Polymorphisms of six Y-chromosome STRs in a Chinese population

The polymorphic short tandem repeat (STR) loci of six Y-chromosome markers were investigated in 112 unrelated Chinese males using a multiplex polymerase chain reaction (PCR). Allele and haplotype frequencies for the Y-specific STR loci DYS19, DYS385, DYS389II, DYS390, DYS391 and DYS393 were analyzed by the Y-PLEX 6 Kit. The commonest allele for each locus was: DYS19, allele 15; DYS385, allele 12; DYS389II, allele 28; DYS390, allele 23; DYS391, 10; and DYS393, allele 12. Gene diversity value was calculated from the allelic frequency for each locus. The DYS385 locus proved to be highly polymorphic (0.890), DYS391 showed the lowest value (0.489), and the other loci showed values ranging from 0.646 to 0.897. A total of 99 haplotypes were observed in six Y-specific STR loci, the haplotype diversity was raised to 0.999. The results revealed that a set of six Y-specific STR loci were able to discriminate most of the male individuals in the Chinese population.     

Genetic polymorphisms of 17 Y-STRs haplotypes in Tibetan ethnic minority group of China

Haplotypes and allele frequencies for the 17 Y-chromosomal STRs loci, namely DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385a,b, DYS393, DYS391, DYS439, DYS635, DYS392, Y GATA H4, DYS437, DYS438, DYS448 were determined in a population sample of 112 healthy unrelated autochthonous Tibetan ethnic male individuals from Tibet of China. No shared haplotypes were observed. The gene diversity values for the Y-STRs loci ranged from 0.2052(DYS391) to 0.9301(DYS385a,b). The results demonstrate that these loci will be very useful for human identification in forensic cases and paternity tests in Tibetan population of China.     

Y-chromosome STR haplotype profiling in the Mongolian population

Eleven Y-chromosome STR loci (DYS19, DYS388, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, two DYS385 loci and DXYS156Y) were analyzed in 92 randomly chosen males from Mongolia. Allelic frequencies and gene diversity for each Y-STR locus and haplotype diversity were determined to evaluate their usefulness in forensic casework. A total of 84 different haplotypes were identified, among which 77 (83.7%) were individual-specific. The most frequent haplotype surveyed here was found in three individuals (3.6%), of which the 'minimal haplotype' (excluding DYS388 and DXYS156Y) was not found in the worldwide Y-STR haplotype reference database (YHRD) available at .     

Population study of Y-chromosome STR haplotypes in Japanese from the Tokushima

The Y-chromosome short tandem repeat (STR) systems including DYS19, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS385 and YCAII were investigated in 121 Japanese males (Tokushima area). Analysis of the nine loci permitted classification of the samples into 107 haplotypes, and the haplotype diversity was estimated to be 0.989. DYS385 showed the highest gene diversity (GD) value (GD=0.946), while DYS391 showed the lowest GD value (GD=0.27). Furthermore, in DYS392, we found a new mutant allele that added a T within the repeat region (a mutation in the repetitive region), and the allele was designated 13.1 according to the sequence structure. We also detected allele 20 in DYS392 as a new allele. In DYS385, a new allele 26 that has not been previously reported was observed.     

Highly informative Y-chromosomal haplotypes by the addition of three new STRs DYS437, DYS438 and DYS439

The Y chromosome STRs DYS437, DYS438 and DYS439 were selected from publicly available genome databases and used to analyse an Italian population sample. A tetraplex PCR reaction including the highly informative DYS385 locus, was set up and used for the analysis of 131 male samples to determine allele frequencies and STR diversity values. The number of different haplotypes and the haplotype diversity value found from the analysis of the STRs included in the tetraplex reaction were very similar to those found from the analysis of the basic set of 7 Y-STRs (DYS19, DYS389I/II, DYS390, DYS391, DYS392 and DYS393) previously carried out on the same population sample. By combining the allelic states of the 11 Y-chromosomal STRs we could construct highly informative haplotypes that allowed the discrimination of 93.8% (120 out of 128) of the samples tested. This approach represents a very powerful tool for individual identification and paternity testing in forensic medicine. Received: 29 November 1999 / Accepted: 17 March 2000     

Genetic polymorphisms of 17 Y-STRs haplotypes in Chinese Han population residing in Shandong province of China

We have co-amplified (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a,b, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, and Y GATA H4) in a single PCR using the AmpFLSTR Yfiler PCR Amplification system. Allelic frequency distribution and haplotype diversity of 17 Y-chromosomal STR from a sample of 131 unrelated individuals of Chinese Han population living in Shandong province of China were obtained. A total of 129 haplotypes were observed in the 131 individuals studied, of which 127 were unique and two were found in two individuals. The gene diversity values ranged from 0.3560 (DYS391) to 0.9675 (DYS385a,b), The overall haplotype diversity for the 17 Y-STR loci was 0.9998, and the discrimination capacity was 0.9695. These results are compared with those observed in worldwide populations at both the locus and the haplotype level.     

