Typing the 1.1 kb control region of human mitochondrial DNA in Japanese individuals

Forensic evaluation of mitochondrial DNA heteroplasmy in Gujarat population, India

BACKGROUND

Owing to its high copy number and its small size, mtDNA analysis is the most reliable choice when biological materials from crime scenes are degraded or have mixed STR profiles.

AIM

To examine the occurrence of heteroplasmy along with its frequency and pattern in both HV1 and HV2 regions of the mtDNA among unrelated individuals from India.

SUBJECTS AND METHODS

Mitochondrial DNA control region [hypervariable region one (HV1) and hypervariable region two (HV2)] were analysed in blood and buccal tissues of 104 unrelated individuals from the Indian state of Gujarat.

RESULTS

A high frequency of point heteroplasmy (PH) and length heteroplasmy (LH) was revealed. PH was detected in 7.69% of the population, with a higher frequency observed in blood than in buccal samples. However, there were no statistically significant differences in PH between the two tissues (Chi-square = 0.552, p ≥ 0.05). A total of six PH positions were detected: three at HV1, and another three at HV2. The studied population showed 46.15% LH in the HV1 and HV2 regions of both tissues. The LH positions observed in the Gujarat population were the same as those previously reported at HV1 np16184-16193 and HV2 np303-315.

CONCLUSIONS

Our findings suggest that differences in the pattern of heteroplasmy found in different tissues can complicate the forensic analysis, on the other hand, the probability of a match between the questioned and reference samples increases when the heteroplasmy is identical in both tissues. Variability of PH among persons and even within tissues recommends analysing multiple tissue samples before drawing a conclusion in forensic mtDNA analyses.

Degradation of nuclear and mitochondrial DNA after γ-irradiation and its effect on forensic genotyping

Forensic genotyping can be impeded by γ-irradiation of biological evidence in the event of radiological crime; that is, criminal activity involving radioactive material. Oxidative effects within the mitochondria of living cells elicits greater damage to mitochondrial DNA (mtDNA) than nuclear DNA (nuDNA) at low doses. This study presents a novel approach for the assessment of nuDNA versus mtDNA damage from a comparison of genotype and quantity data, while exploring likely mechanisms for differential damage after high doses of γ-irradiation. Liquid (hydrated) and dried (dehydrated) whole blood samples were exposed to high doses of γ-radiation (1-50 kilogray, kGy). The GlobalFiler PCR Amplification Kit was used to evaluate short tandem repeat (STR) genotyping efficacy and nuDNA degradation; a comparison was made to mtDNA degradation measured using real-time PCR assays. Each assay was normalized before comparison by calculation of integrity indices relative to unirradiated controls. Full STR profiles were attainable up to the highest dose, although DNA degradation was noticeable after 10 and 25 kGy for hydrated and dehydrated blood, respectively. This was manifested by heterozygote imbalance more than allele dropout. Degradation was greater for mtDNA than nuDNA, as well as for hydrated than dehydrated cells, after equivalent doses. Oxidative effects due to water radiolysis and mitochondrial function are dominant mechanisms of differential damage to nuDNA versus mtDNA after high-dose γ-irradiation. While differential DNA damage was reduced by cell desiccation, its persistence after drying indicates innate differences between nuDNA and mtDNA radioresistance and/or continued oxidative effects within the mitochondria.

Munda languages are father tongues, but Japanese and Korean are not

Over two decades ago, it was observed that the linguistic affinity of the language spoken by a particular population tended to correlate with the predominant paternal, i.e. Y-chromosomal, lineage found in that population. Such correlations were found to be ubiquitous but not universal, and the striking exceptions to such conspicuous patterns of correlation between linguistic and genetic phylogeography elicit particular interest and beg for clarification. Within the Austroasiatic language family, the Munda languages are a clear-cut case of father tongues, whereas Japanese and Korean are manifestly not. In this study, the cases of Munda and Japanese are juxtaposed. A holistic understanding of these contrasting cases of ethnolinguistic prehistory with respect to the father tongue correlation will first necessitate a brief exposition of the phylogeography of the Y chromosomal lineage O. Then triangulation discloses some contours and particulars of both long lost episodes of ethnolinguistic prehistory.

Complete hydatidiform moles are composed of paternal chromosomes and maternal mitochondria

Mitochondrial DNA (mtDNA) and genomic DNA are produced in separate subcellular compartments. Human mtDNA is transmitted via maternal transmission in general. Complete hydatidiform moles (CHMs) represent major trophoblastic diseases that are cytogenetically exceptional because the chromosomal genomic DNA is derived only from sperm cells, making them strikingly different from normal concepti. However, few reports have described the mtDNA-transmission pattern in hydatidiform moles. To evaluate mtDNA transmission in androgenetic CHMs, we compared the sequences of hypervariable regions in 16 trios sets of mtDNAs from maternal, paternal, and villous samples of androgenetic CHMs diagnosed by short tandem repeat-polymorphism analysis. All mtDNAs in androgenetic CHMs were maternally derived, in line with the general human inheritance pattern. Three maternal mtDNAs were heteroplasmic. The heterozygous status of maternal mtDNA was reflected in villous tissue, in which variants status was also heterozygous. CHMs are composed of paternal chromosomes and maternal mitochondria.

