RMSS 2017

We are using a combination of genome-wide genotyping, sequencing and imputation in population cohorts with high kinship to search for quantitative trait loci (QTL) variants of clinical and biological relevance. The Generation Scotland Scottish Family Health Study (GS:SFHS) is a family-based cohort with biological samples, socio-demographic, clinical and genetic data from approximately 24,000 adult volunteers across Scotland (www.generationscotland.org). Although data collection (from 2006-2011) was cross-sectional, GS:SFHS becomes a prospective cohort as a result of the ability to link to routine NHS electronic health record (EHR) data.

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GS:SFHS participants were analysed by genome-wide chip genotyping using the Illumina OMNI+exome chip. QC analyses were performed, data cleaned using quality scores and proportions typed, sample identity verified against recorded gender and pedigree, and data checked for unknown relationships based on estimated identity-by-descent. Genome-wide association studies (GWAS) were run on 20,032 individuals, correcting for family relationships using a polygenic kinship matrix and for population stratification using the first three principal components. Data was imputed to the Haplotype Reference Consortium dataset allowing accurate imputation of rare variants into all the genotyped samples.