Texas Population Substructure and Its Impact on Estimating the Rarity of Y STR Haplotypes from DNA Evidence*

Abstract: Three sampled populations of unrelated males—African American, Caucasian, and Hispanic, all from Texas—were typed for 16 Y short tandem repeat (STR) markers using the AmpFlSTR^® Yfiler^TM kit. These samples also were typed previously for the 13 core CODIS autosomal STR loci. Most of the 16 marker haplotypes (2478 out of 2551 distinct haplotypes) were observed only once in the data sets. Haplotype diversities were 99.88%, 99.89%, and 99.87% for the African American, Caucasian, and Hispanic sample populations, respectively. F_ST values were very small when a haplotype comprised 10–16 markers. This suggests that inclusion of substructure correction is not required. However, haplotypes consisting of fewer loci may require the inclusion of F_ST corrections. The testing of independence of autosomal and Y STRs supports the proposition that the frequencies of autosomal and Y STR profiles can be combined using the product rule.     

常染色体STR和X染色体STR联合应用于姑侄和叔侄关系鉴定

目的通过对常染色体STR和X染色体STR基因座进行分型检验,探讨姑侄、叔侄关系的鉴定策略。方法提取案例中被检女孩和另外3名个体（女性2名,疑为被检女孩的姑姑;男性1名,疑为被检女孩的叔父）的血样DNA,采用Goldeneye 20A系统和AGCU 21＋1系统分别进行常染色体STR基因座的复合PCR扩增,用Mentype○RArgus X-12试剂盒和本室自主研制的16重X染色体STR扩增体系分别进行X染色体STR基因座的复合PCR扩增,用3130 XL遗传分析仪进行毛细管电泳和基因型分析。结果依据常染色体STR基因型结果及姑侄、叔侄关系指数计算结果,不排除2名被检姑姑和与被检女性存在姑侄关系;不排除被检叔叔和与被检女性存在叔侄关系,X染色体STR分型结果支持此鉴定意见。结论对于姑侄、叔侄关系鉴定案例,X染色体STR基因座是常染色体STR基因座的良好补充,两者联合运用可获得可靠的鉴定意见。     

1066例新疆汉族人群21个常染色体STR基因座遗传多态性分析

目的研究21个常染色体STR基因座(CSF1PO,D3S1358,D5S818,D7S820,D8S1179,D13S317,D16S539,D18S51,D21S11,FGA,TH01,VWA,D2S1338,D19S433,D1S1656,D12S391,D2S441,D10S1248,TPOX,D22S1045,SE33)在新疆汉族人群中的遗传多态性。方法用GlobalFiler^TM R PCR Amplification荧光标记试剂盒对1066例新疆汉族无关个体的DNA进行PCR扩增,3500遗传分析仪电泳分析,用GeneMapper■ID-X v1.4软件分析等位基因片段大小,用Modified-Powerstates和Arlequin v3.5分析软件进行等位基因频率和法医学常用参数统计分析。结果在新疆汉族人群中,21个常染色体STR基因座不存在连锁不平衡现象,基因型分布符合Hardy–Weinberg平衡,共检出282个等位基因和1147种基因型,杂合度期望值(He)范围从0.6291(TPOX)到0.9428(SE33),多态信息含量(PIC)范围从0.5648(TPOX)到0.9393(SE33),累计个体识别率(CDP)>0.99999999999999999999。结论新疆汉族人群21个常染色体STR基因座具有较高多态性,可以用于法医学亲权鉴定和个体识别,也可以用于人类学和遗传学研究。     

Multiplexing of Y chromosome specific STRs and performance for mixed samples

A combination of four Y-specific polymorphic STR loci was amplified simultaneously using fluorescently labeled primers. Multiplex conditions required optimization to eliminate constant bands and amplification products for female DNA. A series of experiments was carried out for mixtures of DNA from two males, and from male and female individuals for the Y-specific STRs and an autosomal locus. For the male/male mixtures amplified with the Y specific system, and amplified for an autosomal locus, the minor component in the mixture could only be identified up to a ratio of 1:10, 1:50 respectively. In male/female DNA mixtures the Y STR alleles could be identified for the highest ratio tested, 400 pg male in DNA in 800 ng female DNA which amounts to a ratio of 1:2000.     

