The Diversity of REcent and Ancient huMan (DREAM): A New Microarray for Genetic Anthropology and Genealogy, Forensics, and Personalized Medicine

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The Diversity of REcent and Ancient huMan (DREAM) : A New Microarray for Genetic Anthropology and Genealogy, Forensics, and Personalized Medicine. / Elhaik, Eran; Yusuf, Leeban; Anderson, Ainan I.J.; Pirooznia, Mehdi; Arnellos, Dimitrios; Vilshansky, Gregory; Ercal, Gunes; Lu, Yontao; Webster, Teresa; Baird, Michael L.; Esposito, Umberto.

I: Genome Biology and Evolution, Vol. 9, Nr. 12, 01.12.2017, s. 3225-3237.

Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

Harvard

Elhaik, E, Yusuf, L, Anderson, AIJ, Pirooznia, M, Arnellos, D, Vilshansky, G, Ercal, G, Lu, Y, Webster, T, Baird, ML & Esposito, U 2017, 'The Diversity of REcent and Ancient huMan (DREAM): A New Microarray for Genetic Anthropology and Genealogy, Forensics, and Personalized Medicine', Genome Biology and Evolution, vol. 9, nr. 12, s. 3225-3237. https://doi.org/10.1093/gbe/evx237

APA

CBE

Elhaik E, Yusuf L, Anderson AIJ, Pirooznia M, Arnellos D, Vilshansky G, Ercal G, Lu Y, Webster T, Baird ML, Esposito U. 2017. The Diversity of REcent and Ancient huMan (DREAM): A New Microarray for Genetic Anthropology and Genealogy, Forensics, and Personalized Medicine. Genome Biology and Evolution. 9(12):3225-3237. https://doi.org/10.1093/gbe/evx237

MLA

Vancouver

Author

Elhaik, Eran ; Yusuf, Leeban ; Anderson, Ainan I.J. ; Pirooznia, Mehdi ; Arnellos, Dimitrios ; Vilshansky, Gregory ; Ercal, Gunes ; Lu, Yontao ; Webster, Teresa ; Baird, Michael L. ; Esposito, Umberto. / The Diversity of REcent and Ancient huMan (DREAM) : A New Microarray for Genetic Anthropology and Genealogy, Forensics, and Personalized Medicine. I: Genome Biology and Evolution. 2017 ; Vol. 9, Nr. 12. s. 3225-3237.

RIS

TY - JOUR

T1 - The Diversity of REcent and Ancient huMan (DREAM)

T2 - Genome Biology and Evolution

AU - Elhaik, Eran

AU - Yusuf, Leeban

AU - Anderson, Ainan I.J.

AU - Pirooznia, Mehdi

AU - Arnellos, Dimitrios

AU - Vilshansky, Gregory

AU - Ercal, Gunes

AU - Lu, Yontao

AU - Webster, Teresa

AU - Baird, Michael L.

AU - Esposito, Umberto

PY - 2017/12/1

Y1 - 2017/12/1

N2 - The human population displays wide variety in demographic history, ancestry, content of DNA derived from hominins or ancient populations, adaptation, traits, copy number variation, drug response, and more. These polymorphisms are of broad interest to population geneticists, forensics investigators, and medical professionals. Historically, much of that knowledge was gained from population survey projects. Although many commercial arrays exist for genome-wide single-nucleotide polymorphism genotyping, their design specifications are limited and they do not allow a full exploration of biodiversity. We thereby aimed to design the Diversity of REcent and Ancient huMan (DREAM) - an all-inclusive microarray that would allow both identification of known associations and exploration of standing questions in genetic anthropology, forensics, and personalized medicine. DREAM includes probes to interrogate ancestry informative markers obtained from over 450 human populations, over 200 ancient genomes, and 10 archaic hominins. DREAM can identify 94% and 61% of all known Y and mitochondrial haplogroups, respectively, and was vetted to avoid interrogation of clinically relevant markers. To demonstrate its capabilities, we compared its F ST distributions with those of the 1000 Genomes Project and commercial arrays. Although all arrays yielded similarly shaped (inverse J) F ST distributions, DREAM's autosomal and X-chromosomal distributions had the highest mean F ST, attesting to its ability to discern subpopulations. DREAM performances are further illustrated in biogeographical, identical by descent, and copy number variation analyses. In summary, with approximately 800,000 markers spanning nearly 2,000 genes, DREAM is a useful tool for genetic anthropology, forensic, and personalized medicine studies.

AB - The human population displays wide variety in demographic history, ancestry, content of DNA derived from hominins or ancient populations, adaptation, traits, copy number variation, drug response, and more. These polymorphisms are of broad interest to population geneticists, forensics investigators, and medical professionals. Historically, much of that knowledge was gained from population survey projects. Although many commercial arrays exist for genome-wide single-nucleotide polymorphism genotyping, their design specifications are limited and they do not allow a full exploration of biodiversity. We thereby aimed to design the Diversity of REcent and Ancient huMan (DREAM) - an all-inclusive microarray that would allow both identification of known associations and exploration of standing questions in genetic anthropology, forensics, and personalized medicine. DREAM includes probes to interrogate ancestry informative markers obtained from over 450 human populations, over 200 ancient genomes, and 10 archaic hominins. DREAM can identify 94% and 61% of all known Y and mitochondrial haplogroups, respectively, and was vetted to avoid interrogation of clinically relevant markers. To demonstrate its capabilities, we compared its F ST distributions with those of the 1000 Genomes Project and commercial arrays. Although all arrays yielded similarly shaped (inverse J) F ST distributions, DREAM's autosomal and X-chromosomal distributions had the highest mean F ST, attesting to its ability to discern subpopulations. DREAM performances are further illustrated in biogeographical, identical by descent, and copy number variation analyses. In summary, with approximately 800,000 markers spanning nearly 2,000 genes, DREAM is a useful tool for genetic anthropology, forensic, and personalized medicine studies.

KW - ancient DNA

KW - archaic DNA

KW - biogeography

KW - CNVs

KW - forensics

KW - population genetics

UR - http://www.scopus.com/inward/record.url?scp=85042685107&partnerID=8YFLogxK

U2 - 10.1093/gbe/evx237

DO - 10.1093/gbe/evx237

M3 - Article

VL - 9

SP - 3225

EP - 3237

JO - Genome Biology and Evolution

JF - Genome Biology and Evolution

SN - 1759-6653

IS - 12

ER -