Sequence analysis of mitochondrial DNA hypervariable region I in Thai individuals

Nucleotide sequence analysis of hypervariable region I (HVRI) in human mitochondrial DNA (mtDNA) was investigated in 100 unrelated Thai individuals. A total of 85 variable sites and 423 base substitutions, which consisted of 390 nucleotide transitions and 33 nucleotide transversions were found. The following nucleotide substitutions were found: 48% at 16,223, 31% at 16,304, 30% at 16,332, and 26% at 16,129, respectively. Transition from T to C (43.7%) was the most frequent substitution. The nucleotide insertions were found at two sites with T at position 16,188 and C at position 16,194. Eighty-two haplotypes were investigated of which 72 haplotypes were unique. The most frequent haplotypes (16,108T-16,129A-16,162G-16,172C-16,304C and 16,260T-16,298C-16,355T-16,362C) were observed. From position 16,180 to 16,193, thirteen patterns of polycytosine or C-stretch were observed, whereas 68 Thai individuals were found to be similar to the references. The genetic diversity, random match probability, and discrimination power were estimated to be 0.9943, 0.0156, and 0.9844, respectively.     

A novel dimorphism in the human SRY gene: usefulness in human migration studies

A nucleotide polymorphism of C or T was detected at position 465 in the sex-determining region Y (SRY) gene. To evaluate the utility of this dimorphism in human population studies, the frequency and the frequency of the haplotype combined with the two polymorphic loci YAP and M9 were examined in a total of 130 unrelated Japanese and 130 unrelated German males. The T nucleotide was found in 24.6% (32/130) of the Japanese but not in any of the 130 German males. Accordingly, four of the eight possible combination haplotypes of SRY/YAP/M9 were identified in the Japanese population, but one of the four haplotypes comprising SRY(T) was absent in the German samples. This suggests that the C to T transition may be more recent than the YAP insertion or the M9 transversion and the change might have occurred in an ancestral Asian population. These results imply that the dimorphism at the SRY gene is one of the Y-linked markers useful for human population studies and also for ethnic identification of forensic samples. Received: 9 March 1999 / Accepted: 9 September 1999     

Sequence polymorphism of mitochondrial DNA in Japanese individuals from Gifu Prefecture

Sequence polymorphisms of the hypervariable region HV1 in mitochondrial DNA (mtDNA) were analyzed in a sample of 137 unrelated Japanese individuals living in Gifu Prefecture (central region of Japan) using polymerase chain reaction amplification and direct sequencing. Eighty-two different haplotypes resulting from 81 variable sites were found in the mtDNA HV1 region between positions 16061 and 16450. The most frequent haplotype (16223T, 16362C) was shared by ten individuals. The genetic diversity and the genetic identity were 0.985 and 0.022, respectively. The C-stretch region located around position 16189 was observed in 23.4% of this population sample. Sequence heteroplasmy at the position 16103 (A/G) was found in one individual.     

Mitochondrial DNA control region sequences in Koreans: identification of useful variable sites and phylogenetic analysis for mtDNA data quality control

We have established a high-quality mtDNA control region sequence database for Koreans. To identify polymorphic sites and to determine their frequencies and haplotype frequencies, the complete mtDNA control region was sequenced in 593 Koreans, and major length variants of poly-cytosine tracts in HV2 and HV3 were determined in length heteroplasmic individuals by PCR analysis using fluorescence-labeled primers. Sequence comparison showed that 494 haplotypes defined by 285 variable sites were found when the major poly-cytosine tract genotypes were considered in distinguishing haplotypes, whereas 441 haplotypes were found when the poly-cytosine tracts were ignored. Statistical parameters indicated that analysis of partial mtDNA control region which encompasses the extended regions of HV1 and HV2, CA dinucleotide repeats in HV3 and nucleotide position 16497, 16519, 456, 489 and 499 (HV1ex+HV2ex+HV3CA+5SNPs) and the analysis of another partial mtDNA control region including extended regions of HV1 and HV2, HV3 region and nucleotide position 16497 and 16519 (HV1ex+HV2ex+HV3+2SNPs) can be used as efficient alternatives for the analysis of the entire mtDNA control region in Koreans. Also, we collated the basic informative SNPs, suggested the important mutation motifs for the assignment of East Asian haplogroups, and classified 592 Korean mtDNAs (99.8%) into various East Asian haplogroups or sub-haplogroups. Haplogroup-directed database comparisons confirmed the absence of any major systematic errors in our data, e.g., a mix-up of site designations, base shifts or mistypings. Electronic supplementary material Supplementary material is available for this article at and accessible for authorised users.     

