Analysis of single nucleotide polymorphisms and haplotypes in HOXC gene cluster within susceptible region 12q13 of simple congenital heart disease.
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In the candidate region 12q13 of simple congenital heart disease(CHD), four single nucleotide polymorphisms(SNPs) in HOXC4 gene were chosen in order to investigate the distribution of SNP and haplotypes in simple CHD patients and normal people.The genotype of 4 SNPs in 108 simple CHD patients and 200 normal people were analyzed by restriction fragment length polymorphism(RFLP) and denaturing high-performance liquid chromatography(DHPLC). The statistical contingency table method was used to analyze SNP genotype frequency and gene frequency in patients and control group; then, the haplotypes were established and their frequencies in the two groups were assessed by PHASE software.C16476T polymorphism was not detected; A17860G located in 3' flanking sequence of HOXC5 gene displayed significant difference between the two groups. The G allele frequency in simple CHD patients was higher than that in healthy controls(P < 0.05); the distribution of frequencies of 4 haplotypes showed significant difference(P < 0.01).The A17860G located in 3'flanking sequence of HOXC5 gene is associated with simple CHD; the risk of CHD in the persons with G17860 is higher than that in those with A17860. the haplotype of 3 SNPs may be linked with the susceptible gene of simple CHD.Keywords:
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In the candidate region 12q13 of simple congenital heart disease(CHD), four single nucleotide polymorphisms(SNPs) in HOXC4 gene were chosen in order to investigate the distribution of SNP and haplotypes in simple CHD patients and normal people.The genotype of 4 SNPs in 108 simple CHD patients and 200 normal people were analyzed by restriction fragment length polymorphism(RFLP) and denaturing high-performance liquid chromatography(DHPLC). The statistical contingency table method was used to analyze SNP genotype frequency and gene frequency in patients and control group; then, the haplotypes were established and their frequencies in the two groups were assessed by PHASE software.C16476T polymorphism was not detected; A17860G located in 3' flanking sequence of HOXC5 gene displayed significant difference between the two groups. The G allele frequency in simple CHD patients was higher than that in healthy controls(P < 0.05); the distribution of frequencies of 4 haplotypes showed significant difference(P < 0.01).The A17860G located in 3'flanking sequence of HOXC5 gene is associated with simple CHD; the risk of CHD in the persons with G17860 is higher than that in those with A17860. the haplotype of 3 SNPs may be linked with the susceptible gene of simple CHD.
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Objectives To explore the possible relationship between cytokines IL-1β and IL-1Ra gene single nucleotide polymorphism(SNP) and susceptibility to ulcerative colitis (UC). Methods Fifty-six UC patients and forty-four healthy subjects(HS) were enrolled. SNP of cytokines, including IL-1β(-511 T/C), IL-1β(+3962T/C)and IL-1Ra (11100C/T) were studied with sequence specific primers-polymerase chain reaction (PCR-SSP) respectively. Results ①C/T genotype frequency and T allele gene frequency in IL-1β+3962 site in UC patients was found significantly higher than those in HS (P=0.000, P=0.02). ②Haplotypes analysis revealed H1 Haplotype which contained IL-1B+3962T was assositated with disease (haplotype frequency patients 21.4% vs controls 2.3% P=0.039). Homozygosity for the haplotype H2 was negatively associated with disease (patients 30.5% vs. controls 50.0% P0.05). ③The frequence distributional difference of gene polymorphisms between serious extent and invaded locations of UC wasn’t significant (P0.05).④The frequence distribution difference of gene genotypes and allele genes between patients and controls in IL-1β –511 and IL-1Ra 11100 wasn’t significant (P0.05). Conclusions ①There is susceptibility correlation between the UC patients of North Chinese and the rising of CT gene polymorphisms and T allele gene frequency in IL-1β+3962 site. There isn’t correlation between the gene polymorphisms in IL-1β+3962 site and different invasion location and different serious extent of UC patients ②Gene polymorphisms in IL-1β-511 and IL-1Ra 11100 aren’t correlated with UC.
