Background:The role of DNA analysis for ethnicity inferencing is a topic that attracts much interest from researchers in forensic identification,especially for identifying unknown bodies and trace evidence.So far,the ...Background:The role of DNA analysis for ethnicity inferencing is a topic that attracts much interest from researchers in forensic identification,especially for identifying unknown bodies and trace evidence.So far,the approaches considered effective for ethnic inferencing are autosomal single-nucleotide polymorphisms,Y-chromosome short-tandem repeats(STRs),and mitochondrial DNA haplotyping,which successfully demonstrates the association of specific nucleotides or patterns with population groups.Ethnic inferencing based on autosomal STRs is complex due to the nature of recombination in gamete formation.Aim:This study attempts to use clustering analysis to associate alleles and loci of autosomal STRs with population groups.Materials and Methods:We examined the allele frequency data from 19 STRs loci from the Malay Indonesian population(n=470)to compare with other populations,namely,Chinese Indonesian(n=133)and four reference populations(Malay Malaysian,Filipino,Chinese,and Caucasian).K-Medoids clustering analysis was carried out to pinpoint alleles and loci affecting the population clustering process.Results:The first stage of clustering results placed Malay Indonesians and four other Asian populations,namely,Chinese Indonesian,Malay Malaysian,Filipino,and Chinese,in Cluster 1,whereas the Caucasian group was in Cluster 2.It indicates that the CSF1PO,D5S818,and D8S1179 loci significantly distinguished the five Asian population groups from the Caucasian group,whereas D2S441,D8S1179,and D22S1045 were the three loci that significantly influenced the separation between Malay Indonesians and other groups.Conclusions:We conclude that K-medoids clustering analysis has the potential to play a role in ethnicity estimation by pinpointing specific STRs alleles.展开更多
目的探讨短串联重复序列(short tandem repeat,STR)三带型基因座同一认定似然比(likelihood ratio,LR)的不同计算策略。方法通过忽略三带型基因座、基于人群中不同类型的观测值、基于三带型基因座形成机制推导公式三个模型,对三带型基...目的探讨短串联重复序列(short tandem repeat,STR)三带型基因座同一认定似然比(likelihood ratio,LR)的不同计算策略。方法通过忽略三带型基因座、基于人群中不同类型的观测值、基于三带型基因座形成机制推导公式三个模型,对三带型基因座似然比进行计算。结果得到三个模型六种策略的LR计算方法,并分析其保守性与局限性。结论根据三体综合征发生机制推导的三带型基因座LR计算公式,可得到较为准确且可用于司法鉴定的LR值。展开更多
目的 建立基于常用STR分型试剂盒的肿瘤组织身源鉴定方法。方法 采用ForenSeq^(TM) DNA Signature Prep试剂盒检测55例配对肿瘤组织样本(肿瘤组织和同一个体正常组织成对)以及75例无关个体全血样本27个常染色体STR基因座的分型情况,并模...目的 建立基于常用STR分型试剂盒的肿瘤组织身源鉴定方法。方法 采用ForenSeq^(TM) DNA Signature Prep试剂盒检测55例配对肿瘤组织样本(肿瘤组织和同一个体正常组织成对)以及75例无关个体全血样本27个常染色体STR基因座的分型情况,并模拟55例肿瘤组织的全同胞、亲子对分型数据,统计成对肿瘤(paired carcinoma,PC)、肿瘤-无关个体(tumor-unrelated individual,UI)、肿瘤-全同胞(tumor-simulated full sibling,FS)与肿瘤-亲子(tumor-simulated parent-offspring,PO)的共有等位基因个数(number of total identical alleles,A_n)及状态一致性(identity by state,IBS)评分。以上述统计结果作为参照,建立8个常用STR分型试剂盒的肿瘤组织身源鉴定预测模型,并尝试构建一个专用于肿瘤组织身源鉴定的模型。使用另外23例配对肿瘤组织样本的检测结果对鉴定模型的准确性、灵敏度及特异度进行验证与评估。结果 (1)在任一试剂盒中,全不同基因座数量(A_0)在PC组与PO组之间差异无统计学意义。1个相同基因座数量(A_(1))、2个相同基因座数量(A_(2))和IBS评分在PC组与UI、FS、PO组之间差异均有统计学意义。(2)不同STR基因座的A_n与IBS评分在不同组别存在差异,其中,13个STR基因座(CSF1PO、D12S391、D19S433、D20S482、D2S1338、D3S1358、D4S2408、D7S820、D8S1179、FGA、TH01、TPOX、vWA)的A_(2)在PC组均高于其他STR基因座;2个STR基因座(D6S1043、PentaE)的A_(2)在UI组低于其他STR基因座。(3)成功构建了8个常用STR分型试剂盒的肿瘤组织身源鉴定预测模型以及15个STR基因座的肿瘤组织身源鉴定模型(15-STRs),灵敏度均达100%,特异度为97.56%~99.88%,准确度为97.59%~99.89%。其中,15-STRs模型的灵敏度为100%,特异度为99.88%,准确率为99.89%,高于常用商业化试剂盒。结论 本研究成功建立了8个常用STR分型试剂盒的肿瘤组织身源鉴定方法,拓展了肿瘤组织身源鉴定的应用范围。通过比较不同基因座在肿瘤组织身源鉴定中的差异,筛选出了15个特别适用于肿瘤组织身源鉴定的STR基因座,为未来肿瘤组织溯源的试剂盒构建提供了数据基础。展开更多
