title: Genetic differences between five European populations.
abstract: OBJECTIVE
  We sought to examine the magnitude of the differences in SNP allele frequencies between five European populations (Scotland, Ireland, Sweden, Bulgaria and Portugal) and to identify the loci with the greatest differences.
  
  
  METHODS
  We performed a population-based genome-wide association analysis with Affymetrix 6.0 and 5.0 arrays. We used a 4 degrees of freedom χ(2) test to determine the magnitude of stratification for each SNP. We then examined the genes within the most stratified regions, using a highly conservative cutoff of p < 10(-45).
  
  
  RESULTS
  We found 40,593 SNPs which are genome-wide significantly (p ≤ 10(-8)) stratified between these populations. The largest differences clustered in gene ontology categories for immunity and pigmentation. Some of the top loci span genes that have already been reported as highly stratified: genes for hair color and pigmentation (HERC2, EXOC2, IRF4), the LCT gene, genes involved in NAD metabolism, and in immunity (HLA and the Toll-like receptor genes TLR10, TLR1, TLR6). However, several genes have not previously been reported as stratified within European populations, indicating that they might also have provided selective advantages: several zinc finger genes, two genes involved in glutathione synthesis or function, and most intriguingly, FOXP2, implicated in speech development.
  
  
  CONCLUSIONS
  Our analysis demonstrates that many SNPs show genome-wide significant differences within European populations and the magnitude of the differences correlate with the geographical distance. At least some of these differences are due to the selective advantage of polymorphisms within these loci.
authors.affiliation: MRC Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, UK.
authors.forename: Valentina
authors.initials: V
authors.lastname: Moskvina
authors.forename: Michael
authors.initials: M
authors.lastname: Smith
authors.forename: Dobril
authors.initials: D
authors.lastname: Ivanov
authors.forename: Douglas
authors.initials: D
authors.lastname: Blackwood
authors.forename: David
authors.initials: D
authors.lastname: StClair
authors.forename: Christina
authors.initials: C
authors.lastname: Hultman
authors.forename: Draga
authors.initials: D
authors.lastname: Toncheva
authors.forename: Michael
authors.initials: M
authors.lastname: Gill
authors.forename: Aiden
authors.initials: A
authors.lastname: Corvin
authors.forename: Colm
authors.initials: C
authors.lastname: O'Dushlaine
authors.forename: Derek W
authors.initials: DW
authors.lastname: Morris
authors.forename: Naomi R
authors.initials: NR
authors.lastname: Wray
authors.forename: Patrick
authors.initials: P
authors.lastname: Sullivan
authors.forename: Carlos
authors.initials: C
authors.lastname: Pato
authors.forename: Michele T
authors.initials: MT
authors.lastname: Pato
authors.forename: Pamela
authors.initials: P
authors.lastname: Sklar
authors.forename: Shaun
authors.initials: S
authors.lastname: Purcell
authors.forename: Peter
authors.initials: P
authors.lastname: Holmans
authors.forename: Michael C
authors.initials: MC
authors.lastname: O'Donovan
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Owen
authors.forename: George
authors.initials: G
authors.lastname: Kirov
mesh_terms: D005828:Genetics, Population; D006801:Humans; D043322:Lactase / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D044465:White People / Q000235:genetics*
chemical_list: D043322:Lactase