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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
The GenoChip: A new tool for genetic anthropology
Genome Biology and Evolution, Volume 5, No. 5, Year 2013
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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. © The Author(s) 2013. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Available Materials
https://efashare.b-cdn.net/share/pmc/articles/PMC3673633/bin/supp_5_5_1021__index.html
https://efashare.b-cdn.net/share/pmc/articles/PMC3673633/bin/supp_evt066_Elhaik2013_-_Supplementary_Materials2.doc
https://efashare.b-cdn.net/share/pmc/articles/PMC3673633/bin/supp_evt066_Elhaik2013_-_Table_S1.xlsx
https://efashare.b-cdn.net/share/pmc/articles/PMC3673633/bin/supp_evt066_Elhaik2013_-_Table_S2.xlsx
Authors & Co-Authors
Elhaik, Eran
United States, Baltimore
Johns Hopkins University
Greenspan, Elliott
United States, Houston
Family Tree Dna
Staats, Sean
United States, Houston
Family Tree Dna
Krahn, Thomas
United States, Houston
Family Tree Dna
Tyler-Smith, Chris
United Kingdom, London
Wellcome Trust
Xue, Yali
United Kingdom, London
Wellcome Trust
Tofanelli, Sergio
Italy, Pisa
Università Di Pisa
Francalacci, Paolo
Italy, Sassari
Università Degli Studi Di Sassari
Cucca, Francesco
Italy, Monserrato
Cnr Istituto Di Ricerca Genetica e Biomedica
Pagani, Luca
United Kingdom, London
Wellcome Trust
United Kingdom, Cambridge
University of Cambridge
Jin, Li
China, Shanghai
School of Life Sciences Fudan University
Li, Hui
China, Shanghai
School of Life Sciences Fudan University
Schurr, Theodore G.
United States, Philadelphia
University of Pennsylvania
Greenspan, Bennett
United States, Houston
Family Tree Dna
Wells, R. Spencer
United States, Washington, D.c.
National Geographic Society
Acosta, Oscar
Peru, Lima
Universidad de San Martín de Porres
Adhikarla, Syama
India, Madurai
Madurai Kamaraj University
Adler, Christina J.
Australia, Adelaide
The University of Adelaide
Balanovska, Elena V.
Russian Federation, Moscow
Research Centre for Medical Genetics
Balanovsky, Oleg P.
Russian Federation, Moscow
Research Centre for Medical Genetics
Bertranpetit, Jaume
Spain, Barcelona
Universitat Pompeu Fabra Barcelona
Clarke, Andrew C.
New Zealand, Dunedin
University of Otago
Comas, D.
Spain, Barcelona
Universitat Pompeu Fabra Barcelona
Cooper, Alan C.
Australia, Adelaide
The University of Adelaide
Dulik, Matthew C.
United States, Philadelphia
University of Pennsylvania
Gaieski, Jill Bennett
United States, Philadelphia
University of Pennsylvania
Ganesh Prasad, Arun Kumar
India, Madurai
Madurai Kamaraj University
Haak, Wolfgang
Australia, Adelaide
The University of Adelaide
Haber, Marc E.
Lebanon, Beirut
Lebanese American University
Kaplan, Matthew E.
United States, Tucson
The University of Arizona
Lacerda, Daniela Rodrigues
Brazil, Belo Horizonte
Universidade Federal de Minas Gerais
Li, Shilin
China, Shanghai
Fudan University
Martínez-Cruz, Begoña
Spain, Barcelona
Universitat Pompeu Fabra Barcelona
Matisoo-Smith, Elizabeth A.
New Zealand, Dunedin
University of Otago
Merchant, Nirav C.
United States, Tucson
The University of Arizona
Mitchell, John R.
United States, Philadelphia
University of Pennsylvania
Owings, Amanda C.
United States, Philadelphia
University of Pennsylvania
Parida, Laxmi P.
United States, Armonk
International Business Machines
Pitchappan, Ramasamy M.
India, Madurai
Madurai Kamaraj University
Platt, Daniel E.
United States, Armonk
International Business Machines
Quintana-Murci, Lluís
France, Paris
Institut Pasteur, Paris
Renfrew, Colin
United Kingdom, Cambridge
University of Cambridge
Royyuru, Ajay K.
United States, Armonk
International Business Machines
Sandoval, José Raul
Peru, Lima
Universidad de San Martín de Porres
Brazil, Belo Horizonte
Universidade Federal de Minas Gerais
Santhakumari, Arun Varatharajan
India, Madurai
Madurai Kamaraj University
Santos, Fabrício Rodrigues Dos
Brazil, Belo Horizonte
Universidade Federal de Minas Gerais
Der Sarkissian, Clio S.I.
Australia, Adelaide
The University of Adelaide
Soodyall, Himla
South Africa, Johannesburg
National Health Laboratory Service
Soria-Hernanz, David F.
United States, Columbia
National Geographic Society
Swamikrishnan, Pandikumar
United States, Armonk
International Business Machines
Vieira, Pedro Paulo R.
Brazil, Rio de Janeiro
Universidade Federal do Rio de Janeiro
Vilar, Miguel G.
United States, Philadelphia
University of Pennsylvania
Zalloua, Pierre A.
Lebanon, Beirut
Lebanese American University
Ziegle, Janet S.
United States, Foster City
Vitapath Genetics
Statistics
Citations: 55
Authors: 54
Affiliations: 26
Identifiers
Doi:
10.1093/gbe/evt066
e-ISSN:
17596653
Research Areas
Genetics And Genomics
Study Design
Cross Sectional Study