Y-STR Haplotype Reference Database Research Articles

Comparison of Allele Frequencies of Benghazi Population with Other Metapopulation

This is, to our knowledge, the first in-depth and largest study (238 samples) of genetic diversity in Y-STR haplotypes in an eastern Libyan population (recorded in Afro-Asiatic group from Metapopulation published in Y-STR Haplotype Reference Database-YHRD). Two previous studies, of a Tripoli population (West of Libya) and a Fezzan population (South Libya) analyzed a smaller number of inhabitants (63 samples and 47 samples, respectively) and (YHRD). Recently, (April 2011) YHRD recorded 47 and 82 haplotypes from Tripoli (Berber and Arabs 2011) respectively. Method: We Compare allele frequencies of Benghazi population with Y-STR Haplotype Reference Database -metapopulation. Conclusion: Benghazi population is similar to other Asian groups, such as Euro-Asian and East Asian. Hence, the Benghazi population shows genetic affinity to Asian and Middle Eastern rather than African and West North African groups.

Revealing genetic structure in the paternal lineages and forensic profiling of Bhotra tribe by the analysis of Y-STR multiplex platform

India has a diverse reservoir of genetic components, ethnicity and linguistic affiliations. Y-STR (Short Tandem Repeat) markers serve as a potential tool in the fields of anthropological genetics, ancestry exploration, as well as in forensic investigations. The present study was conducted to explore the molecular diversity in respect to male lineage, genomic heritage and forensic profiling of Bhotra tribe of Odisha, India, by using 23 Y-STR molecular markers. Blood samples were collected randomly from 133 unrelated healthy adult male individuals of Bhotra population following the ethical standards.Out of 133 individuals, 109 unique haplotypes were observed. Discrimination Capacity (DC) was observed at 0.8195; mean Gene Diversity (GD) was observed to be 0.615 along with the Standard Error (SE) of 0.027. The locus DYS385a/b showed the highest genetic diversity (0.887). To assess the genetic affinity of the Bhotra population with other Indian population that were reported to Y-STR Haplotype Reference Database (YHRD) before, Multidimensional Scaling plot (MDS), Neighbor Joining (NJ) tree, and Principal Coordinate Analysis (PCoA) were performed. The study population exhibited a high degree of genetic diversity and indicated genetic affinity with the Majhi and Dorla tribes of Chhattisgarh. Study population characterized by 12 different haplogroups and H1a1a (33.03%) was the most frequently observed haplogroup, indicating the ancestral relationship of Bhotra with the European Romani population.To the best of our knowledge, this is the first global report of the genetic diversity of the Bhotra tribe on 23 Y STR genetic markers, which would be profoundly useful in forensic investigation, medical, and anthropological studies and would also enrich the Indian Y-STR database.

Genetic analysis of 29 Y-STR loci in Qiang population from Beichuan Qiang Autonomous County in China.

This study reported the forensic parameters of the 29 Y-STR loci of 242 unrelated Qiang males in Beichuan Qiang Autonomous County. Qiang population is a minority with small size populations and has never been reported. The overall haplotype diversity of Qiang population was measured to be 0.9992 while a discrimination capacity was 0.9215. According to the haplotypic analysis of the 29 Y-STR loci, 223 different haplotypes were obtained, of which 207 (92.83%) were unique. A total of 242 different alleles were checked at all loci, the corresponding allele frequencies ranged from 0.0041 to 0.7603. In addition, pairwise genetic distances, multidimensional scaling plots and neighbor-joining dendrogram were performed to analyze interpopulation differentiation between Qiang population and 16 other ethnic groups. These data can fill the gap in the Y-STR Haplotype Reference Database of the Qiang population and may be of reference value for forensic and population genetic analysis.

