Y-chromosome STR Loci Research Articles

Forensic characteristics of 38 Y-STR loci in the Hui population from Shaanxi Province, Northwest China

In this study, we genotyped 939 unrelated healthy individuals to investigate the genetic polymorphisms of 38 Y chromosome short tandem repeats(Y-STRs) loci included in the Yfiler™ Platinum kit in the Hui population of Shaanxi Province. Comprehensive population comparisons were performed using analysis of molecular variance(AMOVA), multidimensional scaling(MDS), and molecular evolutionary genetics analysis(MEGA) to explore population relationships. The allele frequencies of the single-copy loci ranged from 0.001 to 0.940 (DYS645), while those of the multi-copy loci ranged from 0.001 to 0.138 (DYS527). The highest genetic diversity (GD) value was observed for DYS385 (0.9723), and the lowest for DYS645 (0.1138). A total of 849 distinct haplotypes were identified among the 939 Hui individuals, with 808 (95.2 %) being unique. Haplotype diversity (HD), haplotype match probability, and discriminatory power (DC) in the Shaanxi Hui population were 0.9996, 0.0015, and 0.9041, respectively. Interpopulation comparisons based on Rst genetic distance values, phylogenetic trees, and MDS indicated that the Shaanxi Hui population has a close genetic relationship with the Ningxia Hui, Qinghai Hui, Xinjiang Hui, and Yunnan Hui populations. The population genetic stratification largely coincides with geographic distribution and language families. Our study revealed that the 38 Y-STR loci exhibit high genetic polymorphisms in the Hui population from Shaanxi Province.

Retraction: Haplotypic diversity and population genetic study of a population in Kashi region by 27 Y-chromosomal short tandem repeat loci.

Liu, Y., Jin, X., Guo, Y., Zhang, X., Zhu, W., Zhang, W., Mei, T. (2020). Haplotypic diversity and population genetic study of a population in Kashi region by 27 Y-chromosomal short tandem repeat loci. Molecular Genetics & Genomic Medicine, 8(8), e1338. https://doi.org/10.1002/mgg3.1338. The above article, published online on 14 June 2020 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the journal Editor in Chief, Suzanne Hart, and Wiley Periodicals LLC. Following publication of this article, concerns were raised by a third party regarding consent and ethical approval for the research undertaken and reported in the article. The publisher and representatives of the journal's editorial board undertook a review of the consent documentation provided, against the research performed and reported in the article. The review uncovered inconsistencies between the consent documentation and the research reported; the documentation was not sufficiently detailed to resolve the concerns raised. As a result, the parties have made the decision to retract the article. In addition, consent documentation did not give approval for data associated with this article to be shared publicly. The associated data for this article has been withdrawn from the publication record following a concern that the data could be used to identify those who have participated in the research. The authors were informed of the retraction but did not respond.

Retraction: Genetic structure and forensic characterization of 36 Y-chromosomal STR loci in Tibeto-Burman- speaking Yi population.

Song, Z., Wang, Q., Zhang, H., Tang, J., Wang, Q., Zhang, H., Yang, M., Ji, J., Ren, Z., Wu, Y., Huang, J. (2021). Genetic structure and forensic characterization of 36 Y-chromosomal STR loci in Tibeto-Burman-speaking Yi population. Molecular Genetics & Genomic Medicine, 9(2), e1572. https://doi.org/10.1002/mgg3.1572. The above article, published online on 15 January 2021 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the journal Editor in Chief, Suzanne Hart, and Wiley Periodicals LLC. Following publication of this article, concerns were raised by a third party regarding consent and ethical approval for the research undertaken and reported in the article. The publisher and representatives of the journal's editorial board undertook a review of the consent documentation provided, against the research performed and reported in the article. The review uncovered inconsistencies between the consent documentation and the research reported; the documentation was not sufficiently detailed to resolve the concerns raised. As a result, the parties have made the decision to retract the article. In addition, consent documentation did not give approval for data associated with this article to be shared publicly. The associated data for this article has been withdrawn from the publication record following a concern that the data could be used to identify those who have participated in the research. The authors were informed of the retraction but did not respond.

