Article

European Journal of Human Genetics (2010) 18, 1322–1326; doi:10.1038/ejhg.2010.112; published online 28 July 2010

NordicDB: a Nordic pool and portal for genome-wide control data

Monica Leu1,2, Keith Humphreys1, Ida Surakka2,3, Emil Rehnberg1, Juha Muilu2, Päivi Rosenström2, Peter Almgren4, Juha Jääskeläinen5, Richard P Lifton6, Kirsten Ohm Kyvik7, Jaakko Kaprio2,8,9, Nancy L Pedersen1, Aarno Palotie2,10,11, Per Hall1, Henrik Grönberg1, Leif Groop4, Leena Peltonen2,3,10,11, Juni Palmgren1,12 and Samuli Ripatti2,3

  1. 1Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
  2. 2Institute for Molecular Medicine, Finland, FIMM, University of Helsinki, Helsinki, Finland
  3. 3Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland
  4. 4Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Malmö, Sweden
  5. 5Department of Neurosurgery, Kuopio University Hospital, Kuopio, Finland
  6. 6Department of Genetics, Howard Hughes Medical Institute, Yale University, Chevy Chase, MD, USA
  7. 7Department of Epidemiology, Institute of Public Health, University of Southern Denmark, Odense Area, Denmark
  8. 8Mental Health Problems and Substance Abuse Services Unit, National Institute for Health and Welfare, Helsinki, Finland
  9. 9Department of Public Health, University of Helsinki, Helsinki, Finland
  10. 10The Broad Institute of Harvard and MIT, Cambridge, MA, USA
  11. 11Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
  12. 12Department of Mathematical Statistics, Stockholm University, Stockholm, Sweden

Correspondence: Dr M Leu, Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, PO Box 281, Nobels vag 12a, SE-17177, Stockholm, Sweden. Tel: +46 8 524 82 337; Fax: +46 8 31 49 75; E-mail: monica.leu@ki.se; Dr S Ripatti, FIMM, PO Box 20, FIN-00014 University of Helsinki, Helsinki, Finland. Tel: +358 20 610 8159; Fax: +358 9 47448480; E-mail: samuli.ripatti@thl.fi

Received 29 October 2009; Revised 24 March 2010; Accepted 4 June 2010; Published online 28 July 2010.

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Abstract

A cost-efficient way to increase power in a genetic association study is to pool controls from different sources. The genotyping effort can then be directed to large case series. The Nordic Control database, NordicDB, has been set up as a unique resource in the Nordic area and the data are available for authorized users through the web portal (http://www.nordicdb.org). The current version of NordicDB pools together high-density genome-wide SNP information from ~5000 controls originating from Finnish, Swedish and Danish studies and shows country-specific allele frequencies for SNP markers. The genetic homogeneity of the samples was investigated using multidimensional scaling (MDS) analysis and pairwise allele frequency differences between the studies. The plot of the first two MDS components showed excellent resemblance to the geographical placement of the samples, with a clear NW–SE gradient. We advise researchers to assess the impact of population structure when incorporating NordicDB controls in association studies. This harmonized Nordic database presents a unique genome-wide resource for future genetic association studies in the Nordic countries.

Keywords:

common controls; genome-wide data; Nordic Control Database; population stratification