Evaluation of 12 Y-chromosome STR loci in Western Mediterranean populations

With the aim to establish a Y-STR haplotype database, a total of 554 males from seven Western Mediterranean populations were genotyped for the 12 Y-chromosome STR loci (minimal haplotype extended by loci DYS437, DYS438 and DYS439) included in the Powerplex Y System (Promega).Among the 554 males analyzed, 443 different haplotypes were obtained, of which 372 were unique. The other haplotypes were shared by two to seven men. The two most frequent haplotypes were both found in seven Ibiza men. A remarkable haplotype diversity of 0.9988 ± 0.0002 was observed.The haplotypes were searched against the Y-haplotype reference database (YHRD) and 149 haplotypes matched to at least one YHRD sample.     

Correlation of surnames and Y-chromosome in Central-Brazil

In patrilineal societies, surnames and Y-specific haplotypes and haplogroups are expected to be correlated. This characteristic could help defining an initial pool of suspects in forensic genetics analysis. Here we evaluated this correlation in a sample of Central-Brazilian men. Surnames and Y-SNP haplogroup and Y-STR haplotype were analyzed in 55 pairs of Central-Brazilian men sharing surnames (n = 110). Seven haplogroups and thirty-two haplotypes have been observed, none correlated solely to any of the twenty-eight surnames represented here. In this sample, two men with the same surname showed a chance of 0.41 of sharing a Y-specific haplogroup. This chance is higher for surnames of intermediate frequencies, whereas rare surnames show distinct chances as zero and one. Observed results may be over-estimated due to a predominance of a specific haplogroup (P92R7 = 49%) in the sample, what makes it possible for two men with no coancestry to share this haplogroup. Considering STR, only three pairs of men shared haplotypes. The average difference between the haplotypes in each pair was 2.45 mutational steps. This relatively low correlation is due to some historical and cultural peculiarities of the country, what makes it improper for forensic purposes in Brazil.     

Diversity of 26-locus Y-STR haplotypes in a Nepalese population sample: isolation and drift in the Himalayas

Twenty-six Y-chromosomal short tandem repeat (STR) loci were amplified in a sample of 769 unrelated males from Nepal, using two multiplex polymerase chain reaction (PCR) assays. The 26 loci gave a discriminating power of 0.997, with 59% unique haplotypes, and the highest frequency haplotype occurring 12 times. We identified novel alleles at four loci, microvariants at a further two, and nine examples of amelogenin-Y deletions (1.2%). Comparison with a similarly sized Bhutanese sample typed with the same markers suggested histories of isolation and drift, with drift having a greater effect in Bhutan. Extended (11-locus) haplotypes for the Nepalese samples have been submitted to the Y-STR Haplotype Reference Database (YHRD).     

Optimization and validation of a fast amplification protocol for AmpFlSTR Profiler Plus for rapid forensic human identification

The goal of this work was to optimize and validate a fast amplification protocol for the multiplex amplification of the STR loci included in AmpFlSTR^® Profiler Plus^® to expedite human DNA identification. By modifying the cycling conditions and by combining the use of a DNA polymerase optimized for high speed PCR (SpeedSTAR™ HS) and a more efficient thermal cycler instrument (Bio-RAD C1000™), we were able to reduce the amplification process from 4 h to 26 min. No modification to the commercial AmpFlSTR^® Profiler Plus^® primer mix was required. When compared to the current Royal Canadian Mounted Police (RCMP) amplification protocol, no differences with regards to specificity, sensitivity, heterozygote peak height ratios and overall profile balance were noted. Moreover, complete concordance was obtained with profiles previously generated with the standard amplification protocol and minor alleles in mixture samples were reliably typed. An increase in n − 4 stutter ratios (2.2% on average for all loci) was observed for profiles amplified with the fast protocol compared to the current procedure. Our results document the robustness of this rapid amplification protocol for STR profiling using the AmpFlSTR^® Profiler Plus^® primer set and demonstrate that comparable data can be obtained in substantially less time. This new approach could provide an alternative option to current multiplex STR typing amplification protocols in order to increase throughput or expedite time-sensitive cases.     

