Loci DYS19 Research Articles

Genetic Diversity Based on the Analysis of 27 Y- Short Tandem Repetition (STR) Loci in Two Populations in the Apuseni Mountains, Romania.

Y chromosome analysis is used in various fields of forensic genetics, genetic genealogy, and evolutionary research, due to its unique characteristics. Short tandem repetitions (STR) are particularly relevant in population genetic studies. The aimof this study is to analyze the genetic profile of two populations in the Apuseni Mountains area, Băița and Roșia Montană, Romania. 27 STR loci of the Y chromosome were analyzed to investigate the genetic profile of two populations from the Apuseni Mountains area. Investigating genetic diversity by analyzing allele frequency, haplotype frequency, calculating forensic parameters, and presenting the main haplogroups identified based on Y-STR markers. Gene diversity in the batch from Băița varies from 0.515 for the DYS393 locus to 0.947 for the DYS385 locus. In the Roșia Montană population, gene diversity ranges from 0.432 for DYS393 to 0.931 for DYS385. The haplotype diversity in Roșia Montană was 0.991, and the haplotype diversity was 1.000 in the population from Băița. A total of nine haplogroups was identified in the batch from Băița, while only seven haplogroups were observed in the batch from Roșia Montană. Both groups are based on the same five major haplogroups (E, G, I, J, and R) and the most common haplogroup is R1b in both populations. In this study, the genetic diversity of two distinct populations was assessed using genetic analyses based on different markers. Analysis of Y-STR profiles revealed significant genetic diversity in both studied groups. All haplogroups identified were similar to those present in other Romanian populations.

Y chromosome haplogroup N in a Japanese population is classified into three subclades, and two DYS385 loci, a duplicated Y-STR, are duplicated again in subclade N-M1819

DYS385 is one of the major Y chromosome short tandem repeats (Y-STRs) in forensic genetics and exists as 2 copies in the human Y chromosome palindrome P4 region. In this study, we found that some samples were estimated to have ≥ 4 copies of DYS385 in Y chromosome haplogroup N in a Japanese population. Y chromosome haplogroup N is distributed widely in eastern/central Asia, Siberia, and eastern/northern Europe, and is also observed in Japan; however, little is known about haplogroup N subclades in the Japanese population. To reveal the link between increased DYS385 copy number and haplogroup N subclades, we sequenced single nucleotide polymorphisms to classify the subclades. As a result, the Japanese Y chromosomes of haplogroup N were classified into three subclades, and an increased DYS385 copy number was specific to subclade N-M1819* (N1b2*). These results are of use in forensic DNA analysis because Y-STR copy number is important for the interpretation of Y-STR typing results of male DNA mixtures and kinship analysis. We also found that DYS458.1 microvariants (DYS458 intermediate alleles with single-nucleotide insertion) were observed only in subclade N-CTS962 (N1b1b∼) samples. Given that previous studies reported that DYS458.1 microvariants are observed in Y chromosomes of haplogroup N in other populations, DYS458.1 might be used to infer haplogroup N subclades without limitation to the Japanese population. The results of this study will be beneficial not only to forensic genetics but also to anthropological studies.

Genetic Polymorphism of 38 Y-chromosome Short Tandem Repeats in Beijing Han Population from China

Abstract Objective: To investigate 38 Y-chromosome short tandem repeat (Y-STR) genetic polymorphisms in Beijing Han and analyze the genetic distance with neighboring or linguistically similar populations. Materials and Methods: In the study, we selected 531 unrelated male individuals of Beijing Han, and the results were statistically analyzed by testing with GSTAR™ 41Y reagents. Results: The allele peak heights were balanced among the Y loci, the amplified fragment ranged from 100 to 500 bps. A total of 531 haplotypes were detected in 531 samples. Eight null genotypes were observed on locus DYS448. One and three double alleles were observed on single-copy locus DYS576 and DYS19, respectively. DYS385 a/b, DYF387S1 a/b, and DYS527 a/b were more common in double copies, but 3, 13, and 11 triple alleles were detected, respectively. The gene diversity values of Y-STRs except DYS391, DYS438, and DYS645 were >0.5. Twenty-seven Y-STRs of Beijing Han population were selected for genetic distance comparison with 17 populations including Changchun Han, with Rst values ranging from 0.0002 to 0.1703. Conclusion: The 38 Y-STRs in this study have strong male lineage identification ability and have great potential for individual identification, kinship identification, Y-STR database construction, and genetic relationship research.

