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The GenoChip: a new tool for genetic anthropology

Elhaik, Eran and Greenspan, Elliott and Staats, Sean and Krahn, Thomas and Tyler-Smith, Chris and Xue, Yali and Tofanelli, Sergio and Francalacci, Paolo and Cucca, Francesco and Pagani, Luca and Jin, Li and LI, Hui and Schurr, Theodore G. and Greespan, Bennett and Wells, R. Spencer (2013) The GenoChip: a new tool for genetic anthropology. Genome Biology and Evolution, Vol. 5 (5), p. 1021-1031. eISSN 1759-6653. Article.

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DOI: 10.1093/gbe/evt066

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.

Item Type:Article
ID Code:9527
Status:Published
Refereed:Yes
Uncontrolled Keywords:Genetic anthropology, GenoChip, genographic project, population genetics, AimsFinder, haplogroups
Subjects:Area 06 - Scienze mediche > MED/03 Genetica medica
Area 05 - Scienze biologiche > BIO/18 Genetica
Divisions:001 Università di Sassari > 01-a Nuovi Dipartimenti dal 2012 > Scienze Biomediche
001 Università di Sassari > 01-a Nuovi Dipartimenti dal 2012 > Scienze della Natura e del Territorio
Publisher:Oxford University Press on behalf of the Society for Molecular Biology and Evolution
eISSN:1759-6653
Copyright Holders:© The Author(s) 2013
Deposited On:04 Dec 2013 13:00

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