Mitochondrial DNA hypervariable region 1 polymorphism in Singapore Chinese population

Sequence polymorphisms of hypervariable region 1 were analyzed in 100 unrelated Singaporean Chinese. Ninety-five different haplotypes resulting from 113 variable sites were found between nucleotide positions 16045 and 16364. Single nucleotide polymorphism at nucleotide positions 16223, 16045, 16129, 16362 and 16189 was amongst the five highest frequencies observed in the sequences, whilst the most frequent haplotype was 16045-16223. Based on polymorphic sites observed at HV1, haplogroups A, F1a, M7b1, B5a and D4b were the most commonly observed clusters. The haplotype, nucleotide diversity and the average number of nucleotide differences were found to be 0.999, 0.028 and 9.082, respectively. The cytosine-stretch region located around nucleotide position 16189 was observed in 22% of this population sample. Transitions were found to be more predominant than transversions.     

Association of genetic variants in VEGF-A with clinical recurrence in prostate cancer patients treated with definitive radiotherapy

Background and purpose

Vascular endothelial growth factor-A (VEGF-A), a key regulator of tumor-induced angiogenesis, is critical for tumor growth and metastasization. The goal of the present study was to evaluate the prognostic value of VEGF single nucleotide polymorphisms (SNPs) and haplotypes for clinical recurrence after definitive radiotherapy for prostate cancer.

Patients and methods

The association of seven VEGF-A polymorphisms and their haplotypes with clinical recurrence (defined as the occurrence of local recurrence and/or distant metastases) in 496 prostate cancer patients treated with definitive radiotherapy were investigated. Genotypes were determined by 5’-nuclease (TaqMan) assays; haplotypes were analyzed using the Haploview program.

Results

Within a median follow-up time of 80 months, 44 patients (9?%) developed clinical recurrences. Haplotype analysis showed two separate blocks of high-linkage disequilibrium, formed by five polymorphisms (??2578C > A, ??2489C > T, ??1498C > T, ??634G > C, ??7C > T) upstream of the coding sequence (CCCCC, ATTGC, CCCGC, ATTGT) and two polymorphisms (936C > T, 1612G > A) downstream of the coding sequence (CA, CG, TG). Carriers of at least 1 copy of the ATTGC haplotype were at higher risk of recurrence (hazard ratio [HR] 3.83; 95?%CI 1.48–9.90, p?=?0.006); for carriers of 2 copies, the HR was 4.85 (95?%CI 1.72–13.6; p?=?0.003). In multivariate analysis, patients harboring at least one copy of the ATTGC haplotype remained at increased risk of recurrence (HR 3.63, 95?%CI 1.38–9.55, p?=?0.009); in patients carrying 2 copies, the HR was 4.72 (95?%CI 1.64–13.6, p?=?0.004).

Conclusion

Our findings indicate that the VEGF-A ATTGC haplotype may predict clinical recurrence in prostate cancer patients treated with radiotherapy.     

