The effectiveness of various strategies to improve DNA analysis of formaldehyde-damaged tissues from embalmed cadavers for human identification purposes

Formalin-fixed tissues provide the medical and forensic communities with alternative and often last resort sources of DNA for identification or diagnostic purposes. The DNA in these samples can be highly degraded and chemically damaged, making downstream genotyping using short tandem repeats (STRs) challenging. Therefore, the use of alternative genetic markers, methods that pre-amplify the low amount of good quality DNA present, or methods that repair the damaged DNA template may provide more probative genetic information. This study investigated whether whole genome amplification (WGA) and DNA repair could improve STR typing of formaldehyde-damaged (FD) tissues from embalmed cadavers. Additionally, comparative genotyping success using bi-allelic markers, including INDELs and SNPs, was explored. Calculated random match probabilities (RMPs) using traditional STRs, INDEL markers, and two next generation sequencing (NGS) panels were compared across all samples. Overall, results showed that neither WGA nor DNA repair substantially improved STR success rates from formalin-fixed tissue samples. However, when DNA from FD samples was genotyped using INDEL and SNP-based panels, the RMP of each sample was markedly lower than the RMPs calculated from partial STR profiles. Therefore, the results of this study suggest that rather than attempting to improve the quantity and quality of severely damaged and degraded DNA prior to STR typing, a more productive approach may be to target smaller amplicons to provide more discriminatory DNA identifications. Furthermore, an NGS panel with less loci may yield better results when examining FD samples, due to more optimized chemistries that result in greater allelic balance and amplicon coverage.     

Investigating DNA barcodes of plants growing in some areas of Iran with high crime rate: Quercus brantii,Curpressus arizonica,Crataegus pentagyna,Ziziphus Spina-chtista,and Buxus hyrcana

According to criminal botany, the offender unknowingly carries plant samples from the crime scene. Therefore, studying the genetic data of plants native to the crime scene can solve many ambiguities in the criminal files. In this regard, the aim of this study was to investigate the genome of 5 endemic plants in some areas of Iran with high crime rate. Quercus brantii, Curpressus arizonica, Crataegus pentagyna, Ziziphus Spina-chtista, and Buxus hyrcana were assessed using 1 genetic fragment on plastid regions (trnH-psbA) as well as 1 gene on nuclear chromosome called ITS. The alignment of DNA sequences of trnH-psbA and ITS genes was done using BioEdit, Clustal X, and Muscle v4.0 software programs. The phylogenetic analysis was performed on aligned data using Maximum Parsimony (MP) and the Bayesian methods. The Splits Tree v.4.14.4 software program was used for phylogenetic network analysis. Finally, the data combinability test was conducted using the Incongruence Length Difference (ILD) test by PAUP* software program. All data from nrDNA ITS and trnH-psbA sequences were consistent with Information Compatibility Test (ICT) results. Moreover, the nrDNA ITS indicated more resolved relationship than trnH-psbA. The results from MP and Bayesian analyses did not differ significantly between singular and combined forms, except for a slight variance in confidence interval of branches. As the phylogenetic trees provide more thorough and deeper conception of species relations, it is hoped that they would be useful to illuminate some forensic gaps in regions with high crime rates enriched by these plants, not only in Iran, but also in all areas over the world with this vegetation.     

湖南省华支睾吸虫线粒体cox1和nad1基因的克隆及进化分析

为了研究湖南省华支睾吸虫分离株线粒体细胞色素c氧化酶第Ⅰ亚基(cox1)基因部分序列(pcox1)和烟酰胺腺嘌呤二核苷酸脱氢酶亚单位Ⅰ基因(nad1)部分序列(pnad1)的遗传变异情况,并用pcox1和pnad1序列构建华支睾吸虫与其他吸虫的种群遗传进化树。应用聚合酶链反应扩增华支睾吸虫虫株的pcox1和pnad1,应用ClustalX 1.81程序对序列进行比对,然后用Phylip3.67程序中的MP法和MEGA4.0程序NJ法绘制种系发育树,并用Puzzle5.2程序构建最大似然树。结果显示,所获得的pcox1和pnad1序列长度分别为1 100bp和790bp,种系发育进化表分析表明,25个华支睾吸虫分离株位于同一分枝。证实华支睾吸虫pcox1和pnad1序列种内相对保守,种间差异较大,故可作为种间遗传变异研究的标记,从而为华支睾吸虫的分类鉴定以及进一步的分子流行病学调查和群体遗传研究奠定基础。     

