Developmental validation of the PowerPlex ESX 16 and PowerPlex ESX 17 Systems

We describe the developmental validation study performed on the PowerPlex^® ESX 16 (European Standard Extended 16) and the PowerPlex^® ESX 17 Systems, part of a suite of four new DNA profiling kits developed by Promega in response to the ENFSI and EDNAP groups’ call for new STR multiplexes for Europe. The PowerPlex^® ESX 16 System combines the 11 loci compatible with the UK National DNA Database, contained within the AmpFlSTR^® SGM Plus^® PCR Amplification Kit, with five additional loci: D2S441, D10S1248, D22S1045, D1S1656 and D12S391. The multiplex was designed to incorporate these five new loci as mini- and midi-STRs while maintaining the loci found in the AmpFlSTR^® SGM Plus^® kit as standard size. The PowerPlex^® ESX 17 System amplifies the same loci as the PowerPlex^® ESX 16 System, but with the addition of a primer pair for the SE33 locus. Tests were designed to address the developmental validation guidelines issued by the Scientific Working Group on DNA Analysis Methods (SWGDAM), and those of the DNA Advisory Board (DAB). Samples processed include DNA mixtures, PCR reactions spiked with inhibitors, a sensitivity series, and 306 United Kingdom donor samples to determine concordance with data generated with the AmpFlSTR^® SGM Plus^® kit. Allele frequencies from 242 white Caucasian samples collected in the United Kingdom are also presented. The PowerPlex^® ESX 16 and ESX 17 Systems are robust and sensitive tools, suitable for the analysis of forensic DNA samples. Full profiles were routinely observed with 62.5 pg of a fully heterozygous single source DNA template. In mixture analysis, a range of 52-95% of unique minor contributor alleles was observed at 19:1 mixture ratios where only 25 pg of the minor component was present. Improved sensitivity combined with the robustness afforded by smaller amplicons has substantially improved the quantity of information obtained from degraded samples, and the improved chemistry confers exceptional tolerance to high levels of laboratory prepared inhibitors.     

HLA血型亲权鉴定系统分析软件的开发及应用

应用FoxPro2．5系统开发了HLA亲权鉴定软件,程序运行中有汉字提示,使用方便。对63例HLA亲权鉴定案例进行复核计算,所得结果与人工计算结果一致,证明程序计算结果可靠,可在实际检案中应用。     

对Cofiler体系在亲子鉴定中应用价值的研究

将商品化 Profiler Plus和 Cofiler扩增检测试剂盒用于亲子鉴定案例和无关个体血样的分析。 186例亲子鉴定案中,母－子－假设父三联体 149例,假设父－子二联体 37例。在 149例含双亲和孩子的鉴定中,有 127例认定存在亲生血缘关系,其 RCP值平均为 99.98％;其余 22例排除了被检父为孩子生父,排除机率为 14.77％,排除指标平均为 6.1个。在 37例含单亲及孩子的鉴定中,有 23例认定存在亲生血缘关系,其 RCP值平均为 99.92％;其余 14例排除被检父为孩子生父,排除机率为 37.84％,平均有 5个不吻合的 STR位点出现。若特意省去三人组合案例中的母亲,将其作为单亲案件进行统计,仅检测 Profiler Plus体系的 9个 STR位点时,则 RCP值平均为 99.1959％,案例中 21.51％将不能得出明确的结论。同时检测 Profiler Plus和 Cofiler体系共 13个 STR位点,则案例中 97.31％能排除或认定生父,案例中 2.69％通过补充母亲样本能排除或认定生父。 Cofiler体系中 6个 STR位点的累积排除率达 0.9825。上述数据表明, Cofiler试剂盒在单亲鉴定案件中有着重要的应用价值。     

