PCR产物纯化增强STR分型强度的研究

目的研究PCR产物纯化对微量DNA的STR分型的影响。方法使用25pg/μL的9947标准基因组DNA为模板,标准程序扩增和STR分型检测。设立对照组A和实验组B、C、D。实验组分别使用分子筛(Qiagen DyeEX2.0spin kit)、超滤膜(Amicon Ultra-0.5,100KD)、亲和层析(Qiagen MinElute Column)3种DNA纯化方法,对照组不做任何处理。结果与对照组相比,3种方法均可显著提高STR分型强度(P峰高<0.001),平均峰高约为对照组的4倍,并且3种方法对提高STR分型强度无显著差异(P峰高=0.249)。结论 PCR产物纯化能显著提高微量DNA的STR分型强度,可用于骨骼、脱落细胞等微量DNA检材的检验。     

快速PCR扩增体系的建立及法医学应用

目的建立快速PCR扩增体系,探讨其在法医实践中的应用价值。方法设置不同的缓冲液、酶浓度与Mg SO4浓度、热循环参数等,观察不同参数对扩增结果的影响,建立快速PCR扩增体系。使用该体系对常见检材进行STR分型,与常规方法扩增的结果比较,考察其分型准确性与扩增用时。结果本文建立的快速PCR扩增体系含DNA TyperTM19试剂盒的Primer Mix(5×)2μL;Ta KaRa试剂的Fast BufferⅡ(10×)1μL,Speed STARTMHS DNA Polymerase(5U/μL)0.3μL,Mg SO4(50mmol/L)为0.1μL。扩增程序为95℃120s;95℃2s、61℃15s,27个循环;72℃60s。结论快速PCR扩增体系分型结果准确,用时仅19min,缩短了常规扩增用时,有较大的法医学应用价值。     

快速PCR扩增检验体系的建立及技术指标验证

目的建立PCR快速扩增程序和体系,并对其技术指标进行验证。方法运用快速扩增酶Fast Start与DNA TyperTM15 plus primer mix组合并优化建立快速扩增体系,对50份静脉血卡和35份案例检材提取的DNA进行扩增,并对体系检测结果的准确性、稳定性和检材适应性进行验证;采用不同稀释浓度的标准品9947,采用快速扩增方法进行检测,验证体系的灵敏度。结果模板DNA浓度达到0.50ng/μL,采用快速扩增体系可能获得准确分型;扩增耗时仅为69min,比常规扩增方法明显缩短;不同种类检材,经检测均获得良好分型图谱,同一份样本重复实验结果一致、稳定。结论本文建立的快速扩增体系可显著提升检测速率,其灵敏度、准确性、稳定性、检材适用性等技术性能,可满足实际检验的需求。     

AmpFISTR Sinofiler快速PCR扩增初探

<正>本文实验选择AmpFISTR Sinofiler试剂盒作为研究对象,对如何缩短PCR扩增时间进行了初步探讨。1材料与方法1.1主要材料AmpFISTR Sinofile试剂盒,QIAGEN Fast CyclingPCR试剂盒,9947A DNA模板(100pg/μL),均为美国AB公司产品。     

PCR扩增循环数与低拷贝模板DNA的STR分型

目的探讨PCR扩增循环数对低拷贝模板DNA的STR分型的影响。方法模板DNA(9947A)的不同扩增用量(含低拷贝模板量),采用ProfilerPlus试剂盒,扩增循环数分别为28、30、32、34、38次,3100型基因分析仪(ABI,美国)检测结果。结果循环数从28次增至38次,模板DNA量最低检出量可从0.25ng减少至0.0312ng;先循环28次后,每反应加0.3μlAmpliTaqGoldDNA聚合酶,再循环6次较1次34个循环的检测灵敏度高,相当于1次38个循环的效果。结论增加PCR扩增循环数,可能影响低拷贝模板DNA的STR分型。     

磁珠法自动化纯化现场检材DNA方法研究

目的利用TE-MAGS在TECAN工作站上结合磁珠试剂盒,建立自动化工作站批量纯化现场检材DNA的方法,并探讨其在法医物证检案中的应用。方法灵敏度测试:标准品使用0.1ng/μL 9947A,用200μL TES稀释制备DNA总量0.1ng~1ng共10种的标准样品,采用本文方法提取纯化,使用IdentifilerTM试剂盒扩增,用3130XL型测序仪检测,Gene Mapper ID-X分析,分析STR图谱质量;纯化能力测试:在1ng总量的标准样品中加入腐殖酸、血红素,采用本文方法提取纯化、扩增检测,分析STR图谱质量;实际案件应用对比:收集304份现场检材,分别采用本方法和硅珠法进行提取纯化,经扩增检测,统计对比两种提取纯化方法 STR分型成功率。结果灵敏度测试:0.1ng~0.2ng总量标准样品提取的DNA模板,扩增后可检测到部分基因座STR图谱,0.3ng~1ng总量标准样品提取的DNA模板,扩增后可以得到完整的STR图谱;纯化能力测试:对混合有一定浓度的腐殖酸、血红素的标准样品的提取产物检测图谱未见明显抑制;实际案件应用对比测试:304份现场检材工作站磁珠法检出成功率(50%)高于硅珠法(40.8%)。结论本文所建立的方法缓冲范围较大,回收率高,纯化能力强,提取产物STR分型成功率高,适合现场检材批量化DNA检验。     

