Date of this Version
Genome Biology and Evolution
The Genographic Project is an international effort aimed at charting human migratory history. The project is nonprofit and non-medical, and, through its Legacy Fund, supports locally led efforts to preserve indigenous and traditional cultures. Although the first phase of the project was focused on uniparentally inherited markers on the Y-chromosome and mitochondrial DNA (mtDNA), 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 single-nucleotide polymorphism (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 FST distributions of GenoChip SNPs to those of two commercial arrays. Although 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 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 approximately 12,000 Y-chromosomal and approximately 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.
© The Author(s) 2013. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License , which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.
genetic anthropology, GenoChip, Genographic Project, population genetics, AimsFinder, haplogroups
Elhaik, E., Greenspan, E., Staats, S., Krahn, T., Tyler-Smith, C., Xue, Y., Tofanelli, S., Cucca, F., Pagani, L., Jin, L., Li, H., Schurr, T. G., Greenspan, B., Wells, R., & Genographic Consortium (2013). The GenoChip: A New Tool for Genetic Anthropology. Genome Biology and Evolution, 5 (5), 1021-1031. https://doi.org/10.1093/gbe/evt066
Additional FilesElhaik2013_-_Supplementary_Materials2.doc (1159 kB)
Elhaik2013_-_Table_S1.xlsx (35 kB)
Supplemental Data Table 1
Elhaik2013_-_Table_S2.xlsx (4220 kB)
Supplmental Data Table 2
Date Posted: 10 July 2014