The GenoChip

A new tool for genetic anthropology

the Genographic Consortium

Research output: Contribution to journalArticle

32 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)1021-1031
Number of pages11
JournalGenome Biology and Evolution
Volume5
Issue number5
DOIs
StatePublished - Jan 1 2013

Fingerprint

anthropology
Anthropology
Single Nucleotide Polymorphism
Mitochondrial DNA
genotyping
mitochondrial DNA
Y Chromosome
Medical Genetics
Population Genetics
Y chromosome
population genetics
Neanderthals
Genome
chromosome
genome
Aptitude
Hominidae
Neanderthal
Principal Component Analysis
human population

Keywords

  • Aimsfinder
  • Genetic anthropology
  • GenoChip
  • Genographic project
  • Haplogroups
  • Population genetics

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

Cite this

The GenoChip : A new tool for genetic anthropology. / the Genographic Consortium.

In: Genome Biology and Evolution, Vol. 5, No. 5, 01.01.2013, p. 1021-1031.

Research output: Contribution to journalArticle

the Genographic Consortium. / The GenoChip : A new tool for genetic anthropology. In: Genome Biology and Evolution. 2013 ; Vol. 5, No. 5. pp. 1021-1031.
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