Xiaoye Jin

Phylogenic analysis and forensic genetic characterization of Chinese Uyghur group via autosomal multi STR markers

We investigated the allelic frequencies and forensic descriptive parameters of 23 autosomal short tandem repeat loci in a randomly selected sample of 1218 unrelated healthy Uyghur individuals residing in the Xinjiang Uyghur Autonomous Region, northwest China. A total of 281 alleles at these loci were identified and their corresponding allelic frequencies ranged from 0.0004 to 0.5390. The combined match probability and combined probability of exclusion of all loci were 5.192 × 10-29 and 0.9999999996594, respectively. The results of population genetic study manifested that Uyghur had close relationships with those contiguous populations, such as Xibe and Hui groups. In a word, these autosomal short tandem repeat loci were highly informative in Uyghur group and the multiplex PCR system could be used as a valuable tool for forensic caseworks and population genetic analysis.We investigated the allelic frequencies and forensic descriptive parameters of 23 autosomal short tandem repeat loci in a randomly selected sample of 1218 unrelated healthy Uyghur individuals residing in the Xinjiang Uyghur Autonomous Region, northwest China. A total of 281 alleles at these loci were identified and their corresponding allelic frequencies ranged from 0.0004 to 0.5390. The combined match probability and combined probability of exclusion of all loci were 5.192 × 10−29 and 0.9999999996594, respectively. The results of population genetic study manifested that Uyghur had close relationships with those contiguous populations, such as Xibe and Hui groups. In a word, these autosomal short tandem repeat loci were highly informative in Uyghur group and the multiplex PCR system could be used as a valuable tool for forensic caseworks and population genetic analysis.

Autosomal InDel polymorphisms for population genetic structure and differentiation analysis of Chinese Kazak ethnic group

In the present study, we assessed the genetic diversities of the Chinese Kazak ethnic group on the basis of 30 well-chosen autosomal insertion and deletion loci and explored the genetic relationships between Kazak and 23 reference groups. We detected the level of the expected heterozygosity ranging from 0.3605 at HLD39 locus to 0.5000 at HLD136 locus and the observed heterozygosity ranging from 0.3548 at HLD39 locus to 0.5283 at HLD136 locus. The combined power of discrimination and the combined power of exclusion for all 30 loci in the studied Kazak group were 0.999999999999128 and 0.9945, respectively. The dataset generated in this study indicated the panel of 30 InDels was highly efficient in forensic individual identification but may not have enough power in paternity cases. The results of the interpopulation differentiations, PCA plots, phylogenetic trees and STRUCTURE analyses showed a close genetic affiliation between the Kazak and Uigur group.

Forensic efficiency estimate and phylogenetic analysis for Chinese Kyrgyz ethnic group revealed by a panel of 21 short tandem repeats

Short tandem repeats (STRs) with a high level of polymorphisms and convenient detection method play an indispensable role in human population and forensic genetics. Recently, we detected the 21 autosomal non-combined DNA index system (non-CODIS) STR loci in a Kyrgyz ethnic group, calculated their forensic parameters and analysed its genetic relationships with reference populations from China. In total, 168 alleles were observed at 21 non-CODIS STRs with corresponding allelic frequencies from 0.0016 to 0.4788. No significant deviations at these STRs were observed from the Hardy–Weinberg equilibrium. The values of cumulative power of discrimination and probability of exclusion for all the 21 non-CODIS STRs were 0.99999999999999999998835 and 0.9999994002, respectively. Furthermore, the analyses of phylogenetic trees, genetic distances and interpopulation differentiations demonstrated that the Kyrgyz group had relatively close genetic relationships with the Uygur and Kazak groups. These 21 non-CODIS STRs were characterized by high genetic diversities in the Kyrgyz group and could be applied as a robust tool for individual identification and kinship testing in forensic sciences.

Genetic structure and polymorphism analysis of Xinjiang Hui ethnic minority based on 21 STRs

In the present study, we calculated the allelic frequencies and forensic descriptive parameters of Hui ethnic minority on the basis of 21 short tandem repeat (STR) loci aiming at understanding population structure better and enriching population genetic database. Bloodstain samples of 506 unrelated healthy Hui individuals in Xinjiang Uygur Autonomous Region were collected. Altogether 268 alleles were observed and the allelic frequencies ranged from 0.0010 to 0.5306. The combined power of discrimination and the cumulative probability of exclusion of the 21 STR loci in Hui ethnic minority were 0.9999999999999999999999998697 and 0.9999999968, respectively. Population data obtained manifested that the panel of 21 STR loci could provide robust genetic information for individual identification and paternity testing involved in forensic applications for Huis of Xinjiang Region. Furthermore, the present results of interpopulation differentiations, phylogenetic trees and principal component analysis which were conducted based on the overlapping 16 STR loci revealed that Hui group was genetically close to Xibe ethnic group and Han populations from different regions.

