Polymorphism and heteroplasmy of mitochondrial DNA in the D-loop region in Taiwanese

Background and Purpose: Although the displacement loop (D-loop) of mitochondrial DNA (mtDNA) is known to have a large number of sequence variations, data on this variation are lacking. This study investigated D-loop sequence polymorphism in Taiwanese subjects. Methods: The D-loop mtDNA region was amplified from whole blood samples of 63 unrelated Taiwanese individuals using the polymerase chain reaction (PCR). PCR products were sequenced and analyzed. Sequence electropherograms of nucleotides 303 to 315 that showed particularly high background after C-stretch were subcloned to the PGEM-TE vector for sequencing analysis. Results: A total of 126 variable sites in 788 polymorphisms including 19 novel sites were found. The genetic diversity of the highly variable region (HVR)-I, HVR-II, HVR-III, and a region elsewhere were 0.999, 0.993, 0.850, and 0.707, respectively. The power of discrimination of these regions was 0.983, 0.977, 0.837, and 0.696, respectively. Both HVR-I and HVR-II contained segments of homopolymeric sequence. A high frequency (30%) of heteroplasmy made up of cytosine between nucleotides 303 and 315 appeared to be a unique feature of the Taiwanese population. Nucleotide substitutions at position 16362 (T to C) in HVR-I have been found with high frequency in Taiwanese. Conclusion: In this study, 19 polymorphisms in the D-loop of mtDNA in Taiwanese were newly identified, and an unusually high frequency of heteroplasmy was found in the region between nucleotides 303 and 315 in this population.