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.

Analysis of Y-STR diversity and DNA methylation variation among Black and Indian males from KwaZulu-Natal, South Africa

Y-chromosome short tandem repeats (Y-STRs) are essential in understanding genetic structure and diversity of human populations and, most importantly, in identification of male perpetrators in criminal investigations. DNA methylation differences have been reported in human populations and methylation pattern at the CpG sites found within or flanking the Y-STR sites could also aid in human identification. Studies based on DNA methylation (DNAm) at Y-STRs are currently limited. The current study aimed to analyze the Y-STR diversity in South African Black and Indian individuals living in KwaZulu-Natal, Durban, South Africa, with the Yfiler™ Plus Kit and to analyze DNAm patterns in Y-STR markers CpG sites. DNA from 247 stored saliva samples were isolated and quantified. Across the 27 Y-STR loci in the Yfiler™ Plus Kit, 253 alleles were observed in 113 South African Black and Indian males, 112 unique haplotypes were observed, and one haplotype appeared twice (two Black individuals). No statistically significant differences were observed in the genetic diversity between the two population groups (Fst = 0.028, p-value ≥ 0.05). The kit showed a high discrimination capacity (DC) of 0.9912 and an overall haplotype diversity (HD) = 0.9995 among the sampled population groups. DYS438 and DYS448 markers displayed 2 and 3 CpG sites, respectively. Based on the two-tailed Fisher’s Exact test, there were no statistically significant differences in the DNAm levels at DYS438 CpGs of Black and Indian males (p > 0.05). The Yfiler™ Plus Kit can be considered highly discriminatory among South African Black and Indian males. Studies on the South African population using Yfiler™ Plus Kit are scarce. Hence, accumulating Y-STR data on the diverse South African population will enhance the representation of South Africa in STR databases. Knowing which Y-STR markers are significantly informative for South Africa is essential for developing Y-STR kits better suited for the different ethnic groups. And to the best of our knowledge, DNA methylation analysis in Y-STR for different ethnic groups has never been done before. Complementing Y-STR data with methylation knowledge could provide population-specific information for forensic identification.

Phylogenetic analyses of 41 Y-STRs and machine learning-based haplogroup prediction in the Qingdao Han population from Shandong province, Eastern China

Background Known for its rich history and culture, Qingdao is a typical symbol of Chinese maritime culture. Its unique genetic landscape has aroused interest among geneticists and forensic scientists. However, the genetic landscape of Qingdao has never been uncovered. Aim This investigation intends to provide light on Qingdao’s paternal genetic diversity and its evolutionary connections to other Han subgroups. Subjects and methods The genetic polymorphisms of 41 Y-chromosomal short tandem repeat (STR) loci in the Qingdao Han were investigated using SureID® PathFinder Plus Kit. Phylogenetic studies were performed using genotype data from 52 East Asian groups at 23 common Y-STR loci. A multidimensional scaling plot and cladogram were constructed. Linear Discriminant Analysis (LDA) was carried out for predicting categories among the Han people. The k-nearest neighbour (kNN) algorithm was utilised to designate Y-SNP haplogroups for each haplotype. Results The Qingdao Han were genetically far from the Tibeto-Burman populations and close with the Han people from northern China. LDA indicated a deep integration among the present-day Han people. By the kNN model, the predicted O2a2 and O2a1 were shown to be the predominant Y-SNP haplogroups. Conclusions This study would be helpful for reconstructing the patrilineal history in China and establishing a more comprehensive Y-STR database.

