Genetic diversities of 20 novel autosomal STRs in Chinese Xibe ethnic group and its genetic relationships with neighboring populations

Forensic Characterization, Genomic Variability and Ancestry Analysis of Six Populations from Odisha Using mtDNA SNPs and Autosomal STRs

Located on India's eastern coast, Odisha is known for its diverse tribes and castes. In the early days of genome sequencing technology, researchers primarily studied the Austroasiatic communities inhabiting this region to reconstruct the ancient origins and dispersal of this broad linguistic group. However, current research has shifted towards identifying population and individual-specific genome variation for forensic applications. This study aims to analyze the forensic efficiency and ancestry of six populations from Odisha. We assessed the SF mtDNA-SNP60™ PCR Amplification Kit by comparing it with PowerPlex® Fusion 6C System, a widely used autosomal STR (aSTR) kit, in an Indian cohort. Although the mtDNA SNP kit showed low discriminating power for individuals of a diverse population, it could identify deep lineage divergence. Also, we utilized mitochondrial and autosomal variation information to analyze the ancestry of six endogamous ethnic groups in Odisha. We observe two extremities-populations with higher West Asian affinity and those with East Asian affinity. This observation is in congruence with the existing information of their tribal and non-tribal affiliation. When compared with neighbouring populations from Central and Eastern India, multivariate analysis showed that the Brahmins clustered separately or with the Gopala, Kaibarta appeared as an intermediate, Pana and Kandha clustered with the Gonds, and Savara with the Munda tribes. Our findings indicate significant deep lineage stratification in the ethnic populations of Odisha and a gene flow from West and East Asia. The artefacts of unique deep lineage in such a diverse population will help in improving forensic identification. In addition, we conclude that the SF mtDNA-SNP60 PCR Amplification Kit may be used only as a supplementary tool for forensic analysis.

Forensic applicability of autosomal insertion/deletion loci in Chinese Daur ethnic group and genetic affinity evaluations between Daur group and reference populations

In present study, we evaluated the genetic diversities of 30 insertion/deletion (InDel) loci and analyzed the genetic relationships between Daur and other comparison populations. In the studied Daur group, any two InDel loci showed no linkage disequilibrium, and all loci showed no deviations from exact tests of Hardy-Weinberg equilibrium. Insertion allele frequencies at 30 InDel loci ranged from 0.1459 (HLD39) to 0.8774 (HLD118). The observed heterozygosity and expected heterozygosity values were ranged from 0.1984 (HLD118) to 0.5564 (HLD6) and 0.2155 (HLD118) to 0.5000 (HLD92 and HLD6), respectively. The combined power of discrimination and power of exclusion values were 0.999999999993428 and 0.9878, respectively, which indicated that this panel of 30 InDels could be used for individual identifications in Daur group. Population genetic analyses including pairwise fixation index, STRUCTURE analysis, principal component analysis, genetic distance, multidimensional scaling analysis and phylogenetic analysis demonstrated that the Daur group had the closer genetic relationships with the groups from western China in comparison with other continental populations.

Analysis of forensic genetic parameters of 22 autosomal STR markers (PowerPlex® Fusion System) in a population sample from Bosnia and Herzegovina

Background: Bosnia and Herzegovina is a multinational and multireligious country, located in the western part of the Balkan Peninsula. Migrations through history were a key factor in the genetic identity of the Bosnian-Herzegovinian population.Aim: To analyse genetic polymorphisms of 22 autosomal short tandem repeat (STR) loci in the population of Bosnia and Herzegovina and to compare STR allele frequencies for STR loci with the reference data for European populations.Subjects and methods: The study was conducted among 600 unrelated individuals from all regions of Bosnia and Herzegovina. Genotyping was performed using the PowerPlex^® Fusion amplification kit. Allele frequencies and statistical parameters were calculated, as well as the genetic distance among analysed populations through the construction of a neighbor-joining dendrogram.Results: STR loci included in the PowerPlex^® Fusion amplification kit showed high discriminatory power indicating their reliability for human identification and paternity testing. The neighbor-joining dendrogram based on the results of genetic distance analysis showed that the Bosnian and Herzegovinian population has the greatest genetic distance from Turkish and Hungarian populations and greatest similarity with Croatian, Slovenian, and Serbian populations.Conclusion: The results of this study strongly support the application of 22 autosomal genetic markers for paternity testing and personal identity testing and are in agreement with most previous human studies in the investigated human populations.

