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。     

低拷贝DNA模板检验方法探讨

目的探讨扩增及检测方法对低拷贝DNA模板分型检测灵敏度的影响。方法Control DNA 9947A按比例稀释,采用IdentifilerTM和DNATyper15TM试剂扩增,循环参数设置为28和28+6个循环,平行扩增3次,分别单独检测及3次合并检测,使用310及3130分析仪检测。结果28+6个循环的基因座检出率高于28个循环;等位基因不平衡及丢失与基因座没有特异性的关联,随着DNA模板量的减少,等位基因不平衡及丢失增多;将3次扩增产物混合后检测,等位基因不平衡及丢失情况减少,分型正确率增高。结论模板DNA分3次扩增后混合检测、循环数为28+6,可提高低拷贝模板基因座的检出率。     

多重置换扩增技术用于法医学微量DNA检测效果

目的探讨多重置换扩增(MDA)技术对法医学微量DNA样品STR检测分型的效果。方法用MDA技术对不同模板量DNA进行全基因组扩增(WGA),扩增产物用实时荧光定量PCR技术定量、用Profiler PlusTM试剂盒检测基因型。结果该方法可对模板DNA增加104～106倍。1ng样品DNA的MDA产物可获得9个STR基因座和Amelogenin性别基因座的准确分型结果;低于0.1ng的样品DNA经MDA扩增后,基因座检出数增加,但可见等位基因不平衡或丢失现象。结论MDA技术可有效增加DNA模板量和提高微量DNA分型效果。但样品DNA量低于0.1ng时,MDA产物的STR分型结果判读须慎重。     

石蜡包埋人体组织STR检验的探讨

目的 探讨普通甲醛对人体组织DNA的影响及提高STR检出率的手段。方法 取少量石蜡包埋组织。65℃水浴脱蜡。Chelex-100法提取DNA，PCR扩增，循环次数分别为28次和28＋6次，扩增产物经310型测序检测。结果 普通甲醛固定5d以内的组织基本上可检出Amel及15个STR基因座，固定时间延长，检出率下降；PCR循环次数增加，灵敏度增加，但有错误分型的情况。结论 普通甲醛固定时间长短直接影响PCR—STR的检验，减少模板量有利于PCR反应成功，PCR次数为28＋6时，灵敏度增加。但应谨慎判读结果，以免错误分型。     

多重置换扩增技术用于法医学微量DNA检测效果

目的探讨多重置换扩增（MDA）技术对法医学微量DNA样品STR检测分型的效果。方法用MDA技术对不同模板量DNA进行全基因组扩增（WGA）．扩增产物用实时荧光定量PCR技术定量、用Prrfiler Plus^TM试剂盒检测基因型。结果该方法可对模板DNA增加10^4～10^6倍。1ng样品DNA的MDA产物可获得9个STR基因座和Amelogenin性别基因座的准确分型结果；低于0．1ng的样品DNA经MDA扩增后，基因座检出数增加。但可见等位基因不平衡或丢失现象。结论MDA技术可有效增加DNA模板量和提高微量DNA分型效果。但样品DNA量低于0．1ng时，MDA产物的STR分型结果判读须慎重。     

石蜡包埋人体组织STR检验的探讨

目的探讨普通甲醛对人体组织DNA的影响及提高STR检出率的手段。方法取少量石蜡包埋组织,65℃水浴脱蜡,Chelex-100法提取DNA,PCR扩增,循环次数分别为28次和28 6次,扩增产物经310型测序检测。结果普通甲醛固定5d以内的组织基本上可检出Amel及15个STR基因座,固定时间延长,检出率下降;PCR循环次数增加,灵敏度增加,但有错误分型的情况。结论普通甲醛固定时间长短直接影响PCR-STR的检验,减少模板量有利于PCR反应成功,PCR次数为28 6时,灵敏度增加,但应谨慎判读结果,以免错误分型。     

DNA提取方法和PCR循环次数对STR扩增成功率的影响

目的探讨常见载体上的微量血痕DNA的提取方法、PCR循环次数对STR扩增成功率的影响。方法分别应用Chelex-100法及Chelex-100结合纯化法对8种载体上不同大小的血痕样本进行DNA提取,并采用28次、30次及34次PCR循环进行STR扩增,分别观察其扩增成功率。结果经28次、30次及34次PCR循环,Chelex-100法提取DNA后的STR扩增成功率分别为0.2917,0.3333,0.4583,Chelex-100结合纯化法的STR扩增成功率分别为0.3750,0.4583,0.8750。结论用Chelex-100结合纯化法提取DNA,用34次循环扩增可提高STR基因座的检测成功率。     