Haplotypic polymorphisms and forensic applications in Chinese Hunan Han population based on a series of Y-STR loci: a perspective of paternal inheritance

Background Hunan, a multinational province in China, possesses more than fifty ethnic groups, such as the Han, Yao, Tujia, Miao, and so on. Aims To evaluate the forensic efficiency of the novel panel and investigate the genetic relationships between Hunan Han population and 12 other reference populations from China. Subjects and methods Haplotypic data of 153 unrelated males of Hunan Han population were investigated using the AGCU Y SUPP Plus amplification system containing 27 Y-chromosomal short tandem repeat (STR) loci. Forensic parameters were calculated to evaluate the application efficiency of this panel in Hunan Han population. Results Haplotype diversity, discrimination capability, and match probability values were 0.9999999977, 1.0000, and 0.0065, respectively. Pairwise fixation index values demonstrated that the minimal genetic differentiation (0.0073) was found between Hunan Han population and Hunan Yao group, while the maximal genetic differentiation (0.0651) was observed between Hunan Han and Guangxi Yao group from the perspective of the patrilineal DNA analysis. Conclusions The haplotype distributions of 27 Y-STR loci in Hunan Han population exhibited remarkable polymorphisms. Moreover, this panel has potential advantages for the forensic applications regarding family investigations, paternity testing of the paternal line, and population genetics.

Genetic polymorphisms and phylogenetic characteristics of Tibeto-Burman-speaking Lahu population from southwest China based on 41 Y-STR loci

Background Male sex-linked Y-chromosome short tandem repeats (Y-STRs) have been widely used in forensic cases and population genetics research. At present, the forensic-related Y-STR data in the Chinese Lahu population are still poorly understood. Aim To enrich the available Y-STR data of this Chinese minority population and investigate its phylogenetic relationships with other reported populations. Subjects and methods The genetic polymorphisms of 41 Y-STR loci were analysed in 299 unrelated healthy Lahu male individuals from Southwest China. Phylogenetic analyses were performed by multidimensional scaling analysis and neighbor-joining phylogenetic tree construction. Results A total of 379 alleles were observed at the 41 Y-STR loci. The allele frequencies ranged from 0.0033 to 0.9666. The genetic diversity values ranged from 0.0653 to 0.9072. A total of 254 different haplotypes of the 41 Y-STR loci were observed in 299 individuals. The values of haplotype diversity, haplotype match probability, and discrimination capacity were 0.9987, 0.0047, and 0.8495, respectively. The phylogenetic analysis indicated that the Tibeto-Burman-speaking Lahu population showed a close genetic relationship with the Yunnan Yi population. Conclusions The haplotype data of the present study can enrich the forensic databases of this Chinese minority population and will be useful for population genetics and forensic DNA application.

Genetic analysis of 23 Y-STR loci in the Va population from Yunnan Province, Southwest China

Background Y-chromosomal short tandem repeat (Y-STR) polymorphisms are widely used in forensic DNA analysis. However, there is a lack of information about the Chinese Va population in the Y-STR Haplotype Reference Database. Aim To establish the Y-chromosome Haplotype Reference Database of the Yunnan Va population and investigate the population genetic relationships with other geographically adjacent groups. Subjects and methods In total, 23 Y-STR loci were genotyped with the PowerPlex Y23 Kit in 368 unrelated healthy Va males from Yunnan Province, Southwest China. Genetic polymorphism was analysed using the YHRD’s AMOVA tools and the MEGA 6.0 software. Results The gene diversity (GD) of the 23 Y-STR loci ranged from 0.3092 (DYS19) to 0.7868 (DYS385a/b). According to haplotype analysis, 204 different haplotypes were obtained, out of which 144 were unique. The haplotype diversity (HD) and discrimination capacity (DC) were 0.9852 and 0.5543, respectively. By comparing the Yunnan Va group with the other 22 referential groups, the results revealed that Yunnan Va was isolated from other groups. Conclusions The 23 Y-STR loci were highly polymorphic and informative in the Yunnan Va population, and the results enriched the basic genetic information for forensic investigation and population genetic studies.

