Haplotype analysis of single nucleotide polymorphisms of mitochondrial DNA

: Mitochondrial DNA (mtDNA) mutations observed in both non-coding control and coding regions are being used widely to characterize human evolution and for identification. Several methodological approaches have been available for detection of single nucleotide polymorphisms (SNPs). SNPs of the non-coding region were mainly analyzed by means of direct sequencing. Especially, sequence analysis of D-loop is often the final resort in forensic and ancient personal identification. However, sequencing is relatively expensive and time-consuming. Furthermore, because the mtDNA molecule is a single linked unit, the statistical significance in forensic cases requires mtDNA matching in comparison with large sequence data. In this study, we developed a procedure of technique simultaneous typing to 11 SNPs and 2 tandem repeat sites in the non-coding and coding region by use of allele-specific amplification. In an analysis to 631 unrelated Japanese individuals the 180 haplotypes were defined in this study, and the level of haplotypic diversity and random mach probability was similar to that obtained by sequencing of the human hypervariable region 1 in mtDNA. These results show the usefulness of mtDNA haplotype analysis by the presented method for personal identification.