Development of a pentaplex X-chromosomal short tandem repeat typing system and population genetic studies

Quadruplex and pentaplex systems for polymerase chain reaction amplification of X-chromosomal short tandem repeats DXS101, HPRTB, DXS8377, DXS981 (STRX1) and DXS6789 were developed for automated profiling of liquid and membrane-bound DNA samples. Chinese, Japanese and Thai populations were typed using a quadruplex system, while German and Philippine populations were analyzed using a five-locus system. Out of 88 meioses studied in Philippine family samples at each locus, a possible one repeat deletion (allele 51 to 50) at DXS8377 was observed in a father-daughter pair. Exact tests performed on genotype data from females in the Philippine, German and Thai populations indicated that these groups conform to Hardy-Weinberg equilibrium. Exact tests for population differentiation indicate significant variations in allele distributions, particularly at loci DXS101, DXS981 and DXS6789. Considered individually, DXS8377 was the most polymorphic and HPRTB the least polymorphic locus in these five populations. When the forensic efficiency of the quadruplex system was calculated, the combined power of discrimination among males (PD(M)) was no lower than 0.998, while among females the combined PD(F) was at least 0.9999 in all populations. The combined power of paternity exclusion was a minimum of 0.998 in trio cases and 0.98 in motherless cases. The addition of locus DXS6789 to the German and Philippine population databases using a pentaplex increased the forensic efficiency of the analysis system.     

广东汉族DXS10011和DXS8377单体型

目的调查DX10011和DXS8377两个X染色体STR在广东汉族男性群体中的遗传多态性。方法DNA样本来自广东汉族男性无关个体,PCR后用聚丙烯酰胺凝胶电泳和银染法进行DNA分型。结果在113名个体中,DXS10011和DXS8377分别检出20和12个等位基因。DXS10011-DXS8377共有72种不同的单体型,最多见的单体型只出现了3次。在没有母亲时,DXS10011-DXS8377的女孩的非父排除率为0.9588。在83个孩子为女孩的三联体家系和29个有两个孩子的家系中,DXS10011和DXS8377均表现为共显性连锁遗传,且没有发现突变。结论本数据表明DXS10011和DXS8377在复杂的亲权鉴定中可提供高的遗传多态性信息。     

西安汉族X染色体上6个STR位点的遗传多态性

目的调查西安汉族人群6个位于X染色体上的短串联重复序列:DXS8378、DXS7132、DXS6789、DXS101、HPRTB和DXS7423的基因及基因型频率分布。方法应用PCR和变性聚丙烯酰胺凝胶电泳及银染技术检测结果。结果在120例女性无关个体中,DXS8378、DXS7132、DXS6789、DXS101、HPRTB和DXS7423分别检出5、6、11、10、8和4个等位基因;分别检出10、17、29、32、22和7种基因型;此6个位点女性的基因型频率分布均符合Hardy-Weinberg平衡。结论此6个X染色体STR位点均有较高的个体识别率,在个体识别和女孩的亲权鉴定中有应用价值,对疾病相关研究有实际意义。     

Validation of the X-linked STR DXS6801

This paper presents sequence and population genetic data of the X-linked microsatellite marker DXS6801 (GDB:G00-365-276) which is a tetranucleotide repeat polymorphism representing eight alleles 109-141 bp in length. Data were obtained from a sample of 1146 unrelated German individuals. DXS6801 is located 99.7 cM from Xptel, nearby DXS6809 [Int. J. Legal Med. 117 (2003) 241] and DXS6789 [Forensic Sci. Int. 119 (2001) 42] in Xq21. The new marker could be added to the panel of ChrX STRs, especially usable as a part of the Xq21 linkage group.     

Sequence variation at three X chromosomal short tandem repeats in Caucasian and African populations

Sequence variation for the X chromosome short tandem repeats (X-STRs) DXS9898, DXS6789 and GATA172D05 was studied in two major population groups, namely Caucasians and Africans. DXS6789 revealed two different subtype sequence polymorphisms: for shorter alleles, with less than 17 repeats, results showed a simple composition with the following structure: (TATG)_m-(TATC)_n. For longer alleles, a constant TATC insertion was observed at the beginning of the variable repeat unit. Additionally, alleles identical in size revealed structural variations regarding the TATG/TATC proportion. Africans showed a higher intra-allelic variation at this locus than the Caucasian population group. For all three loci, DXS9898, DXS6789 and GATA172D05, no unique structure was found among Africans and Caucasians.     

