The GenoChip: a new tool for genetic anthropology

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; Genographic Consortium; Bertranpetit, Jaume, 1952-; Comas, David, 1969-; Martínez Cruz, Begoña

The GenoChip: a new tool for genetic anthropology

Mostra el registre complet Registre parcial de l'ítem

dc.contributor.author Elhaik, Eran
dc.contributor.author Greenspan, Elliott
dc.contributor.author Staats, Sean
dc.contributor.author Krahn, Thomas
dc.contributor.author Tyler-Smith, Chris
dc.contributor.author Xue, Yali
dc.contributor.author Tofanelli, Sergio
dc.contributor.author Francalacci, Paolo
dc.contributor.author Cucca, Francesco
dc.contributor.author Pagani, Luca
dc.contributor.author Jin, Li
dc.contributor.author Li, Hui
dc.contributor.author Schurr, Theodore G.
dc.contributor.author Greenspan, Bennett
dc.contributor.author Wells, R. Spencer
dc.contributor.author Genographic Consortium
dc.contributor.author Bertranpetit, Jaume, 1952-
dc.contributor.author Comas, David, 1969-
dc.contributor.author Martínez Cruz, Begoña
dc.date.accessioned 2019-01-08T09:41:40Z
dc.date.available 2019-01-08T09:41:40Z
dc.date.issued 2013
dc.description.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.
dc.description.sponsorship This work was supported by the National Geographic Society, by SAR-LR 7/09, cRP2-597 to P.F., and by The Wellcome Trust (098051) to C.T.S. and Y.X.
dc.format.mimetype application/pdf
dc.identifier.citation Elhaik E, Greenspan E, Staats S, Krahn T, Tyler-Smith C, Xue Y et al. The GenoChip: a new tool for genetic anthropology. Genome Biol Evol. 2013;5(5):1021-31. DOI: 10.1093/gbe/evt066
dc.identifier.doi http://dx.doi.org/10.1093/gbe/evt066
dc.identifier.issn 1759-6653
dc.identifier.uri http://hdl.handle.net/10230/36214
dc.language.iso eng
dc.publisher Oxford University Press
dc.relation.ispartof Genome Biology and Evolution. 2013;5(5):1021-31
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.rights.uri http://creativecommons.org/licenses/by-nc/3.0/
dc.subject.other Genètica humana
dc.subject.other Antropologia
dc.subject.other Genographic Project
dc.subject.other Genètica de poblacions
dc.title The GenoChip: a new tool for genetic anthropology
dc.type info:eu-repo/semantics/article
dc.type.version info:eu-repo/semantics/publishedVersion

Col·leccions

Articles (Departament de Medicina i Ciències de la Vida)