cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24272174
title: Population genetic analysis of 12 X-STR markers in Slovakia

description: <b>Background:</b> During the last 20 years, X-chromosomal STR markers have become widely used in forensic genetics and paternity testing. Nevertheless, to exploit their full potential in any given population, a reliable reference dataset needs to be established. Since no relevant studies concerning these markers have been performed on the Slovak population so far, we decided to analyse several commonly used markers in this population. <b>Aim:</b> To create an informative set of Slovak population data concerning X-STR markers. <b>Subjects and methods:</b> We genotyped 378 individuals and analysed 12 loci (DXS10148, DX10135, DXS8378, DXS7132, DXS10079, DXS10074, DXS10103, HPRTB, DXS10101, DXS10146, DXS10134 and DXS742) localised in four distinct linkage groups. <b>Results:</b> Our analysis showed that the most informative marker is DXS10135 (PIC = 0,927) and the most informative linkage group (LG) is LG1 with 149 different haplotypes. This analysis also confirmed linkage disequilibrium for two pairs of markers (DX10101-DX10103 and DX10101-HPRTB) within LG3 in female samples. No statistically significant departure from HWE was observed for any locus. Moreover, the interpopulation comparison of 8 European populations based on haplotype frequencies showed no statistically significant F<sub>ST</sub> values in any LG, except for LG2 in comparison with the German population. <b>Conclusion:</b> We created a haplotype database for forensic analyses and kinship testing in Slovakia, as well as the CE dataset which can be used to further increase the decision power in similar analyses in the future.
DOI: 10.6084/m9.figshare.23660544.v1
title: Diversity in matrilineages among the Jomon individuals of Japan

description: The Jomon period of Japan is characterised by a unique combination of sedentary and hunting/gathering lifestyles, spanning for more than 10,000 years from the final Pleistocene to the Holocene. The transition from the preceding Palaeolithic period to the Jomon period is known to have begun with the appearance of pottery usage. However, knowledge of the genetic background of the Jomon people is still limited. We aimed to determine the population-scale complete mitogenome sequences of the Initial Jomon human remains and compare the occurrence of mitochondrial haplogroups in the Jomon period from temporal and regional perspectives. For human remains dated to 8200–8600 cal BP, we determined their complete mitogenome sequences using target enrichment-coupled next-generation sequencing. We successfully obtained the complete mitogenome sequences with high depth of coverage and high concordance on consensus sequences. These sequences differed by more than three bases each, except for two individuals having completely identical sequences. Co-existence of individuals with haplogroups N9b and M7a was first observed at the same archaeological site from the Initial Jomon period. The genetic diversity within the population was not found to be low even in the Initial Jomon period.
DOI: 10.6084/m9.figshare.24272174.v1
title: Population genetic analysis of 12 X-STR markers in Slovakia

description: <b>Background:</b> During the last 20 years, X-chromosomal STR markers have become widely used in forensic genetics and paternity testing. Nevertheless, to exploit their full potential in any given population, a reliable reference dataset needs to be established. Since no relevant studies concerning these markers have been performed on the Slovak population so far, we decided to analyse several commonly used markers in this population. <b>Aim:</b> To create an informative set of Slovak population data concerning X-STR markers. <b>Subjects and methods:</b> We genotyped 378 individuals and analysed 12 loci (DXS10148, DX10135, DXS8378, DXS7132, DXS10079, DXS10074, DXS10103, HPRTB, DXS10101, DXS10146, DXS10134 and DXS742) localised in four distinct linkage groups. <b>Results:</b> Our analysis showed that the most informative marker is DXS10135 (PIC = 0,927) and the most informative linkage group (LG) is LG1 with 149 different haplotypes. This analysis also confirmed linkage disequilibrium for two pairs of markers (DX10101-DX10103 and DX10101-HPRTB) within LG3 in female samples. No statistically significant departure from HWE was observed for any locus. Moreover, the interpopulation comparison of 8 European populations based on haplotype frequencies showed no statistically significant F<sub>ST</sub> values in any LG, except for LG2 in comparison with the German population. <b>Conclusion:</b> We created a haplotype database for forensic analyses and kinship testing in Slovakia, as well as the CE dataset which can be used to further increase the decision power in similar analyses in the future.
DOI: 10.6084/m9.figshare.22225224
title: Haplotypic polymorphisms and forensic applications in Chinese Hunan Han population based on a series of Y-STR loci: a perspective of paternal inheritance

description: Hunan, a multinational province in China, possesses more than fifty ethnic groups, such as the Han, Yao, Tujia, Miao, and so on. 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. 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. 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. 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.
DOI: 10.6084/m9.figshare.23660292.v1
title: Genetic polymorphism and forensic efficiency of 21 autosomal STR loci from Shandong Han population in Northern China