Updated allelic structures of the DXS10135 and DXS10078 STR loci

DXS10135 and DXS10078 are two highly polymorphic STR loci situated in two different linkage groups on the short arm of the human X chromosome. Both loci comprise complex tetrameric repeat units which may partially explain their high degree of polymorphism. DXS10135 is relatively well characterized and is included in a commercially available kit, while DXS10078 has not been well described. We sequenced a large number of alleles of both loci to try and understand the allelic variation and as a prelude to construct allelic ladders from cloned alleles. Our data show interesting features and should encourage other workers to use these loci in forensic genetic investigations.     

The X-linked STRs DXS7130 and DXS6803

This paper presents sequence and population genetic data of two new X-linked microsatellite markers, suitable for forensic purposes. Data were obtained from a sample of unrelated German individuals (male and female). Two highly informative markers could be added to the panel of ChrX STRs [J. Edelmann, S. Hering, M. Michael, R. Lessig, D. Deichsel, G. Meier-Sundhausen, L. Roewer, I. Plate, R. Szibor, 16 X-chromosome STR loci frequency data from a German population, For. Sci. Int. 124 (2001) 215-218; J. Edelmann, D. Deichsel, S. Hering, I. Plate, R. Szibor, Sequence variation and allele nomenclature for the X-linked STRs DXS9895, DXS8378, DXS7132, DXS6800, DXS7133, GATA172D05, DXS7423 and DXS8377, For. Sci. Int. 129 (2002) 99-103].     

24个X-STR及7个Y-STR基因座复合扩增体系建立及法庭科学有效性验证

目的建立24个X-STR基因座及7个Y-STR基因座的复合扩增体系,进行24个X-STR基因座的遗传多态性调查,并评价该体系的法医学应用价值。方法采用六色荧光标记技术,对24个X-STR基因座(DXS6803,DXS10159,DXS10146,DXS7132,DXS10075,DXS8378,DXS7424,DXS101,DXS6795,HUMARA,DXS10074,DXS6801,DXS6789,DXS10135,GATA144D04,DXS7423,DXS10101,HPRTB,DXS10148,GATA165B12,DXS10103,DXS8377,DXS6797,DXS6810)进行复合扩增和毛细管电泳检测;调查山东汉族1057名无关男性个体24个X-STR基因座的遗传多态性,并对系统性能进行评价。结果本文建立的复合扩增体系中的24个X-STR基因座,在1057名个体中共检出1057种单倍型。方法特异性好,分型结果准确稳定,灵敏度达0.0625ng,实际案例常见生物检材的检验结果良好。结论该复合扩增检测体系可以用于实际案例检验,弥补商品化X-STR基因座复合扩增检测体系的不足,联合应用加入的Y-STR基因座适用于混合斑的鉴别。     

Analysis of 8 STR of the X-chromosome in two Italian regions (Umbria and Sardinia)

Eight X-chromosome STR were investigated in two groups of individuals from two Italian regions, Umbria and Sardinia. These two regions have a very different history. Umbria, situated in the centre of Italy and without defensive natural barriers, in the course of the centuries has been object of many invasions and appropriations by foreign people. On the contrary, Sardinia, an island in the centre of the Mediterranean sea, has endured a minor number of foreign invasions. The ChrX markers were amplified in a pentaplex (DXS6789, DXS7423, DXS6807, DXS101, DXS8377) and a triplex (DXS10074, DXS10075, DXS10079) that represents a haplotype. The DNA was extracted from 200 blood samples using the QIAmp DNA Minikit (Qiagen™). Amplification products were detected on an ABI PRISM 310 Genetic Analyzer (Applied Biosystems), using the same dye labels, run conditions, standard (GeneScan 500 Liz) and matrix file of AmpFlSTRIdentifiler. Statistical analyses for all the loci and intergroup comparisons between the two regional groups of individuals were performed.     

