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

Research output: Contribution to journalArticle

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 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.

Details

Authors
  • Eran Elhaik
  • Leeban Yusuf
  • Ainan I.J. Anderson
  • Mehdi Pirooznia
  • Dimitrios Arnellos
  • Gregory Vilshansky
  • Gunes Ercal
  • Yontao Lu
  • Teresa Webster
  • Michael L. Baird
  • Umberto Esposito
External organisations
  • University of Sheffield
  • Johns Hopkins University
  • No affiliation available (private)
  • Lund University
  • National Geographic Society
  • Southern Illinois University, Edwardsville
  • Thermo Fisher Scientific Inc.
  • DNA Diagnostics Center, Fairfield
Research areas and keywords

Subject classification (UKÄ) – MANDATORY

  • Genetics

Keywords

  • ancient DNA, archaic DNA, biogeography, CNVs, forensics, population genetics
Original languageEnglish
Pages (from-to)3225-3237
Number of pages13
JournalGenome Biology and Evolution
Volume9
Issue number12
Publication statusPublished - 2017 Dec 1
Publication categoryResearch
Peer-reviewedYes
Externally publishedYes