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。     

改良IPEP法用于痕量DNA检测的实验研究

目的探讨改良扩增前引物延伸(IPEP)法对痕量DNA样本STR检测分型的效果。方法用改良IPEP法对痕量样品DNA进行全基因组扩增(WGA),扩增产物用实时荧光定量PCR技术定量、用AmpFLSTR~ Indentifiler~试剂盒作基因型检测。结果该方法可增加模板DNA约200~1100倍。基因组DNA不低于0.025ng时,可获得15个STR基因座和Amelogenin性别基因座的分型结果。基因组DNA0.01~0.025ng时,可获得9个以上基因座的分型结果。结论改良IPEP法可有效提高痕量DNA样本STR分型检验的灵敏度,有较好的实用价值。     

PCR扩增循环数增加对低拷贝模板STR分型的影响

低拷贝模板(low copy number,LCN)最初由Gill等[1]定义为低于100pg的DNA模板量.但Budowle等人[2]认为LCN定义为"正常分析随机阈值以下的任何结果的分析和解释"更为合适.应用低于试剂盒规定的最小DNA模板量进行STR扩增检验,并对结果加以分析解释,被定义为低拷贝模板STR分型[3].     

Direct comparison of post-28-cycle PCR purification and modified capillary electrophoresis methods with the 34-cycle “low copy number” (LCN) method for analysis of trace forensic DNA samples

The investigation of samples with low amounts of template DNA remains at the forefront of forensic DNA research and technology as it becomes increasingly important to gain DNA profile information from exceedingly trace levels of DNA. Previous studies have demonstrated that it is possible to obtain short tandem repeat (STR) profiles from <100 pg of template DNA by increasing the number of amplification cycles from 28 to 34, a modification often referred to as “low copy number” or LCN analysis. In this study, we have optimised post-PCR purification techniques applied after only 28 cycles of PCR, as well as using modified capillary electrophoresis injection conditions and have investigated the progressive application of these enhanced approaches. This paper reviews the characteristics of the profiles obtained by these methods compared with those obtained on the same samples after 34-cycle PCR. We observed comparable sensitivity to 34-cycle PCR in terms of the number of profiles with evidence of DNA and the number of allelic peaks per profile and we noted improved peak height and area magnitude with some sample types. Certain parameters reported to be adversely affected in 34-cycle LCN investigations, such as non-donor allele peaks and increased stutter peak ratio, were reduced by this approach. There are a number of advantages for trace samples in progressing from the standard 28-cycle process to the post-PCR processing method as compared to 34-cycle PCR method, including reduced sample consumption, reduced number of PCR amplifications required, and a staged approach to sample processing and profile interpretation.     

Simplified low-copy-number DNA analysis by post-PCR purification

Frequently, evidentiary items contain an insufficient quantity of DNA to obtain complete or even partial DNA profiles using standard forensic gentotyping techniques. Such low-copy-number (LCN) samples are usually subjected to increased amplification cylces to obtain genetic data. In this study, a 28-cycle polymerase chain reaction (PCR) was used to evaluate various methods of post-PCR purification for their effects on the sensitivity of fluorophore-based allelic detection subsequent to capillary electrophoretic separation. The amplified product was purified using filtration, silica gel membrane, and enzyme mediated hydrolysis purification techniques and evaluated for their effect on fluorescent allelic signal intensity. A purification method was selected and its effect on fluorescent allelic signal intensity was compared with that of the unpurified PCR product. A method of post-PCR purification is described which increases the sensitivity of standard 28-cycle PCR such that profiles from LCN DNA templates (<100 pg DNA) can be obtained. Full DNA profiles were consistently obtained with as little as 20 pg template DNA without increased cycle number. In mock case type samples with dermal ridge fingerprints, genetic profiles were obtained by amplification with 28 cycles followed by post-PCR purification whereas no profiles were obtained without purification of the PCR product. Allele dropout, increased stutter, and sporadic contamination typical of LCN analysis were observed; however, no contamination was observed in negative amplification controls. Post-PCR purification of the PCR product can increase the sensitivity of capillary electrophoresis to such an extent that DNA profiles can be obtained from <100 pg of DNA using 28-cycle amplification.     

