Genetic diversity at two pentanucleotide STR and thirteen tetranucleotide STR loci by multiplex PCR in four predominant population groups of central India

Genetic diversity study at STR loci in 208 individuals belonging to two backward groups, one caste and one tribal community of Central India called "Chhattisgarh" has been carried out to evaluate significance of Powerplex System loci in human identification and population diversity. Populations are Agharia (72), Satmani (50), Dheria Gond (36) and Teli (50). Fifteen loci (Powerplex 16 Kit) studied are Penta E, D18S51, D21S11, THO1, D3S1358, FGA, TPOX, D8S1179, vWA, Amelogenin, Penta D, CSF1PO, D16S539, D7S820, D13S317 and D5S818. The studied penta nucleotide STR (two) and 13 tetranucleotide (CODIS ) STR are found to be highly polymorphic genetic markers in all studied populations. Most common allele for the four studied population has been found to be same at THO1 (allele 9), D8S1179 (allele 14), CSF1PO (allele 12), Penta E (allele 11) and D16S539 (allele 11). Penta E is found to be most polymorphic (PD=0.89373) among studied 15 STR loci in four populations of Central India.     

Distribution of alleles of 15 STR loci of the Powerplex 16 Multiplex system in four predominant population groups of South India

Allele distribution of the 15 STR loci of Powerplex 16 Multiplex System were studied in four predominant population groups of South India for evaluating their significance in human identification and population study: Iyengar Brahmin (65), Gowda (59), Lingayat (98) and Muslim (45) from the state of Karnataka. The loci analyzed are--D3S1358, THOI, D2ISI I, D18S51, D5S818, Penta E, D13S317, D7S820, D16S539, CSFIPO, Penta D, vWA, D8S179, TPOX and FGA. Out of 15 STR loci Penta D and D18S51 were found highly polymorphic in the studied populations.     

DNATyper^TM15基因座的研究与选择

目的为研发复合扩增荧光检测试剂盒,对现有的STR基因座进行分析研究并优选新的高鉴别力基因座。方法收集汉族、锡泊族、畲族、壮族、藏族等5个民族群体血样共1200份,提取DNA,应用复合扩增方法检测1200名5个民族群体无关个体的24个基因座的等位基因分布。结果TPOX和TH01基因座的等位基因在5个民族群体中分布不平衡;D2S1338、D6S1043和Penta E等3个STR基因座在5个民族群体中均具有高度遗传多态性,等位基因频率分布均匀,在各群体间无显著差异,而且等位基因传递遵循孟德尔遗传规律。结论确定出DNATyperTM15试剂盒中的14个适合中国人群体遗传学特征和法医学应用的STR基因座。     

用新设计引物调查武汉汉族Penta D和Penta E基因座遗传多态性

目的　研究PentaD和PentaE基因座分型引物设计 ,调查PentaD和PentaE基因座在武汉汉族人群中的遗传多态性。方法　用重新设计的PentaD和PentaE基因座分型引物 ,采用热启动PCR和PAGE技术对 2 81名武汉地区汉族无关个体进行分型调查 ,并将其分型结果与Promega公司的PowerPlexTM16系统荧光标记复合扩增试剂盒分型结果进行比较。结果　新设计引物扩增产物的片段大小范围分别为 15 3～ 198bp和 10 7～ 2 12bp ,其分型结果与PowerPlexTM16系统的分型结果完全一致 ,且用银染法检测的灵敏度显著提高 (由 0 5ng提高到 0 2ng)。PentaD和PentaE基因座在武汉汉族群体分别检出 10个和 2 1个等位基因 ,其基因型频率分布均符合Hardy Weinberg平衡。家系调查证实了其等位基因的传递符合孟德尔遗传规律。两基因座的个体识别能力 (DP)分别为 0 92 62、 0 9860 ,非父排除率 (PE)分别为 0 665 1、 0 83 2 5。结论　新设计引物用于PentaD和PentaE基因座的分型检测准确可靠 ,两基因座多态性程度高 ,在法医学个人识别和亲子鉴定中具有使用价值。     

Population genetic analysis of 15 autosomal STRs loci in the central region of Argentina

Allele frequencies, together with some parameters of forensic interest, for 15 STRs included in the Powerplex-16 System (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, Penta D, Penta E, TH01, TPOX and VWA) were estimated from a sample set of 1368 unrelated individuals from three of the most densely populated provinces of Argentina. No deviations from Hardy-Weinberg equilibrium were observed using the Bonferroni correction for the number of loci analyzed. Comparative analyses between our population data and that of other Argentinean databases previously published are presented and discussed. The most informative loci in our data set is the Penta E Loci with discrimination power larger than 0.98 and typical paternity index larger than 4.3. Our results demonstrate that these loci are robust since different laboratories and sample sets provided highly consistent results. This observation underscores the usefulness of these markers systems for human identification and parentage testing.     

