Population genetic data for 17 Y STR markers from Benghazi (East Libya)

The seventeen Y-STR loci included in the AmpF?STR^® Yfiler? PCR Amplification kit (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a/b, DYS438, DYS439, DYS437, DYS448, DYS458, DYS456, DYS635, and Y-GATA-H4) were used to type a sample population of 238 males from eastern Libya (Benghazi region). Of 238 observed haplotypes, 214 were unique (90%) and 24 (10%) were found more than once. The 17 loci gave a discriminating power of 0.999. DYS458 showed the highest diversity as a single-locus marker (0.73). Allelic frequencies and gene diversities for each Y-STR locus were determined. The high haplotype diversity and discrimination capacity (0.996) demonstrate the utility of these loci for human identification in forensic applications. Comparative analysis with Y-STR datasets of relevant populations and submission of the haplotypes to the Y-STR Haplotype Reference Database (YHRD) was undertaken.     

Genetic analysis of 17 Y-chromosomal STR loci of Chinese Tujia ethnic group residing in Youyang Region of Southern China

Y-STR haplotype data were obtained in a population sample of 197 unrelated healthy male individuals of Chinese Tujia ethnic minority group residing in an autonomous county of Southern China using 17 Y-chromosome STR markers. A total of 197 haplotypes were identified in the set of Y-STR loci. The overall haplotype diversity for the Tujia population at 17 Y-STR loci was 1.0000 ± 0.0005. Genetic distance was estimated between this population and other 14 Chinese populations including Paiwan and Atayal populations of Taiwan, and Southern Han, Dong, Jing, Miao, Yao, Zhuang, Yi, Maonan, She, Hui, Sala, and Tibetan ethnic groups. The results demonstrated that the 17 Y-STR loci analyzed were highly polymorphic in Tujia ethnic group examined and hence useful for forensic cases, paternity testing, and population genetic studies.     

Population genetics for 17 Y-STR loci(AmpFISTR®Y-filerTM) in Luzhou Han ethnic group

In this study, 17 Y-STR loci(AmpFISTR^®Y-filerTM)—DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385a/b, DYS393, DYS391, DYS439, DYS635, DYS392, Y-GATA H4, DYS437, DYS438, DYS448 were analyzed in 424 unrelated males from Luzhou Han ethnic group, Southwest China. 365 haplotypes were observed. The discrimination capacity was 0.8608 and the haplotype diversity was 0.9992.     

Haplotype diversity and phylogenetic relationship analysis of Chinese Yulin Han population using 59 Y-STR loci of two novel Y-STR typing systems

To investigate the genetic polymorphisms of 59 Y-chromosomal short tandem repeat (Y-STR) loci in the Yulin Han population, 229 unrelated healthy male individuals were analyzed using AGCU Y37 kit and AGCU Y-SUPP Plus kit. A total of 227 different haplotypes were obtained at the 59 Y-STR loci. Among them, 225 haplotypes were unique and 2 haplotypes occurred twice. The overall haplotypic diversity and discrimination capacity were 0.9999 and 0.9913, respectively. The phylogenetic relationships between the studied Yulin Han population and 17 previously reported reference populations were evaluated via multidimensional scaling and Neighbor-Joining analyses based on the haplotypic frequencies of ‘YHRD Maximal Loci’. Phylogenetic analysis revealed that Yulin Han population was closely related to Chinese Han and Hunan Yao populations. These results demonstrated that the 59 Y-STR loci were useful for forensic applications and population genetic studies.     