Y-chromosomal STR haplotypes in a Northeast Italian population sample using 17plex loci PCR assay

One hundred fifty-five unrelated, autochthonous healthy males from Northeast Italy were typed for the 17 Y-chromosome short tandem repeat (STR) (Y-STR) loci DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385, DYS393, DYS391, DYS439, DYS635, DYS392, Y GATA H4, DYS437, DYS438, DYS448 using the AmpFLSTR Yfiler polymerase chain reaction amplification kit. A total of 153 different haplotypes were observed, and among these, 151 were unique, while 2 were found two times. The overall haplotype diversity was 0.9997. Furthermore, 50 father–son pairs, previously confirmed by autosomal STR analysis, were typed using the same set of 17 Y-STR loci, and, among 850 allele transfers, three mutation events were identified, giving an average mutation rate of 3.53×10⁻³ per locus per generation (95% confidence interval 0.73–1.03). Electronic supplementary material Supplementary material is available for this article at     

Genetic population study of 11 Y chromosome STR loci in Greece

Statistical properties of eleven Y chromosome Short Tandem Repeat (STR) markers were analyzed (DYS391, DYS389I, DYS439, DYS389II, DYS438, DYS437, DYS19, DYS392, DYS393, DYS390 and DYS385) in a Greek population sample. The 200 subjects where distributed across Greece, from various Peripheries. 182 distinct haplotypes were found. To validate our results gene diversity has been calculated for the whole population, as well as for each locus individually. Genetic distance has been estimated between this population and Albanian, Egyptian, Italian and Turkish populations. The results indicate that all Y loci are useful for forensic sciences.     

Genetic diversity of 17 Y-short tandem repeats in Indian population

Seventeen short tandem repeats (DYS389I, DYS390, DYS389II, DYS19, DYS385a/b, DYS393, DYS391, DYS392, DYS439, DYS438, DYS456, DYS458, DYS635, Y(GATA)H4, DYS437, and DYS448) from the non-recombining region of the human Y-chromosome were analyzed in 750 unrelated males representing four major linguistic families of India using AmpFlSTR(?) Yfiler(?) PCR Amplification kit. A total of 612 distinct haplotypes were observed, of which 545 were unique. Rare alleles for the loci DYS456, DYS458, DYS635, Y(GATA)H4, and duplication at the loci DYS389I and DYS389II were also observed. To understand the genetic diversity of the Indian population, and utility of Y-STRs in forensics, the locus diversity, haplotype diversity, and discrimination capacity in all populations was determined. MDS plot based on pairwise Φ(st) and AMOVA revealed the high genetic heterogeneity among the Indian populations due to linguistic diversity and social stratification.     

Y chromosome microsatellite genetic variation in two Native American populations from Argentina: Population stratification and mutation data

Two Native American populations from North and northwest regions of Argentina (Toba and Colla) were analyzed for 17 Y chromosome short tandem repeat loci (Y-STRs), namely, DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4.1. Over 357 allele transfers, two one-step mutations could be detected at DYS456 and GATA H4.1 loci. A new 16.1 ‘micro-variant’ allele was observed for DYS385, characterized by an insertion at the fifth GAAA repeat. We also observed two alleles at the DYS448 locus in three samples (two from Toba and one from Colla). A total of 34 and 16 different haplotypes were detected for Toba and Colla, respectively, the former with a haplotype diversity value of 0.9769 ± 0.01, whereas 0.9497 ± 0.02 for the latter. Significant population differences were observed between Colla and Toba, at least in part, due to a more prevalent European input in the Colla. In agreement with this observation is the fact that the genetic distances between Colla and Iberian populations are lower than those observed between Iberian and any other Native American population. The results of multiscaling dimensional analysis and genetic distances (Rst) among Native American population samples also reflect this fact. The data show the existence of clear population stratification in the Argentina, a fact that should be taken into account in forensic casework.     