Population data and phylogenetic analysis of 37 Y-STR loci in the Hui population from Yunnan Province, Southwest China

Background Previous studies of the genetic polymorphism of the Y-chromosomal short tandem repeat (Y-STR) of Huis were focussed on the northwest of China. However, the population genetic characteristics of Chinese Hui residing in Yunnan province, Southwest China, remain unclear. Aim To provide genetic data for 37 Y-STRs in the Chinese Hui population of Yunnan province, as well as to investigate population genetic relationships between the Chinese Hui and another 26 populations from China and neighbouring countries. Subjects and methods In total, 326 unrelated healthy male individuals were genotyped using the GoldeneyeTM Y Plus PCR Amplification Kit. Genetic relationships between different populations were analysed using YHRD’s AMOVA tools. Results A total of 279 haplotypes were detected, out of which 244 were unique. The overall haplotype diversity (HD) and discrimination capacity (DC) were 0.9989 and 0.8611, respectively. The gene diversity (GD) ranged from 0.0544 (DYS645) to 0.9656 (DYS385). Conclusions The population comparison indicated that Muslim populations (Hui, Salar and Uighur) showed significantly more genetic affinity than other populations. Our results could be applied in forensic practice and population genetic studies.

Allelic and haplotypic polymorphisms and paternal genetic analysis of Chinese Shaanxi Han population utilizing a multiplex Y-STR set

Background The analysis of Y chromosomal genetic markers is of great significance in human genetic fields related to male individuals. The Han nationality is the most populous ethnic group. It is critical to investigate the Y-chromosome short tandem repeat (Y-STR) genetic informativeness of Han nationalities in different Chinese regions in order to gain a comprehensive understanding of their paternal genetic relationships and origin. Aim To assess the allelic and haplotypic polymorphisms of the novel AGCU Y SUPP STR amplification system containing seven Y-STRs in the maximal dataset of the Y-STR Haplotype Reference Database (YHRD) and 17 newly included Y-STRs, and explore the genetic relationships among the Shaanxi Han population and 12 reference populations from China. Subjects and methods A total sample of 220 Han male subjects were obtained from the Shaanxi Province, China, and genotyped by the novel AGCU Y SUPP STR amplification system. Multiplex population genetic analyses derived from the same 16 Y-STR loci were carried out among the Shaanxi Han population and 12 reference populations from China. Results The gene diversities (GD) ranged from the maximum value of 0.9609 (DYS385a,b) to the minimum value of 0.5441 (DYS531). Besides, 217 distinct haplotypes were detected wholly in 220 individuals, of which 214 (98.62%) were exclusive. The entire haplotype diversity (HD) and discrimination capacity (DC) were 0.9999 and 0.9864, respectively, while the haplotype match probability (HMP) was 0.0045. Among the reference populations, the obtained results of population genetic analyses revealed that the Shaanxi Han population had the largest genetic distance with the Guangxi Yao group, but the smallest genetic distance with the Hunan Tujia group. Conclusions These Y-STR loci in the AGCU Y SUPP STR amplification system were of high genetic polymorphisms and the amplification system could be used as a prospective complementary tool for forensic application and paternal genetics in the Shaanxi Han population.

Distribution of Y-chromosome haplogroups in Serbian population groups originating from historically and geographically significant distinct parts of the Balkan Peninsula