Seventeen Y-chromosomal short tandem repeat haplotypes in seven groups of population living in Taiwan

The analysis of Y-chromosome short tandem repeat (Y-STR) loci is a powerful tool in forensic casework. The aim of this study was to present the 17 Y-STR loci haplotype distributions of groups of population living in Taiwan and to demonstrate genetic distances between the groups as well as multidimensional scaling plot based on Y-STR genotype data. Five hundred and fifteen DNA samples from unrelated males of seven groups of population, including Taiwanese Han, two groups of indigenous Taiwanese of Taiwan Island, Tao, mainland Chinese, Filipinos, and a group of people with European, Near Eastern, or South Asian ancestry, were analyzed using a commercial kit that co-amplifies 17 Y-STRs. A total of 471 different haplotypes with 440 unique haplotypes were identified. The overall haplotype diversity was 0.9995 ± 0.0002. High haplotype diversity was observed in six groups of population, except the Tao. These Y-STRs revealed a low discrimination capacity in the Tao population (36.84%), which should be considered in forensic practice. The multidimensional scaling plot of these seven groups of population constructed based on the genetic distances according to 17 Y-STR loci presented a clear patrilineal genetic substructure in the area. Partial Y-STRs profiling reduced the discrimination capacity in most groups of population and distorted the multidimensional scaling plot.     

Genetic variations of 15 autosomal and 17 Y-STR markers in Sindhi population of Pakistan

This study comprises genetic characterization of 15 autosomal and 17 Y-chromosomal STR loci in 103 unrelated male inhabitants of the Sindhi population to establish its lineage and parameters of forensic interest. The examined autosomal STRs revealed high combined power of discrimination, combined power of exclusion, and the combined matching probability as 0.99999999999999999042580, 0.9999977141, and 9.5742 × 10⁻¹⁸, respectively. A total of 89 unique haplotypes were obtained, of which 84 were observed once with a haplotype diversity value of 0.999677. The resulted Y-STR haplotypes exhibited a high degree of geographical demarcation by comparing with other populations at the local and global levels.

     

Genetic analysis of 39 Y-STR loci in a Han population from Henan province,central China

A total of 39 Y-chromosomal short tandem repeat (Y-STR) loci included in the advanced commercial six-dye multiplex system (AGCU Database Y30 kit) and a custom-designed four-dye multiplex system were investigated in 259 unrelated healthy Chinese males residing in Henan Province, central China. The haplotype diversity (HD) values were 0.99997 and 1.0000 for the six and four fluorescent-multiplex amplification systems, respectively. The discrimination capacity (DC) values were 0.9961 and 1.0000, respectively. When the 39 Y-STR loci were considered, 259 unique haplotypes were obtained in Henan Han individuals with both the haplotype diversity and discrimination capacity being 1.000. The gene diversity (GD) of 39 Y-STR loci in the studied group ranged from 0.3956 (DYS588) to 0.9990 (DYF403S1). Population comparisons between the Henan Han and 24 reference groups were performed. Both multidimensional scaling plots and phylogenetic analysis demonstrated that significant genetic differences existed between Henan Han and reference ethnic minorities of China, particularly the Tibetan, Uighur, and Mongolian populations. Moreover, the results indicated that 39 Y-STRs included in the two fluorescent-multiplex amplification systems are highly polymorphic and informative in the studied populations and can be employed as complementary tools for forensic application and human genetics research.

     

Phylogenetic and forensic studies of the Southeast Florida Hispanic population using the next-generation forensic PowerPlex® Y23 STR marker system

The purpose of this study is to examine the robustness and sensitivity of the newly available Y-STR multiplex kit, the PowerPlex® Y23 System, by comparing our data at the 23-loci level to the routinely used 17 loci provided by the AmpFlSTR® Yfiler® PCR Amplification kit. For the first time, allelic and genotypic frequencies for the 23 Y-STR loci included in the PowerPlex® Y23 System are provided for the Southeast Florida Hispanic (SFH) population. In addition, we have characterized the SFH population in terms of intra-population and inter-population parameters. We also compared these indices of forensic and population genetics interest in the SFH population to comparable data of previously published populations to assess their phylogenetic relationships. Our 23-loci data was shown to provide more discriminatory values as compared to the data when using only 17 loci. Also, the R_ST distance values demonstrate the superior capacity of the PowerPlex® Y23 system to discriminate among populations.     

