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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ftunisanmartinpo:oai:repositorio.usmp.edu.pe:20.500.12727/6332 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 pp. 1021-1031 application/pdf https://hdl.handle.net/20.500.12727/6332 eng eng Oxford University Press (OUP) https://hdl.handle.net/20.500.12727/6332 info:eu-repo/semantics/openAccess Repositorio Académico USMP Universidad San Martín de Porres - USMP Genética de población Haplotipos Genética humana Especiación genética info:eu-repo/semantics/article ftunisanmartinpo https://doi.org/20.500.12727/6332 2021-07-02T10:44:17Z 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. Article in Journal/Newspaper Saqqaq Universidad San Martín de Porres: Repositorio Academico USMP The ''Y'' ENVELOPE(-112.453,-112.453,57.591,57.591) |
institution |
Open Polar |
collection |
Universidad San Martín de Porres: Repositorio Academico USMP |
op_collection_id |
ftunisanmartinpo |
language |
English |
topic |
Genética de población Haplotipos Genética humana Especiación genética |
spellingShingle |
Genética de población Haplotipos Genética humana Especiación genética 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 The GenoChip: A new tool for genetic anthropology |
topic_facet |
Genética de población Haplotipos Genética humana Especiación genética |
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. |
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 |
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 |
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 (OUP) |
url |
https://hdl.handle.net/20.500.12727/6332 |
long_lat |
ENVELOPE(-112.453,-112.453,57.591,57.591) |
geographic |
The ''Y'' |
geographic_facet |
The ''Y'' |
genre |
Saqqaq |
genre_facet |
Saqqaq |
op_source |
Repositorio Académico USMP Universidad San Martín de Porres - USMP |
op_relation |
https://hdl.handle.net/20.500.12727/6332 |
op_rights |
info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/20.500.12727/6332 |
_version_ |
1766188134009143296 |