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

Developmental validation of the STRSeqTyper122 kit for massively parallel sequencing of forensic STRs

Massively parallel sequencing allows for integrated genotyping of different types of forensic markers, which reduces DNA consumption, simplifies experimental processes, and provides additional sequence-based genetic information. The STRseqTyper122 kit genotypes 63 autosomal STRs, 16 X-STRs, 42 Y-STRs, and the Amelogenin locus. Amplicon sizes of 117 loci were below 300 bp. In this study, MiSeq FGx sequencing metrics for STRseqTyper122 were presented. The genotyping accuracy of this kit was examined by comparing to certified genotypes of NIST standard reference materials and results from five capillary electrophoresis-based kits. The sensitivity of STRseqTyper122 reached 125 pg, and > 80% of the loci were correctly called with 62.5 pg and 31.25 pg input genomic DNA. Repeatability, species specificity, and tolerance for DNA degradation and PCR inhibitors of this kit were also evaluated. STRseqTyper122 demonstrated reliable performance with routine case-work samples and provided a powerful tool for forensic applications.

Genetic Polymorphism Analysis of 24 Y-STRs in a Han Chinese Population in Luzhou, Southwest China

Han is the largest of China's 56 ethnic groups and the most populous ethnic group in the world. The Luzhou region is located in southwest China, at the junction of three provinces. The unique historical factors contribute to the genetic polymorphism information. Short tandem repeats (STRs) are highly polymorphic, but the polymorphism of the Y chromosomal STRs (Y-STRs) loci in the Luzhou region is still unclear. It is of great significance to provide Y-STRs genetic data for the Han population from the Luzhou areas of southwest China. A total of 910 unrelated male individuals of the Han population from the Luzhou area were recruited, and 24 Y-STRs were analyzed. The population structure and phylogenetic relationships were compared with those of another 11 related Han populations. A total of 893 different haplotypes were achieved from 910 samples, of which 877 (98.21%) haplotypes were unique. Haplotype diversity and discrimination were 0.999956 and 0.981319, respectively. The lowest genetic diversity of DYS437 is 0.4321, and the highest genetic diversity of DYS385a/b is 0.9642. Pair-to-pair genetic distance and relative probability values indicate that Luzhou Han people are close to Sichuan Han people, Guangdong Han people, and Hunan Han people, which is consistent with geographical distribution, historical influence, and economic development. The 24 Y-STR markers of the southwest Luzhou Han population were highly polymorphic, which provided us with genetic polymorphism information and enriched the population genetic database. Therefore, it is of great value to our forensic applications and population genetics research.

Loop-mediated isothermal amplification assay for fluorescence analysis and lateral flow detection of male DNA

Male DNA screening is important in forensic investigations, such as sexual assault cases. Although quantitative real-time PCR is a robust method for detection of male DNA, it is time-consuming and labor-intensive. We herein report the development of a male DNA-targeted loop-mediated isothermal amplification (LAMP) assay that can be used for both laboratory-based fluorescence analysis and on-site lateral flow detection. The two detection systems are independent, but we streamlined the reaction before the detection by introducing a fluorescence probe and biotin-labeled primer into a single reaction. This allowed the evaluation of fluorescence signal followed by lateral flow detection. Both the fluorescence and lateral flow analyses detected as low as 10 pg of male DNA. We also integrated an alkaline lysis method with our LAMP assay. The direct assay successfully detected male DNA from forensic samples without purification. The workflow requires only <40 min for fluorescence analysis and <45 min for lateral flow detection. Furthermore, when combined with a lateral flow strip, this workflow does not require any sophisticated instruments. These findings suggest that our assay is a promising strategy for on-site male DNA screening as well as laboratory-based testing.

Population genetic study of 17 Y-STR Loci of the Sorani Kurds in the Province of Sulaymaniyah, Iraq

Background

The Kurds as an ethnic group are believed to be a combination of earlier Indo-European tribes who migrated and inhabited a mountainous area thousands of years ago. However, as it is difficult to describe the precise history of their origin, it is necessary to investigate their population relationship with other geographical and ethnic groups.

Results

Seventeen Short Tandem Repeat markers on the Y chromosome (Y-STR) included in the AmpFLSTR™ Yfiler™ PCR Amplification Kit (Thermo Fisher Scientific, USA) were used to type DNA samples from the Sorani (Central) Kurdish population in Sulaymaniyah province. One hundred fifty-seven haplotypes were obtained from 162 unrelated male individuals. The highest and lowest gene diversities were DYS385a/b (GD = 0.848) and DYS392 (GD = 0.392), respectively. The haplotypes were used to predict the most likely haplogroups in the Sulaymaniyah population.

