Overall, GAWMerge presents a practical application of integrating case-only array-genotyped data with WGS data as public controls to enable new GWAS and enhance the potential for discovering novel genetic loci. It is a general approach for integrating array and WGS genotyping technologies. The substantial availability of case-only datasets in public repositories and collected across many consortia makes the protocol broadly applicable. With >155,000 samples with WGS data in the TOPMed program, this is an ample resource for selecting public controls for a variety of case-only disease datasets. With WGS data the overlap of measured variants across genotyping platforms is overcome. Furthermore, the diversity of individuals within the TOPMed (>47,000 African, >23,000 Hispanic/Latino, and >13,000 Asian ancestries) and increasing representation in other resources make widespread use of non-European public controls realistic. With many other WGS resources being launched and released, the potential to use public controls to increase sample size and leverage case-only cohorts is just beginning.