Genetic polymorphisms for 17 Y-chromosomal STRs haplotypes in Chinese Hui population

We have co-amplified 17 Y-chromosomal STRs (including DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a,b, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, and Y GATA H4) for samples of 143 unrelated male individuals of Chinese Hui Ethnic Minority Group. We obtained allelic frequency distribution and haplotype diversity of 17 Y-chromosomal STR for Hui population. A total of 136 different haplotypes were identified in 143 individuals, among which 129 were found only once, and seven haplotypes were found twice. The gene diversity values of STR loci ranged from 0.4161 (DYS391) to 0.9571 (DYS385a,b). The overall haplotype diversity for the 17 Y-STR loci was 0.9933, and the discrimination capacity was 0.9511.     

Genetic analysis of 17 Y-chromosomal STRs haplotypes of Chinese Tibetan ethnic minority group

We have co-amplified and analyzed 17 Y-chromosomal STRs loci (DYS19, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS438, DYS439, DYS437, DYS448, DYS456, DYS458, DYS635, YGATA-H4 and DYS385a/b) in 132 healthy unrelated autochthonous male individuals of Chinese Tibetan ethnic group residing in Lassa area of China. The gene diversity values for the Y-STRs loci ranged from a minimum 0.206 for DYS391 locus to a maximum of 0.912 for DYS385a/b locus in the populations. A total of 123 haplotypes were identified, among which 115 were unique and 8 occurred more than once. The overall haplotype diversity for 17 Y-STRs loci was 0.998. Research results will be valuable for forensic use in the regions and for Chinese population genetic study.     

Increased forensic efficiency of a STR-based Y-specific haplotype by addition of the highly polymorphic DYS385 locus

The polymorphic short tandem repeat (STR) locus DYS385 mapping to the male-specific region of human Y chromosome, was used to reinvestigate 125 unrelated Italian males, from our data archive, who had been previously typed for 7 different Y-specific STRs (DYS19, DYS389 I and II, DYS390, DYS391, DYS392, DYS393), defining a haplotype now widely adopted in the forensic context. The aim of this study was to improve the information value of the original haplotype in view of its application to issues of personal identification and parental analysis. DYS385 proved to be highly polymorphic (94.5% gene diversity) and the overall individualization capacity of the 8-loci haplotype was raised to 93.6%, with 117 unique assets out of 125 tested samples. Received: 4 August 1997 / Received in revised form: 29 September 1997     

Population and mutation analysis of 17 Y-STR loci from Rio de Janeiro (Brazil)

The 17 Y chromosome STR loci DYS19, DYS385, DYS389I and II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS460, DYS461, GATA C4, GATA H4 and GATA A10 were analyzed in a male sample of 126 unrelated individuals from Rio de Janeiro. No shared haplotypes were observed, demonstrating the usefulness and informative power of these Y-STRs in male lineage identification in Rio de Janeiro. Pairwise haplotype analysis showed no significant differences in the comparison of Rio de Janeiro with Iberian samples from different regions of Portugal and Spain, as well as with other Caucasian samples from South America, namely Costa Rica, Buenos Aires (Argentina) and São Paulo (Brazil). The same set of Y-STRs was also typed in 119 father/son pairs and among 2,023 allele transfers, 8 mutations were observed with an overall mutation rate of 0.003955±0.001396 per locus/meiosis across the 17 loci. Except in one case, all mutations were single step. For DYS438 a four-step mutation was found which has never been reported before, where allele 10 mutated to allele 6.     

Genetic sub-structure in western Mediterranean populations revealed by 12 Y-chromosome STR loci

Haplotype and allele frequencies of 12 Y-chromosome short tandem repeat (Y-STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385 a/b, DYS437, DYS438 and DYS439) included in the Powerplex® Y System were determined in seven western Mediterranean populations from Valencia, Majorca, Ibiza (eastern Spain), Sicily and three Calabrian provinces (southern Italy). Amongst the 554 males included in the study, 443 different haplotypes were observed of which 372 were only observed once. The other haplotypes were shared by two to seven men. The overall haplotype diversity was 0.9988?±?0.0002. These Y-STRs markers showed a low capacity of discrimination (56.3%) in the Ibiza population probably due to genetic drift. Comparisons between the populations studied and other neighbouring populations showed a clear genetic sub-structure in the western Mediterranean area.     