Conclusion

Haplogroup prediction indicated predominance (28%) of subclade J2 (44/157) in the Sorani Kurds, northeast of Iraq. The pairwise genetic distance results showed that the Kurdish group clustered along with Asian populations, whereas the furthest countries were Europeans and Africans.

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.

The Y chromosome and its use in forensic DNA analysis

Originally relatively ignored in forensic investigations because its genetic analysis lacks inference of individual identification, the value of Y chromosome analysis has been proven in cases of sexual assault, particularly where the amount of material left by a male assailant is limited in comparison with female DNA. All routine analysis of autosomal DNA, however, targets a gene (AMELY) on the Y chromosome in order to identify the sex of the DNA source and this is discussed in the context of the genetic structure of this male-specific chromosome. Short-tandem repeat markers on the chromosome are tested in dedicated multiplexes that have developed over time and these are described alongside international guidance as to their use in a forensic setting. As a marker of lineage, the Y chromosome provides additional tools to assist in the inference of ancestry, both geographical and familial and the value of Y chromosome testing is illustrated through descriptions of cases of criminal and historical interest. A decision to analyse the Y chromosome has to be considered in the context, not only of the circumstances of the case, but also with regard to the ethical questions it might raise, and these are discussed in relation to the cases that have been described in more detail in the accompanying online supplementary material.

Genetic characterisation for Yan'an Han population in Northern Shaanxi Province, China, via 38Y-STRs using Yfiler™ Platinum

BACKGROUND

Haplotype/allele frequency data of Y-chromosomal STR loci in ethnically diverse populations are essential for forensics, anthropology and genealogy. However, genetic structure and forensic characterisation of the Chinese Han population residing in Yan'an, in the Northern Shaanxi Province, remain unclear.

AIM

To assess forensic efficiency for 38 Y-Chromosomal STR loci in Yan'an Han population and reveal the population genetic relationships between Yan'an Han and other populations at a nationwide and worldwide level.

SUBJECTS AND METHODS

719 healthy unrelated males were genotyped using the Yfiler™ Platinum system. Haplotype/allele frequencies and forensic parameters were calculated. Multi-dimensional scaling plots (MDS) and neighbor-joining (N-J) tree were used to explore the population structure based on the pairwise gene distances (Rst).

RESULTS

A total of 707 haplotypes were identified, among which 697 unique haplotypes were observed (98.59%). The overall haplotype diversity (HD) and discrimination capacity (DC) were 0.9999 and 0.9833, respectively. Comprehensive population comparisons showed Yan'an Han is genetically closer to linguistically similar populations in China, and more related to East Asian populations around the world.

CONCLUSION

The present results give a unique insight into the Yan'an Han population via the set of 38 Y-STRs, which can be used for forensic practice and human genetics research.

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

BACKGROUND

Male-specifically inherited Y-STRs have been widely used in population genetics and forensic investigations.

METHODS

We genotyped and analyzed Y chromosome haplotypes of 408 unrelated Tibeto-Burman-speaking Yi male individuals from Guizhou using Goldeneye® Y-PLUS kit. Population comparisons between the Guizhou Yi and 67 reference groups were performed via the AMOVA, MDS, and phylogenetic relationship reconstruction.

RESULTS

A total of 389 alleles and 396 haplotypes could be detected, and the allelic frequencies ranged from 0.0025 to 0.9875. The haplotype diversity, random match probability, and discrimination capacity values were 0.9999, 0.0026, and 0.9900, respectively. The gene diversity (GD) of 36 Y-STR loci in the studied group ranged from 0.0248 (DYS645) to 0.9601 (DYS385a/b). Our newly genotyped Yi samples show a close affinity with other Tibeto-Burman speaking groups in China and Southeast Asia.

CONCLUSIONS

The population stratification was almost consistent with the geographic distribution and language-family, both among Chinese and worldwide ethnic groups. Our data may provide useful information for paternal lineage in the forensic application and population genetics, as well as evidence for archaeological and historical research.

Genetic structure and forensic characterisation of 36 Y-chromosomal STR loci in Hmong-Mien-speaking Miao population

BACKGROUND

Y-chromosomal short tandem repeats (Y-STRs) are widely used in paternity identification, pedigree investigation, and human population genetic history.

