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

Autor:	Svensson D; Department of Chemistry, Computational Life Science Cluster, Umeå University, Umeå, Sweden., Rentoft M; Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden., Dahlin AM; Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden., Lundholm E; Centre for Demography and Ageing, Umeå University, Umeå, Sweden., Olason PI; Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden., Sjödin A; Department of Chemistry, Computational Life Science Cluster, Umeå University, Umeå, Sweden.; Division of CBRN Security and Defence, FOI-Swedish Defence Research Agency, Umeå, Sweden., Nylander C; Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden., Melin BS; Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden., Trygg J; Department of Chemistry, Computational Life Science Cluster, Umeå University, Umeå, Sweden., Johansson E; Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden.
Jazyk:	angličtina
Zdroj:	PloS one [PLoS One] 2020 Sep 11; Vol. 15 (9), pp. e0237721. Date of Electronic Publication: 2020 Sep 11 (Print Publication: 2020).
DOI:	10.1371/journal.pone.0237721
Abstrakt:	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 < 5%). ACpop was initially designed for cancer disease studies, but the genetic structure within the cohort will be of general interest for all genetic disease studies in northern Sweden. Competing Interests: The authors have declared that no competing interests exist.
Databáze:	MEDLINE
Externí odkaz: