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 un...

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Bibliographic Details
Published in:Genome Biology and Evolution
Main Authors: Elhaik, Eran, Greenspan, Elliott, Staats, Sean, Krahn, Thomas, Tyler Smith, Chris, Xue, Yali, Tofanelli, Sergio, FRANCALACCI, Paolo, CUCCA, Francesco, Pagani, Luca, Jin, Li, Li, Hui, Schurr, Theodore G., Greenspan, Bennett, Wells, R. Spencer
Other Authors: Krahn, Thoma, Tyler Smith, Chri, Francalacci, Paolo, Cucca, Francesco
Format: Article in Journal/Newspaper
Language:English
Published: 2013
Subjects:
Aimsfinder
Genetic anthropology
GenoChip
Genographic project
Haplogroup
Population genetic
DNA
mitochondrial
Genes
Y-Linked
History
ancient
Human Genome Project
Human migration
Human
Polymorphism
single nucleotide
Anthropology
cultural
Oligonucleotide array sequence analysi
Ecology
evolution
behavior and systematic
Genetics
Saqqaq
Online Access:http://hdl.handle.net/11584/254018
https://doi.org/10.1093/gbe/evt066
http://gbe.oxfordjournals.org/
Description
Summary: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 ...

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