Ethnic derivation of the Ainu inferred from ancient mitochondrial DNA data

Objectives

The Ainu, the indigenous people living on the northernmost island of Japan, Hokkaido, have long been a focus of anthropological interest because of their cultural, linguistic, and physical identity. A major problem with genetic studies on the Ainu is that the previously published data stemmed almost exclusively from only 51 modern‐day individuals living in Biratori Town, central Hokkaido. To clarify the actual genetic characteristics of the Ainu, individuals who are less influenced by mainland Japanese, who started large‐scale immigration into Hokkaido about 150 years ago, should be examined. Moreover, the samples should be collected from all over Hokkaido.

Materials and methods

Mitochondrial DNA haplogroups of 94 Ainu individuals from the Edo era were successfully determined by analyzing haplogroup‐defining polymorphisms in the hypervariable and coding regions. Thereafter, their frequencies were compared to those of other populations.

Results

Our findings indicate that the Ainu still retain the matrilineage of the Hokkaido Jomon people. However, the Siberian influence on this population is far greater than previously recognized. Moreover, the influence of mainland Japanese is evident, especially in the southwestern part of Hokkaido that is adjacent to Honshu, the main island of Japan.

Discussion

Our results suggest that the Ainu were formed from the Hokkaido Jomon people, but subsequently underwent considerable admixture with adjacent populations. The present study strongly recommends revision of the widely accepted dual‐structure model for the population history of the Japanese, in which the Ainu are assumed to be the direct descendants of the Jomon people.

Analysis of human mitochondrial DNA polymorphisms in the Japanese population

The highly polymorphic nature and high amplification efficiency of mitochondrial DNA (mtDNA) is valuable for the analysis of biological evidence in forensic casework, such as the identification of individuals and assignment of race/ethnicity. To be useful, a mtDNA polymorphism database for the Japanese population requires an understanding of the range of haplotype variation and phylogenies of mtDNA sequences. To extend current knowledge on the haplotypes in the Japanese population, this study defines new lineages and provides more detail about some of those previously described. We compared the hypervariable regions (HVRs) of 270 healthy, unrelated Japanese individuals and demonstrated 192 haplotypes. Combining HVR1 and HVR2, the genetic diversity was 0.9935, thus providing a high level of identification capability. Haplogroup status was defined for 160 individuals using HVR1, HVR2, and particular coding region polymorphisms; these individuals belonged to 94 haplotypes, four of which were new lineages. The complete mtDNA sequence was also determined from seven individuals.

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

To clarify the colonizing process of East/Northeast Asia as well as the peopling of the Americas, identifying the genetic characteristics of Paleolithic Siberians is indispensable. However, no genetic information on the Paleolithic Siberians has hitherto been reported. In the present study, we analyzed ancient DNA recovered from Jomon skeletons excavated from the northernmost island of Japan, Hokkaido, which was connected with southern Siberia in the Paleolithic period. Both the control and coding regions of their mitochondrial DNA (mtDNA) were analyzed in detail, and we confidently assigned 54 mtDNAs to relevant haplogroups. Haplogroups N9b, D4h2, G1b, and M7a were observed in these individuals, with N9b being the predominant one. The fact that all these haplogroups, except M7a, were observed with relatively high frequencies in the southeastern Siberians, but were absent in southeastern Asian populations, implies that most of the Hokkaido Jomon people were direct descendants of Paleolithic Siberians. The coalescence time of N9b (ca. 22,000 years) was before or during the last glacial maximum, implying that the initial trigger for the Jomon migration in Hokkaido was increased glaciations during this period. Interestingly, Hokkaido Jomons lack specific haplogroups that are prevailing in present-day native Siberians, implying that diffusion of these haplogroups in Siberia might have been after the beginning of the Jomon era, about 15,000 years before present.

Mitochondrial C150T polymorphism increases the risk of cervical cancer and HPV infection

During a survey of control region (D-loop) sequence variances in 142 cervical cancer (CC) patients and 136 controls, all Chinese women, including both HPV-positive (human papillomavirus) and HPV-negative subjects, we determined that the C150T polymorphism increased the CC risk in a case-control study (OR=3.0, 95% CI=1.8-5.0, P<0.05). HPV-positive individuals were more likely to carry the C150T polymorphism than HPV-negative controls (OR=5.8, 95% CI=2.6-13.2, P=2.3×10(-5)). HPV-positive CC patients were more likely to carry the C150T polymorphism than HPV-negative controls (OR=4.9, 95% CI=2.6-9.3, P=9.9×10(-7)). In all subjects, an increased risk of HPV infection was also associated with the C150T polymorphism (OR=4.5, 95% CI=2.5-8.1, P=6.6×10(-7)). However, no significant difference in the frequency of other alleles was found at the variable sites in D146, D152, D310 and D514. These results indicated that the C150T polymorphism increased the risk of HPV infection and CC progression. Additionally, we assessed the association of mtDNA copy number with CC risk or the C150T polymorphism in 45 CC patients and 43 controls. There was no significant association of mtDNA copy number with CC risk or the C150T polymorphism. To the best of our knowledge, this is the first report to suggest that mtDNA C150T polymorphism was positively associated with HPV infection and subsequent CC risk among Chinese women.

