HED, Hofman, A, Oostra, BA, 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, Bakker, PIW, Swertz, M & 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

TY - JOUR

T1 - Whole-genome sequence variation population structure and demographic history of the Dutch population

AU - Francioli, L.C.

AU - Menelaou, A.

AU - Pulit, S.L.

AU - Dijk, F.

AU - Palamara, P.F.

AU - Elbers, C.C.

AU - Neerincx, P.B.T.

AU - Ye, K.

AU - Guryev, V.

AU - Kloosterman, W.P.

AU - Deelen, P.

AU - Abdellaoui, A.

AU - van Leeuwen, E.

AU - van Oven, M.

AU - Vermaat, M.

AU - Li, M.

AU - Laros, J.F.J.

AU - Karssen, L.C.

AU - Kanterakis, A.

AU - Amin, N.

AU - Lameijer, E.W.

AU - Kattenberg, V.M.

AU - Dijkstra, M.

AU - Byelas, H.

AU - van Setten, J.

AU - van Schaik, B.D.C.

AU - Bot, J.

AU - Nijman, I.J.

AU - Renkens, I.

AU - Marschall, T.

AU - Schönhuth, A.

AU - Hehir-Kwa, J.Y.

AU - Handsaker, R.E.

AU - Polak, P.

AU - Sohail, M.

AU - Vuzman, D.

AU - Hormozdiari, F.

AU - van Enckevort, D.

AU - Mei, H.

AU - Koval, V.

AU - Moed, M.H.

AU - van der Velde, K.J.

AU - Rivadeneira, F.

AU - Estrada, K.

AU - Medina-Gomez, C.

AU - Isaacs, A.

AU - McCarroll, S.A.

AU - Beekman, M.

AU - de Craen, A.J.

AU - Suchiman, H.E.D.

AU - Hofman, A.

AU - Oostra, B.A.

AU - Uitterlinden, A.G.

AU - Willemsen, G.

AU - Platteel, M.

AU - Veldink, J.H.

AU - Van den Berg, L.H.

AU - Pitts, S.J.

AU - Potluri, S.

AU - Sundar, P.

AU - Cox, D.R.

AU - Sunyaev, S.R.

AU - den Dunnen, J.T.

AU - Stoneking, M.

AU - de Knijff, P.

AU - Kayser, M.

AU - Li, Q.

AU - Li, Y.

AU - Du, Y.

AU - Chen, R.

AU - Cao, H.

AU - Li, N.

AU - Cao, S.

AU - Wang, J.

AU - Bovenberg, J.A.

AU - Pe'er, I.

AU - Slagboom, P.E.

AU - van Duijn, C.M.

AU - Boomsma, D.I.

AU - van Ommen, G.J.B

AU - Bakker, P.I.W.

AU - Swertz, M.

AU - Wijmenga, C.

PY - 2014

Y1 - 2014

N2 - 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. © 2014 Nature America, Inc.

AB - 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. © 2014 Nature America, Inc.

U2 - 10.1038/ng.3021

DO - 10.1038/ng.3021

M3 - Article

SN - 1061-4036

VL - 46

SP - 818

EP - 825

JO - Nature Genetics

JF - Nature Genetics

IS - 8

ER -

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

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