The polymorphisms of various short tandem repeats on the Y chromosome in Japanese and German populations

In the present study we have analyzed the genotypes at the DYS389-I, DYS389-II, DYS390, DYS391, DYS393 and DYS19 loci on the Y chromosome in Japanese and German populations. The genotypes were determined in the white blood cell DNA of 200 Japanese and 111 German males. The 8-locus haplotype combination of these six loci with our previous data on DYS388 and DYS392 revealed much lower maximum matching probability (0.0053 in Japanese and 0.0092 in Germans), much higher minimum diversity (dw_min) (0.9947 in Japanese and 0.9908 in Germans) and more haplotypes (194 in Japanese and 110 in Germans). These very high abilities for discrimination could provide ideal tools for forensic analysis and population studies. Received: 8 October 1998 / Received in revised form: 7 June 1999 / Accepted: 30 June 1999     

Characterization and haplotype analysis of the polymorphic Y-STRs DYS443, DYS444 and DYS445 in a Japanese population

From sequence database information we have newly identified three male-specific and polymorphic tetranucleotide STRs, DYS443 (GDB: 10807127), DYS444 (GDB: 10807128) and DYS445 (GDB: 10807129) on the Y chromosome. Analysis of 190 Japanese males revealed 6, 5 and 4 alleles in the DYS443, DYS444 and DYS445 systems, with calculated STR diversities of 0.68, 0.57 and 0.53, respectively. The cumulative haplotype diversity of the five Y-STRs DYS441, DYS442, DYS443, DYS444 and DYS445 was calculated to be 0.95 and therefore application of these STRs may yield very useful information for forensic individualization. Received: 17 July 2001 / Accepted: 20 September 2001     

DYS19 marker in Japanese populations

Allele frequencies of the Y chromosome-specific short tandem repeat system DYS19 (Y-27H39) were determined from blood samples obtained from 251 unrelated Japanese in Fukui and Gunma Prefectures. Five alleles that contained 10, 11, 12, 13 and 14 repeats of GATA were detected. Allele frequency distributions in Japanese populations were different from those in other Asian and Caucasian populations. Received: 16 September 1996 / Received in revised form: 6 January 1997     

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     

The Y-STRs DYS19 and DYS390 in a south-east Hungarian (Szeged area) population

The allele frequencies of DYS19 and DYS390 located on the Y chromosomes were determined from male bloodstain samples of 308 (DYS19) and 268 (DYS390) unrelated male adults in south-east Hungary. Six alleles could be distinguished in both systems, yielding 22 DYS19/ DYS390 halotypes in a subset of 239 males. Received: 23 March 1998 / Accepted: 22 June 1998     

Bimodal allele frequency distribution at Y-STR loci DYS392 and DYS438: no evidence for a deviation from the stepwise mutation model

A deviation from the stepwise mutation model (SMM) has been suggested for the trinucleotide Y-STR locus DYS392, based upon its bimodal allele frequency distribution in various populations. The same type of distribution is also observed for the pentanucleotide Y-STR DYS438. In order to verify whether a departure from an SMM is likely for these two loci, we studied a large number of Portuguese male DNA samples typed for the two loci and in addition, for the Y-STR loci DYS19, DYS389I/II, DYS390, DYS391 and DYS393. The compatibility of the observed allele frequency spectrum with an SMM was assessed by an apportionment of the molecular variance among, and consideration of the molecular distances between, haplotype groups defined according to their allelic state at each of the two markers of interest. For haplotypes carrying either modal alleles 11 or 13 of DYS392, 18.6% of the molecular variance of the remaining Y-STR background could be attributed to variation between the two groups. When all pairwise _st values between haplotype groups were compared, group 12 was found to be closer to 11 than to 13, and group 14 was much closer to 13 than to 12 and 11. It may therefore be concluded that DYS392 allele 13 represents an evolutionary lineage with little or no relationship to 11 and 12. Furthermore, allele 14 is a one-step neighbour of 13 and is therefore likely to represent an offshoot from group 13. For haplotypes carrying either modal allele 10 or modal allele 12 of DYS438, 27.7% of the molecular variance of the Y-STR background was found to be due to variation between the two groups. Comparison of the other pairwise _st values indicated that group 10 was closer to 9 and 11 than to 12, and that group 12 was closer to 11 and 13 than to 10. The lineages defined by the two modal alleles of DYS438 therefore also seem to be phylogenetically distant. When the two loci were analysed in combination, using the standardised linkage disequilibrium measure (D'), a strong association was noted between alleles DYS392*11 and DYS438*10 (D'=0.70) and between DYS392*13 and DYS438*12 (D'=0.72). Taken together, these results show that the bimodal allele frequency distributions of DYS392 and DYS438 are explicable in terms of (probably the same) historical and demographic causes, rather than a mutational mechanism other than SMM. The loci do therefore not appear to warrant any special attention when applied in population genetic or forensic studies.     