Estimation of allele and haplotype frequencies for 23 YSTR markers of Iraqi populations in Baghdad

Specialized class of short tandem repeats located on human Y (male) chromosomes called Y-chromosome short tandem repeats (Y-STRs) are transferred from one generation to the next with unchanged (barring a mutation). Also, these loci have high discriminatory capacities among individuals of the same population or ethnicity due to the non-recombining nature of it. Peripheral blood sample from 160 unrelated Iraqi males in Baghdad are collected and DNA was extracted from it. Amplification of 23 Y-STR markers (DYS576, DYS3891, DYS448, DYS389II ,DYS19, DYS481, DYS549, DYS533, DYS438, DYS437, DYS570, DYS635, DYS390, DYS439, DYS392, DYS643, DYS393, DYS458a/b, DYS456 and YGATAH4) was performed using PowerPlex Y 23 System (Promega Corporation), PCR amplicons were analyzed on 4-capillary ABI Prism® 3100 Genetic Analyzer. Collected data were analyzed and haplotypes were obtained using Gene Mapper ID-X software version 1.4 (Applied Biosystems). Results indicated that the most polymorphic loci were DYS385a/b with 43 alleles and The GD value was 0.929, while 4 alleles at the DYS576 and DYS391, with the genetic diversity of 0.459 and 0.480 respectively. At the loci DYS570 and DYS458 the allele frequency were 10 and 12 alleles with a genetic diversity 0.780 and 0.844 respectively. Gene diversity values for the South of Iraq males ranged from 0.447 to 0.844. The highest GD was detected at DYS458loci with a value of 0.856 and the lowest GD at DYS448 locus with a value of 0.447, 143 Haplotype was identified, 130 (81, 25%) as a unique Haplotype and 13 (18, 75%) as replicated haplotype among individuals. The highest haplotype were found in sample H19, H43, H72 and H122 at frequency 0.01875, While 130 haplotype with 0.00625 frequency and haplotype diversity was 0.99835 with a discrimination capacity 0.91. The study revealed that the loci under study and the used kit are suitable for use in identification, discrimination and forensic applications in the Iraqi population.

RETRACTED ARTICLE: Y Chromosomal STR haplotypes in Chinese Uyghur, Kazakh and Hui ethnic groups and genetic features of DYS448 null allele and DYS19 duplicated allele.

Y Chromosomal short-tandem repeats (Y-STRs) provide valuable information that can be used for forensic investigation and population studies. The Yfiler® Plus PCR Amplification Kit allows the multiplex amplification of 27 Y-STRs, including seven rapidly mutating markers. With the kit, 447 unrelated males of three minorities (161 Uyghurs, 130 Kazakhs and 156 Huis) from the Xinjiang Uighur Autonomous Region of China were analysed in this study. The gene diversity values of the 27 Y-STRs in the Uyghur, Kazakh and Hui groups ranged from 0.4770 to 0.9545, 0.3897 to 0.9375 and 0.4621 to 0.9725, respectively. One specific sequence pattern of null alleles at the DYS448 locus was confirmed. The individuals carrying the null alleles at the DYS448 locus belonged to haplogroups C2b and C2b1a1b1, while those carrying duplicated alleles at the DYS19 locus belonged to haplogroups C2b1a2 and G2a. A total of 155, 118 and 146 distinct haplotypes were obtained in these three groups, respectively, with overall haplotype diversities of 0.9998, 0.9993 and 0.9996, respectively. Compared with 17 Y-plex, 27 Y-plex demonstrated an increased power of discrimination, especially for the Kazakh group. Visualisation of pairwise genetic distances between 24 ethnic groups in China using multidimensional scaling (MDS) demonstrates the distribution of various groups, which is largely in keeping with ethno-geographic patterns.

Analysis of Mutation Rate of 17 Y-Chromosome Short Tandem Repeats Loci Using Tanzanian Father-Son Paired Samples.

Hundred unrelated father-son buccal swab sample pairs collected from consented Tanzanian population were examined to establish mutation rates using 17 Y-STRs loci DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a, DYS385b, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, and Y-GATA-H4 of the AmpFlSTRYfiler kit used in forensics and paternity testing. Prior to 17 Y-STRs analysis, father-son pair biological relationships were confirmed using 15 autosomal STRs markers and found to be paternally related. A total of four single repeat mutational events were observed between father and sons. Two mutations resulted in the gain of a repeat and the other two resulted in a loss of a repeat in the son. All observed mutations occurred at tetranucleotide loci DYS389II, DYS385a, and DYS385b. The locus specific mutation rate varied between 0 and 1.176 x10−3 and the average mutation rate of 17Y-STRs loci in the present study was 2.353x10−3 (6.41x10−4 - 6.013x10−3) at 95% CI. Furthermore the mean fathers' age with at least one mutation at son's birth was 32 years with standard error of 2.387 while the average age of all fathers without mutation in a sampled population at son's birth was 26.781 years with standard error of 0.609. The results shows that fathers' age at son's birth may have an effect on Y-STRs mutation rate analysis, though this age difference was statistically not significant using unpaired samples t-test (p = 0.05). As a consequence of observed mutation rates in this study, the precise and reliable understanding of mutation rate at Y-chromosome STR loci is necessary for a correct evaluation and interpretation of DNA typing results in forensics and paternity testing involving males. The criterion for exclusion in paternity testing should be defined, so that an exclusion from paternity has to be based on exclusion constellations at a minimum of two 17 Y-STRs loci.