Genetic polymorphism and phylogenetic analyses of 21 non-CODIS STR loci in a Chinese Han population from Shanghai

BACKGROUND

Short tandem repeats (STRs) are essential genetic markers for forensic applications and population estimations; thus the population genetics of STR loci have been extensively studied and discussed.

METHODS

In the present study, we detected 21 autosomal noncombined DNA index system (non-CODIS) STR loci in a Chinese Han population from Shanghai, calculated their forensic parameters and analyzed their genetic relationships with reported reference populations in mainland China.

RESULTS

A total of 173 alleles were observed, with corresponding allele frequencies from 0.0020 to 0.5512. The cumulative power of discrimination (CPD) and the cumulative probability of exclusion (CPE) values of the 21 STR loci were 0.999999999999999999997337058271 and 0.99999953732495, respectively. The results of interpopulation differentiation, phylogenetic, multidimensional scaling, and structure analyses indicated a closer genetic relationship of the studied population with Han populations from other regions of China than with other populations.

CONCLUSIONS

The 21 STR loci exhibited high genetic polymorphism in the studied Shanghai_Han population and could be used for forensic applications and population genetic studies.

Forensic parameters and mutation analysis of 23 short tandem repeat (PowerPlex® Fusion System) loci in Fujian Han Chinese population

Kinship testing based on genetic markers has valuable practical applications. Short tandem repeat polymorphisms (STRPs) can have large number of alleles, and become the dominant marker for kinship identification. However, the high mutation rates affect the identification accuracy. Thus, accurate investigation of the mutation rate of STR loci in different populations is crucial for the reliability of phylogenetic relationships. In present study, forensic parameters and mutation rates (include 95% CI) of 23 short tandem repeats (STR) loci (D3S1358, D1S1656, D2S441, D10S1248, D13S317, D16S539, D18S51, D2S1338, CSF1PO, TH01, vWA, D21S11, D7S820, D5S818, TPOX, D8S1179, D12S391, D19S433, FGA, D22S1045, PentaE, PentaD and DYS391) were investigated through PowerPlex® Fusion System in Fujian Han population. The high level of CDP (0.999999999999999999999999992) and CPE (0.999999993) indicated the panel was high efficiency in forensic DNA identification and paternity testing. In mutation analysis, 43 mutation cases were found through 54,124 parent-child meiotic transfers. The observed mutation rates ranged from 0 (D3S1358, D1S1656, D13S317, TH01, D19S433 and D22S1045) to 0.0025 (PentaE and FGA). The overall mutation rate across all loci was 0.0008 and the average mutation rate for the 23 loci was estimated to be 0.00078 per meiosis. The vast majority of mutations were single-step (88.4%) mutation and also include double-step (9.3%) and triple-step (2.3%) mutations. Paternal mutation rate was more common than maternal mutation rate with a ratio of 7.2:1. In addition, mutation rates indicated positive correlation (r = 0.633, p = 0.009) with the expected heterozygosity (H_e).

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.