AIM

To investigate the Y-STR polymorphisms in a typical Miao population, and explore the genetic differentiation between the Miao population and reference groups.

SUBJECTS AND METHODS

We detected 36 Y-STRs genotyping in 455 unrelated Miao individuals from Guizhou province, and analysed genetic differentiation between the Miao population and 76 reference groups.

RESULTS

A total of 369 alleles were obtained, and the allele frequencies ranged from 0.0022 to 0.9802. In addition, the haplotype diversity, random match probability, and discrimination capacity values were 0.99997, 0.0022, and 0.9934, respectively. Moreover, the genetic relationships between Guizhou Miao and 76 ethnic populations showed that the population stratification was almost consistent with geographic distribution and language-family.

CONCLUSIONS

The 36 Y-STR loci in this study have good polymorphism distributions in the Guizhou Miao population, and therefore would be a useful tool in forensic identification and male parentage testing and even pedigree investigation.

The Y-chromosomal haplotype and haplogroup distribution of modern Switzerland still reflects the alpine divide as a geographical barrier for human migration

A sample of 606 Swiss individuals has been characterized for 27 Y-STR and 34 Y-SNPs, defining major European haplogroups. For the first time, a subsample from the southernmost part of Switzerland, the Italian speaking canton Ticino, has been included. The data reveals significant intra-national differences in the distribution of haplogroups R1b-U106, R1b-U152, I1 and J2a north and south of the alpine divide, with R1b-U152 being the most frequent haplogroup among all Swiss subpopulations, reaching 26 % in average and 53 % in the Ticino sample. In addition, a high percentage of haplogroup E1b1b-M35 in Eastern Switzerland corresponds well with data reported from Western Austria. In general, we detected a low level of differentiation between the subgroups north of the alpine divide. The dataset also revealed a variety of microvariants. Some of them were previously known to be associated with particular haplogroups. However, we discovered one microvariant in DYS533 that seems to be closely associated with haplogroup I2-P215 (xM223). This association had not yet been reported to date. The concordance study with two STR-kits suggests that the DYS533 microvariant is due to an InDel in the flanking regions of the marker. One individual carried a large deletion, frequently detected in people of East Asian ancestry, encompassing the amelogenin locus. To our knowledge, this is the first time that such a deletion has been observed within European haplogroup R1b-U152. This is the first comprehensive Y chromosomal dataset for Switzerland, demonstrating significant population substructure due to an intra-national geographical barrier.

Haplotype diversity and phylogenetic characteristics for Guanzhong Han population from Northwest China via 38 Y-STRs using Yfiler™ Platinum Amplification System

BACKGROUND

For better application in human forensic cases and population genetics research, it is imperative to investigate the genetic characteristics of Guanzhong Han population using enhanced Y-chromosomal short tandem repeats (Y-STR) detecting system with higher discriminating power than previous ones.

METHODS

In this study, 38 Y-STRs were profiled in 430 unrelated Chinese Han male individuals from Guanzhong region of Shaanxi Province, Northwest China, using the Yfiler™ Platinum PCR Amplification Kit. Haplotype frequencies and forensic parameters were calculated. Comprehensive population comparisons with geographically/ethnically different populations in China and other worldwide countries were performed.

RESULTS

A total of 422 different haplotypes were observed with the overall haplotype diversity (HD), discriminatory power (DC) and haplotype match probability (HMP) were 0.9999, 0.9814, and 0.0024, respectively. Guanzhong Han showed genetically affinity with Han ethnicity from Shanxi and Henan provinces, while far distant from Tibetan populations.

CONCLUSION

This study offered a unique insight into Guanzhong Han population, the 38 Y-STRs included in the the Yfiler™ Platinum system are highly polymorphic and informative and can be used for forensic practice and human genetic research.

Forensic characteristics and genetic affinity analyses of Xinjiang Mongolian group using a novel six fluorescent dye-labeled typing system including 41 Y-STRs and 3 Y-InDels

BACKGROUND

Y-chromosomal genetic marker haplotypes of individuals can define the paternal kinship or genealogies to which they belong and further provide clues for forensic individual identifications. Studying the genetic structure of the Mongolian group will help to bring to light the Mongolian ethnic origin, and explicate the genetic affinities among the studied and compared populations. Some forensic scientists have studied the genetic background of the Mongolian group based on different molecular genetic markers. These studies were of very great reference significance for the Mongolian group genetic research, whereas the investigation of Y-STR haplotype data in the Xinjiang Mongolian group is still insufficient.

