Short tandem repeat (STR) genotyping of keratinised hair. Part 2. An optimised genomic DNA extraction procedure reveals donor dependence of STR profiles

A feasibility study of short tandem repeat (STR) genotyping of telogen phase hairs in particular, and hair shaft in general, is presented. A number of extraction procedures in common use were investigated and the quantities of nuclear DNA (nuDNA) delivered were quantified via a real-time PCR assay. The extracts were subjected to two variations on AmpFlSTR Profiler Plus PCR amplification strategies (extended cycles, two rounds of PCR) and the genotypes compared. Nuclear DNA was found to persist in human hair shafts, albeit at very low levels. Full Profiler Plus profiles consistent with the hair donor were obtained from 100 mg hair shaft samples (bleached and unbleached). These were, however, mixed profiles, indicating low copy number (LCN) contamination in the extracts. Single telogen hair clubs and single hair shafts delivered partial profiles with usually only one allele of heterozygous loci. Telogen phase hairs yielded the same amount of nuDNA (and no more) as hair shafts (either anagen or telogen). Whether hair shafts dissolved or not in lysis buffer had no effect on either the quantitated yield of DNA or on the chance of obtaining a correct genotype. These results provide evidence that genomic DNA resides on the exterior of the hair shaft and we use this information to suggest an optimal procedure for nuDNA extraction from keratinised hair samples: soaking hairs in simple digestion buffers containing Tris-HCl, a salt and a chelating agent without prior cleaning of the hair shafts. It is proposed that cleaning removes most of the recoverable DNA. This procedure was applied to obtain genotypes from 3 cm hair shafts which matched reference profiles from the donors at up to 9 out of 10 AmpFlSTR Profiler Plus STR loci. When the genotyping success was measured by counting the number of matches between the two dominant alleles at each locus for each extract with the reference DNA profile of the hair donor, the success was found to be highly dependent on the donor. The number of matching alleles varied between not less than 10 for one donor to no more than two for another donor. These results may well be linked to the environmental experience of the hairs from each donor prior to removal.     

Nondestructive Methods for Recovery of Biological Material from Human Teeth for DNA Extraction

The extraction of DNA from human skeletal remains applied to forensic, and evolutionary studies do not exclude risks, which are to be evaluated when working with unique specimens that could be damaged or even destroyed. In the present study were evaluated several nondestructive methods for recovering DNA instead of the most currently used pulverization method. Three different procedures to access inside the dental pieces (occlusal perforation, cervical perforation, and cervical cut) have been compared with the aim of recovering as many cell remains as possible to carry out a DNA extraction. Given the DNA quantitation results, a method was proposed that consists of a cervical cut to facilitate the access to the pulp cavity and a subsequent filing of the root canals down to the apex of the dental root. This methodology allows the recovery of both mitochondrial and nuclear DNA, with the minimum deterioration for the dental pieces.     

Nuclear and mitochondrial DNA quantification of various forensic materials

Due to the different types and quality of forensic evidence materials, their DNA content can vary substantially, and particularly low quantities can impact the results in an identification analysis. In this study, the quantity of mitochondrial and nuclear DNA was determined in a variety of materials using a previously described real-time PCR method. DNA quantification in the roots and distal sections of plucked and shed head hairs revealed large variations in DNA content particularly between the root and the shaft of plucked hairs. Also large intra- and inter-individual variations were found among hairs. In addition, DNA content was estimated in samples collected from fingerprints and accessories. The quantification of DNA on various items also displayed large variations, with some materials containing large amounts of nuclear DNA while no detectable nuclear DNA and only limited amounts of mitochondrial DNA were seen in others. Using this sensitive real-time PCR quantification assay, a better understanding was obtained regarding DNA content and variation in commonly analysed forensic evidence materials and this may guide the forensic scientist as to the best molecular biology approach for analysing various forensic evidence materials.     

The effects of skeletal preparation techniques on DNA from human and non-human bone

The forensic pathologist increasingly relies on the forensic anthropologist to be the consulting expert in human identification. Likewise, if identification is not possible from visual inspection of skeletal remains, the forensic biologist may be called upon to conduct DNA analysis. The possibility of downstream DNA testing needs to be considered when skeletal preparation techniques are employed to deflesh human remains, as they have the potential to strongly impact genetic analyses and subsequent identification. In this study, three cleaning techniques, boiling bone in water, in bleach, and in powdered detergent/sodium carbonate, were tested for their effect on nuclear and mtDNA recovery from a variety of human and non-human bones. A statistically significant reduction in DNA yields occurred in non-human bones cleaned with bleach, and DNA degradation was apparent electrophoretically. The human bones also showed much lower yields from bleach cleaning, while the detergent/carbonate method allowed the largest segments of DNA to be amplified, indicating it may have a less degradative effect on bone DNA than either of the other cleaning processes.     