description: Highly polymorphic autosomal STR loci are useful for understanding population structure better and for forensic application, however the non-CODIS STR loci in the Han population of Shandong, located in Northern China, are not well-characterised. To investigate population genetic polymorphism and forensic efficiency of 21 autosomal STR loci from the Shandong Han population in Northern China and reveal the genetic relationships with other populations both at home and abroad. In this study, population genetic data of 21 autosomal STR loci included in the Goldeneye DNA ID 22NC Kit that includes four CODIS loci and 17 non-CODIS loci were determined for 523 unrelated Han individuals in Shandong. Significant deviations from Hardy–Weinberg equilibrium were not observed. A total of 233 alleles were detected with allele frequencies ranging from 0.0010 to 0.3728. The combined power of discrimination was 0.99999999999999999999999990011134, and the combined power of exclusion was 0.99999999788131. Furthermore, in an analysis of population differentiation Nei’s standard genetic distance and multidimensional scaling analysis, which were conducted based on the overlapping 15 STR loci, revealed that the Shandong Han population was most closely related to populations in close geographic proximity. This study demonstrated that the 21 autosomal STR loci included in the Goldeneye<sup>TM</sup> DNA ID 22NC system are highly polymorphic and suitable for forensic identification and paternity testing in the Shandong Han population. Additionally, the present results enrich the population genetic database.
DOI: 10.6084/m9.figshare.23660544
title: Diversity in matrilineages among the Jomon individuals of Japan

description: The Jomon period of Japan is characterised by a unique combination of sedentary and hunting/gathering lifestyles, spanning for more than 10,000 years from the final Pleistocene to the Holocene. The transition from the preceding Palaeolithic period to the Jomon period is known to have begun with the appearance of pottery usage. However, knowledge of the genetic background of the Jomon people is still limited. We aimed to determine the population-scale complete mitogenome sequences of the Initial Jomon human remains and compare the occurrence of mitochondrial haplogroups in the Jomon period from temporal and regional perspectives. For human remains dated to 8200–8600 cal BP, we determined their complete mitogenome sequences using target enrichment-coupled next-generation sequencing. We successfully obtained the complete mitogenome sequences with high depth of coverage and high concordance on consensus sequences. These sequences differed by more than three bases each, except for two individuals having completely identical sequences. Co-existence of individuals with haplogroups N9b and M7a was first observed at the same archaeological site from the Initial Jomon period. The genetic diversity within the population was not found to be low even in the Initial Jomon period.
DOI: 10.6084/m9.figshare.24272170
title: Development of an Okinawa panel for biogeographic inference of Okinawans

description: The Precision ID Ancestry Panel with 165 SNP markers was unable to differentiate between mainland Japanese and Okinawa Japanese or to distinguish either of them from other East Asian populations. An Okinawa panel was developed with the aim of further separating Okinawa Japanese individuals from mainland Japanese and other Asian groups. Seventy-five SNPs were selected using the most informative markers from the literature. Further, 22 SNPs were selected to separate Okinawa Japanese at minimum SNPs. Samples were collected from 48 unrelated individuals from mainland Japan and 46 unrelated residents of the Okinawa prefecture. Data were evaluated by STRUCTURE, principal component, and GenoGeographer analyses. The 22 SNP set had similar levels of differentiation in STRUCTURE and PCA analyses as the 75 SNP set. GenoGeographer analysis showed that, out of the 46 Okinawa Japanese individuals, the 75 SNP and 22 SNP sets correctly assigned the Okinawan population as the most likely population of origin for 32 and 31 individuals, respectively. Neither SNP set could completely differentiate between Okinawa Japanese and other Asian groups, however, these sets should be useful for crime investigation, when the sample, cost and time are limited.
DOI: 10.6084/m9.figshare.22225224.v1
title: Haplotypic polymorphisms and forensic applications in Chinese Hunan Han population based on a series of Y-STR loci: a perspective of paternal inheritance

description: Hunan, a multinational province in China, possesses more than fifty ethnic groups, such as the Han, Yao, Tujia, Miao, and so on. 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. 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. 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. 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.
DOI: 10.6084/m9.figshare.22922489
title: Population data and phylogenetic analysis of 37 Y-STR loci in the Hui population from Yunnan Province, Southwest China

description: 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. 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. In total, 326 unrelated healthy male individuals were genotyped using the Goldeneye<sup>TM</sup> Y Plus PCR Amplification Kit. Genetic relationships between different populations were analysed using YHRD’s AMOVA tools. 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). 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.
DOI: 10.6084/m9.figshare.22922489.v1
title: Population data and phylogenetic analysis of 37 Y-STR loci in the Hui population from Yunnan Province, Southwest China

description: 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. 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. In total, 326 unrelated healthy male individuals were genotyped using the Goldeneye<sup>TM</sup> Y Plus PCR Amplification Kit. Genetic relationships between different populations were analysed using YHRD’s AMOVA tools. 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). 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.
DOI: 10.6084/m9.figshare.23660292
title: Genetic polymorphism and forensic efficiency of 21 autosomal STR loci from Shandong Han population in Northern China

