中国汉族人mtDNA控制区异质性遗传规律

目的探讨中国汉族人mtDNA控制区异质性分布情况和遗传规律。方法将人mtDNA控制区扩增成6个部分互相重叠的片段,利用已建立的DHPLC技术分析其异质性规律。结果对150例汉族无关个体的多种组织检测,发现异质性个体的发生率达34%(51/150);个体的组织mtDNA异质性检出率最高为脑(50/150)、心肌(48/150)、最低为骨骼(22/150);本组共发现mtDNA控制区异质性位点有36个;同一个体可有多个异质性位点,最多的不超过3个;未发现异质性发生率有性别差异;超过41岁的高年龄组的异质性发生率(27/59)高于低年龄组(24/91);同一个体在2年前后取的血样,异质性检测结果一致;同一母系不同成员的异质性位点相同,但异质性mtDNA的含量有差异。结论DHPLC检测mtDNA控制区异质性具有高分辩力;mtDNA控制区异质性在中国汉族人中广泛存在;上述结果可作为mtDNA控制区多态性作个人认定和亲权鉴定的指导性资料。     

Critique of interpretation of high levels of heteroplasmy in the human mitochondrial DNA hypervariable region I from hair

The phenomenon known as heteroplasmy can be operationally observed in some human mitochondrial DNA (mtDNA) samples. Typically, heteroplasmy manifests itself in an individual presenting two mtDNA species that differ at a single base. Heteroplasmy at two, and even possibly three sites, also may occur, but at very low rates. A recent report (Grzybowski, 2000, see ref. [13]) suggests that much higher levels of mtDNA (point substitution) heteroplasmy can occur in hair. This observation is contrary to the experience of the forensic mtDNA community. There are several explanations for the unusual findings of high levels of heteroplasmy. First, the template quantities of DNA are approximately three orders of magnitude higher than required for mtDNA sequencing, and an excessive number of amplification cycles were used. Thus, the protocol used did not follow routine practices by the forensic community. Second, there are misidentifications and tabular errors that call into question the reliability of the findings. Third, by comparing the natural human mtDNA variation with a reference sample population with that observed in the heteroplasmy in hair study, the data are inconsistent with population genetic expectations. The observation of high levels of heteroplasmy may be due to contamination of the samples and/or possibly the amplification of nuclear pseudogenes. The results observed in the heteroplasmy in hair study do not apply to other methods of mtDNA analysis and cannot be used to question the reliability of the current forensic mtDNA practices.     

Detection and quantification of the age-related point mutation A189G in the human mitochondrial DNA

Mutation analysis in the mitochondrial DNA (mtDNA) control region is widely used in population genetic studies as well as in forensic medicine. Among the difficulties linked to the mtDNA analysis, one can find the detection of heteroplasmy, which can be inherited or somatic. Recently, age-related point mutation A189G was described in mtDNA and shown to accumulate with age in muscles. We carried out the detection of this 189 heteroplasmic point mutation using three technologies: automated DNA sequencing, Southern blot hybridization using a digoxigenin-labeled oligonucleotide probe, and peptide nucleic acid (PNA)/real-time PCR combined method on different biological samples. Our results give additional information on the increase in mutation frequency with age in muscle tissue and revealed that the PNA/real-time PCR is a largely more sensitive method than DNA sequencing for heteroplasmy detection. These investigations could be of interest in the detection and interpretation of mtDNA heteroplasmy in anthropological and forensic studies.     

人类线粒体DNA异质性研究进展及在法医学中的应用

线粒体DNA(mtDNA)异质性的存在使其在法医学应用变得复杂。本文对mtDNA异质性形成的可能原因、异质性的分布和遗传特点、异质性的筛查和定量方法、异质性对法医学的影响以及异质性的研究和展望等方面进行综述,探讨异质性在法医学上的应用价值。     