Sequence polymorphism in the coding region of mitochondrial genome encompassing position 8389–8865

Analysis of the polymorphic sequences in mitochondrial DNA (mtDNA) has been widely applied to forensic tests and anthropology studies. However, these polymorphic data in human have thus far been derived from the displacement-loop and intergenic regions only. Here, we report the identification of clustered polymorphic sites in the mitochondria coding region encompassing position 8389–8865. The DNA sequences of 119 unrelated Chinese were determined by PCR amplification and direct sequencing. The results showed that heteroplasmy was found in five individuals, 39 sites were noted in this 477 bp region, and 41 haplotypes were identified. The probability of identity and allelic diversity were estimated as 0.1265 and 0.8809, respectively. The results suggest that sequence polymorphism from position 8389–8865 in human mtDNA can be used as a marker for identity investigation.     

线粒体DNA分型技术

综述了线粒体DNA的遗传特性,线粒体DNA分型技术发展历程以及线粒体DNA分型技术相关质量控制、命名原则、异质型影响、结论诠释、数据统计,并展望了线粒体DNA分型技术的未来发展.     

法医学难检样品的处理及检测方法研究

在法医物证检验中常常会遇到一些量微而保存条件差的检材,这类检材的成功分析对案件的调查和侦破常起着至关重要的作用,其关键在于能否正确提取和处理检材、并采用适当的分析方法进行检测.笔者结合多年的物证检验经验和研究,综述了常见的牙齿、烟头、毛发、微量血痕等检材的有效处理方法.     

大鼠肾细胞DNA含量与死亡时间关系的图像分析

运用计算机图像分析技术,对大鼠死后肾细胞DNA的变化进行观测,以寻找一种客观、量化的推断早期死亡时间的标准.实验选择15只大鼠,处死后,在24小时内每隔1小时取肾组织进行细胞学涂片,福尔马林液固定,Feulgen染色,自动图象分析仪测量,所得数据进行统计学分析处理.实验结果证明大鼠的早期死亡时间与肾细胞核DNA降解速率呈线性关系,其中积分光密度、平均灰度、异形指数提示此方法有可能作为辅助手段,使死亡时间推断更为精确.     

一种改良的骨组织DNA提取方法

骨组织耐腐败,当其他软组织已完全腐败后,只能用骨组织进行种属鉴定,性别鉴定和个人识别.骨组织DNA提取是骨组织DNA分析的关键.作者曾用多种方法提取过骨组织DNA,本文报道一种改良的骨组织DNA提取方法.     

大鼠脑细胞DNA含量与死亡时间关系的图像分析

运用计算机图像分析技术 ,对大鼠死后脑细胞DNA的变化进行观测 ,以寻找一种客观、量化的推断早期死亡时间的标准。实验选择 1 5只大鼠。处死后 ,在 2 4h内每隔 1h分别取脑细胞进行细胞学涂片、福尔马林液固定、Feulgen染色、自动图象分析仪测量、统计学处理。结果显示 :大鼠的早期死亡时间与其脑细胞DNA降解速率呈线性关系 ,其中积分光密度 (IOD)、平均灰度 (AG)、异形指数 (ID)提示本法有可能作为精确推断死亡时间 (PMI)的辅助手段。     

Quantifiler observations of relevance to forensic casework

The Quantifiler (QF) kit is regularly used by forensic scientists for DNA quantitation. We performed in-house validation studies which revealed some interesting observations. The QF standard displayed a two-fold difference between two different lot numbers which suggests that every standard should be tested prior to use. The Promega K562 DNA standard works well with the QF kit. c. 41% of samples that inhibited the internal PCR control (IPC) system within the QF kit still produced good Profiler Plus reactions. QIAquick was effective at removing inhibitors. The presence of dyes within casework samples were observed not to inhibit QF amplifications. Template DNA greater than 100 ng/muL appeared to inhibit the IPC. Close to identical concentration results were obtained when alternative analysis settings were used. These validation findings will assist DNA processes involved in forensic casework.