Comparison of STR polymorphism among a Kirgiz ethnic group from Sinkiang and other groups

Objective To study the genetic relationship between Kirgiz individuals living in Sinkiang China and analyze the difference among Kirgiz and the other population with STR polymorphisms.Methods PCR amplification was performed using PE9700,the PCR products were typed by automated sequencer and genescan.Results A database of nine STR loci of Kirgiz was established.It shows there are at least 73 STR alleles and 191 genotypes in Kirgiz.Genotype frequencies distribution showed no deviation from Hardy-Weinberg equilibrium by χ2-test.Kirgiz was compared with the other Chinese ethnic groups,then the American Black and the White.Conclusion These results suggested that the nine STR loci and Amelogenin locus were very useful in human identification,biological archaeology and gene resource studies.

A NORTHWEST DATABASE MODEL OF SHORT TANDEM REPEAT LOCI IN FORENSIC MEDICINE

Objective To establish the northwest database of short tandem repeat(STR) loci in forensic medicine. Methods Bloodstains or whole blood samples were collected from the unrelated prisoners in Xi'an city. Genetic distribution for 13 STR loci and amelogenin locus were determined in prisons based on GeneScan. One primer for each locus was labeled with the fluorescent by 5 FAM, JOE, or NED. The forensic database were generated by using multiple amplification, GeneScan, genotype, and genetic distribution analysis. Results 113 alleles and 302 genotypes were observed, with the corresponding frequency between 0.0050-0.5250 and 0.0100-0.4100. The mean H was 0.7667. The accumulative DP was 0.9999999,. The accumulative EPP was 0.9999999. The scope of PIC was 0.6036- 0.8562 . PM was less than 10 -11 . The observed and expected genotype frequencies were evaluated using χ 2 test and all were in accordance with Hardy Weinberg equilibrium ( P > 0.05 ). Conclusion STR loci is an ideal genetic marker with powerful polymorphism and stable heredity. It can be used for individual identification and paternity in forensic medicine. The forensic DNA database model can be established successfully.

Identification and characterization of short tandem repeats in the Tibetan macaque genome based on resequencing data

The Tibetan macaque, which is endemic to China, is currently listed as a Near Endangered primate species by the International Union for Conservation of Nature （IUCN）（2017）. Short tandem repeats （STRs） refer to repetitive elements of genome sequence that range in length from 1-6 bp. They are found in many organisms and are widely applied in population genetic studies. To clarify the distribution characteristics of genome-wide STRs and understand their variation among Tibetan macaques, we conducted a genome-wide survey of STRs with next-generation sequencing of five macaque samples. A total of 1 077 790 perfect STRs were mined from our assembly, with an N50 of 4 966 bp. Mono-nucleotide repeats were the most abundant, followed by tetra- and di-nucleotide repeats. Analysis of GC content and repeats showed consistent results with other macaques. Furthermore, using STR analysis software （IobSTR）, we found that the proportion of base pair deletions in the STRs was greater than that of insertions in the five Tibetan macaque individuals （P〈0.05, t-test）. We also found a greater number of homozygous STRs than heterozygous STRs （P〈0.05, t-test）, with the Emei and Jianyang Tibetan macaques showing more heterozygous loci than Huangshan Tibetan macaques. The proportion of insertions and mean variation of alleles in the Emei and Jianyang individuals were slightly higher than those in the Huangshan individuals, thus revealing differences in STR allele size between the two populations The polymorphic STR loci identified based on the reference genome showed good amplification efficiency and could be used to study population genetics in Tibetan macaques. The neighbor-joining tree classified the five macaques into two different branches according to their geographical origin, indicating high genetic differentiation between the Huangshan and Sichuan populations. We elucidated the distribution characteristics of STRs in the Tibetan macaque genome and provided an effective method for screening polymorphic STRs. Our results also lay a foundation for future genetic variation studies of macaques.

Genetic Polymorphisms of 15 STR Loci in Gansu Hui Population

The short tandem repeat (STR) markers are widely used in human identification and paternity testing in the field of forensic genetics[1].Recent researches on polymorphic STRs have led to their applications to population genetics,forensic DNA database,human individual identification,paternity testing,genetic mapping,disease linkage analysis,archaeology and potential inference of the ethnic origin of an individual[2].