Our study enrolled 1200 Serbian males originating from three geographical regions in the Balkan Peninsula inhabited by Serbs: present-day Serbia, regions of Old Herzegovina and Kosovo and Metohija. These samples were genotyped using the combination of 23 Y-chromosomal short tandem repeats (Y-STRs) loci and 17 Ychromosomal single nucleotide polymorphisms (Y-SNPs) loci for the haplotype and haplogroup analysis in order to characterize in detail Y chromosome flow in the recent history. Serbia’s borders have changed through history, forcing Serbs constantly to migrate to different regions of Balkan Peninsula. The most significant migration waves in the recent history towards present-day Serbia occurred from the regions of Old- Herzegovina and Kosovo and Metohija that lie in the south-west/south. High haplotype diversity and discrimination capacity were observed in all three datasets, with the highest number of unique haplotypes (381) and discrimination capacity (0.97) detected in the samples originating from the present-day Serbia. Haplogroup composition didn’t differ significantly among datasets, with three dominant haplogroups (I-M170, E-P170 and R-M198), and haplogroup I-M170 being the most frequent in all three datasets. Haplogroup E-P170 was the second most dominant in the dataset originating from geographical region of Kosovo and Metohija, whereas haplogroup R-M198 was the second most prevalent in the dataset from historical region of Old Herzegovina. Based on the phylogenetic three for haplogroup I constructed within this study, haplogroup I2a1-P37.2 was the most dominant within all three datasets, especially in the dataset from historical region of Old Herzegovina, where 182 out of 400 samples were derived for SNP P37.2. Genetic distances between three groups of samples, evaluated by the Fst and Rst statistical values, and further visualized through multidimensional scaling plot, showed great genetic similarity between datasets from Old Herzegovina and present-day Serbia. Genetic difference in the haplogroup distribution and frequency between datasets from historical region of Old Herzegovina and from geographical region of Kosovo and Metohija was confirmed with highest Fst and Rst vaules. In this study we have distinguished genetic structure, diversity and haplogroup frequencies within 1200 Serbian males from three datasets, relationships among them as well as with other Balkan and European populations, which is useful for studying recent demographic history.

Development and validation of a new multiplex Y-STR panel designed to increase the power of discrimination.

In an attempt to increase the discrimination capacity (DC) and reduce the adventitious match probability, a 6-dye multiplex Y-chromosomal short tandem repeat (Y-STR) panel named Y34plex was constructed that combined 25 Y-chromosomal markers (DYS456, DYS627, DYS390, DYS570, DYS635, DYS385a/b, DYS448, DYS437, DYS533, DYS449, DYS481, DYS392, DYS391, DYS389I, DYS460, YGATAH4, DYS438, DYS389II, DYS19, DYS458, DYF387S1a/b, DYS439, DYS393, DYS576, and DYS518) in widely used commercial kits, with nine highly polymorphic Y-STR loci (DYS557, DYS527a/b, DYS593, DYS444, DYS596, DYS643, DYS447, DYS549, and DYS645). The Y34plex is a promising type system to distinguish both unrelated and related male individuals due to the incorporation of rapidly mutatedY-STR loci. A validation study of the Y34plex was performed and followed the guidelines of the Scientific Working Group on DNA analysis methods. Results show that full Y-STR profiles were obtained from male/female DNA mixtures with 125pg of male DNA in the presence of 50ng of female DNA. The ability to tolerate polymerase chain reaction inhibitors commonly contained in forensic casework samples demonstrated the applicability and robustness of the Y34plex. Compared with the Yfiler Plus kit, the novel panel showed an increased power of discrimination in Chinese Wuxi Han population (n=434). The overall haplotype diversity of the Y34plex was 0.999606, whereas DC value was 0.956221, which is suitable for use on forensic paternal investigation.

Forensic Analysis and Genetic Structure Construction of Chinese Chongming Island Han Based on Y Chromosome STRs and SNPs.

