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

Author

Listed:
  • 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
    Framingham Heart Study)

  • 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
    Julius Center for Health Sciences and Primary Care, 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)

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

Suggested Citation

  • 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, 2015. "Genome of the Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels," Nature Communications, Nature, vol. 6(1), pages 1-6, May.
    • Handle: RePEc:nat:natcom:v:6:y:2015:i:1:d:10.1038_ncomms7065
    DOI: 10.1038/ncomms7065
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