文摘Background:The role of DNA analysis for ethnicity inferencing is a topic that attracts much interest from researchers in forensic identification,especially for identifying unknown bodies and trace evidence.So far,the approaches considered effective for ethnic inferencing are autosomal single-nucleotide polymorphisms,Y-chromosome short-tandem repeats(STRs),and mitochondrial DNA haplotyping,which successfully demonstrates the association of specific nucleotides or patterns with population groups.Ethnic inferencing based on autosomal STRs is complex due to the nature of recombination in gamete formation.Aim:This study attempts to use clustering analysis to associate alleles and loci of autosomal STRs with population groups.Materials and Methods:We examined the allele frequency data from 19 STRs loci from the Malay Indonesian population(n=470)to compare with other populations,namely,Chinese Indonesian(n=133)and four reference populations(Malay Malaysian,Filipino,Chinese,and Caucasian).K-Medoids clustering analysis was carried out to pinpoint alleles and loci affecting the population clustering process.Results:The first stage of clustering results placed Malay Indonesians and four other Asian populations,namely,Chinese Indonesian,Malay Malaysian,Filipino,and Chinese,in Cluster 1,whereas the Caucasian group was in Cluster 2.It indicates that the CSF1PO,D5S818,and D8S1179 loci significantly distinguished the five Asian population groups from the Caucasian group,whereas D2S441,D8S1179,and D22S1045 were the three loci that significantly influenced the separation between Malay Indonesians and other groups.Conclusions:We conclude that K-medoids clustering analysis has the potential to play a role in ethnicity estimation by pinpointing specific STRs alleles.
文摘目的探讨短串联重复序列(short tandem repeat,STR)三带型基因座同一认定似然比(likelihood ratio,LR)的不同计算策略。方法通过忽略三带型基因座、基于人群中不同类型的观测值、基于三带型基因座形成机制推导公式三个模型,对三带型基因座似然比进行计算。结果得到三个模型六种策略的LR计算方法,并分析其保守性与局限性。结论根据三体综合征发生机制推导的三带型基因座LR计算公式,可得到较为准确且可用于司法鉴定的LR值。
文摘目的 建立基于常用STR分型试剂盒的肿瘤组织身源鉴定方法。方法 采用ForenSeq^(TM) DNA Signature Prep试剂盒检测55例配对肿瘤组织样本(肿瘤组织和同一个体正常组织成对)以及75例无关个体全血样本27个常染色体STR基因座的分型情况,并模拟55例肿瘤组织的全同胞、亲子对分型数据,统计成对肿瘤(paired carcinoma,PC)、肿瘤-无关个体(tumor-unrelated individual,UI)、肿瘤-全同胞(tumor-simulated full sibling,FS)与肿瘤-亲子(tumor-simulated parent-offspring,PO)的共有等位基因个数(number of total identical alleles,A_n)及状态一致性(identity by state,IBS)评分。以上述统计结果作为参照,建立8个常用STR分型试剂盒的肿瘤组织身源鉴定预测模型,并尝试构建一个专用于肿瘤组织身源鉴定的模型。使用另外23例配对肿瘤组织样本的检测结果对鉴定模型的准确性、灵敏度及特异度进行验证与评估。结果 (1)在任一试剂盒中,全不同基因座数量(A_0)在PC组与PO组之间差异无统计学意义。1个相同基因座数量(A_(1))、2个相同基因座数量(A_(2))和IBS评分在PC组与UI、FS、PO组之间差异均有统计学意义。(2)不同STR基因座的A_n与IBS评分在不同组别存在差异,其中,13个STR基因座(CSF1PO、D12S391、D19S433、D20S482、D2S1338、D3S1358、D4S2408、D7S820、D8S1179、FGA、TH01、TPOX、vWA)的A_(2)在PC组均高于其他STR基因座;2个STR基因座(D6S1043、PentaE)的A_(2)在UI组低于其他STR基因座。(3)成功构建了8个常用STR分型试剂盒的肿瘤组织身源鉴定预测模型以及15个STR基因座的肿瘤组织身源鉴定模型(15-STRs),灵敏度均达100%,特异度为97.56%~99.88%,准确度为97.59%~99.89%。其中,15-STRs模型的灵敏度为100%,特异度为99.88%,准确率为99.89%,高于常用商业化试剂盒。结论 本研究成功建立了8个常用STR分型试剂盒的肿瘤组织身源鉴定方法,拓展了肿瘤组织身源鉴定的应用范围。通过比较不同基因座在肿瘤组织身源鉴定中的差异,筛选出了15个特别适用于肿瘤组织身源鉴定的STR基因座,为未来肿瘤组织溯源的试剂盒构建提供了数据基础。
