title: Haplotyping of TNFalpha gene promoter using melting temperature analysis: detection of a novel -856(G/A) mutation.
abstract: Tumor necrosis factor alpha (TNFalpha) is a potent cytokine with a wide range of pro-inflammatory activities and plays a critical role in the pathogenesis of a number of infectious, inflammatory, autoimmune, and metabolic diseases. We determined four single-nucleotide polymorphisms (SNPs), -1031(C/T), -863(C/A), -857(C/T), and -308(G/A) in the TNFalpha promoter region using melting temperature analysis, among 1451 geriatric autopsy samples. Two adjacent SNPs, -863(C/A) and -857(C/T), were directly assayed by a single probe reaction, which correctly determined three of four expected haplotypes. Sequence confirmation related that the most rare haplotype (8/2902 chromosomes, frequency: 0.26%) contains a novel mutation of -856(G/A), instead of the predicted haplotype. These results indicate that melting temperature analysis provides a robust method to determine the polymorphisms in the TNFalpha promoter.
authors.affiliation: Department of Molecular Epidemiology, Medical Research Institute, Tokyo Medical and Dental University, Chiyoda-ku, Tokyo, Japan.
authors.forename: Y
authors.initials: Y
authors.lastname: Song
authors.forename: J
authors.initials: J
authors.lastname: Araki
authors.forename: L
authors.initials: L
authors.lastname: Zhang
authors.forename: T
authors.initials: T
authors.lastname: Froehlich
authors.forename: M
authors.initials: M
authors.lastname: Sawabe
authors.forename: T
authors.initials: T
authors.lastname: Arai
authors.forename: T
authors.initials: T
authors.lastname: Shirasawa
authors.forename: M
authors.initials: M
authors.lastname: Muramatsu
mesh_terms: D006239:Haplotypes / Q000235:genetics / Q000276:immunology; D006801:Humans; D017354:Point Mutation / Q000235:genetics* / Q000276:immunology; D016133:Polymerase Chain Reaction / Q000379:methods; D020641:Polymorphism, Single Nucleotide / Q000235:genetics* / Q000276:immunology; D011401:Promoter Regions, Genetic / Q000235:genetics* / Q000276:immunology; D014409:Tumor Necrosis Factor-alpha / Q000235:genetics* / Q000276:immunology
chemical_list: D014409:Tumor Necrosis Factor-alpha