贵州汉族19个STR基因座多态性及法医学应用

目的调查19个常染色体STR基因座在贵州汉族人群中的等位基因分布,评估其在法医学中的应用价值。方法应用Goldeneye~(TM) DNA身份鉴定系统20A试剂盒,研究贵州520名汉族无关健康个体19个常染色体STR基因座多态性。用310型遗传分析仪进行毛细管电泳,Gene Mapper~ID v3.1进行基因分型。结果 19个常染色体STR基因座的杂合度为0.603 8~0.916 4,个体识别率为0.790 0~0.985 6,非父排除率为0.295 5~0.826 9,多态信息含量为0.553 5~0.908 9,累积个体识别率为1-1.230 0×10~(-22),累积非父排除率为0.999 999 99。贵州汉族和其他五个地域的汉族两两之间等位基因频率比较,仅贵州汉族与山东汉族、辽宁汉族、山西汉族之间存在基因频率差异具有统计学意义。结论 D19S433等19个常染色体STR基因座在贵州汉族人群中具有良好的遗传多态性,对群体遗传学和法医物证学研究有应用价值。     

Effectiveness of Coupled Application of AmpFℓSTR Yfiler Kit and Reduced Size Y‐chromosomal Short Tandem Repeat Analysis for Archeological Human Bones

The AmpF?STR Yfiler PCR Amplification (Yfiler) kit continues to be improved for a better analytical efficiency in cases of highly degraded DNA. The authors endeavored to determine whether coupling of the Yfiler kit with supplemental multiplex amplification of some Y‐STR loci is a more efficient analytical mode for poorly preserved human femurs (n = 15) discovered at Korean archeological sites. To reveal locus profiles not easily obtained by Yfiler analysis, custom‐designed primers were adopted for the DYS390, DYS391, DYS392, DYS438, DYS439, and DYS635 loci. The success rate for 16 Y‐STR locus profiles obtained from the 15 femurs was improved from 18.33% (in the use of Yfiler kit only) to 49.17% (the coupled use of Yfiler and custom‐designed primers). In this study, the authors established that the custom‐designed primers offer a markedly improved success rate for obtainment of Y‐STR profiles from degraded aDNA not easily identified by sole use of the Yfiler assay.     

中国北方汉族与维吾尔族群体8个STR位点的遗传多态性

目的调查中国北方汉族与维吾尔族群体8个STR位点的遗传多态性。方法应用荧光标记引物试剂盒及基因扫描技术检测vWA、TH01、TPOX、CSF1PO、D5S818、D13S317、D7S820、D16S539位点等位基因。结果100例汉族群体共检出62个等位基因,累计非父排除率为0.9975;50例维吾尔族群体共检出52个等位基因,累计非父排除率为0.9973。2群体总个人识别机率均超过0.9999。基因频率分布2群体间存在显著性差异。结论8个STR位点在汉族与维吾尔族群体中具有较高的遗传多态性,频率分布有民族差别。     

Internal validation study of the PowerPlex® Y23 system

The PowerPlex Y23 System is a 23-loci, 5-color Y-STR multiplex designed for genotyping forensic casework samples, database samples and paternity samples. The kit contains: all 12 loci in the current PowerPlex Y System, the additional 5 loci found in AmpFlSTR Y-filer, plus 6 new loci. An internal validation study of the PowerPlex Y23 kit was therefore conducted including the following aspects: sensitivity, mixture studies of male–male and female–male DNA, performance with simulated inhibition and stutter calculations. 100 Caucasians living in Switzerland were also typed using the PowerPlex Y23 kit.     

A Y‐Chromosomal Haplotype with Two Short Tandem Repeat Mutations*

Abstract:  The male‐specific Y‐chromosomal short tandem repeat (STR) is a useful tool in forensic casework. The Y haplotype comprised of 16 loci, which is amplified simultaneously by AmpFlSTR^® Yfiler^TM PCR kit and provides strong exculpatory evidence in individual identification. We reported a rare Y‐STR profile with a null allele at the DYS448 locus and an off‐ladder allele at the DYS456 locus, when genotyping material from a vaginal swab in an alleged rape case. Sequence analysis revealed that the DYS448 null allele was a true type of null allele because of a total deletion of 11 upstream repeats and 9 bp of the N₄₂ region, and there were numerous primer binding site mutations as well. The amplicon of the DYS456 locus was a small 92‐bp fragment that was off‐ladder, and sequencing analysis showed that there were only 10 repeats (AGAT)₁₀. This Y chromosome haplotype that was comprised of two variations provided helpful evidence for personal identification.     

