Analysis of mitochondrial DNA (mtDNA) has been used successfully for a number of years in anthropology and forensic genetics (Budowle et al., 2003). The high copy number of mitochondrial genomes (typically more than 3000) in a somatic cell makes it more likely to amplify mtDNA markers than nuclear DNA markers from old and highly degraded sample materials. In addition, mtDNA can also be collected from hair shafts, which do not contain any nuclear DNA, and hair shafts are one of the frequent samples recovered from scenes of violent crimes. Mitochondrial DNA is maternally inherited, and there is no recombination between mitochondrial genomes, because there is only one chromosome per mitochondria. Therefore, the variation of mtDNA genomes among humans is relatively small and the power of discrimination is limited compared to the analysis of autosomal chromosomes. The mtDNA genome is approximately 16 569 bp long and it was sequenced already in 1981. It encodes 13 genes, two rRNAs and 22 tRNAs and has a 1100 bp non-coding sequence, known as the mtDNA control region, where the mutation rate is unusually high. Within the control region there are at least three hypervariable (HV) regions with a high number of SNPs (Brandstätter et al., 2004) and these regions can be amplified by PCR and sequenced. In 1999, EDNAP's mitochondrial DNA population database project (EMPOP) (www.empop.org) was initiated with the purpose of creating a common forensic standard for mtDNA sequencing and an on-line mtDNA database with high-quality mtDNA population data. The initiative was a reaction to the significant number of errors in public mtDNA databases (Brandstätter et al., 2004) and only forensic laboratories qualified by successful participation in EMPOP collaborative exercises have permission to submit mtDNA sequences (Parson et al., 2004). Today, the typical targets for forensic and anthropological investigations are HV-I (position 16 024-16 400) and HV-II (position 44-340). However, there is a growing interest for SNPs in the mtDNA coding region, because certain sequences in HV-I and HV-II are very common (e.g. 7% of all Caucasians have the same HV1/HV2 haplotype). Several SNP panels have been proposed (Grignani et al., 2006; Brandstätter et al., 2006) and a selection of coding region SNPs for forensic caseworks are likely to be recommended in the near future.
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