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The GenoChip : a new tool for genetic anthropology

Elhaik, Eran LU ; Greenspan, Elliott ; Staats, Sean ; Krahn, Thomas ; Tyler-Smith, Chris ; Xue, Yali ; Tofanelli, Sergio ; Francalacci, Paolo ; Cucca, Francesco and Pagani, Luca , et al. (2013) In Genome Biology and Evolution 5(5). p.31-1021
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... (More)

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.

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publishing date
type
Contribution to journal
publication status
published
keywords
Anthropology, Cultural, DNA, Mitochondrial/genetics, Genes, Y-Linked, History, Ancient, Human Genome Project, Human Migration/history, Humans, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide/genetics
in
Genome Biology and Evolution
volume
5
issue
5
pages
31 - 1021
publisher
Oxford University Press
external identifiers
  • scopus:84888821239
  • pmid:23666864
ISSN
1759-6653
DOI
10.1093/gbe/evt066
language
English
LU publication?
no
id
f7b228c4-561d-47d7-980b-8f158b1e4960
date added to LUP
2019-11-10 16:57:05
date last changed
2020-07-01 05:24:27
@article{f7b228c4-561d-47d7-980b-8f158b1e4960,
  abstract     = {<p>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.</p>},
  author       = {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 Greenspan, Bennett and Spencer Wells, R},
  issn         = {1759-6653},
  language     = {eng},
  number       = {5},
  pages        = {31--1021},
  publisher    = {Oxford University Press},
  series       = {Genome Biology and Evolution},
  title        = {The GenoChip : a new tool for genetic anthropology},
  url          = {http://dx.doi.org/10.1093/gbe/evt066},
  doi          = {10.1093/gbe/evt066},
  volume       = {5},
  year         = {2013},
}