Generation Scotland (Scottish Family Health Study) is an intensively phenotyped, family-based cohort for the study of the genetic basis of common complex diseases and response to treatments. Recruitment began early in 2006 and was completed in 2011. The cohort includes just over 24,000 participants, with most consenting to record linkage and recontact. Each participant gave blood or saliva samples (for processing, biochemistry and cryopreservation) and a urine sample. The blood or saliva samples were processed to DNA and extensive genotyping was carried out in 2015. Generation Scotland has worked with a number of collaborators on generating genetic data on its resource, in particular with the MRC Institute of Genetics and Molecular Medicine Quantitative Trait Locus (QTL) group. DNA from over 20,000 GS:SFHS participants has been analysed by high density genome-wide chip genotyping, Illumina OmniExpress SNP GWAS (700k) and exome chip (250K), with low failure and high call rates. QC analyses were performed, data cleaned using quality scores and proportions typed. Sample identity was verified against recorded gender and pedigree and data checked for unknown relationships based on estimated identity-by-descent. Population stratification was assessed by analysis of principal components and imputing all data to the 1000 Genome data set. The quality of the checked data was assessed by GWAS analysis on anthropometric and lipid phenotypic quantitative traits. Family relationships were corrected for using a polygenic kinship matrix and for population stratification using principal component analysis. These results are being compared with those in published meta-analyses and the genome-wide data are being used by the QTL group in a range of research projects involving both international consortia and local experts. For example, cognition research is being led by colleagues at the University of Edinburgh, and a wide range of phenotypes is being analysed in collaboration with the CHARGE consortium. Methylation data is available on a subset of 19,500 samples. Study website:

https://www.generationscotland.orgThe

Scottish Family Health Study (GS:SFHS) is an intensively phenotyped, family-based cohort for the study of the genetic basis of common complex diseases and response to treatments. Recruitment began early in 2006 and was completed in 2011. The cohort includes just over 24,000 participants, with most consenting to record linkage and recontact. Each participant gave blood or saliva samples (for processing, biochemistry and cryopreservation) and a urine sample. The blood or saliva samples were processed to DNA and extensive genotyping was carried out in 2015. Generation Scotland has worked with a number of collaborators on generating genetic data on its resource, in particular with the MRC Institute of Genetics and Molecular Medicine Quantitative Trait Locus (QTL) group. DNA from over 20,000 GS:SFHS participants has been analysed by high density genome-wide chip genotyping, Illumina OmniExpress SNP GWAS (700k) and exome chip (250K), with low failure and high call rates. QC analyses were performed, data cleaned using quality scores and proportions typed. Sample identity was verified against recorded gender and pedigree and data checked for unknown relationships based on estimated identity-by-descent. Population stratification was assessed by analysis of principal components and imputing all data to the 1000 Genome data set. The quality of the checked data was assessed by GWAS analysis on anthropometric and lipid phenotypic quantitative traits. Family relationships were corrected for using a polygenic kinship matrix and for population stratification using principal component analysis. These results are being compared with those in published meta-analyses and the genome-wide data are being used by the QTL group in a range of research projects involving both international consortia and local experts. For example, cognition research is being led by colleagues at the University of Edinburgh, and a wide range of phenotypes is being analysed in collaboration with the CHARGE consortium. Methylation data is available on a subset of 19,500 samples. Study website:

https://www.generationscotland.org