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Body: Background: We investigated the role of protein C (PC) polymorphism in patients with PTE in order to find out the correlation between its polymorphism and the susceptibility of the Chinese population to develop PTE. Methods: Sixty three consecutive patients with PTE were enrolled as the investigated group and eighty six healthy people as the control group. C/T at the position of 2405 and A/G at the position of 2418in the PC gene promoter region were detected through polymerase chain reaction-restriction fragment length polymorphism analysis. Results: (1) The results suggested that the genotype frequencies of the two SNPs when combined together were not significantly different between two group (P > 0.05).However, the allele frequency of the C2405T SNP was significantly different between the case and control group. The frequency of T allele in the PTE group was higher. (2) These results suggested that there were six different kinds of genotype distribution (TA - TA, TA - CA, TA - CG, CG - CG, CA - CG, CA - CA) and three different kinds of haplotype (TA, CG, CA). Conclusions: These results suggest that the two polymorphisms present in the control region of PC gene are associated with an increased susceptibility to PTE in the Chinese population. The2405T allele may be a possible risk factor for the development of PTE while the C allele may probably be a protective factor of PTE.Moreover, the TA haplotype may also be associated with an increased risk for developing PTE.
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To examine if there is any correlation between ankylosing spondylitis (AS) and TNF-a gene promoter single-nucleotide polymorphisms (SNP) and their associ- ated haplotypes. Using restriction fragment length poly- morphism—polymerase chain reaction method, the polymorphism of TNF-a-238, -308, -850, -857, -863 locus, and TNF-b ?252 were analyzed in patients with progres- sive AS, stable AS and control. (1) Neither the genotypes nor the allele frequencies of TNF-a (-308), (-238), (-863), and TNF-b ?252 showed differences in each group. TNF-a (-850) CC genotype and C allele frequency distribution was significantly higher in healthy controls group than in the stable and progressive groups. TNF-a (-857) CT, CC genotype, and C, T allele frequency showed differences in all groups. (2) Polymorphism linkage equilibrium test revealed that association of six TNF-a, b gene SNPs with haplotype GACTCG in progressive group is significantly higher than in the stable group and healthy control group (P 0.05). TNF-a (-857), (-850) gene polymorphism may increase the susceptibility to AS, but do not reflect the disease active state. The CC genotype and C allele may play a protective role in the pathogenesis of AS. TNF-a (-308) may be a weak indicator reflecting the active state of AS. Haplotype GACTCG may indicate both the suscepti- bility and the activity of AS.
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Objectives To investigate the effect on childhood asthma of single nucleotide polymorphisms(SNPs)in IL-13 gene and β2-adrenoreceptor(β2-AR)gene,and the combined effect of the two SNPs.Methods A total of 182 children with 96 asthma subjects and 96 control subjects were recruited.PCR-RFLP was used to detect the IL-13 A2044G SNPs and the β2-AR R16G SNPs.The difference of haplotype and allele frequency between two groups were analyzed.The combined effect of these two SNPs was examined.Results(1)The frequency of IL-13 A2044G G/G genotype in the asthma group was significantly higher than that in the control group(OR = 2.40,P = 0.005);(2)The frequencies of both β2-AR R16G A/A genotype and A allele in asthma patients were significantly higher than those in the control subjects(OR = 2.87,P = 0.011;OR = 1.82,P = 0.004);(3)The relative risk of developing asthma in the carrier of both IL-13 A2044G G/G + and β2-AR R16G A/A was significantly higher than that in the carriers of either IL-13 A2044G G/G or β2-AR R16G A/A(OR = 5.33,P = 0.009;OR = 4.80,P = 0.017).Conclusions Both IL-13 A2044G G/G and β2-AR R16G A/A are statistically related with the development of childhood asthma and there is the enhancing effect between them.