Validation of a 17-locus Y-STR multiplex system

Internal validation of a commercial 17-locus Y-STR system (AmpFlSTR^® Yfiler™, Applied Biosystems) has been performed on the ABI PRISM^® 3130 Genetic Analyzer for use in forensic cases. The Yfiler™ kit was validated according to SWGDAM guidelines. Our results show that it is possible to obtain full profiles with as little as 30 pg of male DNA even in the presence of 20,000-fold amounts of female DNA. Reaction volume was optimized for 10 μl. Male-male mixtures yielded full profiles of the minor contributor with 10-fold excess of the major contributor. Stutter values for each locus were determined from data generated for the population study which included Y-STR profiles from 156 caucasian males from the Montreal and Lac St.-Jean areas of Québec, Canada. The study recorded 141 different haplotypes of which 131 were unique with a haplotype diversity of 0.9965. A number of non-probative forensic samples from rape kit epithelial fractions and fingernail scrapings were also successfully tested.     

Population genetics for Y-chromosomal STRs haplotypes of Chinese Tujia ethnic group

Allele and haplotype frequencies of 11 Y-chromosomal short tandem repeats (STRs) included in the PowerPlex^® Y Systems (Promega) were determined in a sample of 215 unrelated healthy male individuals of Chinese Tujia ethnic group living in Chongqing (Southwest of China). The gene diversity values of the Y-STRs loci ranged from 0.3757(DYS391) to 0.9170 (DYS385a/b). A total of 195 haplotypes were identified in the Y-STR loci, among which 180 were unique, 11 were found in two individuals, 3 were shared in three individuals and 1 was shared in four individuals. The observed haplotype diversity value and discrimination capacity were 0.9942 and 0.9070, respectively.     

Analysis of 16 Y-chromosomal STRs in an African descent sample population of Chocó (Colombia)

We studied and established a database and some parameters of forensic importance were calculated of 16 Y-STR (DYS19, DYS385, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS460, DYS461, GATA-A10, GATA-H4 and DYS635) in a population of 298 unrelated males of African descent of Chocó (Colombia) and a total of 257 haplotypes were identified using the present set of Y-STR markers, of which 224 were represented only once in the database. Twenty-six haplotypes were presents two times, six haplotypes were presents in three individuals and one haplotype in four men. The haplotype diversity was 0.9987 ± 0.0004. By combining the allelic states of the 16 Y-chromosomal STRs we could construct highly informative haplotypes that allowed the discrimination of 86.2% of the samples tested. With this work we established a database of Y-STR and some parameters of forensic importance. This approach represents a very powerful tool for individual identification and paternity testing in forensic genetic.     

云南白族群体Y-STR及Y-SNP关联性探讨

目的探讨Y-STR与Y-SNP单倍群间的关联性及其法医学应用价值。方法用Y-filer的17个Y-STR基因座及6个Y-SNPs（M122、M95、M9、M130、M119和M45）对云南白族146名无关男性个体样本进行检测。结果①17个Y-STR基因座构成的单倍型在146名男性个体中共检出114种单倍型,其中93种仅出现于一名个体中。②6个Y-SNPs在白族中的频率为4.1%～47.3%,其中O3-M122频率最高,占47.3%。③综合两类遗传标记结果,出现于2名或2名以上个体的21种Y-STR单倍型中,有5种其Y-SNP不同;分别只有一个Y-STR基因座分型不同的29对单倍型中,有8对其Y-SNP分别不同。Y-SNP单倍群间部分Y-STR基因座等位基因频率分布存在一定差异。结论 Y-STR单倍型相同或相近的个体间其Y-SNP分型可不相同,结合两者进行检测分析对于男性嫌疑人家系排查具有重要意义。     

