3 research outputs found
The GenoChip: A New Tool for Genetic Anthropology
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. TheGenoChip includes ancestry informativemarkers obtained
for over 450 human populations, an ancient human (Saqqaq), and two archaic hominins (Neanderthal and Denisovan) and was
designed to identify all knownY-chromosome andmtDNAhaplogroups. The chip was carefully vetted to avoid inclusion ofmedically
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 highestmean 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 SNPswithout any known health,medical, or phenotypic relevance, the GenoChip
is a useful tool for genetic anthropology and population genetics