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The minor allele T of rs113420705 (C/T) in caspase-3 gene (CASP3) has been found to significantly increase the risk of Kawasaki disease (KD) and complicate coronary artery lesions (CALs) in Japanese children. In this study, we have explored association of single nucleotide polymorphisms (SNPs) of CASP3 gene and clinic phenotypes of KD.A total of 238 unrelated KD patients and 364 healthy controls with matched age, gender and ethnic origins were recruited. Genotypes of the 3 SNPs were determined with PCR-restriction fragment length polymorphism (PCR-RFLP) and DNA sequencing. Allelic, genotypic and haplotypic frequencies were compared between patients and controls, patients with and without CALs, and patients resistant to and responsive to intravenous immunoglobulin (IVIG) treatment.The T allele and T carriers of rs113420705 were significantly more common in KD patients than controls. A significant difference was also detected in haplotype distribution between patients and controls, where two haplotypes involving the T allele of rs113420705 showed higher frequencies in the patient group. Allelic and genotypic frequencies of the 3 SNPs were similar between patients with and without CALs and those resistant to and responsive to IVIG treatment.Our results suggested that CASP3 probably plays an important role in KD. The T allele of rs113420705 may provide a useful marker for KD susceptibility, although no association between this SNP and clinical prognosis and treatment effect of KD has been found among the selected Chinese children patients.
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Objective To investigate the genetic association between the polymorphism of rs4132604 site,rs2218404 site and rs1373336 site on NTNG1 gene and schizophrenia in Han population from the north of China.Methods PCR-RFLP analysis was used to detect the genotype of NTNG1 gene in 316 patients and 311 controls.Inheritance statistics methods were used to analysis the genotype,allele frequencies and haplotype.Results The genotypic frequency of the NTNG1 gene did not deviate from Hardy-Weinberg equilibrium in both patient group and control group(P 0.05).The allele and genotype frequencies for rs2218404 and rs1373336 were not significantly different between the patients and the controls.However,SNP rs4132604 showed significant association with schizophrenia(G T,χ2=7.86,P =0.01,genotype χ2=7.67,P=0.02).Significant haplotype differences between case and control groups were observed.It include GG(χ2=6.11,P=0.01),TG(χ2=5.28,P =0.02)between rs4132604 and rs2218404,GT(χ2=5.38,P =0.02),GC(χ2=4.72,P =0.03)between rs1373336 and rs2218404,GGT(χ2=13.40,P =0.00,TGT(χ2=6.56,P =0.01)between three SNPs.Conclusion Rs4132604 variations in NTNG1 may play a role in schizophrenia in the Chinese Northern population.The frequencies of haplotypes between the three SNPs have differences between case and control groups.
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Background : We investigated the role of protein C (PC) polymorphism in patients with PTE in order to find out the correlation between its polymorphism and the susceptibility of the Chinese population to develop PTE. Methods : Sixty three consecutive patients with PTE were enrolled as the investigated group and eighty six healthy people as the control group. C/T at the position of 2405 and A/G at the position of 2418in the PC gene promoter region were detected through polymerase chain reaction-restriction fragment length polymorphism analysis. Results: (1) The results suggested that the genotype frequencies of the two SNPs when combined together were not significantly different between two group (P > 0.05).However, the allele frequency of the C2405T SNP was significantly different between the case and control group. The frequency of T allele in the PTE group was higher. (2) These results suggested that there were six different kinds of genotype distribution (TA - TA, TA - CA, TA - CG, CG - CG, CA - CG, CA - CA) and three different kinds of haplotype (TA, CG, CA). Conclusions: These results suggest that the two polymorphisms present in the control region of PC gene are associated with an increased susceptibility to PTE in the Chinese population. The2405T allele may be a possible risk factor for the development of PTE while the C allele may probably be a protective factor of PTE.Moreover, the TA haplotype may also be associated with an increased risk for developing PTE.
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