Base specific variation rates at mtDNA positions 16093 and 16183 in human hairs

Small variations between haplotypes detected in different tissues from the same individual have been previously described. These differences complicate the interpretation of mtDNA results in real forensic casework. mtDNA haplotypes detected in hair strands collected at the crime scene have to be frequently compared with haplotypes of reference samples (buccal swabs) from victims or suspects. Nucleotide position 16093 is a well-known hot spot where differences can accumulate between different tissues of the same individual. Intra individual variation was also detected at positions 16182 and 16183 in haplotypes showing an uninterrupted HV1 poly-C stretch (with 16189C).In order to better characterize the type of variation in these positions between buccal cells and hair strands from the same individual, we have performed Sanger sequencing in 25–28 hair strands (411 in total) from 15 individuals showing either an uninterrupted HV1 polyC-stretch (16189C) or 16093C/Y in their buccal cells. The results have been evaluated by also taking into account our previous results published in [19]. We have found that no variation among hair strands was detected in individuals showing T16093 in buccal cells, while variation in hair strands (T16093, 16093C and 16093Y) were detected in individuals showing 16093C or 16093Y in buccal cells. Regarding nucleotide positions 16182 and 16183 in combination with an uninterrupted polyC-stretch, no variation was detected in hairs from individuals showing A16182 16183C in their buccal cells. In contrast, individuals A16182 A16183 showed hair strands with A16182 16183 M and A16182 16183C. And finally, individuals with 16182C 16183C showed some variation in a small amount of their hair strands (some hairs with 16182 M 16183C). These results can be relevant for forensic practitioners when comparing reference samples with hair strands, which is the type of sample most tested by using mtDNA analysis in forensic casework.     

维吾尔族和汉族人群RANTES基因多态性特征及其对HIV-1感染的意义

目的　分析RANTES启动子区等位基因在中国维吾尔族和汉族健康人和HIV 1感染者中的分布特点 ,以期阐明RANTES基因突变型和人类免疫缺陷病毒(HIV 1 )感染在不同民族人群的关系。方法　利用PCR RFLP法对维吾尔族和汉族HIV 1感染者和健康人群的 86 5份样品的RANTES 4 0 3、 2 8等位基因进行检测。结果　两个位点在维吾尔族和汉族人群均有较高的等位基因频率 ,分布基本一致 ;RANTES等位基因具有 6个基因表型 ,分别为AC/AC、AC/AG、AC/GC、AG/GC、GC/GC和AG/AG ;从单倍型看 ,汉族和维吾尔族均以GC为最高 ,占 6 2 7% ,AC分别为 2 8 7%和 30 4 % ,AG分别为 8 6 %和 6 8%。但是从单个位点看 ,HIV感染者和健康人、吸毒者差异均无统计学意义(P >0 0 5 ) ;从基因表型分析 ,与AC/AC比较 ,AC/AG、AC/GC、AG/GC、GC/GC的OR值显示都有不同程度的关联(OR =0 33～0 81 )。结论　汉族和维吾尔族中RANTES启动子区 4 0 3/ 2 8均有较高的突变频率 ;与AC/AC比较 ,AC/AG、AC/GC、AG/GC、GC/GC的OR值显示都有不同程度的保护作用     

Effects in vivo of iohexol and diatrizoate on human plasma acetyl- and butyryl-cholinesterase activity