北京汉族人群三个Y染色体STR基因座的遗传多态性研究

目的　获得DYS4 37,A7 1,H4三个Y染色体STR基因座及其单倍型在北京汉族人群中的遗传多态性分布 ,并探讨其法医学应用价值。方法　应用自行建立的Y STR 15 plex复合扩增体系 ,对用酚 /氯仿法提取的 132份北京地区汉族无关男性个体血样DNA样品进行复合扩增 ,用ABI310型遗传分析仪对扩增产物进行检测 ,统计分析 3个Y STR基因座的群体遗传学参数。结果　DYS4 37,A7 1,H4三个Y STR基因座在该群体中分别检出 4 ,5 ,4个等位基因 ,GD值分别为 0 4 977,0 6 731,0 5 42 0 ;观察到 32种单倍型 ,其中 17种单倍型出现 1次 ,最多 1种单倍型出现 2 0次 ,单倍型累积GD值为 0 9118。结论　 3个Y STR基因座具有较强的个体识别能力 ,在法医学个体识别和亲权鉴定中具有很高的应用价值     

Human Y-specific STR haplotypes in the Western Croatian population sample

Nine Y-chromosome STR loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385 and YCAII) were analysed in a sample of 101 unrelated males from Croatia. Allelic frequencies and gene diversities for each Y-STR locus and haplotype diversity were determined. Ninety-one different haplotypes were obtained from 101 unrelated males and 84 haplotypes were unique. Three most common haplotypes were shared by 3% of the sample, one of them was not found in the online Y-STR Haplotype Reference Database (http://www.ystr.org/).     

Population genetics of 25 Y-STR loci in Chinese Han population from Liaoning Province,Northeast China

In this study, we investigated the genetic characteristics of 25 Y-chromosomal short tandem repeat loci in 305 unrelated Chinese Han male individuals from Liaoning Province, using AmpFISTR® Yfiler® Plus amplification kit. A total of 293 different haplotypes were observed at the 25 Y-STR loci; among them, 281 were unique and 12 were occurred twice. The overall haplotype diversity was 0.9997 and the discrimination capacity was 0.9607. The gene diversity values ranged from 0.4525 (DYS391) to 0.9617 (DYS385). Population relationships between our data and other published populations were measured by Rst and visualized in two multi-dimensional scaling plots. The results showed that the 25 Y-STR loci in Liaoning Han population are valuable for forensic application and human genetics.     

广东汉族群体24个Y-STR基因座的多态性及突变率

目的调查24个Y-STR基因座在广东汉族群体中的遗传多态性和突变现象。方法收集800对经常染色体STR检验确定父子关系的血滤纸样本,用于突变现象观察;其中父亲样本视为无关个体,用于多态性调查。采用GFS 24Y荧光标记复合扩增体系进行扩增及Y-STR分型,并对分型结果进行相关统计分析。结果 800名广东汉族男性无关个体在24个Y-STR基因座中共检出794种单倍型,其中788种为唯一单倍型,总的单倍型多样性（HD）和识别能力（DC）分别为0.999 98和0.992 5。24个基因座共检出296个等位基因,基因多样性值（GD）在0.552 1-0.960 9之间。800对父子中共19 219次等位基因传递中,观察到41对父子共42个突变事件,各基因座总突变率为2.185 310^-3（95%CI 1.575 410^-3-2.952 810^-3）。结论本研究24个Y-STR基因座在广东汉族群体具有较高的遗传多态性,在法医学个体识别、父系亲缘关系鉴定等方面具有很高的应用价值。     