Allele frequencies of 13 short tandem repeat (STR) loci in the Romanian population

A population study on 13 tetra- and pentameric STR loci (D3S1358, VWA, D8S1179, D21S11, D18S51, D16S539, D2S1338, D19S433, THO1, FGA, ACTBP2 (SE33), Penta D and Penta E) was performed with Romanians from the Bucharest area.     

Allele frequencies for 15 STR loci in Van-Ağri districts of the Eastern Anatolia region of Turkey

Allele frequencies of 13 tetrameric short tandem repeat (STR) loci (D3S1358, TH01, D21S11, D18S51, D5S818, D13S317, D7S820, D16S539, CSF1PO, vWA, D8S1179, TPOX, FGA) and 2 pentameric short tandem repeat loci (Penta E and Penta D) included in the PowerPlex 16 kit were obtained from a sample of 116 unrelated individuals in Van-A?ri districts of the Eastern Anatolia region of Turkey. The expected performance of these loci for personal identification and paternity testing in this population was estimated.     

Forensic genetic analysis of the population of Gujarat with PowerPlex 21 multiplex system

The present investigation assessed the allele frequencies and forensic parameters for the loci included in PowerPlex 21 multiplex system (Promega, USA) in 101 unrelated individuals residing in the state of Gujarat, India. The study likewise introduces the first global report on polymorphism on Penta D and Penta E autosomal STR loci from the population of Gujarat, India. The obtained outcomes in the study revealed that the considered STR multiplex system is highly polymorphic and suitable for forensic genetic analysis.     

STR primer concordance study.

Over 1500 population database samples comprising African Americans, Caucasians, Hispanics, Native Americans, Chamorros and Filipinos were typed using the PowerPlex 16 and the Profiler Plus/COfiler kits. Except for the D8S1179 locus in Chamorros and Filipinos from Guam, there were eight examples in which a typing difference due to allele dropout was observed. At the D8S1179 locus in the population samples from Guam, there were 13 examples of allele dropout observed when using the Profiler Plus kit. The data support that the primers used in the PowerPlex 16, Profiler Plus, and COfiler kits are reliable for typing reference samples that are for use in CODIS. In addition, allele frequency databases have been established for the STR loci Penta D and Penta E. Both loci are highly polymorphic.     

Population genetics data of 23 autosomal STR loci for three Populations in United Arab Emirates

In the present study, forensic parameters were estimated for three populations residing in the United Arab Emirates (UAE) including UAE Arabs, Pakistanis and Indians based on the population data of 23 autosomal short tandem repeats (STRs). The UAE Arabs is a vital population to study due to high rates of consanguineous marriages. Therefore, it is essential to estimate the allele distribution and frequencies within this population. In addition, it is crucial to study the largest communities living in the UAE such as Indians and Pakistanis. A total of 1272 blood samples were collected on FTA® cards, comprising of 571 UAE Arabs, 352 Indians and 349 Pakistanis. All of these samples were amplified directly using Verifiler® Express PCR Amplification Kit that focuses on 23 autosomal STR loci, namely D3S1358, vWA, D16S539, CSF1PO, TPOX, D8S1179, D21S11, D18S51, D2S441, D19S433, TH01, FGA, D22S1045, D5S818, D13S317, D7S820, D10S1248, D1S1656, D12S391, D2S1338, D6S1043, Penta D and Penta E loci. The PCR products were electrophoresed on ABI 3500 Genetic Analyzer and analyzed using GeneMapper ID-X v1.4 software. Arlequin v3.5 and PowerStats software were utilized to determine the forensic parameters and population structure using AMOVA. Gene diversity, ranged from 0.67406 (TPOX) to 0.9226 (Penta E) in the UAE Arabs, 0.69955 (TPOX) to 0.9214 (Penta E) in Indian and 0.69853 (TPOX) to 0.921 (Penta E) in Pakistani population. The most discriminating autosomal STR loci observed was Penta E (PD = 0.985), (PD = 0.986), (PD = 0.986) in the UAE Arabs, Indian and Pakistani population, respectively. The obtained results showed the 23 STR loci had a relatively high genetic variation, confirming the suitability for forensic identification and kinship analysis, in the relevant populations. The significance of this study is to build an allelic frequency database for one of the most powerful commercially available STR amplification kits by using the current forensic workflow.     

Population data for 11 STR loci in northeast China Han

Allele frequencies for the nine tetrameric short tandem repeats (STR) loci D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, and D7S820 (AmpFlSTR Profiler Plus PCR amplification kit, PE Applied Biosystems) and two pentameric STR loci Penta D and Penta E (PowerPlex 16 system, Promega Corporation) were determined in a population sample of unrelated China Han.     

STR data for the power plex-16 loci in a population from Central Poland

The allele frequencies for the 13 CODIS core loci and two recently developed but not extensively validated in Central European populations pentanucleotide STRs (Penta E and D) were determined using the Power Plex-16 (Promega) kit in a sample of 430 unrelated individuals born in Central Poland. The calculated parameters of polymorphism showed Penta E to be the most valuable marker from the studied set. The obtained distribution of Penta E and D alleles was statistically significantly different from that previously reported for a population of Southern Poland. Analysis of Hardy-Weinberg equilibrium revealed a deviation for the D5S818 locus which may reflect presence of a null allele.     