UK and Irish Y-STR population data—A catalogue of variant alleles

A total of 3128 Y-STR profiles from three UK and one Irish population have been analysed with the PowerPlex Y23 system and are reported here. Instances of haplotype sharing between apparently unrelated individuals were identified and further investigated with the use of the 5 additional markers within the Yfiler Plus kit, resulting in a reduction by 76% in the number of shared haplotypes. Furthermore, Yfiler Plus was also employed to verify locus deletions and duplications observed in Y23 genotypes while inconsistencies between the two kits were sequenced, revealing underlying Y23 primer binding site mutations in loci DYS392 and DYS576. Finally, the mechanism behind a previously reported population specific peak shift observed in DYS481 in South Asian samples has been evaluated and further investigated in a novel case of this phenomenon seen in a Black British individual featuring a different flanking region mutation.

Mutation rates and segregation data on 16 Y-STRs: An update to previous GHEP-ISFG studies

The increasing relevance of human Y-STRs in forensic science demands reliable estimates of their mutation rates. Therefore, a collaborative study was carried out by the Spanish and Portuguese working group of the International Society for Forensic Genetics (GHEP-ISFG) in the interest of extending the data on Y-chromosomal short tandem repeat (Y-STR) mutation rates. Sixteen Y-STRs were considered in the analyses: DYS456, DYS389I, DYS389II, DYS390, DYS458, DYS19, DYS385, DYS391, DYS392, DYS393, DYS439, DYS635, DYS437, DYS438, DYS448, GATA H4. Among the sample of 1598 father-son duos analyzed, 46 mutations were observed, 45 of which were a single-step change and 1 was a double-step change. A total of 28 repeat losses were observed against 18 gains, with a ratio of 1:1.5. Eleven duos showing double alleles at the Y-STR loci DYS19, DYS391, DYS439 and DYS448 without allelic discrepancy between the father-son duo were also observed. This new data was added to the previous studies from the GHEP-ISFG working group, totalizing 63 496 allele transmissions (varying between 2298 and 7347 per locus). The average mutation rate across all 16 Y-STRs loci was 0.00187 (95% CI 0.00155–0.00224). The average mutation rates per marker varied between 0.00057 (95% CI 0.00007–0.00206) at DYS438 and 0.00606 (95% CI 0.00375–0.00925) at DYS439.

Genomic portrait of population of Jharkhand, India, drawn with 15 autosomal STRs and 17 Y-STRs.

We analysed 15 autosomal STRs in 200 unrelated individuals (102 males and 98 females) and 17 Y-STRs in 102 unrelated males living in Jharkhand, India, to establish parameters of forensic interest. The examined autosomal STRs revealed high combined power of exclusion (CPE) and combined power of discrimination (CPD) as equal to 0.9999 and greater than 0.99999, respectively. The combined probability of match (CPm) and combined paternity index (CPI) for all 15 autosomal STR loci were found to be 5.15×10-18 and 6.83×105, respectively. A total of 97 unique haplotypes were obtained, of which 93 were observed only once. The haplotype diversity, discrimination capacity and matching probability for 17 Y-STR loci were 0.999, 0.951 and 1.09×10-2, respectively. The highest gene diversity values at the single copy locus DYS635 and multi-copy locus DYS385 a/b were 0.785 and 0.823, respectively.

17 to 23: A novel complementary mini Y-STR panel to extend the Y-STR databases from 17 to 23 markers for forensic purposes.