Validation and casework application of a Y chromosome specific STR multiplex

A series of validation experiments was performed for a Y chromosome specific STR multiplex system following the suggestions made by the Technical Working Group DNA Analysis Methods (TWGDAM). The multiplex PCR products were detected on Perkin-Elmer 373 and 377 automated sequencers using two labeling colors. No problems regarding the stability, robustness and sensitivity of the Y STR multiplex were observed. Mixture studies revealed a cut off rate similar to autosomal STRs for mixtures of male DNAs and no interference of any female admixture. The comparison of the Y STR results to the autosomal typing results for 56 nonprobative semen stains and swabs, showed a slightly higher success rate in detecting the semen donor’s alleles for the Y STR multiplex. Two examples are shown to illustrate the usefulness of Y STR typing for DNA mixtures. In one case the Y STR results confirmed an isolated exclusion; in the other case, the interpretation of a mixture was clarified since the Y STR results proved the presence of DNA from at least two semen donors. Y STR typing is a valuable addition to the forensic DNA testing panel.     

A novel platform for the modular integration of forensic assay setup and medium- to high-throughput purification of nucleic acids

With its extraction and assay setup modules, the QIAsymphony^® provides a highly flexible solution for processing forensic samples in a medium- to high-throughput scale. We tested the sensitivity of extraction, precision of sample processing, and accuracy of automated assay setup of this integrated system. Results attest to QIAsymphony's ability to isolate DNA from a spectrum of common forensic samples and process these samples without cross-contamination. Furthermore, accurate assay setup for downstream applications, like PCR, make this system highly suited for enhancing laboratory workflow.     

Forensic genetic analysis of the population of Gujarat with PowerPlex 21 multiplex system

The present investigation assessed the allele frequencies and forensic parameters for the loci included in PowerPlex 21 multiplex system (Promega, USA) in 101 unrelated individuals residing in the state of Gujarat, India. The study likewise introduces the first global report on polymorphism on Penta D and Penta E autosomal STR loci from the population of Gujarat, India. The obtained outcomes in the study revealed that the considered STR multiplex system is highly polymorphic and suitable for forensic genetic analysis.     

亲子鉴定中STR基因座的基因突变分析

目的探讨Identifiler^TM荧光标记复合扩增试剂盒15个STR基因座在亲子鉴定中的基因突变特点。方法应用Identifiler^TM荧光标记复合扩增试剂盒检测676例亲子鉴定案，对其中1～2个突变基因座加做HLA等位基因检测或Y—STR基因座检测。结果在认定亲子关系的676例中，观察1304次减数分裂，Identifiler^TM荧光标记复合扩增试剂盒中的15个基因座确定19例突变，其中D18S51基因座4例，D2S1338基因座3例，D8S1179、D16S539、vWA、D7S820、D13S317基因座各2例，D5S818和TH01基因座各1例，D21S11、FGA、D3S1358、D19S433、TPOX、CSF1P0基因座未见突变；一步突变的17例，二步突变的为1例，四步突变的1例；1个基因座发生突变的18例，2个基因座同时发生基因突变的为1例；突变来自父亲与来自母亲的比例为13：2，4例来源不能确定。结论用Identifiler^TM荧光标记复合扩增试剂盒检测到1—2个基因座发生突变，须增加对其它遗传标记的检测。     

PowerPlex~(TM) 16体系在亲子鉴定中的应用评估

目的 评估PowerPlexTM16体系在亲子鉴定中的检验能力。方法 以633例亲子鉴定案例为基础,调查PowerPlexTM16体系15个STR基因座的群体遗传学数据资料,并对该体系在亲子鉴定中的排除能力及遗传稳定性进行评估。结果 879名无关个体共检出197个等位基因,739种基因型,累计个体识别力为1×10-30,累计非父排除率为0.999999999999987。633例亲子鉴定案件中有95例确定为排除亲权,平均排除指标为6个。18例表现出1个STR基因座突变的现象,1例表现出2个STR基因座突变的现象。结论 PowerPlexTM16体系应用于亲子鉴定是高效、可靠的。     

An inter-laboratory study of DNA-based identity,parentage and species testing in animal forensic genetics

