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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Online Access: | http://hdl.handle.net/10230/36214 https://doi.org/10.1093/gbe/evt066 |
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ftupompeufabra:oai:repositori.upf.edu:10230/36214 2023-05-15T18:15:05+02:00 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 application/pdf http://hdl.handle.net/10230/36214 https://doi.org/10.1093/gbe/evt066 eng eng Oxford University Press Genome Biology and Evolution. 2013;5(5):1021-31 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 1759-6653 http://hdl.handle.net/10230/36214 http://dx.doi.org/10.1093/gbe/evt066 © Eran Elhaik et al. 2013. Published by Oxford University Press. This is an Open Access article distributed under the terms of a Creative Commons Attribution License http://creativecommons.org/licenses/by-nc/3.0/ info:eu-repo/semantics/openAccess CC-BY CC-BY-NC Genètica humana Antropologia Genographic Project Genètica de poblacions info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion ftupompeufabra https://doi.org/10.1093/gbe/evt066 2021-08-03T23:18:56Z 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. 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. Article in Journal/Newspaper Saqqaq UPF Digital Repository (Universitat Pompeu Fabra, Barcelona) The ''Y'' ENVELOPE(-112.453,-112.453,57.591,57.591) Genome Biology and Evolution 5 5 1021 1031 |
institution |
Open Polar |
collection |
UPF Digital Repository (Universitat Pompeu Fabra, Barcelona) |
op_collection_id |
ftupompeufabra |
language |
English |
topic |
Genètica humana Antropologia Genographic Project Genètica de poblacions |
spellingShingle |
Genètica humana Antropologia Genographic Project Genètica de poblacions 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 |
topic_facet |
Genètica humana Antropologia Genographic Project Genètica de poblacions |
description |
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. 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. |
format |
Article in Journal/Newspaper |
author |
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 |
author_facet |
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 |
author_sort |
Elhaik, Eran |
title |
The GenoChip: a new tool for genetic anthropology |
title_short |
The GenoChip: a new tool for genetic anthropology |
title_full |
The GenoChip: a new tool for genetic anthropology |
title_fullStr |
The GenoChip: a new tool for genetic anthropology |
title_full_unstemmed |
The GenoChip: a new tool for genetic anthropology |
title_sort |
genochip: a new tool for genetic anthropology |
publisher |
Oxford University Press |
url |
http://hdl.handle.net/10230/36214 https://doi.org/10.1093/gbe/evt066 |
long_lat |
ENVELOPE(-112.453,-112.453,57.591,57.591) |
geographic |
The ''Y'' |
geographic_facet |
The ''Y'' |
genre |
Saqqaq |
genre_facet |
Saqqaq |
op_relation |
Genome Biology and Evolution. 2013;5(5):1021-31 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 1759-6653 http://hdl.handle.net/10230/36214 http://dx.doi.org/10.1093/gbe/evt066 |
op_rights |
© Eran Elhaik et al. 2013. Published by Oxford University Press. This is an Open Access article distributed under the terms of a Creative Commons Attribution License http://creativecommons.org/licenses/by-nc/3.0/ info:eu-repo/semantics/openAccess |
op_rightsnorm |
CC-BY CC-BY-NC |
op_doi |
https://doi.org/10.1093/gbe/evt066 |
container_title |
Genome Biology and Evolution |
container_volume |
5 |
container_issue |
5 |
container_start_page |
1021 |
op_container_end_page |
1031 |
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1766188135588298752 |