A Y-STR multiplex system has been developed with the purpose of complementing the widely used 17 Y-STR haplotyping (AmpFlSTR Y Filer® PCR Amplification kit) routinely employed in forensic and population genetic studies. This new multiplex system includes six additional STR loci (DYS576, DYS481, DYS549, DYS533, DYS570, and DYS643) to reach the 23 Y-STR of the PowerPlex® Y23 System. In addition, this kit includes the DYS456 and DYS385 loci for traceability purposes. Male samples from 625 individuals from ten worldwide populations were genotyped, including three sample sets from populations previously published with the 17 Y-STR system to expand their current data. Validation studies demonstrated good performance of the panel set in terms of concordance, sensitivity, and stability in the presence of inhibitors and artificially degraded DNA. The results obtained for haplotype diversity and discrimination capacity with this multiplex system were considerably high, providing further evidences of the suitability of this novel Y-STR system for forensic purposes. Thus, the use of this multiplex for samples previously genotyped with 17 Y-STRs will be an efficient and low-cost alternative to complete the set of 23 Y-STRs and improve allele databases for population and forensic purposes.

Genetic portrait of Majhi tribe of Chhattisgarh, India based on 15 autosomal STRs and 23 Y-STRs.

The aim of this study was to contribute new data on autosomal STR and Y-STR markers of the Majhi tribal community of Chhattisgarh, a state of central India. In order to improve available databases of forensic interest, we analyzed 15 autosomal STR markers in a population sample of 129 unrelated indigenous Majhi tribe and 23 Y-chromosomal STR markers in the 107 males of the sample. The combined power of discrimination (CPD) and combined power of exclusion (CPE) were greater than 0.999999 and 0.999998 respectively for autosomal STRs. In addition, a total of 64 distinct Y-STR haplotypes were observed out of which 31 Y-STR haplotypes were observed only once. The haplotypes diversity and discrimination capacity for 23 Y-STR loci was 0.989 and 0.589, respectively. The highest gene diversity values at the single copy locus DYS570 and the multi-copy locus DYS385 a/b were 0.805 and 0.952, respectively. Average gene diversity over loci was 0.652304±0.325572.

Genetic polymorphism of 8 Y-STR loci in native population of Isfahan province in central part of Iran

Background: Y-chromosome short tandem repeats (Y-STRs) are genetic markers with practical applications in human identification and population studies.Aim: Here we present the allelic and haplotype frequencies of 8 Y-STR loci most commonly used in forensic medicine in 103 unrelated native males of Isfahan province, central part of Iran.Subjects and methods: The cases were selected on the basis of strict criteria to assure pure native populations of Isfahan origin. DNA extracted from peripheral blood samples and PCR amplified for each marker. Y-specific STR loci DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392 and DYS393 were included in this study.Results: The most common alleles for each locus were: DYS19, allele 12; DYS385, allele 12; DYS389I, allele 13; DYS389II, allele 29; DYS390, allele 24; DYS391, allele 10; DYS392, allele 11; and DYS393, allele 13. Gene diversity value was calculated from the allelic frequency for each locus. The average gene diversity was 0.6518. A total of 101 haplotypes were observed in eight Y-specific STR loci, the haplotype diversity was raised to 0.986.Conclusion: The results revealed that a set of eight Y-specific STR loci were able to discriminate most of the male individuals in the population studied. A search through the Y Haplotype Reference Database demonstrated 21 matched haplotypes to 160,693 haplotypes, exclusively with Eurasian-European, Eurasian, and Eurasian-Indo Iranian populations.

Y STRs mutation events in father-son pairs in Ecuadorian individuals

Eleven Y-STR loci were applied to 417 confirmed father-son pairs. Seven mutations that comprise single step were observed in a total of 2532 allelic transfers, in locus DYS385, DYS390, DYS391, DYS392, and DYS389II. The total mutation rate estimated in this study was 2.8×10−3 (95% CI, 1.1×10−3 to 5.7×10−3); this result is similar to other populations. Q haplogroup lineage was more frequent than others in this study. These results will contribute the forensic and paternity areas database in Ecuador.

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.

English

Samples of 320 random healthy unrelated Iraqi male persons from the Arab ethic group of Iraqi population were collected for Y chromosomal STRs typing. FTA® Technology was utilized to extract DNA from blood collected on FTA™ paper. We analyzed 11 Y chromosomal STR loci for evaluating allele frequencies and gene diversity for each Y-STR locus of the Y-Plex™ PCR amplification kit. The 11 loci include DYS389I, DYS389II, DYS19, DYS391, DYS438, DYS390, DYS439, DYS392, DYS393, DYS385a and DYS385b. A total of 299 unique haplotypes was identified among the 320 individuals studied. The DYS385b had the highest diversity (GD = 0.8392), while loci DYS392 had the lowest (D = 0.2695). The study focuses to establish the basic forensic genetic informations, knowledge, data and statistics which might be so ultimately helpful practically in forensic science and criminology and to let evaluate and present the DNA weight evidences in Iraq medico-legal institute and courts of law.   Key words: Allele frequency, gene diversity, Iraq, STR DNA typing, Y-Plex™.