Forensic genetic investigation of human skeletal remains recovered from the La Belle shipwreck

In 1995, the historical shipwreck of La Belle was discovered off the coast of Texas. One partial human skeleton was recovered from alongside cargo in the rear portion of the ship; a second (complete) skeleton was found atop coiled anchor rope in the bow. In late 2015, comprehensive forensic genetic testing began on multiple samplings from each set of remains. For the partial skeleton recovered from the ship’s rear cargo area, results were obtained for 26/27 Y-STRs using traditional CE; with MPS technology, results were obtained for 18/24 Y-STRs, 56/56 ancestry-informative SNPs (aiSNPs), 22/22 phenotype-informative SNPs (piSNPs), 22/27 autosomal STRs, 4/7 X-STRs, and 94/94 identity-informative SNPs (iiSNPs). For the complete skeleton of the second individual, results were obtained for 7/17 Y-STRs using traditional CE; with MPS technology, results were obtained for 5/24 Y-STRs, 49/56 aiSNPs, 18/22 piSNPs, 15/27 autosomal STRs, 1/7 X-STRs, and 66/94 iiSNPs. Biogeographic ancestry for each set of skeletal remains was predicted using the ancestry feature and metapopulation tool of the Y-STR Haplotype Reference Database (YHRD), Haplogroup Predictor, and the Forensic Research/Reference on Genetics knowledge base (FROG-kb). Phenotype prediction was performed using piSNP data and the HIrisplex eye color and hair color DNA phenotyping webtool. mtDNA whole genome sequencing also was performed successfully. This study highlights the sensitivity of current forensic laboratory methods in recovering DNA from historical and archaeological human remains. Using advanced sequencing technology provided by MiSeq™ FGx (Verogen) and Ion S5™ (Thermo Fisher Scientific) instrumentation, degraded skeletal remains can be characterized using a panel of diverse and highly informative markers, producing data which can be useful in both forensic and genealogical investigations.

Population data of 23 Y chromosome STR loci for the five major human subpopulations of Ghana.

In this study, 268 samples for unrelated males belonging to the five major human subpopulation groups in Ghana (Akan, Ewe, Mole-Dagbon, Ga-Dangme and Guang) were genetically characterised for 23 Y chromosome short tandem repeat (STR) loci using the Powerplex® Y23 STR kit. A total of 263 complete haplotypes were recorded of which 258 were unique. The haplotype diversity, discriminating capacity and match probability for the pooled population data were 0.9998, 0.9627 and 0.0039, respectively. The pairwise genetic distance (RST) for the Ghanaian datasets and other reference populations deposited in the Y-STR Haplotype Reference Database (YHRD) were estimated and mapped using multidimensional scaling (MDS) plot. The Guang and Ewe were significantly different from the Akan, Mole-Dagbon and Ga-Dangme. However, the five Ghanaian datasets were all plotted close together with other African populations in the MDS data mapping.

Phylogenetic analysis and forensic evaluation among Rakhine, Marma, Hajong, and Manipuri tribes from four culturally defined regions of Bangladesh using 17 Y-chromosomal STRs.

We have analyzed haplotypes for 17 Y chromosomal STR loci in Bangladeshi mainstream Bengali population and four largest ethnic groups inhabiting the North-Eastern and Southern region of Bangladesh using AmpFlSTR® Yfiler® PCR amplification systems. A total of 667 haplotypes from Bangladeshi Bangali, 157 from Rakhine, 144 from Marma, 112 from Hajong, and 136 from Manipuri individuals were observed with corresponding discrimination capacity (DC) of 0.973 for Bengali, 0.723 for Rakhine, 0.743 for Marma, 0.794 for Hajong, and 0.720 for Manipuri groups, respectively. In order to investigate genetic relationship and the pattern of paternal contributions of the studied population, a comparison of the studied data with the published data from Y-STR haplotype reference database (YHRD) was conducted based on analysis of molecular variance (AMOVA). Construction of neighbour-joining tree revealed that the Rakhine population lies closer to a clade consisting, Korean and Japanese population. The Hajong population showed close affinity with Riang (Tripura, India) tribe followed by Marma population. On the other hand, Manipuri group is closely related to Thai population followed by Tamil and mainstream Bengali population.

