Recent genomic heritage in Scotland

BMC Genomics

Chris S Haley¹  Pau Navarro²  Caroline Hayward²  Veronique Vitart²  Nick Hastie²  James F Wilson³  David Porteous²  Archie Campbell²  Holly Trochet²  Jennifer Huffman²  Carmen Amador² 

[1] Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK;MRC IGMM, University of Edinburgh, Edinburgh EH4 2XU, UK;Centre for Population Health Sciences, University of Edinburgh, Edinburgh EH8 9AG, UK

关键词: Population structure;    Rare variants;    Admixture;    Genetic ancestry;    Principal component analysis;    Generation Scotland;   

Others  :  1211967
DOI  :  10.1186/s12864-015-1605-2

 received in 2014-11-07, accepted in 2015-05-01,  发布年份 2015

【 摘 要 】

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.

【 授权许可】

   
2015 Amador et al.

【 图 表 】

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