The Y-STR landscape of coastal southeastern Han: Forensic characteristics, haplotype analyses, mutation rates, and population genetics.

The Y-STR landscape of Coastal Southeastern Han (CSEH) living in Chinese southeast areas (including Guangdong, Fujian, and Zhejiang provinces) is still unclear. We investigated 62 Y-STR markers in a reasonably large number of 1021 unrelated males and 1027 DNA-confirmed father-son pairs to broaden the genetic backgrounds of CSEH. In total, 85 null alleles, 121 off-ladder alleles, and 95 copy number variants were observed, and 1012 distinct haplotypes were determined with the overall HD and DC values of 0.999974 and 0.9912. We observed 369 mutations in 76 099 meiotic transfers, and the average estimated Y-STR mutation rate was 4.85 × 10-3 (95% CI, 4.4 × 10-3 -5.4 × 10-3 ). The Spearman correlation analyses indicated that GD values (R2 = 0.6548) and average allele sizes (R2 = 0.5989) have positive correlations with Y-STR mutation rates. Our RM Y-STR set including 8 candidate RM Y-STRs, of which DYS534, DYS630, and DYS713 are new candidates in CSEH, distinguished 18.52% of father-son pairs. This study also clarified the population structures of CSEH which isolated in population-mixed South China relatively. The strategy, SM Y-STRs for familial searching and RM Y-STRs for individual identification regionally, could be applicable based on enough knowledge of the Y-STR mutability of different populations.

Deletions and duplications of 42 Y chromosomal short tandem repeats in Chinese Han population.

Genotypes of 42 Y chromosome STR (Y-STR) loci were analyzed for a sample of 1420 unrelated males and 1160 father-son pairs from a Chinese Han population. Deletions of Y-STR loci were detected at DYS389I, DYS389II, DYS437, DYS446, DYS447, DYS448, and DYS557 loci. The most common deletion occurred at DYS448 and DYS557 with a frequency of 0.0056 and 0.0035, respectively. On the other hand, duplications of alleles were observed at DYF387S1a/b, DYS385a/b, DYS460, DYS527a/b, DYS459a/b, and DYS557 loci. The DYF387S1a/b, DYS527a/b, and DYS385a/b showed the highest duplicated frequencies of 0.0148, 0.0134, and 0.0099, respectively. The Y-STRs located on palindromes significantly exhibited more deletions or duplications than those non-palindromic loci. Also, duplications were more frequent than deletions. Hence, deletions or duplications of Y-STRs related to their positions on the Y chromosome. All the 52 deleted or duplicated events occurred in the two-generation families inherited stably. Furthermore, the deletions may show the Chinese Han population specificity, but the duplications may not have a similar phenomenon. Our results will be helpful to correct interpretation of the genetic profile of Y-STR loci in forensic casework.

[Method of Identifying Male Lineages Based on Main Haplotype and Analysis of the Distribution of Y-STR Haplotype Mismatch Based on the Bayesian Theory].

OBJECTIVE: To establish a classification method to identify different male lineages in a large population, to study the distribution patterns of Y-STR loci mismatches among Han Chinese male lineage members and to explore the mismatch probability distribution among the members with different meiosis intervals in the family. METHODS: Peripheral blood samples of 269 male individuals from 12 lineages in Han Chinese population and 45 unrelated male individuals were collected. Then, Yfiler Plus TM and ZGWZ FSY or Yfiler Platinum amplification kits were used, obtaining 314 Y-STR haplotypes. The Y-STR haplotype with 3 or more repetitions were selected as the main haplotype, in which the largest number was selected as the first data center. According to the standard of Y-STR genotype, those with mismatches within five loci and six steps were clustered and merged. Then, the main haplotype of the largest number in the remaining data was taken as the second data center, and cluster analysis is carried out in turn until there is no main haplotype remained. Pair comparison was conducted between lineage members and unrelated individuals, and the mismatch distribution among lineage members and unrelated individuals was calculated respectively. The average mismatch rate of each locus was subsequently calculated, as well as the mismatch probability distribution among members with different meiosis intervals within the lineage. RESULTS: 269 out of the 314 individuals were divided into 12 groups by cluster analysis method, accomplishing 100% accuracy between the cluster groups thus identified and the 12 known lineages. The remaining 45 unrelated individuals were scattered. The mismatch loci was within 0-7 loci and 0-7 steps among lineage members and the mismatch between unrelated individuals was at least 11 loci and 15 steps. The mismatch loci with the largest number of one-step and two-step mismatch were different in each lineage and had features that were specific to each lineage. The minimum mutation count and average mismatch rate of each locus were significantly correlated with the mutation rate. Two individuals with no mismatch had a 19.7% probability of 1 meiosis interval and a 71.2% probability of less than 6 meiosis interval. Two individuals with 3 loci mismatches had a 65.2% probability of more than 10 meiosis intervals. CONCLUSION: The cluster analysis method based on main haplotypes provided in this paper can quickly and effectively differentiate large male lineage samples. The clustering method and the mismatch probability distribution of different meiosis intervals obtained thus can provide new ideas for research and screening instruments, and important reference for lineage investigation, data analysis and practical application of Y-STR database in the future.