The probative value of animal forensic genetic evidence relies on laboratory accuracy and reliability. Inter-laboratory comparisons allow laboratories to evaluate their performance on specific tests and analyses and to continue to monitor their output. The International Society for Animal Genetics (ISAG) administered animal forensic comparison tests (AFCTs) in 2016 and 2018 to assess the limitations and capabilities of laboratories offering forensic identification, parentage and species determination services. The AFCTs revealed that analyses of low DNA template concentrations (≤300 pg/µL) constitute a significant challenge that has prevented many laboratories from reporting correct identification and parentage results. Moreover, a lack of familiarity with species testing protocols, interpretation guidelines and representative databases prevented over a quarter of the participating laboratories from submitting correct species determination results. Several laboratories showed improvement in their genotyping accuracy over time. However, the use of forensically validated standards, such as a standard forensic short tandem repeat (STR) kit, preferably with an allelic ladder, and stricter guidelines for STR typing, may have prevented some common issues from occurring, such as genotyping inaccuracies, missing data, elevated stutter products and loading errors. The AFCTs underscore the importance of conducting routine forensic comparison tests to allow laboratories to compare results from each other. Laboratories should keep improving their scientific and technical capabilities and continuously evaluate their personnel’s proficiency in critical techniques such as low copy number (LCN) analysis and species testing. Although this is the first time that the ISAG has conducted comparison tests for forensic testing, findings from these AFCTs may serve as the foundation for continuous improvements of the overall quality of animal forensic genetic testing.     

Real-time forensic DNA analysis at a crime scene using a portable microchip analyzer

An integrated lab-on-a-chip system has been developed and successfully utilized for real-time forensic short tandem repeat (STR) analysis. The microdevice comprises a 160-nL polymerase chain reaction reactor with an on-chip heater and a temperature sensor for thermal cycling, microvalves for fluidic manipulation, a co-injector for sizing standard injection, and a 7-cm-long separation channel for capillary electrophoretic analysis. A 9-plex autosomal STR typing system consisting of amelogenin and eight combined DNA index system (CODIS) core STR loci has been constructed and optimized for this real-time human identification study. Reproducible STR profiles of control DNA samples are obtained in 2 h and 30 min with ≤0.8 bp allele typing accuracy. The minimal amount of DNA required for a complete DNA profile is 100 copies. To critically evaluate the capabilities of our portable microsystem as well as its compatibility with crime scene investigation processes, real-time STR analyses were carried out at a mock crime scene prepared by the Palm Beach County Sheriff's Office (PBSO). Blood stain sample collection, DNA extraction, and STR analyses on the portable microsystem were conducted in the field, and a successful “mock” CODIS hit was generated on the suspect's sample within 6 h. This demonstration of on-site STR analysis establishes the feasibility of real-time DNA typing to identify the contributor of probative biological evidence at a crime scene and for real-time human identification.     

青岛地区汉族人群13个STR基因座的频率分布及法医学应用

目的　调查青岛地区汉族人群无关个体的 13个STR基因座 (D3S135 8、VWA、FGA、D8S1179、D2 1S11、D18S5 1、D5S818、D13S317、D7S82 0、D16S5 39、TH0 1、TPOX、CSFIPO)的基因频率分布 ,研究其遗传多态性及其在法医学个体识别及亲子鉴定中的应用价值。　方法　用美国ABI - 310型遗传分析仪对ProfilerPlus和Cofiler两个系统的 13个STR基因座的复合扩增产物进行毛细管电泳及四色荧光自动分析检测 ,基因分型软件为GeneScanv3.1和Genotyperv2 .5 .2。　 结果　获得 13个STR基因座在青岛地区汉族人群的基因频率分布数据 ,13个STR基因座的PIC >0 .5 ,DP >0 .71,CCE =0 .999999,TDP值接近 1,TPm =1.2× 10 -14 ,家系调查符合孟德尔遗传规律。　结论　ProfilerPlus和Cofiler两个系统的 13个STR基因座在法医学个体识别及亲子鉴定中具有较高的应用价值。     