ANALYSIS ON GENETIC POLYMORPHISM OF 6 STR LOCI ON CHROMOSOME 12 IN CHINESE HAN POPULATION

Objective To analyze the genetic polymorphism of 6 STR loci (D12S358, D12S1675, D12S1663, D12S1697, D12S1725 and D12S1613) on chromosome 12 in Chinese Han population. Methods EDTA-blood specimens were collected from 153 unrelated individuals of Chinese Han population in Shaanxi province. Allele and genotype frequencies for the 6 STR loci were estimated and statistical parameters of polymorphism were calculated. Results 8 alleles and 18 genotypes, 10 alleles and 17 genotypes, 9 alleles and 15 genotypes, 12alleles and 29 genotypes, 12 alleles and 31 genotypes, 8 alleles and 11 genotypes were observed at D12S358, D12S1675, D12S1663, D12S1697, D12S1725 and D12S1613, respectively. No deviations of the observed allele frequency from Hardy-weinberg equilibrium expectations were found for any of these loci. The Heterozygotes of these 6 loci were 78.89%, 66.10%, 54.95%, 79.10%, 71.98% and 59.48%, respectively. It indicated the high genetic polymorphism of the loci in Chinese Han population. Conclusion The 6 STR loci belonged to the genetic marker system of high discriminutesation and high information in Chinese Han population and can be used in the study of gene-related diseases.

Genetic Polymorphisms of 22 Novel Autosomal Short Tandem Repeat Loci in Sierra Leone Population

Background:Exploring and identifying novel alleles of noncombined DNAIndex System(CODIS)short tandem repeat(STR)loci in different ethnic groups is important for the establishment of forensic reference databases and study of population genetics.Aim:This study is aimed to explore the genetic polymorphism of 22 non-CODIS autosomal STR loci(D6S477,D18S535,D19S253,D15S659,D11S2368,D20S470,D1S1656,D22-GATA198B05,D8S1132,D4S2366,D21S1270,D13S325,D9S925,D3S3045,D14S608,D10S1435,D12S391,D7S3048,D17S1290,D5S2500,D2S1338,and D16S539)in Sierra Leone population and analyze the population genetic relationships in comparison with otherpopulations.Materialsand ethods:The amples of a total of 495 unrelated individuals(274 females and 221 males)from Sierra Leonewere examined by the Microreader^(TM)23SPID System,and their genetic polymorphisms and associated forensic parameters were calculated.The genetic relationships between Sierra Leonepopulation and other populations were evaluated as well.Results:Atotal of 287 alleles were observed with allelic frequencies ranging from 0.001 to 0.399.The cumulative power of discrimination(CPD)of the 22 autosomal STR loci was 0.99999999999999999999999999999538.The cumulative probability of exclusion(CPE)of the 22 autosomal STR loci was 0.9999998514(CPEdous)and 0.9999999999826(CPEtrios).All of the STR loci reached the Hardy–Weinberg equilibrium after Bonferroni correction.The population genetics analysis results demonstrated that Sierra Leone population exhibited distinctive genetic characteristics compared to those of East Asian populations and it had relatively close genetic distances to the Uygur population.Conclusion:The results of this study could enrich the forensic databases with Sierra Leone population.The 22 STR loci are highly polymorphic and could be used for forensic practice and population genetics studies.

