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...
Published in: | Genome Biology and Evolution |
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Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
Other Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
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2013
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Online Access: | http://hdl.handle.net/11568/209049 https://doi.org/10.1093/gbe/evt066 https://academic.oup.com/gbe/article/5/5/1021/611342 |
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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. TheGenoChip includes ancestry informativemarkers obtained for over 450 human populations, an ancient human (Saqqaq), and two archaic hominins (Neanderthal and Denisovan) and was designed to identify all knownY-chromosome andmtDNAhaplogroups. The chip was carefully vetted to avoid inclusion ofmedically 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 highestmean 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 SNPswithout any known health,medical, or phenotypic relevance, the GenoChip is a useful tool for genetic ... |
author2 |
Elhaik, E Greenspan, E Staats, S Krahn, T Tyler-Smith, C Xue, Y Tofanelli, S Francalacci, P Cucca, F Pagani, Luca Jin, L Li, H Schurr, Tg Greenspan, B Spencer Wells, R Acosta, O Adhikarla, S Adler, Cj Balanovska, E Balanovsky, O Bertranpetit, J Clarke, Ac Comas, D Cooper, A Dulik, Mc Gaieski, Jb Ganesh Prasad, Ak Haak, W Haber, M Kaplan, Me Lacerda, Dr Li, S Martinez-Cruz, B Matisoo-Smith, Ea Merchant, Nc Mitchell, Jr Owings, Ac Parida, L Pitchappan, R Platt, De Quintana-Murci, L Renfrew, C Royyuru, Ak Sandoval, Jr Santhakumari, Av Santos, Fr Der Sarkissian, Csi Soodyall, S Soria Hernanz, Df Swamikrishnan, P |
format |
Article in Journal/Newspaper |
author |
Elhaik E Greenspan E Staats S Krahn T Tyler-Smith C Xue Y Tofanelli S Francalacci P Cucca F Pagani Luca Jin L Li H Schurr TG Greenspan B Spencer Wells R Acosta O Adhikarla S Adler CJ Balanovska E Balanovsky O Bertranpetit J Clarke AC Comas D Cooper A Dulik MC Gaieski JB Ganesh Prasad AK Haak W Haber M Kaplan ME Lacerda DR Li S Martinez-Cruz B Matisoo-Smith EA Merchant NC Mitchell JR Owings AC Parida L Pitchappan R Platt DE Quintana-Murci L Renfrew C Royyuru AK Sandoval JR Santhakumari AV Santos FR Der Sarkissian CSI Soodyall S Soria Hernanz DF Swamikrishnan P Vieira PP Vilar MG Zalloua PA Ziegle JS |
spellingShingle |
Elhaik E Greenspan E Staats S Krahn T Tyler-Smith C Xue Y Tofanelli S Francalacci P Cucca F Pagani Luca Jin L Li H Schurr TG Greenspan B Spencer Wells R Acosta O Adhikarla S Adler CJ Balanovska E Balanovsky O Bertranpetit J Clarke AC Comas D Cooper A Dulik MC Gaieski JB Ganesh Prasad AK Haak W Haber M Kaplan ME Lacerda DR Li S Martinez-Cruz B Matisoo-Smith EA Merchant NC Mitchell JR Owings AC Parida L Pitchappan R Platt DE Quintana-Murci L Renfrew C Royyuru AK Sandoval JR Santhakumari AV Santos FR Der Sarkissian CSI Soodyall S Soria Hernanz DF Swamikrishnan P Vieira PP Vilar MG Zalloua PA Ziegle JS The GenoChip: A New Tool for Genetic Anthropology |
author_facet |
Elhaik E Greenspan E Staats S Krahn T Tyler-Smith C Xue Y Tofanelli S Francalacci P Cucca F Pagani Luca Jin L Li H Schurr TG Greenspan B Spencer Wells R Acosta O Adhikarla S Adler CJ Balanovska E Balanovsky O Bertranpetit J Clarke AC Comas D Cooper A Dulik MC Gaieski JB Ganesh Prasad AK Haak W Haber M Kaplan ME Lacerda DR Li S Martinez-Cruz B Matisoo-Smith EA Merchant NC Mitchell JR Owings AC Parida L Pitchappan R Platt DE Quintana-Murci L Renfrew C Royyuru AK Sandoval JR Santhakumari AV Santos FR Der Sarkissian CSI Soodyall S Soria Hernanz DF Swamikrishnan P Vieira PP Vilar MG Zalloua PA Ziegle JS |
