TY - JOUR
T1 - The GenoChip
T2 - A new tool for genetic anthropology
AU - the Genographic Consortium
AU - Elhaik, Eran
AU - Greenspan, Elliott
AU - Staats, Sean
AU - Krahn, Thomas
AU - Tyler-Smith, Chris
AU - Xue, Yali
AU - Tofanelli, Sergio
AU - Francalacci, Paolo
AU - Cucca, Francesco
AU - Pagani, Luca
AU - Jin, Li
AU - Li, Hui
AU - Schurr, Theodore G.
AU - Greenspan, Bennett
AU - Spencer Wells, R.
AU - Acosta, Oscar
AU - Adhikarla, Syama
AU - Adler, Christina J.
AU - Balanovska, Elena
AU - Balanovsky, Oleg
AU - Bertranpetit, Jaume
AU - Clarke, Andrew C.
AU - Comas, David
AU - Cooper, Alan
AU - Dulik, Matthew C.
AU - Gaieski, Jill B.
AU - Ganesh Prasad, Arun Kumar
AU - Haak, Wolfgang
AU - Haber, Marc
AU - Kaplan, Matthew E.
AU - Lacerda, Daniela R.
AU - Li, Shilin
AU - Martinez-Cruz, Begona
AU - Matisoo-Smith, Elizabeth A.
AU - Merchant, Nirav C.
AU - Mitchell, John R.
AU - Owings, Amanda C.
AU - Parida, Laxmi
AU - Pitchappan, Ramasamy
AU - Platt, Daniel E.
AU - Quintana-Murci, Lluis
AU - Renfrew, Colin
AU - Royyuru, A. K.
AU - Sandoval, Jose Raul
AU - Santhakumari, Arun Varatharajan
AU - Santos, Fabrıcio R.
AU - Der Sarkissian, Clio S.I.
AU - Soodyall, Himla
AU - Soria Hernanz, David F.
AU - Swamikrishnan, Pandikumar
PY - 2013/5/1
Y1 - 2013/5/1
N2 - 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.
AB - 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.
KW - Aimsfinder
KW - Genetic anthropology
KW - GenoChip
KW - Genographic project
KW - Haplogroups
KW - Population genetics
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UR - http://www.scopus.com/inward/citedby.url?scp=84888821239&partnerID=8YFLogxK
U2 - 10.1093/gbe/evt066
DO - 10.1093/gbe/evt066
M3 - Article
C2 - 23666864
AN - SCOPUS:84888821239
SN - 1759-6653
VL - 5
SP - 1021
EP - 1031
JO - Genome biology and evolution
JF - Genome biology and evolution
IS - 5
ER -