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     

Haplotype analysis with 14 Y-STR loci using 2 multiplex amplification and typing systems in 2 regional populations in Japan

In this study 14 Y-STR loci (DYS393, DYS19, DYS391, DYS437, DYS435, DYS439, DYS389II, DYS438, DYS436, DYS390, Y-GATA-H4, DYS385, Y-GATA-A7.1 and DYS392) were analysed in 207 Japanese males from Honshu (main island of Japan, Nagoya City) and 87 Japanese males from Okinawa (southernmost islands of Japan) using two multiplex PCR typing systems, a novel 10-plex amplification system and a new commercially available 6-plex typing kit which had two loci in common. The allele frequency distributions were similar at almost all of the 14 loci. Of the haplotypes observed, 244 were unique in both Japanese populations and 17 haplotypes were observed more than once but the 2 populations shared only 7 haplotypes. The haplotype diversities for the 14 loci were 0.9987 and 0.9976 in Honshu and Okinawa Japanese, respectively. The haplotype analysis at 14 Y-STR loci would be useful for personal identification in forensic fields and for population genetics because of the high divergence of these haplotypes.     

Identification and characterization of two novel human polymorphic STRs on the Y chromosome

From sequence database information, we have identified two male-specific and polymorphic tetranucleotide STRs, DYS 441 (GDB:10013873) and DYS 442 (GDB: 10030304), on the Y chromosome. Analysis of 184 males allowed 7 and 5 alleles to be distinguished in the DYS 441 and DYS 442 systems, respectively, yielding 21 haplotypes. The gene diversities were 0.72 and 0.51, respectively and the haplotype diversity was 0.85. Received: 16 October 2000 / Accepted: 7 January 2001     

Y-STR haplotyping in two Hungarian populations

A set of seven Y-chromosomal STR loci (DYS19, DYS389-I, DYS389-II, DYS390, DYS391, DYS392, DYS393) with the addition of the bilocal marker DYS385 was used to generate male-specific haplotype databases for two Hungarian population samples, Caucasians from the Budapest area and Romanies from Baranya county. At the locus DYS385 three types of intermediate sized alleles were detected in six males. The presence of a (GA) dinucleotide, probably due to an (AA) deletion in the second (GAAA) repeat of the polymorphic repeat region leads to an intermediate allelle 17.2. The intermediate alleles 17.-1 and 18.-1 with the consensus repeat structure of (GAAA)₁₇ and (GAAA)₁₈, respectively, were found to lack a T in the same (T)₇ stretch located within the 3′ flanking region of each allele. The forensic efficiency values for the Romany population were significantly lower than those found in the Central Hungarian and other non-isolated Causasian populations, which may imply a possible common paternal ancestry of some haplotypes in the Romany sample. With pairwise comparisons of inter-population molecular variance, the two populations analyzed here and an Italian population sample, could be clearly distinguished using the seven monolocal Y-STRs. A sizing precision of ≤ 0.14 nucleotide standard deviation was obtained with capillary electrophoresis carried out on an ABI Prism 310 Genetic Analyzer. Objective and accurate genotyping is thus possible using an internal size standard with a high density of fragments. Received: 14 July 1998 / Received in revised form: 8 March 1999     

