The Genome of the Netherlands: design, and project goals

被引：192

作者：

Boomsma, Dorret I. ^{[1
]}

Wijmenga, Cisca ^{[2
]}

Slagboom, Eline P. ^{[3
]}

Swertz, Morris A. ^{[2
]}

Karssen, Lennart C. ^{[4
]}

Abdellaoui, Abdel ^{[1
]}

Ye, Kai ^{[3
]}

Guryev, Victor ^{[5
,6
]}

Vermaat, Martijn ^{[7
,8
,9
]}

van Dijk, Freerk ^{[2
]}

Francioli, Laurent C. ^{[10
]}

Hottenga, Jouke Jan ^{[1
]}

Laros, Jeroen F. J. ^{[7
,8
,9
]}

Li, Qibin ^{[11
]}

Li, Yingrui ^{[11
]}

Cao, Hongzhi ^{[11
]}

Chen, Ruoyan ^{[11
]}

Du, Yuanping ^{[11
]}

Li, Ning ^{[12
]}

Cao, Sujie ^{[12
]}

van Setten, Jessica ^{[10
]}

Menelaou, Androniki ^{[10
]}

Pulit, Sara L. ^{[10
]}

Hehir-Kwa, Jayne Y. ^{[15
]}

Beekman, Marian ^{[16
]}

Elbers, Clara C. ^{[10
]}

Byelas, Heorhiy ^{[2
]}

de Craen, Anton J. M. ^{[16
]}

Deelen, Patrick ^{[2
]}

Dijkstra, Martijn ^{[2
]}

den Dunnen, Johan T. ^{[8
,9
]}

de Knijff, Peter ^{[8
,9
]}

Houwing-Duistermaat, Jeanine ^{[17
]}

Koval, Vyacheslav ^{[18
]}

Estrada, Karol ^{[18
]}

Hofman, Albert ^{[4
]}

Kanterakis, Alexandros ^{[2
]}

van Enckevort, David ^{[7
]}

Mai, Hailiang ^{[7
]}

Kattenberg, Mathijs ^{[1
]}

van Leeuwen, Elisabeth M. ^{[4
]}

Neerincx, Pieter B. T. ^{[2
]}

Oostra, Ben ^{[19
]}

Rivadeneira, Fernanodo ^{[18
]}

Suchiman, Eka H. D. ^{[3
]}

Uitterlinden, Andre G. ^{[18
]}

Willemsen, Gonneke ^{[1
]}

Wolffenbuttel, Bruce H. ^{[20
,21
]}

Wang, Jun ^{[11
,13
,14
]}

de Bakker, Paul I. W. ^{[10
]}

机构：

[1] Vrije Univ Amsterdam, Dept Biol Psychol, Netherlands Twin Register, NL-1081 BT Amsterdam, Netherlands

[2] Univ Groningen, Univ Med Ctr Groningen, Dept Genet, Groningen, Netherlands

[3] Leiden Univ, Med Ctr, Mol Epidemiol Sect, Netherlands Consortium Hlth Ageing, Leiden, Netherlands

[4] Erasmus MC, Dept Epidemiol, Rotterdam, Netherlands

[5] Univ Groningen, Univ Med Ctr Groningen, European Res Inst Biol Ageing, Groningen, Netherlands

[6] Univ Med Ctr Utrecht, Royal Netherlands Acad Arts & Sci, Hubrecht Inst, Utrecht, Netherlands

[7] Netherlands Bioinformat Ctr, Nijmegen, Netherlands

[8] Leiden Univ, Dept Human Genet, Ctr Human & Clin Genet, Med Ctr, NL-2300 RA Leiden, Netherlands

