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Genome of the Netherlands Project Overview - Mapping Dutch Genetic Variation

The Genome of the Netherlands Project aims to establish a comprehensive map of Dutch genetic diversity through whole-genome sequencing of 1000 independent Dutch genomes. The project utilizes a unique family-based design with trio setups for accurate haplotype determination and aims to explore structural variation, de novo mutations, and more. This national project welcomes collaboration and analysis ideas from interested parties.

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Genome of the Netherlands Project Overview - Mapping Dutch Genetic Variation

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  1. Genome of the Netherlands Your name Meeting June 21, 2011

  2. Mission: Establish a map of Dutch genetic variation by whole genome-sequencing of 1000 independent Dutch genomes • Unique family-based design: 250 trios • 230 x 2 parents – 1 offspring • 10 x 2 parents – 2 offspring • 10 x 2 parents – 1 MZ twin offspring • Specifications: • Families equally distributed over the Dutch provinces • Genomic DNA, paired-end sequencing on HiSeq2000, 12x coverage • Trios allow phase information; accurate haplotypes • Other results: Structural variation, detection de novo variants

  3. Project overview • Sequence analysis • 230 trio’s (690) • 10 quartets (40) • 10 MZ twin (40) • Immunochip GWAS data for QC (UMCG) • Data analysis & • Method development • ~ 50% of data aligned to reference (hg19) • In-depth analysis on 20 trio’s (pilot) Imputation existing GWAS ~100,000 Dutch samples with GWAS data

  4. Project overview • Sequence analysis • 230 trio’s (690) • 10 quartets (40) • 10 MZ twin (40) • Data analysis & • Method development • ~ 50% of data aligned to reference (hg19) • In-depth analysis on 20 trio’s (pilot) Imputation existing GWAS ~100,000 Dutch samples with GWAS data Further analysis Structural variation, Population Genetics, De novo mutations, Mitochondrial DNA This is an open national project: please contact debakker@broadinstitute.orgm.a.swertz@rug.nl and cisca.wijmenga@gmail.com for analysis ideas.

  5. BBMRI-GoNL is a national projectsee http://www.bbmriwiki.nl & www.nlgenome.com • Analysis team (creating protocols and pipelines) • Laurent Francioli (UU), Kai Ye (LUMC), Jeroen Laros (LUMC), Lennart Karssen (EMC), Martijn Dijkstra (UMCG), JoukeJan Hottenga (VU), Mathijs Kattenberg (VU), David van Encvort (NBIC), Leon Mei (NBIC), Elise van Leeuwen (EMC), … and many, many others • Production team (data production) • Freerk van Dijk (UMCG), Barbera van Schaik (AMC), Ies Nijman (Hubrecht), Jan Bot (LUMC), Slavik Koval (EMC) • Steering group (coordination) • Cisca Wijmenga (PI GoNL), Morris Swertz (PI analysis), Gertjan van Ommen (LUMC), Eline Slagboom (LUMC), Jasper Bovenberg (ELSI issues), Cornelia van Duijn (EMC), Dorret Boomsma (VU), Paul de Bakker (co-PI analysis, UU)

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