Chelex-100提取生物检材DNA实时PCR定量研究

目的研究Chelex-100法提取的生物检材DNA用量与复合STR分型成功率的关系。方法113份各种生物检材采用Chelex-100法提取DNA，应用Quantifiler人类DNA定量试剂盒在ABI 7500荧光定量PCR仪上进行实时PCR定量，同时用Identifiler复合扩增系统在ABI 3100遗传分析仪上对这些DNA样品进行STR分型。结果各种生物检材提取的DNA浓度分别为：37份滤纸、纱布血痕0．042～5．28ng／μl，16份口腔拭子1．15—4．21ng／μl，18份烟头0．016～1．46ng／μl，10份肋软骨0．531—14．40ng／μl，8份肌肉5．75—24．80ng／μl，7份指甲0．788—11．50ng／μl，17份精斑0．79～99．50ng／μl。在建立的8μl扩增体系中，根据上述结果，调整用于复合STR扩增的DNA模板量在0．5—3ng之间，大部分样品可获得完全的STR分型。结论Chelex-100法提取的检材DNA模板用量在0．5—3ng之间可得到有效STR扩增，浓度为0．5ng／μl以上的DNA样品，用小体积模板（1μl）比大体积（3μl）模板扩增效果好。     

AmpF(l)STR(R) Identifiler(R) Plus试剂盒快速直接PCR扩增初探

目的 探索可应用于法医实践的快速直接PCR扩增方法,以缩短扩增时间,提高STR分型速率.方法 联合运用AmpF(l)STR(R) Identifiler(R) Plus试剂盒与TaKaRa快速PCR检测试剂构建快速直接PCR体系,以FTA血卡为模板,采用优化后的扩增程序在快速PCR仪上进行扩增,分型结果与常规直接扩增方法相比较.结果 AmpF(l)fSTR(R) Identifiler(R) Plus试剂盒与TaKaRa的快速PCR检测试剂针对血卡的联合扩增,所得STR分型结果与常规方法一致,扩增用时由常规直接扩增所需的175 min缩短为55 min.结论 采用快速直接PCR方法进行扩增,可得到与常规直接扩增一致的DNA分型,扩增时间明显缩短,DNA分型速率大幅提高.     

微腔型PCR芯片用于法医DNA分析的初步研究

目的为了克服传统PCR热循环仪体积大,运行电压高,耗时长,只能在实验室中应用的缺点,研究了一种微腔型PCR芯片,以期实现现场对STR片段的复合扩增。方法采用在PCR反应缓冲液中加入不同浓度的BSA溶液对芯片进行表面优化处理的方法及不同酶量优化实现对STR片段的有效扩增。结果使用浓度为0．5mg／mL的BSA可得到清晰完整的STR分型结果;加大酶量有益于扩增效率的提高。结论该种微腔型PCR芯片经初步优化后可有效地对STR片段进行复合扩增,经进一步优化可真正实现法医DNA分析的更加微量化和快速化。     

模板DNA用量对荧光STR复合扩增检测的影响

目的 探讨模板DNA用量对荧光STR复合扩增检测的影响,寻求荧光STR复合扩增检测的最适扩增模板DNA用量。方法 采用模板DNA(9947A)不同的扩增用量,对Profiler Plus试剂盒的基因座进行扩增,在3100型全自动遗传分析仪上作了检测。结果 3100型遗传分析仪检测的最适扩增模板DNA用量在0.31～2.5ng之间。结论 模板DNA量过高或过低均会影响荧光STR复合扩增检测结果的可靠性。     

2种陈旧骨骼、牙齿DNA纯化方法的比较

目的比较有机法+QIAquick纯化法和DNA IQ磁珠法对陈旧骨骼和牙齿DNA的纯化效果。方法选择10份陈旧骨骼和12份牙齿样本,进行消化后分别采用有机法+QIAquick纯化法和DNA IQ磁珠法进行提取纯化,进行DNA定量后用SinofilerTM试剂盒进行检测。结果 2种方法纯化的骨骼、牙齿DNA的IPC CT值无显著差异。有机法+QIAquick纯化法纯化的骨骼、牙齿DNA平均浓度分别为0.180ng/μL±0.068ng/μL和0.132ng/μL±0.027ng/μL,所有样品均获得全部基因分型。DNA IQ磁珠法纯化的DNA平均浓度分别为0.038ng/μL±0.028ng/μL和0.036ng/μL±0.007ng/μL,有5份骨骼和6份牙齿样本仅获得部分基因分型或未能分型。结论有机法+QIAquick纯化法对陈旧骨骼、牙齿DNA的纯化效果优于DNA IQ磁珠法。     

