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

LC Francioli; A Menelaou; SL Pulit; Femke Dijk; PF Palamara; CC Elbers; PBT Neerincx; K Ye; V Guryev; WP Kloosterman; P Deelen; A Abdellaoui; Elisa Leeuwen; Mannis Oven; M Vermaat; M Li; JFJ Laros; Lennart Karssen; A Kanterakis; Najaf Amin; JJ (Jouke Jan) Hottenga; EW Lameijer; M Kattenberg; M Dijkstra; H Byelas; J Van Settenl; BDC van Schaik; J Bot; IJ Nijman; I Renkens; T Marscha; A Schonhuth; JY Hehir-Kwa; RE Handsaker; P Polak; M Sohail; D Vuzman; F Hormozdiari; D van Enckevort; Hailang Mei; Slavik Koval; MTH Moed; KJ Van der Velde; Fernando Rivadeneira; Karol Estrada Gil; C Medina-Gomez; Aaron Isaacs; SA McCarroll; M Beekrnan; AJM de Craen; HED Suchiman; Bert Hofman; Ben Oostra; André Uitterlinden; G Willemsen; M Plattee; JH Veldink; LH van den Berg; SJ Pitts; S Potluri; P Sundar; DR Cox; SR Sunyaev; JT Dunnen; M Stoneking; P de Knijff; Manfred Kayser; QB Li; YR Li; YP Du; Ruoqing Chen; H Cao; N (Nan) Li; S Cao; Johnny Wang; JA Bovenberg; I Peer; PE (Eline) Slagboom; Cornelia Duijn; DI Boomsma; GJB van Ommen; PIW de Bakker; MA Swertz; C Wijmenga

doi:10.1038/ng.3021

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

LC Francioli, A Menelaou, SL Pulit, Femke Dijk, PF Palamara, CC Elbers, PBT Neerincx, K Ye, V Guryev, WP Kloosterman, P Deelen, A Abdellaoui, Elisa Leeuwen, Mannis Oven, M Vermaat, M Li, JFJ Laros, Lennart Karssen, A Kanterakis, Najaf AminJJ (Jouke Jan) Hottenga, EW Lameijer, M Kattenberg, M Dijkstra, H Byelas, J Van Settenl, BDC van Schaik, J Bot, IJ Nijman, I Renkens, T Marscha, A Schonhuth, JY Hehir-Kwa, RE Handsaker, P Polak, M Sohail, D Vuzman, F Hormozdiari, D van Enckevort, Hailang Mei, Slavik Koval, MTH Moed, KJ Van der Velde, Fernando Rivadeneira, Karol Estrada Gil, C Medina-Gomez, Aaron Isaacs, SA McCarroll, M Beekrnan, AJM de Craen, HED Suchiman, Bert Hofman, Ben Oostra, André Uitterlinden, G Willemsen, M Plattee, JH Veldink, LH van den Berg, SJ Pitts, S Potluri, P Sundar, DR Cox, SR Sunyaev, JT Dunnen, M Stoneking, P de Knijff, Manfred Kayser, QB Li, YR Li, YP Du, Ruoqing Chen, H Cao, N (Nan) Li, S Cao, Johnny Wang, JA Bovenberg, I Peer, PE (Eline) Slagboom, Cornelia Duijn, DI Boomsma, GJB van Ommen, PIW de Bakker, MA Swertz, C Wijmenga

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

532 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 (similar to 13x) 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 language	Undefined/Unknown
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

Research programs

EMC MGC-02-26-01
EMC MGC-02-96-01
EMC MM-01-39-09-A
EMC NIHES-01-64-02

Access to Document

10.1038/ng.3021

http://hdl.handle.net/1765/58974

Cite this

Francioli, LC., Menelaou, A., Pulit, SL., Dijk, F., Palamara, PF., Elbers, CC., Neerincx, PBT., Ye, K., Guryev, V., Kloosterman, WP., Deelen, P., Abdellaoui, A., Leeuwen, E., Oven, M., Vermaat, M., Li, M., Laros, JFJ., Karssen, L., 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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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 (similar to 13x) 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.",

author = "LC Francioli and A Menelaou and SL Pulit and Femke Dijk and PF Palamara and CC Elbers and PBT Neerincx and K Ye and V Guryev and WP Kloosterman and P Deelen and A Abdellaoui and Elisa Leeuwen and Mannis Oven and M Vermaat and M Li and JFJ Laros and Lennart Karssen and A Kanterakis and Najaf Amin and Hottenga, {JJ (Jouke Jan)} and EW Lameijer and M Kattenberg and M Dijkstra and H Byelas and {Van Settenl}, J and {van Schaik}, BDC and J Bot and IJ Nijman and I Renkens and T Marscha and A Schonhuth and JY Hehir-Kwa and RE Handsaker and P Polak and M Sohail and D Vuzman and F Hormozdiari and {van Enckevort}, D and Hailang Mei and Slavik Koval and MTH Moed and {Van der Velde}, KJ and Fernando Rivadeneira and {Estrada Gil}, Karol and C Medina-Gomez and Aaron Isaacs and SA McCarroll and M Beekrnan and {de Craen}, AJM and HED Suchiman and Bert Hofman and Ben Oostra and Andr{\'e} Uitterlinden and G Willemsen and M Plattee and JH Veldink and {van den Berg}, LH and SJ Pitts and S Potluri and P Sundar and DR Cox and SR Sunyaev and JT Dunnen and M Stoneking and {de Knijff}, P and Manfred Kayser and QB Li and YR Li and YP Du and Ruoqing Chen and H Cao and Li, {N (Nan)} and S Cao and Johnny Wang and JA Bovenberg and I Peer and Slagboom, {PE (Eline)} and Cornelia Duijn and DI Boomsma and {van Ommen}, GJB and {de Bakker}, PIW and MA Swertz and C Wijmenga",

