The GenoChip: A New Tool for Genetic Anthropology

• Published in: Genome Biology and Evolution
• Main Authors: Elhaik, Eran, Greenspan, Elliott, Staats, Sean, Krahn, Thomas, Tyler-Smith, Chris, Xue, Yali, Tofanelli, Sergio, Francalacci, Paolo, Cucca, Francesco, Pagani, Luca, Jin, Li, Li, Hui, Schurr, Theodore G., Greenspan, Bennett, Wells, R. Spencer, the Genographic Consortium
• Format: Text
• Language: English
• Published: Oxford University Press 2013
• Subjects: Letter; The ''Y''; Saqqaq
• Online Access: http://gbe.oxfordjournals.org/cgi/content/short/evt066v2; https://doi.org/10.1093/gbe/evt066

The Genographic Project is an international effort aimed at charting 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. While the first phase of the project was focused on uniparentally-inherited markers on the Y-chromosome and mitochondrial DNA, the current phase focuses 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 inappropriate 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. The GenoChip includes ancestry informative markers obtained for over 450 human populations, an ancient human (Saqqaq), and two archaic hominins (Neanderthal and Denisovan) and was designed to identify all known Y-chromosome and mtDNA haplogroups. The chip was carefully vetted to avoid inclusion of medically relevant markers. To demonstrate its capabilities, we compared the F ST distributions of GenoChip SNPs to those of two commercial arrays. While all arrays yielded similarly shaped (inverse J) F ST distributions, the GenoChip autosomal and X-chromosomal distributions had the highest mean F ST , attesting to its ability to discern subpopulations. The chip performances are illustrated in a principal component analysis for 14 worldwide populations. In summary, the GenoChip is a dedicated genotyping platform for genetic anthropology. With an unprecedented number of ∼12,000 Y-chromosomal and ∼3,300 mtDNA SNPs and over 130,000 autosomal and X-chromosomal SNPs without any known health, medical, or phenotypic relevance, the GenoChip is a useful tool for genetic anthropology and population genetics.