Y-chromosome short tandem repeat (Y-STR) and Y-chromosome single nucleotide polymorphism (Y-SNP) are genetic markers on the male Y chromosome for individual identification, forensic applications, and paternal genetic history analysis. In this study we successfully genotyped 38 Y-STR loci and 24 Y-SNP loci of Pudong Han (n = 689) and Chongming Han (n = 530) in Shanghai. The haplotype diversity of the Y filer platinum genotyping system was the highest in the Han population in the Pudong area of Shanghai (0.99996) and Chongming Island (0.99997). The proportion of unique haplotypes was 97.10% (Pudong) and 98.49% (Chongming), respectively. The multidimensional scaling analysis and phylogenetic analysis were performed according to the genetic distance Rst, which was calculated based on the Y-STR gene frequency data. Moreover, we made a comparison on the frequency distribution analysis and principal component analysis of haplogroups in both populations. As a result, Shanghai Pudong Han, Chongming Island Han, and Jiangsu Han were determined to have a strong genetic affinity. The haplogroup distribution characteristics of the Pudong Han and Chongming Han populations were similar to those of the southern Han population. The results of haplotype network analysis showed that Jiangsu Wujiang Han and Jiangsu Changshu Han had more paternal genetic contributions to the formation of Shanghai Pudong Han and Chongming Island Han. Through the joint analysis of SNPs and STRs, this study deeply analyzed the paternal genetic structure of the Pudong Han and Chongming Han populations. The addition of Y-SNP haplogroups to forensic applications can provide information for pedigree investigation.

Development and validation of a multiplex typing system with 32 Y-STRs for forensic application

Y-chromosomal short tandem repeats (Y-STRs) with high mutation rates will increase the potential to distinguish related males and improve discrimination capacity. The newly developed Y32 kit is a six-dye multiplex amplification kit that contains 21 rapidly mutating Y-STR loci (DYF387S1a/b, DYF399S1a/b/c, DYF403S1a1/a2/a3/b, DYF404S1a/b, DYS449, DYS518, DYS526a/b, DYS547, DYS570, DYS576, DYS612, DYS626, and DYS627), 8 fast mutating Y-STR loci (DYS458, DYS464a/b/c/d, DYS516, DYS534, and DYS713), and 3 moderately mutating Y-STR loci (Y-GATA-A10, DYS630, and DYS446). To verify the efficiency and accuracy of the Y32 kit, PCR reaction conditions, sensitivity, mixture, concordance, inhibition, species specificity, case samples, reproducibility, sizing precision, stutter, and population study were studied according to the SWGDAM developmental validation guidelines. The results showed that the Y32 kit is efficient, accurate, reliable, and highly informative for forensic applications.

Sequence polymorphisms of forensic Y-STRs revealed by a 68-plex in-house massively parallel sequencing panel

Sequence polymorphisms of Y chromosome short tandem repeat (Y-STR) markers can be unveiled using next generation sequencing (NGS). Compared to capillary electrophoresis, NGS has the advantage of distinguishing between some alleles of the same length. Here, a 68-plex in-house panel covering 67 Y-STR loci and the sex determinant Amelogenin locus, was developed. The accuracy of this panel was 100% concordant with three standard reference samples. The sensitive was as low as 250 pg. A total of 466 length-based alleles, 806 sequence-based alleles, and 149 haplotypes were observed across 149 Chinese Han individuals. The total haplotype diversity and discrimination capacity was 1.0000 in detected samples. The DYS710 locus possessed the highest diversity by sequence among these Y-STRs, with 109 sequence-based alleles observed. Micro-variant alleles with the same length were observed in 39 Y-STR loci, with their sequence variations mainly attributable to repeat pattern variations. While the number of sequence-based alleles identified for DYS447, DYS449, DYS710, DYS720 and DYF387S1a/b was approximately three times that of their length-based alleles, flanking sequence variations were observed in 18 alleles. In addition, 201 sequence-based alleles in 42 loci were newly discovered. This significantly expanded the knowledge of human Y-STR sequence polymorphisms. Collectively, the 68-plex panel provided reliable Y-STR results as well as higher resolution for paternal lineage analysis.

