Candidate array (384 SNPs)
An initial genotyping study of 384 SNPs in ~100K DNA samples from CKB participants was conducted in 2013 at the BGI laboratory in Shenzen, China. SNPs were selected based on previous associations with chronic diseases (e.g. stroke, IHD, diabetes), intermediate phenotypes (e.g. blood pressure, BMI, lung function), metabolic pathways (e.g. vitamin D), and risk exposures (e.g. alcohol, smoking), with priority given to replicated results from large-scale GWAS in East Asians (if available), functional genetic variants (e.g. PLA2G7 V279F), and SNPs in key genes of interest (e.g. FTO, MTHFR).
GWAS array (880K SNPs)
Following the candidate array work, a custom-designed biobank array, to provide optimised genome-wide coverage for Chinese populations, was developed by CTSU in collaboration with BGI and Affymetrix. This ~700K SNP array has been used to genotype ~32,000 individuals including: 5,000 haemorrhagic stroke cases; 5,000 ischaemic stroke cases; 5,000 cases of hospitalisation for chronic obstructive pulmonary disease; and 15,000 CKB controls. Completion of this phase of genotyping is expected by mid-October 2015. A major grant from the MRC Newton Fund will extend genotyping to over 100,000 participants, including all 25,000 subjects who attended the 2014-2015 second resurvey. This will use a revised and updated version of the original array, now covering ~803K SNPs. This second phase of genotyping is expected to be completed by mid-2016.