Bofeng Zhu

Y-chromosomal STR haplotypes in Chinese Uigur ethnic group

We have already coamplified minimal haplotypes (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385I/II), two additional loci, namely, DYS438, DYS439, and Amelogenin, in a single PCR using the Y-PLEX 12 kit. We investigated 107 unrelated male individuals from the Uigur ethnic group and studied the allelic frequency distribution and haplotype diversity of 11 Y-chromosomal STRs. A number of 43 alleles (nine STR loci) and 27 phenotypes (including DYS385) were detected, with frequencies ranging from 0.0092 to 0.6296. A total of 103 haplotypes were identified, among which 99 were individual-specific and four haplotypes were found twice. The haplotype diversity for these 12 Y-STR loci was 0.9993.

Genetic diversities of 21 non-CODIS autosomal STRs of a Chinese Tibetan ethnic minority group in Lhasa

In the present study, we investigated 21 short tandem repeat (STR) loci (D6S474, D12ATA63, D22S1045, D10S1248, D1S1677, D11S4463, D1S1627, D3S4529, D2S441, D6S1017, D4S2408, D19S433, D17S1301, D1GATA113, D18S853, D20S482, D14S1434, D9S1122, D2S1776, D10S1435, D5S2500), which are not included in the Combined DNA Index System and Amelogenin locus in 104 randomly selected healthy autochthonous individuals from the Tibetan ethnic minority group residing in the Lhasa region, Tibet Autonomous Region of China. Allelic frequencies, common forensic statistical parameters, and the Hardy–Weinberg equilibrium in this population were calculated with a modified PowerState V12.xls. A total of 143 alleles were found in the Tibetan group with corresponding allelic frequencies ranging from 0.005 to 0.582. The observed heterozygosity, the expected heterozygosity, the power of discrimination, the power of exclusion, and the polymorphic information content ranged from 0.615 to 0.817, 0.559 to 0.787, 0.727 to 0.926, 0.310 to 0.632, and 0.488 to 0.760, respectively. Chi-square tests of the observed genotype frequencies and expected genotype frequencies in the samples showed no departure from the Hardy–Weinberg equilibrium at all loci except for D5S2500. Our results demonstrate that these 21 STRs are highly polymorphic and suitable for anthropological research, population genetics, and forensic paternity testing and human individual identification in this region, and can enrich Chinese ethnical genetic informational resources.

Population data of 15 STR loci of Chinese Yi ethnic minority group

Allele frequency data and statistical parameters for D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA loci were determined in a sample of 120 healthy unrelated individuals of Chinese Yi ethnic minority group living in Yunnan province, China. We observed 132 alleles with allelic frequencies ranging from 0.0042 to 0.5333. The forensic statistical parameters from the data of all the loci showed high values. All loci were in accordance with Hardy-Weinberg equilibrium (p>0.05). The obtained frequency distributions were compared with previously published other population data, and significant differences were found between Yi population and Korean, Chinese Tibetan, Uigur, Ewenki, Han, Hui population at some STR loci. Our results of present study were valuable for forensic application and Chinese population genetic studies. These population data enriched Chinese genetic informational resources.

Population data of 15 STR in Chinese Han population from north of Guangdong.

The samples were obtained from 102 unrelated, healthy individuals of Chinese Han population living in north of Guangdong province of China. Genomic DNA was extracted using the Chelex100 protocol as described by Walsh et al. (1). Fifteen STR loci and Amelogenin locus were co-amplified by using the AmpFLSTR Identifiler kit following the amplification conditions recommended by the manufacturer. Detection and genotyping of all PCR products were accomplished using ABI3100 DNA Genetic Analyzer (Applied Biosystem). Allele designation was done using GeneScan 3.7 and Genotyper 3.7. Evaluation of Hardy—Weinberg equilibrium expectations was carried out using the exact test and further statistical parameters of forensic interest were determined by using Arlequin version 1.1 (2).

