High-throughput Y-STR typing of U.S. populations with 27 regions of the Y chromosome using two multiplex PCR assays

Two Y-chromosome short tandem repeat (STR) multiplex polymerase chain reaction (PCR) assays were used to generate haplotypes for 19 single copy and 3 multi-copy Y-STRs. A total of 27 PCR products were examined in each sample using the following loci: DYS19, DYS385 a/b, DYS388, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS426, DYS437, DYS438, DYS439, DYS447, DYS448, DYS450, DYS456, DYS458, DYS460, DYS464 a/b/c/d, H4, and YCAII a/b. The first multiplex is the Y-STR 20plex previously described by Butler et al. [Forensic Sci. Int. 129 (2002) 10]. The second multiplex is a novel Y-STR 11plex and includes DYS385 a/b, DYS447, DYS448 and the new markers DYS450, DYS456, DYS458, and DYS464 a/b/c/d. These two multiplexes were tested on 647 males from three United States population sample sets: 260 African Americans, 244 Caucasians, and 143 Hispanics. Haplotype comparisons between common loci included in the 20plex and 11plex assays as well as commercially available kits found excellent agreement across a sampling of the population samples. The multi-copy loci DYS464, DYS385, and YCAII were the most polymorphic followed by the following single copy Y-STRs: DYS458, DYS390, DYS447, DYS389II, DYS448, and DYS456. Samples containing the most common type in the European database could be well resolved with additional markers beyond the minimal haplotype loci.     

Haplotype analysis of 17 Y-STR loci in a Japanese population

We analyzed 17 Y-STR loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a/b, DYS438, DYS439, DYS456, DYS458 and DYS464a/b/c/d) in 252 Japanese males using three multiplex PCR typing systems. Two variants were found at DYS385a/b. A total of 244 different haplotypes were observed, of which 239 were found in single individuals. The haplotype diversity for the 17 loci was 0.996.     

Genetic analysis of 17 Y-chromosomal STRs haplotypes of Chinese Tibetan ethnic group residing in Qinghai province of China

We have co-amplified and analyzed 17 Y-chromosomal STRs loci including European 'extended haplotypes' (DYS19, DYS389 I, DYS389 II, DYS390, DYS391, DYS392, DYS393, DYS385a,b, DYS438, and DYS439) and also six additional loci DYS437, DYS448, DYS456, DYS458, DYS635 and YGATA H4 in a population sample of 167 healthy unrelated autochthonous male individuals of Chinese Tibetan ethnic minority group residing in Qinghai province of China using a multiplex PCR system. The gene diversity values for the Y-STRs loci ranged from a minimum 0.3581 for DYS391 locus to a maximum of 0.8702 for DYS385a,b loci in Tibetan population. A total of 163 haplotypes were identified in the set of Y-STR loci, of which 159 were unique and 4 found in two individuals. The overall haplotype diversity for the set of Y-STRs loci was 0.9998, and the discrimination capacity was 0.9938. Research results will be valuable for human identification and paternity tests in the region and for Chinese population genetic study in the future.     

Forensic evaluation and haplotypes of 19 Y-chromosomal STR loci in Koreans

In this study, 19 Y-specific STR loci (DYS19, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS388, DYS434, DYS435, DYS436, DYS437, DYS438, DYS439, DYS446, DYS449, and DYS464) were analyzed in 301 unrelated Korean males by three multiplex PCR systems. The haplotype diversity using the classical set of Y-STRs (DYS19, DYS389I/II, DYS390, DYS391, DYS392, DYS393, and DYS385; multiplex I) was 0.9963. For the same individuals, the haplotype diversity value using the new set of highly informative Y-STRs (DYS385, DYS446, DYS449, and DYS464; multiplex III) was 0.9989, while that using the combined set of Y-STRs by adding DYS388 to the previously studied DYS434, DYS435, DYS436, DYS437, DYS438, and DYS439 (multiplex II) was 0.9509. A total of 297 different haplotypes were identified using the 19 Y-STR markers, of which 293 were unique and 4 were found twice. The overall haplotype diversity was 0.9999. The evaluation of the information of selected markers by combination of each marker with the minimal haplotype showed that DYS434, DYS435, DYS436, DYS437, and DYS438 do not significantly contribute to increment of haplotype diversity. However, respective conjunction of DYS464, DYS449, and DYS446 with the minimal haplotype considerably increased the haplotype diversity. Especially, DYS464 is expected to be the most useful marker that can be included in the expanded minimal haplotype. These results including the haplotype data at 19 Y-STR loci in the present study would provide useful information in forensic practice in a Korean population.     

