cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22225191.v1
title: Forensic efficiency evaluation of a novel multiplex panel of InDels and STRs in the Guizhou Han population and its phylogenetic relationships with other reference populations

description: Insertion/deletion polymorphism (InDel), as the third genetic marker, has been given a lot of attention by forensic geneticists since it has the advantages of extensive distributions in the human genome, small amplicon, and low mutation rate. However, the extant InDel panels were only viewed as supplemental tools for kinship analyses. In addition, these panels were not conductive to mixture deconvolution because InDels in these panels mainly displayed two alleles. The purpose of this study is to investigate genetic distributions of a novel panel of InDels and STRs in the Guizhou Han population; assess the forensic application value of the panel; and conduct population genetic analyses of the Guizhou Han and other reference populations based on the overlapping loci. The bloodstain samples of 209 Guizhou Han were gathered and genotyped by the novel panel. Allelic frequencies and forensic parameters of two miniSTRs and 59 InDels in the panel were estimated. In addition, we assessed phylogenetic relationships among the Guizhou Han and other reference populations by principal component analysis, <i>D<sub>A</sub></i> genetic distance, and neighbor-joining tree. A total of 139 alleles of 61 loci could be observed in the Guizhou Han population. Polymorphic information content values of 59 InDels were greater than 0.3 in the Guizhou Han population. The cumulative power of discrimination and probability of exclusion of two miniSTRs and 59 InDels in the Guizhou Han population were 0.999999999999999999999999997984 and 0.9999986, respectively. Principal component analysis of 14 populations showed that the Guizhou Han population located closer to Hunan Han and Southern Han Chinese (CHS) populations. Similar results were also discerned from <i>D<sub>A</sub></i> genetic distances and the neighbor-joining tree. To sum up, the novel panel could be employed for forensic personal identification and paternity testing in the Guizhou Han population as a promising independent tool. Besides, the principal component analysis and phylogenetic tree of the Guizhou Han and other compared populations revealed that the Guizhou Han population possesses close genetic affinities with Hunan Han, CHS, and Han Chinese in Beijing (CHB) populations.
DOI: 10.6084/m9.figshare.23622819
title: Sex-dependent association of DNA methylation in the coding region of the corticotropin-releasing hormone gene and schizophrenia spectrum disorder

description: Schizophrenia spectrum disorder (SSD) is a common mental disorder causing severe and chronic disability. Epigenetic changes in genes related to the hypothalamic–pituitary–adrenal (HPA) axis are believed to play an important role in SSD pathogenesis. The methylation status of the corticotropin-releasing hormone (<i>CRH</i>) gene, which is central to the HPA axis, has not been investigated in patients with SSD. We investigated the methylation status of the coding region of the <i>CRH</i> gene (hereafter, <i>CRH</i> methylation) using peripheral blood samples from patients with SSD. We used sodium bisulphite and MethylTarget to determine <i>CRH</i> methylation after collecting peripheral blood samples from 70 patients with SSD who had positive symptoms and 68 healthy controls. <i>CRH</i> methylation was significantly increased in patients with SSD, especially in male patients. Differences in <i>CRH</i> methylation were detectable in the peripheral blood of patients with SSD. Epigenetic abnormalities in the <i>CRH</i> gene were closely related to positive symptoms of SSD, suggesting that epigenetic processes may mediate the pathophysiology of SSD.
DOI: 10.6084/m9.figshare.22039337
title: Genetic polymorphisms of 19 X-STRs in populations of Hubei Han and Guangxi Zhuang and their comparisons with 13 other Chinese populations

description: A prerequisite for applying short tandem repeat (STR) kits is obtaining population allele and/or haplotype frequencies and forensic parameters. Firstly, we aimed to investigate the population data of 19 X-chromosomal STRs (X-STRs) included in the AGCU X19 STR kit in the Han people residing in Hubei Province, Central China, and the Zhuang people residing in the Guangxi Zhuang Autonomous Region of South China. Furthermore, we compared these population data with those for other Chinese populations. In total, 509 unrelated Han males and 266 unrelated Zhuang males were genotyped using the AGCU X19 STR kit. Allele frequencies, haplotype frequencies, and forensic parameters were computed, and genetic differences among 15 Chinese populations were analysed. The 19 X-STRs showed a high power of discrimination and high mean chance of exclusion, whether calculated using allele or haplotype frequencies. Major differences were found between Han and Oroqen, Uyghur, Mongolian, Tibetan, Li, and Yi populations. Aberrant biallelic patterns at DXS10159, DXS10134, and DXS10079 and allelic dropouts at DXS10164 were observed. The 19 X-STRs were highly polymorphic in the Hubei Han and Guangxi Zhuang populations, and the AGCU X19 STR kit was shown to be suitable for forensic casework.
DOI: 10.6084/m9.figshare.22225222.v1
title: Genetic polymorphisms and phylogenetic characteristics of Tibeto-Burman-speaking Lahu population from southwest China based on 41 Y-STR loci

