在法医DNA分析领域,混合短串联重复序列(short tandem repeats,STR)图谱的分析一直是研究难点。当前,国内主要依靠法医进行人工分析,不仅效率低下,分析结果还存在着主观性偏好,难以满足日益增长的STR图谱分析的需求。本文提出一种新的混...在法医DNA分析领域,混合短串联重复序列(short tandem repeats,STR)图谱的分析一直是研究难点。当前,国内主要依靠法医进行人工分析,不仅效率低下,分析结果还存在着主观性偏好,难以满足日益增长的STR图谱分析的需求。本文提出一种新的混合STR图谱分析方法——全局最小残差法,不仅可以计算出分析结果,还可以预测出每个组分的混合比例。该方法首先给混合比例赋予了新的定义,然后对等位基因模型进行优化,进而综合考虑STR图谱中的所有基因座,将每个基因座的残差值进行累加求和,选择累加和最小的混合比例作为推断结果,并使用灰狼优化算法快速寻找混合比例的最优值。对于二组分STR图谱,全局最小残差法能够兼顾分析的准确性和分析速度,有利于实现大量的图谱分析。本文提出的算法在实际应用中取得了不错的效果,具有较高的应用价值,可为混合STR图谱分析领域的研究提供新的解决方案。展开更多
We describe the optimization and validation of the DNATyper^(TM)15 multiplex polymerase chain reaction(PCR)genotyping system for autosomal short tandem repeat(STR)amplification at 14 autosomal loci(D6S1043,D21S11,D7S8...We describe the optimization and validation of the DNATyper^(TM)15 multiplex polymerase chain reaction(PCR)genotyping system for autosomal short tandem repeat(STR)amplification at 14 autosomal loci(D6S1043,D21S11,D7S820,CSF1PO,D2S1338,D3S1358,D13S317,D8S1179,D16S539,Penta E,D5S818,vWA,D18S51,and FGA)and amelogenin,a sex‑determining locus.Several DNATyper^(TM)15 assay variables were optimized,including hot start Taq polymerase concentration,Taq polymerase activation time,magnesium concentration,primer concentration,annealing temperature,reaction volume,and cycle number.The performance of the assay was validated with respect to species specificity,sensitivity to template concentration,stability,accuracy,influence of the DNA extraction methods,and the ability to genotype the mixture samples.The performance of the DNATyper^(TM)15 system on casework samples was compared with that of two widely used STR amplification kits,Identifiler^(TM)(Applied Biosystems,Carlsbad,CA,USA)and PowerPlex 16®(Promega,Madison,WI,USA).The conditions for PCR‑based DNATyper^(TM)15 genotyping were optimized.Contamination from forensically relevant nonhuman DNA was not found to impact genotyping results,and full profiles were generated for all the reactions containing≥0.125 ng of DNA template.No significant difference in performance was observed even after the DNATyper^(TM)15 assay components were subjected to 20 freeze‑thaw cycles.The performances of DNATyper^(TM)15,Identifiler^(TM),and PowerPlex 16®were comparable in terms of sensitivity and the ability to genotype the mixed samples and case‑type samples,with the assays giving the same genotyping results for all the shared loci.The DNA extraction methods did not affect the performance of any of the systems.Our results demonstrate that the DNATyper^(TM)15 system is suitable for genotyping in both forensic DNA database work and case‑type samples.展开更多
文摘在法医DNA分析领域,混合短串联重复序列(short tandem repeats,STR)图谱的分析一直是研究难点。当前,国内主要依靠法医进行人工分析,不仅效率低下,分析结果还存在着主观性偏好,难以满足日益增长的STR图谱分析的需求。本文提出一种新的混合STR图谱分析方法——全局最小残差法,不仅可以计算出分析结果,还可以预测出每个组分的混合比例。该方法首先给混合比例赋予了新的定义,然后对等位基因模型进行优化,进而综合考虑STR图谱中的所有基因座,将每个基因座的残差值进行累加求和,选择累加和最小的混合比例作为推断结果,并使用灰狼优化算法快速寻找混合比例的最优值。对于二组分STR图谱,全局最小残差法能够兼顾分析的准确性和分析速度,有利于实现大量的图谱分析。本文提出的算法在实际应用中取得了不错的效果,具有较高的应用价值,可为混合STR图谱分析领域的研究提供新的解决方案。
基金the National Science and Technology Supporting Program during the 10th 5‑year plan period(2001BA801B02)。
文摘We describe the optimization and validation of the DNATyper^(TM)15 multiplex polymerase chain reaction(PCR)genotyping system for autosomal short tandem repeat(STR)amplification at 14 autosomal loci(D6S1043,D21S11,D7S820,CSF1PO,D2S1338,D3S1358,D13S317,D8S1179,D16S539,Penta E,D5S818,vWA,D18S51,and FGA)and amelogenin,a sex‑determining locus.Several DNATyper^(TM)15 assay variables were optimized,including hot start Taq polymerase concentration,Taq polymerase activation time,magnesium concentration,primer concentration,annealing temperature,reaction volume,and cycle number.The performance of the assay was validated with respect to species specificity,sensitivity to template concentration,stability,accuracy,influence of the DNA extraction methods,and the ability to genotype the mixture samples.The performance of the DNATyper^(TM)15 system on casework samples was compared with that of two widely used STR amplification kits,Identifiler^(TM)(Applied Biosystems,Carlsbad,CA,USA)and PowerPlex 16®(Promega,Madison,WI,USA).The conditions for PCR‑based DNATyper^(TM)15 genotyping were optimized.Contamination from forensically relevant nonhuman DNA was not found to impact genotyping results,and full profiles were generated for all the reactions containing≥0.125 ng of DNA template.No significant difference in performance was observed even after the DNATyper^(TM)15 assay components were subjected to 20 freeze‑thaw cycles.The performances of DNATyper^(TM)15,Identifiler^(TM),and PowerPlex 16®were comparable in terms of sensitivity and the ability to genotype the mixed samples and case‑type samples,with the assays giving the same genotyping results for all the shared loci.The DNA extraction methods did not affect the performance of any of the systems.Our results demonstrate that the DNATyper^(TM)15 system is suitable for genotyping in both forensic DNA database work and case‑type samples.
