De-Jian Lu

Mutation analysis of 24 short tandem repeats in Chinese Han population

Germline mutations of 24 short tandem repeat (STR) loci (TPOX, D3S1358, FGA, D5S818, CSF1PO, D7S820, D8S1179, TH01, vWA, D13S317, Penta E, D16S539, D18S51, Penta D, D21S11, D2S1772, D6S1043, D7S3048, D8S1132, D11S2368, D12S391, D13S325, D18S1364, and GATA198B05) were studied for 6,441 parent–child meioses taken from the paternity testing cases in Chinese Han population. In total, 195 mutations were identified at 22 of the 24 loci. Among them, 189 (96.92%) mutations were one step, five mutations (2.56%) were two step, and one mutation (0.51%) was three step. No mutation was found at the TH01 and TPOX loci. The overall mutation rate estimated was 0.0013 (95% CI 0.0011–0.0015), and the locus-specific mutation rate estimated ranged from 0 to 0.0034. There was a bias in the STR mutations that repeat gains were more common than losses (∼1.7:1). Mutation events in the male germline were more frequent than in the female germline (∼4.3:1). Furthermore, loci with a larger heterozygosity tended to have a higher mutation rate. Mutation in short alleles was biased towards expansion, whereas mutation in long alleles favored contraction. The long alleles have a higher allelic mutational probability than short alleles.

Genetic data of nine non-CODIS STRs in Chinese Han population from Guangdong Province, Southern China

Nine non-combined DNA index system tetranucleotide short tandem repeat (STR) loci D2S1772, D6S1043, D7S3048, D8S1132, D11S2368, D12S391, D13S325, D18S1364, and GATA198B05 were amplified in a multiplex polymerase chain reaction system. The distribution of alleles of the nine STRs was reported from a Chinese Han population in Guangdong Province, Southern China. The combined power of exclusion in trios and duos for the nine loci was 0.999981 and 0.999025, respectively. Mutation rates range from 0 to 0.005618. Pairwise analysis of linkage disequilibrium, which included PowerPlex 16 System loci, did show statistically significant deviation from independence even though loci locate on the same chromosomes. The nine STRs are highly informative and suitable to extend the results obtained with other STRs commonly analyzed for difficult paternity and kinship analysis.

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.

Development of the nine X-STR loci typing system and genetic analysis in three nationality populations from China

This study is to develop a new multiplex polymerase chain reaction (PCR) system that simultaneously amplifies the nine X-chromosome short tandem repeats loci in the same PCR reaction, and to explore their polymorphism and mutation rate among three nationality populations from China. These loci included DXS6854, DXS9902, DXS6809, GATA172D05, HPRTB, DXS7423, DXS6807, DXS8378, and DXS8377. The samples of 890 (484 males and 406 females) unrelated individuals from Guangdong Han population, Xinjiang Uigur, and Inner-Mongolia Mongol were successfully analyzed using this multiplex system. The allele frequencies and mutation rates of the nine loci were investigated, and the comparison of allele frequency distribution among different populations was performed. There were 87 alleles for all the loci, and six to 18 alleles for each locus observed by our new multiplex PCR system. Polymorphism information content was 0.4998–0.9101, and power of discrimination in females was 0.6518–0.9846. Five cases with mutation of above loci were detected in 5,310 meioses. Pair-wise comparisons of allele frequencies distribution showed significant differences for most loci among different populations. Our results indicate that this multiplex system is very useful for identification analysis, and that the information about polymorphism and mutation rate is necessary for forensic application in three nationality populations from China.

Development of multiplex PCR system with 15 X-STR loci and genetic analysis in three nationality populations from China

The aim of this study is to develop a new multiplex PCR system that simultaneously amplifies the 15 X‐chromosome short tandem repeats (X‐STRs) loci in the same PCR reaction, and to obtain the 15 X‐STR loci database in three nationality populations from China. This multiplex system includes DXS7133, DXS6801, DXS981, DXS6809, DXS7424, DXS6789, DXS9898, DXS7132, GATA165B12, DXS101, DXS10075, DXS6800, GATA31E08, DXS10074, and DXS10079, which were successfully analyzed on 1251 DNA samples (670 males and 581 females) from Guangdong Han population, Xinjiang Uigur and Kazakh. The allele frequencies and mutation rates of the 15 loci were investigated, and the allele frequency distribution among different populations was compared. A total of 6–17 alleles for each locus were observed and altogether 170 alleles for all the selected loci were found. Thirteen cases with mutation of the above loci were detected in 11 850 meioses. Pairwise comparisons of the allele frequencies distribution showed significant differences in most loci among different populations. The results indicate that this multiplex system 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.