27 Y-chromosomal STR haplotypic structure for the Chinese Han population from Changchun,Northeastern China

Y- Changchun is the capital and largest city of Jilin Province in the northeast China. In this study, we genotyped and investigated haplotypes of 27 Y-STR loci in 1037 Changchun Han male individuals using commercially available AmpFlSTR Yfiler® Plus kit. We calculated the Gene diversity (GD) values and haplotype diversity (HD) as important forensic parameters. Furthermore, we observed genetic affinities between Changchun Han with other Northern Han Chinese populations and also Korans in Yanbian in the Multidimensional scaling and phylogenetic tree analysis.     

Population genetic polymorphisms of 17 Y-chromosomal STR loci in South Koreans

Haplotypes and allele frequencies of 17 Y-chromosomal STR loci included in the AmpFlSTR^® Yfiler^® system were obtained from a sample of 1021 unrelated individuals living in 6 provinces of South Korea. A total of 938 haplotypes were observed in the 1021 individuals studied, of which 885 were unique. The overall haplotype diversity for the 17 Y-STR loci was 0.9998, and the discrimination capacity was 0.9187. We found 11 atypical alleles (null, duplicated, triplicated, and microvariant alleles), that have not previously been reported in South Korean populations. It seems that these 17 loci are useful genetic markers for forensic personal identification and paternity testing in the South Korean population.     

Y-STR markers from Ladakh in the Himalayas

A total of 223 samples from the general population of Ladakh in Northwestern India were amplified at 17 Y-STR loci using the AmpFlSTR® Yfiler™ system. The DNA profiles generated were employed to generate allelic frequencies, gene diversity, haplotype diversity and discrimination capacity values as well as number of different haplotypes, fraction of unique haplotypes and Rst pair wise genetic distances. Multidimensional Scaling (MDS) and Correspondence Analysis (CA) were performed with the Rst values and allelic frequencies, respectively. The 17-loci discrimination capacity of Ladakh was found to be 0.8093. Eleven out of the 16 loci have diversity values greater than 0.6, and 13 loci possess values greater than 0.5. Ladakh exhibits no significant genetic difference to seven of the 15 reference forensic databases after Bonferroni correction, three of which are located in South Central Asian and four are from the Himalayan region. Rst genetic distance values before and after Bonferroni corrections illustrate the capacity of the Yfiler system to discriminate among Himalayan populations. The intermediate position of the Ladakh population in the MDS and CA plots likely reflects genetic flow and admixture with neighboring populations. In addition, the longitudinal partition of populations in the MDS and CA plots likely reflect human dispersals such as the silk road migrations.     

Analysis of 24 Y chromosomal STR haplotypes in a Chinese Han population sample from Henan Province,Central China

We analyzed haplotypes for 24 Y chromosomal STRs (Y-STRs), including 17 Yfiler loci (DYS19, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DY438, DYS439, DYS448, DYS456, DYS458, DYS635 and Y-GATA-H4) and 7 additional STRs (DYS388, DYS444, DYS447, DYS449, DYS522 and DYS527a/b) in 1100 unrelated Chinese Han individuals from Henan Province using AGCU Y24 STR kit systems. The calculated average gene diversity (GD) values ranged from 0.4105 to 0.9647 for the DYS388 and DYS385a/b loci, respectively. The discriminatory capacity (DC) was 72.91% with 802 observed haplotypes using 17 Yfiler loci, by the addition of 7 Y-STRs to the Yfiler system, the DC was increased to 79.09% while showing 870 observed haplotypes. Among the additional 7 Y-STRs, DYS449, DYS527a/b, DYS444 and DYS522 were major contributors to enhancing discrimination. In the analysis of molecular variance, the Henan Han population clustered with Han origin populations and showed significant differences from other Non-Han populations. In the present study, we report 24 Y-STR population data in Henan Han population, and we emphasize the need for adding additional markers to the commonly used 17 Yfiler loci to achieve more improved discriminatory capacity in a population with low genetic diversity.     

