Document

Genome of the Netherlands
Your name
Meeting
June 21, 2011
http://www.nlgenome.com/
http://www.bbmriwiki.nl
GoNL
Mission: Establish a map of Dutch genetic variation by whole genomesequencing 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
http://www.nlgenome.com/
http://www.bbmriwiki.nl
GoNL
Project overview
Sequence analysis
Data analysis &
Method development
Imputation
existing GWAS
•~ 50% of data aligned to
reference (hg19)
•In-depth analysis on 20
trio’s (pilot)
~100,000 Dutch samples
with GWAS data
•230 trio’s (690)
•10 quartets (40)
•10 MZ twin (40)
•Immunochip GWAS
data for QC (UMCG)
http://www.nlgenome.com/
http://www.bbmriwiki.nl
GoNL
Project overview
Sequence analysis
Data analysis &
Method development
Imputation
existing GWAS
•~ 50% of data aligned to
reference (hg19)
•In-depth analysis on 20
trio’s (pilot)
~100,000 Dutch samples
with GWAS data
•230 trio’s (690)
Further
analysis
•10
quartets
(40)
•10 MZ twin (40) Structural variation, Population Genetics,
De novo mutations, Mitochondrial DNA
This is an open national project: please contact
http://www.nlgenome.com/
debakker@broadinstitute.org
http://www.bbmriwiki.nl
m.a.swertz@rug.nl and
GoNL
BBMRI-GoNL is a national project
see 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)
http://www.nlgenome.com/
http://www.bbmriwiki.nl
GoNL