Heteroplasmy in hair: study of mitochondrial DNA third hypervariable region in hair and blood samples

Mitochondrial DNA (mtDNA) analysis has proved useful for forensic identification especially in cases where nuclear DNA is not available, such as with hair evidence. Heteroplasmy, the presence of more than one type of mtDNA in one individual, is a common situation often reported in the first and second mtDNA hypervariable regions (HV1/HV2), particularly in hair samples. However, there is no data about heteroplasmy frequency in the third mtDNA hypervariable region (HV3). To investigate possible heteroplasmy hotspots, HV3 from hair and blood samples of 100 individuals were sequenced and compared. No point heteroplasmy was observed, but length heteroplasmy was, both in C-stretch and CA repeat. To observe which CA "alleles" were present in each tissue, PCR products were cloned and re-sequenced. However, no variation among CA alleles was observed. Regarding forensic practice, we conclude that point heteroplasmy in HV3 is not as frequent as in the HV1/HV2.

Sequence-length variation of mtDNA HVS-I C-stretch in Chinese ethnic groups

The purpose of this study was to investigate mitochondrial DNA (mtDNA) hypervariable segment-I (HVS-I) C-stretch variations and explore the significance of these variations in forensic and population genetics studies. The C-stretch sequence variation was studied in 919 unrelated individuals from 8 Chinese ethnic groups using both direct and clone sequencing approaches. Thirty eight C-stretch haplotypes were identified, and some novel and population specific haplotypes were also detected. The C-stretch genetic diversity (GD) values were relatively high, and probability (P) values were low. Additionally, C-stretch length heteroplasmy was observed in approximately 9% of individuals studied. There was a significant correlation (r=-0.961, P<0.01) between the expansion of the cytosine sequence length in the C-stretch of HVS-I and a reduction in the number of upstream adenines. These results indicate that the C-stretch could be a useful genetic maker in forensic identification of Chinese populations. The results from the Fst and dA genetic distance matrix, neighbor-joining tree, and principal component map also suggest that C-stretch could be used as a reliable genetic marker in population genetics.

MtDNA control region sequence polymorphisms and phylogenetic analysis of Malay population living in or around Kuala Lumpur in Malaysia

Control region polymorphisms in the mitochondrial DNA of 124 unrelated individuals from the Malay population living in or around Kuala Lumpur in Malaysia were investigated and phylogenetic haplogroup lineages were determined. The intergenic COII/tRNALys 9-bp deletion, 3010 and 5178 mutations, and several coding region polymorphisms were examined to discriminate some phylogenetic haplogroups. Sequence comparison of the control regions led to the identification of 117 mitochondrial haplotypes, in which 103 types were observed in only one individual and the other nine types were shared by more than two individuals. Gene diversity was estimated to be 0.997. Phylogenetic haplogroup determination revealed that the gene pool of the modern Malay population in Malaysia consisted mainly of southeast Asian, east Asian, unidentified and unique, and aboriginal southeast-specific haplogroups. These results suggest a multi-original nature for the modern Malay population. The present database may help not only in personal identification but also in determining geographic origin in forensic casework in Malaysian, Southeast Asian and East Asian populations.

Molecular analysis of mitochondrial hypervariable region 1 in 394 Japanese individuals

Mitochondrial DNA (mtDNA) is a powerful tool for forensic casework when the resource is highly putrefied or very limited. It is important that mtDNA sequence databases continue to be generated and published, to extend mtDNA typing capability to additional populations and to increase the size of existing databases. The aim of this study was to analyze hypervariable region 1 (HV1) of mtDNA and establish a new database of mtDNA in Japanese population. Three hundred and ninety-four unrelated Japanese individuals were investigated. They were classified into 193 haplotypes based on HV1 sequence. Nucleotide substitutions were clustered in several positions and were 79% at 16,223, 50% at 16,362, and 29% at 16,189. Transition accounts for 81% of all the mutations and especially transition from cytosine to thymine (33%) was the most frequent substitution. 16,223-16,362 was observed in 34 individuals, following 16,129-16,223-16,362 in 29 individuals, and haplotype 16,223-16,278-16,362 in 14 individuals. Genetic diversity and random match probability in this population were estimated to 0.987% and 1.95%, respectively. In conclusion, HV1 of mitochondria sequence has a high discrimination power, but in addition to HV1, analysis of other region such as HV2 and HV3 are required in certain cases.