Forensic characterization of 15 autosomal STRs in four populations from Xinjiang, China, and genetic relationships with neighboring populations

The Xinjiang Uyghur Autonomous Region of China (XUARC) harbors 47 ethnic groups including the Manchu (MCH: 0.11%), Mongols (MGL: 0.81%), Kyrgyz (KGZ: 0.86%) and Uzbek (UZK: 0.066%). To establish DNA databases for these populations, allele frequency distributions for 15 autosomal short tandem repeat (STR) loci were determined using the AmpFlSTR Identifiler PCR amplification kit. There was no evidence of departures from Hardy-Weinberg equilibrium (HWE) in any of the four populations and minimal departure from linkage equilibrium (LE) for a very small number of pairwise combinations of loci. The probabilities of identity for the different populations ranged from 1 in 1.51 × 1017 (MCH) to 1 in 9.94 × 1018 (MGL), the combined powers of discrimination ranged from 0.99999999999999999824 (UZK) to 0.9999999999999999848 (MCH) and the combined probabilities of paternal exclusion ranged from 0.9999979323 (UZK) to 0.9999994839 (MCH). Genetic distances, a phylogenetic tree and principal component analysis (PCA) revealed that the MCH, KGZ and UZK are genetically closer to the Han population of Liaoning and the Mongol population of Mongolia while the MGL are closer to Han, Japanese, Korean, Malaysian, Hong Kong Han and Russians living in China.

Genetic polymorphism of 21 non-CODIS STR loci in Chengdu Han population and its interpopulation analysis between 25 populations in China

AGCU 21+1 STR kit contains 21 non-combined DNA index system (non-CODIS) short tandem repeats (STR) loci and a sex-determining locus amelogenin. In this study, we evaluated the genetic diversity and forensically relevant population statistics of 21 non-CODIS loci in 210 Chinese Han individuals from Chengdu city, Sichuan province, Southwest China. No significant deviations from Hardy-Weinberg equilibrium were observed within the 21 non-CODIS STR loci. The combined power of discrimination (CPD) and combined power of exclusion (CPE) were 0.99999999999999999994278, 0.999999355 respectively. To reveal interpopulation differentiations of mainland population of China, a neighbor-joining (N-J) phylogenetic tree was constructed based on Nei's genetic distances among Chengdu Han and 25 published populations. The phylogenetic analyses indicated that Chengdu Han population keeps a close genetic relationship with other Han 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 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.

Chinese Xibe population genetic composition according to linkage groups of X-chromosomal STRs: population genetic variability and interpopulation comparisons

BACKGROUND

The Xibe population is one of China's officially recognised populations and is now distributed separately from west to east in the northern part of China. X-chromosomal short tandem repeats have a special inheritance pattern, and could be used as complements in forensic application, especially for complex or deficiency cases.

SUBJECTS AND METHODS

This study obtained the allelic and haplotypic frequencies of 19 X-STR loci in the Xibe population from Xinjiang Uygur Autonomous Region, China, and studied the genetic differentiations between the Xibe and other populations.

RESULTS

The combined power of discrimination in females and males and mean exclusion chances in deficiency cases, normal trios and duo cases was at least 0.999 999 994. In the haplotypic study, the Xibe population showed a more similar pattern of haplotype distribution with Asian populations than populations from other continents, while allelic study also indicated a closer relationship between the Xibe and Asian populations.

CONCLUSIONS

The 19 X-STR loci would be useful in forensic application in the studied population. The Xibe population showed a closer genetic relationship with Asian populations in the study, and more population data would be necessary for more detailed genetic relationship studies.

Genetic polymorphisms of 54 mitochondrial DNA SNP loci in Chinese Xibe ethnic minority group

We analyzed the genetic polymorphisms of 54 mitochondrial DNA (mtDNA) variants in Chinese Xibe ethnic minority group. A total of 137 unrelated healthy volunteers from Chinese Xibe group were the objects of our study. Among the selected loci, there were 51 variable positions including transitions and transversions, and single nucleotide transitions were common (83.93%) versus transversions. These variations defined 64 different mtDNA haplotypes exclusive of (CA)n and 9 bp deletion variation. The haplotype diversity and discrimination power in Xibe population were 0.9800 ± 0.004 and 0.9699, respectively. Besides, we compared Xibe group with 18 other populations and reconstructed a phylogenetic tree using Neighbor-Joining method. The result revealed that Xibe group was a close to Xinjiang Han and Yanbian Korean groups. Our data also indicated that Xibe group has a close relationship with Daur and Ewenki groups, which is reflected by the history that Xibe was influenced by Daur and Ewenki groups during the development of these groups. In conclusion, the variants we studied are polymorphic and could be used as informative genetic markers for forensic and population genetic application.