Paternal genetic structure of the Bosnian‐Herzegovinian Roma: A Y‐chromosomal STR study

Studies indicate the complex nature of the genetic structure of the European Roma which has been shaped by different effects of their demographic history, while preserving their ancestral Indian origin. The primary aims of this study were to present for the first time the paternal profiles of the Roma from Bosnia and Herzegovina based on the data from Y-chromosome STR loci, identify the components of non-Roma paternal gene flow into the Roma, and evaluate the genetic relationships with other European Roma populations. In this study, 110 DNA samples of unrelated males from Roma populations residing in different regions of Bosnia and Herzegovina were genotyped using the 23 Y-STR loci included in the PowerPlex Y23 system. The analysis of the genetic structure of the Bosnian-Herzegovinian Roma revealed intra-country population substructuring and indicated differing genetic affinities between the Bosnian-Herzegovinian Roma and other European Roma populations. The paternal genetic structure of the Bosnian-Herzegovinian Roma has two components: an ancestral component represented by haplogroup H1a1a-M82, and European component presented by haplogroups I1-M253, I2a1a2b-L621, J2a1a-L26, J2a1a1a2b2a3~Z7671, J2b2a-M241, G2a2b2a1a1b-L497, and E1b1b-M215. Genetic relations between the Bosnian-Herzegovinian Roma and other European Roma are shaped by different influences on their demographic history. The data suggest that the paternal gene pool of the Roma from Bosnia and Herzegovina might be a consequence of an early separation of the proto-Roma population and the later gene flow as well as factors of the isolation that accompany the Roma populations in some Bosnian-Herzegovinian regions.

Improving the regional Y-STR haplotype resolution utilizing haplogroup-determining Y-SNPs and the application of machine learning in Y-SNP haplogroup prediction in a forensic Y-STR database: A pilot study on male Chinese Yunnan Zhaoyang Han population

Improving the resolution of the current widely used Y-chromosomal short tandem repeat (Y-STR) dataset is of great importance for forensic investigators, and the current approach is limited, except for the addition of more Y-STR loci. In this research, a regional Y-DNA database was investigated to improve the Y-STR haplotype resolution utilizing a Y-SNP Pedigree Tagging System that includes 24 Y-chromosomal single nucleotide polymorphism (Y-SNP) loci. This pilot study was conducted in the Chinese Yunnan Zhaoyang Han population, and 3473 unrelated male individuals were enrolled. Based on data on the male haplogroups under different panels, the matched or near-matching (NM) Y-STR haplotype pairs from different haplogroups indicated the critical roles of haplogroups in improving the regional Y-STR haplotype resolution. A classic median-joining network analysis was performed using Y-STR or Y-STR/Y-SNP data to reconstruct population substructures, which revealed the ability of Y-SNPs to correct misclassifications from Y-STRs. Additionally, population substructures were reconstructed using multiple unsupervised or supervised dimensionality reduction methods, which indicated the potential of Y-STR haplotypes in predicting Y-SNP haplogroups. Haplogroup prediction models were built based on nine publicly accessible machine-learning (ML) approaches. The results showed that the best prediction accuracy score could reach 99.71% for major haplogroups and 98.54% for detailed haplogroups. Potential influences on prediction accuracy were assessed by adjusting the Y-STR locus numbers, selecting Y-STR loci with various mutabilities, and performing data processing. ML-based predictors generally presented a better prediction accuracy than two available predictors (Nevgen and EA-YPredictor). Three tree models were developed based on the Yfiler Plus panel with unprocessed input data, which showed their strong generalization ability in classifying various Chinese Han subgroups (validation dataset). In conclusion, this study revealed the significance and application prospects of Y-SNP haplogroups in improving regional Y-STR databases. Y-SNP haplogroups can be used to discriminate NM Y-STR haplotype pairs, and it is important for forensic Y-STR databases to develop haplogroup prediction tools to improve the accuracy of biogeographic ancestry inferences.

