A study on ten short tandem repeat systems: African immigrant and Spanish population data

This work presents the results obtained from a genetic–population study for the D1S1656 system in the population of Southwest Spain (Huelva, Cádiz and Sevilla), Spaniards of Caucasian origin from North Africa (Ceuta), as well as in the black Central West African and Moroccan immigrant populations in Spain. The results of a study of the autochtonous population of the Canary Islands (n=138), and immigrant Central West African populations in Spain (n=132), obtained for nine short tandem repeat (STR) loci (D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820), as well as the amelogenin locus, all contained in Profiler Plus™ (Perkin-Elmer) PCR amplification kits, are also presented. Except for the FGA and VWA data on immigrant Central West African populations in Spain, no deviations from the Hardy–Weinberg equilibrium were detected.     

Turkish population data with the CODIS multiplex short tandem repeat loci.

Allele frequencies for 13 tetrameric short tandem repeat (STR) loci, CSF1PO, D18S51, D3S1358, D21S11, D5S818, FGA, D7S820, HUMTH01, D8S1179, TPOX, D13S317, VWA, and D16S539 were determined on 198 Turkish blood samples.     

5个STR基因座的遗传多态性及其法医学应用

目的获得D11S4951、D11S4957、GATA193H05、D2S2951、D6S2421基因座的群体遗传学数据,并分析其在法医学中的应用价值。方法随机抽取成都地区汉族群体无血缘关系个体的静脉血,EDTA抗凝,用Chelex-100法提取DNA,应用PCR技术,扩增上述5个短串联重复序列基因座,聚丙烯酰胺凝胶垂直板电泳分型。结果5个基因座在中国成都汉族人群中分别发现了7、10、8、6、8个等位基因,5个基因座的基因型分布符合Hardy-Weinberg平衡(P>0.05)。各基因座的杂合度分别为0.743、0.772、0.833、0.650和0.800;非父排除概率分别为0.497、0.549、0.662、0.356和0.599;个人识别几率分别为0.863、0.912、0.947、0.829和0.931。结论5个基因座在中国汉族群体中具有法医学应用价值。     

Sequence analysis and population data on the 'new' short tandem repeat locus D5S2360

We have studied the sequence structure and population genetics of a 'new' short tandem repeat polymorphism at locus D5S2360 in German Caucasians. Sequencing at this locus revealed a considerable variation, which is characterized by a tetranucleotide (AGAT)(n) repeat pattern with (GAT), (AGATT), and (AG) repeats dispersed throughout the alleles. These microvariations do not necessarily alter the size of the alleles. They may vary by one or two pairs or they may remain unchanged in size. At locus D5S2360 we observed 33 allelic lengths comprising at least 36 different alleles. Population data revealed a high polymorphism with a heterozygosity rate of approximately 92.5%.     

Italian population data on two new short tandem repeat loci: D2S1338 and Penta E

A population study on two new short tandem repeat (STR) loci D2S1338 (a tetranucleotide repeat) and Penta E (a pentanucleotide repeat) was performed on 208 unrelated Italian Caucasians. The DNA was amplified by polymerase chain reaction (PCR) and separation and detection of the amplified STR fragments were carried out by use of a PE/ABD PRISM 377 DNA Sequencer 377 automated system (Applied Biosystems Division/Perkin-Elmer). Both loci meet Hardy-Weinberg expectations. There is no evidence for departures from expectations between the two loci. The combined Probability of Discrimination and Probability of Exclusion for the two STR loci are 0.999155 and 0.944925, respectively. The results demonstrate that these two regions can be useful for differentiating among individuals, particularly in concert with other STR loci.     

Genetic variation and population genetic data of the short tandem repeat locus D8S320

The locus D8S320 is an STR system first described in 1993 as a simple (AAAG) repeat. Sequencing data revealed that the D8S320 locus is a complex STR system consisting of (AAAG)- and (AAAC)-repeat units. A total of 22 different alleles were found in a population survey of 210 unrelated individuals from the Rhine area with frequencies ranging from <0.01 to 0.198. The population data revealed the existence of variant alleles differing by 1 and 2bp from the consensus allele. Due to the complex repeat structure consisting of three variable regions and one constant region, electrophoresis under denaturing conditions is strongly recommended. The statistical values were calculated to be 0.89 (observed heterozygosity rate), 0.96 (discrimination index) and 0.71 (mean exclusion chance). No deviation from Hardy-Weinberg equilibrium (HWE) was observed.     

