Haplotyping of mitochondrial DNA in the D-loop region by PCR: forensic application

A rapid and simple method using restriction enzymes to detect the restriction fragment length polymorphism (RFLP) pattern of hypervariable segment 1 in the D-loop region of human mitochondrial DNA (mtDNA) was developed. We first focused on the investigation of variations of DNA sequence in the D-loop region among Chinese subjects, as well as on the determination of RFLP patterns of each restriction enzyme. Seven restriction enzymes were used to digest a 618 bp polymerase chain (PCR) reaction product of the D-loop region of mtDNA. Frequency distribution of RFLP patterns of each restriction enzyme among 145 unrelated Chinese subjects in Taiwan was also established. For the purposes of practical forensic application, a routine typing system was designed on the basis of the RFLP data. Two short hypervariable, mtDNA fragments, which were contained within the 618 bp region, were selected for this purpose. In this haplotyping system, a 281 bp PCR-amplified DNA product was analyzed by five restriction enzymes: Mnl I, Nla III, Rsa l, Mse I and Hinf I, and a 237 bp fragment was analyzed by Kpn I. The RFLP patterns were determined by agarose gel electrophoresis of the restriction enzyme-digested DNA fragments. Six restriction enzymes. Mul I, Nla III, Rsa I. Msc I, Hinf I and Kpn 1, defined eight, four, four, five, two and four polymorphic patterns, respectively among the 145 Chinese subjects. The RFLP patterns of restriction fragments for each individual were systematically analyzed and the mtDNAs of the 145 Chinese subjects were grouped into 52 haplotypes. This PCR-RFLP haplotyping system revealed a high degree of variability and diversity of segment I in the D-loop region of human mtDNA. The power of discrimination and allelic diversity values were 0.923 and 0.929, respectively. Successful application of this haplotyping system in a murder case is also discussed.