PURPOSE: The aim of this study was to evaluate the effects of two iodinate contrast agents (CA), iohexol and diatrizoate, on human plasma acetyl-(AC) and butyrylcholinesterase(BC) activity. MATERIAL AND METHODS: Forty-eight patients (24 males and 24 females) scheduled for intravenous pyelography were randomly divided into four groups of 6 males and 6 females each, receiving as CA, respectively: iohexol (Omnipaque, Schering) 0.6 ml/kg body weight (G1); iohexol 1.2 mg/kg (G2); sodium and meglumine diatrizoate 58% (Urografin, Schering) 0.6 ml/kg (G3); sodium and meglumine diatrizoate 58% 1.2 ml/kg (G4). Blood samples were taken before and 5, 10, and 20 min after the injection. Enzymatic activity of AC and BC were measured by spectrophotometry. Plasma concentration of K, Na, Ca, and Mg was measured in all blood samples; blood pressure and plasma pH were measured after each sample collection. Statistical analysis was performed by Student's test. RESULTS: In G1 a reversible decrease of AC (12.9%) and BC (8.2%) plasma activity was observed at 10 min. In G2 a progressive decrease of AC (13.9%) and BC (18.4%) plasma activity was observed with a maximum at 20 min. In G3 a modest reversible decrease of BC plasma activity (5.4%) was observed. In G4 a modest progressive decrease of AC (7.3%) and BC (6.5%) plasma activities was observed. In all cases, AC and BC plasma activities remained within the normal range of values. Plasma concentration of K, Na, Ca, and Mg, as well as pH and systolic and diastolic pressure, did not show any change. No adverse effects was observed in our patients. CONCLUSIONS: Iohexol and diatrizoate induce in vivo a significant decrease of AC and BC plasma activities. The decrease is more pronounced for iohexol, a non ionic CA, which has a lower pharmacotoxicity than diatrizoate and adverse effects rate. No inference can be drawn about the relationship between plasma cholinesterase activity and adverse effects.     

Sequence polymorphism of the mitochondrial DNA control region in the population of Vojvodina Province,Serbia

In order to generate and establish the database for forensic identification purposes in Vojvodina Province (Serbia), the sequence of the hypervariable regions 1 (HV1) and 2 (HV2) of the mtDNA control region were determined in a population of 104 unrelated individuals from Vojvodina Province, using a fluorescent-based capillary electrophoresis sequencing method. A total of 93 different haplotypes were found, of these 83 mtDNA types were unique, nine haplotypes were shared by two individuals and one haplotype by three individuals. The variation of mtDNA HV1 and HV2 regions was confined to 116 nucleotide positions, of which 72 were observed in the HV1 and 44 in the HV2. A statistical estimate of the results for this population showed the genetic diversity of 0.9977 and the random match probability of 1.18%. Haplogroup H was the most common haplogroup (43.3%). Haplogroups observed at intermediate levels included clusters U (13.5%), T (10.6%), J (8.6%) and W (5.8%).     

Sequence polymorphism of the mitochondrial DNA hypervariable regions I and II in 205 Singapore Malays

Mitochondrial DNA sequences of the hypervariable regions HV1 and HV2 were analyzed in 205 unrelated ethnic Malays residing in Singapore as an initial effort to generate a database for forensic identification purposes. Sequence polymorphism was detected using PCR and direct sequencing analysis. A total of 152 haplotypes was found containing 152 polymorphisms. Out of the 152 haplotypes, 115 were observed only once and 37 types were seen in multiple individuals. The most common haplotype (16223T, 16295T, 16362C, 73G, 146C, 199C, 263G, and 315.1C) was shared by 7 (3.41%) individuals, two haplotypes were shared by 4 individuals, seven haplotypes were shared by 3 individuals, and 27 haplotypes by 2 individuals. Haplotype diversity and random match probability were estimated to be 0.9961% and 0.87%, respectively.     

Sequence polymorphisms of mtDNA HV1, HV2, and HV3 regions in the Malay population of Peninsular Malaysia

The uniparentally inherited mitochondrial DNA (mtDNA) is in the limelight for the past two decades, in studies relating to demographic history of mankind and in forensic kinship testing. In this study, human mtDNA hypervariable segments 1, 2, and 3 (HV1, HV2, and HV3) were analyzed in 248 unrelated Malay individuals in Peninsular Malaysia. Combined analyses of HV1, HV2, and HV3 revealed a total of 180 mtDNA haplotypes with 149 unique haplotypes and 31 haplotypes occurring in more than one individual. The genetic diversity was estimated to be 99.47%, and the probability of any two individuals sharing the same mtDNA haplotype was 0.93%. The most frequent mtDNA haplotype (73, 146, 150, 195, 263, 315.1C, 16140, 16182C, 16183C, 16189, 16217, 16274, and 16335) was shared by 11 (4.44%) individuals. The nucleotide diversity and mean of pair-wise differences were found to be 0.036063 ± 0.020101 and 12.544022 ± 6.230486, respectively.     