description: 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. To enrich the available Y-STR data of this Chinese minority population and investigate its phylogenetic relationships with other reported populations. 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. 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. 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.
DOI: 10.6084/m9.figshare.23622821.v1
title: Geolocation prediction from STR genotyping: a pilot study in five geographically distinct global populations

description: Traditional CE-based STR profiles are highly useful for the purpose of individualisation. However, they do not give any additional information without the presence of the reference sample for comparison. To assess the usability of STR-based genotypes for the prediction of an individual’s geolocation. Genotype data from five geographically distinct populations, i.e. Caucasian, Hispanic, Asian, Estonian, and Bahrainian, were collected from the published literature. A significant difference (<i>p</i> &lt; 0.05) in the observed genotypes was found between these populations. D1S1656 and SE33 showed substantial differences in their genotype frequencies across the tested populations. SE33, D12S391, D21S11, D19S433, D18S51, and D1S1656 were found to have the highest occurrence of “unique genotype’s” in different populations. In addition, D12S391 and D13S317 exhibited distinct population-specific “most frequent genotypes.” Three different prediction models have been proposed for genotype to geolocation prediction, i.e. (i) use of unique genotypes of a population, (ii) use of the most frequent genotype, and (iii) a combinatorial approach of unique and most frequent genotypes. These models could aid the investigating agencies in cases where no reference sample is available for comparison of the profile.
DOI: 10.6084/m9.figshare.22225189
title: Genetic polymorphism of 27 Y-STR loci in Kazakh populations from Eastern Kazakhstan

description: The establishment of a national haplotype database is important for forensic and genetic applications and requires studying genetic polymorphisms at Y-STR sites. However, the genetic structure of the Eastern Kazakhstan population is poorly characterised. To investigate the genetic polymorphisms of 27 Y-STR loci in the Kazakh population from Eastern Kazakhstan and analyse the population genetic relationships of the Eastern Kazakhs with other populations. The Yfiler Plus kit was utilised to genotype 246 healthy, unrelated males from Eastern Kazakhstan. Based on the raw data, haplotype and allele frequencies along with forensic parameters were calculated, and an MDS plot was constructed. A total of 207 haplotypes were detected, of which 186 were unique. The haplotype diversity and discrimination capacity were 0.997 and 0.841, respectively. Population comparisons showed that Eastern Kazakhs have close genetic relationships with Kazakhs from Xinjiang, China. At the same time, a difference was found between the studied population and the previous one in the same part of Kazakhstan. The obtained haplotypes will help to expand the Kazakhstan Y-chromosome reference database and will be useful for future genetic research and forensic applications.
DOI: 10.6084/m9.figshare.22225189.v1
title: Genetic polymorphism of 27 Y-STR loci in Kazakh populations from Eastern Kazakhstan

description: The establishment of a national haplotype database is important for forensic and genetic applications and requires studying genetic polymorphisms at Y-STR sites. However, the genetic structure of the Eastern Kazakhstan population is poorly characterised. To investigate the genetic polymorphisms of 27 Y-STR loci in the Kazakh population from Eastern Kazakhstan and analyse the population genetic relationships of the Eastern Kazakhs with other populations. The Yfiler Plus kit was utilised to genotype 246 healthy, unrelated males from Eastern Kazakhstan. Based on the raw data, haplotype and allele frequencies along with forensic parameters were calculated, and an MDS plot was constructed. A total of 207 haplotypes were detected, of which 186 were unique. The haplotype diversity and discrimination capacity were 0.997 and 0.841, respectively. Population comparisons showed that Eastern Kazakhs have close genetic relationships with Kazakhs from Xinjiang, China. At the same time, a difference was found between the studied population and the previous one in the same part of Kazakhstan. The obtained haplotypes will help to expand the Kazakhstan Y-chromosome reference database and will be useful for future genetic research and forensic applications.
DOI: 10.6084/m9.figshare.22225222
title: Genetic polymorphisms and phylogenetic characteristics of Tibeto-Burman-speaking Lahu population from southwest China based on 41 Y-STR loci

description: 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. To enrich the available Y-STR data of this Chinese minority population and investigate its phylogenetic relationships with other reported populations. 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. 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. 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.
DOI: 10.6084/m9.figshare.23622821
title: Geolocation prediction from STR genotyping: a pilot study in five geographically distinct global populations