基于不同STR分型试剂盒的肿瘤组织身源鉴定方法

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。

浙江省汉族人群18-STR基因座的分型资料及其应用

【目的】建立浙江地区汉族人群18个STR基因座(D8S1179、D21S11、D7S820、CSF1PO、D3S1358、TH01、D13S317、D16S539、D2S1338、D19S433、VWA、TPOX、D18S51、D5S818、FGA、PentaE、PentaD、SE33)的遗传多态性数据资料,并探讨18-STR鉴定分析系统在亲子鉴定、产前诊断等领域的应用。【方法】对浙江汉族598例无血缘关系个体,采用2组荧光标记STR-PCR复合扩增系统及毛细管电泳基因分型技术,获取18个STR基因座数据资料;在497个亲子鉴定案例中,比较18-STR与15-STR鉴定系统在亲子鉴定和产前诊断中的应用。【结果】18个STR基因座基因型频率分布均符合Hardy-Weinberg平衡(P>0.05)。18个STR基因座的杂合度在0.630～0.942之间,累积个体识别力大于0.9999999999,基因型分布与中国其它地区汉族人群存在差异。与15-STR鉴定系统相比,18-STR鉴定系统更有利于二联体亲缘关系的认定及可疑突变的判断。在胎儿亲子鉴定中偶然发现的1例21三体胎儿在D21S11、PentaD两个STR基因座出现了特征性峰型。【结论】18个STR基因座在浙江汉族人群中呈高度多态性,对法医学亲子关系的认定或排除具有较大价值,部分STR基因座的检测也有助于非整倍染色体的产前诊断。

华南地区汉族群体15个STR基因座的遗传多态性调查

【目的】调查获得华南地区汉族群体遗传多态性参数,并与以往相关文献报道的群体资料进行统计比较。同时评估PowerPlex誖16体系应用于华南汉族人群进行法医学个体识别及亲子鉴定的价值。【方法】应用PowerPlex誖16荧光标记复合扩增系统检测4786名华南地区汉族无关个体15个STR基因座的多态性,统计计算群体遗传学参数,并将获得的等位基因频率与文献报道的群体资料进行统计比较。【结果】15个STR基因座的基因型分布均符合Hardy-Weinberg平衡(P﹥0.05),共检出241个等位基因,频率在0.0001～0.5458;共1043种基因型。在13个基因座上检出共60个等位基因阶梯以外的等位基因。15个基因座的杂合度观察值(Ho)在0.6030～0.9076之间,多态信息含量(PIC)在0.5428～0.9044之间,累计个人识别率(TDP)达0.9999999999999999971,三联体累计非父排除概率(CPE)达到0.99999981,单亲鉴定累计亲权排除概率(CPE*)为0.9543。本文调查结果与以往文献报道的人群等位基因频率资料有不同程度的差异。【结论】15个STR基因座在华南汉族人群中有较高的多态性,PowerPlex誖16荧光标记复合扩增系统对华南汉族人群的个体识别及亲子鉴定具有很高的应用价值。本文调查获得的群体遗传学数据可为法医学个人识别和亲子鉴定提供结果评估的依据。

中国南方汉族群体27个Y-STR基因座的遗传多态性及突变研究

【目的】调查27个Y-STR基因座在中国南方汉族群体的遗传多态性及突变情况。【方法】采集885名中国南方汉族无关男性个体血样和911对父子血样,采用YfilerPlus扩增体系对样本进行扩增,并进行毛细管电泳检测与分型,统计相关遗传多态性参数,观察Y-STR基因座突变情况。【结果】885名无关男性个体中共观察到880种单倍型,其中875种单倍型为唯一单倍型,5种单倍型分别出现两次。单倍型多样性（HD）为0.999 987 2,系统识别能力（DC）为0.994 350 3。27个Y-STR基因座基因多态性（GD）在0.434 4（DYS438）-0.960 5（DYS385a/b）之间。在911个父子对共246 23次等位基因传递中共观察到113次突变事件,其中108次突变事件为一步突变,5次突变事件为二步突变。11个父子对观察到2个基因座同时突变,1个父子对发生3个基因座同时突变。平均突变率为4.6×10-3（95%CI：3.8×10-3-5.5×10-3）。【结论】YfilerPlus体系包含的27个Y-STR基因座在中国南方汉族群体中具有高度遗传多态性,对于法医学实践中个体识别、父系亲缘关系鉴定等具有重要意义。

Polymorphism Profile of Nine Short Tandem Repeat Loci in the Han Chinese

Nine short tandem repeat (STR) markers (D3S1358, VWA, FGA, THO1, TPOX, CSFIPO, D5S818, D13S317, and D7S820) and a sex-identification marker (Amel-ogenin locus) were amplified with multiplex PCR and were genotyped with a four-color fluorescence method in samples from 174 unrelated Han individuals in North China. The allele frequencies, genotype frequencies, heterozygosity, probability of discrimination powers, probability of paternity exclusion and Hardy-Weinberg equilibrium expectations were determined. The results demonstrated that the genotypes at all these STR loci in Han population conform to Hardy-Weinberg equilibrium expectations. The combined discrimination power (DP) was 1.05×10-10 within nine STR loci analyzed and the probability of paternity exclusion (EPP) was 0.9998. The results indicate that these nine STR loci and the Amelo-genin locus are useful markers for human identification, paternity and maternity testing and sex determination in forensic sciences.