Population structure of Han population in China revealed by 41 STR loci.

Background: Currently, the Han population in China may be comprised of different genetic groups due to geographic, cultural and economic factors. Understanding population structure is very important for forensic purposes. However, knowledge of the genetic substructure within the whole Han population in China is still limited.Aim: This study is designed to ascertain the genetic structure of the Han population in China through genetic data from autosomal short tandem repeats (STRs).Subjects and methods: A set of 41 STR markers were analysed in 8725 unrelated Han Chinese males from the seven geographic regions of Northeast, North, East, Central, South, Southwest and Northwest in mainland China. Allele frequencies and F-statistics were estimated. Principal coordinate analysis (PCoA), phylogenetic analyses, analysis of molecular variance (AMOVA) and discriminant analysis of principal components (DAPC) were performed to explore the population structure.Results: Rare alleles that have not been observed in previous samples were detected. The small overall Fst values (0.0008), AMOVA and DAPC indicated that there is no population structure in Han Chinese. However, the PCoA and phylogenetic tree disclose a genetic differentiation pattern from north to south.Conclusions: There is no apparent population substructure in the Han population in China. However, genetic distances among the Han populations correlate with geographic locations.

Mutation rates at 42 Y chromosomal short tandem repeats in Chinese Han population in Eastern China.

Mutation analysis of 42 Y chromosomal short tandem repeats (Y-STRs) loci was performed using a sample of 1160 father-son pairs from the Chinese Han population in Eastern China. The results showed that the average mutation rate across the 42 Y-STR loci was 0.0041 (95% CI 0.0036-0.0047) per locus per generation. The locus-specific mutation rates varied from 0.000 to 0.0190. No mutation was found at DYS388, DYS437, DYS448, DYS531, and GATA_H4. DYS627, DYS570, DYS576, and DYS449 could be classified as rapidly mutating Y-STRs, with mutation rates higher than 1.0 × 10-2. DYS458, DYS630, and DYS518 were moderately mutating Y-STRs, with mutation rates ranging from 8 × 10-3 to 1 × 10-2. Although the characteristics of the Y-STR mutations were consistent with those in previous studies, mutation rate differences between our data and previous published data were found at some rapidly mutating Y-STRs. The single-copy loci located on the short arm of the Y chromosome (Yp) showed relatively higher mutation rates more frequently than the multi-copy loci. These results will not only extend the data for Y-STR mutations but also be important for kinship analysis, paternal lineage identification, and family relationship reconstruction in forensic Y-STR analysis.

Analysis of linkage and linkage disequilibrium for syntenic STRs on 12 chromosomes.

The purpose of this study is to evaluate allelic association and linkage of 18 adjacent syntenic short tandem repeat (STR) pairs form out of 30 markers located on 12 different autosomes. Linkage disequilibrium was tested by using the unknown gametic phase genotypes and phased haplotypes from 290 unrelated individuals from Chinese Han population. Genetic linkage analysis between syntenic STRs was performed based on 145 two-generation families which involved 628 meioses. The results showed no significant linkage disequilibrium at any STR pairs and independent inheritance between syntenic STR pairs was indicated. Significant linkage (maximum logarithm of odd (LOD) scores >3.0) was found in 6 out of the 18 adjacent syntenic STR pairs (D1S1627-D1S1677, CSF1PO-D5S818, D6S1017-D6S1043, D6S1043-D6S474, D12S391-vWA, and D19S253-D19S433). These significant linkage marker pairs had a genetic distance ranged from 11.94 to 41.33 cM deduced from HapMap. When recombination fractions determined in families were compared to those derived from Kosambi mapping function based on HapMap data, the latter may have an overestimation. In summary, our results demonstrated that product rule included syntenic STRs can be used for unrelated individual profile probability and the recombination fraction based on family data was superior to the estimation from HapMap for kinship analysis.

