Recently, the -160 C/A polymorphism, located within the regulatory region of E-cadherin promoter, has been shown to influence E-cadherin transcription by altering transcription factor binding. We examined the effect of this polymorphism on risk of gastric cancer and on histological classification of intestinal- and diffuse-type gastric cancer in 146 normal healthy individuals and 292 Korean gastric cancer patients. Genomic DNA samples were examined by polymerase chain reaction (PCR)-single strand conformational polymorphism (SSCP)-sequencing and confirmed by restriction fragment length polymorphism (RFLP). Unexpectedly, there was no significant difference in the genotype frequencies of the polymorphism between normal control and gastric cancer patients (x(2) test, p=0.433). The estimated odd ratio of C/C to A/A genotype in gastric cancer cases was 1.07 (95% confidence interval, 0.396-2.870). We also found no evidence for differences in risk for the intestinal- and diffuse-type gastric cancer. These results suggest that the -160 C/A polymorphism of the E-cadherin has no direct effect on the risk of Korean gastric cancer development and on its histological classification.
Alleles ; Cadherins/*genetics ; DNA/metabolism ; Genetic Predisposition to Disease ; Genotype ; Homozygote ; Human ; Korea ; Odds Ratio ; Polymerase Chain Reaction ; Polymorphism (Genetics) ; Polymorphism, Restriction Fragment Length ; *Polymorphism, Single Nucleotide ; Polymorphism, Single-Stranded Conformational ; *Promoter Regions (Genetics) ; Risk ; Stomach Neoplasms/*genetics ; Transcription, Genetic

Autoimmune diseases (AID) are a group of complex disorders due to antibodies acting on self-antigens causing damage to the body. AID has long been considered as the outcome of genetic and environmental interactions. In recent years, studies have shown that increased susceptibility to AID may be associated with single nucleotide polymorphisms and copy number variations of Toll like receptor 7 (TLR7) gene, which provided a clue to further understanding of the pathogenesis of AID. This paper provides a review of the recent advances in understanding of the roles of TLR7 gene single nucleotide polymorphisms and copy number variations in AID.
Animals ; Autoimmune Diseases ; genetics ; DNA Copy Number Variations ; Genetic Predisposition to Disease ; Humans ; Polymorphism, Single Nucleotide ; Toll-Like Receptor 7 ; genetics

OBJECTIVETo investigate the sequence polymorphism of mtDNA HV1,HV2 overlapping fragments and coding region encompassing position 8430-8673 in Hebei Han population.

METHODSPolymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) combined with sequencing method was used to detect the haplotype distribution of mtDNA in 100 Hebei Han individuals.

RESULTSNinety-one haplotypes were noted in 100 unrelated individuals. The gene diversity is 0.9985 and the random match probability is 0.0115. Compared with the Anderson sequence, 65 sites of different nucleotide sequences were noted, of which 44 sites were previously registered in MITOMAP, 12 sites were not registered and the gene mutations were different from MITOMAP at 9 positions.

CONCLUSIONThe obtained data suggest that these loci are valuable genetic markers for personal identification and thus could be used as basic data for the forensic application of mtDNA in Hebei province.

China ; DNA, Mitochondrial ; genetics ; Humans ; Polymorphism, Genetic ; Polymorphism, Single Nucleotide ; Polymorphism, Single-Stranded Conformational