常染色体STR突变率的研究

【目的】观察10 000例肯定亲子关系的三联体案例中STR基因座的突变事件,获取STR基因座的突变率资料。【方法】采用PowerPlexTM16系统进行15个STR基因座的检测,从10 000例肯定亲子关系的三联体案例中筛查出包含STR基因座突变的案例,确定突变等位基因的来源和步数,统计各STR基因座特异性、父源和母源特异性及等位基因特异性的突变率及其95%置信区间,分析突变的特点。【结果】10 000例三联体亲子鉴定中检出368例发生突变的案件,共计379个突变事件。突变案件的发生率为3.68%,15个STR基因座的突变率为0.10×10-3～2.30×10-3,平均突变率为1.26×10-3。各基因座的父源和母源突变率分别为0.05×10-3～1.35×10-3和0.05×10-3～0.70×10-3。统计FGA、vWA和D18S51等三个基因座一步突变的等位基因突变率分别为5.0×10-5～40.0×10-5、5.0×10-5～50.0×10-5和5.0×10-5～35.0×10-5。15个基因座的父源/母源突变比值为1.3∶1～17.0∶1,平均为3.57∶1。【结论】STR基因座突变现象普遍存在于亲子鉴定中,各基因座的突变率、父源和母源的突变率、各等位基因的突变率均存在差异,获取这些数据资料对于更准确地评判亲子鉴定结果非常必要。

中国汉族人群15个STR基因座的等位基因频率调查

目的 调查10071名中国汉族无关个体15个STR基因座的等位基因的类型及其频率，并与以往相关文献报道的汉族群体资料进行统计比较。方法 应用PowerPlex^(TM)16荧光标记复合扩增系统，对10071份中国汉族无关个体的血样DNA进行15个STR基因座的复合扩增；用ABI 377或3100遗传分析仪对扩增产物进行分型，统计15个STR基因座的基因频率。结果 15个STR基因座共发现226个等位基因，频率在0.0001～0.5512；除D8S1179基因座外，其它基因座均发现稀有等位基因，数目1～7个不等，共34个。在中国汉族人群，稀有D21S11基因座的等位基因32.1和36.2，D18S51基因座的等位基因15.2和17.2，Penta E基因座的等位基因15.2、17.4、18.4、19.4、26和27，D7S820基因座的等位基因9.2、10.1、11.1和15，Penta D基因座的等位基因18、19和20，TPOX基因座的等位基因14，FGA基因座的等位基因13，以及较常见但欧洲稀有的D21S11基因座的等位基因30.3和D7S820基因座的等位基因9.1和9.2等均为首次报道。结论 大样本基因频率调查有利于观察STR基因座的稀有等位基因；本研究结果与以往相关文献报道的结果有不同程度的差异。

2个新Y-STR基因座的序列分析和在广东汉族群体中的多态性研究

分析了Y染色体2个新STR基因座DYS522和DYS527的序列结构及其在151例广东汉族男性无关个体中的遗传多态性。结果显示,DYS522基因座为单拷贝,核心序列gata,观察到重复数目为9-13次。DYS527基因座有双拷贝,每一个拷贝的序列结构有6个稳定的重复序列和2个数目变异的重复序列,如(GGAA)3…(GGAA)2…(GGAA)2…(GGAA)3…(GGAA)4…(GGAA)3…(GAAA)m(GGAA)n。在广东汉族男性群体中观察到2个数目变异的核心序列重复总数目(m+n)为18～26次。还发现1个稀有的拷贝“15．3”。在广东汉族男性群体中,2个基因座所组成的单倍型有63种,出现最多的单倍型为11/21-22,频率为0．0728,仅出现1次的单倍型有29种,频率为0．0066。本系统单倍型多样性(HD)为0．9780,个体识别力(DP)达0．9715。在38对父子遗传中未发现DYS522和DYS527基因座发生变异。这2个Y-STR具有种属差异,能够区分“男人”和“非人”雄性动物。因此,DYS522和DYS527基因座具有高度的多态性,适用于法医学实践和人类进化的研究。

