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

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

PLOS ONE, 2020, vol. 15, issue 9, 1-18

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

Date: 2020
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0237721

DOI: 10.1371/journal.pone.0237721

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