[9] Leiden Univ, Leiden Genome Technol Ctr, Med Ctr, Leiden, Netherlands

[10] Univ Med Ctr Utrecht, Dept Med Genet, Utrecht, Netherlands

[11] BGI Shenzhen, Shenzhen, Peoples R China

[12] BGI Europe, Copenhagen, Denmark

[13] Univ Copenhagen, Dept Biol, Copenhagen, Denmark

[14] Univ Copenhagen, Novo Nordisk Fdn Ctr Basic Metab Res, Copenhagen, Denmark

[15] Radboud Univ Nijmegen Med Ctr, Dept Human Genet, Nijmegen, Netherlands

[16] Leiden Univ, Dept Gerontol & Geriatr, Med Ctr, Leiden, Netherlands

[17] Leiden Univ, Dept Med Stat & Bioinformat, Med Ctr, Leiden, Netherlands

[18] Erasmus MC, Genet Lab Internal Med, Rotterdam, Netherlands

[19] Erasmus Univ, Sch Med, Dept Clin Genet, Rotterdam, Netherlands

[20] Univ Groningen, Univ Med Ctr Groningen, LifeLines Cohort Study, Groningen, Netherlands

[21] Univ Groningen, Univ Med Ctr Groningen, Dept Endocrinol, Groningen, Netherlands

[22] Leiden Univ, Dept Human Genet, Med Ctr, NL-2300 RA Leiden, Netherlands

来源：

EUROPEAN JOURNAL OF HUMAN GENETICS | 2014年 / 22卷 / 02期

关键词：

whole-genome sequence; trio-design; population genetics; SUSCEPTIBILITY VARIANTS; WIDE ASSOCIATION; COMMON SNPS; HERITABILITY; DISEASE; TWIN; MUTATIONS; FAMILY; RISK;

D O I：

10.1038/ejhg.2013.118

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Within the Netherlands a national network of biobanks has been established (Biobanking and Biomolecular Research Infrastructure-Netherlands (BBMRI-NL)) as a national node of the European BBMRI. One of the aims of BBMRI-NL is to enrich biobanks with different types of molecular and phenotype data. Here, we describe the Genome of the Netherlands (GoNL), one of the projects within BBMRI-NL. GoNL is a whole-genome-sequencing project in a representative sample consisting of 250 trio-families from all provinces in the Netherlands, which aims to characterize DNA sequence variation in the Dutch population. The parent-offspring trios include adult individuals ranging in age from 19 to 87 years (mean = 53 years; SD = 16 years) from birth cohorts 1910-1994. Sequencing was done on blood-derived DNA from uncultured cells and accomplished coverage was 14-15x. The family-based design represents a unique resource to assess the frequency of regional variants, accurately reconstruct haplotypes by family-based phasing, characterize short indels and complex structural variants, and establish the rate of de novo mutational events. GoNL will also serve as a reference panel for imputation in the available genome-wide association studies in Dutch and other cohorts to refine association signals and uncover population-specific variants. GoNL will create a catalog of human genetic variation in this sample that is uniquely characterized with respect to micro-geographic location and a wide range of phenotypes. The resource will be made available to the research and medical community to guide the interpretation of sequencing projects. The present paper summarizes the global characteristics of the project.

引用

页码：221 / 227

页数：7

共 29 条

[21] The Young Netherlands Twin Register (YNTR): Longitudinal Twin and Family Studies in Over 70,000 Children [J].

van Beijsterveldt, Catharina E. M. ;

Groen-Blokhuis, Maria ;

Hottenga, Jouke Jan ;

Franic, Sanja ;

Hudziak, James J. ;

Lamb, Diane ;

Huppertz, Charlotte ;

de Zeeuw, Eveline ;

Nivard, Michel ;

Schutte, Nienke ;

Swagerman, Suzanne ;

Glasner, Tina ;

van Fulpen, Michelle ;

Brouwer, Cyrina ;

Stroet, Therese ;

Nowotny, Dustin ;

Ehli, Erik A. ;

Davies, Gareth E. ;

Scheet, Paul ;

Orlebeke, Jacob F. ;

Kan, Kees-Jan ;

Smit, Dirk ;

Dolan, Conor V. ;

Middeldorp, Christel M. ;

de Geus, Eco J. C. ;

Bartels, Meike ;

Boomsma, Dorret I. .

TWIN RESEARCH AND HUMAN GENETICS, 2013, 16 (01) :252-267

[22]

Vermaat M, 2012, EUR J HUM GENET, V20, P276

[23] Five Years of GWAS Discovery [J].