广州汉族人群12个Y-STR基因座多态性及法医学应用研究

目的研究广州地区汉族人群12个Y-STR基因座的等位基因频率分布、单倍型遗传多样性及其法医学应用价值。方法采用PowerPlexYSystem荧光标记复合扩增系统检测401例广州汉族无关个体的12个Y-STR基因座,并用3100遗传分析仪进行基因分型。结果获得了广州地区汉族无关男性个体的12个Y-STR基因座的频率分布资料,观察到398个单倍型,其基因多样性为0.99997;检测13种动物血样,在特异性区域均无扩增产物;55个父系样本,未观察到突变基因;同一男性个体的不同组织基因分型相同且女性DNA成分不影响Y-STR的扩增分型。结论该12个Y-STR基因座检测系统具有很高的识别能力,在群体遗传学研究及法医学混合检材的个人识别和父系亲缘关系鉴定中有重要应用价值。

云南汉族人群11个Y-STR基因座遗传多态性调查及法医学应用

目的调查11个Y-STR基因座及其单倍型在云南汉族人群中的遗传多态性分布,探讨其法医学应用价值,为法医学应用提供基础数据。方法应用Powerplex!Y系统对云南汉族201名无关男性个体进行11个Y-STR基因座的复合扩增,用ABI310型基因分析仪对扩增产物进行检测,统计其群体遗传学参数。结果Powerplex!Y系统前10个Y-STR基因座分别检出3、5、6、8、5、4、5、8、4、7个等位基因,DYS385a/b基因座检出56种单倍型;GD值最低为0.4273(DYS438),最高为0.9747(DYS385a/b);观察到11个Y-STR基因座共同构成的单倍型175种,其中有154种单倍型只出现1次,16种出现2次,5种出现3次,累计GD值为0.9984。结论11个Y-STR基因座具有较强的个体识别能力,可应用于云南地区汉族人群的个体识别与亲权鉴定。

成都地区汉族人群X染色体3个STR基因座的遗传多态性及其法医学应用

目的 了解 X染色体 3个 STR基因座在中国成都汉族群体的遗传多态性及其法医学应用价值。方法 利用 PCR和非变性聚丙烯酰胺凝胶电泳对中国成都地区无亲缘关系汉族个体 X染色体 3个 STR基因座进行分型 ,自动激光荧光测序仪测定 DNA序列 ,并检验女性基因型频率分布是否符合 Hardy- Weinberg平衡 ,计算法医学常用各种概率。结果 3个 STR基因座在成都地区汉族群体均具有遗传多态性 ,χ2检验表明女性的基因型频率分布符合 Hardy- Weinberg平衡。结论 为人类群体研究提供了 X染色体 3个 STR基因座的中国成都汉族群体数据 。

Y染色体STR基因座DYS385等位基因分型标准物的制备及群体遗传学研究

目的 采用分子克隆技术大量制备优质标准 STR基因座等位基因分型标准物 ,解决长期困扰STR分型上存在的准确性和标准化问题。方法 先用 PCR扩增出 Y染色体上 DYS385基因座的 9个等位基因片段 ,将其插入 p U C重组质粒中 ,经 DNA测序分析证实插入片段的结构及大小 ,按国际标准将插入的等位基因片段进行命名 ,最后经转染、扩大培养、扩增及再鉴定后制备出标准的 DYS385等位基因分型标准物。结果 应用此法制备出大量的 DYS385等位基因分型标准物 ,并将其成功地应用于该基因座在中国成都地区汉族及德国美茵茨地区高加索人群体中的基因型分布频率调查。结论 该法制备的 STR基因座等位基因分型标准物在法科学实践中应用价值极高 。