中国汉族及日本群体7个Y—STR位点及单倍型的遗传多态性和群体差异

目的调查Y染色体7个STR位点及单倍型的遗传多态性并分析其群体差别。方法应用PCR、变性聚丙烯酰胺凝胶电泳结合银染显色分型技术,检测45例中国汉族及59例日本男性DNA样品。结果在DYS393、DYS389Ⅰ、DYS19、DYS390、DYS389Ⅱ、DYS392等6个位点中共检出33个等位基因,DYS385位点检出39个等位基因组,其频率分布在0.0169～0.6444之间,DP值分布在0.5406～0.9579之间,以DYS385位点最高。7个位点数据综合比较,二组群体间在遗传学上存在显著性差异P<0.05。由7个位点组成的单倍型有95种,中国汉族有41种,DP值为0.9960,日本群体有54种,DP值为0.9965,2群体间未发现相同的单倍型。结论上述7个STR位点属于高鉴别能力位点,单倍型具有很高的遗传多态性并显示出明显的民族特征。     

Developmental validation of the PowerPlex ESX 16 and PowerPlex ESX 17 Systems

We describe the developmental validation study performed on the PowerPlex^® ESX 16 (European Standard Extended 16) and the PowerPlex^® ESX 17 Systems, part of a suite of four new DNA profiling kits developed by Promega in response to the ENFSI and EDNAP groups’ call for new STR multiplexes for Europe. The PowerPlex^® ESX 16 System combines the 11 loci compatible with the UK National DNA Database, contained within the AmpFlSTR^® SGM Plus^® PCR Amplification Kit, with five additional loci: D2S441, D10S1248, D22S1045, D1S1656 and D12S391. The multiplex was designed to incorporate these five new loci as mini- and midi-STRs while maintaining the loci found in the AmpFlSTR^® SGM Plus^® kit as standard size. The PowerPlex^® ESX 17 System amplifies the same loci as the PowerPlex^® ESX 16 System, but with the addition of a primer pair for the SE33 locus. Tests were designed to address the developmental validation guidelines issued by the Scientific Working Group on DNA Analysis Methods (SWGDAM), and those of the DNA Advisory Board (DAB). Samples processed include DNA mixtures, PCR reactions spiked with inhibitors, a sensitivity series, and 306 United Kingdom donor samples to determine concordance with data generated with the AmpFlSTR^® SGM Plus^® kit. Allele frequencies from 242 white Caucasian samples collected in the United Kingdom are also presented. The PowerPlex^® ESX 16 and ESX 17 Systems are robust and sensitive tools, suitable for the analysis of forensic DNA samples. Full profiles were routinely observed with 62.5 pg of a fully heterozygous single source DNA template. In mixture analysis, a range of 52-95% of unique minor contributor alleles was observed at 19:1 mixture ratios where only 25 pg of the minor component was present. Improved sensitivity combined with the robustness afforded by smaller amplicons has substantially improved the quantity of information obtained from degraded samples, and the improved chemistry confers exceptional tolerance to high levels of laboratory prepared inhibitors.     

Allelic frequencies and statistical data obtained from 48 AIM INDEL loci in an admixed population from the Brazilian Amazon

Allelic frequencies of 48 informative insert-delete (INDEL) loci were obtained from a sample set of 130 unrelated individuals living in Macapá, a city located in the northern Amazon region, in Brazil. The values of heterozygosity (H), polymorphic information content (PIC), power of discrimination (PD), power of exclusion (PE), matching probability (MP) and typical paternity index (TPI) were calculated and showed the forensic efficiency of these genetic markers. Based on the allele frequency obtained for the population of Macapá, we estimated an interethnic admixture for the three parental groups (European, Native American and African) of, respectively, 50%, 21% and 29%. Comparing these allele frequencies with those of other Brazilian populations and the parental populations, statistically significant distances were found. The interpopulation genetic distance (F_ST coefficients) to the present database ranged from F_ST = 0.0431 (p < 0.00001) between Macapá and Belém to F_ST = 0.266 (p < 0.00001) between Macapá and the Native American group.     