Gender-specific amplification of Japanese macaque genes using primers for the human DYS391 and DYS438 loci

The species specificity of 10 human Y chromosomal short tandem repeat loci, DYS19, DYS385, DYS389, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439, was examined in the Japanese macaque, Macaca fuscata. Primers for loci DYS391 and DYS438 only yielded an amplification product from male samples. The PCR products amplified with the DYS391 primers showed no inter-individual differences in migration rate in electrophoretic experiments. Sequence analysis revealed that these PCR products consisted of 287 bases containing tandem repeats of TC and TATC. The numbers of TC and the TATC repeats varied between individuals. The TC repeat does not exist in human and chimpanzee sequences. The PCR products amplified by the DYS438 primers provided no evidence of inter-individual variation between the six male Japanese macaque samples. In the Japanese macaque, PCR gives a 184 base pair product, in contrast to human sample from which the products are 203-233 bases in size. The primers for four loci, DYS19, DYS385, DYS389 and DYS437 produced PCR products from both male and female Japanese macaques. The primers for the other loci, DYS390, DYS392, DYS393 and DYS439, did not yield PCR products.     

Haplotype frequencies of nine Y-chromosome STR loci in the Taiwanese Han population

Haplotype frequencies of nine Y-chromosome STR loci (DYS19, DYS385, DYS388, DYS389I, DYS389II, DYS390, DYS391, DYS392 and DYS393) in the Taiwanese Han population were established. A total of 183 unrelated individuals produced 162 haplotypes, of which 146 were unique, 1 was found in 5 individuals, 2 were found in 3 individuals and 13 were found in 2 individuals. The haplotype diversity (99.99%) and discrimination capacity (88.5%) were calculated. A family study of 109 father/son pairs in 100 families showed 2 mutational events in the DYS389II locus and 1 in the DYS392 locus. Received: 20 February 2001 / Accepted: 15 May 2001     

Population study and evaluation of 20 Y-chromosome STR loci in Germans

The nine European minimal haplotype (EMH) loci, the two SWGDAM loci and five further single-copy Y-chromosomal short tandem repeats (Y-STRs) DYS446, DYS447, DYS448, DYS449, DYS463, and the multicopy loci DYS464 were evaluated in the German population groups Dresden, Hamburg, Rostock, Munich, and the Sorbs who are a Slavic-speaking minority in Lusatia. Highest gene diversities in all populations were shown for DYS464, DYS385, and DYS449 (D=0.8559–0.9486). The haplotype diversity for the European minimal haplotype loci ranged between 0.9852 for Sorbs and 0.9983 for the Hamburg population showing that there is a significant portion of haplotypes which could not be resolved. Advanced typing using DYS446, DYS447, DYS448, DYS449, DYS463, and DYS464 discriminated all non-related individuals of the Dresden, Hamburg, and Rostock populations. Evaluation of the Y-STRs was accomplished by sequence analysis of all allelic fragments of the allelic ladders and microvariant alleles of DYS385 and the determination of the amounts of stutter products of the loci. Electronic Supplementary Material Supplementary material is available for this article at     