An alternative for the extraction and storage of DNA from insects in forensic entomology

An important area of recent research in forensic entomology has been the use of insect DNA to provide identification of insects for fast and accurate estimation of time since death. This requires DNA to be extracted efficiently and in a state suitable for use in molecular procedures, and then stored on a long-term basis. In this study, Whatman FTA cards were tested for use with the Calliphoridae (Diptera). In particular, testing examined their ability to effectively extract DNA from specimens, and store and provide DNA template in a suitable condition for amplification using the polymerase chain reaction (PCR). The cards provided DNA that was able to be amplified from a variety of life stages, and thus appears to be of sufficient quality and quantity for use in subsequent procedures. FTA cards therefore appear suitable for use with calliphorids, and provide a new method of extraction that is simple and efficient and allows for storage and transportation without refrigeration, consequently simplifying the handling of DNA in forensic entomological cases.     

Use of computer software for indirect molecular genetic identification of unidentified bodies

The authors discuss the development and use of computer software for realization of indirect DNA identification, based on identification of biological relation. Estimated algorithms of this method are based on regularities of parental signs inheritance by children and consist in comparative analysis of allele states of nuclear DNA typed locuses in unidentified bodies and probable parents of these dead subjects and subsequent estimation of the coefficients of the likelihood of hypotheses of their probable blood relationship. Available software maintain the database with identification characteristics of VNTR and STR locuses, HLA DQA1 locuses, and PM system (potential set of 23 locuses). The results of identification are presented as lists of exclusions and tables with estimated likelihood coefficients for the probability expert evaluation of relationship. The suggested computer-aided method of indirect identification is a new highly effective tool for personality identification by chromosome markers under conditions of mass information processing in examinations of unidentified corpses.     

大鼠脑细胞DNA含量与死亡时间关系的图像分析

应用计算机图像分析技术 ,测定 15只大鼠死后 48h内不同时间点大鼠脑细胞核DNA含量的面积(Area)、等效直径 (Mean Dia ,MD)、异形指数 (Indexofdensity ,ID)、平均光度 (Averageopticaldensity ,AOD)、积分光度 (Integralopticaldensity ,IOD)、密度变化数 (L Den Coe ,LDC)和平均灰度 (Averagegray ,AG)等七项参数的变化值。结果证明 ,在大鼠死亡后 2 8h内 ,其脑细胞核DNA降解速率与PMI具有一定相关性。将每个参数的测量值进行多项式运算 ,获得了更能体现DNA降解趋势的二项式回归方程。其结果表明 ,应用计算机图像分析技术 ,测量机体死后DNA含量变化 ,将会成为推断PMI精确、客观的新方法。     

用引物Y_3,Y_4和DNA扩增技术作血液(痕)和毛根性别鉴定的研究

作者用引物Y_3、Y_4和DNA聚合酶链式反应(PCR)作微量人类血液(痕)和毛根的性别鉴定。扩增的靶序列位于Y染色体DNA特异3.4kb重复序列中,扩增产物为460bp。检材用量为:新鲜血液0.5μl、血痕纱纤维1mm、毛根单个。20例保存4个月的血痕与2例保存6年半的血痕性别判定结果均正确,无性别记载的保存9～11年的3例血痕显现了清晰的460bpY特异DNA扩增带。15例保存20天的自然脱落毛根性别判定结果均正确。本法省略了检材处理中的酚-氯仿抽提DNA等纯化步骤,既简化了实验操作,又减少了检验过程中外源DNA的污染机会和样品DNA的损耗,使这一性别鉴定方法更符合法医学实践的需要。     

Rapid quantification and sex determination of forensic evidence materials

DNA quantification of forensic evidence is very valuable for an optimal use of the available biological material. Moreover, sex determination is of great importance as additional information in criminal investigations as well as in identification of missing persons, no suspect cases, and ancient DNA studies. While routine forensic DNA analysis based on short tandem repeat markers includes a marker for sex determination, analysis of samples containing scarce amounts of DNA is often based on mitochondrial DNA, and sex determination is not performed. In order to allow quantification and simultaneous sex determination on minute amounts of DNA, an assay based on real-time PCR analysis of a marker within the human amelogenin gene has been developed. The sex determination is based on melting curve analysis, while an externally standardized kinetic analysis allows quantification of the nuclear DNA copy number in the sample. This real-time DNA quantification assay has proven to be highly sensitive, enabling quantification of single DNA copies. Although certain limitations were apparent, the system is a rapid, cost-effective, and flexible assay for analysis of forensic casework samples.     