基于Ion Torrent PGM~(TM)测序系统的人mtDNA全测序分析

目的应用Ion Torrent PGM~(TM)测序系统对人线粒体DNA(mitochondria DNA,mtDNA)全序列进行分析检测,研究不同组织间mt DNA序列差异情况。方法通过法医尸体检验采集6名无关个体的组织样本,包括胸腔血液、头发、肋软骨、指甲、骨骼肌和口腔上皮。使用4对引物对线粒体全序列进行扩增,应用Ion Shear~(TM)Plus Reagents试剂盒和Ion Plus Fragment Library试剂盒等构建文库,并在Ion Torrent PGM~(TM)测序系统上进行线粒体基因组全序列测序,并针对异质性位点和在HVⅠ区域突变位点,进行Sanger测序验证。结果所有样本的全基因组mtDNA都扩增成功,6名无关个体分属于6种不同的单倍型,同一个体不同组织之间mtDNA存在异质性差异。异质性位点和HVⅠ区域突变位点采用Sanger测序结果均得到验证。通过Kappa统计方法进行一致性检验后发现,相同个体不同组织的mtDNA序列检验结果仍具有较好的一致性。结论本研究所采用的人线粒体基因组全序列的测序检验方法,可以检测出同一个体不同组织间mtDNA的异质性差异,该差异具有较高的一致性,该结果对mtDNA在法庭科学中的应用具有指导作用。     

DHPLC检测人体线粒体DNA异质性研究

目的建立筛选线粒体DNA异质性的DHPLC方法;检测线粒体DNA高变区的异质性频率。方法选取尸体18例,分别提取血、心、肝、脾、肺、肾、胰腺、脑、肌肉、皮肤、肋骨、指甲及毛发的mtDNA,用DHPLC筛选异质型样本,并用直接测序法进行验证。结果9例个体存在异质性,肌肉组织出现的异质性频率最高。结论正确认识线粒体DNA异质性对于法医学应用领域具有指导意义。     

Optimization of a duplex amplification and sequencing strategy for the HVI/HVII regions of human mitochondrial DNA for forensic casework

A duplex primer set for the amplification of mitochondrial DNA HVI and HVII control regions was evaluated for the optimization of a DNA sequencing protocol suitable for forensic casework. HVI and HVII products, with the absence of non-specific products, could be detected by agarose gel electrophoresis when as little as 0.5 and 0.1pg of DNA were amplified for 34 and 38 cycles, respectively. Because HVI and HVII amplicons are co-synthesized in the duplex PCR, fewer steps are required (lessening the risk of cross contamination events) and more frugal use of precious extracted DNA samples is possible, both desirable features for forensic casework. The ABI Prism BigDyetrade mark version 1.1 chemistry provided high quality sequencing data, with little or no background noise and uniform peak heights, outcomes that favored reliable detection of heteroplasmy, particularly at early sequence reads (<40 bases). Optimal compromise between sensitivity and sequence accuracy in the absence of noise was achieved starting at 150 mitochondrial genome copies. The protocol is effective (no sequence errors) with highly degraded DNA (average detectable template size of 200bp). Dual artificial template mixtures with the minor component at 15% suggests that heteroplasmy should be detected at this level with confidence.     

Heteroplasmy in Hair: Study of Mitochondrial DNA Third Hypervariable Region in Hair and Blood Samples*†

Abstract: 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.     

人线粒体DNA序列分析在法医学中的应用研究及其进展

综述人线粒体DNA(m tDNA)序列分析在法医学种属鉴别、个体识别,以及个体年龄推断中的应用研究及其进展,展望对m tDNA异质性的研究及建立人m tDNA数据库,并具有重要的法医学实践意义。     

人类mtDNA控制区异质性

目的观察mtDNA的点突变异质性和长度异质性。方法运用直接测序法对50名无关个体及16名母系家族成员的血液、口腔上皮细胞、头发的mtDNAHVI、HVII区序列进行分析,并对20例HVI区直接测序失败的无关个体进行克隆后测序分析。结果同一个体的三种检材样本及16名母系家族成员的序列一致,未见异质性存在;同一个体的不同克隆的C延伸区的长度有差异,存在长度异质性。但同一个体的血液和头发具有相似的长度变异类型,即长度异质性在组织间无差异。结论mtDNA碱基序列具有同质性及稳定性,适用于法医学检案。     

Current Next Generation Sequencing technology may not meet forensic standards

In a Nature paper of 2010, the concern was raised that intra-individual mtDNA variation may be more pronounced than previously believed, in that heteroplasmies are common and vary markedly from tissue to tissue. This claim taken at face value would have considerable impact on forensic casework. It turns out however that the employed technology detected the germ-line variation relative to the reference sequence only incompletely: on average at least five mutations were missed per sample, as an in silico reassessment of the data reveals. Before one can really set out to access to entire mtDNA genome data with relative ease for forensic purposes, one needs careful calibration studies under strict forensic conditions—or might have to wait for another generation.     