PCR扩增3因素对低拷贝模板STR分型的影响研究

目的探讨低拷贝模板(low copy number,LCN)STR扩增方法,提高LCN检材的检验成功率。方法采用Profiler P lusTM试剂盒与9947A对照DNA,改变Taq酶量、体系、循环次数3个因素进行扩增检验,了解各变量对扩增检测的影响。结果对低拷贝模板DNA,单纯增加Taq酶量或反应体系,扩增效率改善不明显;增加循环数,显著提高检验灵敏度;低于0.01ng的模板DNA,同时增加扩增体系、Taq酶量、循环数在一定程度上提高扩增效率。结论对于影响扩增的Taq酶量、体系、循环次数3个因素中,循环数影响最大,但应慎用34次及以上循环数;三者同时增加,对于低于0.01ng模板DNA的扩增可有效改善。     

Rapid amplification of commercial STR typing kits

Forensic DNA typing is currently conducted in approximately 8–10 h. The process includes DNA extraction, quantitation, multiplex PCR amplification, and fragment length detection. Today's commercial multiplex short tandem repeat (STR) typing kits are not optimized for rapid PCR thermal cycling. Current protocols require approximately 3 h for amplifying a multiplex containing 15 STR loci plus amelogenin. With the continuing development of miniaturization technologies such as microfluidic and micro-capillary devices, there is a desire to reduce the overall time required to type DNA samples. Such miniature devices could be used for initial screening at a crime scene, at a border, and at airports. There is also the benefit of reducing the required PCR amplification time for labs typing single-source reference samples. Surveys of fast processing polymerases working in combination with rapid cycling protocols have resulted in the development of a ‘rapid’ PCR amplification protocol. Results are obtained in less than 36 min run on a standard peltier-based thermal cycler employing a heating rate of 4 °C/s. Capillary electrophoresis characterization of the PCR products indicates good peak balance between loci, strong signal intensity and minor adenylation artifacts. Genotyping results are concordant with standard amplification conditions utilizing a standard 3 h (non-rapid) thermal cycling procedure. The rapid assay conditions are robust enough to routinely amplify 0.5 ng of template DNA (with 28 cycles).     

运用酚-氯仿法结合磁珠法提取蝇蛆体内人类DNA

目的建立运用酚-氯仿法结合磁珠法从蝇蛆嗉囊内提取人类DNA的方法,从而提高STR分型检验的灵敏度。方法采用酚-氯仿法对蝇蛆嗉囊内容物中的人类DNA进行提取,提取产物经磁珠法纯化浓缩后用QuantifilerTM人类DNA定量试剂盒在7500型实时荧光定量PCR仪上进行PCR定量,再用AmpF■STR IndentifilerTM试剂盒在3130XL-Avant遗传分析仪上对这些DNA样本进行STR分型。结果本研究建立的方法可增加模板DNA浓度约为单独使用酚-氯仿法的2倍。用此方法提取到的DNA浓度[（0.218±0.041）ng/μL]可获得全部16个STR分型结果。结论酚-氯仿法结合磁珠法可以有效地提高提取到的人类DNA样本STR分型检验的灵敏度,对于从事法医昆虫学方面研究的工作者有较好的实用价值。     

A multiplexed system for quantification of human DNA and human male DNA and detection of PCR inhibitors in biological samples

Forensic analysts routinely encounter samples containing DNA mixtures from male and female contributors. To obtain interpretable Short Tandem Repeat (STR) profiles and select the appropriate STR analysis methodology, it is desirable to determine relative quantities of male and female DNA, and detect PCR inhibitors. We describe a multiplex assay for simultaneous quantification of human and human male DNA using the ribonuclease P RNA component H1 (RPPH1) human target and the sex determining region Y (SRY) male-specific target. A synthetic oligonucleotide sequence was co-amplified as an internal PCR control. Standard curves were generated using human male genomic DNA. The SRY and RPPH1 assays demonstrated human specificity with minimal cross-reactivity to DNA from other species. Reproducible DNA concentrations were obtained within a range of 0.023-50 ng/μl. The assay was highly sensitive, detecting as little as 25 pg/μl of human male DNA in the presence of a thousand-fold excess of human female DNA. The ability of the assay to predict PCR inhibition was demonstrated by shifted IPC Ct values in the presence of increasing quantities of hematin and humic acid. We also demonstrate the correlation between the multiplex assay quantification results and the strength of STR profiles generated using the AmpF?STR^®PCR Amplification kits.     

