Chinese Han Population Sample Research Articles

Gamma-glutamyl transpeptidase to platelet and gamma-glutamyl transpeptidase to lymphocyte ratio in a sample of Chinese Han population

BackgroundGamma-glutamyl transpeptidase to platelet ratio (GPR) and gamma-glutamyl transpeptidase to lymphocyte ratio (GLR) are assumed to be prognostic factors in liver fibrosis, cirrhosis and hepatocellular carcinoma. However, the reference values of GPR and GLR were not known.ObjectivesThe study aimed to investigate the reference ranges of GPR and GLR in Chinese Han population in Chaoshan region in South China.MethodsA retrospective study was conducted in the First Affiliated Hospital of Shantou University Medical College in South China. 2400 healthy adults aged 20~79 years were included. GPR and GLR were determined.ResultsOf 2400 healthy adults, 1200 men and 1200 women were included. The median GPR and GLR for men were 0.22 and 11.28, for women were 0.18 and 7.86, respectively. The 95% reference range of GPR in normal male and female are 0.09~0.54 and 0.08~0.55, GLR are 4.55~29.64 and 3.52~23.08, respectively. The male had a higher GPR at age 20~49 than the female while the GPR at age 60~79 was higher in the female than in the male. The GPR was affected by age, decreased with aging in male and increased in female. The GLR was higher in the male than in the female and varied with aging in the female but not in the male.ConclusionThe study provides reference data on GPR and GLR from different age and sex groups in South China. GPR and GLR varied with age and sex.

NOTCH1 Gene MicroRNA Target Variation and Ventricular Septal Defect Risk.

Birth defects, the ventricular septal defect (VSD) in particular, have major public health significance. There is evidence that genetic factors play a role in VSD risk. We report here our findings on the relationship between VSD and microRNA (miRNA)-3691-3p target sequence single-nucleotide polymorphisms (SNPs) in the 3' untranslated region of the NOTCH1 gene. Functional SNPs in NOTCH1 target sequence were screened from the SNP database. A case-control study in a large Chinese Han population sample of 350 children with VSD and 430 healthy controls examined the association between rs6563 SNPs and VSD. NOTCH1 wild and mutant recombinant expression vectors were constructed by the luciferase reporter gene system. The effects of miRNA on gene regulatory effects were also analyzed. The allelic distributions at the locus rs6563 showed statistically significant susceptibility to VSD (odds ratio [OR] = 1.502, 95% confidence interval [CI] = 1.209-1.866, p < 0.001). Compared with the subjects with G/G genotype, individuals with G/A genotype or A/A genotype showed ORs 1.414 (95% CI = 1.047-1.908, p = 0.020) and 2.366 (95% CI = 1.430-3.914, p < 0.001), respectively. The miRNA-3691-3p reduced luciferase activity of the A allele. The rs6563G > A genetic variation appears to be associated with congenital VSD through gene regulatory effects of miR-3691-3p on the NOTCH1 gene. Further studies in other population samples are called for diagnostics and public health innovation in relation to birth defects.

Analysis of 24 Y chromosomal STR haplotypes in a Chinese Han population sample from Henan Province, Central China

We analyzed haplotypes for 24 Y chromosomal STRs (Y-STRs), including 17 Yfiler loci (DYS19, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DY438, DYS439, DYS448, DYS456, DYS458, DYS635 and Y-GATA-H4) and 7 additional STRs (DYS388, DYS444, DYS447, DYS449, DYS522 and DYS527a/b) in 1100 unrelated Chinese Han individuals from Henan Province using AGCU Y24 STR kit systems. The calculated average gene diversity (GD) values ranged from 0.4105 to 0.9647 for the DYS388 and DYS385a/b loci, respectively. The discriminatory capacity (DC) was 72.91% with 802 observed haplotypes using 17 Yfiler loci, by the addition of 7 Y-STRs to the Yfiler system, the DC was increased to 79.09% while showing 870 observed haplotypes. Among the additional 7 Y-STRs, DYS449, DYS527a/b, DYS444 and DYS522 were major contributors to enhancing discrimination. In the analysis of molecular variance, the Henan Han population clustered with Han origin populations and showed significant differences from other Non-Han populations. In the present study, we report 24 Y-STR population data in Henan Han population, and we emphasize the need for adding additional markers to the commonly used 17 Yfiler loci to achieve more improved discriminatory capacity in a population with low genetic diversity.

Developing a multiplex mtSNP assay for forensic application in Han Chinese based on mtDNA phylogeny and hot spot.