Allele and haplotype diversity of 17 Y-STRs loci in the northern region Pashtun (Pathans) population of Pakistan

A total of 17 Y-linked short tandems repeat (Y-STRs) loci (DYS19, DYS385a, DYS385b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, and GATA H4) were genotyped in the Pashtun (Pathans) male population residing in the northern region of Pakistan. The Pashtun population, in spite of its decisive geographic location for repopulation movements between Pakistan, Afghanistan and India over time, has been insufficiently characterised at the genetic level, especially for Y chromosomal DNA variation. To understand the genetic structure characterisation of the Pashtun resident population of the northern region, we have utilised the Y chromosome STRs diversity, haplotype diversity and discrimination capacity. In this work, a total of 67 distinct haplotypes were observed in the resident population of Pashtun living in the northern region of the country, and they showed a high haplotype diversity (0.9756) and discrimination capacity (89.3%); five individuals shared a single haplotype. Genetic distances between the studied population and 11 other populations were calculated based on haplogroup frequencies with Analysis of Molecular Variance (AMOVA).     

A method for genotyping Y chromosome-linked DYS385a and DYS385b loci

We developed a method for genotyping Y chromosome-linked homologous DYS385 loci individually, combining locus-specific polymerase chain reaction (PCR) amplification and previously reported procedures. Duplicated DYS385a (5'-end) and DYS385b (3'-end) loci were located about 41 kb apart and inverted to each other in the Y chromosome, which data was obtained from the human genome sequence in National Center for Biotechnology Information (NCBI), and sequence differences were found at 424 bp down- and upstream of each locus. The locus-specific amplifications were performed using primers designed for this intergenic region, and fragments about 900 bp in length were produced. Polymorphic tetranucleotide arrays in the PCR products were typed according to procedures reported previously. Twenty male subjects were genotyped using this method. Alleles (GAAA)13-(GAAA)21 were observed at the DYS385a locus, and those at DYS385b included alleles (GAAA)9-(GAAA)15. DYS385a alleles, excluding those of identical arrays, were always larger than DYS385b alleles in the same subjects. These data suggest that the DYS385a and DYS385b loci can be amplified completely for discrimination, and the genotypes of the alleles provide information useful for forensic case work and population genetics.     

Genetic polymorphisms for 17 Y-chromosomal STR haplotypes in Jammu and Kashmir Saraswat Brahmin population

In this study 17 Y-chromosomal STRs (including DYS19, DYS389I, DS389II, DYS390, DYS391, DYS392, DYS393, DYS385a/b, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and Y GATA H4) were analysed using blood samples of 122 unrelated male individuals belonging to Saraswat Brahmin community from Jammu (ID YP000599) and Kashmir (ID YP000600) region of J&K state of India. The allelic frequency distribution and haplotype diversity of 17 Y-chromosomal STR for both the populations were calculated. In the Kashmiri Saraswat group, a total of 109 haplotypes were identified in 122 individuals, of these haplotypes, 101 were found only once. The gene diversity values of STR loci ranged from 0.4813 (DYS391) to 0.8645 (DYS385a/b) for Jammu & Kashmiri Saraswat Brahmins.     

Forensic evaluation and population data on the new Y-STRs DYS434, DYS437, DYS438, DYS439 and GATA A10

The Y-specific STR loci DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS434, DYS437, DYS438, DYS439 and GATA A10 were studied in a northern Portuguese population. Haplotype and allele frequencies of these 14 Y-chromosome STRs were estimated. In a sample of 212 individuals it was possible to define 196 different haplotypes of which 182 were found only once, 12 were found in 2 samples and the 2 most frequent haplotypes were shared by only 3 individuals. The observed haplotype diversity value was 0.9992. The usefulness of the inclusion of each of these new markers for forensic purposes is discussed by comparing expected and observed increases in haplotype diversity. When combining the new markers (DYS434, DYS437, DYS438, DYS439 and GATA A10) with the classical set (DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392 and DYS393) a 0.68% increase in haplotype diversity was obtained and the number of different haplotypes rose from 157 to 196. When DYS434 was not considered the haplotype diversity was not affected. Received: 18 June 2001 / Accepted: 23 October 2001     

Population data for Y-chromosome haplotypes defined by 17 STRs in South-East Romania

Haplotypes and allele frequencies for 17 STR loci included in AmpFlSTR YFiler kit (DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385a/b, DYS393, DYS391, DYS439, DYS635, DYS392, Y GATAH4, DYS437, DYS438 and DYS448) were determined in a sample of 122 unrelated males living in the South-East Romania. Genetic distances had been calculated and dendrograms had been generated for South-East Romanian population and other eighteen surrounding populations.