Forensic molecular genetic diversity analysis of Chinese Hui ethnic group based on a novel STR panel

In present study, the genetic polymorphisms of 22 autosomal short tandem repeat (STR) loci were analyzed in 496 unrelated Chinese Xinjiang Hui individuals. These autosomal STR loci were multiplex amplified and genotyped based on a novel STR panel. There were 246 observed alleles with the allele frequencies ranging from 0.0010 to 0.3609. All polymorphic information content values were higher than 0.7. The combined power of discrimination and the combined probability of exclusion were 0.999999999999999999999999999426766 and 0.999999999860491, respectively. Based on analysis of molecular variance method, genetic differentiation analysis between the Xinjiang Hui and other reported groups were conducted at these 22 loci. The results indicated that there were no significant differences in statistics between Hui group and Northern Han group (including Han groups from Hebei, Henan, Shaanxi provinces), and significant deviations with Southern Han group (including those from Guangdong, Guangxi provinces) at 7 loci, and Uygur group at 10 loci. To sum up, these 22 autosomal STR loci were high genetic polymorphic in Xinjiang Hui group.

Genetic characteristics of 19 STRs in Chinese Uzbek ethnic and its phylogenetic relationships with other 24 populations

Allelic frequencies and genetic polymorphisms of 19 short tandem repeats loci were investigated so as to provide more genetic data for forensic applications in Chinese Uzbek group; besides, we evaluated phylogenetic relationships of Uzbek group with other populations. All loci were observed to conform to Hardy-Weinberg equilibrium after Bonferroni’s correction. Two hundred and nine alleles were identified in 212 unrelated healthy Uzbek individuals and their allelic frequencies ranged from 0.0024 to 0.5259. The cumulative discrimination power and cumulative probability of exclusion were 0.999999999999999999999996501 and 0.999999998759, respectively. The results of population differentiation comparison, principal component analysis, and phylogenetic tree revealed that Uzbek group had close relationships with Uyghur and Kazakh groups.

Genetic differentiation and forensic efficiency evaluation for Chinese Salar ethnic minority based on a 5-dye multiplex insertion and deletion panel

The present study investigated the genetic diversities of 30 autosomal insertion and deletion (InDel) loci of Investigator DIPplex kit (Qiagen) in Chinese Salar ethnic minority and explored the genetic relationships between the studied Salar group and other populations. The allelic frequencies of deletion alleles at the 30 InDel loci were in the range of 0.1739 (HLD64) to 0.8478 (HLD39). The discrimination power, polymorphism information content and probability of exclusion ranged from 0.4101 (HLD39) to 0.6447 (HLD136), 0.2247 (HLD39) to 0.3750 (HLD92) and 0.0400 (HLD39) to 0.2806 (HLD92), respectively. The observed and expected heterozygosity were in the range of 0.2348 (HLD39) to 0.5913 (HLD92), and 0.2580 (HLD39) to 0.5000 (HLD92), respectively. The cumulative discrimination power and probability of exclusion of the 30 loci reached 0.999999999993418 and 0.99039, respectively. The results of population genetic differentiation comparisons revealed that Salar group had similar allele distributions with Qinghai Tibetan, Xibe and Yi groups. Population Bayesian cluster analysis showed that there were similar ancestry components between Salar group and most Chinese populations. Besides, the principal components analysis and phylogenetic reconstructions further indicated that Salar group had intimate genetic relationships with Qinghai Tibetan and Xibe groups. In short, the results of the current studies indicated the genetic distributions of the 30 InDel loci in Salar group were relatively high genetic polymorphisms, which could be used in forensic individual identifications and as a supplementary tool for complex paternity testing.

Population Genetic Diversity and Clustering Analysis for Chinese Dongxiang Group With 30 Autosomal InDel Loci Simultaneously Analyzed

In comparison with the most preferred genetic marker utilized in forensic science (STR), insertion/deletion analysis possesses further benefits, like absence of stutter peak, low mutation rate, and enabling mixed stain analysis. At present, a total of 169 unrelated healthy Dongxiang individuals dwelling in Dongxiang Autonomous county of Gansu province were recruited in our study to appraise the forensic usefulness of the panel including 30 autosomal diallelic genetic markers. The insertion allele frequencies were in the range of 0.1598 at HLD 111 to 0.8550 at HLD 118. The cumulative match of probability and the combined probability of exclusion were estimated based on independence of pairwise loci, with the values of 3.96 × 10-11 and 0.9886, respectively, which showed tremendous potential of this panel to be qualified for forensic personal identification in Chinese Dongxiang group. And it could also be used as a complementary tool for forensic parentage testing when combined with standard STR genetic markers. Furthermore, calculation of the DA distance and Fst values of pairwise populations, phylogenetic reconstruction, multidimensional scaling analysis, structure clustering analysis were also conducted to probe the genetic relationships between Dongxiang group and the other 30 reference populations. Results demonstrated that Dongxiang ethnic group might be genetically closer related with most Chinese populations involved in our study, especially Tibet groups, Xibe group, and several Han populations.