OBJECTIVE: There is asingle nucleotide polymorphism (SNP) in the exon 2 of the vitamin D receptor (VDR) gene that can be distinguished using the restriction endonuclease FokI, and accordingly divided into three genotypes: FF, Ff and ff. VDR-FokI polymorphism was the only known SNP that could alter the protein structure of VDR. CYP24A1 is the gene encoding vitamin D 24 hydroxylase and is a vitamin D responsive gene. The influence of rs2228570 on transcriptional activation by VDR in human gingival fibroblasts (hGF) and periodontal ligament cells (hPDLC) was investigated in this study. METHODS: hGF and hPDLC of 12 donors' were primarily cultured and genomic DNA was extracted. A part of genomic DNA with the length of 267 bp was obtained using PCR, which contained the SNP. VDR-Fok I genotypes were determined according to the results of restriction fragment length polymorphism. hGF and hPDLC were stimulated with 10 nmol/L 1α,25 dihydroxy vitamin D₃ (1,25OH₂D₃) or 1 000 nmol/L 25 hydroxy vitamin D₃ (25OHD₃) for 48 h before RNA was extracted. Then VDR antagonist ZK159222 was used or not used during 1,25OH₂D₃ or 25OHD₃ stimulation with hGF and hPDLC. After 1,25OH₂D₃ stimulation for 48 h, the proteins in hGF and hPDLC were also collected. The protein expressions of CYP24A1 and VDR were detected using Western blot. RESULTS: Among the 12 donors' cell cultures, the number of FF, ff and Ff genotypes was 4, 3 and 5, respectively.After stimulation with 1,25OH₂D₃ or 25OHD₃ for 48 h,CYP24A1 mRNA levels in FF-hGF were significantly higher than those in other hGF genotypes(1,25OH₂D₃: F=31.147, P<0.01; 25OHD₃: F= 32.061,P <0.01), as was in FF-hPDLC (1,25OH₂D₃: F=23.347, P<0.01; 25OHD₃: F=32.569,P<0.01). When ZK159222 was used before 1,25OH₂D₃ stimulation, this statistically significant difference disappeared (hGF: F=0.246, P=0.787; hPDLC: F=0.574, P=0.583). When ZK159222 was used before 25OHD₃ stimulation, the trend was similar (hGF: F=1.636, P=0.248; hPDLC: F=0.582, P=0.578).After stimulation with 1,25OH₂D₃ for 48 h, CYP24A1 protein levels in FF-hGF were significantly higher than those in the other hGF genotypes (F=12.368, P <0.01), as was in FF-hPDLC (F=15.749, P <0.01). In hGF and hPDLC, the mRNA or protein expression of VDR of different genotypes was not significantly different under different stimulation conditions.The paired comparison showed that there was no statistically significant difference between the expression of CYP24A1 in hGF and that in hPDLC under all the stimulation conditions, as was the expression of VDR. CONCLUSION In hGF and hPDLC, the FF-VDR genotype is associated with the more remarkable up-regulation of CYP24A1than the other genotypes, indicating that transcriptional activation of FF-VDR might be higher than those of other vitamin D receptors.
Fibroblasts/metabolism* ; Genotype ; Humans ; Periodontal Ligament/metabolism* ; Polymorphism, Genetic ; Polymorphism, Restriction Fragment Length ; Polymorphism, Single Nucleotide ; Receptors, Calcitriol/genetics* ; Vitamin D3 24-Hydroxylase/metabolism*

The development of Human Genome Project (HGP) makes it possible and more important to reveal the variations or polymorphisms precisely between different individuals and populations. Due to the characters of their high polymorphism and value in disease-linkage analysis as well as pharmacogenomnics, genetic markers on X chromosome have attracted much more attention of current medical and forensic scientists. This report summarized the proceeding of research on X chromosome genetic markers in the clinical and forensic context.
Chromosomes, Human, X/genetics* ; Female ; Genetic Markers ; Genetic Variation/genetics* ; Humans ; Microsatellite Repeats/genetics* ; Polymorphism, Restriction Fragment Length ; Polymorphism, Single Nucleotide

OBJECTIVETo investigate the genetic association for schizophrenia within the long arm region 1 band 1 of chromosome 22 (22q11) in a Han Chinese population.

METHODSPolymerase chain reaction (PCR)-based restriction fragment length polymorphism (RFLP) analysis was used to detect three single nucleotide polymorphism (SNPs), rs165655 (A/G base change) and rs165815 (C/T base change) present in the ARVCF (armadillo repeat gene deletion in velocardiofacial syndrome) locus, and rs756656 (A/C base change) in the LOC128979 (expressed sequence tags, EST) locus, among 100 nuclear families composed of fathers, mothers and affected offspring with schizophrenia. Genotyping data were analyzed by linkage disequilibrium methods including haplotype relative risk (HRR) analysis, transmission disequilibrium test (TDT) and haplotype transmission analysis.

RESULTSThe genotype frequency distributions of three SNPs were all in Hardy-Weinberg equilibrium; Both HRR and TDT analysis showed that rs165815 was associated with schizophrenia (P < 0.05), whereas the other two SNPs did not show any allelic association. The haplotype transmission analysis showed a biased transmission for the rs165655-rs165815 haplotype system and for the rs756656-rs165655-rs165815 haplotype system (P < 0.01).

CONCLUSIONEither ARVCF gene itself or a nearby locus might confer susceptibility to schizophrenia in a Han Chinese population.

Adult ; Chromosomes, Human, Pair 22 ; genetics ; Female ; Genetic Predisposition to Disease ; genetics ; Haplotypes ; Humans ; Linkage Disequilibrium ; genetics ; Male ; Polymorphism, Restriction Fragment Length ; Polymorphism, Single Nucleotide ; Schizophrenia ; genetics

OBJECTIVE: To explore the genetic etiology for a newborn with corneal opacity. METHODS: The neonate and her parents were subjected to routine G-banding chromosomal karyotyping analysis. Copy number variation (CNV) was analyzed with low-coverage whole-genome sequencing (WGS) and single nucleotide polymorphism microarray (SNP array). RESULTS: No karyotypic abnormality was found in the newborn and her parents. Low-coverage WGS has identified a de novo 5.5 Mb microdeletion at chromosome 8q21.11-q21.13 in the neonate, which encompassed the ZFHX4 and PEX2 genes. The result was confirmed by SNP array-based CNV analysis. CONCLUSION The newborn was diagnosed with chromosome 8q21.11 deletion syndrome. ZFHX4 may be one of the key genes underlying this syndrome.
Chromosome Banding ; Chromosomes, Human, Pair 8/genetics* ; DNA Copy Number Variations ; Female ; Genetic Testing ; Homeodomain Proteins/genetics* ; Humans ; Infant, Newborn ; Karyotyping ; Monosomy/genetics* ; Peroxisomal Biogenesis Factor 2/genetics* ; Polymorphism, Single Nucleotide ; Transcription Factors/genetics*

