Genome of the Netherlands

The Dept of Genetics, UMCG, is the coordinator and host of the biggest genomics project in the Netherlands (500 TB data, 200,000 computing hours), together with LUMC, UMCU, EMC, VU and others. Its mission is to unravel the genetic variation found in the Dutch indigenous population. A detailed knowledge of this is not only interesting in itself, it will also help to extract biomedical information from Dutch biobanking analyses. The Dutch biobank collaboration, BBMRI-NL, has initiated the extensive Rainbow Project called “Genome of the Netherlands” (GoNL) because it offers unique opportunities for science and for the development of new medical treatments and diagnostic techniques. A close-up look at the DNA of 750 Dutch people (250 trio’s of two parents and an adult child) plus a global genetic profile of large numbers of Dutch individuals is disclosing a wealth of new information, new insights, and possible applications.

The Genome of the Netherlands is a consortium funded as part of the Netherlands Biobanking and Biomolecular Research Infrastructure (BBMRI-NL). The work is being led by Prof Cisca Wijmenga. All the sequencing work is being done by BGI Hong Kong. The project started at the end of 2010, and preliminary results have been published.

Selected publications

• A high-quality human reference panel reveals the complexity and distribution of genomic structural variants Hehir-Kwa JY et al. Nat Commun. 2016
• Genome-wide patterns and properties of de novo mutations in humans Francioli LC et al. Nat Genet. 2015
• Population-specific genotype imputations using minimac or IMPUTE2 van Leeuwen EM et al. Nat Protoc. 2015
• van Leeuwen EM et al. Genome of The Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels. Nat Commun. 2015;6:6065. doi: 10.1038/ncomms7065.
• Genome of the Netherlands Consortium. Whole-genome sequence variation, population structure and demographic history of the Dutch population. Nat Genet. 2014;46(8):818-25. doi: 10.1038/ng.3021.
• Deelen P et al. Improved imputation quality of low-frequency and rare variants in European samples using the ‘Genome of The Netherlands’. Eur J Hum Genet. 2014;22(11):1321-6.
• Boomsma, D I, Wijmenga, C, Slagboom, EP, Swertz, MA, Karssen, LC, Abdellaoui, A, et al. (2014). The Genome of the Netherlands: design, and project goals. Eur J Hum Genet. (position paper)
• Van Setten J et al. From GWAS to WGS: a whole-genome association study in 250 trios of the Genome of the Netherlands Project. Eur J Human Genetics 2013;21(Suppl2): 389.
• Deelen P. The ‘Genome of The Netherlands’ outperforms ’1000 genomes’ as a reference set for imputing rare variants in the European population. Eur J Human Genetics 2013;21(Suppl2): 48.
• Kanterakis A, Ricaño-Ponce I, Gutierrez J, Westra H, Franke L, Wijmenga C, and Swertz MA. Identifying additional variants associated to celiac disease by imputation-based GWAS. Eur J Human Genetics 2013;21(Suppl2): 371.
• Kiezun A et al. Deleterious alleles in the human genome are on average younger than neutral alleles of the same frequency. PLoS Genet. 2013;9(2):e1003301.
• Ganesh SK. Loci influencing blood pressure identified using a cardiovascular gene-centric array. Hum Mol Genet. 2013;22(8):1663-78.
  
• Neerincx PBT, van Dijk F, Rengaw T, Francioli LC, de Bakker PIW, Wijmenga C, and Swertz MA. GenomeNL variant database; towards a deep genetic encyclopedia of Dutch variation. Eur J Human Genetics 20(Suppl): 287. IF: 4.319.
• Asselbergs FW et al. Large-scale gene-centric meta-analysis across 32 studies identifies multiple lipid loci. Am J Hum Genet. 2012;91(5):823-38.
  
• Dolmans GH, Werker PM, de Jong IJ, Nijman RJ; LifeLines Cohort Study, Wijmenga C, Ophoff RA. WNT2 locus is involved in genetic susceptibility of Peyronie’s disease. J Sex Med. 2012;9(5):1430-4.
  
• Dolmans GH, … LifeLines Cohort Study; BSSH-GODD Consortium. Wnt signaling and Dupuytren’s disease. N Engl J Med. 2011;365(4):307-17.
• Brandsma M, van Ommen GJ, Wijmenga C, Kiemeney LA. [Dutch government invests in existing biobanks]. Ned Tijdschr Geneeskd. 2010;154:A2825; in Dutch. Abstract in English

More papers from Genome of the Netherlands consortium