Visscher, Peter M. ;

Brown, Matthew A. ;

McCarthy, Mark I. ;

Yang, Jian .

AMERICAN JOURNAL OF HUMAN GENETICS, 2012, 90 (01) :7-24

[24] The Adult Netherlands Twin Register: Twenty-Five Years of Survey and Biological Data Collection [J].

Willemsen, Gonneke ;

Vink, Jacqueline M. ;

Abdellaoui, Abdel ;

den Braber, Anouk ;

van Beek, Jenny H. D. A. ;

Draisma, Harmen H. M. ;

van Dongen, Jenny ;

van't Ent, Dennis ;

Geels, Lot M. ;

van Lien, Rene ;

Ligthart, Lannie ;

Kattenberg, Mathijs ;

Mbarek, Hamdi ;

de Moor, Marleen H. M. ;

Neijts, Melanie ;

Pool, Rene ;

Stroo, Natascha ;

Kluft, Cornelis ;

Suchiman, H. Eka D. ;

Slagboom, P. Eline ;

de Geus, Eco J. C. ;

Boomsma, Dorret I. .

TWIN RESEARCH AND HUMAN GENETICS, 2013, 16 (01) :271-281

[25] The Netherlands Twin Register Biobank: A Resource for Genetic Epidemiological Studies [J].

Willemsen, Gonneke ;

de Geus, Eco J. C. ;

Bartels, Meike ;

van Beijsterveldt, C. E. M. Toos ;

Brooks, Andy I. ;

Estourgie-van Burk, G. Frederique ;

Fugman, Douglas A. ;

Hoekstra, Chantal ;

Hottenga, Jouke-Jan ;

Kluft, Kees ;

Meijer, Piet ;

Montgomery, Grant W. ;

Rizzu, Patrizia ;

Sondervan, David ;

Smit, August B. ;

Spijker, Sabine ;

Suchiman, H. Eka D. ;

Tischfield, Jay A. ;

Lehner, Thomas ;

Slagboom, P. Eline ;

Boomsma, Dorret I. .

TWIN RESEARCH AND HUMAN GENETICS, 2010, 13 (03) :231-245

[26] Genome partitioning of genetic variation for complex traits using common SNPs [J].

Yang, Jian ;

Manolio, Teri A. ;

Pasquale, Louis R. ;

Boerwinkle, Eric ;

Caporaso, Neil ;

Cunningham, Julie M. ;

de Andrade, Mariza ;

Feenstra, Bjarke ;

Feingold, Eleanor ;

Hayes, M. Geoffrey ;

Hill, William G. ;

Landi, Maria Teresa ;

Alonso, Alvaro ;

Lettre, Guillaume ;

Lin, Peng ;

Ling, Hua ;

Lowe, William ;

Mathias, Rasika A. ;

Melbye, Mads ;

Pugh, Elizabeth ;

Cornelis, Marilyn C. ;

Weir, Bruce S. ;

Goddard, Michael E. ;

Visscher, Peter M. .

NATURE GENETICS, 2011, 43 (06) :519-U44

[27] Common SNPs explain a large proportion of the heritability for human height [J].

Yang, Jian ;

Benyamin, Beben ;

McEvoy, Brian P. ;

Gordon, Scott ;

Henders, Anjali K. ;

Nyholt, Dale R. ;

Madden, Pamela A. ;

Heath, Andrew C. ;

Martin, Nicholas G. ;

Montgomery, Grant W. ;

Goddard, Michael E. ;

Visscher, Peter M. .

NATURE GENETICS, 2010, 42 (07) :565-U131

[28] Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads [J].

Ye, Kai ;

Schulz, Marcel H. ;

Long, Quan ;

Apweiler, Rolf ;

Ning, Zemin .

BIOINFORMATICS, 2009, 25 (21) :2865-2871

[29] Founder mutations among the Dutch [J].

Zeegers, MPA ;

van Poppel, F ;

Vlietinck, R ;

Spruijt, L ;

Ostrer, H .

EUROPEAN JOURNAL OF HUMAN GENETICS, 2004, 12 (07) :591-600

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