Genetic analysis of the 10 ChrX STRs loci in Chinese Han nationality from Guangdong province.

This study is to explore the polymorphic nature of X-Chromosome short tandem repeats (ChrX STRs) loci, and to determine its application in kinship tests for forensic cases. A new fluorescent multiplex PCR that simultaneously amplifies the 10 ChX STRs loci in the same PCR reaction had been set up. DXS7132, DXS981, DXS6801, DXS6809, DXS6789, DXS7424, DXS101, DXS7133, GATA165B12 and GATA31E08 were analyzed in a sample of 511 (399 males and 112 females) unrelated individuals from Guangdong Han nationality in China. One hundred and one alleles were observed in all the loci. Here, we investigated the allele frequencies and mutation rates of the ten loci, and then made the comparison of allele frequencies distribution among different populations. The results show the ten loci in the multiplex systems may provide high polymorphism information for kinship testing and relationship investigations, and it is necessary to gain allele frequency and mutation rate of different population for forensic application.

Validation of a 6-Dye Short Tandem Repeat System: A Dry Kit With Lyophilized Amplification Reagent.

The SureID®S6 system used a lyophilized pellet as the amplification reagent to enable multiplexing of sex-determining marker Amelogenin, 21 autosomal short tandem repeats (STRs), and one Y-STR. To assess the performance, reliability, and limitation of the dry amplification system, the validation studies including PCR condition, reproducibility, sizing and precision, analytical threshold calculation, sensitivity and stochastic threshold calculation, species specificity, stability, mixture, case sample, and population and concordance were conducted according to the Scientific Working Group on DNA Analysis Methods (SWGDAM) Validation Guidelines. Experimental data suggested that the optimal range of total input DNA was from 125 to 500 pg; the appropriate analytical threshold was 80 relative fluorescence units (RFUs) while the stochastic threshold was 260 RFUs; for the stability studies, SureID®S6 system could resist against less than 500 µmol/L of hematin, 100 ng/µl of humic acid, 4 mM of indigotin, 800 mM of tannic acid, and 800 mM of calcium ion. Population and concordance studies using 500 unrelated individuals showed that the combined probability of discrimination (CPD) and cumulative probability of exclusion (CPE) values were 0.999999999999 and 0.999999998416, respectively. The genotypes for the same sample were concordant with the previously validated HUAXIA™ Platinum kit. The validation results demonstrated that the SureID®S6 system could be used for forensic applifications.

Population genetics of 17 Y-STR loci in a large Chinese Han population from Zhejiang Province, Eastern China.

Seventeen Y-STRs (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a, DYS385b, DYS438, DYS439, DYS437, DYS448, DYS456, DYS458, DYS635 and YGATAH4) were analyzed for 4451 Chinese Han unrelated males from Zhejiang Province, Eastern China, with the AmpFlSTR Yfiler™ PCR Amplification kit. A total of 3389 different haplotypes was identified, of which 2877 were unique and 512 repeatedly found among different individuals. The overall haplotype diversity (HD) and discrimination capacity (DC) were 0.999696 and 0.761402, respectively. Analysis of molecular variance (AMOVA) tests demonstrated that genetic distance between Zhejiang Han and most Chinese Han populations is closer than that between Zhejiang Han and non-Han populations. This study provides information for the application of Y-chromosomal STRs to forensic identification, indicating that the extended genotyping of Y-STRs is needed for forensic practice.

Allele frequencies of seven X-linked STR loci in Chinese Han population from Zhejiang Province.

Allele frequencies and forensic parameters of seven X-chromosome STRs (DXS981, DXS7424, DXS101, DXS7133, DXS6789, GATA165B12 and GATA31E08) were estimated from a sample of unrelated individuals (383 females and 313 males) belonging to Chinese Han population in Zhejiang Province, a region located in the east of China. Combining the seven X-linked markers, high mean exclusion chance and power of discrimination values were obtained. Amplification was performed in a single multiplex PCR reaction. Due to the small PCR products (<202bp), the use of these STRs can increase the probability that a degraded sample can be typed.