Developmental validation of the DNATyper™Y26 PCR amplification kit: An enhanced Y-STR multiplex for familial searching

The DNATyper^™Y26 PCR Amplification kit, which including 26 low-medium mutating Y-STRs, is designed for Y-STR familial searching casework. The kit combines nine new Y-STR loci in addition to the 17 Y-STR loci from the commercially available AmpFlSTR®Yfiler® kit. The validation of the DNATyper^™Y26 kit was performed in terms of technical index, including accuracy, stability, species specificity, sensitivity, adaptability for various samples, and mixture. Further, mutations of the 26 Y-STRs were analyzed by 1167 DNA-confirmed father-son pairs, and the results indicated that these loci had low or medium mutation rates. Furthermore, these Y-STRs loci were also tested in 1072 random male samples from Henan, Shanxi, Inner Mongolia, and Chongqing in China, showing their high power for forensic discrimination in the Chinese population. Thus, the DNATyper^™Y26 PCR Amplification kit is a powerful tool for ‘Y-STRs familial searching’ in actual sexual-assault cases, indicating its unique advantage in familial searching due to Y-STR loci with only low-medium mutation rates.     

Forensic characteristics and genetic analysis of both 27 Y-STRs and 143 Y-SNPs in Eastern Han Chinese population

Y-chromosome short tandem repeat (Y-STR) and Y-chromosome single nucleotide polymorphism (Y-SNP) frequency distributions provide resources for assessment of male population stratification among world-wide populations. Currently, the Y-STR Haplotype Reference Database (YHRD) contains numerous Y-chromosome haplotype profiles from various populations and countries around the world. However, for many of the recently discovered and already phylogenetically mapped Y-SNPs, the population data are scarce. Herein, the typing of 27 Y-STRs (Yfiler Plus) and 143 Y-SNPs (self-designed Y-SNP panel) was performed on 1269 unrelated males from 11 Han Chinese populations. Haplogroup O-M175 was the most predominant haplogroup in our Han Chinese data, ranging from 67.34% (Henan Han) to 93.16% (Guangdong Han). The highest haplogroup diversity (0.967056) was observed in Heilongjiang Han, with a discrimination capacity (DC) value of 0.3723. The number of alleles at single-copy loci varied from 2 for DYS391 (Guangdong Han) to 16 for DYS518 (Henan Han). For the majority of the populations (8/11), both the haplotype diversity and DC values are 1.0000. Furthermore, genetic differentiations were observed between Northern and Southern Han Chinese. These genetic differences were mainly reflected in haplogroup distribution and frequency, and they were confirmed by statistical analysis.     

Genetic polymorphism of Y-chromosomal STRs in Gujjar population of Punjab

Y-STR polymorphism of Gujjar population was determined by using AmpFISTR®YfilerTM PCR amplification kit. A total 176 haplotypes were obtained after the analysis of 17 Y-STR loci in 176 genetically unrelated individuals. Haplotype diversity and discrimination capacity attained was 0.99730 and 0.652201325, respectively. The comparison of Gujjar population with 16 other populations revealed that Gujjars have low genetic distance from Punjabi, Sindhi, and Pakhtun population of Pakistan; Azad Kashmir, Saraswat Brahmin from India; Bangladeshi population; north and south of Afghanistan; and Uttar Pradesh India which hints toward the migrational route Gujjars took over the centuries. This data is of significant value for population studies and forensic applications.     

Distribution of Y-chromosomal haplotypes in the Central Portuguese population using 17-STRs

17 Y-chromosome STR loci (DYS19, DYS389I, DYS389II, DYS390, DYS456, DYS391, DYS392, DYS393, DYS385 a/b, DYS458, DYS439, DYS635, GATA H4.1, DYS437, DYS438 and DYS448) were determined for 303 unrelated males, living in Central Portugal, using the AmpFlSTR^® YFiler™ PCR Amplification kit (Applied Biosystems). A total of 287 different haplotypes were found, 272 being unique. The overall haplotype diversity (HD) was determined as 0.9996, a value similar to other YFiler data sets. Y-STR polymorphisms in Central Portugal population, using YFiler, provide a powerful discrimination tool for routine forensic applications.     