Forensic characteristics and phylogenetic analysis of two Han populations from the southern coastal regions of China using 27 Y-STR loci

Currently, the largest national database within the Y-STR Haplotype Reference Database (YHRD, https://yhrd.org, release 55) is China, which has a very large Y-STR haplotype profiles. However, no haplotype data was available for Hainan province, the smallest and southernmost province of China. Herein, 280 unrelated male Chinese Han individuals residing in Hainan province were recruited and genotyped with 27 Y-STR loci. Moreover, 136 Han individuals from Shenzhen, the largest migrant city in China, also investigated. 279 distinct haplotypes were obtained in the Hainan Han individuals with the overall haplotype diversity (HD) and discrimination capacity (DC) were 0.999974 and 0.9964, respectively. 136 unique haplotypes were observed in the Shenzhen individuals, and thus both of the related HD and DC values were 1.0. The two multi-copy loci (DYS385a/b and DYF387S1a/b) and rapidly mutating Y-STRs (RM Y-STRs, DYS449, DYS518, DYS570, DYS576, DYS627) exhibited high genetic diversity (GD) values (GD>0.7) in two Han populations. Furthermore, genetic relationships along Chinese administrative and ethnic divisions were analyzed, and we also combined our data with existing datasets of non-Chinese groups to explore the genetic variance. Genetic differentiations were observed between Northern and Southern Han nationality, and genetic differences existed between the two Han populations and some ethnic groups, most prominently for the Tibetans and Kazakhs, as well as non-Chinese groups, especially African groups.

Forensic application of Y-chromosomal STR analysis in Lithuanian population

This paper presents a comprehensive Y-chromosomal STR haplotype analysis in the Lithuanian population in order to evaluate Lithuanians’ Y chromosome diversity, to infer genetic relations between Lithuanian and other European neighbouring populations and to introduce population reference data for generation of reliable Y-STR haplotype frequency estimates to be used in the quantitative assessment of Y-STR haplotype match in the forensic casework. Data were collected from the peripheral blood samples of 194 unrelated males throughout various regions of Lithuania. The amplification of 17 Y-STRs was carried out in one multiplex PCR using an AmpFlSTR® Yfiler<sup>TM</sup> PCR Amplication Kit according to the supplier’s protocol. The results indicated that the Y-chromosomal haplotype diversity in the Lithuanian population rises as the number of the analyzed Y-STRs is increased. However, all additional Y-STR loci are not hypervariable and only their whole makes a large diversity of Y-STR haplotypes in Lithuanian males. The analysis of molecular variance revealed low but significant interpopulation differences except the pair of Lithuanian and Latvian populations. The phylogenetic analysis showed that the clustered Y chromosome gene pool of Lithuanians and Latvians has a closer phylogenetic relation to Russian and Estonian populations and is less genetically related to other neighbouring populations of Belarus and Poland. Yet Y-STRs alleles and haplotypes differentiate effectively inside the Lithuanian population and between Lithuanians and its geographical neighbours excluding the Latvian population. Comparison of the Y-STR data suggests that Lithuanian and Latvian populations are closely related not only by geography and language but also by the Y chromosome gene pool represented by forensic Y-STR markers. Consequently, more forensic Y-STR markers should be included in the Y-STR haplotype in order to achieve a resolution between the Y chromosomes of Lithuanian and Latvian males. Lithuanian Y-STR haplotype data were submitted to the 34th release of the Y-STR Haplotype Reference Database 3.0 for match probability calculations in the forensic casework.

Phylogenetic analysis and forensic characteristics of 12 populations using 23 Y-STR loci

Genetic analysis of Y-STRs has the potential to be used to explore the complexity in population substructures and to perform forensic ancestry inference. In this study, 334 individuals from 12 populations were typed using the PowerPlex® Y23 System (Promega, USA) to investigate their relationship. Population comparisons with other East Asian populations collated from YHRD (Y-STR Haplotype Reference Database) were also performed. Variant alleles, including seven intermediate alleles in 15 samples were observed, while the novel allele 11.3 at the DYS549 locus was confirmed by sequencing. Our results showed that the fraction of unique haplotypes differed among the 12 populations studied here. A close relationship was found between Chinese and other East Asian populations. The present study contributed to the enrichment of the forensic Y-chromosome databases with a high resolution 23 Y-STR marker set, which is informative in forensic casework, such as familial searching and estimating the geographical origin of the offender.

