1. Discrimination of a single nucleotide polymorphism in the haptoglobin promoter region, rs5472, using a competitive fluorophore-labeled probe hybridization assay following loop-mediated isothermal amplification
- Author
-
Yasuyoshi Mori, Satoru Michiyuki, Tsugunori Notomi, Norihiro Tomita, Hidetoshi Kanda, and Kosuke Tashiro
- Subjects
0301 basic medicine ,Loop-mediated isothermal amplification ,Single-nucleotide polymorphism ,Polymorphism, Single Nucleotide ,Applied Microbiology and Biotechnology ,Biochemistry ,Analytical Chemistry ,03 medical and health sciences ,symbols.namesake ,0302 clinical medicine ,Humans ,Nucleotide ,Promoter Regions, Genetic ,Saliva ,Molecular Biology ,Fluorescent Dyes ,chemistry.chemical_classification ,Sanger sequencing ,Haptoglobins ,biology ,Hybridization probe ,Organic Chemistry ,Haptoglobin ,Promoter ,General Medicine ,Molecular biology ,SNP genotyping ,030104 developmental biology ,Molecular Diagnostic Techniques ,chemistry ,030220 oncology & carcinogenesis ,biology.protein ,symbols ,Nucleic Acid Amplification Techniques ,Biotechnology - Abstract
Personalized peptide vaccination, which involves activation of the host immune system against cancer cells using personalized peptide vaccines (PPVs), can improve overall survival in multiple cancer types. However, the clinical efficacies of PPVs vary for unknown reasons. Recently, a single nucleotide polymorphism (NG_012651.1:g.4461_5460[4960A>G]) in the haptoglobin promoter region, rs5472, was significantly associated with clinical response of PPV. Therefore, rs5472 is expected to be a predictive biomarker for PPV therapy. Here, we described a single nucleotide discrimination method for rs5472 analysis by combining the loop-mediated isothermal amplification and quenching probe methods. In evaluation of saliva samples, this method showed high concordance with the results of Sanger sequencing (100%, n = 36). Importantly, this method did not require calculation of melting temperature for single nucleotide discrimination and could therefore be carried out on a simple instrument. Accordingly, this method may be more robust and applicable to near-patient testing.
- Published
- 2021
- Full Text
- View/download PDF