English

Analysis of 17 Y chromosomal STR loci in a population sample of 400 unrelated male living in the middle and south of Iraq was done to evaluate allele frequencies and gene diversity for each Y-STR locus of the Y filer™ PCR amplification kit. The seventeen loci include DYS635, DYS437, DYS448, DYS456, DYS458, YGATA H4, DYS389I, DYS389II, DYS19, DYS391, DYS438, DYS390, DYS439, DYS392, DYS393, DYS385a and DYS385b. Total DNA from blood cells was extracted using the FTA™ paper DNA extraction. A total of 361 unique haplotypes were identified among the four hundred individuals studied. The DYS385b had the highest diversity (GD = 0.8392), while loci DYS392 had the lowest (D = 0.2695). Key words: Allele frequency, gene diversity, Iraq, Y filer™.

Haplotype diversity of 17 Y-STR loci in a Chinese Han population sample from Shanxi Province, Northern China

The distribution of 17 Y-chromosome STR loci DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385a/b, DYS393, DYS391, DYS439, DYS635, DYS392, Y-GATA-H4, DYS437, DYS438, and DYS448 haplotypes was determined in a population sample of 222 unrelated Chinese Han from Shanxi Province, Northern China. A total of 219 haplotypes were observed, and of these, 216 were unique, while 3 were found two times. The overall haplotype diversity was 0.9999 and the discrimination capacity was 0.9865, indicating a high potential for differentiating between male individuals in this population. Comparison analysis via Analysis of Molecular Variance (AMOVA) and construction of MDS plot revealed that Shanxi Han sample clusters with Chinese origin populations and stands far apart of the non-Chinese populations, justifying the establishment of local databases in Shanxi Han population for any future forensic and genetic epidemiology efforts in this region.

Prototype PowerPlex® Y23 System: A concordance study

The Prototype PowerPlex(®) Y23 System (Promega Corporation, Madison, WI) is a polymerase chain reaction-based amplification kit that targets the 23 Y STR loci DYS19, DYS385a/b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS481, DYS533, DYS549, DYS570, DYS576, DYS635, DYS643, and Y-GATA-H4. A total of 951 samples from six populations were typed to evaluate the kit and examine concordance for 17 of the loci that are in common with those that can be typed using the AmpFlSTR(®) Yfiler™ kit (Life Technologies, Carlsbad, CA). A total of 16,167 loci were analyzed for each multiplex, and overall concordance was observed. Because of different kit designs, and although concordant for the genetic type, discordant calls can occur due to a deletion at the DYS448 locus. Users should take into consideration such nomenclature anomalies when comparing Y STR profiles. This new kit allows a large battery of Y STR loci to be analyzed using the same basic technologies already employed in forensic laboratories.

Haplotype data for 16 Y-chromosome STR loci in Aboriginal and Caucasian populations in South Australia

Y-STR haplotype data was obtained using the AmpFlSTR(®) YFiler™ PCR Amplification Kit (Applied Biosystems, Foster City, CA) for 1079 Caucasian and 766 Australian Aboriginal individuals. Haplotype diversity was similar in both populations, however discrimination capacity was higher in Caucasians than Aborigines (0.946 compared to 0.692). Locus DYS385, which was considered as a single locus, was the most diverse marker in both populations (0.836 in Caucasians and 0.905 in Aborigines). The South Australian Aboriginal and Caucasian databases were compiled from casework reference profile information held on the South Australian Criminal, Reference and Evidence DNA Database (SACREDD). Ethnicity was assigned based on self-declaration.

A Y‐Chromosomal Haplotype with Two Short Tandem Repeat Mutations*

The male-specific Y-chromosomal short tandem repeat (STR) is a useful tool in forensic casework. The Y haplotype comprised of 16 loci, which is amplified simultaneously by AmpFlSTR(®) Yfiler(TM) PCR kit and provides strong exculpatory evidence in individual identification. We reported a rare Y-STR profile with a null allele at the DYS448 locus and an off-ladder allele at the DYS456 locus, when genotyping material from a vaginal swab in an alleged rape case. Sequence analysis revealed that the DYS448 null allele was a true type of null allele because of a total deletion of 11 upstream repeats and 9bp of the N(42) region, and there were numerous primer binding site mutations as well. The amplicon of the DYS456 locus was a small 92-bp fragment that was off-ladder, and sequencing analysis showed that there were only 10 repeats (AGAT)(10). This Y chromosome haplotype that was comprised of two variations provided helpful evidence for personal identification.