This study assessed the utility of using two newly available screening assays for the rapid exclusion of nonmatching samples in mitochondrial DNA (mtDNA) analysis.
The primary advantage of mtDNA is its presence in high copy number within cells, such that it is more likely to be recovered from highly degraded specimens. A significant disadvantage to traditional forensic mtDNA analysis, however, is the time-consuming, labor-intensive procedure for generating and reviewing the 610 nucleotides of sequence information commonly targeted in hypervariable regions I and II (HVI and HVII) of the control region. In addition, common haplotypes exist in HVI/HVII mtDNA sequences that can reduce the ability to differentiate two unrelated samples. This paper describes a number of interrelated technologies associated with the use of the newly available Linear Array Mitochondrial DNA HVI/HVII Region-Sequence Typing Kit (Roche Applied Science, Indianapolis, IN). The utility of a new microchip CE method for quantifying PCR products that are then hybridized to immobilized sequence specific oligonucleotide (SSO) probes is demonstrated. Also, a semiautomated sample-processing method for the Linear Arrays was developed and is demonstrated. The utility of this typing kit is shown by differentiating several hundred unrelated individuals from U.S. Caucasian, African-American, and Hispanic groups. These results are compared with previous work with similar mtDNA SSO typing probes. In addition, a new coding region single nucleotide polymorphism (SNP) assay was used to help subdivide 51 individuals having the most common Caucasian mtDNA haplotype. The authors conclude that these types of screening assays produce a more rapid evaluation of samples, because only samples not excluded would be subjected to further characterization through full HVI/HVII mtDNA sequence analysis. 7 tables, 5 figures, and 32 references