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.     

Sub-Saharan Africa descendents in Rio de Janeiro (Brazil): population and mutational data for 12 Y-STR loci

A male sample of 135 African descendents from the Rio de Janeiro population were typed for the 12 Y-chromosome short tandem repeat (STR) loci included in the PowerPlex Y System. A high haplotype diversity was observed (0.9971), with 91% of haplotypes being unique, demonstrating the usefulness and informative power of this Y-STR set in male lineage identification. Samples with shared haplotypes were additionally typed with the Yfiler kit, which includes five extra markers. The haplotype diversity when using the 17-Yfiler loci increased to (0.9998) with 97% unique haplotypes. The same set of Y-STRs was also typed in 135 father/son pairs and three single-step mutations were observed: one at DYS19 and two at DYS385. Genetic distance analysis showed highly significant differences in all pairwise comparisons between this sample of African descendents and the general population from Rio de Janeiro, as well as with Iberian and African samples from Portugal, Mozambique, Angola and Equatorial Guinea. Comparisons with samples from other regions in Brazil showed that heterogeneity does exist, indicating that a Y-haplotype database for the whole country should take into account the population sub-structure. Moreover, a strong European influence was detected, and thus, a Y-chromosome STR profile proves a rather poor indicator for the ethnic origin of an individual in Rio de Janeiro. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Extending STR markers in Y chromosome haplotypes

Two multiplex reactions were developed to amplify 16 Y-STRs (DYS19, DYS385, DYS389 I and II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, GATA A7.1, GATA A7.2, GATA A10, GATA C4, GATA H4). Here we extend previous population studies done in a sample from northern Portugal for the GATA A7.1, GATA A7.2, GATA C4 and GATA H4 loci. A total of 199 different haplotypes identified by the 16 Y-STR markers were observed in a sample of 208 male individuals, of which 190 were unique and 9 were found twice. The overall haplotype diversity was 0.9996. The haplotype diversity of the Y-STR set composed of the 8 new markers is higher than the Y-STR core set included in the Y-STR haplotype reference database. Sequence structure of new alleles for GATA C4 and GATA H4 is reported. The usefulness of the inclusion of this new set of Y-STRs in forensic casework was also assessed. The increase in haplotype diversity with the addition of any new Y-STR marker to the 8 Y-STR core set is dependent not only on the gene diversity (positively) but also (negatively) on the degree of gametic association between the markers and the haplotypes previously defined. For instance, in our sample the addition of the DYS437, DYS438 and GATA A7.2 to a 13-locus set increased haplotype diversity only by 0.0001.     

Haplotype and mutation analysis for newly suggested Y-STRs in Korean father–son pairs

In this study, 363 Korean father–son haplotype transfers in 351 families were analyzed using an in-house multiplex PCR system for 14 Y-STRs (DYS385a/b, DYF387S1, DYS391, DYS449, DYS460, DYS481, DYS518, DYS533, DYS549, DYS570, DYS576, DYS627 and DYS643), that included 11 loci newly added to the PowerPlex Y23 system or the Yfiler Plus system. The Y-STRs showed gene diversity values ranging from 0.2499 to 0.9612; the multicopy Y-STR loci DYS385 and DYF387S1 had high gene diversity of 0.9612 and 0.9457, respectively. In addition, DYF387S1, which has two copies, showed three alleles in seven individuals, and micro-variant alleles were observed in 14 individuals at four loci (DYS448, DYS518, DYS570 and DYS627). Among 351 haplotypes for the 11 newly added Y-STRs, 350 different haplotypes were observed, with an overall haplotype diversity of 0.9999 and discrimination capacity of 99.72%. In 363 haplotype transfers from 351 pedigrees, 29 single-step mutations were observed at 11 Y-STRs. Locus-specific mutation rate estimates varied from 0.0 to 1.93 × 10⁻², with an average estimated mutation rate of 6.66 × 10⁻³. Two father–son pairs had mutations at two different loci in 11 Y-STRs. The number of pairs with mutations at multiple loci increased to five when the mutation event was investigated for haplotype transfer at 28 Y-STRs including 17 Yfiler loci and 11 Y-STRs examined in this study: four father–son pairs had mutations at two loci, and one pair had mutations at three loci. Overall, mutations were frequently observed at DYS449, DYS576 and DYS627 loci, which are known to be rapidly mutating Y-STRs. Mutation rate estimates at most loci were not significantly different from rates in other populations, but estimates for DYF387S1, DYS518 and DYS570 were considerably lower in the Korean population than in other populations.     