We designed one multiplex assay with a reduced number of SNPs from whole mitochondrial genome as a screening approach for forensic purposes and developed a multiplex SNaPshot assay with 26 mitochondrial SNPs (mtSNPs). This assay included 16 target mtSNPs that defined the main haplogroups in Chinese population and ten hot-spot mtSNPs found by pyrosequencing. To validate our multiplex mtSNP assay, we not only analyzed a Chinese Han population sample, but also sequenced the complete control region of same set of individuals. Fifty-one haplotypes were observed in 204 individuals using our multiplex mtSNP assay and the haplotype diversity was estimated to be 0.9626. Our multiplex mtSNP assay could also distinguish some individuals sharing the same control region sequences. The same mtSNP profiles were obtained from the bloodstain, hair shaft, and salivary swab from same individuals. A good profile could be obtained with 50 pg of DNA. It was evident that our multiplex mtSNP assay not only improved the discrimination power, but also allowed allocating mitochondrial DNA profiles to particular haplogroups not clearly defined with the control region alone. We highlight the importance of the balance of target mtSNPs for haplogroup assignment and hot-spot mtSNPs for increasing discrimination power.

A promoter polymorphism (rs3806798) of interleukin-15 gene is associated with chronic hepatitis B virus infection in the Chinese Han population.

This study aimed to investigate the association between the polymorphisms of IL-15 gene and susceptibility to chronic hepatitis B virus (HBV) infection in the Chinese Han population. A total of 234 patients with chronic HBV infection and 150 age- and sex-matched healthy controls in the Chinese population were enrolled in this case-control study. Genotyping of ten single nucleotide polymorphisms (SNPs) in the IL-15 gene was carried out via Sequenom MassARRAY system. The association analysis demonstrated that SNP rs3806798 (A/T) had a significant difference in the distribution between patients and healthy controls (P = 0.033). Moreover, a significantly increased risk of HBV infection was found to be associated with IL-15 rs3806798 A allele among male patients and HBeAg-negative patients, compared with IL-15 rs3806798 T allele (P = 0.003; P = 0.046, respectively). Furthermore, haplotype analysis revealed that haplotype ATAGG (rs3806798, rs12508866, rs1519551, rs6819823 and rs2857261, respectively) in block 1 was significantly associated with HBV infection (P = 0.022). In conclusion, we found an association between IL-15 rs3806798 and the risk of chronic HBV infection in a sample of Chinese Han population.

Haplotype diversity of 17 Y-STR loci in a Chinese Han population sample from Shanxi Province, Northern China

The distribution of 17 Y-chromosome STR loci DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385a/b, DYS393, DYS391, DYS439, DYS635, DYS392, Y-GATA-H4, DYS437, DYS438, and DYS448 haplotypes was determined in a population sample of 222 unrelated Chinese Han from Shanxi Province, Northern China. A total of 219 haplotypes were observed, and of these, 216 were unique, while 3 were found two times. The overall haplotype diversity was 0.9999 and the discrimination capacity was 0.9865, indicating a high potential for differentiating between male individuals in this population. Comparison analysis via Analysis of Molecular Variance (AMOVA) and construction of MDS plot revealed that Shanxi Han sample clusters with Chinese origin populations and stands far apart of the non-Chinese populations, justifying the establishment of local databases in Shanxi Han population for any future forensic and genetic epidemiology efforts in this region.

Effects of genetic variants on lipid parameters and dyslipidemia in a Chinese population

A number of recent genome-wide association (GWA) studies have identified several novel genetic determinants of plasma lipid and lipoprotein concentrations in European populations. However, it is still unclear whether these loci identified in Caucasian GWA studies also exert the same effect on lipid and lipoprotein concentrations in a Chinese population. We genotyped 10 single-nucleotide polymorphisms (SNPs) in nine loci in a Chinese Han population sample (n = 4,192) and assessed the associations of these SNPs with metabolic traits, using linear regression adjusted for age, gender, diabetes status, and body mass index. Three variants (rs12654264, P ∼ 1.7 × 10(-6); rs3764261, P ∼ 7.1 × 10(-7); and rs4420638, P ∼ 1.1 × 10(-3)) showed strong evidence for association with total cholesterol; four variants (rs780094, P ∼ 1.8 × 10(-11); rs17145738, P ∼ 5.0 × 10(-7); rs326, P ∼ 2.3 × 10(-6); and rs439401, P ∼ 2.2 × 10(-5)) showed strong evidence for association with triglycerides, four variants (rs17145738, P ∼ 1.9 × 10(-4); rs326, P ∼ 9.7 × 10(-4); rs1800588, P ∼ 1.5 × 10(-7); and rs3764261, P ∼ 4.3 × 10(-14)) showed strong evidence for association with HDL-cholesterol (HDL-C), two variants (rs12654264, P ∼ 2.3 × 10(-5); and rs4420638, P ∼ 3.6 × 10(-4)) showed strong evidence for association with LDL-C, and four variants (rs326, P ∼ 2.8 × 10(-3); rs1800588, P ∼ 6.1 × 10(-4); rs3764261, P ∼ 2.0 × 10(-3); and rs4420638, P ∼ 9.4 × 10(-5)) showed strong evidence for association with total cholesterol-HDL-C-related ratio. These SNPs generated strong combined effects on lipid traits and dyslipidemia. Our findings indicate that the variants that associated with metabolic traits in Europeans may also play a role in a Chinese Han population.

