Guanglin He

Genetic polymorphism investigation of the Chinese Yi minority using PowerPlex® Y23 STR amplification system

Twenty-three Y-STR loci (DYS576, DYS389I, DYS389 II, DYS448, DYS19, DYS391, DYS481, DYS549, DYS533, DYS438, DYS437, DYS570, DYS635, DYS390, DYS439, DYS392, DYS393, DYS458 DYS456, DYS643, Y-GATA-H4, and DYS385a/b) included in the next-generation PowerPlex® Y23 System were first investigated in 311 unrelated, healthy male individuals from the Yi minority population residing in the Liangshan Yi Autonomous Prefecture, Sichuan, China. A total of 179 alleles and 297 haplotypes were discovered in the Yi group. In total, 285 haplotypes among them were unique, and the remaining 12 haplotypes were observed in two or three individuals. Haplotype discrimination capacity and haplotype diversity were 0.9550 and 0.9989, respectively. Genetic diversity ranged from 0.4550 (DYS437) to 0.9556 (DYS385a/b). Population comparisons between the Yi minority group and 10 Asian meta-populations comprising 58 individual populations were performed. Both multidimensional scaling plots and phylogenetic analyses demonstrated that the genetic structure of the Chinese Yi ethnicity was extremely different compared to Taiwan indigenous inhabitants among 10 Asian meta-populations. Additionally, the genetic structure resemblance of the Yi group was obtained from a geographically close population (Xuanwei Han) or similar language family groups (Thai populations). Besides, our study has demonstrated that the PowerPlex® Y23 System has high polymorphism in a Chinese Yi ethnic population and high discriminatory power for forensic purposes. Population data of the 23 Y-STR obtained from a Yi ethnic population has enriched the Chinese ethnic genetic information.

Forensic characteristics and phylogenetic analyses of the Chinese Yi population via 19 X-chromosomal STR loci

The demographic characteristics and genetic polymorphism data of 56 Chinese nationalities or 31 administrative divisions in Chinese mainland have repeatedly been the genetic research hotspots. While most genetic studies focused on some particular Chinese populations based on autosomal or Y-chromosomal genetic markers, the forensic characteristics and phylogenetic analyses of the seventh largest Chinese population (Yi ethnicity) on the X-chromosomal genetic markers are scarce. Here, allele frequencies and forensic statistical parameters for 19 X-chromosomal short tandem repeat loci (DXS7424-DXS101, DXS6789-DXS6809, DXS7423-DXS10134, DXS10103-HPRTB-DXS10101, DXS10159-DXS10162-DXS10164, DXS10148-DXS10135-DXS8378, and DXS7132-DXS10079-DXS10074-DXS10075) of 331 Chinese Yi individuals were obtained. All 19 X-chromosomal short tandem repeat (STR) loci in females were consistent with the Hardy-Weinberg equilibrium test. A total of 214 alleles were identified with the corresponding allele frequencies spanned from 0.0019 to 0.6106. The combined PE, PDF, and PDM were 0.9999999214, 0.9999999999999999999993, and 0.9999999999998, respectively. The high combined MECKrüger, MECKishida, MECDesmarais, and MECDesmarais Duo were achieved as 0.9999999617638, 0.9999999999971, 0.9999999999971, and 0.9999999931538, respectively. The findings suggested that the panel of 19 X-STR loci is highly polymorphic and informative in the Yi ethnic population and can be considered to be a powerful tool in forensic complex kinship identification. Population differentiation analyses among 12 populations indicated that significant differences in genetic structure were observed in between the Yi ethnicity and the Chinese Uyghur as well as Kazakh, and genetic homogeneity existed in similar ethno-origin or geographic origin populations.

Phylogenetic analysis among 27 Chinese populations and genetic polymorphisms of 20 autosomal STR loci in a Chinese Uyghur ethnic minority group

Abstract Allele frequency data and forensic statistical parameters were determined for 20 autosomal short tandem repeat (STR) loci of the PowerPlex 21 System in 214 unrelated healthy individuals of a Uyghur ethnic minority group living in Xinjiang province, northwest China. A total of 232 alleles were observed with the corresponding allele frequencies ranging from 0.0023 to 0.5304. All loci were consistent with Hardy–Weinberg equilibrium (HWE) after the Bonferroni correction (p > 0.0025). The combined probability of exclusion, power of discrimination, probability of matching value were 0.999999999, 0.9999999999999999999999995, and 4.78246 × 10−25, respectively. Our results revealed that the 20 STRs were highly polymorphic and informative, and could be suitable for forensic application, especially parentage test and personal identification. The further population comparison between the Uyghur and other 26 reference populations revealed that the loci of D13S317, TH01 and D6S1043 showed high ethnical specificity. Phylogenetic analysis based on 19 shared loci demonstrated that the Uyghur had a close genetic relationship with the Kazakh, but a distinct genetic distance with other Chinese populations from different ethnicity and regions.