A 30-InDel Assay for Genetic Variation and Population Structure Analysis of Chinese Tujia Group

In the present study, thirty autosomal insertion and deletion polymorphic loci were simultaneously amplified and genotyped in a multiplex system, and their allelic frequencies as well as several forensic parameters were obtained in a sample of 236 unrelated healthy Tujia individuals. All the loci were in Hardy-Weinberg equilibrium after applying a Bonferroni correction and all pair-wise loci showed no significant linkage disequilibrium. These loci were observed to be relatively informative and discriminating, quite efficient for forensic applications. Allelic frequencies of 30 loci were compared between the Tujia group and other reference populations, and the results of analysis of molecular variance indicated the Tujia group showed the least significant differences with the Shanghai Han at one locus, and the most with Central Spanish population at 22 loci. We analyzed the population genetic structure by the principal component analysis, the clustering of STRUCTURE program and a Neighbor-Joining tree, and then evaluated the genetic relationships among Tujia and other 15 populations.

Allele and haplotype diversity of new multiplex of 19 ChrX-STR loci in Han population from Guanzhong region (China)

X-chromosomal short tandem repeats (X-STRs) have been proved to be useful for some deficiency paternity cases in recent years. Here, we studied the genetic polymorphisms of 19 X-STR loci (DXS10148-DXS10135-DXS8378, DXS10159-DXS10162-DXS10164, DXS7132-DXS10079-DXS10074-DXS10075, DXS6809-DXS6789, DXS7424-DXS101, DXS10103-HPRTB-DXS10101 and DXS7423-DXS10134) in 252 male and 222 female individuals from Guanzhong Han population, China. No deviation for all 19 loci was observed from the Hardy-Weinberg equilibrium. The polymorphism information content values of the panel of 19 loci were more than 0.5 with the exception of the locus DXS7423. The combined power of discrimination were 0.9999999999999999999994340 in females and 0.9999999999997662 in males, respectively; and the combined mean exclusion chances were 0.999999993764 in duos and 0.999999999997444 in trios, respectively. The haplotype diversities for all the seven clusters of linked loci were more than 0.9. The results showed that the panel of 19 X-STR loci were powerful for forensic applications in Guanzhong Han population. Locus by locus population comparisons showed significant differences at more than seven loci between Guanzhong Han population and the groups from North America, Europe and Africa.

Mutation rate estimation for 15 autosomal STR loci in a large population from Mainland China

STR, short tandem repeats, are well known as a type of powerful genetic marker and widely used in studying human population genetics. Compared with the conventional genetic markers, the mutation rate of STR is higher. Additionally, the mutations of STR loci do not lead to genetic inconsistencies between the genotypes of parents and children; therefore, the analysis of STR mutation is more suited to assess the population mutation. In this study, we focused on 15 autosomal STR loci. DNA samples from a total of 42,416 unrelated healthy individuals (19,037 trios) from the population of Mainland China collected between Jan 2012 and May 2014 were successfully investigated. In our study, the allele frequencies, paternal mutation rates, maternal mutation rates and average mutation rates were detected. Furthermore, we also investigated the relationship between paternal ages, maternal ages, area, the time of pregnancy and average mutation rate. We found that the paternal mutation rate was higher than the maternal mutation rate and the paternal, maternal, and average mutation rates had a positive correlation with paternal age, maternal age and the time of pregnancy respectively. Additionally, the average mutation rate of coastal areas was higher than that of inland areas.

•

15 autosomal STR loci were analyzed in a large scale population in Mainland China.

•

With increases of repeat units the event of loss is more than that of gain.

•

The paternal mutation rate is higher than the maternal mutation rate.

•

There is a positive correlation between mutation rates and age and pregnancy time.

•

The average mutation rates of coastal areas are higher than that of inland areas.