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pages = "818--825",

journal = "Nature Genetics",

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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, Leeuwen, E, Oven, M, Vermaat, M, Li, M, Laros, JFJ, Karssen, L, Kanterakis, A, Amin, N, Hottenga, JJ, Lameijer, EW, Kattenberg, M, Dijkstra, M, Byelas, H, Van Settenl, J, van Schaik, BDC, Bot, J, Nijman, IJ, Renkens, I, Marscha, T, Schonhuth, A, Hehir-Kwa, JY, Handsaker, RE, Polak, P, Sohail, M, Vuzman, D, Hormozdiari, F, van Enckevort, D, Mei, H, Koval, S, Moed, MTH, Van der Velde, KJ, Rivadeneira, F, Estrada Gil, K, Medina-Gomez, C, Isaacs, A, McCarroll, SA, Beekrnan, M, de Craen, AJM, Suchiman, HED, Hofman, B, Oostra, B, Uitterlinden, A, Willemsen, G, Plattee, M, Veldink, JH, van den Berg, LH, Pitts, SJ, Potluri, S, Sundar, P, Cox, DR, Sunyaev, SR, Dunnen, JT, Stoneking, M, de Knijff, P, Kayser, M, Li, QB, Li, YR, Du, YP, Chen, R, Cao, H, Li, N, Cao, S, Wang, J, Bovenberg, JA, Peer, I, Slagboom, PE, Duijn, C, 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

TY - JOUR

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

AU - Francioli, LC

AU - Menelaou, A

AU - Pulit, SL

AU - Dijk, Femke

AU - Palamara, PF

AU - Elbers, CC

AU - Neerincx, PBT

AU - Ye, K

AU - Guryev, V

AU - Kloosterman, WP

AU - Deelen, P

AU - Abdellaoui, A

AU - Leeuwen, Elisa

AU - Oven, Mannis

AU - Vermaat, M

AU - Li, M

AU - Laros, JFJ

AU - Karssen, Lennart

AU - Kanterakis, A

AU - Amin, Najaf

AU - Hottenga, JJ (Jouke Jan)

AU - Lameijer, EW

AU - Kattenberg, M

AU - Dijkstra, M

AU - Byelas, H

AU - Van Settenl, J

AU - van Schaik, BDC

AU - Bot, J

AU - Nijman, IJ

AU - Renkens, I

AU - Marscha, T

AU - Schonhuth, A

AU - Hehir-Kwa, JY

AU - Handsaker, RE

AU - Polak, P

AU - Sohail, M

AU - Vuzman, D

AU - Hormozdiari, F

AU - van Enckevort, D

AU - Mei, Hailang

AU - Koval, Slavik

AU - Moed, MTH

AU - Van der Velde, KJ

AU - Rivadeneira, Fernando

AU - Estrada Gil, Karol

AU - Medina-Gomez, C

AU - Isaacs, Aaron

AU - McCarroll, SA

AU - Beekrnan, M

AU - de Craen, AJM

AU - Suchiman, HED

AU - Hofman, Bert

AU - Oostra, Ben

AU - Uitterlinden, André

AU - Willemsen, G

AU - Plattee, M

AU - Veldink, JH

AU - van den Berg, LH

AU - Pitts, SJ

AU - Potluri, S

AU - Sundar, P

AU - Cox, DR

AU - Sunyaev, SR

AU - Dunnen, JT

AU - Stoneking, M

AU - de Knijff, P

AU - Kayser, Manfred

AU - Li, QB

AU - Li, YR

AU - Du, YP

AU - Chen, Ruoqing

AU - Cao, H

AU - Li, N (Nan)

AU - Cao, S

AU - Wang, Johnny

AU - Bovenberg, JA

AU - Peer, I

AU - Slagboom, PE (Eline)

AU - Duijn, Cornelia

AU - Boomsma, DI

AU - van Ommen, GJB

AU - de Bakker, PIW

AU - Swertz, MA

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 (similar to 13x) 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.

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 (similar to 13x) 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.

U2 - 10.1038/ng.3021

DO - 10.1038/ng.3021

M3 - Article

C2 - 24974849

SN - 1061-4036

VL - 46

SP - 818

EP - 825

JO - Nature Genetics

JF - Nature Genetics

IS - 8

ER -