Evaluation of a microhaplotypes panel for forensic genetics using massive parallel sequencing technology

Abstract

Massive parallel DNA sequencing (MPS) makes it possible to explore a new type of genetic marker, known as microhaplotypes or microhaps. These loci were recently introduced in the landscape of forensic genetic and appear to be useful for identification purposes, reconstruction of family relationships, ancestry prediction and DNA mixtures deconvolution. Microhaplotypes loci, based on 89 loci in ALFRED, were selected and their genetic variations in 100 Italian individuals were evaluated by using MPS, in order to make inference about utility of a set of microhaps in forensic genetics. After MPS, the panel was reduced to 87 microhaps, comprised of 266 different SNPs and spread across 22 human autosomes. Genotype and haplotype frequencies were estimated, as well as the effective number of alleles at each locus (A_e), which relates to the usefulness of the locus in resolution of relationships and deconvolution of DNA mixtures. Overall, the A_e values for the 87 microhaps range from 1.010 to 8.344, with about 80% showing values greater than 2.0. Noteworthy, 32 microhaps display A_e values greater than 3.0 and 18 loci A_e above 4.0. To explore the suitability of microhaplotypes in mixture deconvolution, the probability of detecting a mixture, as a function of A_e, was inferred for different groups of loci. Considering the fourteen loci with A_e between 3.0 and 3.999 the probability of detecting a mixture was at least 0.99973, while considering the ten loci with Ae between 4.0 and 4.999 the probability was at least 0.99998. Moreover, when considering just the six loci with A_e between 5.0 and 5.999 the probability of detecting a mixture was at least 0.99984, while when considering just the two loci with A_e above 6 the probability was 0.97228. Combining these 32 MH loci, the theoretical probability of detecting a mixture was 0.999999999999973. These results make the subset of 32 loci with A_e above three informative for mixture resolution. The individual matching probabilities (PI) of the 87 microhaps ranged from 0.032 to 0.9802. Considering the 32 microhap loci with A_e greater than 3.0, the cumulative PI value was 1.6 × 10^-33, while considering the 18 microhap loci with A_e above 4.0, the cumulative PI value was 2.34 × 10^-21. Overall the results of this study confirmed the utility of microhaps in forensic genetics.

Keywords: Individual identification; Massive parallel sequencing; Matching probability.; Microhaplotypes; Mixture deconvolution; Single nucleotide polymorphisms.