Genetic diversity of 21 autosomal STR loci in the Han population from Sichuan province, Southwest China

Exploration of the ethnic origin and genetic differentiation of 56 Chinese officially recognized nationalities populations played a fundamental role in the research field of population genetics, forensic science, linguistics, anthropology, and archaeology. In the present study, population data of 21 autosomal STR loci (CSF1PO, D10S1248, D12S391, D13S317, D16S539, D18S51, D19S433, D21S11, D2S1338, D2S441, D3S1358, D5S818, D6S1043, D7S820, D8S1179, FGA, Penta D, Penta E, TH01, TPOX, and vWA) included in the AGCU EX22 kit in 2793 Southwest Han Chinese individuals was obtained and population genetic relationships among 28 Chinese populations were investigated. Our study indicated that the twenty-one autosomal STRs are highly polymorphic in the Sichuan Han population and can be used as a powerful tool in the routine forensic usage. MDS and phylogenetic analysis suggested that the Sichuan Han population kept a close genetic relationship with the southwest populations.

Genetic Diversity and Phylogenetic Differentiation of Southwestern Chinese Han: a comprehensive and comparative analysis on 21 non-CODIS STRs

Short tandem repeats (STRs), with high polymorphism and complex evolution information, play a significant role in genetic association studies like population genetics, molecular anthropology and human forensics. However, human genetic diversity has only been partially sampled and available for Southwest Chinese Han population, as well as the genetic architecture of this population remains uncharacterized. In this work, 368 unrelated Han individuals from Sichuan province were firstly genotyped with 21 non-CODIS autosomal STRs, and phylogenetic relationships along administrative (Han Chinese from different regions) and ethnic divisions (minority ethnic groups) were subsequently investigated. The CMP and CPE were 6.2796 × 10−20 and 0.9999999, respectively. Analysis of molecular variance (AMOVA), principal component analysis (PCA), multidimensional scaling plots (MDS) and phylogenetic analysis consistently demonstrated that the Southwest Han population had a close genetic relationship with the geographically close population (Hunan Han) and kept a distant genetic relationship with some ethnic groups, most prominently for Gansu Yugu and Fujian She. Furthermore, no significant genetic distinction between the Northern Han and Southern Han was observed. Aforementioned results suggested that these 21 STRs are highly polymorphic and informative, which are suitable for human identification and population genetics.

Genetic polymorphisms for 19 X-STR loci of Sichuan Han ethnicity and its comparison with Chinese populations

X-chromosomal short tandem repeats (X-STRs) can be serviced as a complementary tool in forensic deficiency cases and other complicated kinship identification. To investigate the genetic variation of the western Chinese Han population, genetic polymorphisms of 19 X-STR loci (DXS8378, DXS7423, DXS10148, DXS10159, DXS10134, DXS7424, DXS10164, DXS10162, DXS7132, DXS10079, DXS6789, DXS101, DXS10103, DXS10101, HPRTB, DXS6809, DXS10075, DXS10074 and DXS10135) included in the AGCU X19 PCR amplification kit were obtained from 201 Chinese Han individuals (108 females and 93 males) residing in Sichuan province, western China. A total of 211 alleles were found from the 19 X-STR loci, and 4-22 alleles were found for each locus with the corresponding allele frequencies spanned from 0.0034 to 0.6395. The combined PDF and PDM were 0.9999999999999999999992 and 0.9999999999997, respectively. The combined MECKrüger, MECKishida, MECDesmarais as well as MECDesmarais Duo were 0.999999958110254, 0.999999999996533, 0.999999999996695 and 0.999999992428394, respectively. The number of haplotypes observed in the seven linkage groups varied from 27 to 97 for 108 male individuals with the corresponding haplotype diversities spanned from 0.9424 (DXS7424-DXS101) to 0.9979 (DXS7132-DXS10079-DXS10075-DXS10074). The above-mentioned results indicated that the 19 X-STR loci and the seven linkage groups are highly polymorphic and informative in the Sichuan Han population. Results from population comparisons and phylogenetic analyses demonstrated that genetic heterogeneity widely existed between the Sichuan Han population and Xinjiang minority ethnic groups (Uyghur and Kazakh) and genetic affinity was identified in populations which possessed the same ethno-origin or close geographic origin.

