The Diversity of REcent and Ancient huMan (DREAM) : A New Microarray for Genetic Anthropology and Genealogy, Forensics, and Personalized Medicine
Elhaik, Eran LU
; Yusuf, Leeban
; Anderson, Ainan I.J.
; Pirooznia, Mehdi
; Arnellos, Dimitrios
; Vilshansky, Gregory
; Ercal, Gunes
; Lu, Yontao
; Webster, Teresa
and Baird, Michael L.
, et al.
(2017)
In Genome Biology and Evolution
9(12).
p.3225-3237
- Abstract
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... (More)
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.
(Less)
- author
- Elhaik, Eran
LU
; Yusuf, Leeban
; Anderson, Ainan I.J.
; Pirooznia, Mehdi
; Arnellos, Dimitrios
; Vilshansky, Gregory
; Ercal, Gunes
; Lu, Yontao
; Webster, Teresa
and Baird, Michael L.
, et al. (More)
- Elhaik, Eran
LU
; Yusuf, Leeban
; Anderson, Ainan I.J.
; Pirooznia, Mehdi
; Arnellos, Dimitrios
; Vilshansky, Gregory
; Ercal, Gunes
; Lu, Yontao
; Webster, Teresa
; Baird, Michael L.
and Esposito, Umberto
(Less)
- publishing date
- 2017-12-01
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- ancient DNA, archaic DNA, biogeography, CNVs, forensics, population genetics
- in
- Genome Biology and Evolution
- volume
- 9
- issue
- 12
- pages
- 13 pages
- publisher
- Oxford University Press
- external identifiers
-
- pmid:29165562
- scopus:85042685107
- ISSN
- 1759-6653
- DOI
- 10.1093/gbe/evx237
- language
- English
- LU publication?
- no
- id
- 3cefc823-8b98-43bf-a5a9-00126095ecc5
- date added to LUP
- 2018-03-15 14:31:58
- date last changed
- 2024-07-08 10:56:33
@article{3cefc823-8b98-43bf-a5a9-00126095ecc5,
abstract = {{<p>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.</p>}},
author = {{Elhaik, Eran and Yusuf, Leeban and Anderson, Ainan I.J. and Pirooznia, Mehdi and Arnellos, Dimitrios and Vilshansky, Gregory and Ercal, Gunes and Lu, Yontao and Webster, Teresa and Baird, Michael L. and Esposito, Umberto}},
issn = {{1759-6653}},
keywords = {{ancient DNA; archaic DNA; biogeography; CNVs; forensics; population genetics}},
language = {{eng}},
month = {{12}},
number = {{12}},
pages = {{3225--3237}},
publisher = {{Oxford University Press}},
series = {{Genome Biology and Evolution}},
title = {{The Diversity of REcent and Ancient huMan (DREAM) : A New Microarray for Genetic Anthropology and Genealogy, Forensics, and Personalized Medicine}},
url = {{http://dx.doi.org/10.1093/gbe/evx237}},
doi = {{10.1093/gbe/evx237}},
volume = {{9}},
year = {{2017}},
}