Analysis of mutation rates and haplotypes of 23 Y-chromosomal STRs in Korean father–son pairs

Y-chromosomal short tandem repeats (Y-STRs) have been widely used in forensic genetics, and accurate knowledge of mutation rates at Y-STR loci is essential in kinship analysis. The main aim of this study was to estimate Y-STR mutation rates in Korean males. To obtain locus-specific mutations and haplotypes at 23 Y-STRs, we analyzed samples from 620 Korean father–son pairs. In addition, we also analyzed 476 unrelated individuals using the PowerPlex® Y23 System, with the aim of augmenting the available data for the Korean population. The PowerPlex® Y23 system facilitates analysis of the 23 Y-STR loci (DYS576, DYS570, DYS458, DYS635, DYS389 II, DYS549, DYS385, DYS481, DYS439, DYS456, DYS389 I, DYS19, DYS393, DYS391, DYS533, DYS437, DYS390, Y GATA H4, DYS448, DYS438, DYS392, and DYS643). Locus-specific mutation rate estimates varied from 0.00 to 8.06 × 10⁻³ per generation, with an average mutation rate of 2.17 × 10⁻³ (95% CI, 1.5–3.1 × 10⁻³). To obtain comprehensive genetic values for the Korean population, we combined data obtained in this study with previously reported values, thereby enabling us to estimate the locus-specific mutation rates regarding 22,711 allele transmissions. By combining these data, we obtained an overall average mutation rate of 2.91 × 10⁻³ (95% CI, 2.3–3.7 × 10⁻³). In addition, among the 476 unrelated Korean males, we detected 467 different haplotypes, with an overall haplotype diversity value of 0.9999. By extracting haplotypes of Y-STRs described in previous literature on 23 Y-STR reported in Korea, we obtained gene diversities for 1133 Korean individuals. We believe that the values and characteristics of the 23 Y-STRs analyzed in this study will contribute to establishing criteria for forensic genetic interpretation, including kinship analysis.     

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.     

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     

Population and segregation data on 17 Y-STRs: results of a GEP-ISFG collaborative study

A collaborative work was carried out by the Spanish and Portuguese International Society for Forensic Genetics Working Group in order to extend the existing data on Y-short tandem repeat (STR) mutations at the 17 Y chromosome STR loci included in the AmpFlSTR YFiler kit (Applied Biosystems): DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, and GATA H4.1. In a sample of 701 father/son pairs, 26 mutations were observed among 11,917 allele transfers across the 17 loci. After summing previously reported mutation data with our sample, mutation rates varied between 4.25 × 10⁻⁴ (95% CI 0.05 × 10⁻³–1.53 × 10⁻³) at DYS438 and 6.36 × 10⁻³ (95% CI 2.75 × 10⁻³–12.49 × 10⁻³) at DYS458. All mutations were single step, and mutations in the same father/son pair were found twice. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Mutation rate at 17 Y-STR loci in “Father/Son” pairs from moroccan population

Precise knowledge of mutation rate at Y-STRs loci is essential for a correct evaluation of typing results in forensic casework and specially kinship genetic studies. In this study, we have examined 252 confirmed and unrelated father/son sample pairs from Moroccan population using the 17 Y-STR markers DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a, DYS385b, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, and Y-GATA-H4 of the AmpFlSTR Yfiler? kit used in routine casework. We observed a total of 15 single repeat mutations between fathers and sons as mutational events. Nine mutations resulted in the gain of a repeat in the son and six resulted in a loss of a repeat. The average mutation rate in the studied sample is 3.5 × 10^?3 (95% CI 2–5.8 × 10^?3). Furthermore, Y-STRs mutation occurrence seems to be 4 times more frequent than autosomal STRs mutation in this sample.     

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.     

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.     

Developmental validation of the Yfiler® Plus PCR Amplification Kit: An enhanced Y-STR multiplex for casework and database applications

Y-chromosomal loci have proven useful in solving investigations where low levels of male DNA are present in a high female DNA background. An intrinsic limitation of Y-STRs compared with autosomal STRs is a reduced power of discrimination due to a lack of recombination throughout most of the Y-chromosome. Thus, in an effort to increase the power of discrimination we have developed a new 6-dye, 27-plex Y-STR system that includes the 17 loci from the Yfiler^® and Yfiler^® Direct kits (DYS19, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 (Y GATA C4), and Y GATA H4) plus three highly polymorphic Y-STR loci (DYS460, DYS481, and DYS533), and seven rapidly mutating Y-STR loci (DYF387S1a/b, DYS449, DYS518, DYS570, DYS576, DYS627) which allow for improved discrimination of related individuals. The Yfiler^® Plus PCR Amplification Kit is a dual application assay designed to amplify DNA from extracted casework and database samples from storage cards and swab lysates via direct amplification. Compared to the Yfiler PCR Amplification Kit, the new multiplex shows increased discrimination of male lineages and also improved performance in inhibited samples, improved balance in male DNA samples mixed with female DNA at ratios >1:1000, and faster time to results. The Yfiler Plus Kit shows very high concordance to the Yfiler Kit but discordance with the PowerPlex^® Y23 Kit at the DYS481 locus was observed in 2 out of 30 samples tested. This developmental validation work follows the SWGDAM guidelines and demonstrates that the assay is robust and suitable for use on forensic casework and database samples.     