Heteroplasmy in hair: differences among hair and blood from the same individuals are still a matter of debate

The analysis of mitochondrial DNA (mtDNA) is a useful tool in forensic cases when sample contents too little or degraded nuclear DNA to genotype by autosomal short tandem repeat (STR) loci, but it is especially useful when the only forensic evidence is a hair shaft. Several authors have related differences in mtDNA from different tissues within the same individual, with high frequency of heteroplasmic variants in hair, as also in some other tissues. Is still a matter of debate how the differences influence the interpretation forensic protocols. One difference between two samples supposed to be originated from the same individual are related to an inconclusive result, but depending on the tissue and the position of the difference it should have a different interpretation, based on mutation-rate heterogeneity of mtDNA. In order to investigate it differences in the mtDNA control region from hair shafts and blood in our population, sequences from the hypervariable regions 1 and 2 (HV1 and HV2) from 100 Brazilian unrelated individuals were compared. The frequency of point heteroplasmy observed in hair was 10.5% by sequencing. Our study confirms the results related by other authors that concluded that small differences within tissues should be interpreted with caution especially when analyzing hair samples.     

PCR结合变性梯度凝胶电泳法检测人血mtDNA HVⅡ

目的建立简单、有效的mtDNA单倍型检测及异质性筛查技术,并获取其相应的汉族人群频率分布。方法用PCR结合变性梯度凝胶电泳(DGGE)技术对200例武汉汉族无关个体外周血mtDNA HVⅡ29～290nt区域进行分型检测。结果200例汉族无关个体中,检出17种单倍型,其单倍型多样性(HD值)为0.8826;有4名个体观察到异质性,其发生率为2%。结论PCR-DGGE是一种简单、灵敏、高效的mtDNA多态性及异质性检测技术,可应用于法医学实践。     

用PCR-DGGE技术检测人外周血mtDNA HVⅠ单倍型及异质性

目的建立简单、有效的m tDNA单倍型检测及异质性筛查技术,并获取其相应的汉族人群频率分布。方法用PCR-DGGE技术对200例武汉汉族无关个体外周血m tDNA HVⅠ15997~16174nt和16208~16401nt区域进行分型检测。结果200例汉族无关个体中,15997~16174nt和16208~16401nt区域分别检出20种和22种单倍型,其单倍型多样性(HD值)分别为0.8159和0.8844;m tDNA HVⅠ组合单倍型共90种,其HD值达0.9803。两区域分别有4名和2名个体观察到异质性,其发生率为3%。结论PCR-DGGE是一种简单、灵敏、高效的m tDNA多态性及异质性检测技术,可应用于法医学实践。     

Sequencing strategy of mitochondrial HV1 and HV2 DNA with length heteroplasmy

We describe a method to obtain reliable mitochondrial DNA (mtDNA) sequences downstream of the homopolymeric stretches with length heteroplasmy in the sequencing direction. The method is based on the use of junction primers that bind to a part of the homopolymeric stretch and the first 2-4 bases downstream of the homopolymeric region. This junction primer method gave clear and unambiguous results using samples from 21 individuals with length heteroplasmy in the hypervariable regions HV1, HV2 or both. The method is of special value for forensic casework, because sequencing of both strands of an mtDNA region is preferable in order to reduce ambiguities in sequence determination.     

