Performance of ancestry-informative SNP and microhaplotype markers

Elaine Y Y Cheung; Christopher Phillips; Mayra Eduardoff; Maria Victoria Lareu; Dennis McNevin

doi:10.1016/j.fsigen.2019.102141

Performance of ancestry-informative SNP and microhaplotype markers

Forensic Sci Int Genet. 2019 Nov:43:102141. doi: 10.1016/j.fsigen.2019.102141. Epub 2019 Aug 8.

Authors

Elaine Y Y Cheung¹, Christopher Phillips², Mayra Eduardoff³, Maria Victoria Lareu², Dennis McNevin⁴

Affiliations

¹ National Centre for Forensic Studies, Faculty of Science and Technology, University of Canberra, Canberra, Australia. Electronic address: Elaine.Cheung@canberra.edu.au.
² Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain.
³ Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.
⁴ Centre for Forensic Science, School of Mathematical and Physical Sciences (MaPS), Faculty of Science, University of Technology Sydney, Sydney, Australia.

PMID: 31442930
DOI: 10.1016/j.fsigen.2019.102141

Abstract

The use of microhaplotypes (MHs) for ancestry inference has added to an increasing number of ancestry-informative markers (AIMs) for forensic application that includes autosomal single nucleotide polymorphisms (SNPs) and insertions/deletions (indels). This study compares bi-allelic and tri-allelic SNPs as well as MH markers for their ability to differentiate African, European, South Asian, East Asian, and American population groups from the 1000 Genomes Phase 3 database. A range of well-established metrics were applied to rank each marker according to the population differentiation potential they measured. These comprised: absolute allele frequency differences (δ); Rosenberg's informativeness for (ancestry) assignment (I_n); the fixation index (F_ST); and the effective number of alleles (A_e). A panel consisting of all three marker types resulted in the lowest mean divergence per population per individual (MDPI = 2.16%) when selected by I_n. However, when marker types were not mixed, MHs were the highest performing markers by most metrics (MDPI < 4%) for differentiation between the five continental populations.

Keywords: Allele frequency; Ancestry-informative markers; Biogeographical ancestry; Microhaplotype; Population differentiation potential; Single nucleotide polymorphism (SNP).

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Databases, Nucleic Acid
Forensic Genetics / methods
Gene Frequency
Genetic Markers*
Haplotypes*
Humans
Polymorphism, Single Nucleotide*
Racial Groups / genetics*

Substances

Genetic Markers