The GenoChip: A New Tool for Genetic Anthropology

Are you curious to know your ‘personal’ history from your genome? An extremely accurate way to nail the ancestral origin of individuals has been developed by Dr. Eran Elhaik of Johns Hopkins and his colleagues. Their paper is available from the early edition of Genome Biology and Evolution.

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 genomewide 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 Projects 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. While 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 ~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.

How accurate is the chip? The paper says -

The accuracy of the autosomal genotypes obtained by the GenoChip, was assessed by

genotyping 168 worldwide samples from the 1000 Genomes Project and cross- validating the

results. The concordance rate per sample was over 99.5%. We did not observe any position with

mismatching homozygote alleles. The marginal error rate was expected due to the low coverage

of the 1000 Genomes Project data, particularly for rare alleles (Durbin et al. 2010). We thus

confirmed that genotypes reported by the GenoChip are accurate.