GWAS

In 2013/2014, an Illumina Omni 2.5–8 chip (Illumina Inc, San Diego, Ca.,USA) was used to perform genome-wide genotyping of around 2.5 million single nucleotide polymorphisms (SNPs) and related genomic features on approximately 7,400 consenting ELSA participants who provided blood samples at wave 2 or waves 3 and 4 (refreshment samples) . The same genotyping chip had previously been used in HRS, enabling direct comparisons of the ELSA and HRS samples to be carried out. The ELSA GWAS data have been deposited in the European Genome-phenome Archive (EGA) and are available to bona fide researchers. Applicants can request access to the ELSA GWAS data by applying to the *Managing Ethico-social, Technical and Administrative issues in Data Access Committee (METADAC).

A second data set of imputed SNPs is also available on request. Imputation was performed with Shapeit and IMPUTE2 using reference data from 1092 samples included in the worldwide 1000 Genomes phase I data set. Imputation was carried out as described by Howie et al. (Nat. Genet. 44, 955–9 (2012)) in 1 MB chunked intervals with a 20 kb overlap between chunks. Both probability files and hard called imputed genotypes (in PLINK format) are available. This guide describes steps that can be taken to explore, catalogue and impute data in the version of the ELSA genome wide genotyping data set that is provided via the European Genome/Phenome Archive (EGA). Download report

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