title: The genetic structure of the Swedish population.
abstract: Patterns of genetic diversity have previously been shown to mirror geography on a global scale and within continents and individual countries. Using genome-wide SNP data on 5174 Swedes with extensive geographical coverage, we analyzed the genetic structure of the Swedish population. We observed strong differences between the far northern counties and the remaining counties. The population of Dalarna county, in north middle Sweden, which borders southern Norway, also appears to differ markedly from other counties, possibly due to this county having more individuals with remote Finnish or Norwegian ancestry than other counties. An analysis of genetic differentiation (based on pairwise F(st)) indicated that the population of Sweden's southernmost counties are genetically closer to the HapMap CEU samples of Northern European ancestry than to the populations of Sweden's northernmost counties. In a comparison of extended homozygous segments, we detected a clear divide between southern and northern Sweden with small differences between the southern counties and considerably more segments in northern Sweden. Both the increased degree of homozygosity in the north and the large genetic differences between the south and the north may have arisen due to a small population in the north and the vast geographical distances between towns and villages in the north, in contrast to the more densely settled southern parts of Sweden. Our findings have implications for future genome-wide association studies (GWAS) with respect to the matching of cases and controls and the need for within-county matching. We have shown that genetic differences within a single country may be substantial, even when viewed on a European scale. Thus, population stratification needs to be accounted for, even within a country like Sweden, which is often perceived to be relatively homogenous and a favourable resource for genetic mapping, otherwise inferences based on genetic data may lead to false conclusions.
authors.affiliation: Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
authors.forename: Keith
authors.initials: K
authors.lastname: Humphreys
authors.forename: Alexander
authors.initials: A
authors.lastname: Grankvist
authors.forename: Monica
authors.initials: M
authors.lastname: Leu
authors.forename: Per
authors.initials: P
authors.lastname: Hall
authors.forename: Jianjun
authors.initials: J
authors.lastname: Liu
authors.forename: Samuli
authors.initials: S
authors.lastname: Ripatti
authors.forename: Karola
authors.initials: K
authors.lastname: Rehnström
authors.forename: Leif
authors.initials: L
authors.lastname: Groop
authors.forename: Lars
authors.initials: L
authors.lastname: Klareskog
authors.forename: Bo
authors.initials: B
authors.lastname: Ding
authors.forename: Henrik
authors.initials: H
authors.lastname: Grönberg
authors.forename: Jianfeng
authors.initials: J
authors.lastname: Xu
authors.forename: Nancy L
authors.initials: NL
authors.lastname: Pedersen
authors.forename: Paul
authors.initials: P
authors.lastname: Lichtenstein
authors.forename: Morten
authors.initials: M
authors.lastname: Mattingsdal
authors.forename: Ole A
authors.initials: OA
authors.lastname: Andreassen
authors.forename: Colm
authors.initials: C
authors.lastname: O'Dushlaine
authors.forename: Shaun M
authors.initials: SM
authors.lastname: Purcell
authors.forename: Pamela
authors.initials: P
authors.lastname: Sklar
authors.forename: Patrick F
authors.initials: PF
authors.lastname: Sullivan
authors.forename: Christina M
authors.initials: CM
authors.lastname: Hultman
authors.forename: Juni
authors.initials: J
authors.lastname: Palmgren
authors.forename: Patrik K E
authors.initials: PK
authors.lastname: Magnusson
mesh_terms: D005828:Genetics, Population; D006239:Haplotypes; D006720:Homozygote; D006801:Humans; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide; D011786:Quality Control; D013548:Sweden