Sequence polymorphism of the mitochondrial DNA control region in the Slovenian population

The forensic application of mitochondrial DNA (mtDNA) typing requires large and regionally well-defined databases. To expand the database for forensic identification purposes in Slovenia, the mtDNA control region sequences of the hypervariable regions HVI and HVII were determined in a population of 129 maternally unrelated Slovenians, using a fluorescent-based capillary electrophoresis sequencing method. A total of 111 different haplotypes resulting from 124 polymorphic positions (80 polymorphic positions in HVI and 44 in HVII) were found. Of these, 101 mtDNA types were unique, 6 haplotypes were shared by 2 individuals, 1 haplotype by 3 individuals, 2 haplotypes by 4 individuals, and the most common haplotype was found in 5 individuals. The most frequent haplotypes in the Slovenian population ,263(G), 315.1(C) and 263(G), 309.1(C), 315.1(C) are also the most common in other European populations. The data support the concept that these haplotypes may represent a common European mtDNA sequence types. The sequence poymorphisms were compared to the databases of west Austria and central Italy and the HVI and HVII sequence matching probabilities within and between populations were calculated. It is 1.1–4.5 times more likely to find a sequence match in a random pair of Slovenians than in a random Slovenian-Italian pair and in a random Slovenian-Austrian pair. The length heteroplasmy in the homopolymeric C-stretch regions located at nucleotide positions 16184–16193 in HVI and at positions 303–315 in HVII was observed in 17% and 8% of individuals, respectively. A statistical estimate of the results for this population showed the random match probability and the genetic diversity of 1.16% and 0.996, respectively.Electronic Supplementary Material Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00414-003-0394-3     

Discrimination of haplotype in mitochondrial DNA mixtures using LNA-mediated PCR clamping

Locked nucleic acid (LNA) has been widely used for various genetic analyses, and has many benefits, in terms of the specificity or sensitivity of amplification, because LNA-containing primers/probes form more stable duplexes with template DNA than probes lacking LNA. Here, we developed a new method for discriminating HV1 haplotypes from mitochondrial DNA (mtDNA) mixtures by applying PCR clamping using LNA. PCR clamping is based on the selective inhibition of amplification using LNA-containing probes, which can discriminate single-nucleotide differences. Before designing probes, we selected 171 sequences with single-nucleotide variations from the HV1 region, and evaluated the specificity of LNA-containing probes for them by predicting Tm values. The differences of Tm between mismatched and exactly matched probe–template duplexes depended markedly on the type of LNA nucleotides for discriminating single-nucleotide differences, and the cytosine LNA nucleotide at the site of variations in the probes was most effective to discriminate these differences. For mixture analysis, each probe targeted one or two variations (16209C, 16217C, 16257A/16261T, 16297C/16298C, 16304C, 16362C, or 16362T) that are particularly common in the Japanese population, and seven designed probes completely inhibited the amplification of exactly matched templates. We prepared mixed samples by mixing DNA from two individuals at a ratio of 1:9, 1:4, 1:1, 4:1, or 9:1, and then performed Sanger sequencing analysis after PCR clamping with each probe. Our method distinguished each haplotype at lower ratios from two-person mixtures, and enabled sensitive detection at 12 pg of total DNA including 600 copies of mtDNA. Moreover, we analyzed three-person mixtures with representative sequences, and detected the minor haplotype of one individual present at a rate of 10% by adding two selected probes. The ability to discriminate haplotypes in mixed samples by using LNA-mediated PCR clamping indicates the potential value of mtDNA analysis in criminal investigations.     