Population genetics of 17 Y-chromosomal STRs loci in Garo and Santal tribal populations in Bangladesh

Allele frequencies and haplotype diversity of 17 Y-chromosomal short tandem repeat (STR) loci included in Y-filer™ PCR amplification kit were studied in 120 Garo and 139 Santal male individuals residing in two distinct regions of Bangladesh. A total of 99 different haplotypes from Garo and 129 different haplotypes from Santal individuals were observed with a corresponding discrimination capacity (DC) of 0.825 and 0.928, respectively. A comparison of the studied data with the published data from Y-STR haplotype reference database (YHRD) based on AMOVA revealed that the Garo population is closely related to Tripuri population from Tripura, India and Santal population moderately close to Munda population from Jharkhand, India. The mainstream Bengali population resides at a significant genetic distance from these two studied populations.

Population genetic data for 17 Y STR markers from Benghazi (East Libya)

The seventeen Y-STR loci included in the AmpFℓSTR® Yfiler™ PCR Amplification kit (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a/b, DYS438, DYS439, DYS437, DYS448, DYS458, DYS456, DYS635, and Y-GATA-H4) were used to type a sample population of 238 males from eastern Libya (Benghazi region). Of 238 observed haplotypes, 214 were unique (90%) and 24 (10%) were found more than once. The 17 loci gave a discriminating power of 0.999. DYS458 showed the highest diversity as a single-locus marker (0.73). Allelic frequencies and gene diversities for each Y-STR locus were determined. The high haplotype diversity and discrimination capacity (0.996) demonstrate the utility of these loci for human identification in forensic applications. Comparative analysis with Y-STR datasets of relevant populations and submission of the haplotypes to the Y-STR Haplotype Reference Database (YHRD) was undertaken.

Diversity of 17-locus Y-STR haplotypes in Upper (Southern) Egyptians

Seventeen Y-STR loci included in the AmpFℓSTR ® Yfiler™ PCR Amplification kit were typed in a population sample of 208 males from Upper (South) Egypt. Of 204 observed haplotypes, 200 were unique (96.6%) and 4 were found twice each. The 17 loci gave a discriminating power of 0.9998. DYS458 showed the highest diversity as a single-locus marker ( h = 0.868) along with a high frequency of microvariants and new alleles (22% of the sample). Other loci revealed duplicated and null alleles. Comparative analysis with Y-STR datasets of relevant populations and submission of the haplotypes to the Y-STR Haplotype Reference Database (YHRD) were undertaken.

Population data for 15 Y-chromosome STRs in a population sample from Quito (Ecuador)

Population frequencies for the 9 Y-STR loci included in the “minimal haplotype” from Y-STR Haplotype Reference Database (YHRD), plus other 6 Y-STRs (DYS437, DYS438, DYS439, GATA A7.2, GATA H4 and GATA A10) were obtained for a sample of 120 males from Quito (Ecuador). One hundred and sixteen unique haplotypes were identified within the sample. Haplotype diversity (0.9994) was among the highest in comparison to other populations from Iberia and South-America. Genetic distances were calculated and our sample presented significative differences with all other samples, the lowest values being with a Guinean sample.

Diversity of 26-locus Y-STR haplotypes in a Nepalese population sample: Isolation and drift in the Himalayas

Twenty-six Y-chromosomal short tandem repeat (STR) loci were amplified in a sample of 769 unrelated males from Nepal, using two multiplex polymerase chain reaction (PCR) assays. The 26 loci gave a discriminating power of 0.997, with 59% unique haplotypes, and the highest frequency haplotype occurring 12 times. We identified novel alleles at four loci, microvariants at a further two, and nine examples of amelogenin-Y deletions (1.2%). Comparison with a similarly sized Bhutanese sample typed with the same markers suggested histories of isolation and drift, with drift having a greater effect in Bhutan. Extended (11-locus) haplotypes for the Nepalese samples have been submitted to the Y-STR Haplotype Reference Database (YHRD).