OBJECTIVE: The aim of this study was to investigate the association of JAK1 polymorphisms with allergic rhinitis in China Han population. METHOD: A total of 450 patients with AR and 615 healthy subjects as control were genotyped for the presence of three single nucleotide polymorphisms using polymerase chain reaction restriction fragment length polymorphism (PGR-RFLP) analysis of DNA extracted from blood samples. RESULT: All control subjects were in Hardy-Weinberg equilibrium, but high frequencies of JAK1 the homozygous rs310241 CC genotype were observed in AR patients compared to controls (P < 0.05). The results also revealed that there was no association between the rest of two investigated SNPs and AR. CONCLUSION Our results suggested that JAK1 gene rs310241 CC genotype was associated with patients with AR.
Asian Continental Ancestry Group ; genetics ; China ; Genetic Predisposition to Disease ; Genotype ; Humans ; Janus Kinase 1 ; genetics ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Polymorphism, Single Nucleotide ; Rhinitis, Allergic ; genetics

BACKGROUNDGenetic factors contribute to the development of coronary artery disease (CAD). Recently, a missense mutation in the low density lipoprotein receptor related protein 6 (LRP6) gene, encoding low density lipoprotein receptor related protein 6, has been implicated in an autosomal dominant form of early-onset CAD. The aim of this study was to determine whether the common variants in LRP6 are associated with sporadic CAD in Chinese.

METHODSA total of 766 CAD patients and 806 healthy controls were included in this study. The presence of angiographic CAD was determined by coronary angiographic analysis. Six signal nucleotide polymorphisms (SNPs) were genotyped using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique.

RESULTSA significant association was detected between rs11054731 in LRP6 intron 2 and CAD in our cohort (P = 0.001). The CC genotype and C allele frequency in the case group were 52% and 72%. Using a dominant model of inheritance, the C allele of rs11054731 was shown to be an independent risk factor for CAD with an OR of 1.45 (95%CI: 1.19 - 1.77, P = 0.0002). With the stratification according to the number of affected coronary arteries, an association was observed between rs11054731 and CAD (P = 0.0002). No significant association was observed between any other SNPs and the risk of CAD.

CONCLUSIONThe C allele of the rs11054731 within the LRP6 gene was associated with increased risk and extent of CAD in Chinese.

Aged ; Asian Continental Ancestry Group ; genetics ; Coronary Artery Disease ; genetics ; Female ; Genetic Predisposition to Disease ; genetics ; Genotype ; Humans ; Low Density Lipoprotein Receptor-Related Protein-6 ; genetics ; Male ; Middle Aged ; Polymorphism, Genetic ; genetics ; Polymorphism, Restriction Fragment Length ; genetics ; Polymorphism, Single Nucleotide ; genetics

OBJECTIVETo study the relationship between the polymorphisms of single nucleotide polymorphisms(SNPs) in rs2240424, rs2057951, rs2240427 and rs714909 loci in the PATZ1 gene and azoospermia.

METHODSThe allele and genotype frequencies of the four SNPs were investigated in 180 patients with azoospermia and 190 normal men as controls by polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) analysis. The allele and genotype frequencies of the four SNPs were investigated in 180 patients with azoospermia and 190 normal men as controls by polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) analysis.

RESULTSThe frequencies of allele C (35.0% vs. 27.6%, P=0.031) and individuals with allele C (TC+CC) (57.8% vs. 46.3%, P=0.027) at the rs2057951 locus in azoospermic patients were significantly higher than that in normal men. There was a significant difference in distribution of haplotypes of the four SNPs between the two groups (P=0.01). Hapoltypes ACAC (11.1% vs. 6.6%, P=0.029) and ACGC (11.2% vs. 5.2%, P=0.003) increased significantly in azoospermic patients compared with controls.

CONCLUSIONThe allele C of rs2057951 locus and haplotypes ACAC and ACGC of the four SNPs in PTAZ1 gene increased the susceptibility to azoospermia, suggesting that PATZ1gene may be associated with azoospermia.

Alleles ; Azoospermia ; genetics ; Gene Frequency ; genetics ; Genetic Predisposition to Disease ; genetics ; Genotype ; Haplotypes ; Humans ; Kruppel-Like Transcription Factors ; genetics ; Male ; Polymorphism, Genetic ; Polymorphism, Restriction Fragment Length ; genetics ; Polymorphism, Single Nucleotide ; genetics ; Repressor Proteins ; genetics