Cheung,E.Y.Y.; Phillips,C.; Eduardoff,M.; Lareu,M.V.; McNevin,D.;
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 (delta); 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.
Forensic Sci Int Genet 2019 43:102141