26-Locus Y-STR typing in a Bhutanese population sample

26 Y chromosome short tandem repeat (STR) loci were amplified in a sample of 856 unrelated males from Bhutan, using two multiplex polymerase chain reaction (PCR) assays. The first multiplex is the Y-STR 20plex described by Butler et al. [J.M. Butler, R. Schoske, P.M. Vallone, M.C. Kline, A.J. Redd, M.F. Hammer, A novel multiplex for simultaneous amplification of 20 Y chromosome STR markers, Forensic Sci. Int. 129 (2002) 10–24], and the second is a novel (but overlapping) 14plex that targets six additional Y-STRs (DYS425, DYS434, DYS435, DYS436, DYS461, DYS462) and also amplifies the amelogenin locus. The 26-loci give a discriminating power of 0.9957, though even at this resolution one haplotype occurs 24 times. We identify novel alleles at five loci and microvariants at a further three, which were characterised by sequencing. Extended (11-locus) haplotypes for these samples have been submitted to the Y-STR Haplotype Reference Database (YHRD).

Y-chromosome STR haplotype profiling in the Mongolian population

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

Population data for Y-chromosome STR haplotypes from Piedmont (Italy)

Eight Y-chromosome STR loci (DYS19, DYS389-I, DYS389-II, DYS390, DYS391, DYS392, DYS393 and DYS385) were analysed in a sample of 236 unrelated males from four towns of Piedmont (Trino, Biella, Cavaglià, Postua). One hundred and fifty six different haplotypes were observed and 55 of them were not previously observed in the Y-STR Haplotype Reference Database ( http://www.ystr.org/).

Human Y-specific STR haplotypes in the Western Croatian population sample

Nine Y-chromosome STR loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385 and YCAII) were analysed in a sample of 101 unrelated males from Croatia. Allelic frequencies and gene diversities for each Y-STR locus and haplotype diversity were determined. Ninety-one different haplotypes were obtained from 101 unrelated males and 84 haplotypes were unique. Three most common haplotypes were shared by 3% of the sample, one of them was not found in the online Y-STR Haplotype Reference Database ( http://www.ystr.org/).

Portuguese population study with 16 Y-STR loci

The aim of this study was to present a Portuguese Population Database of 214 Southern Portugal samples studied with 16 Y-STR loci including the eight minimal Y-STR haplotype—DYS19, DYS390, DYS391, DYS392, DYS393, DYS389I/II, DYS385 and other Y-STR loci—GATA A7.1 (DYS460), GATA C4, GATA A7.2 (DYS461), GATA A10, GATA H4, DYS437, DYS438 and DYS439. In this study, 209 different haplotypes could be defined and 205 haplotypes were found just once. This database has a discrimination power of 97.7%, a haplotype diversity of 99.6% and 2.3% of shared haplotypes. Some samples do not match any sample in the Y-STR Haplotype Reference Database which assigned specific region characteristics to these population samples. Forty-three alleged father–child non-exclusion cases were also studied and two possible mutations have been detected in DYS439 and DYS393. Complex paternity investigation cases without alleged father have also been studied. In an autosomal STR exclusion case, the same 16 Y-STR haplotype was obtained between the excluded alleged father and the child.

How much more should the Y-STR Haplotype Reference Database increase to reach a pragmatic saturation level?

Empirical saturation curves can be a valuable tool for estimation of sampling effort required to detect an adequate number of Y-STR haplotypes, since they are independent of theoretical models. Nevertheless, they were shown to be highly dependent on current sample size, as detected when applied to the study of the Y-STR Haplotype Reference Database, at a European scale. The influence of geography on sampling saturation was difficult to evaluate due to high heterogeneity of the sample sizes in the database, but at the European level, it is probably very slight. Concerning the present status of the database, it is expected that a fivefold increase in the sample size of the database (up to 60,000 individuals) will reveal twice the current number of haplotypes (11,308 haplotypes), reaching a pragmatic saturation level of 5% (that is, when along with a sample increment of M individuals, no more than 0.05× M “new” haplotypes are added).