Allele and Haplotype Diversity of 26 X-STR Loci in Four Nationality Populations from China

Background Haplotype analysis of closely associated markers has proven to be a powerful tool in kinship analysis, especially when short tandem repeats (STR) fail to resolve uncertainty in relationship analysis. STR located on the X chromosome show stronger linkage disequilibrium compared with autosomal STR. So, it is necessary to estimate the haplotype frequencies directly from population studies as linkage disequilibrium is population-specific. Methodology and Findings Twenty-six X-STR loci including six clusters of linked markers DXS6807-DXS8378-DXS9902(Xp22), DXS7132-DXS10079-DXS10074-DXS10075-DXS981 (Xq12), DXS6801-DXS6809-DXS6789-DXS6799(Xq21), DXS7424-DXS101-DXS7133(Xq22), DXS6804-GATA172D05(Xq23), DXS8377-DXS7423 (Xq28) and the loci DXS6800, DXS6803, DXS9898, GATA165B12, DXS6854, HPRTB and GATA31E08 were typed in four nationality (Han, Uigur, Kazakh and Mongol) samples from China (n = 1522, 876 males and 646 females). Allele and haplotype frequency as well as linkage disequilibrium data for kinship calculation were observed. The allele frequency distribution among different populations was compared. A total of 5–20 alleles for each locus were observed and altogether 289 alleles for all the selected loci were found. Allele frequency distribution for most X-STR loci is different in different populations. A total of 876 male samples were investigated by haplotype analysis and for linkage disequilibrium. A total of 89, 703, 335, 147, 39 and 63 haplotypes were observed. Haplotype diversity was 0.9584, 0.9994, 0.9935, 0.9736, 0.9427 and 0.9571 for cluster I, II, III, IV, V and VI, respectively. Eighty-two percent of the haplotype of cluster IIwas found only once. And 94% of the haplotype of cluster III show a frequency of <1%. Conclusions These results indicate that allele frequency distribution for most X-STR loci is population-specific and haplotypes of six clusters provide a powerful tool for kinship testing and relationship investigation. So it is necessary to obtain allele frequency and haplotypes data of the linked loci for forensic application.

X chromosomal recombination—A family study analyzing 26 X‐STR Loci in Chinese Han three‐generation pedigrees

The aim of this study is to investigate genetic linkage and recombination fractions of 26 X chromosomal (X‐STR) loci with two multiplex PCR systems (MX15‐STR and MX12‐STR). MX15‐STR (including DXS7133, DXS6801, DXS981, DXS6809, DXS7424, DXS6789, DXS9898, DXS7132, GATA165B12, DXS101, DXS10075, DXS6800, GATA31E08, DXS10074, and DXS10079) and MX12‐STR (including DXS6854, DXS9902, DXS6800, GATA172D05, DXS7423, HPRTB, DXS6807, DXS6803, DXS6804, DXS6799, DXS8378, and DXS8377) were successful analyzed on 206 two‐generation families with two or more children and 33 three‐generation families with 72 grandsons. Segregation analysis and calculation of recombination fractions between pairs of markers were performed. Linkage analysis of pairs of markers showed that there existed significant linkage (maximum LOD scores >2.0) within the physical distance of 48.5 Mb. Recombination events could be observed within the clusters of closed linked makers spanning <1.0 Mb. These results indicate that close cluster X‐STRs used and recombination fractions of the selected loci will be very useful for biostatistical calculations in complex kinship analysis.

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.

Population data and mutation rates of 19 STR loci in seven provinces from China based on Goldeneye™ DNA ID System 20A.

Short tandem repeat (STR) analysis is a primary tool in forensic casework. Population data and mutation rates of STRs are very important for paternity testing and forensic genetics. However, the population data and mutation rates of STRs in Han nationality based on large samples have still not been fully described in China. In this study, the allelic frequencies, forensic parameters, and mutation rate of 19 STR loci (D19S433, D5S818, D21S11, D18S51, D6S1043, D3S1358, D13S317, D7S820, D16S539, CSFIPO, PentaD, vWA, D8S1179, TPOX, Penta E, TH01, D12S391, D2S1338, and FGA) based on the Goldeneye™ DNA ID System 20A in Southern China Han nationality among seven provinces were investigated. Furthermore, population stratification of Southern China Han nationality among seven provinces was established. The multidimensional scaling (MDS) plot based on genetic distances (Fst) showed that the studied populations can be clustered into two major groups. However, relationships among populations were weak (Fst < 0.0043). A total of 376 cases of mutation were detected from the 19 selected loci in 15,396 meioses. The average mutation rate for the 19 loci was estimated to be 1.3 × 10−3 per meiosis. The mutation was mainly single step; the paternal mutation rate was higher than the maternal; and paternal mutation rate increases with paternal age.

Genetic polymorphism of 22 autosomal STR markers in a Han population of Southern China.

Population genetic data and forensic statistics of 22 autosomal short tandem repeat (STR) loci (D1S1656, D2S1338, D3S3045, D4S2366, D5S2500, D6S477, D7S3048, D8S1132, D9S925, D10S1435, D11S2368, D12S391, D13S325, D14S608, D15S659, D16S539, D17S1290, D18S535, D19S253, D20S470, D21S1270 and GATA198B05) were determined for a sample of 515 unrelated individuals from Han population in Southern China. The expected heterozygosity and the discrimination power varied from 0.7358 to 0.8733 and 0.8915 to 0.9702, respectively. The probability of excluding an unrelated man as the true father (assuming no background relatedness in the population) for trios and for duos ranged from 0.5126 to 0.7415 and 0.3331 to 0.5864, respectively. The studied STRs appear to provide a significant improvement in the statistical power of kinship analysis.