Population genetics for Y-chromosomal STRs haplotypes of Chinese Tibetan ethnic minority group in Tibet

Y-chromosomal STRs loci were analyzed from a sample of 119 healthy unrelated autochthonous male individuals of Chinese Tibetan ethnic minority group using a multiplex PCR system. Allele and haplotype frequencies for DYS19, DYS389 I, DYS389 II, DYS390, DYS391, DYS392, DYS393, DYS385a,b, DYS438, and DYS439 were determined by the Y-PLEXtrade mark 12 kit. The gene diversity values for the Y-STRs loci ranged from 0.3347 (DYS438) to 0.9547 (DYS385a,b). A total of 110 haplotypes were identified in the Y-STR loci, among which 104 were unique, while six occurred more than once. The overall haplotype diversity for the Y-STRs loci was 0.9981, and the discrimination capacity was 0.9897. The results in the present study can be used for routine forensic application in the region, and enrich Chinese ethnical genetic informational resources.     

Genetic polymorphism of 12 Y-chromosomal STR loci in the Minnan Han Chinese in Southeast China

The 12Y-chromosomal short tandem repeat (STR) loci DYS19, DYS389I and II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS385a and b were analyzed in a sample of 109 unrelated male individuals from mountainous areas of Minnan, Southeast China. A total of 95 haplotypes were identified. The allele diversity values for each locus ranged from 0.3205 (DYS391) to 0.9553 (DYS385), the haplotype diversity was 0.9863, and the discrimination capacity 0.8716.     

Y chromosome STR haplotypes in three UK populations

Eleven Y chromosome short tandem repeat markers: DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439, have been typed in the three main UK population groups: Caucasians, Afro-Caribbeans and South Asians. Existing PCR reactions were adapted to incorporate DYS437, DYS438 and DYS439. The observed 11 loci haplotypes and the individual allele frequencies for each locus are presented. Distinct differences for most markers were observed between the population groups studied.     

7个Y-STR基因座单倍型及其法医学应用

目的调查7个Y-STR基因座单倍型及其法医学应用。方法利用二组复合扩增体系,(Ⅰ:DYS391、GATA-A4、GATA-A10和GATA-H4;Ⅱ:DYS439、DYS437和DYS434)检测7个Y染色体特异性的STR基因座,并用聚丙烯酰胺凝胶电泳和银染显色技术进行基因分型。结果在广东汉族372名无关男性个体中,二组7个基因座分别检出5、7、6、5和6、4、4个等位基因,共检出254种单倍型,其中201种为唯一的。单倍型基因多样性为0.9960。结论7个Y-STR基因座具有很高的识别能力,对建立Y染色体STR数据库,研究群体遗传学和进行法医学鉴定有重要意义。     

Y-STRs haplotypes of Chinese Mongol ethnic group using Y-PLEX 12

Eleven Y-chromosome STR loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a,b, DYS438, DYS439) have been co-amplified in 96 healthy unrelated males of Chinese Mongol ethnic group, in order to investigate allele and haplotype frequencies of them, evaluate their usefulness in forensic casework.     

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。     

Tunisian population data on 10 Y-chromosomal loci

Alleles and haplotypes frequencies for 10 Y-chromosome STR loci (DYS19, DYS385 I/II, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS438 and DYS439), included in the Y-Plex6 and Y-Plex5 kits were determined for a Tunisian population sample of 100 male individuals.     

Population genetics for Y-chromosomal STRs haplotypes of Chinese Korean ethnic group in northeastern China

Y-chromosomal STRs loci were analyzed from a sample of 201 healthy unrelated male individuals of Chinese Korean ethnic group. Allele and haplotype frequencies for DYS19, DYS385a/b, DYS388, DYS389 I, DYS389 II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439 were determined by the general PCR and silver staining methods. The gene diversity values for the Y-STRs loci ranged from 0.4146 (DYS437) to 0.9631 (DYS385a/b). A total of 194 haplotypes were identified in the Y-STR loci, among which 188 were unique, while 6 occurred more than once. And the combined haploytpes diversity was 0.9996. The results in the present study can be used for routine forensic application in the region, and enrich Chinese ethnical genetic informational resources.     

Population data for 12 Y-chromosome STRs in a sample from Brescia (northern Italy)

Twelve Y-chromosome STRs--DYS19, DYS389-I, DYS389-II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438, DYS439--were typed in a population sample (n=104) of unrelated males from Brescia (northern Italy). A total of 91 haplotypes were identified by the 12 Y-STR loci. The haplotype diversity (98.68%), discrimination capacity (87.50%) and gene diversity were calculated.     

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。     

Y chromosome STR haplotype data for an Irish population

Y chromosome haplotype data was collected for 155 Irish males residing in the Republic of Ireland. Eleven short tandem repeat (STR) markers: DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439 were analysed and the allele and haplotype frequencies calculated. This Irish data is presented here and was found to be less diverse when compared with the neighbouring UK population.     

