Comparison of mitotyper rules and phylogenetic-based mtDNA nomenclature systems

A consistent nomenclature scheme is necessary to characterize a forensic mitochondrial DNA (mtDNA) haplotype. A standard nomenclature, called the Mitotyper Rules™, has been developed that applies typing rules in a hierarchical manner reflecting the forensic practitioner's nomenclature preferences. In this work, an empirical comparison between the revised hierarchical nomenclature rules and the phylogenetic approach to mtDNA type description has been conducted on 5173 samples from the phylogenetically typed European Mitochondrial DNA Population database (EMPOP) to identify the degree and significance of any differences. The comparison of the original EMPOP types and the results of retyping these sequences using the Mitotyper Rules demonstrates a high degree of concordance between the two alignment schemes. Differences in types resulted mainly because the Mitotyper Rules selected an alignment with the fewest number of differences compared with the rCRS. In addition, several identical regions were described in more than one way in the EMPOP dataset, demonstrating a limitation of a solely phylogenetic approach in that it may not consistently type nonhaplogroup-specific sites. Using a rule-based approach, commonly occurring as well as private variants are subjected to the same rules for naming, which is particularly advantageous when typing partial sequence data.