Typing the 1.1 kb Control Region of Human Mitochondrial DNA in Japanese Individuals

Abstract

This study presents a reliable method that uses high-fidelity long-range PCR and optimized primers to assess polymorphism and to genotype human mitochondrial DNA (mtDNA). This method was used to analyze polymorphic sites in the human mtDNA control region, including hypervariable regions I, II, and III (HVI, HVII, and HVIII), from 124 unrelated Japanese individuals. In HVI, HVII, and HVIII, 80, 37, and 14 polymorphic sites were identified, respectively, excluding those in the homopolymeric cytosine stretch (C-stretch) regions. The region between HVI and HVII also contained 15 polymorphic sites. On the other hand, C-stretch length heteroplasmy in HVI or HVII was observed in 66 of 124 Japanese individuals (53%), which is much higher than in Caucasian populations. The variants in the C-stretch regions were characterized by counting the number of heteroplasmic peaks split from the single peak in homoplasmic sequences (i.e., 16244G and 16255G in HVI and 285G in HVII). Including the C-stretch length heteroplasmy, the 124 Japanese mtDNA samples were classified into 116 distinct haplotypes. The random match probability and the genetic diversity were estimated to be 0.95% and 0.998581, respectively, indicating that the method presented here has higher discrimination than the conventional method for mtDNA typing using HVI and HVII. [Correction added after publication 30 January 2007: in the preceding sentence random match probability and genetic diversity estimates were corrected from 0.95 and 0.998581%, respectively, to 0.95% and 0.998581, respectively.] The haplogroups and their frequencies observed in this study (i.e., D4; 13.7%, M7a1; 11.3%, D4a; 9.7% and M7b2; 8.9%) were similar to those observed in other studies of Japanese mtDNA polymorphism. The method described here is suitable for forensic applications, as shown by successful analysis of tissues from highly putrefied remains of an infant, which allowed maternal relationship to be determined via mtDNA haplotyping.

Identification of Human Bone Remains by Autosomal STRs and Mitochondrial DNA SNPs

“…In the present study, C-stretch length heteroplasmy was found at two positions within HVS-II. This finding agreed with that of several previous studies [23][24][25] . C-stretch length heteroplasmy increases the difficulties of DNA sequencing 19,20,36) and individual identification.…”

Mitochondrial DNA analysis of Hokkaido Jomon skeletons: Remnants of archaic maternal lineages at the southwestern edge of former Beringia

“…e Sequence of the segment 16,195 is particularly shown in the parenthesis as described by Mabuchi et al (2007) except that the number of cytosines in the C-stretches are ignored and described as ''poly C. '' population. However, gene diversity among the Hokkaido Jomons (1.000 6 0.004) is higher than that among the native Siberians, suggesting that a certain level of genetic variation is maintained in the Hokkaido Jomon population studied.…”

Genetic structure of native circumpolar populations based on autosomal, mitochondrial, and Y chromosome DNA markers

“…Additional data obtained from previously published sources and used in this study included for mtDNA sequences: Chinese and Vietnamese (Oota et al, 2002); Japanese and Korean (Mabuchi et al, 2007); Itel'men and Koryak (Schurr et al, 1999); Bering Aleut (Zlojutro et al, 2006); Chukchi and Siberian Eskimo (Starikovskaya et al, 1998); Aleutian Aleut (Rubicz et al, 2003); Athabascan (Shields et al, 1993); Bella Coola and Haida ; West Greenland Eskimos (Saillard et al, 2000); Arsario, Ijka, Kogi, and Wayuú (Melton et al, 2007); and for Y chromosomes: Chinese, Japanese, Korean, Greenland Eskimo, and Amerindian (Willuweit et al, 2007); Aleutian Aleut (Rubicz, 2007); Apache, Dogrib, and Tanana (Malhi et al, 2008).…”