Haplotype analysis of the polymorphic 24 Y-STR markers in six ethnic populations from China

Twenty-four Y-STR loci were analysed in 1446 males from the following six Chinese ethnic populations: Guangxi Han (n=600), Gin (n=161), Maonan (n=135), Miao (n=186), Zhuang (n=226) and Yao (n=138) using the AGCU Y24 STR amplification kit. The lowest estimates of genetic diversity (below 0.5) correspond to markers DYS391 (0.4006), DYS438 (0.4300), and DS388 (0.4907), and the greatest diversity corresponds to markers DYS385a/b (0.9636) and DYS527a/b (0.9439). Moreover, there were 1331 different haplotypes identified from the 1446 total samples, of which 1233 were unique. Notably, we observed shared haplotypes between the four ethnic populations (Maonan, Miao, Zhuang, Yao ethnic population), except between the Guangxi Han and Gin population. The estimated overall haplotype diversity (HD) was 0.9997. A multidimensional scaling (MDS) plot based on the genetic distances between populations demonstrates the genetic similarity of the Maonan, Miao and Zhuang populations with genetic distance below 3.0. No substructure correction is required to estimate the rarity of a haplotype comprising 24 markers. In summary, the results of our study indicate that the 24 Y-STRs have a high level of polymorphism in these six Chinese ethnic populations and could therefore be a powerful tool for forensic applications and population genetic studies.     

Investigation of extended Y chromosome STR haplotypes in Sardinia

Y-chromosomal variation of selected single nucleotide polymorphisms (SNPs) and 32 short tandem repeat (STR) loci was evaluated in Sardinia in three open population groups (Northern Sardinia, n = 40; Central Sardinia, n = 56; Southern Sardinia, n = 91) and three isolates (Desulo, n = 34; Benetutti, n = 45, Carloforte, n = 42). The tested Y-STRs consisted of Yfiler^® Plus markers and the seven rapidly mutating (RM) loci not included in the YFiler^® Plus kit (DYF399S1, DYF403S1ab, DYF404S1, DYS526ab, DYS547, DYS612, and DYS626).As expected, inclusion of additional Y-STR loci increased haplotype diversity (h), though complete differentiation of male lineages was impossible even by means of RM Y-STRs (h = 0.99997).Analysis of molecular variance indicated that the three open populations were fairly homogeneous, whereas signs of genetic heterogeneity could be detected when the three isolates were also included in the analysis.Multidimensional scaling analysis showed that, even for extended haplotypes including RM Y-STR markers, Sardinians were clearly differentiated from populations of the Italian peninsula and Sicily. The only exception was represented by the Carloforte sample that, in accordance with its peculiar population history, clustered with Northern/Central Italian populations.The introduction of extended forensic Y-STR panels, including highly variable RM Y-STR markers, is expected to reduce the impact of population structure on haplotype frequency estimations. However, our results show that the availability of geographically detailed reference databases is still important for the assessment of the evidential value of a Y-haplotype match.     

Allele frequency data of 15 autosomal STR loci in four major population groups of South Africa

Allele frequency distributions for 15 tetrameric short tandem repeat (STR) loci were determined using the AmpFlSTR® Identifiler Plus? PCR amplification kit. There was little evidence of departures from Hardy–Weinberg equilibrium or association of alleles of different loci in the population samples. The probability of identity values for the different populations range from 1/3.3?×?10¹⁷ (White) to 1/1.88?×?10¹⁸ (Coloured). The combined probability of paternal exclusion for the different population groups ranges from 0.9995858 (Coloured) to 0.9997874 (Indian).     

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.