Inferring biogeographic ancestry with compound markers of slow and fast evolving polymorphisms

Bio-geographic ancestry is an area of considerable interest in the medical genetics, anthropology and forensics. Although genome-wide panels are ideal as they provide dense genotyping data, small sets of ancestry informative marker provide a cost-effective way to investigate genetic ancestry and pop...

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Bibliographic Details
Published in:European journal of human genetics : EJHG 2018-11, Vol.26 (11), p.1697-1707
Main Authors: Moriot, Amandine, Santos, Carla, Freire-Aradas, Ana, Phillips, Christopher, Hall, Diana
Format: Article
Language:English
Subjects:
Biogeography
Evolution, Molecular
Forensic science
Genetic Markers
Genome, Human
Genomes
Genotyping
Genotyping Techniques - methods
Genotyping Techniques - standards
Haplotypes
Human Migration
Humans
Mutation
Polymorphism, Genetic
Population genetics
Population structure
Short tandem repeats
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Summary:Bio-geographic ancestry is an area of considerable interest in the medical genetics, anthropology and forensics. Although genome-wide panels are ideal as they provide dense genotyping data, small sets of ancestry informative marker provide a cost-effective way to investigate genetic ancestry and population structure. Here, we investigate the performance of a reduced marker set that combine different types of autosomal markers through haplotype analysis. In particular, recently described DIP-STR markers should offer the advantage of comprising both, low mutation rate Indels (DIPs), to study human history over longer time scale; and high mutation rate STRs, to trace relatively recent demographic events. In this study, we assessed the ability of an initial set of 23 DIP-STRs to distinguish major population groups using the HGDP-CEPH reference samples. The results obtained applying the STRUCTURE algorithm show that the discrimination capacity of the DIP-STRs is comparable to currently used small-scale ancestry informative markers by approaching seven major demographic groups. Yet, the DIP-STRs show an improved success rate in assigning individuals to populations of Europe and Middle East. These data show a remarkable ability of a preliminary set of 23 DIP-STR markers to infer major biogeographic origins. A novel set of DIP-STRs preselected to contain ancestry information should lead to further improvements.
ISSN:1018-4813
1476-5438
DOI:10.1038/s41431-018-0215-2