STR typing of ancient DNA extracted from hair shafts of Siberian mummies

The aim of this study was to determine if ancient hair shafts could be suitable for nuclear DNA analysis and to develop an efficient and straightforward protocol for DNA extraction and STR typing of ancient specimens. The developed method was validated on modern and forensic samples and then successfully applied on ancient hairs collected from Siberian mummies dating from the 16th to the early 19th centuries. In parallel extractions including or excluding a washing step were performed at least two times for each sample in order to evaluate the influence on the quantity of nuclear DNA yielded and on the typing efficiency. Twelve ancient individuals were analyzed through our approach and full and reliable profiles were obtained for four of them. These profiles were validated by comparison with those obtained from bone and teeth DNA extracted from the same ancient specimens. The present study demonstrates that the washing step cannot be considered as deleterious for DNA retrieval since the same results were obtained by the two approaches. This finding challenges the hypothesis that recoverable nuclear DNA is only found on the outer surface of hair shafts and provides evidence that nuclear DNA can be successfully extracted from ancient hair shafts. The method described here constitutes a promising way for non-invasive investigations in ancient DNA analysis for precious or historical samples as well as forensic casework analyses.     

The ultrastructure of tissue attached to telogen hair roots

Most tissues encountered in forensic biology laboratories have been previously characterized with electron microscopy due to their medical importance. Anagen hair root cells, epithelial cells, erythrocytes, neutrophils, osteocytes, and spermatozoa have received considerable research attention at the ultrastructural level. There is no literature indicating that cells attached to removed telogen hair roots have been characterized with transmission electron microscopy. Nonetheless, telogen hairs are a frequent submission item to forensic laboratories for DNA typing. The amount of tissue attached to a telogen hair root usually determines whether that hair is suitable for nuclear DNA typing methods or mitochondrial DNA typing methods. This study used transmission and scanning electron microscopy to characterize the tissues found in three commonly occurring telogen hair root forms. The tissues were found to consist of keratinized remnant follicle, nonnucleated epithelial cells, nucleated epithelial cells, and trichilemmal keratin. These findings were consistent with the known principles of hair follicle regression. The recognition of the root structures that contain these specific tissue types may assist in the DNA typing of telogen hairs inasmuch as the quality of tissue present may be more important than the amounts of tissue present.     

Comparison of the M-Vac® Wet-Vacuum-Based Collection Method to a Wet-Swabbing Method for DNA Recovery on Diluted Bloodstained Substrates*†‡

A wet-vacuum-based collection method with the M-Vac^® was compared to a wet-swabbing collection method by examining the recovery of diluted blood on 22 substrates of varying porosity. The wet-vacuum method yielded more total nuclear DNA than wet-swabbing on 18 porous substrates, recovering on average 12 times more DNA. However, both methods yielded comparable amounts of total DNA on two porous and two nonporous substrates. In no instance did wet-swabbing significantly recover more DNA. The wet-vacuum method also successfully collected additional DNA on previously swabbed substrates. Mitochondrial DNA yields were assessed, and outcomes were generally similar to the nuclear DNA outcomes described above. Results demonstrate that wet-vacuuming may serve as an alternative collection method to swabbing on difficult porous substrates and could potentially recover additional DNA on previously swabbed substrates. However, swabbing remains the preferred collection method on substrates with visible stains and/or nonporous surfaces for reasons of convenience, simplicity, and lower cost relative to the wet-vacuum method.     

茚三酮显现汗潜指印的三种操作方法对DNA检测的影响

目的探讨并比较茚三酮显现汗潜指印的3种操作方法,即溶液浸泡法、涂抹法和喷雾法对后续DNA检测带来的影响。方法取16名志愿者的指印分4组,分为茚三酮浸泡法、涂抹法和喷雾法以及空白组,然后提取DlNA进行定量和STR分型检测。结果3种操作方法都会减少汗潜指印DNA的量,喷雾法的损失量最大,浸泡法和涂抹法结果比较接近。结论现场可疑指印检材,应根据检验需要决定指印显现和DNA提取的先后顺序。     

Possibilities of DNA sex determination in hair roots

Species- and sex-determination on hair roots were simultaneously performed using extracted DNA and a human Y chromosomespecific probe. (pH Y 2.1) After Southern hybridization, Hae III-digested DNA fragments were detected by non-radioactive digoxigenin detection system. DNA was extracted from one to five freshly plucked hair roots. The specific 2.12 kb fragment was successfully detected in male DNA samples from a single hair root. A positive identification of female DNA was more difficult. The hair root DNA was revealed to be stable at room temperature for at least 2 weeks (examination time) and produced the same specific band pattern as the DNA of fresh hair roots. In the blind tests with DNA samples from randomly plucked one to four hair roots, the rate of successful sex-determination was 95.8% on male samples (23 out of 24 samples) and 25% on female samples (4 out of 16 samples).     