Evaluation of population variation at 17 autosomal STR and 16 Y-STR haplotype loci in Croatians

Seventeen autosomal STR loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818, FGA, Penta E and Penta D) and 16 Y-STR haplotype loci (DYS19, DYS385, DYS389I, DYS398II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4.1) were analyzed in the sample of 200 unrelated Croatians. The agreement with HWE was confirmed for all autosomal STR loci. The combined power of discrimination (PD) and the combined power of exclusion (PE) for the 17 autosomal STR loci were 0.999999999999999999682299331476 and 0.99999995, respectively. Penta E proved to be the most informative autosomal STR locus. Among 200 Croatian males, 197 Y-STR haplotypes were identified and haplotype diversity was estimated at 0.9998 ± 0.0005.     

Data for 15 autosomal STR markers (Powerplex 16 System) from two Tunisian populations: Kesra (Berber) and Zriba (Arab)

Allele frequencies, together with some parameters of forensic interest, for 15 STRs included in the Powerplex 16 System (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, Penta D, Penta E, TH01, TPO and VWA) were estimated from two samples of unrelated individuals from Tunisia, of different ethnicity: Kesra (Berber) and Zriba (Arab). No deviations from Hardy-Weinberg equilibrium were observed after Bonferroni's correction for the number of loci analysed. Comparative analyses between our population data and other North African databases showed that significant differences were concentrated on loci with lowest values of diversity (mainly CSF1PO and D13S317), irrespective of ethnicity and geographic location.     

PowerPlex~(TM) 16体系在中国人群中罕见等位基因及其类型

目的 分析PowerPlexTM 16体系基因座在中国人群中的罕见等位基因及其类型。方法 应用PCR-STR和DNA序列分析技术,对4650个无关个体在15个STR基因座中的罕见等位基因进行检测。结果 在PowerPlexTM16体系中的D7S820、D16S539、Penta E基因座,检测到2种类型的罕见等位基因,而TH01、D21S11、D5S818、D13S317、Penta D、D8S1179、TPOX、FGA基因座检测出1种类型。其等位基因频率均较低(0.215‰-7.097‰)。结论 超出ladder范围的罕见等位基因序列比相邻等位基因增加(或减少)1个或数个重复单位,因碱基的插入或缺失的罕见等位基因出现在两等位基因之间。     

Allele frequencies for 15 short tandem repeat loci in a representative sample of Bosnians and Herzegovinians

Allele frequencies for the 15 STR loci (D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, vWA, D8S1179, TPOX, FGA) included in the PowerPlex 16 kit were obtained from a multiethnic sample of 100 unrelated individuals born in Bosnia and Herzegovina.     

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。     

单亲鉴定案例STR选择探讨和PI值计算方法评价

作者对STR位点的个体识别能力(DP)、杂合度(H)、非父排除率(PE)、多态信息含量(PIC)等进行统计学分析,探寻了适合中国人群单亲子鉴定、且有利于国内外DNA实验室数据交流的STR位点,并对现行的PI值计算方法进行了评价。     

Genetic polymorphisms of 20 STR loci in Chinese Han population in Tianjin,North China

The PowerPlex^® 21 System PCR Amplification Kit was a new PCR Amplification Kit developed for forensic laboratories, but there was a lack of data about this kit in Chinese people in Tianjin, North China. This kit contained 20 STR loci, D3S1358, D1S1656, D6S1043, D13S317, Penta E, D16S539, D18S51, D2S1338, CSF1PO, Penta D, TH01, vWA, D21S11, D7S820, D5S818, TPOX, D8S1179, D12S391, D19S433 and FGA. In order to evaluate this kit and to get basic population data for its use in forensic practice in Chinese Han population, 360 unrelated Chinese Han individuals from Tianjin were typed using the Kit. Allele frequencies of the 20 STR loci and further population forensic genetic parameters were obtained. The observed genotype frequencies and expected genotype frequencies were evaluated by χ² test. No significant deviation from the Hardy–Weinberg equilibrium was observed in the population sample for the 20 STR loci. The population data in the present study can be used for routine forensic practice in Tianjin, North China.     

Genetic profile of the Madeira Archipelago population using the new PowerPlex16 System kit

Allele and haplotype frequencies of 17 chromosome STR loci, 15 of them included in the kit PowerPlex 16 System from Promega, were determined in a sample of unrelated males from Madeira and Porto Santo Islands. PowerPlex 16 includes STRs not studied before in the Madeira population. The-kit includes two new allele markers (Penta D and Penta E), which proved to be extremely useful for paternity testing (PD = 0.952 and 0.977, respectively). The study revealed that the Madeira population does not differ from that of the north Portugal. Nevertheless, some loci presented alleles found in sub-Saharan and North European populations which were not reported so far in Portugal.