Forensic characteristics and phylogenetic analysis of Hubei Han population in central China using 17 Y-STR loci

Currently, the largest national database within the Y chromosome haplotype reference database (YHRD, https://yhrd.org, release 53) is China, which has approximately 38000 Y chromosomal 17-marker (Yfiler) haplotypes. These haplotype profiles derived from the vast majority of Chinese administrative divisions, but no haplotype data was available for Hubei province, which is located in the Central China region. Herein, 429 unrelated male Chinese Han individuals residing in Hubei province were recruited and genotyped with 17 Y-STR loci. 115 alleles were identified with corresponding allele frequencies spanned from 0.0023 to 07506. The gene diversity (GD) values ranged from 0.3988 at DYS438 to 0.9573 at DYS385a/b. A total of 410 distinct haplotypes were obtained with the overall haplotype diversity (HD) and discrimination capacity (DC) was 0.9995 and 0.9557, respectively. Additionally, genetic relationships along administrative (Han Chinese from different provinces) and ethnic divisions (minority ethnic groups) were analyzed using analysis of molecular variance (AMOVA) tests and visualized by multidimensional scaling plots (MDS). The Han ethnicity including the Hubei Han shows a high genetic homogeneity all across China and significant genetic differences existed between the Hubei Han and some ethnic groups, most prominently for the Kazakhs and the Tibetans.

X-chromosomal STR-based genetic structure of Sichuan Tibetan minority ethnicity group and its relationships to various groups

The X-chromosomal short tandem repeats (STRs) with more informative than autosomal STRs in some complicated biological relationships identification due to its specific mode of genetic transmission can be used as a complementary tool in forensic case practices. In this study, we presented the population genetic data of 19 X-STRs, consisting of DXS10174, DXS10075, DXS10079, DXS101, DXS10101, DXS10103, DXS10134, DXS10135, DXS10148, DXS10159, DXS10162, DXS10164, DXS6789, DXS6809, DXS7132, DXS7423, DXS7424, DXS8378, and HPRTB loci, in a sample of 235 individuals of Tibetan nationality from Sichuan province, Southwest China. All 19 X-STR loci were consistent with Hardy-Weinberg equilibrium. The results showed that the combined power of discrimination in females and males are 0.999999999999999999997 and 0.9999999999997, respectively. In addition, the mean paternity exclusion chances based on the formula of MECKrüger, MECKishida, and MECDesmarais as well as MECDesmarais Duo are 0.99999991, 0.9999999999924, 0.9999999999929, and 0.999999985, respectively. In summary, our findings suggested that the AGCU X19 kit can be considered to serve as a high polymorphic information tool for forensic identification and kinship testing in the Sichuan Tibetan population. Furthermore, population genetic structure investigation between Sichuan Tibetan population and other 19 populations using PCA, MDS, and phylogenetic tree illustrated that significant genetic difference was observed between the Sichuan Tibetan and Malay, as well as the Xinjiang Uyghur 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.

Genetic diversity and phylogenetic characteristics of Chinese Tibetan and Yi minority ethnic groups revealed by non-CODIS STR markers

Non-CODIS STRs, with high polymorphism and allele frequency difference among ethnically and geographically different populations, play a crucial role in population genetics, molecular anthropology, and human forensics. In this work, 332 unrelated individuals from Sichuan Province (237 Tibetan individuals and 95 Yi individuals) are firstly genotyped with 21 non-CODIS autosomal STRs, and phylogenetic relationships with 26 previously investigated populations (9,444 individuals) are subsequently explored. In the Sichuan Tibetan and Yi, the combined power of discrimination (CPD) values are 0.9999999999999999999 and 0.9999999999999999993, and the combined power of exclusion (CPE) values are 0. 999997 and 0.999999, respectively. Analysis of molecular variance (AMOVA), principal component analysis (PCA), multidimensional scaling plots (MDS) and phylogenetic analysis demonstrated that Sichuan Tibetan has a close genetic relationship with Tibet Tibetan, and Sichuan Yi has a genetic affinity with Yunnan Bai group. Furthermore, significant genetic differences have widely existed between Chinese minorities (most prominently for Tibetan and Kazakh) and Han groups, but no population stratifications rather a homogenous group among Han populations distributed in Northern and Southern China are observed. Aforementioned results suggested that these 21 STRs are highly polymorphic and informative in the Sichuan Tibetan and Yi, which are suitable for population genetics and forensic applications.