State of the Art for Microhaplotypes

Abstract

In recent years, the number of publications on microhaplotypes has averaged more than a dozen papers annually. Many have contributed to a significant increase in the number of highly polymorphic microhaplotype loci. This increase allows microhaplotypes to be very informative in four main areas of forensic uses of DNA: individualization, ancestry inference, kinship analysis, and mixture deconvolution. The random match Probability (RMP) can be as small as 10−100 for a large panel of microhaplotypes. It is possible to measure the heterozygosity of an MH as the effective number of alleles (Ae). Ae > 7.5 exists for African populations and >4.5 exists for Native American populations for a smaller panel of two dozen selected microhaplotypes. Using STRUCTURE, at least 10 different ancestral clusters can be defined by microhaplotypes. The Ae for a locus is also identical to the Paternity Index (PI), the measure of how informative a locus will be in parentage testing. High Ae loci can also be useful in missing persons cases. Finally, high Ae microhaplotypes allow the near certainty of seeing multiple additional alleles in a mixture of two or more individuals in a DNA sample. In summary, a panel of higher Ae microhaplotypes can outperform the standard CODIS markers.

An MPS-Based 50plex Microhaplotype Assay for Forensic DNA Analysis

“…Therefore, the selection of the most informative marker for familial identification depends on the A e value. The A e value is also an important index for evaluating the ability of a mixture analysis [ 49 ]. For our 50-plex MH panel, Het values of more than 98% (49/50) of MHs were >0.40, A e values of more than 80% (40/50) MHs > 3.0, and CDP and CPE were 1–3.109 × 10 −49 and 1–8.727 × 10 −16 , respectively ( Supplementary Table S4 ).…”

Recent advances in forensic biology and forensic DNA typing: INTERPOL review 2019–2022

“…Compared to STR markers, MHs do not have stutter artifacts (which complicate mixture interpretation), can be designed with shorter amplicon lengths in some cases (which benefits recovery of genetic information from degraded DNA samples), possess a higher degree of polymorphism compared to single SNP loci (which benefits discrimination power), and exhibit low mutation rates (which enables relationship testing and biogeographical ancestry inference). Thus, MH markers bring advantages to human identification, ancestry inference, kinship analysis, and mixture deconvolution to potentially assist missing person investigations, relationship testing, and forensic casework as discussed in several recent reviews [ 16 , 511 ]. A new database, MicroHapDB, has compiled information on over 400 published MH markers and frequency data from 26 global population groups [ 512 ].…”