title: Recent genomic heritage in Scotland.
abstract: BACKGROUND
  The Generation Scotland Scottish Family Health Study (GS:SFHS) includes 23,960 participants from across Scotland with records for many health-related traits and environmental covariates. Genotypes at ~700 K SNPs are currently available for 10,000 participants. The cohort was designed as a resource for genetic and health related research and the study of complex traits. In this study we developed a suite of analyses to disentangle the genomic differentiation within GS:SFHS individuals to describe and optimise the sample and methods for future analyses.
  
  
  RESULTS
  We combined the genotypic information of GS:SFHS with 1092 individuals from the 1000 Genomes project and estimated their genomic relationships. Then, we performed Principal Component Analyses of the resulting relationships to investigate the genomic origin of different groups. We characterised two groups of individuals: those with a few sparse rare markers in the genome, and those with several large rare haplotypes which might represent relatively recent exogenous ancestors. We identified some individuals with likely Italian ancestry and a group with some potential African/Asian ancestry. An analysis of homozygosity in the GS:SFHS sample revealed a very similar pattern to other European populations. We also identified an individual carrying a chromosome 1 uniparental disomy. We found evidence of local geographic stratification within the population having impact on the genomic structure.
  
  
  CONCLUSIONS
  These findings illuminate the history of the Scottish population and have implications for further analyses such as the study of the contributions of common and rare variants to trait heritabilities and the evaluation of genomic and phenotypic prediction of disease.
authors.affiliation: MRC IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK. Carmen.Amador@igmm.ed.ac.uk.
authors.forename: Carmen
authors.initials: C
authors.lastname: Amador
authors.affiliation: MRC IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK. Jennifer.Huffman@igmm.ed.ac.uk.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Huffman
authors.affiliation: MRC IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK. HTrochet@gmail.com.
authors.forename: Holly
authors.initials: H
authors.lastname: Trochet
authors.affiliation: MRC IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK. Archie.Campbell@igmm.ed.ac.uk.
authors.forename: Archie
authors.initials: A
authors.lastname: Campbell
authors.affiliation: MRC IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK. David.Porteous@igmm.ed.ac.uk.
authors.forename: David
authors.initials: D
authors.lastname: Porteous
authors.affiliation: Centre for Population Health Sciences, University of Edinburgh, Edinburgh, EH8 9AG, UK. Jim.Wilson@ed.ac.uk.
authors.forename: James F
authors.initials: JF
authors.lastname: Wilson
authors.affiliation: MRC IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK. Nick.Hastie@igmm.ed.ac.uk.
authors.forename: Nick
authors.initials: N
authors.lastname: Hastie
authors.affiliation: MRC IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK. Veronique.Vitart@igmm.ed.ac.uk.
authors.forename: Veronique
authors.initials: V
authors.lastname: Vitart
authors.affiliation: MRC IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK. Caroline.Hayward@igmm.ed.ac.uk.
authors.forename: Caroline
authors.initials: C
authors.lastname: Hayward
authors.affiliation: MRC IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK. Pau.Navarro@ed.ac.uk.
authors.forename: Pau
authors.initials: P
authors.lastname: Navarro
authors.affiliation: MRC IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK. Chris.Haley@roslin.ed.ac.uk.|Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK. Chris.Haley@roslin.ed.ac.uk.
authors.forename: Chris S
authors.initials: CS
authors.lastname: Haley
mesh_terms: D044466:Asian People / Q000235:genetics*; D044383:Black People / Q000235:genetics*; D005260:Female; D015894:Genome, Human; D005838:Genotype; D006801:Humans; D008297:Male; D008957:Models, Genetic; D058974:Phylogeography; D020641:Polymorphism, Single Nucleotide; D011157:Population Dynamics; D025341:Principal Component Analysis; D019655:Quantitative Trait, Heritable; D012606:Scotland / Q000208:ethnology; D044465:White People / Q000235:genetics*