Analysis of 16 Y-STRs in a sample of Colombian males

We studied and stablished a data base of 16 Y-STR (DYS19, DYS385, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS460, DYS461, GATA-A10, GATA-H4 and DYS635) in 133 unrelated Colombian males. The haplotype diversity was 0.9997 ± 0.0010. One hundred thirty one different haplotypes were found and only one was found three times. Good allelic representation in all the systems was observed, between 3 and 7 alleles, with the exception of the DYS385 with 35 allelic classes. DYS385 displayed the greater genic diversity (0.9012), whereas the system that displayed the smaller (0.4570) was the DYS393. This approach represents a very powerful tool for individual identification and paternity testing in forensic genetic.     

湖北地区汉族人群24个 Y-STR基因座遗传多态性研究

目的 对湖北汉族人群24个Y-STR基因座多态性进行调查,并获得相关的基础遗传学数据.方法 应用AGCU Y24 STR荧光标记复合直接扩增系统及3130XL型DNA测序仪,对湖北地区320对已确定父子关系的640个男性个体血样进行24个Y-STR检测分型.结果 在320名父亲男性个体中,在DYS391、DYS389工、DYS439、DYS389Ⅱ、DYS438、DYS449、DYS456、DYS458、DYS437、DYS635、DYS448、Y-GATA-H4、DYS447、DYS19、DYS392、DYS522、DYS393、DYS388、DYS390、DYS444基因座在湖北地区汉族人群分别检出4～17个等位基因,DYS527a/b检出45个等位基因组,DYS385a/b检出57个等位基因组,各基因座基因多样性最低为0.3838,最高为0.9650;并检出320种单倍型.比对320对父子Y-STR分型,在7680次基因遗传传递中,在DYS449、DYS527、DYS444、DYS389Ⅱ、DYS447、DYS522、DYS385、Y-GATA-H4等10个基因座中检出16个突变,突变率为1.5625‰～1.5653％,平均突变率为2.0833‰;等位基因增加突变与等位基因减少突变比为1∶1.结论 24个基因座单倍型在湖北地区汉族人群中具有丰富的遗传多态性,其数据对法医学应用、Y-STR数据库建设和群体遗传学等研究应用具有重要意义.     

Population data for six X-chromosome STR loci in a Rio de Janeiro (Brazil) sample: Usefulness in forensic casework

This study presents data for the X-chromosome STR loci DXS7133, DXS7424, DXS8378, DXS6807, DXS7423 and DXS8377. In order to establish a database, unrelated individuals (males and females) from Rio de Janeiro were typed for the above loci. No significant differences were observed between allele frequencies in male and female samples (non-differentiation exact P values ≥ 0.156). Hardy-Weinberg equilibrium was tested in the female sample and no significant deviations were found. All six markers have shown to be highly polymorphic in our sample with gene diversities varying between 0.6797 for DXS7133, and 0.9260 for DXS8377. Pairwise linkage disequilibrium analysis did not allow discharging a possible association between DXS7133 and DXS7424 alleles in Rio de Janeiro population. Parameters of forensic interest, like PD_M, PD_F, Het_obs, Het_exp, were calculated for each locus. The high discrimination power estimated in both males and females, as well as mean exclusion chance in father/daughter duos and in father/mother/daughter trios, demonstrates the usefulness of these six markers in forensic investigation.     

珠海地区汉族人群10个Y-STR基因座的多态性

目的 调查珠海地区汉族人群10个Y-STR基因座及其单倍型的遗传多态性，探讨其法医学应用价值。方法 应用Y-PLEX荧光标记复合扩增系统，对珠海地区汉族200名无关男性个体进行10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10个Y-STR基因座的群体遗传学参数。结果 9个Y-STR基因座分别检出5、6、6、5、4、5、5、5、7个等位基因，DYS385基因座检出44种单倍型；GD值最低为0.3904(DYS391)，最高为0.9497(DYS385)；10个Y-STR基因座共同构成的单倍型161种，其中134种单倍型只出现1次，20种单倍型出现2次，3种单倍型出现3次，3种单倍型出现4次，1种单倍型出现5次，累计GD值为0.9948。结论 10个Y-STR基因座具有较高的个体识别能力，可应用于法庭科学中的个体识别与亲权鉴定。     

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。