11个Y—STR基因座遗传多态性研究

目的 调查11个Y染色体STR基因座的遗传多态性。方法 利用PCR扩增和聚丙烯酰胺凝胶电泳技术对广州地区汉族群体无关男性血样进行11个Y—STR基因座的分型。结果 11个Y—STR基因座在广州地区汉族群体分别发现3～5个等位基因,GD值最低为0.3037(DYS434),最高为0.8455(DYS390)。结论 11个Y—STR基因座在广州地区汉族群体均具有较高的遗传多态性,可应用于法科学个体识别和亲子鉴定。     

STR data for PowerPlex 16 System from Neuquen population,SW Argentina

Allele frequencies for the 15 autosomic STR loci included in the PowerPlex 16 System kit (Promega) were estimated from a sample of 111 unrelated individuals living in Neuquen province, southwest of Argentina. Population showed to be in HWE.     

SiFa~(TM) 23 Plex试剂盒(提取测试版)在汉族人群中的法医学调查

目的评估SiFa~(TM) 23 Plex试剂盒(提取测试版)的性能及其所包含的STR基因座在汉族人群中的群体遗传学信息。方法应用试剂盒对1 000名汉族健康无关个体进行分型检测,检测试剂盒有效性并统计分析STR基因座的频率数据及群体遗传学参数信息。结果该试剂盒最小扩增体系可以为6.25μL,标准体系25μL中DNA含量低至125 pg可获取理想分型图谱。试剂盒中包含的21个常染色体STR基因座在1000人份中共检测到267个等位基因,均符合Hardy-Weinberg平衡。新增加的两个STR基因座D1S1656和D10S1248分别检测到15和11个等位基因,多态信息含量丰富。结论 SiFa~(TM) 23 Plex试剂盒(提取测试版)对于血液样本检测性能优越,准确性、重复性、灵敏度均可满足法医学检案需求,可以应用于法医学实际检案及DNA建库工作。     

Autosomal short tandem repeat analysis of ancient DNA by coupled use of mini- and conventional STR kits

Abstract: Multiplex autosomal short tandem repeat (STR) genotyping enables researchers to obtain genetic information from ancient human samples. In this study, we tested newly developed AmpF?STR^® MiniFiler? kit for autosomal STR analysis of ancient DNA (aDNA), using human femurs (n = 8) collected from medieval Korean tombs. After extracting aDNA from the bones, autosomal STR analyses were repeated for each sample using the AmpF?STR^® MiniFiler? and Identifiler? kits. Whereas only 21.87% of larger‐sized loci profiles could be obtained with the Identifiler? kit, 75% of the same loci profiles were determined by MiniFiler? kit analysis. This very successful amplification of large‐sized STR markers from highly degraded aDNA suggests that the MiniFiler? kit could be a useful complement to conventional STR kit analysis of ancient samples.     

广西地区3个群体15个STR基因座频率多态性

目的调查广西地区仡佬族、仫佬族、瑶族无关个体的15个STR基因座(D8S1179、1321S11、D7S820、CSF1PO、D3S1358、TH01、D13S317、D16S539、D2S1338、D19S433、vWA、TPOX、D18S51、D5S818、FGA)多态性,研究其在法医学检验中的应用价值。方法 应用AmpFISTR IdentifilerTM荧光标记复合扩增系统,对314例仡佬族、332例仫佬族、238例瑶族无关个体血样DNA进行15个STR基因座的复合扩增,用ABI 3100遗传分析仪对扩增产物进行检测,GeneScan、GenoTyper软件进行基因分型,统计计算15个STR基因座的群体遗传学参数。结果IdertifilerTM系统的15个STR基因座在仡佬、仫佬、瑶族的累积偶合率为1.839×10-16~5.073×10-17,累积非父排除率为0.9999983~0.9999991。结论该15个STR基因座足可满足仡佬族、仫佬族、瑶族法医学的个体识别及亲权鉴定的需要。     

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.     