Extended PCR conditions to reduce drop-out frequencies in low template STR typing including unequal mixtures

Forensic laboratories employ various approaches to obtain short tandem repeat (STR) profiles from minimal traces (<100 pg DNA input). Most approaches aim to sensitize DNA profiling by increasing the amplification level by a higher cycle number or enlarging the amount of PCR products analyzed during capillary electrophoresis. These methods have limitations when unequal mixtures are genotyped, since the major component will be over-amplified or over-loaded. This study explores an alternative strategy for improved detection of the minor components in low template (LT) DNA typing that may be better suited for the detection of the minor component in mixtures. The strategy increases the PCR amplification efficiency by extending the primer annealing time several folds. When the AmpF?STR^® Identifiler^® amplification parameters are changed to an annealing time of 20 min during all 28 cycles, the drop-out frequency is reduced for both pristine DNA and single or multiple donor mock case work samples. In addition, increased peak heights and slightly more drop-ins are observed while the heterozygous peak balance remains similar as with the conventional Identifiler protocol. By this extended protocol, full DNA profiles were obtained from only 12 sperm heads (which corresponds to 36 pg of DNA) that were collected by laser micro dissection. Notwithstanding the improved detection, allele drop-outs do persist, albeit in lower frequencies. Thus a LT interpretation strategy such as deducing consensus profiles from multiple independent amplifications is appropriate. The use of extended PCR conditions represents a general approach to improve detection of unequal mixtures as shown using four commercially available kits (AmpF?STR^® Identifiler, SEfiler Plus, NGM and Yfiler). The extended PCR protocol seems to amplify more of the molecules in LT samples during PCR, which results in a lower drop-out frequency.     

A stochastic model of the processes in PCR based amplification of STR DNA in forensic applications

In forensic DNA profiling use is made of the well-known technique of PCR. When the amount of DNA is high, generally unambiguous profiles can be obtained, but for low copy number DNA stochastic effects can play a major role. In order to shed light on these stochastic effects, we present a simple model for the amplification process. According to the model, three possible things can happen to an individual single DNA strand in each complete cycle: successful amplification, no amplification, or amplification with the introduction of stutter. The model is developed in mathematical terms using a recursive approach: given the numbers of chains at a given cycle, the numbers in the next can be described using a multinomial probability distribution. A full set of recursive relations is derived for the expectations and (co)variances of the number of amplicon chains with no, 1 or 2 stutters. The exact mathematical solutions of this set are given, revealing the development of the expectations and (co)variances as function of the cycle number. The equations reveal that the expected number of amplicon chains without stutter grows exponentially with the cycle number, but for the chains with stutter the relation is more complex. The relative standard deviation on the numbers of chains (coefficient of variation) is inversely proportional to the square root of the expected number of DNA strands entering the amplification. As such, for high copy number DNA the stochastic effects can be ignored, but they play an important role at low concentrations. For the allelic peak, the coefficient of variation rapidly stabilizes after a few cycles, but for the chains with stutter the decrease is more slowly. Further, the ratio of the expected intensity of the stutter peak over that of the allelic peak increases linearly with the number of cycles. Stochastic models, like the one developed in the current paper, can be important in further developing interpretation rules in a Bayesian context.     

A comparison of the characteristics of profiles produced with the AMPFlSTR SGM Plus multiplex system for both standard and low copy number (LCN) STR DNA analysis.

DNA STR profiles have been generated from 1 ng and low copy number (LCN) templates using 28 and 34 cycles of amplification, respectively. Characteristics which facilitate the interpretation of profiles, such as heterozygous balance, allelic dropout and stutter proportions have been quantified. We demonstrate that a reduction in DNA template coupled with an increase in amplification cycle number produces an increased rate of allelic dropout out which can be correlated to the peak areas of those alleles observed. In addition, the LCN conditions increase the degree of peak area asymmetry observed from heterozygotes and the size range of stutters. Analysis of the data allows us to develop sets of guidelines appropriate for interpreting both single and mixed DNA profiles.     