人胰岛素样生长因子-I基因P1启动子区域单核苷酸多态性-705T>C和-603T>A对启动子活性的影响(英文)

目的探讨人胰岛素样生长因子-I(IGF-I)基因P1启动子区域单核苷酸多态性(SNP)-705T>C和-603T>A对启动子活性的影响。方法招募152名健康志愿者参与本研究,取静脉血样品,使用基因组DNA提取试剂盒从血样中提取全基因组DNA。通过限制片段长度多态性分析(RFLP),对每名志愿者的SNP-705T>C和-603T>A进行基因分型,统计各基因型的频率。使用PHASE v2.1软件程序分析P1启动子单体型的类型和频率。通过荧光素酶报告基因测定不同P1启动子单体型的活力差异。结果成功提取了每名志愿者的全基因组DNA并测定了SNP-705T>C和-603T>A的基因型。基因型-705T/T、705T/C、-705C/C的频率分别与-603T/T、-603T/A、-603A/A相同,分别为43.4%、45.4%、11.2%。等位基因-705T、-705C的频率分别与-603T、-603A相同,分别为66.1%、33.9%。SNP-705T>C和-603T>A之间存在完全的连锁不平衡,其组成的P1启动子单体型只有-705T/-603T和-705C/-603A两种,频率分别为66.1%和33.9%。报告基因分析结果表明,P1启动子-705C/-603A单体型的活力显著高于-705T/-603T单体型。结论人IGF-I基因P1启动子区域SNP-705T/C和-603T/A能够影响P1启动子的活性。     

Effects of cell membrane disruption on the relaxation rates of blood and clot with various methemoglobin concentrations

The magnetic resonance imaging (MRI) characteristics of hemorrhage and clotted blood change with age. The effects of methemoglobin and cell membrane lysis, factors which in part may underlie this evolution of imaging characteristics, were studied using clotted and heparinized dog blood at various methemoglobin concentrations. Cell lysis did not alter the longitudinal relaxation rate (1/T1) in clotted or unclotted samples. Membrane lysis altered significantly the transverse relaxation rate (1/T2) in both clotted and unclotted samples. Lysed samples of oxygenated blood at 0% methemoglobin had significantly higher T2 values than intact samples. At 0% methemoglobin, clotted samples had slightly but significantly shorter relaxation times than unclotted samples. Within the samples studied, large changes in the state of oxygenation and methemoglobin content were observed in less than 24 h. Such changes necessitate frequent monitoring of these parameters if serial studies are to be done.     

Steroid profile analysis and UGT2B17 genotyping of the same urine sample to determine testosterone abuse

When testing a urine sample for testosterone abuse, a ratio of testosterone glucuronide (T) to epitestosterone glucuronide (ET) of 4.0 or above is considered suspicious. A degree of variation, however, has been observed in T/ET ratio between individuals from both the same and different ethnic backgrounds. The majority of this variation might be due to UGT2B17 deletion genotype (UGT2B17 deletion-type). The aim of this study was to investigate the use of the same urine sample for the analysis of T/ET ratio and UGT2B17 deletion-type. Japanese men were deletion-typed via a UGT2B17 copy number assay using DNA from blood. Urinary T and ET levels were determined using gas chromatography–mass spectrometry before (n = 112) and after a testosterone injection (n = 25). Basal T level and the increase in T/ET ratio after injection were dependent on UGT2B17 deletion-type, being lower in subjects with deletion (del/del) than nondeletion (ins/del or ins/ins) genotype. UGT2B17 deletion-typing was first performed using DNA from urine cryopreserved for 1–1.5 years (n = 66). The concentration of DNA required for discrimination between the deletion and nondeletion genotype by copy number assay was more than 0.1 ng/ml urine. Discrimination was possible in 94.0 % of urine samples (5–7 ml each). These findings show that T/ET ratio and UGT 2B17 deletion-type can be analyzed exclusively via urine samples, removing the need for the collection of other samples, such as blood or buccal cells. The combination of T/ET ratio and UGT 2B17 deletion-type may help inform decisions regarding a genotype-specific T/ET cutoff ratio.     

Evaluation of in vivo P-glycoprotein function at the blood-brain barrier among MDR1 gene polymorphisms by using 11C-verapamil.

