Genome of the Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels

Elisabeth M. van Leeuwen, Lennart C. Karssen, Joris Deelen, Aaron Isaacs, Carolina Medina-Gomez, Hamdi Mbarek, Alexandros Kanterakis, Stella Trompet, Iris Postmus, Niek Verweij, David J. van Enckevort, Jennifer E. Huffman, Charles C. White, Mary F. Feitosa, Traci M. Bartz, Ani Manichaikul, Peter K. Joshi, Gina M. Peloso, Patrick Deelen, Freerk van Dijk, Gonneke Willemsen, Eco J. de Geus, Yuri Milaneschi, Brenda W.J.H. Penninx, Laurent C. Francioli, Androniki Menelaou, Sara L. Pulit, Fernando Rivadeneira, Albert Hofman, Ben A. Oostra, Oscar H. Franco, Irene Mateo Leach, Marian Beekman, Anton J.M. de Craen, Hae-Won Uh, Holly Trochet, Lynne J. Hocking, David J. Porteous, Naveed Sattar, Chris J. Packard, Brendan M. Buckley, Jennifer A. Brody, Joshua C. Bis, Jerome I. Rotter, Josyf C. Mychaleckyj, Harry Campbell, Qing Duan, Leslie A. Lange, James F. Wilson, Caroline Hayward, Ozren Polasek, Veronique Vitart, Igor Rudan, Alan F. Wright, Stephen S. Rich, Bruce M. Psaty, Ingrid B. Borecki, Patricia M. Kearney, David J. Stott, L. Adrienne Cupples, J. Wouter Jukema, Pim van der Harst, Eric J. Sijbrands, Jouke-Jan Hottenga, Andre G. Uitterlinden, Morris A. Swertz, Gert-Jan B. van Ommen, Paul I.W. de Bakker, P. Eline Slagboom, Dorret I. Boomsma, Cisca Wijmenga and Cornelia M. van Duijn ()
Additional contact information
Elisabeth M. van Leeuwen: Erasmus Medical Center
Lennart C. Karssen: Erasmus Medical Center
Joris Deelen: Leiden University Medical Center
Aaron Isaacs: Erasmus Medical Center
Carolina Medina-Gomez: Erasmus Medical Center
Hamdi Mbarek: VU University Amsterdam and EMGO+ Institute for Health and Care Research
Alexandros Kanterakis: Genomics Coordination Center, University of Groningen, University Medical Center Groningen
Stella Trompet: Leiden University Medical Center
Iris Postmus: Leiden University Medical Center
Niek Verweij: University Medical Center Groningen, University of Groningen
David J. van Enckevort: BioAssist, Netherlands Bioinformatics Center
Jennifer E. Huffman: MRC Human Genetics Unit, MRC IGMM, University of Edinburgh
Charles C. White: Boston U School of Public Health
Mary F. Feitosa: Washington University School of Medicine
Traci M. Bartz: University of Washington
Ani Manichaikul: Center for Public Health Genomics, University of Virginia
Peter K. Joshi: Centre for Population Health Sciences, University of Edinburgh
Gina M. Peloso: Center for Human Genetic Research, Massachusetts General Hospital
Patrick Deelen: Genomics Coordination Center, University of Groningen, University Medical Center Groningen
Freerk van Dijk: Genomics Coordination Center, University of Groningen, University Medical Center Groningen
Gonneke Willemsen: VU University Amsterdam and EMGO+ Institute for Health and Care Research
Eco J. de Geus: VU University Amsterdam and EMGO+ Institute for Health and Care Research
Yuri Milaneschi: VU University Medical Center Amsterdam/GGZinGeest, EMGO+ Institute for Health and Care Research, Neuroscience Campus Amsterdam
Brenda W.J.H. Penninx: VU University Medical Center Amsterdam/GGZinGeest, EMGO+ Institute for Health and Care Research, Neuroscience Campus Amsterdam
Laurent C. Francioli: Center for Molecular Medicine, University Medical Center Utrecht
Androniki Menelaou: Center for Molecular Medicine, University Medical Center Utrecht
Sara L. Pulit: Center for Molecular Medicine, University Medical Center Utrecht
Fernando Rivadeneira: Erasmus Medical Center
Albert Hofman: Erasmus Medical Center
Ben A. Oostra: Erasmus Medical Center
Oscar H. Franco: Erasmus Medical Center
Irene Mateo Leach: University Medical Center Groningen, University of Groningen
Marian Beekman: Leiden University Medical Center
Anton J.M. de Craen: Leiden University Medical Center
Hae-Won Uh: Leiden University Medical Center
Holly Trochet: MRC Human Genetics Unit, MRC IGMM, University of Edinburgh
Lynne J. Hocking: University of Aberdeen
David J. Porteous: Centre for Genomic and Experimental Medicine, MRC IGMM, University of Edinburgh
Naveed Sattar: BHF Glasgow Cardiovascular Research Centre, Faculty of Medicine, University of Glasgow
Chris J. Packard: Institute of Cardiovascular and Medical Sciences, University of Glasgow
Brendan M. Buckley: University College Cork
Jennifer A. Brody: University of Washington
Joshua C. Bis: University of Washington
Jerome I. Rotter: Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center
Josyf C. Mychaleckyj: Center for Public Health Genomics, University of Virginia
Harry Campbell: Centre for Population Health Sciences, University of Edinburgh
Qing Duan: University of North Carolina
Leslie A. Lange: University of North Carolina
James F. Wilson: Centre for Population Health Sciences, University of Edinburgh
Caroline Hayward: MRC Human Genetics Unit, MRC IGMM, University of Edinburgh
Ozren Polasek: Faculty of Medicine, University of Split
Veronique Vitart: MRC Human Genetics Unit, MRC IGMM, University of Edinburgh
Igor Rudan: Centre for Population Health Sciences, University of Edinburgh
Alan F. Wright: MRC Human Genetics Unit, MRC IGMM, University of Edinburgh
Stephen S. Rich: Center for Public Health Genomics, University of Virginia
Bruce M. Psaty: University of Washington
Ingrid B. Borecki: Washington University School of Medicine
Patricia M. Kearney: University College Cork
David J. Stott: Institute of Cardiovascular and Medical Sciences, University of Glasgow
L. Adrienne Cupples: Boston U School of Public Health
J. Wouter Jukema: Leiden University Medical Center
Pim van der Harst: University Medical Center Groningen, University of Groningen
Eric J. Sijbrands: Erasmus Medical Center
Jouke-Jan Hottenga: VU University Amsterdam and EMGO+ Institute for Health and Care Research
Andre G. Uitterlinden: Erasmus Medical Center
Morris A. Swertz: Genomics Coordination Center, University of Groningen, University Medical Center Groningen
Gert-Jan B. van Ommen: Leiden University Medical Center
Paul I.W. de Bakker: Center for Molecular Medicine, University Medical Center Utrecht
P. Eline Slagboom: Leiden University Medical Center
Dorret I. Boomsma: VU University Amsterdam
Cisca Wijmenga: University of Groningen, University Medical Center Groningen
Cornelia M. van Duijn: Erasmus Medical Center

Nature Communications, 2015, vol. 6, issue 1, 1-6

Abstract: Abstract Variants associated with blood lipid levels may be population-specific. To identify low-frequency variants associated with this phenotype, population-specific reference panels may be used. Here we impute nine large Dutch biobanks (~35,000 samples) with the population-specific reference panel created by the Genome of the Netherlands Project and perform association testing with blood lipid levels. We report the discovery of five novel associations at four loci (P value

Date: 2015
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DOI: 10.1038/ncomms7065

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