description: Highly polymorphic autosomal STR loci are useful for understanding population structure better and for forensic application, however the non-CODIS STR loci in the Han population of Shandong, located in Northern China, are not well-characterised. To investigate population genetic polymorphism and forensic efficiency of 21 autosomal STR loci from the Shandong Han population in Northern China and reveal the genetic relationships with other populations both at home and abroad. In this study, population genetic data of 21 autosomal STR loci included in the Goldeneye DNA ID 22NC Kit that includes four CODIS loci and 17 non-CODIS loci were determined for 523 unrelated Han individuals in Shandong. Significant deviations from Hardy–Weinberg equilibrium were not observed. A total of 233 alleles were detected with allele frequencies ranging from 0.0010 to 0.3728. The combined power of discrimination was 0.99999999999999999999999990011134, and the combined power of exclusion was 0.99999999788131. Furthermore, in an analysis of population differentiation Nei’s standard genetic distance and multidimensional scaling analysis, which were conducted based on the overlapping 15 STR loci, revealed that the Shandong Han population was most closely related to populations in close geographic proximity. This study demonstrated that the 21 autosomal STR loci included in the Goldeneye<sup>TM</sup> DNA ID 22NC system are highly polymorphic and suitable for forensic identification and paternity testing in the Shandong Han population. Additionally, the present results enrich the population genetic database.
DOI: 10.6084/m9.figshare.24272170.v1
title: Development of an Okinawa panel for biogeographic inference of Okinawans

description: The Precision ID Ancestry Panel with 165 SNP markers was unable to differentiate between mainland Japanese and Okinawa Japanese or to distinguish either of them from other East Asian populations. An Okinawa panel was developed with the aim of further separating Okinawa Japanese individuals from mainland Japanese and other Asian groups. Seventy-five SNPs were selected using the most informative markers from the literature. Further, 22 SNPs were selected to separate Okinawa Japanese at minimum SNPs. Samples were collected from 48 unrelated individuals from mainland Japan and 46 unrelated residents of the Okinawa prefecture. Data were evaluated by STRUCTURE, principal component, and GenoGeographer analyses. The 22 SNP set had similar levels of differentiation in STRUCTURE and PCA analyses as the 75 SNP set. GenoGeographer analysis showed that, out of the 46 Okinawa Japanese individuals, the 75 SNP and 22 SNP sets correctly assigned the Okinawan population as the most likely population of origin for 32 and 31 individuals, respectively. Neither SNP set could completely differentiate between Okinawa Japanese and other Asian groups, however, these sets should be useful for crime investigation, when the sample, cost and time are limited.
DOI: 10.6084/m9.figshare.22310117
title: Forensic characteristics and genetic substructure analysis of the Handan Han population, Northern China

description: We analysed the forensic characteristics and substructure of the Handan Han population based on 36 Y-STR (short tandem repeat) and Y-SNP (single nucleotide polymorphism) markers. The two most dominant haplogroups in Handan Han, O2a2b1a1a1-F8 (17.95%) and O2a2b1a2a1a (21.51%), and their abundant downstream branches, reflected the strong expansion of the precursor of the Hans in Handan. The present results enrich the forensic database and explore the genetic relationships between Handan Han and other neighbouring and/or linguistically close populations, which suggests that the current concise overview of the Han intricate substructure remains oversimplified.
DOI: 10.6084/m9.figshare.22310117.v1
title: Forensic characteristics and genetic substructure analysis of the Handan Han population, Northern China

description: We analysed the forensic characteristics and substructure of the Handan Han population based on 36 Y-STR (short tandem repeat) and Y-SNP (single nucleotide polymorphism) markers. The two most dominant haplogroups in Handan Han, O2a2b1a1a1-F8 (17.95%) and O2a2b1a2a1a (21.51%), and their abundant downstream branches, reflected the strong expansion of the precursor of the Hans in Handan. The present results enrich the forensic database and explore the genetic relationships between Handan Han and other neighbouring and/or linguistically close populations, which suggests that the current concise overview of the Han intricate substructure remains oversimplified.
DOI: 10.6084/m9.figshare.23144109
title: Genetic analysis of 23 Y-STR loci in the Va population from Yunnan Province, Southwest China

description: 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. To establish the Y-chromosome Haplotype Reference Database of the Yunnan Va population and investigate the population genetic relationships with other geographically adjacent groups. 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. 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. 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.
DOI: 10.6084/m9.figshare.23144109.v1
title: Genetic analysis of 23 Y-STR loci in the Va population from Yunnan Province, Southwest China

description: 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. To establish the Y-chromosome Haplotype Reference Database of the Yunnan Va population and investigate the population genetic relationships with other geographically adjacent groups. 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. 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. 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.