The GenoChip: A new tool for genetic anthropology

Eran Elhaik, Elliott Greenspan, Sean Staats, Thomas Krahn, Chris Tyler-Smith, Yali Xue, Sergio Tofanelli, Paolo Francalacci, Francesco Cucca, Luca Pagani, Li Jin, Hui Li, Theodore G. Schurr, Bennett Greenspan, R. Spencer Wells, Oscar Acosta, Syama Adhikarla, Christina J. Adler, Elena Balanovska, Oleg BalanovskyJaume Bertranpetit, Andrew C. Clarke, David Comas, Alan Cooper, Matthew C. Dulik, Jill B. Gaieski, Arun Kumar Ganesh Prasad, Wolfgang Haak, Marc Haber, Matthew E. Kaplan, Daniela R. Lacerda, Shilin Li, Begona Martinez-Cruz, Elizabeth A. Matisoo-Smith, Nirav C. Merchant, John R. Mitchell, Amanda C. Owings, Laxmi Parida, Ramasamy Pitchappan, Daniel E. Platt, Lluis Quintana-Murci, Colin Renfrew, A. K. Royyuru, Jose Raul Sandoval, Arun Varatharajan Santhakumari, Fabrıcio R. Santos, Clio S.I. Der Sarkissian, Himla Soodyall, David F. Soria Hernanz, Pandikumar Swamikrishnan, Pedro Paulo Vieira, Miguel G. Vilar, Pierre A. Zalloua, Janet S. Ziegle

Research output: Contribution to journalArticle

36 Scopus citations

Abstract

The Genographic Project is an international effort aimed at charting human migratory history. The project is nonprofit and nonmedical, 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.
Original languageAmerican English
Pages (from-to)1021-1031
Number of pages11
JournalGenome Biology and Evolution
DOIs
StatePublished - 1 Jan 2013
Externally publishedYes

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    Elhaik, E., Greenspan, E., Staats, S., Krahn, T., Tyler-Smith, C., Xue, Y., Tofanelli, S., Francalacci, P., Cucca, F., Pagani, L., Jin, L., Li, H., Schurr, T. G., Greenspan, B., Spencer Wells, R., Acosta, O., Adhikarla, S., Adler, C. J., Balanovska, E., ... Ziegle, J. S. (2013). The GenoChip: A new tool for genetic anthropology. Genome Biology and Evolution, 1021-1031. https://doi.org/10.1093/gbe/evt066