Genetic polymorphism analysis of 15 STR loci in Chinese Hui ethnic group residing in Qinghai province of China

In the present study, we investigated the diversity distributions of allelic frequencies of 15 short tandem repeats (STRs) loci in a sample of Chinese Hui ethnic group in the Ningxia Hui Autonomous Region. The allelic frequencies of the 15 STR loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA) were obtained from 2975 unrelated healthy Hui individuals. The STR genotyping data of all the samples were generated by DNA extraction, multiple amplification, GeneScan and genotype analysis. The genetic distances among different populations were calculated by using Nei’s method and a phylogenetic tree was constructed based on the allelic frequencies of the same 15 STR loci using the neighbor-joining method. A total of 185 alleles were observed in the Hui population, with the corresponding allelic frequencies ranging from 0.0002 to 0.5322. Chi-Square tests showed that all STR loci were in Hardy–Weinberg equilibrium. The forensic statistical parameters of all the loci showed high values. The population data in this study were compared with the previously published population data from other ethnics or areas. The Hui population showed significant differences from the Minnan Han, Uigur, Ewenki, Yi, Tibetan, Maonan and Malay ethnic minority groups in some loci, and from the South Morocco population and the Moroccan population in all the loci. Our results are valuable for human individual identification and paternity testing in the Chinese Hui population and are expected to enrich the genetic information resources of Chinese populations.

Genetic data provided by 21 autosomal STR loci from Chinese Tujia ethnic group

The aim of this study was to investigate allelic frequency distribution and forensic genetic parameters of autosomal short tandem repeats (STR) loci of the population samples from 107 Tujia individuals from Chinese Hubei Province. Twenty-one autosomal STR genetic markers (D9S1122, D6S474, D6S1017, D5S2500, D4S2408, D3S4529, D2S441, D2S1776, D22S1045, D20S482, D1S1677, D1S1627, D1GATA113, D19S433, D18S853, D17S1301, D11S4463, D12ATA63, D10S1248, D10S1435 and D14S1434) were simultaneously amplified in a new multiplex polymerase chain reaction system. 155 alleles for all the STR loci from the Tujia population were observed and the corresponding allelic frequencies ranged from 0.005 to 0.589. Expected heterozygosity, polymorphic information content, power of discrimination and power of exclusion of the 21 STR loci in the Tujia population were from 0.579 to 0.824, from 0.525 to 0.802, from 0.773 to 0.945 and from 0.257 to 0.641, respectively. Our results indicate that the autosomal STRs multiplex system provides highly informative STR data and could be useful in forensic individual identification and parentage testing in this region.

Allele Polymorphism and Haplotype Diversity of HLA-A, -B and -DRB1 Loci in Sequence-Based Typing for Chinese Uyghur Ethnic Group

Background Previous studies indicate that the frequency distributions of HLA alleles and haplotypes vary from one ethnic group to another or between the members of the same ethnic group living in different geographic areas. It is necessary and meaningful to study the high-resolution allelic and haplotypic distributions of HLA loci in different groups. Methodology/Principal Findings High-resolution HLA typing for the Uyghur ethnic minority group using polymerase chain reaction-sequence-based-typing method was first reported. HLA-A, -B and -DRB1 allelic distributions were determined in 104 unrelated healthy Uyghur individuals and haplotypic frequencies and linkage disequilibrium parameters for HLA loci were estimated using the maximum-likelihood method. A total of 35 HLA-A, 51 HLA-B and 33 HLA-DRB1 alleles were identified at the four-digit level in the population. High frequency alleles were HLA-A*1101 (13.46%), A*0201 (12.50%), A*0301 (10.10%); HLA-B*5101(8.17%), B*3501(6.73%), B*5001 (6.25%); HLA-DRB1*0701 (16.35%), DRB1*1501 (8.65%) and DRB1*0301 (7.69%). The two-locus haplotypes at the highest frequency were HLA-A*3001-B*1302 (2.88%), A*2402-B*5101 (2.86%); HLA-B*5001-DRB1*0701 (4.14%) and B*0702-DRB1*1501 (3.37%). The three-locus haplotype at the highest frequency was HLA-A*3001-B*1302-DRB1*0701(2.40%). Significantly high linkage disequilibrium was observed in six two-locus haplotypes, with their corresponding relative linkage disequilibrium parameters equal to 1. Neighbor-joining phylogenetic tree between the Uyghur group and other previously reported populations was constructed on the basis of standard genetic distances among the populations calculated using the four-digit sequence-level allelic frequencies at HLA-A, HLA-B and HLA-DRB1 loci. The phylogenetic analyses reveal that the Uyghur group belongs to the northwestern Chinese populations and is most closely related to the Xibe group, and then to Kirgiz, Hui, Mongolian and Northern Han. Conclusions/Significance The present findings could be useful to elucidate the genetic background of the population and to provide valuable data for HLA matching in clinical bone marrow transplantation, HLA-linked disease-association studies, population genetics, human identification and paternity tests in forensic sciences.