METHODS

Genetic characteristics of 182 unrelated healthy male Mongolian individuals were revealed by 41 Y-chromosomal short tandem repeat and 3 insertion/deletion molecular genetic markers. Furthermore, analyses of molecular variance programs, multi-dimensional scaling plots, and phylogenetic tree reconstructions were operated to explore the genetic relationships of the Xinjiang Mongolian group with comparative 23 populations from China and 33 populations from worldwide nations.

RESULTS

The genetic diversity values ranged from 0.0641 (rs771783753) to 0.9502 (DYF387S1). A total of 165 distinct haplotypes were identified, of which 150 (90.91%) were unique. The discrimination capacity, match probability, and haplotype diversity of 44 loci were 0.9066, 0.0067, and 0.9988, respectively. Additionally, the Mongolian group had the most intimate relationship with Gansu Dongxiang (RST  = 0.0165), followed by HulunBuir Mongolian (RST  = 0.0187), Inner Mongolia Daur (RST  = 0.0202) as well as other three minority ethnic groups from the Xinjiang region (RST  < 0.05) in all compared Chinese populations, and clustered together with the majority of Asian populations in a worldwide scale.

CONCLUSIONS

Consequently, the 44 loci could be well applied in forensic applications of the Mongolian group. The haplotypes available in here made new contributions to the existing population genetic information and would be of great value in population studies.

Population genetic analysis of 36 Y-chromosomal STRs yields comprehensive insights into the forensic features and phylogenetic relationship of Chinese Tai-Kadai-speaking Bouyei

Male-specifically inherited Y-STRs, harboring the features of haploidy and lack of crossing over, have gained considerable attention in population genetics and forensic investigations. Goldeneye® Y-PLUS kit was a recently developed amplification system focused on the genetic diversity of 36 Y-chromosomal short tandem repeats (Y-STRs) in East Asians. However, no population data and corresponding forensic features were reported in China. Here, 36 Y-STRs were first genotyped in 400 unrelated healthy Tai-Kadai-speaking Bouyei male individuals. A total of 371 alleles and 396 haplotypes could be detected, and the allelic frequencies ranged from 0.0025 to 0.9875. The haplotype diversity, random match probability and discrimination capacity values were 0.9999, 0.0026 and 0.9900, respectively. The gene diversity (GD) of 36 Y-STR loci in the studied group ranged from 0.0248 (DYS645) to 0.9601 (DYS385a/b). Population comparisons between the Guizhou Bouyei and 80 reference groups were performed via the AMOVA, MDS, and phylogenetic relationship reconstruction. The results showed that the population stratification was almost consistent with the geographic distribution and language-family, both among Chinese and worldwide ethnic groups. Our newly genotyped Bouyei samples show a close affinity with other Tai-Kadai-speaking groups in China and Southeast Asia. Our data may provide useful information for paternal lineage in the forensic application and population genetics, as well as evidence for archaeological and historical research.

Profiling of 17 Y-STR loci in Mazandaran and Gilan provinces of Iran

Background/aim

The Y-chromosome mainly consists of heterochromatin regions that have a father-to-son inheritance. Short tandem repeat polymorphic (STRP) markers distributed all over the chromosome provide the opportunity for investigations in forensic medicine and ancestral lineage studies. Due to the existence of wide varieties of geographical and ethnic groups in Iran, studying Y-STRP markers is necessary for further applications. Here we investigated the provinces of Mazandaran and Gilan for the first time.

Materials and methods

Samples included 119 and 90 unrelated males from Mazandaran and Gilan, respectively. Using a PCR amplification kit, 17 Y-STRP markers were amplified and genotyping was conducted by capillary electrophoresis. Allele frequency, haplotype diversity (HD), and haplotype discrimination capacity (DC) were calculated. The populations were compared together and to neighboring countries including Afghanistan and Azerbaijan by F_ST index.

Results

A total of 204 unique haplotypes were observed. No uniqueness was observed between the two provinces. HD was 0.9993 and 0.9998 in Mazandaran and Gilan, respectively. DC was 0.9666 and 0.9888 for Mazandaran and Gilan, respectively. DYS385b and DYS391 had the most and least polymorphic content in both provinces, respectively. There was not a significant difference between these two provinces (F_ST = 0.0006 and P = 0.00) and neighboring countries.

Conclusion

The results highlight the effectiveness of these Y-STRP markers for male discrimination in the north of Iran. Using additional markers along with extended sample size would provide a better opportunity for removing matched haplotypes and introducing the best polymorphic markers in this specific population.