A systematic approach to improve downstream single-cell analysis for the DEPArray™ technology

Most commercially available STR amplification kits have never been fully validated for low template DNA analysis, highlighting the need for testing different PCR kits and conditions for improving single-cell profiling. Here, current strategies rely mainly on adjusting PCR cycle number and analytical threshold settings, with a strong preference for using 30 amplification cycles and thresholds at 30–150 RFU for allele detection. This study aimed to (1) determine appropriate conditions for obtaining informative profiles utilizing a dilution series, and (2) test the outcome on single cells using the DEPArray™ technology. Four routinely applied forensic STR kits were compared by using three different amplification volumes and DNA dilutions down to 3.0 pg, while two well-performing kits were used for single/pooled leucocyte and sperm cell genotyping. Besides reduced costs, the results demonstrate that a 50%–75% PCR volume reduction was beneficial for peak height evaluation. However, this was counteracted by an increased artifact generation in diluted DNA volumes. Regarding profile completeness, the advantage of volume reduction was only prominent in samples processed with Fusion 6C. For single and pooled cells, ESIFast and NGMDetect provided a solid basis for consensus profiling regarding locus failure, although locus dropouts were generally observed as stochastic events. Amplification volume of 12.5 μL was confirmed as appropriate in terms of peak heights and stutter frequencies, with increased stutter peaks being the main artifact in single-cell profiles. Limitations associated with these analyses are discussed, providing a solid foundation for further studies on low template DNA.     

Persisting fetal microchimerism does not interfere with forensic Y-chromosome typing

Forensic Y-chromosome typing applies Y-chromosomal polymorphisms to the analysis of male/female mixed stains such as vaginal swabs in rape cases. The sensitivity of this approach exceeds that of cytological techniques combined with autosomal DNA typing. Y-chromosome typing is based on the assumption that Y-chromosomal DNA found in tissue or secretions of women must originate from a male individual, usually the perpetrator. Nevertheless, it was shown recently that fetal cells can migrate into the female body during pregnancy and can persist for decades ("persisting fetal microchimerism"). The body of a woman after a pregnancy with a male embryo can thus display a small fraction of fetal cells with Y-chromosomes. Using high sensitivity PCR protocols (reamplification with nested primers and up to 60 PCR cycles) fetal cells were previously identified in a number of maternal tissues including skin, blood, muscle and solid organs. It is, however, not clear at present, whether these cells can occur in vaginal secretions, and whether they are capable of producing false positive results in forensic Y-chromosome typing. To evaluate these questions, 66 blood samples of women with at least one son and nine vaginal swabs of women without sexual intercourse in the last 2 weeks were amplified for a stretch of the SRY gene. Eight thyroid gland tissues with already established male fetal microchimerism were used as positive control samples. Blood samples of 10 young girls without history of pregnancy were used as negative controls. Using a PCR with 10 ng of extracted DNA and 30 PCR cycles ("routine sensitivity assay") none of the samples yielded positive results. However, in a PCR with 200 ng of extracted DNA and 45 PCR cycles ("high sensibility assay"), 14% of the blood samples of mothers and 33% of the vaginal swabs amplified for SRY. Our results thus show that increasing the sensitivity of the PCR method and the amount of template DNA produce positive results while protocols used for routine Y-chromosomal typing with small amounts of DNA (approximately 10 ng of DNA) and with a limited number of PCR cycles (approximately 30) can clearly eliminate this peril.     

STR analysis of artificially degraded DNA-results of a collaborative European exercise

Degradation of human DNA extracted from forensic stains is, in most cases, the result of a natural process due to the exposure of the stain samples to the environment. Experiences with degraded DNA from casework samples show that every sample may exhibit different properties in this respect, and that it is difficult to systematically assess the performance of routinely used typing systems for the analysis of degraded DNA samples. Using a batch of artificially degraded DNA with an average fragment size of approx. 200 bp a collaborative exercise was carried out among 38 forensic laboratories from 17 European countries. The results were assessed according to correct allele detection, peak height and balance as well as the occurrence of artefacts. A number of common problems were identified based on these results such as strong peak imbalance in heterozygous genotypes for the larger short tandem repeat (STR) fragments after increased PCR cycle numbers, artefact signals and allelic drop-out. Based on the observations, strategies are discussed to overcome these problems. The strategies include careful balancing of the amount of template DNA and the PCR cycle numbers, the reaction volume and the amount of Taq polymerase. Furthermore, a careful evaluation of the results of the fragment analysis and of automated allele calling is necessary to identify the correct alleles and avoid artefacts.