description: Traditional CE-based STR profiles are highly useful for the purpose of individualisation. However, they do not give any additional information without the presence of the reference sample for comparison. To assess the usability of STR-based genotypes for the prediction of an individual’s geolocation. Genotype data from five geographically distinct populations, i.e. Caucasian, Hispanic, Asian, Estonian, and Bahrainian, were collected from the published literature. A significant difference (<i>p</i> &lt; 0.05) in the observed genotypes was found between these populations. D1S1656 and SE33 showed substantial differences in their genotype frequencies across the tested populations. SE33, D12S391, D21S11, D19S433, D18S51, and D1S1656 were found to have the highest occurrence of “unique genotype’s” in different populations. In addition, D12S391 and D13S317 exhibited distinct population-specific “most frequent genotypes.” Three different prediction models have been proposed for genotype to geolocation prediction, i.e. (i) use of unique genotypes of a population, (ii) use of the most frequent genotype, and (iii) a combinatorial approach of unique and most frequent genotypes. These models could aid the investigating agencies in cases where no reference sample is available for comparison of the profile.
DOI: 10.6084/m9.figshare.24279110
title: Unveiling genetic diversity and forensic utility of SureID® human DNA identification kits: a comprehensive analysis of 44 autosomal STR loci in English and Irish populations

description: <b>Background:</b> Human identification and kinship testing in forensic science rely on Short Tandem Repeat (STR) multiplex kits, typically containing loci recommended by standard sets. However, complementary kits with additional STR loci can be valuable in complex cases. Allele frequency databases specific to the population are essential for accurate forensic analysis. <b>Aim:</b> This study aimed to generate allele frequencies and population genetic data for 44 autosomal STR loci from SureID<sup>®</sup> PanGlobal and 27comp kits in English and Irish populations for forensic casework, human identification, and kinship testing. <b>Subjects and methods:</b> Buccal swab samples from 645 White Caucasians (365 English, 280 Irish) were collected. DNA was extracted and amplified using the mentioned kits. Quality control, statistical analysis, and genetic distance calculations were performed. <b>Results:</b> Both kits demonstrated robustness with no significant deviations from Hardy-Weinberg Equilibrium (HWE). Variant alleles and minor discordances between kits were observed. Syntenic STR pairs were identified but showed no significant linkage. A close genetic relationship was found between English and Irish populations, allowing for combined databases. <b>Conclusions:</b> The SureID<sup>®</sup> PanGlobal and 27comp kits showed high discriminatory power and reliability in the English and Irish populations. Care is needed when handling variant alleles, discordances, and syntenic loci. Combining data from both populations is feasible for a comprehensive database. Further studies are required to explore their effectiveness in diverse populations.
DOI: 10.6084/m9.figshare.22922081.v1
title: The genetic structure and admixture of Manchus and Koreans in northeast China

description: The fine-scale genetic profiles and population history of Manchus and Koreans remain unclear. To infer a fine-scale genetic structure and admixture of Manchu and Korean populations. We collected and genotyped 16 Manchus from Liaoning and 18 Koreans from Jilin province with about 700K genome-wide SNPs. We analysed the data using principal component analysis (PCA), ADMIXTURE, Fst, TreeMix, <i>f</i>-statistics, <i>qpWave</i>, and <i>qpAdm</i>. Manchus and Koreans showed a genetic affinity with northern East Asians. Chinese Koreans showed a long-term genetic continuity with Bronze Age populations from the West Liao River and had a strong affinity with Koreans in South Korea and Japan. Manchus had a different genetic profile compared with other Tungusic populations since the Manchus received additional genetic influence from the southern Chinese but didn’t have West Eurasian-related admixture. The genetic formation of Manchus involving southern Chinese was consistent with the extensive interactions between Manchus and populations from central and southern China. The large-scale genetic continuity between ancient West Liao River farmers and Koreans highlighted the role farming expansion played in the peopling of the Korean Peninsula.
DOI: 10.6084/m9.figshare.24279110.v1
title: Unveiling genetic diversity and forensic utility of SureID® human DNA identification kits: a comprehensive analysis of 44 autosomal STR loci in English and Irish populations