中国鄂温克族DXS7423，DXS7424，DXS7132，DXS7133，DXS6804位点多态性的研究

目的以无关个体为研究对象,研究鄂温克族人群X染色体5个STR位点的遗传多态性,建立群体遗传数据库。方法用聚合酶链反应(PCR)、变性聚丙烯凝胶电泳和银染的方法,检测98名中国鄂温克族DXS7423,DXS7424,DXS7132,DXS7133,DXS6804位点的重复序列长度的变化。结果5个STR位点在鄂温克族群体均具有遗传多态性,χ2检验表明多态性分布符合Hardy-Weinberg平衡定律。结论中国鄂温克族X染色体5个STR基因座群体遗传数据资料,可用于法庭科学个体识别、亲子鉴定及其他人类学研究。     

浙江汉族人群12个X-STR基因座遗传多态性调查

目的调查12个X染色体STR基因座在浙江汉族人群的遗传多态性,为法医学应用提供基础数据。方法应用ZJGA-X12荧光标记复合扩增系统,对浙江汉族468名无关男性个体与449名无关女性个体进行DXS7133、DXS8378、DXS981、DXS7424、DXS6789、DXS10159、GATA165B12、DXS101、DXS7423、GA-TA31E08、DXS10164、DXS10162这12个X-STR基因座的复合扩增,用ABI3130XL型基因分析仪对扩增产物进行检测,并统计这12个X-STR基因座的群体遗传学参数。结果获得12个X-STR基因座的等位基因频率分布,分别检出8、7、13、12、11、8、7、16、6、8、9、11个等位基因,获得男性样本DXS10159-DXS10162-DXS10164与DXS101-DXS7424两组连锁基因座单倍型119、62种;分别统计了12个X-STR基因座的GD、DP、MEC等法医遗传学参数。结论 12个X-STR基因座具有较强个体识别能力,可应用于法庭科学中的个体识别与亲权鉴定。     

Validation of the STR DXS7424 and the linkage situation on the X-chromosome

X-linked microsatellite markers have proven to be powerful tools for parentage testing, mainly in deficiency paternity cases when the disputed child is female. However, only a small number of X-linked short tandem repeats (STRs) have been comprehensively described for forensic applications to date.We present sequence and population genetic data of the DXS7424 STR (GDB-G00-577-633) which is a trinucleotide repeat polymorphism representing 12 alleles of 147-180 bp in length. DXS7424 is located at Xq22 and closely linked to DXS101, corresponding to a genetic localisation of 104.9-121 cM from Xp-tel.PCR fragment length measurements and sequencing were carried out using the automatic gene analyser ABI 310 (Applied Biosystems).The population of 764 unrelated Germans checked for this STR exhibited the following features: polymorphism information content (PIC) = 0.780; heterozygosity (Het) = 0.843; mean exclusion chance (MEC = 0.766. Kinship tests revealed a typical X-linked inheritance. In 300 meioses under investigation, mutations were not found. Significant deviations from the Hardy-Weinberg equilibrium (HWE) were not established.Linkage studies confirmed closely linkage to DXS101. Additional we found linkage disequilibrium between DXS7424 and DXS101. This requires to use the established haplotype frequencies in kinship testing.     

Genetic data of 10 X-STRs in a Spanish population sample

In this work, we present population genetic data of 10 X-chromosome STRs (DXS8378, DXS9898, DXS8377, HPRTB, GATA172D05, DXS7423, DXS6809, DXS7132, DXS101 and DXS6789) obtained from sample of 145 unrelated female individuals belonging to Valencia (Spain), a region located in the east of the Iberian Peninsula. All the markers studied present high genetic diversities, similar to those previously reported in other European population samples. No deviations from Hardy-Weinberg equilibrium were observed, with the exception of DXS101 locus. Allele frequencies and parameters of forensic interest for each X-STR were calculated. High mean exclusion chance and power of discrimination values were obtained by combining these 10 X-linked markers. Population comparisons (exact test of population differentiation; pairwise genetic distances) were carried out and low genetic distances were found between our sample and those from other Spanish or European regions.     

Genetic analysis of 18 X-linked short tandem repeat markers in Korean population

The population genetic data of 18 X-chromosomal short tandem repeat (STR) markers DXS6807, DXS8378, DXS9895, DXS9902, DXS6810, DXS7132, DXS981, DXS6800, DXS9898, DXS6789, DXS101, DXS6797, GATA172D05, GATA165B12, HPRTB, GATA31E08, DXS8377, and DXS7423 were analyzed in samples of unrelated 220 males and 181 females from Korean population. The exact test for genotype distribution of the markers showed no significant deviation from the Hardy-Weinberg equilibrium. Allele frequencies between male and female samples were not significantly different in all examined markers. All examined males and females showed different hemizygotic haplotype and combined genotypes, respectively. Four cases of mutation were found in GATA172D05, GATA31E08, DXS7132, and HPRTB from the analysis of 95 father-child-mother trios. Details of X chromosomal STRs in Koreans would be useful in paternity tests and forensic purposes as well as whole X-chromosomal mapping studies.     