Y chromosomal STRs haplotypes in two populations from Bolivia

In the present study, we typed our previously reported two microsatellite markers, DXYS241 and DXYS266 together with a basic set of nine Y-STRs (DYS19, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DXYS156Y, DYS413) on Y chromosomes from two Bolivian populations. Unrelated males from communities living at high- (N=59) and low- (N=142) altitude, were studied. Combining the alleles into 11 Y-STRs haplotypes revealed that the high-altitude population is significantly less diverse than the low-altitude population. Haplotype diversities of 0.927+/-0.029 and 0.996+/-0.002 were found within the high-altitude, and the low-altitude populations, respectively. Within the high-altitude population 40 haplotypes were detected, whereas in the low-altitude population 113 haplotypes were found. Only three haplotypes were shared between both populations. Haplotyping-based discrimination using the 11 Y-STRs including our new two microsatellite markers DXYS241 and DXYS266 was shown to be powerful than using the conventional 9 Y-STRs, especially for the low-altitude Bolivian population. This 11 Y-STRs-based haplotyping system shows a very high potential for discrimination and could provide an ideal tool for forensic analysis and population studies. Moreover, this study includes data about two Bolivian populations which were not previously reported, this will help in building a world-wide database for future use in forensic and legal studies.     

Improvement of a multiplex PCR system for DYS441, DYS442, DYS443, DYS444 and DYS445, and a population study in 340 Japanese males

A multiplex PCR system for five Y-STRs (DYS441, DYS442, DYS443, DYS444 and DYS445) has been improved to increase the probability of obtaining a DNA typing result from aged samples. Newly designed PCR primers for amplification of the DYS441 and DYS442 loci and optimization of PCR conditions enabled successful typing from blood and semen stains that had been stored for more than seven years at room temperature. Analysis of 340 Japanese males revealed 7, 5, 6, 5 and 4 alleles at the DYS441, DYS442, DYS443, DYS444 and DYS445 loci, respectively, yielding 122 haplotypes with a cumulative haplotype diversity of 0.97.     

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     

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.     

Y-chromosome 10 locus short tandem repeat haplotypes in a population sample from Sicily Italy

This study reports the first data on Y-chromosome-specific short tandem repeat (STR) haplotype frequencies, in the population of the island of Sicily (Italy), based on the combination of alleles at the following 10 Y-chromosome loci DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, and DYS439. In a total of 117 males, 108 unique haplotypes were observed, with 99 of them being singletons. The 10 locus haplotypes generated a diversity value of 0.9987 and discriminatory power (DP) of 92.30%. The data on the seven of the 10 polymorphisms (DYS19; DYS389I; DYS389II; DYS390; DYS391; DYS392 and DYS393) that have been most studied in worldwide populations were compared with similar data from neighboring Mediterranean populations in order to address the question of shared ancestry, gene flow and population affinities. Overall, results indicate Sicily is closest genetically to the mainland Italian population but also with evidence of a significant African component in the male gene pool. These findings are consistent with those obtained from other genetic markers (autosomal and mitochondrial DNA as well as the classical blood groups) and also with the recorded settlement history (either peaceful or due to invasion) of the island.     

Y chromosome STR haplotypes: genetic and sequencing data of the Galician population (NW Spain)

Recently described Y-STR polymorphisms can be analysed as informative haplotypes which are useful in the forensic field. In order to include these systems in our forensic routine, we have carried out a population study in Galicia (NW Spain) analysing seven Y-STR polymorphisms (DYS19, DYS389-I, DYS389-II, DYS390, DYS393 and DYS385: two loci). The results were compared with other population studies. In addition various alleles for each system (except DYS385) were sequenced and the corresponding allelic ladders constructed. Received: 6 October 1997 / Received in revised form: 24 March 1998     

Y-Chromosome STR haplotypes in an Italian population sample

Seven Y-chromosome STRs were investigated in a male population sample from the Modena area by means of one quadruplex reaction (systems DYS19, DYS390, DYS391, DYS393), one duplex reaction (systems DYS389-II, DYS392) and two single PCR reactions (DXYS156 and DYS389-I/II). In 100 males, 71 different haplotypes could be observed, 57 of which were seen only once. The haplotype diversity/discrimination index is 0.97. The resulting database could be used for routine forensic application like paternity testing and stain investigation. Received: 6 November 1997 / Received in revised form: 12 March 1998