浙江汉族人群6个STR基因座的遗传多态性的调查

目的进一步完善浙江省汉族人群STR基因座遗传多态性的调查,为其应用提供基础数据。方法采用AmpF1STRSGMplus和AmpF1STRCoficer反应试剂盒,使用ABI310型基因分析仪对浙江汉族人群200名无关个体血样进行了D16S539、D2S1338、D19S433、TH01、TPOX和CSF1PO6个STR基因座遗传学分析。结果分别发现了9、15、15、11、8、10个等位基因,发现的基因型分别为23、42、35、19、16、17个,其分布经X2检验均符合Hardy-Weinberg平衡定律,并分别统计了6个STR基因座的H、DP、PM、PE及PIC参数。结论6个STR基因座适合法医学应用。     

中国成都地区汉族群体5个STR基因座的遗传多态性

采用PCR扩增,聚丙烯酰胺凝胶电泳分析技术,调查中国成都汉族群体DIS1656、D851179、D9S302、D185535及D195253等5个STR基因座的等位基因频率分布。D1S1656检出11个等位基因,35种基因型;DSS1179检出9个等位基因,32种基因型;D95302检出12个等位基因,50种基因型;D185535检出7个等位基因,20种基因型;D195253检出8个等位基因,28种基因型。5个STR基因座基因型频率分布符合Hardy-weinberg平衡（P＞0．05）。个人识别机率（DP）为0．92～0．98。分析了二代3口之家的遗传模式,证明5个STR基因座均符合孟德尔遗传规律。5个STR基因座PCR扩增采用同一条件,方法简单、快速、灵敏、重复性好,可用于法科学亲子鉴定和个人识别。     

DNA typing of short tandem repeat loci on Y-chromosome of Greek population

Haplotype, allele frequencies and population data of nine Y-chromosome STR loci, DYS385I, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, were determined from a sample of 69 unrelated Greek male individuals.     

Response of short tandem repeat systems to temperature and sizing methods

In capillary gel electrophoresis (CE), changing run conditions such as temperature can result in minor variations in the size determination of an allele. These effects are caused by secondary structure differences that can occur between the amplified sample and the internal standard. The type of method chosen to generate the sizing curve in STR analysis can influence the relationship between estimated allele size and temperature. To better understand the effects of temperature and sizing method on the reproducibility of DNA migration, two fluorescently labeled allelic ladders, CTTv and Y-PLEX 6 were analyzed using the ABI Prism 310 Genetic Analyzer. The default method on the Genetic Analyzer utilizes an electrophoretic temperature of 60 degrees C and a Local Southern method to generate a sizing curve from the fragment migration times of the internal lane standard. In this work, electrophoresis was conducted at 35-70 degrees C using the commercially available POP 4 buffer at pH 8 and two sizing methods, Global Southern and Local Southern, were compared. The slopes of the regression line between estimated allele size and temperature, using either sizing method, were measured in order to demonstrate the temperature sensitivity of migration time and the importance of the operator-chosen method. Our results indicate that the Global Southern method is a better choice in situations where temperature fluctuations can occur. In addition, the temperature dependence of the DNA size estimates using the POP 4 system were compared to results obtained using an experimental buffer consisting of 3% hydroxyethylcellulose at pH 11. These results demonstrate that secondary structure effects are minimized at an elevated pH, increasing the precision of size estimates obtained.     

Maine Caucasian population DNA database using twelve short tandem repeat loci

A population study of Caucasians residing in Maine was conducted using the AmpF1STR Profiler PCR Amplification Kit and the AmpF1STR Profiler Plus PCR Amplification Kit (Applied Biosystems Division (ABD) of Perkin Elmer, Foster City, CA). The kits contain the reagents necessary to amplify 12 different STR loci and the gender marker Amelogenin using two multiplex PCR, each containing nine STR loci. Thus, there is an overlap of six STR loci. The 12 STR loci are TH01, TPOX, CSF1PO, D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, and D7S820. These loci represent 12 of the 13 core loci selected by the CODIS STR standardization project. Dye-labeled amplification products were separated and detected using the capillary electrophoresis instrument ABI Prism 310 Genetic Analyzer. Allele frequencies were determined for the 12 STR loci. Statistical analysis of the data included Hardy-Weinburg equilibrium (HWE) analysis, pairwise independence testing, power of discrimination (PD), and probability of exclusion (PE).