Development of the X-linked tetrameric microsatellite marker HumDXS6789 for forensic purposes

This paper presents sequence and population genetic data of the X-linked DXS6789 short tandem repeat (STR). The tetranucleotide repeat polymorphism DXS6789, also known as CHLC.GATA31F01, is located at the Xq22.3 region. This locus is unlinked with DXS6807 and slightly linked with ARA, DXS9898 and HPRTB. In kinship testing, DXS6789 is suitable for concomitant use with DXS6807. Population genetic data were obtained by analysing 250 unrelated males and 315 females from East Germany. In this population, the STR exhibited 12 clearly distinguishable alleles ranging from 154 to 198bps in length. DXS6789 is characterised by the following data: polymorphic information content (PIC)=0.70; observed heterozygosity (Het)=0.78; mean exclusion chance (MEC)=0.70. A deviation from the Hardy-Weinberg equilibrium could not be detected. The investigations we performed in 243 mother-child and 161 father-child meioses did not reveal any mutations.     

X-chromosome STRs analysis of Ewenke ethnic population

X-chromosome STR, known as microsatellite, is a kind of the most information genetic markers for specific biological materials. Because the size of X-chromosome STR alleles is small, generally including 100-350 nucleotides, it is relatively easy to be amplified and detected with high sensitivity. We have investigated 10 X-chromosome STR loci in an Ewenke ethnic population who live in Neimengu of northeast China. Allele frequencies of 10 X-chromosome STR loci, including DXS7133, DXS6799, DXS8378, DXS7423, DXS6804, HPRTB, DXS7424, DXS7132, DXS6789 and DXS101, were obtained from healthy unrelated individuals (45 females and 53 males) of Ewenke ethnic group.     

Development of a heptaplex PCR system to analyse X-chromosome STR loci from five Italian population samples. A collaborative study

Many X-chromosome short tandem repeats (X-STRs) have been validated for forensic use even if further studies are needed on allele frequencies and mutation rates to evaluate the extent of polymorphism in different populations and to establish reference databases useful for forensic applications and for anthropological studies. A single multiplex reaction of seven X-STRs, which includes the DXS6789, HUMARA, DXS10011, DXS7423, HPRTB, DXS6807, DXS101 loci, is presented and their allele frequency distribution in a large population sample including 556 subjects (268 females and 288 males) analysed by five forensic laboratories of Central and Northern Italy is shown. Our results demonstrate the feasibility of a single amplification/detection reaction involving seven markers of the X chromosome, which can be fruitfully used in complex kinship analysis.     

X-linked microsatellites in two Northern Spain populations

The X-chromosomal microsatellites HPRTB, DXS101, ARA, DXS7423, and DXS8377 were analysed by a pentaplex PCR in an expanded population sample from Cantabria and an independent sample of unrelated individuals from the Basque Country. Allele frequencies showed similar distributions, but minor variations were found for some loci.     

Sequence variation and allele nomenclature for the X-linked STRs DXS9895, DXS8378, DXS7132, DXS6800, DXS7133, GATA172D05, DXS7423 and DXS8377

X-linked DNA markers are increasingly used in forensic kinship testing. This paper presents sequencing data of the short tandem repeats (STRs) DXS9895, DXS8378, DXS7132, DXS6800, DXS7133, GATA172D05, DXS7423, DXS8377 and proposes an allele nomenclature. Alleles were assigned according to the recommendations of the International Society of Forensic Genetics (ISFG) Commission.     

X染色体STR单倍型DXS7424-DXS101遗传多态性

目的研究X染色体STR单倍型DXS7424-DXS101在汉族群体中的法医学特征及其分布特点。方法本实验应用PCR和聚丙烯酰胺凝胶电泳及银染技术对DXS7424和DXS101位点进行基因分型,利用相关统计方法进行数据分析。结果汉族151个男性样本中共检出37种单倍型,频率分布在0.0066～0.1391,GD值为0.9453,DP值达到0.9389,最常见单倍型为16-23。结论DXS7424-DXS101作为单倍型分析在汉族群体中具有较高的个体识别率和非父排除率,在法医学特殊亲权鉴定中具有良好的应用前景。