Improved MtDNA sequence analysis of forensic remains using a "mini-primer set" amplification strategy

Mitochondrial DNA (mtDNA) analysis of highly degraded skeletal remains is often used for forensic identification due largely to the high genome copy number per cell. Literature from the "ancient DNA" field has shown that highly degraded samples contain populations of intact DNA molecules that are severely restricted in size (1-4). Hand et al. have demonstrated the targeting and preferential amplification of authentic human DNA sequences with small amplicon products of 150 bp or less (1,2). Given this understanding of ancient DNA preservation and amplification, we report an improved approach to forensic mtDNA analysis of hypervariable regions 1 and 2 (HV1/HV2) in highly degraded specimens. This "mini-primer set" (MPS) amplification strategy consists of four overlapping products that span each of the HV regions and range from 126 to 170 bp, with an average size of 141 bp. For this study, 11 extracts representing a range of sample quality were prepared from nonprobative forensic specimens. We demonstrate a significant increase in MPS amplification success when compared to testing methods using approximately 250 bp amplicons. Further, 16 of 17 independent amplifications previously "unreported" due to mixed sequences provided potentially reportable sequence data from a single, authentic template with MPS testing.     

Exploring of rare differences in mtGenomes between MZ twins using massively parallel sequencing

Compared with nuclear DNA, fewer DNA repair mechanisms in mitochondria and lack of proofreading capabilities in the mtDNA polymerase help introduce more variability between MZ twins. In our previous study, we used ultra-deep mtGenome sequencing to characterize point heteroplasmy and nucleotide variant in blood samples of MZ twins. In the present study, we characterize minor differences of mtGenomes in saliva and hair shaft samples from six sets of MZ twins using the Precision ID mtDNA Whole Genome Panel, Ion S5 XL system, and Converge Software. Additionally, the effectiveness of different tissue samples for differentiating between MZ twins was evaluated. Point heteroplasmies were observed in all sets of MZ twins regardless of sample type. Overall, more variants were observed in the mtGenome from hair shaft samples than that from blood and saliva samples. The results of this study further support that the mtGenome analysis could be used to distinguish MZ twins from each other.     

Human hair histogenesis for the mitochondrial DNA forensic scientist.

Analysis of mitochondrial DNA (mtDNA) sequence from human hairs has proven to be a valuable complement to traditional hair comparison microscopy in forensic cases when nuclear DNA typing is not possible. However, while much is known about the specialties of hair biology and mtDNA sequence analysis, there has been little correlation of individual information. Hair microscopy and hair embryogenesis are subjects that are sometimes unfamiliar to the forensic DNA scientist. The continual growth and replacement of human hairs involves complex cellular transformation and regeneration events. In turn, the analysis of mtDNA sequence data can involve complex questions of interpretation (e.g., heteroplasmy and the sequence variation it may cause within an individual, or between related individuals. In this paper we review the details of hair developmental histology, including the migration of mitochondria in the growing hair, and the related interpretation issues regarding the analysis of mtDNA data in hair. Macroscopic and microscopic hair specimen classifications are provided as a possible guide to help forensic scientists better associate mtDNA sequence heteroplasmy data with the physical characteristics of a hair. These same hair specimen classifications may also be useful when evaluating the relative success in sequencing different types and/or forms of human hairs. The ultimate goal of this review is to bring the hair microscopist and forensic DNA scientist closer together, as the use of mtDNA sequence analysis continues to expand.     

Validation of the barcoding gene COI for use in forensic genetic species identification

The application of forensics to wildlife crime investigation routinely involves genetic species identification based on DNA sequence similarity. This work can be hindered by a lack of authenticated reference DNA sequence data resulting in weak matches between evidence and reference samples. The introduction of DNA barcoding has highlighted the expanding use of the mtDNA gene, cytochrome c oxidase I (COI), as a genetic marker for species identification. Here, we assess the COI gene for use in forensic analysis following published human validation guidelines. Validation experiments investigated reproducibility, heteroplasmy, mixed DNA, DNA template concentration, chemical treatments, substrate variation, environmental conditions and thermocycling parameters. Sequence similarity searches using both GenBank BLASTn and BOLD search engines indicated that the COI gene consistently identifies species where authenticated reference sequence data exists. Where misidentification occurred the cause was attributable to either erroneous reference sequences from published data, or lack of primer specificity. Although amplification failure was observed under certain sample treatments, there was no evidence of environmentally induced sequence mutation in those sequences that were generated. A simulated case study compared the performance of COI and cytochrome b mtDNA genes. Findings are discussed in relation to the utility of the COI gene in forensic species identification.