尸体胸骨骨髓细胞核DNA含量变化及其与死后经过时间的关系

目的探讨推断腐败尸体死亡时间的新方法。方法应用计算机图像分析技术,对以改良的Feu lgen法染色,死后经过不同时间(<1~14d)的胸骨骨髓细胞核DNA含量进行观测,并对所得数据进行相关分析。结果胸骨骨髓细胞核DNA含量随死亡时间延长逐渐下降,死后2周DNA量达最低值;死后DNA降解速率与死亡时间呈直线相关。结论测定胸骨骨髓细胞核DNA含量有助于腐败尸体的死亡时间推断。     

Evaluation of real-time PCR amplification efficiencies to detect PCR inhibitors

Real-time PCR analysis is a sensitive template DNA quantitation strategy that has recently gained considerable attention in the forensic community. However, the utility of real-time PCR methods extends beyond quantitation and allows for simultaneous evaluation of template DNA extraction quality. This study presents a computational method that allows analysts to identify problematic samples with statistical reliability by comparing the amplification efficiencies of unknown template DNA samples with clean standards. In this study, assays with varying concentrations of tannic acid are used to evaluate and adjust sample-specific amplification efficiency calculation methods in order to optimize their inhibitor detection capabilities. Kinetic outlier detection and prediction boundaries are calculated to identify amplification efficiency outliers. Sample-specific amplification efficiencies calculated over a four-cycle interval starting at the threshold cycle can be used to detect reliably the presence of 0.4 ng of tannic acid in a 25 microL PCR reaction. This approach provides analysts with a precise measure of inhibition severity when template samples are compromised. Early detection of problematic samples allows analysts the opportunity to consider inhibitor mitigation strategies prior to genotype or DNA sequence analysis, thereby facilitating sample processing in high-throughput forensic operations.     

小鼠心肌细胞核DNA变化与死亡时间的关系

目的监测小鼠死后细胞核DNA降解的情况,探讨死后细胞核DNA降解的一般规律。方法应用单细胞凝胶电泳(SCGE)技术结合荧光显微镜和专业的计算机图像分析技术,测定111只小鼠在死后72h内不同时间点小鼠心肌组织细胞头半径、尾长度、头DNA含量比例、尾DNA含量比例、尾矩、Olive矩、头面积、尾面积八项参数的变化值。结果在个体死亡72h内,测定的八项参数指标均显示细胞核DNA降解速率和程度与死亡时间具有高度的相关性,并获得了更能体现DNA降解趋势的二项式回归方程和多元回归方程,均具有高度的统计学意义。结论应用72h内心肌组织DNA变化与死亡时间之间呈线性关系的各组回归方程,可为法医学推断死后经过时间提供一种新的、客观的、精确的方法和参考依据。     

定量PCR技术在法医学中应用的研究

目的研究荧光定量PCR技术在法医学中的应用。方法应用Taqman技术对法医各种生物检材进行DNA定量。结果该定量PCR技术对各种法医生物检材进行了准确定量,并判断检材中是否存在抑制物,从而指导了后续STR的检验。结论定量PCR技术是法医DNA检验中一项不可缺少的辅助技术。     

The primary investigation of material evidence and the evaluation of its suitability for expert biological identification by genomic "dactyloscopy"

Use of DNA "fingerprinting" method for biological analysis of material evidences exhibit new potentials for making concrete expert conclusions. But such expertise is time consuming and difficult to perform that's why it is important to evaluate fitness of expert material for DNA fingerprinting at early stages of object investigation. Method of preliminary treatment of objects sent for DNA fingerprint expertise in case of sexual assault is suggested and tested. This method allows one to evaluate objects easily from the standpoint of possibility to perform such investigation.     

Forensic DNA-typing of dog hair: DNA-extraction and PCR amplification

The forensic application of DNA-typing for the identification of dog hair provides objective evidence in the characterisation of traces found at crime scenes. During the past few years forensic dog identity testing has been improved considerably using multiplex PCR systems. However, DNA-typing from samples of one up to 10 dog hairs is often problematic in forensic science. A single dog hair contains very small quantities of DNA or the hair sample consists of hairs with roots of bad quality or even of broken hairshafts without roots. Here we describe an experimental study about dog hairs by means of a Ca(2+) improved DNA-extraction method, quantification and amplification.