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A whole-genome sequenced control population in northern Sweden reveals subregional genetic differences

Author

Listed:
  • Daniel Svensson
  • Matilda Rentoft
  • Anna M Dahlin
  • Emma Lundholm
  • Pall I Olason
  • Andreas Sjödin
  • Carin Nylander
  • Beatrice S Melin
  • Johan Trygg
  • Erik Johansson

Abstract

The number of national reference populations that are whole-genome sequenced are rapidly increasing. Partly driving this development is the fact that genetic disease studies benefit from knowing the genetic variation typical for the geographical area of interest. A whole-genome sequenced Swedish national reference population (n = 1000) has been recently published but with few samples from northern Sweden. In the present study we have whole-genome sequenced a control population (n = 300) (ACpop) from Västerbotten County, a sparsely populated region in northern Sweden previously shown to be genetically different from southern Sweden. The aggregated variant frequencies within ACpop are publicly available (DOI 10.17044/NBIS/G000005) to function as a basic resource in clinical genetics and for genetic studies. Our analysis of ACpop, representing approximately 0.11% of the population in Västerbotten, indicates the presence of a genetic substructure within the county. Furthermore, a demographic analysis showed that the population from which samples were drawn was to a large extent geographically stationary, a finding that was corroborated in the genetic analysis down to the level of municipalities. Including ACpop in the reference population when imputing unknown variants in a Västerbotten cohort resulted in a strong increase in the number of high-confidence imputed variants (up to 81% for variants with minor allele frequency

Suggested Citation

  • Daniel Svensson & Matilda Rentoft & Anna M Dahlin & Emma Lundholm & Pall I Olason & Andreas Sjödin & Carin Nylander & Beatrice S Melin & Johan Trygg & Erik Johansson, 2020. "A whole-genome sequenced control population in northern Sweden reveals subregional genetic differences," PLOS ONE, Public Library of Science, vol. 15(9), pages 1-18, September.
    • Handle: RePEc:plo:pone00:0237721
    DOI: 10.1371/journal.pone.0237721
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    References listed on IDEAS

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    1. Bryan N Howie & Peter Donnelly & Jonathan Marchini, 2009. "A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies," PLOS Genetics, Public Library of Science, vol. 5(6), pages 1-15, June.
    2. Nick Patterson & Alkes L Price & David Reich, 2006. "Population Structure and Eigenanalysis," PLOS Genetics, Public Library of Science, vol. 2(12), pages 1-20, December.
    3. Keith Humphreys & Alexander Grankvist & Monica Leu & Per Hall & Jianjun Liu & Samuli Ripatti & Karola Rehnström & Leif Groop & Lars Klareskog & Bo Ding & Henrik Grönberg & Jianfeng Xu & Nancy L Peders, 2011. "The Genetic Structure of the Swedish Population," PLOS ONE, Public Library of Science, vol. 6(8), pages 1-11, August.
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