A shared recognition of the value of coordinated efforts and the need for reference genome datasets that would be useful for the complex populations of Asia has led to the formation of the GenomeAsia consortium (http://www.genomeasia100k.com). The consortium serves to facilitate and coordinate sequencing efforts among consortium members to maximize the value of the genomic sequence data that is produced and to facilitate efforts by national or other regional groups. Here we describe the GenomeAsia Pilot (GAsP) project, which consists of analyses of the whole-genome sequencing data of 1,739 individuals from 219 population groups across Asia, with the ultimate goal of providing a useful genomic resource and facilitating genetic studies in Asia. We use the data that was generated in this pilot to analyse population structure and history, and as the basis for designing larger-scale genomic studies. Furthermore, we explore disease-associated loci as an initial comparison of differences between populations. We show that the variant data produced by this project improve variant filtering for the discovery of disease-associated genes of rare diseases. We show that Asia has sizable founder populations
