Biogeographic assignment with the MHappaMundi microhaplotype panel using decomposable graphical models

Ancestry-informative microhaplotypes (MHs) were proposed as an alternative to single nucleotide polymorphisms (SNPs) for biogeographical analysis. However, estimation of biogeographic background from MHs is not supported by current assignment software (e.g., Snipper and GenoGeographer), and there is insufficient population data for MHs to allow robust haplotype frequency estimates. In this study, the biogeographical assignment performance of the MHappaMundi MH ancestry panel was evaluated using decomposable graphical models to account for allelic dependence within MH data and estimate haplotype frequencies for all possible haplotypes, including rare and unobserved ones. MHappaMundi data were collected for eight metapopulations (representing 33 subpopulations). Population assignment of MH profiles consisted of an outlier detection test for each reference population prior to calculation of evidential weights to prevent misassignment of individuals whose origin population is unrepresented in the database. Comparison with SNP-based assignments from the Precision ID Ancestry Panel for the same individuals was performed at inter- and intra-continental levels. Fewer MH profiles than SNP profiles were rejected in all populations using the outlier tests. Concordant assignment rates were similar for both MH (94.9%) and SNP (94.7%) data in metapopulations, however, MHs achieved higher concordance rates for subpopulations compared to SNPs (80.2% vs. 54.3%). A total of 4,100,000 MH profiles were simulated to estimate the expected distribution of likelihood ratio (LR) values and theoretical confidence intervals for each combination of populations, providing a basis for the definition of LR thresholds for population assignment. Our results demonstrated that MHappaMundi outperformed the Precision ID Ancestry Panel for population assignment.