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。     

Validation and implementation of the PowerPlex 16 BIO System STR multiplex for forensic casework

The PowerPlex 16 BIO multiplex short tandem repeat (STR) system contains the 13 CODIS loci (FGA, TPOX, D8S1179, vWA, D18S51, D21S11, TH01, D3S1358, CSF1PO, D16S539, D7S820, D13S317, and DS5S818), plus two pentanucleotide repeat loci (Penta D and Penta E) and the sex-identifying locus. Amelogenin. The PowerPlex 16 BIO System is optimized for use with the Hitachi FMBIO gel imaging systems. A consortium of seven independent laboratories collaborated to perform the studies defined by the FBI standards for performing a developmental validation, including the evaluation of sample concordance, percent stutter determination, nonprobative casework, precision, sensitivity, mixture determination, effect of substrates, the impact of environmental insults, and species specificity. All samples tested for concordance were consistent except for one sample from the Virginia Division of Forensic Science database that displayed discordance at D13S317, a locus whose primer sequence was altered. Stutter values were comparable to those of other STR multiplex systems, the precision was comparable to other multiplexes analyzed by gel electrophoresis, the DNA profiles were unchanged by the substrate upon which the blood samples were placed, and the nonprobative casework samples re-typed for the PowerPlex 16 BIO System were consistent with previous typing results. When greater than 0.125 ng of DNA was placed into the PowerPlex 16 BIO System amplification reaction, a full profile was generated by all laboratories. The mixture study results were comparable to those reported for other multiplex systems, the environmental study demonstrated a loss of larger molecular weight loci when samples were incubated at elevated temperatures for a prolonged period of time, and the only notable cross species hybridization was observed with primate DNA samples. This extensive validation work performed demonstrates that the PowerPlex 16 BIO System provides STR data of a quality comparable with other PowerPlex STR multiplex kits as well as other widely used STR multiplexes and is thus suitable for evidentiary casework analysis as well as database sample profiling.     

Customizing a commercial laboratory information management system for a forensic genetic laboratory

The need for high-throughput laboratories to comply with regulatory requirements makes data management an important aspect of forensic genetics. A Laboratory Information Management System (LIMS) enables efficient workflows and ensures traceability if designed and implemented properly. We customized a commercial LIMS to support STR typing of reference samples according to in-house defined requirements. The customization focused on data validity, traceability and automated solutions.     

Calculation and implementation of sample-wide stochastic thresholds for forensic genetic analysis of STRs and SNPs for massively parallel sequencing platforms

Capillary electrophoresis (CE) analysis of short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) use a stochastic threshold to consider the possibility of missing alleles (dropouts) or detecting additional alleles (drop-ins). In CE, this threshold may be approximately 200 RFU, and peak heights are assessed relative to this threshold. In next generation sequencing (NGS), also known as massively parallel sequencing (MPS), STRs are identified by their sequence, and specific alleles are identified by their repeat number and intra-allelic variation. Abundance is approximated by the number of sequence reads for each allele. The total number of reads generated for each marker in a sample depends on factors such as the numbers of samples pooled for sequencing, the number of markers in the assay, the integrity and quantity of the input DNA sample, and the inter-locus balance of the assay. For multiplexes that contain both autosomal and sex-linked markers, the biological sex of the sample also influences total reads per locus. To normalize these variables and better establish a robust stochastic threshold, a sample-wide metric is proposed for estimating the possibility of dropouts or drop-ins based on the variance of the inter-locus balance of the markers across a sample. The intuition is that samples with variable allele balance globally are more likely to have noisier data and therefore require more stringent read count thresholds. This method is robust to sequencing multiplexity, biological sex and manufacturing lot variation.     

