Journal
NATURE GENETICS
Volume 46, Issue 8, Pages 818-825Publisher
NATURE PORTFOLIO
DOI: 10.1038/ng.3021
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Funding
- BBMRI-NL - Netherlands Organization for Scientific Research (NWO) [184.021.007]
- eBioGrid
- CTMM/TraIT
- Ubbo Emmius Fund
- Netherlands Bioinformatics Center (NBIC)
- BU-BioSHARE
- Samenwerkingsverband Noord Nederland
- European Fund for Regional Development
- Dutch Ministry of Economic Affairs, Pieken in de Delta
- provinces-of Groningen and Drenthe
- Netherlands Organization for Scientific Research (NWO)
- Center for Medical Systems Biology-2
- European Research Council [ERC 230374]
- VIDI awards (NWO) [016.138.318, 016.126.354]
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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.
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