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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Main Authors: 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
Format: Article in Journal/Newspaper
Language:English
Published: Oxford University Press (OUP)
Subjects:
Online Access:https://hdl.handle.net/20.500.12727/6332
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spelling 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
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