Population data of 17 Y-STR loci from Rio Grande do Sul state (South Brazil)

A sample of 255 Brazilian males from Rio Grande do Sul (RS), the Brazilian southernmost state, was typed for 17 Y-STR loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, YGATA_H4.1 and DYS385ab). A total of 247 haplotypes were identified, of which 239 were unique and eight were found in two individuals each. The haplotype diversity (99.98%) and discrimination capacity (96.86%) were calculated. Pairwise haplotype distances showed that the RS population is not significantly different from Brazil, Rio de Janeiro, and Argentina, is different from São Paulo, Italy, and North Portugal, and is very distant from Spain, the Amazon region, Germany, and South Amerindians. When the RS data was separated in the seven geopolitical regions, some pairs of regions were significantly different; however no region was different from the whole Brazilian sample.     

17 Y-STR haplotype data for a population sample of Residents in the Basque Country

Non autochthonous population is the most numerous group in the Basque Country. This group is named "Residents" to distinguish them from the "Autochthonous Basque" population. In this work, the 17 Y-STR loci distribution of Resident population was studied in a sample of 197 individuals, who were concretely genotyped for DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS439, DYS438, DYS437, DYS448, DYS456, DYS458, DYS635 and Y GATA H4. Resident population showed a high haplotype diversity and discrimination capacity. The distribution of Y-STRs haplotypes of the Resident population was statistically significant different to the one of the Autochthonous Basque population. The genetic substructure found between Resident and Autochthonous Basque 17 Y-STR haplotype distributions advises for the use of two different databases in the Basque Country, to ensure the most trustworthy frequency estimate in casework.     

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.     

Understanding the Y chromosome variation in Korea—relevance of combined haplogroup and haplotype analyses

We performed a molecular characterization of Korean Y-chromosomal haplogroups using a combination of Y-chromosomal single nucleotide polymorphisms (Y-SNPs) and Y-chromosomal short tandem repeats (Y-STRs). In a test using DNA samples from 706 Korean males, a total of 19 different haplogroups were identified by 26 Y-SNPs including the newly redefined markers (PK4, KL2, and P164) in haplogroup O. When genotyping the SNPs, phylogenetic nonequivalence was found between SNPs M117 and M133, which define haplogroup O3a3c1 (O3a2c1a according to the updated tree of haplogroup O by Yan et al. (European Journal of Human Genetics 19:1013-1015, 2011)), suggesting that the position of the M133 marker should be corrected. We have shown that the haplotypes consisted of DYS392, DYS393, DYS437, DYS438, DYS448, and DYS388 loci, which exhibit a relatively lower mutation rate, can preserve phylogenetic information and hence can be used to roughly distinguish Y-chromosome haplogroups, whereas more rapidly mutating Y-STRs such as DYS449 and DYS458 are useful for differentiating male lineages. However, at the relatively rapidly mutating DYS447, DYS449, DYS458, and DYS464 loci, unusually short alleles and intermediate alleles with common sequence structures are informative for elucidating the substructure within the context of a particular haplogroup. In addition, some deletion mutations in the DYS385 flanking region and the null allele at DYS448 were associated with a single haplogroup background. These high-resolution haplogroup and haplotype data will improve our understanding of regional Y-chromosome variation or recent migration routes and will also help to infer haplogroup background or common ancestry.     

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).     

Y-STR typing of an Austrian population sample using a 17-loci multiplex PCR assay

Y-chromosomal STR haplotypes were determined from a sample of 135 unrelated men and 70 sons from Tirol (Austria) using the AmpFlSTR Yfiler PCR amplification kit (Applied Biosystems) that coamplifies 17 Y-STRs. The panel of markers includes the 9-loci European minimal haplotype (minHt) and, in addition, the markers DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 (Y GATA C4) and Y GATA H4. A total of 130 different haplotypes (125 were unique) were identified by the 17 Y-STR markers, an increase of 19 compared with the minHt. The gene diversity of DYS635, DYS456 and DYS458 exceeded 0.75 and only that of the duplicated marker DYS385 (0.86) was higher. Consistently high haplotype diversity values were found in all tested Y-SNP haplogroups. Because the simultaneous analysis of 17 Y-STR systems offers a high power of discrimination at minimum sample consumption, the Yfiler kit is a promising tool for forensic applications.     

Haplotypes and mutation analysis of 22 Y-chromosomal STRs in Korean father–son pairs

We analyzed 369 Korean father/son haplotype transfers in 355 families at 22 Y-STRs (DYS19, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS388, DYS437, DYS438, DYS439, DYS446, DYS447, DYS448, DYS449, DYS456, DYS458, DYS464, DYS635, and GATA H4.1). A total of 350 haplotypes were observed with an overall haplotype diversity of 0.9999. Among these, 345 were unique and five were found twice. Furthermore, 36 mutations were identified, giving locus-specific mutation rate estimates between 0.0 and 19.0 × 10⁻³ per generation and an average mutation rate estimate of 3.9 × 10⁻³ (95% CI 2.7–5.4 × 10⁻³). The compilation of Y-STR mutation events for the present study and previous studies demonstrates that DYS449, DYS458, DYS635, DYS456 and DYS439 are the most prone to mutations and that their overall average mutation rate estimate is 2.36 × 10^–3 (95% CI 2.03–2.73 × 10^–33). Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

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.