Performance of ancestry-informative SNP and microhaplotype markers

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

Research output: Contribution to journalArticlepeer-review

35 Citations (Scopus)


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 (In); the fixation index (FST); and the effective number of alleles (Ae). A panel consisting of all three marker types resulted in the lowest mean divergence per population per individual (MDPI = 2.16%) when selected by In. 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.

Original languageEnglish
Article number102141
Pages (from-to)1-7
Number of pages7
JournalForensic Science International: Genetics
Publication statusPublished - Nov 2019


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