Allelic polymorphic investigation of 21 autosomal short tandem repeat loci in a Chinese Bai ethnic group

Population genetic data of 21 autosomal short tandem repeats (STRs) were obtained in a sample of 106 unrelated healthy individuals of Bai ethnic minority born in the Dali Bai Autonomous Prefecture in Yunnan Province. We observed 138 alleles with corresponding allelic frequencies ranging from 0.005 to 0.575. The genotypic frequency distributions at those STR loci were consistent with Hardy-Weinberg equilibrium (Bonferronis correction was used for Hardy-Weinberg equilibrium tests). The combined probability of exclusion, power of discrimination, probability of matching value for all 21 STR loci were 0.9999975729, 0.999999999999999999872 and 1.28×10(-19), respectively. The population data in this study showed significant differences from the previously published population data of Tibetan and Salar groups in some loci.

Allelic frequency distributions of 21 non-combined DNA index system STR loci in a Russian ethnic minority group from Inner Mongolia, China.

We studied the allelic frequency distributions and statistical forensic parameters of 21 new short tandem repeat (STR) loci and the amelogenin locus, which are not included in the combined DNA index system (CODIS), in a Russian ethnic minority group from the Inner Mongolia Autonomous Region, China. A total of 114 bloodstain samples from unrelated individuals were extracted and co-amplified with four fluorescence-labeled primers in a multiplex polymerase chain reaction (PCR) system. Using capillary electrophoresis, the PCR products of the 21 STR loci were separated and genotyped. A total of 161 alleles were observed in the Russian ethnic minority group, and corresponding allelic frequencies ranged from 0.0044 to 0.5965. The 21 non-CODIS STR loci of the Russian ethnic minority group were characterized by high genetic diversity and therefore may be useful for elucidating the population’s genetic background, for individual identification, and for paternity testing in forensic practice.

Developmental validation of the AGCU 21+1 STR kit: A novel multiplex assay for forensic application

In this study, we describe the developmental validation assay performed on a novel designed STR multiplex system, AGCU 21+1 STR kit. This kit contains a sex‐determining locus amelogenin and 21 noncombined DNA index system STR loci, that are, D6S474, D12ATA63, D22S1045, D10S1248, D1S1677, D11S4463, D1S1627, D3S4529, D2S441, D6S1017, D4S2408, D19S433, D17S1301, D1GATA113, D18S853, D20S482, D14S1434, D9S1122, D2S1776, D10S1435, and D5S2500. The 21+1 kit was validated by a series of tests including optimized PCR conditions, sensitivity, precision and accuracy, stutter ratio, DNA mixture, inhibitors, and species specificity according to the revised validation guidelines issued by the Scientific Working Group on DNA Analysis Methods (SWGDAM). Our results in this study show that the kit is a useful tool for forensic application.