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 non-medical, 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 u...
Published in: | Genome Biology and Evolution |
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Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
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2013
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Online Access: | http://hdl.handle.net/11388/45681 https://doi.org/10.1093/gbe/evt066 |
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The Genographic Project is an international effort aimed at charting human migratory history. The project is nonprofit and non-medical, 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 F-ST distributions of GenoChip SNPs to those of two commercial arrays. Although all arrays yielded similarly shaped (inverse J) F-ST distributions, the GenoChip autosomal and X-chromosomal distributions had the highest mean F-ST, 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 ... |
author2 |
Elhaik, E. Greenspan, E. Staats, S. Krahn, T. Tyler-Smith, C. Xue, Y. Tofanelli, S. Francalacci, P. Cucca, F. Pagani, L. Jin, L. Li, H. Schurr, T. Greenspan, B. Spencer Wells, R. Acosta, O. Adhikarla, S. Adler, C. Balanovska, E. Balanovsky, O. Bertranpetit, J. Clarke, A. Comas, D. Cooper, A. Dulik, M. Gaieski, J. Ganesh Prasad, A. Haak, W. Haber, M. Kaplan, M. Lacerda, D. Li, S. Martinez-Cruz, B. Matisoo-Smith, E. Merchant, N. Mitchell, J. Owings, A. Parida, L. Pitchappan, R. Platt, D. Quintana-Murci, L. Renfrew, C. Royyuru, A. Sandoval, J. Santhakumari, A. Santos, F. Der Sarkissian, C. Soodyall, S. Soria Hernanz, D. 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, L. Jin, L. Li, H. Schurr, T. Greenspan, B. Spencer Wells, R. Acosta, O. Adhikarla, S. Adler, C. Balanovska, E. Balanovsky, O. Bertranpetit, J. Clarke, A. Comas, D. Cooper, A. Dulik, M. Gaieski, J. Ganesh Prasad, A. Haak, W. Haber, M. Kaplan, M. Lacerda, D. Li, S. Martinez-Cruz, B. Matisoo-Smith, E. Merchant, N. Mitchell, J. Owings, A. Parida, L. Pitchappan, R. Platt, D. Quintana-Murci, L. Renfrew, C. Royyuru, A. Sandoval, J. Santhakumari, A. Santos, F. Der Sarkissian, C. Soodyall, S. Soria Hernanz, D. Swamikrishnan, P. Vieira, P. Vilar, M. Zalloua, P. Ziegle, J. |
spellingShingle |
Elhaik, E. Greenspan, E. Staats, S. Krahn, T. Tyler-Smith, C. Xue, Y. Tofanelli, S. Francalacci, P. Cucca, F. Pagani, L. Jin, L. Li, H. Schurr, T. Greenspan, B. Spencer Wells, R. Acosta, O. Adhikarla, S. Adler, C. Balanovska, E. Balanovsky, O. Bertranpetit, J. Clarke, A. Comas, D. Cooper, A. Dulik, M. Gaieski, J. Ganesh Prasad, A. Haak, W. Haber, M. Kaplan, M. Lacerda, D. Li, S. Martinez-Cruz, B. Matisoo-Smith, E. Merchant, N. Mitchell, J. Owings, A. Parida, L. Pitchappan, R. Platt, D. Quintana-Murci, L. Renfrew, C. Royyuru, A. Sandoval, J. Santhakumari, A. Santos, F. Der Sarkissian, C. Soodyall, S. Soria Hernanz, D. Swamikrishnan, P. Vieira, P. Vilar, M. Zalloua, P. Ziegle, J. 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, L. Jin, L. Li, H. Schurr, T. Greenspan, B. Spencer Wells, R. Acosta, O. Adhikarla, S. Adler, C. Balanovska, E. Balanovsky, O. Bertranpetit, J. Clarke, A. Comas, D. Cooper, A. Dulik, M. Gaieski, J. Ganesh Prasad, A. Haak, W. Haber, M. Kaplan, M. Lacerda, D. Li, S. Martinez-Cruz, B. Matisoo-Smith, E. Merchant, N. Mitchell, J. Owings, A. Parida, L. Pitchappan, R. Platt, D. Quintana-Murci, L. Renfrew, C. Royyuru, A. Sandoval, J. Santhakumari, A. Santos, F. Der Sarkissian, C. Soodyall, S. Soria Hernanz, D. Swamikrishnan, P. Vieira, P. Vilar, M. Zalloua, P. Ziegle, J. |
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 |
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2013 |
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http://hdl.handle.net/11388/45681 https://doi.org/10.1093/gbe/evt066 |
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Genome Biology and Evolution |
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ftsassariuniiris:oai:iris.uniss.it:11388/45681 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, L. Jin, L. Li, H. Schurr, T. Greenspan, B. Spencer Wells, R. Acosta, O. Adhikarla, S. Adler, C. Balanovska, E. Balanovsky, O. Bertranpetit, J. Clarke, A. Comas, D. Cooper, A. Dulik, M. Gaieski, J. Ganesh Prasad, A. Haak, W. Haber, M. Kaplan, M. Lacerda, D. Li, S. Martinez-Cruz, B. Matisoo-Smith, E. Merchant, N. Mitchell, J. Owings, A. Parida, L. Pitchappan, R. Platt, D. Quintana-Murci, L. Renfrew, C. Royyuru, A. Sandoval, J. Santhakumari, A. Santos, F. Der Sarkissian, C. Soodyall, S. Soria Hernanz, D. Swamikrishnan, P. Vieira, P. Vilar, M. Zalloua, P. Ziegle, J. Elhaik, E. Greenspan, E. Staats, S. Krahn, T. Tyler-Smith, C. Xue, Y. Tofanelli, S. Francalacci, P. Cucca, F. Pagani, L. Jin, L. Li, H. Schurr, T. Greenspan, B. Spencer Wells, R. Acosta, O. Adhikarla, S. Adler, C. Balanovska, E. Balanovsky, O. Bertranpetit, J. Clarke, A. Comas, D. Cooper, A. Dulik, M. Gaieski, J. Ganesh Prasad, A. Haak, W. Haber, M. Kaplan, M. Lacerda, D. Li, S. Martinez-Cruz, B. Matisoo-Smith, E. Merchant, N. Mitchell, J. Owings, A. Parida, L. Pitchappan, R. Platt, D. Quintana-Murci, L. Renfrew, C. Royyuru, A. Sandoval, J. Santhakumari, A. Santos, F. Der Sarkissian, C. Soodyall, S. Soria Hernanz, D. Swamikrishnan, P. 2013 http://hdl.handle.net/11388/45681 https://doi.org/10.1093/gbe/evt066 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/11388/45681 doi:10.1093/gbe/evt066 info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-84888821239 info:eu-repo/semantics/article 2013 ftsassariuniiris https://doi.org/10.1093/gbe/evt066 2024-03-15T04:05:43Z The Genographic Project is an international effort aimed at charting human migratory history. The project is nonprofit and non-medical, 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 F-ST distributions of GenoChip SNPs to those of two commercial arrays. Although all arrays yielded similarly shaped (inverse J) F-ST distributions, the GenoChip autosomal and X-chromosomal distributions had the highest mean F-ST, 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 ... Article in Journal/Newspaper Saqqaq CINECA IRIS Universitá Degli Studi di Sassari The ''Y'' ENVELOPE(-112.453,-112.453,57.591,57.591) Genome Biology and Evolution 5 5 1021 1031 |