Association between the 5-HTR1B gene polymorphisms and alcohol dependence in a Han Chinese population

The human serotonin receptor 1B (HRT1B) plays an important role in regulating serotonin release. Previous research has suggested that the genetic variation of the HTR1B gene may confer susceptibility to alcoholism or some subtypes of alcohol dependence, but the evidence has been inconsistent. The aim of the present study is to examine whether polymorphic variants of the HTR1B gene are associated with alcohol dependence subtypes or drinking-related behaviors in Chinese Han population. Alcohol-dependent (AD) male patients ( n = 135) and controls ( n = 143) were genotyped for two polymorphisms: A161T in the promoter region and the synonymous variation G861C in the coding region of HTR1B. The results showed that the A161T polymorphism was associated with alcohol dependence (T vs. A allele: p = 0.002; OR = 2.18, 95% CI: 1.32–3.60). This association was strengthened in those with positive family history (OR = 3.12, 95% CI: 1.71–5.70) and/or early onset (OR = 4.53, 95% CI: 2.18–9.44) of alcohol dependence. The A161T variant was also significantly associated with age of onset of alcoholism ( p = 0.001). Furthermore, there was a significant difference of haplotypic frequencies between patients and controls ( χ 2 = 14.84, df = 3, p = 0.002), with one common haplotype AG of being significantly underrepresented among the patient group compared to the control group (34% vs. 47.7%, permutation p = 0.0034; OR = 0.56; 95% CI: 0.39–0.79). These findings confirm HTR1B as a susceptibility gene for alcohol dependence in the sample of Chinese Han population. The HTR1B A-161 T polymorphism may be particularly valuable as a functional genetic marker for alcoholism and merits additional study.

Association of the SDF1-3′A polymorphism with susceptibility to myocardial infarction in Chinese Han population

SDF-1 has been demonstrated to be involved in the pathophysiology of atherosclerosis. This study was aimed to investigate whether the SDF1-3'A polymorphism (rs1801157) is associated to myocardial infarction (MI) in a sample of Chinese Han population. A total of 560 patients with MI and 532 controls were enrolled in the study. The SDF1-3'A polymorphism was determined by polymerase chain reaction -restriction fragment length polymorphism (PCR-RFLP) analysis. A significant difference in genotype distribution and allele frequency was observed between patients and controls (P = 0.003 and P = 0.001, respectively). The A allele carriers had a significantly reduced MI risk compared with the GG homozygotes (OR, 0.69; 95% CI, 0.52-0.92; adjusted P = 0.007) in a logistic regression model after controlling conventional risk factors. The present study showed a significant association between the SDF1-3'A polymorphism and MI in Chinese Han population.

Polymorphism of two new Y-STR loci in a Chinese population

Human chromosome Y-specific short tandem repeat (Y-specific STR) markers have useful properties for forensic applications. However, there is a need to develop more Y-specific STR markers because the discriminating power of each STR locus is limited. In the present study, we describe our results on two new Y-specific STR markers, which were initially reported by White et al. [Genomics 57 (1999) 433] as Y-GATA-C4 and Y-GATA-A10. The distributions of alleles and haplotypes for both Y-specific STR loci were studied in a Chinese Han population sample. Allele determination was carried out by comparison with sequenced allelic ladders which were made in-house. Following the recommendations of the International Society of Forensic Genetics, the allele classification for both Y-specific STR loci was based on the number of repeat motifs. The results show that the haplotype diversity, the power of discrimination and the exclusion probability in the Chinese population for both Y-specific STR loci were 0.9090. The implication from this study is that Y-GATA-C4 and Y-GATA-A10 are useful Y-specific STR markers for forensic DNA typing in Chinese populations.

Allele sequences of six new Y-STR loci and haplotypes in the Chinese Han population

Human chromosome Y-specific short tandem repeat (Y-specific STR) markers have useful properties for forensic applications. However, there is a need to develop more Y-specific STR markers, because the discriminating power of each STR locus is limited. In the present study, we describe our results on six new Y-specific STR markers that were initially located using sequence database information by Ayub et al. and were named DYS434, DYS435, DYS436, DYS437, DYS438 and DYS439. Our studies focused on the analysis of the DNA sequence for each allele at all six Y-specific STR loci in order to understand their structures in the human genome and to construct human allelic ladders, which are necessary for forensic DNA typing. In addition, the haplotype distribution for all six analyzed loci was studied in a Chinese Han population sample. The results indicate that DYS434, DYS435, DYS436, DYS437, DYS438 and DYS439 are useful Y-specific STR markers for forensic sciences.