26个Y-STR基因座遗传多态性及突变调查

目的 调查26个Y-STR基因座的突变率和遗传多态性,研究其法医学应用效能.方法 本文以575对蒙古族父子对为模板,统计26个Y-STR基因座的突变率,并且研究26个Y-STR基因座在黑龙江省蒙古族、江西省汉族及福州市汉族等3个地区777个无关男性个体中的遗传多态性,评估该试剂盒的法医学应用价值.结果 26个Y-STR...     

山东汉族人群19个STR基因座的遗传多态性

目的调查山东汉族人群19个STR基因座的群体遗传学资料,为亲权鉴定提供遗传学数据。方法采用GoldeneyeTM20A试剂盒对山东汉族人群中205例无关个体进行基因分型,得到19个STR基因座的等位基因频率及群体遗传学参数。对Identifile一、SinoFilerTM、PowerPlex16和GoldeneyeTM20A4个试剂盒进行比较,并对l例特殊的亲子鉴定案件进行分析。结果获得山东汉族人群19个STR基因座的群体遗传学参数。累积个体识别率（CDP）及累积非父排除率（CPE）从高到低分别为GoldeneyeTM20A、SinoFilerTM、PowerPlex16、IdentifilerTM试剂盒。对实际案件进行分析．作为二联体,IdentifilerTM试剂盒无被排除基因座,而SinoFilerTM、PowerPlex16和GoldeneyeTM20A试剂盒均不能排除父子关系。结论与IdentifilerTM、SinoFilerYn和PowerPlex163种试剂盒进行比较．GoldeneyeTM20A试剂盒效能更高．但不能完全满足二联体鉴定的要求。     

二联体亲权鉴定风险分析

目的探讨二联体亲权鉴定时存在的风险。方法选取22组经Goldeneye~(TM) 20A试剂盒检测后只有一个或没有不符合基因座的无关个体对构建假想家系。对其增加检测STRtyper-10G和/或AGCU 21+1 STR系统直至所有组不符合基因座个数大于3个,累积父权指数(CPI)不大于0.000 1。以三种规则:(1)不符合基因座数大于3个;(2)CPI值小于0.000 1;(3)同时满足(1)和(2),作为排除依据,使用不同数量的基因座(19个、26个、39个和46个)进行检测,讨论无关个体对的排除情况是否存在差异。结果 22组无关个体对,使用19个基因座和39个基因座以上的检测系统达到排除结果的分别为0组和22组。结论二联体亲子鉴定,使用19个基因座进行检测仍存在结果错判,39个基因座以上的检测系统能更有效的避免二联体的鉴定风险。     

24个Y-STR基因座等位基因频率的群体差异分析

目的调查华东地区汉族无关个体24个Y-STR基因座的群体遗传学多态性,比较华东汉族和广东汉族人群间的群体差异性。方法应用GFS 24Y STR荧光检测试剂盒,对华东地区268名汉族无关个体24个Y-STR基因座进行群体遗传学分析。比较华东汉族和广东汉族人群的等位基因频率,进行群体差异分析。结果华东地区268名汉族无关个体24个Y-STR基因座共检出235个等位基因,267种单倍型,GD值范围为0.564 9~0.966 8。华东汉族和广东汉族人群在DYS622、DYS552、DYS443等12个基因座的等位基因间的差异有统计学意义。结论 GFS 24Y STR荧光检测试剂盒中的Y-STR基因座具有良好的遗传多态性,可应用于父系亲缘关系鉴定。     

Reduction of Powerplex® Y23 Reaction Volume for Genotyping Buccal Cell Samples on FTATM Cards

PowerPlex^® Y23 is a novel kit for Y‐STR typing that includes new highly discriminating loci. The Israel DNA Database laboratory has recently adopted it for routine Y‐STR analysis. This study examined PCR amplification from 1.2‐mm FTA punch in reduced volumes of 5 and 10 μL. Direct amplification and washing of the FTA punches were examined in different PCR cycle numbers. One short robotically performed wash was found to improve the quality and the percent of profiles obtained. The optimal PCR cycle number was determined for 5 and 10 μL reaction volumes. The percent of obtained profiles, color balance, and reproducibility were examined. High‐quality profiles were achieved in 90% and 88% of the samples amplified in 5 and 10 μL, respectively, in the first attempt. Volume reduction to 5 μL has a vast economic impact especially for DNA database laboratories.