Population study of 11 Y-chromosomal STR loci in Singapore Chinese

In this study of 212 unrelated Singapore Chinese males, allelic frequencies and gene diversities of 11 Y-chromosome specific STR loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a/b, DYS438 and DYS439) were established. A total of 184 haplotypes were observed in the 212 individuals studied, of which 165 (89.67%) were unique. The most common haplotype was observed in five (2.35%) individuals. The overall haplotype diversity for the 11 Y-STR loci was 99.81%, and the discrimination capacity was 86.79%.     

Genetic polymorphisms for 11 Y-STRs haplotypes of Chinese Yi ethnic minority group

Eleven Y-STRs loci including minimal haplotypes (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, and DYS385a,b) and two additional loci, namely DYS438 and DYS439 have been co-amplified in 100 healthy unrelated males of Chinese Yi minority ethnic group using the Y-PLEX 5 and Y-PLEX 6 kit, in order to investigate allele and haplotype frequencies of Yi population, evaluate their usefulness in forensic paternity testing and human identification, and enrich Chinese population genetic informational resources. Out of a total of 100 individuals 85 showed different haplotypes, while 8 haplotypes occurred more than once. The overall haplotype diversity for 11 Y-STRs loci was 0.9945.     

Validation of a multiplex amplification system of 19 autosomal STRs and 27 Y-STRs

This article describes a newly devised autosomal short tandem repeat (STR) multiplex polymerase chain reaction (PCR) system for 19 autosomal loci (D12S391, D13S317, D16S539, D18S51, D19S433, D2S1338, D21S11, D3S1358, D5S818, D6S1043, D7S820, D8S1179, CSF1PO, FGA, TH01, TPOX, vWA, Penta D and Penta E), 27 Y-chromosome STR loci (DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS460, DYS481, DYS518, DYS533, DYS570, DYS576, DYS635, DYS627, YGATAH4 and DYF387S1) and amelogenin with six-colour fluorescent labelling. Various parameters were evaluated, such as its accuracy, sensitivity, specificity, stability, ability to analysis of mixtures and effects of changes in the PCR-based procedures. All of the 47 selected STR loci were accurately and robustly amplified from 282 bloodstain samples. The species-specificity was high and some ability to inhibit Hematin was identified. The lowest detectable DNA amount was ≥0.125 ng. All of the male loci of the secondary component were revealed precisely when the control DNA was mixed at male/female and male/male ratios of 1:4 or more. We conclude that the present 19-plex autosomal STR and 27 Y-STR assay is both accurate and sensitive. It constitutes an additional powerful tool for forensic applications.     

Haplotype diversity of 16 Y-chromosomal STRs in three main ethnic populations (Malays, Chinese and Indians) in Malaysia

We have analyzed 16 Y-STR loci (DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385a/b, DYS393, DYS391, DYS439, DYS635 or Y-GATA C4, DYS392, Y-GATA H4, DYS437, DYS438 and DYS448) from the non-recombining region of the human Y-chromosome in 980 male individuals from three main ethnic populations in Malaysia (Malay, Chinese, Indian) using the AmpFlSTR((R)) Y-filertrade mark (Applied Biosystems, Foster City, CA). The observed 17-loci haplotypes and the individual allele frequencies for each locus were estimated, whilst the locus diversity, haplotype diversity and discrimination capacity were calculated in the three ethnic populations. Analysis of molecular variance indicated that 88.7% of the haplotypic variation is found within population and 11.3% is between populations (fixation index F(ST)=0.113, p=0.000). This study has revealed Y-chromosomes with null alleles at several Y-loci, namely DYS458, DYS392, DYS389I, DYS389II, DYS439, DYS448 and Y-GATA H4; and several occurrences of duplications at the highly polymorphic DYS385 loci. Some of these deleted loci were in regions of the Y(q) arm that have been implicated in the occurrence of male infertility.     

Haplotypes for 12 Y-chromosomal STR loci in a Korean population (the central region)

Haplotypes and allele frequencies of 12 STR loci included in the PowerPlex Y system (DYS391, DYS389I, DYS439, DYS389II, DYS438, DYS437, DYS19, DYS392, DYS393, DYS390, and DYS385a/b) were obtained from a sample of 569 unrelated individuals living in the central region of Korea. A total of 473 haplotypes were observed in the 569 individuals studied, of which 426 (90.06%) were unique. The overall haplotype diversity for the 12 Y-STR loci was 0.9985, and the discrimination capacity was 0.8313. In DYS439, we found a new intermediate-sized allele that added an A at base 3 upstream from the repeat region's first GATA motif. The allele was named 11 (U3Ains) according to its sequence structure.