A multi-dimensional evaluation of the ‘NIST 1032’ sample set across four forensic Y-STR multiplexes

This manuscript reports Y-chromosomal short tandem repeat (Y-STR) haplotypes for 1032 male U.S. population samples across 30 Y-STR loci characterized by three capillary electrophoresis (CE) length-based kits (PowerPlex Y23 System, Yfiler Plus PCR Amplification Kit, and Investigator Argus Y-28 QS Kit) and one sequence-based kit (ForenSeq DNA Signature Prep Kit): DYF387S1, DYS19, DYS385 a/b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS460, DYS481, DYS505, DYS518, DYS522, DYS533, DYS549, DYS570, DYS576, DYS612, DYS627, DYS635, DYS643, and Y-GATA-H4. The length-based Y-STR haplotypes include six loci that are not reported in the sequence-based kit (DYS393, DYS449, DYS456, DYS458, DYS518, and DYS627), whereas three loci included in the sequence-based kit are not present in length-based kits (DYS505, DYS522, and DYS612). For the latter, a custom multiplex was used to generate CE length-based data, allowing 1032 samples to be evaluated for concordance across the 30 Y-STR loci included in these four commercial Y-STR typing kits. Discordances between typing methods were analyzed further to assess underlying causes such as primer binding site mutations and flanking region insertions/deletions. Allele-level frequency and statistical information is provided for sequenced loci, excluding the multi-copy loci DYF387S1 and DYS385 a/b, for which locus-specific haplotype-level frequencies are provided instead. The resulting data reveals the degree of information gained through sequencing: 88% of sequenced Y-STR loci contain additional sequence-based alleles compared to length-based data, with the DYS389II locus containing the most additional alleles (51) observed by sequencing. Despite these allelic increases, only minimal improvement was observed in haplotype resolution by sequence, with all four commercial kits providing a similar ability to differentiate length-based haplotypes in this sample set. Finally, a subset of 369 male samples were compared to their corresponding additionally sequenced father samples, revealing the sequence basis for the 50 length-based changes observed, and no additional sequence-based mutations. GenBank accession numbers are reported for each unique sequence, and associated records are available in the STRSeq Y-Chromosomal STR Loci National Center for Biotechnology Information (NCBI) BioProject, accession PRJNA380347. Haplotype data is updated in the Y-STR Haplotype Reference Database (YHRD) for the ‘NIST 1032’ data set to now achieve the level of maximal haplotype of YHRD. All supplementary files including revisions to previously published Y-STR data are available in the NIST Public Data Repository: U.S. population data for human identification markers, DOI 10.18434/t4/1500024.

Twenty-Seven Y-Chromosome Short Tandem Repeats Analysis of Italian Mummies of the 16th and 18th Centuries: An Interdisciplinary Research.

Roccapelago (MO) is a small village located in the Northern Central Apennines, with a population of 31 inhabitants (2014). In 2010, more than 400 individuals dated between the end of the 16th and the 18th century, many of which partially mummified, were discovered in the crypt of the church. This small village, because of its geographical location and surrounding environment, seems to possess the characteristics of a genetic isolate, useful for population genetics and genealogical analyses. Thus, a diachronic study of DNA aimed at investigating the structure and dynamics of the population of Roccapelago over the about 4 centuries, was conducted by analyzing ancient and modern inhabitants of the village. The 14 modern samples were selected by considering both the founder surnames of the village, identified thanks to the study of parish registers, and the grandparent’s criterion. From 25 ancient mummies, morphologically assigned to male individuals, the petrous bone, that harbors high DNA amounts, was selected for the DNA extraction. The quantification and qualitative assessment of total human male DNA were evaluated by a real-time PCR assay using the Quantifiler Trio DNA Quantification Kit and multiplex PCR of 27 Y-chromosome short tandem repeat (Y-STR) markers included in the Yfiler Plus PCR Amplification Kit, with seven rapidly mutating Y-STR loci for improving discrimination of male lineages, was performed to genotype the samples. Y-STRs were analyzed according to the criteria of ancient DNA (aDNA) analysis to ensure that authentic DNA typing results were obtained from these ancient samples. The molecular analysis showed the usefulness of the Y chromosome to identify historically relevant remains and discover patterns of relatedness in communities moving from anthropology to genetic genealogy and forensics.