author_sort |
Elhaik E |
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 |
publishDate |
2013 |
url |
http://hdl.handle.net/11568/209049 https://doi.org/10.1093/gbe/evt066 https://academic.oup.com/gbe/article/5/5/1021/611342 |
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ENVELOPE(-112.453,-112.453,57.591,57.591) |
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The ''Y'' |
geographic_facet |
The ''Y'' |
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Saqqaq |
genre_facet |
Saqqaq |
op_relation |
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info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.1093/gbe/evt066 |
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Genome Biology and Evolution |
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1021 |
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ftunivpisairis:oai:arpi.unipi.it:11568/209049 2024-04-14T08:19:04+00:00 The GenoChip: A New Tool for Genetic Anthropology Elhaik E Greenspan E Staats S Krahn T Tyler-Smith C Xue Y Tofanelli S Francalacci P Cucca F Pagani Luca Jin L Li H Schurr TG Greenspan B Spencer Wells R Acosta O Adhikarla S Adler CJ Balanovska E Balanovsky O Bertranpetit J Clarke AC Comas D Cooper A Dulik MC Gaieski JB Ganesh Prasad AK Haak W Haber M Kaplan ME Lacerda DR Li S Martinez-Cruz B Matisoo-Smith EA Merchant NC Mitchell JR Owings AC Parida L Pitchappan R Platt DE Quintana-Murci L Renfrew C Royyuru AK Sandoval JR Santhakumari AV Santos FR Der Sarkissian CSI Soodyall S Soria Hernanz DF Swamikrishnan P Vieira PP Vilar MG Zalloua PA Ziegle JS Elhaik, E Greenspan, E Staats, S Krahn, T Tyler-Smith, C Xue, Y Tofanelli, S Francalacci, P Cucca, F Pagani, Luca Jin, L Li, H Schurr, Tg Greenspan, B Spencer Wells, R Acosta, O Adhikarla, S Adler, Cj Balanovska, E Balanovsky, O Bertranpetit, J Clarke, Ac Comas, D Cooper, A Dulik, Mc Gaieski, Jb Ganesh Prasad, Ak Haak, W Haber, M Kaplan, Me Lacerda, Dr Li, S Martinez-Cruz, B Matisoo-Smith, Ea Merchant, Nc Mitchell, Jr Owings, Ac Parida, L Pitchappan, R Platt, De Quintana-Murci, L Renfrew, C Royyuru, Ak Sandoval, Jr Santhakumari, Av Santos, Fr Der Sarkissian, Csi Soodyall, S Soria Hernanz, Df Swamikrishnan, P 2013 STAMPA http://hdl.handle.net/11568/209049 https://doi.org/10.1093/gbe/evt066 https://academic.oup.com/gbe/article/5/5/1021/611342 eng eng info:eu-repo/semantics/altIdentifier/pmid/23666864 info:eu-repo/semantics/altIdentifier/wos/WOS:000324593500022 volume:5 issue:5 firstpage:1021 lastpage:1031 numberofpages:11 journal:GENOME BIOLOGY AND EVOLUTION http://hdl.handle.net/11568/209049 doi:10.1093/gbe/evt066 info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-84888821239 https://academic.oup.com/gbe/article/5/5/1021/611342 info:eu-repo/semantics/openAccess info:eu-repo/semantics/article 2013 ftunivpisairis https://doi.org/10.1093/gbe/evt066 2024-03-21T19:07:21Z 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. TheGenoChip includes ancestry informativemarkers obtained for over 450 human populations, an ancient human (Saqqaq), and two archaic hominins (Neanderthal and Denisovan) and was designed to identify all knownY-chromosome andmtDNAhaplogroups. The chip was carefully vetted to avoid inclusion ofmedically 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 highestmean 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 SNPswithout any known health,medical, or phenotypic relevance, the GenoChip is a useful tool for genetic ... Article in Journal/Newspaper Saqqaq ARPI - Archivio della Ricerca dell'Università di Pisa The ''Y'' ENVELOPE(-112.453,-112.453,57.591,57.591) Genome Biology and Evolution 5 5 1021 1031 |