Evaluating 130 microhaplotypes across a global set of 83 populations

TLDR

Short tandem repeat markers dominate forensic DNA analysis but suffer from stutter in mixed samples and provide only coarse continental ancestry, prompting interest in more powerful methods such as massively parallel sequencing. The study investigates microhaplotype loci to improve mixture deconvolution and ancestry inference using MPS. The authors identified 130 microhaplotype loci and estimated their allele frequencies across 83 global populations. These loci are highly informative for individual identification and for deconvolving DNA mixtures.

Abstract

Today the primary DNA markers used in forensics are short tandem repeat (STR) polymorphisms (STRPs), initially selected because they are highly polymorphic. However, the increasingly common need to deal with samples with a mixture of DNA from two or more individuals sometimes is complicated by the inherent stutter involved with PCR amplification, especially in strongly unbalanced mixtures when the minor component coincides with the stutter range of the major component. Also, the STRPs in use provide little evidence of ancestry of a single source sample beyond broad "continental" resolution. Methodologies for analyzing DNA have become much more powerful in recent years. Massively parallel sequencing (MPS) is a new method being considered for routine use in forensics. Primarily to aid in mixture deconvolution and avoid the issue of stutter, we have begun to investigate a new type of forensic marker, microhaplotype loci, that will provide useful information on mixtures of DNA and on ancestry when typed using massively parallel sequencing (MPS). We have identified 130 loci and estimated their haplotype (allele) frequencies in 83 different population samples. Many of these loci are shown to be highly informative for individual identification and for mixture identification and deconvolution.