Genetic and structural characterization of 20 autosomal short tandem repeats in the Chinese Qinghai Han population and its genetic relationships and interpopulation differentiations with other reference populations

Abstract China is a multinational country composed of 56 ethnic groups of which the Han Chinese accounts for 91.60%. Qinghai Province is located in the northeastern part of the Qinghai–Tibet Plateau, has an area of 72.12 km2, and is the fourth largest province in China. In the present study, we investigated the genetic polymorphisms of 20 short tandem repeat (STR) loci in a Qinghai Han population, as well as its genetic relationships with other populations. A total of 273 alleles were identified in 2 000 individuals at 20 loci, and the allelic frequency ranged from 0.000 2 to 0.532 7. The 20 STR loci showed a relatively high polymorphic rate in the studied group. Observed and expected heterozygosities ranged 0.613 0–0.907 5 and 0.614 8–0.920 0, respectively. The combined power of discrimination, and the probability of exclusion in duo and trio cases were 0.999 999 999 999 999 999 999 999 34, 0.999 996 0 and 0.999 999 996 5, respectively. Analyses of interpopulation differentiation revealed that the most significant differences were found between the Qinghai Han and Malaysian, while no significant differences were found between the Qinghai Han and Han people from Shaanxi and Jiangsu. The results of principal component analysis, multidimensional scaling analysis and phylogenetic reconstructions also suggested the close relationships between the Qinghai Han and other two Han populations. The present results, therefore, indicated that these 20 STR loci could be used for paternity testing and individual identification in forensic applications, and may also provide information for the studies of genetic relationships between Qinghai Han and other groups.

Genetic variation and forensic characteristic analysis of 25 STRs of a novel fluorescence co-amplification system in Chinese Southern Shaanxi Han population

We analyzed the genetic polymorphisms of 15 autosomal and 10 Y-chromosomal STR loci in 214 individuals of Han population from Southern Shaanxi of China and studied the genetic relationships between Southern Shaanxi Han and other populations. We observed a total of 150 alleles at 15 autosomal STR loci with the corresponding allelic frequencies ranging from 0.0023 to 0.5210, and the combined power of discrimination and exclusion for the 15 autosomal STR loci were 0.99999999999999998866 and 0.999998491, respectively. For the 10 Y-STR loci, totally 100 different haplotypes were obtained, of which 94 were unique. The discriminatory capacity and haplotype diversity values of the 10 Y-STR loci were 0.9259 and 0.998269, respectively. The results demonstrated high genetic diversities of the 25 STR loci in the population for forensic applications. We constructed neighbor-joining tree and conducted principal component analysis based on 15 autosomal STR loci and conducted multidimensional scaling analysis and constructed neighbor-joining tree based on 10 Y-STR loci. The results of population genetic analyses based on both autosomal and Y-chromosome STRs indicated that the studied Southern Shaanxi Han population had relatively closer genetic relationship with Eastern Han population, and distant relationships with Croatian, Serbian and Moroccan populations.We analyzed the genetic polymorphisms of 15 autosomal and 10 Y-chromosomal STR loci in 214 individuals of Han population from Southern Shaanxi of China and studied the genetic relationships between Southern Shaanxi Han and other populations. We observed a total of 150 alleles at 15 autosomal STR loci with the corresponding allelic frequencies ranging from 0.0023 to 0.5210, and the combined power of discrimination and exclusion for the 15 autosomal STR loci were 0.99999999999999998866 and 0.999998491, respectively. For the 10 Y-STR loci, totally 100 different haplotypes were obtained, of which 94 were unique. The discriminatory capacity and haplotype diversity values of the 10 Y-STR loci were 0.9259 and 0.998269, respectively. The results demonstrated high genetic diversities of the 25 STR loci in the population for forensic applications. We constructed neighbor-joining tree and conducted principal component analysis based on 15 autosomal STR loci and conducted multidimensional scaling analysis and constructed neighbor-joining tree based on 10 Y-STR loci. The results of population genetic analyses based on both autosomal and Y-chromosome STRs indicated that the studied Southern Shaanxi Han population had relatively closer genetic relationship with Eastern Han population, and distant relationships with Croatian, Serbian and Moroccan populations.