The GenoChip: A New Tool for Genetic Anthropology

The Genographic Project is an international effort using genetic data to chart human migratory history. The project is non-profit and non-medical, and through its Legacy Fund supports locally led efforts to preserve indigenous and traditional cultures. In its second phase, the project is focusing on markers from across the entire genome to obtain a more complete understanding of human genetic variation. Although many commercial arrays exist for genome-wide SNP genotyping, they were designed for medical genetic studies and contain medically related markers that are not appropriate for global population genetic studies. GenoChip, the Genographic Project's new genotyping array, was designed to resolve these issues and enable higher-resolution research into outstanding questions in genetic anthropology. We developed novel methods to identify AIMs and genomic regions that may be enriched with alleles shared with ancestral hominins. Overall, we collected and ascertained AIMs from over 450 populations. Containing an unprecedented number of Y-chromosomal and mtDNA SNPs and over 130,000 SNPs from the autosomes and X-chromosome, the chip was carefully vetted to avoid inclusion of medically relevant markers. The GenoChip results were successfully validated. To demonstrate its capabilities, we compared the FST distributions of GenoChip SNPs to those of two commercial arrays for three continental populations. While all arrays yielded similarly shaped (inverse J) FST distributions, the GenoChip autosomal and X-chromosomal distributions had the highest mean FST, attesting to its ability to discern subpopulations. The GenoChip is a dedicated genotyping platform for genetic anthropology and promises to be the most powerful tool available for assessing population structure and migration history. 11 pages, 5 Figures, 2 supplementary notes