description: <b>Background:</b> Human identification and kinship testing in forensic science rely on Short Tandem Repeat (STR) multiplex kits, typically containing loci recommended by standard sets. However, complementary kits with additional STR loci can be valuable in complex cases. Allele frequency databases specific to the population are essential for accurate forensic analysis. <b>Aim:</b> This study aimed to generate allele frequencies and population genetic data for 44 autosomal STR loci from SureID<sup>®</sup> PanGlobal and 27comp kits in English and Irish populations for forensic casework, human identification, and kinship testing. <b>Subjects and methods:</b> Buccal swab samples from 645 White Caucasians (365 English, 280 Irish) were collected. DNA was extracted and amplified using the mentioned kits. Quality control, statistical analysis, and genetic distance calculations were performed. <b>Results:</b> Both kits demonstrated robustness with no significant deviations from Hardy-Weinberg Equilibrium (HWE). Variant alleles and minor discordances between kits were observed. Syntenic STR pairs were identified but showed no significant linkage. A close genetic relationship was found between English and Irish populations, allowing for combined databases. <b>Conclusions:</b> The SureID<sup>®</sup> PanGlobal and 27comp kits showed high discriminatory power and reliability in the English and Irish populations. Care is needed when handling variant alleles, discordances, and syntenic loci. Combining data from both populations is feasible for a comprehensive database. Further studies are required to explore their effectiveness in diverse populations.
DOI: 10.6084/m9.figshare.22922081
title: The genetic structure and admixture of Manchus and Koreans in northeast China

description: The fine-scale genetic profiles and population history of Manchus and Koreans remain unclear. To infer a fine-scale genetic structure and admixture of Manchu and Korean populations. We collected and genotyped 16 Manchus from Liaoning and 18 Koreans from Jilin province with about 700K genome-wide SNPs. We analysed the data using principal component analysis (PCA), ADMIXTURE, Fst, TreeMix, <i>f</i>-statistics, <i>qpWave</i>, and <i>qpAdm</i>. Manchus and Koreans showed a genetic affinity with northern East Asians. Chinese Koreans showed a long-term genetic continuity with Bronze Age populations from the West Liao River and had a strong affinity with Koreans in South Korea and Japan. Manchus had a different genetic profile compared with other Tungusic populations since the Manchus received additional genetic influence from the southern Chinese but didn’t have West Eurasian-related admixture. The genetic formation of Manchus involving southern Chinese was consistent with the extensive interactions between Manchus and populations from central and southern China. The large-scale genetic continuity between ancient West Liao River farmers and Koreans highlighted the role farming expansion played in the peopling of the Korean Peninsula.
DOI: 10.6084/m9.figshare.23808605
title: Genetic diversity of 23 Y-STR loci of the Lisu ethnic minority residing in Chuxiong Yi Autonomous Prefecture, Yunnan province, Southwest China

description: The Lisu group is a unique minority in Yunnan province. However, there is a lack of Y-STR population data for Chinese Lisu and the genetic structure of the Lisu group and other populations is unclear. To provide genetic data for 23 Y-STRs in the Chinese Lisu population from Chuxiong Yi Autonomous Prefecture, as well as to analyse population genetic relationships between Chinese Lisu ethnic minority and other reference groups. 423 unrelated healthy Lisu males were genotyped using the PowerPlex® Y23 system. Forensic parameters were calculated according to the previously published studies. Genetic structure analysis among Chinese Lisu and other populations was conducted using the YHRD’s AMOVA tools. Gene diversity (GD) ranged from 0.2,466 (DYS438) to 0.8,945 (DYS385a/b) among the 23 Y-STR loci. According to haplotype analysis, 323 different haplotypes were obtained, out of which 271 were unique. The haplotype diversity (HD) and discrimination capacity (DC) were 0.9,977 and 0.7,636, respectively. MDS plot indicated that the Chuxiong Lisu group is genetically related to the Yunnan Yi group. This is the first report on Y-STR population data for the Chinese Lisu population. These data would be valuable for forensic applications.
DOI: 10.6084/m9.figshare.23808605.v1
title: Genetic diversity of 23 Y-STR loci of the Lisu ethnic minority residing in Chuxiong Yi Autonomous Prefecture, Yunnan province, Southwest China

description: The Lisu group is a unique minority in Yunnan province. However, there is a lack of Y-STR population data for Chinese Lisu and the genetic structure of the Lisu group and other populations is unclear. To provide genetic data for 23 Y-STRs in the Chinese Lisu population from Chuxiong Yi Autonomous Prefecture, as well as to analyse population genetic relationships between Chinese Lisu ethnic minority and other reference groups. 423 unrelated healthy Lisu males were genotyped using the PowerPlex® Y23 system. Forensic parameters were calculated according to the previously published studies. Genetic structure analysis among Chinese Lisu and other populations was conducted using the YHRD’s AMOVA tools. Gene diversity (GD) ranged from 0.2,466 (DYS438) to 0.8,945 (DYS385a/b) among the 23 Y-STR loci. According to haplotype analysis, 323 different haplotypes were obtained, out of which 271 were unique. The haplotype diversity (HD) and discrimination capacity (DC) were 0.9,977 and 0.7,636, respectively. MDS plot indicated that the Chuxiong Lisu group is genetically related to the Yunnan Yi group. This is the first report on Y-STR population data for the Chinese Lisu population. These data would be valuable for forensic applications.