P-glycoprotein (P-gp) is a membrane protein that functions as an adenosine triphosphate-dependent efflux pump for xenobiotics at the blood-brain barrier (BBB). Polymorphisms of MDR1 gene have been reported to be associated with the expression level of P-gp. (11)C-Verapamil is considered to be one of the suitable radioligands for evaluating P-gp functions. However, the metabolites of verapamil might complicate the quantitative analysis because of their possible brain penetration. In the present study, we investigated the P-gp functional differences at the BBB between the haplotypes (1236TT, 2677TT, 3435TT vs. 1236CC, 2677GG, 3435CC) of the MDR1 gene with different quantitative analyses of (11)C-verapamil. METHODS: Thirty-three healthy male volunteers were enrolled in this study after identification of the haplotypes of the MDR1 gene. Brain PET scans with (11)C-verapamil were performed for 16 min. Integration plot analysis, which yields brain uptake clearance, was performed with the first 3-min data. Integration plot analysis was then compared with several other quantitative analyses with 16-min data (1-input, 1-tissue compartment model, and the area under the curve ratio (AUC(ratio)) between brain and plasma). RESULTS: In the integration plot, there was no difference in the absolute values of brain uptake clearance (CL(uptake)) between the haplotypes; CL(uptake) of (11)C-verapamil for the haplotypes (1236TT, 2677TT, 3435TT vs. 1236CC, 2677GG, 3435CC) were 0.053 +/- 0.011 and 0.051 +/- 0.011 mL/g/min, respectively. CL(uptake) of (11)C-verapamil in the integration plot was significantly correlated with K1 and DV(K1/k2) (DV is distribution volume; K1 and k2 are plasma and tissue rate constants) in the 1-input, 1-tissue compartment model and the AUC(ratio). CONCLUSION: On the basis of the several quantitative analyses of (11)C-verapamil, the assumption that the function of P-gp at the BBB is different between the haplotypes (3 single nucleotide polymorphisms: C1236T, G2677T, and C3435T) of MDR1 gene was not supported.     

Helena,the hidden beauty: Resolving the most common West Eurasian mtDNA control region haplotype by massively parallel sequencing an Italian population sample

The analysis of mitochondrial (mt)DNA is a powerful tool in forensic genetics when nuclear markers fail to give results or maternal relatedness is investigated. The mtDNA control region (CR) contains highly condensed variation and is therefore routinely typed. Some samples exhibit an identical haplotype in this restricted range. Thus, they convey only weak evidence in forensic queries and limited phylogenetic information. However, a CR match does not imply that also the mtDNA coding regions are identical or samples belong to the same phylogenetic lineage. This is especially the case for the most frequent West Eurasian CR haplotype 263G 315.1C 16519C, which is observed in various clades within haplogroup H and occurs at a frequency of 3–4% in many European populations.In this study, we investigated the power of massively parallel complete mtGenome sequencing in 29 Italian samples displaying the most common West Eurasian CR haplotype – and found an unexpected high diversity. Twenty-eight different haplotypes falling into 19 described sub-clades of haplogroup H were revealed in the samples with identical CR sequences. This study demonstrates the benefit of complete mtGenome sequencing for forensic applications to enforce maximum discrimination, more comprehensive heteroplasmy detection, as well as highest phylogenetic resolution.     

Mitochondrial DNA population data of HV1 and HV2 sequences from Japanese individuals

Mitochondrial DNA sequences of the hypervariable regions HV1 and HV2 were determined for 1204 unrelated Japanese individuals. A total of 741 different mtDNA haplotypes were found, 157 of which were seen in multiple individuals. Twenty-seven of these individuals showed point heteroplasmy. The most frequent haplotype (16223T-16362C-73G-263G-315.1C) was found in 31 individuals and the second most frequent haplotypes (16129A-16223T- 16362C-73G-152C-263G-309.1C-315.1C) was found in 24 individuals. The haplotypes diversity and random match probability were calculated to be 0.9969 and 0.0040, respectively.