Since a number of investigators have attempted to increase the forensic discrimination of mtDNA testing by accessing variation that occurs outside of the HIV1/HV2 portions of the control region, the work reported in this article sought to determine maximally effective approaches for targeting additional information in the mtDNA-coding region.
Most investigators have attempted to recover addition discrimination in mtDNA coding by sequencing short segments of the coding region that are believed to be particularly variable; however, such efforts have generally failed to appreciate that most variation in the coding region is redundant with information already present in HV1/HV2. This results in an overvaluing of the potential for this approach. An alternative approach involves single nucleotide polymorphism (SNP), which identifies specific bases that provide resolution in specific common HV1/HV2 types and related sequences. The current study examined several relevant data sets wherein the latter approach was found to perform appreciably better than sequencing selected short portions of the coding region. This remained true even when only synonymous variation was targeted to minimize the potential for problems stemming from discovery of mutations that have reportedly been related to disease. Thus, the synonymous SNP strategy described in Coble et al. (2004) is more effective than the sequence-based strategies presented to date. An initial disadvantage of the SNP approach, however, is the large amount of work required to obtain the necessary knowledge of mtGenome variation in order to accurately target maximally discriminatory sites. This disadvantage is tolerable, since once the information is obtained, it is available for applications. 1 figure and 26 references