Internal validation of 29 autosomal SNP multiplex using a ABI 310 genetic analyser

In the last few years genetic identification and paternity testing have begun to make increasing use of autosomal SNP (Single Nucleotide Polymorphism) typing as a supplement or alternative to STR analysis. With the improvement in detection technology SNP analysis is likely to be easier and more sensitive, with the generation of new methods and multiplex systems for a growing array of SNP markers. SNPforID consortium developed 52 SNP PCR multiplex for human identification purposes detected with 23 plex and 29 plex single base extension reactions (Auto1 and 2 respectively). In this study, internal validation for the 29 SNPs of Auto2 was carried out by performing a 29 plex PCR and single base extension reaction on control samples and previously analyzed forensic casework and subsequent detection with an AB 310 Genetic Analyzer. We tested the accuracy, precision, sensitivity and reproducibility of the Auto2 multiplex with this instrument in our laboratory. We used 9947A control DNA samples of the AmpF?STR Identifiler™ kit to test the validation parameters together with non-probative DNA samples from whole blood and buccal swab samples of 29 healthy donors from different parts of Istanbul. Good results were obtained but interpretation of the peak patterns obtained on the AB 310 requires care and thorough optimization before they can be readily compard to those obtained from multiple capillary AB 31xx Analyzers. We succesfully optimized and validated the SNPforID Auto2 multiplex system for identification analyses in our laboratory.     

DNA IQ磁珠法结合Maxwell~（TM） 16自动仪提取接触DNA

目的研究DNA IQ磁珠法结合MaxwellTM 16自动仪对接触DNA提取的应用价值。方法 151份案件接触DNA检材95℃裂解后,采用DNA IQ磁珠法结合MaxwellTM 16自动仪提取DNA,然后进行DNA定量和STR分型检测,统计各种类型的接触DNA含量I、PC CT值和STR分型成功率。结果 151份案件接触DNA检材中,除果核平均DNA获得量为9.51ng以外,其它接触检材的平均DNA获得量均大于10ng,烟蒂检验成功率最高为93%,果核检验成功率较低,为60%。所有DNA样品的IPC CT值均在27左右,纯度高。结论大部分接触DNA检材采用DNA IQ磁珠法结合MaxwellTM 16自动仪可提取到足以进行STR分型的DNA。     

Quantitative PCR overestimation of DNA in samples contaminated with tin

Metals can pose challenges while conducting forensic DNA analysis. The presence of metal ions in evidence-related DNA extracts can degrade DNA or inhibit PCR as applied to DNA quantification (real-time PCR or qPCR) and/or STR amplification, leading to low success in STR profiling. Different metal ions were spiked into 0.2 and 0.5 ng of human genomic DNA in an “inhibition study” and the impact was evaluated by qPCR using the Quantifiler™ Trio DNA Quantification Kit (Thermo Fisher Scientific) and an in-house SYBR Green assay. This study reports on a contradictory finding specific to tin (Sn) ions, which caused at least a 38,000-fold overestimation of DNA concentration when utilizing Quantifiler Trio. This was explained by the raw and multicomponent spectral plots, which indicated that Sn suppresses the Quantifiler Trio passive reference dye (Mustang Purple™, MP) at ion concentrations above 0.1 mM. This effect was not observed when DNA was quantified using SYBR Green with ROX™ as the passive reference, nor when DNA was extracted and purified prior to Quantifiler Trio. The results show that metal contaminants can interfere with qPCR-based DNA quantification in unexpected ways and may be assay dependent. The results also highlight the importance of qPCR as a quality check to determine steps for sample cleanup prior to STR amplification that may be similarly impacted by metal ions. Forensic workflows should recognize the risk of inaccurate DNA quantification of samples that are collected from substrates containing tin.     

Rapid and high-throughput forensic short tandem repeat typing using a 96-lane microfabricated capillary array electrophoresis microdevice

A 96-channel microfabricated capillary array electrophoresis (muCAE) device was evaluated for forensic short tandem repeat (STR) typing using PowerPlex 16 and AmpFlSTR Profiler Plus multiplex PCR systems. The high-throughput muCAE system produced high-speed <30-min parallel sample separations with single-base resolution. Forty-eight previously analyzed single-source samples were accurately typed, as confirmed on an ABI Prism 310 and/or the Hitachi FMBIO II. Minor alleles in 3:1 mixture samples containing female and male DNA were reliably typed as well. The instrument produced full profiles from sample DNA down to 0.17 ng, a threshold similar to that found for the ABI 310. Seventeen nonprobative samples from various evidentiary biological stains were also correctly typed. The successful application of the muCAE device to actual forensic STR typing samples is a significant step toward the development of a completely integrated STR analysis microdevice.