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. 2015 Jun 6;16(1):437.
doi: 10.1186/s12864-015-1605-2.

Recent Genomic Heritage in Scotland

Free PMC article

Recent Genomic Heritage in Scotland

Carmen Amador et al. BMC Genomics. .
Free PMC article


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.


Fig. 1
Fig. 1
Results of the PCA in the GS + 1 kG data set. a Values for PC1 and PC2 in GS + 1 kG individuals; b Values for PC1 and PC2 only in GS:SFHS individuals (open circles were defined as outliers); c Values for PC3 and PC4 in GS + 1 kG individuals; d Values for PC5 and PC6 in GS + 1 kG individuals
Fig. 2
Fig. 2
Results of the PCA in the GS + European data set. Values for PC1 and PC2 in Generation Scotland and the other European samples
Fig. 3
Fig. 3
Score values of individuals 40,280 and 11,786. a Individual marker score of individual 40,280; b Individual marker score of individual 11,786; c Pair marker score of individuals 40,280 and 11,786; d Rarity scores of individual 40,280 and 11,786
Fig. 4
Fig. 4
Origin of rare alleles in GS:SFHS. Frequencies for rare Generation Scotland alleles (p ≤ 0.0004) in the a African, b Asian and c European populations of the 1000 Genomes data set
Fig. 5
Fig. 5
Selected results from chromosomal PCA. Location of GS:SFHS individuals (whole genome and different chromosomes analyses) for PC 1 and 2 (upper row) and several PCs showing a distinct pattern (lower row). The colours show the correspondence between the groups shown in PC 5 and 6 when using the whole genome, and those obtained when analysing only chromosome 8 for PC 2 and 3
Fig. 6
Fig. 6
Locations and predictions within Scotland. a Real location of the 31 different origins of the GS:SFHS individuals. b Predicted latitude and longitude of the individuals using the genomic principal components

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