January 2021, there are at least 217 case-only studies containing >136,000 samples across many genotyping platforms in the database of Genetics and Phenotypes (dbGaP) (query = ‘case set[Study Design]’). As of February 2020, freeze 6a, there are >227,000 public controls with WGS data in resources such as TOPMed (>155,000 samples)15, UK BioBank (>50,000 samples)16, Gabriella Miller Kids First Pediatric Consortium (>21,000 samples), and GenomeAsia 100K Project (>1,700 individuals)17, which are eligible to be combined with these case-only datasets for GWAS. Both the pools of case-only data and WGS public controls will continue to increase. Although the array genotyping may have a lower overall precision due to the poor cluster separation in the genotype assignment pipeline based on a 2-dimensional metrics, the average discordant calls were below 1%18, which supports the feasibility to combine the array genotyping data with WGS data.