单亲案亲权鉴定结果判定策略

目的探讨用STR基因座进行单亲鉴定出现矛盾基因座时下结论的策略。方法根据基因频率和遗传规律,推导单亲案亲权鉴定时的非父排除率。根据平均单亲非父排除率和平均突变率,用二项分布公式分别计算出现不同数目矛盾基因座时真父和假父的概率和似然率(亲权指数)。结果对STR共显性基因座,其单亲非父排除率的计算公式为:PEM=∑i=n1pi2(1-pi)2 ∑i相似文献   

Atomic force microscopy as a biophysical tool for nanoscale forensic investigations

The atomic force microscope (AFM) has found its way to the arsenal of tools available to the forensic practitioner for the analysis of samples at the nano and microscales. As a non-destructive probing tool that requires minimal sample preparation, the AFM is very attractive, particularly in the case of minimal or precious sample. To date, the use of the AFM has primarily been in the arena of imaging where it has been complementary to other microscopic examination tools. Forensic applications in the visual examination of evidence such as blood stains, questioned documents, and hair samples have been reported. While a number of reviews have focused on the use of AFM as an imaging tool for forensic analyses, here we not only discuss these works, but also point to a versatile enhancement in the capabilities of this nanoscale tool – namely its use for force spectroscopy. In this mode, the AFM can determine elastic moduli, adhesion forces, energy dissipation, and the interaction forces between cognate ligands, that can be spatially mapped to provide a unique spatial visualization of properties. Our goals in this review are to provide a context for this capability of the AFM, explain its workings, cover some exemplary works pertaining to forensic sciences, and present a critical analysis on the advantages and disadvantages of this modality. Equipped with this high-resolution tool, imaging and biophysical analysis by the AFM can provide a unique complement to other tools available to the researcher for the analysis and characterization of forensic evidence.     

D6S1043和D12S391基因座在亲权鉴定中的应用

目的研究D6S1043和D12S391基因座在亲权关系鉴定案件中的应用价值。方法应用荧光标记复合扩增系统对日常检案中所收集的192名汉族无关个体血样DNA进行PCR扩增,用ABI3100-Avant遗传分析仪对扩增产物进行毛细管电泳,用GeneMapperv3.2软件进行基因分型,统计分析D6S1043和D12S391基因座的多态信息。结果在D6S1043和D12S391基因座分别发现12个等位基因,它们在中国汉族人群中的个体识别能力分别为0.9656和0.9510,二联体非父排除率分别为0.573和0.510,三联体非父排除率分别为0.731和0.679。结论D6S1043和D12S391基因座具有高度多态性,在亲权鉴定中具有重要应用价值。     

中国法医学会物证专业委员会法医DNA分析的若干建议

中国法医学会法医物证学专业委员会与国际法医遗传学会中文专委会于2006年10月在成都召开学术会议。我们的讨论强调有必要将国际法医遗传学会的信息及时传递到中国。因此,按照国际法医遗传学会的指南,我们推荐混合斑分析,法医DNA数据库及新遗传标记选择标准供同行参考。     

中国5个群体D20S85基因座的遗传多态性

目的 了解中国5个群体D20S85基因座的群体遗传学数据,比较它们之间的遗传学差异,探讨其在法医学应用中的意义。方法 分别收集5个群体622名无关个体的血样,Chelex-100快速抽提法或饱和酚/氯仿法抽提DNA;扩增后经PAGE垂直板电泳、银染,进行D20S85基因座分型。结果 在5个群体622名无关个体中,共检出9个等位基因,并首次在广东汉族和广西壮族群体中检出等位基因14;每个群体基因频率大于0.05的均为6个,D20S85*6为最常见等位基因。5个群体共观察到35种基因型,群体内基因型频率分布均符合Hardy-Weinberg氏平衡,各群体间基因型构成比无显著性差异。观察140次减数分裂未发现突变。各群体的期望杂合度为0.7720～0.7912;非父排除率,在三联体为0.7538～0.7594,二联体为0.3988～0.4297;个人识别率为0.9175～0,9272;多态信息含量为0.7442～0.7656。应用于亲子鉴定和个人识别案例,效果满意。结论 D20S85基因座是法医学应用价值较高的遗传标记系统。