title: Comparison of three different methods for the evaluation of IL28 and ITPA polymorphisms in patients infected with HCV.
abstract: A single nucleotide polymorphism (SNP) upstream of the IL28 gene (rs12979860) has been reported to predict sustained virological response to peginterferon-ribavirin therapy in chronic HCV patients. In addition, two functionally deficient variants (rs1127354 and rs7270101) of inosine triphosphatase (ITPA) were shown to protect against ribavirin (RBV) - induced hemolytic anemia during early stages of treatment. In this study, three methods for detecting IL28 and ITPA mutations were compared to evaluate accuracy, sensitivity costs and turn-around time. IL28 and ITPA variants were detected using genomic DNA from peripheral blood mononuclear cells (PBMCs) of 61 patients with chronic HCV infection by denaturing high-performance liquid chromatography (DHPLC), direct DNA sequencing analysis and Taq Man Real-Time SNP analysis. Complete concordance in the IL28 polymorphism analysis was observed among the three methods. As for ITPA polymorphisms, 60/61 (98.4%) samples were consistent among the three methods, while results for 1/61 (1.64%) samples were concordant by DHPLC and sequencing, and discordant by real-time SNP. All three methods are suitable for routine testing. On the other hand, screening by real-time SNP detection was less expensive and more rapid.
authors.affiliation: Molecular Virology Unit, Virology and Microbiology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.
authors.forename: Loretta
authors.initials: L
authors.lastname: Fiorina
authors.forename: Stefania
authors.initials: S
authors.lastname: Paolucci
authors.forename: Stavros
authors.initials: S
authors.lastname: Papadimitriou
authors.forename: Fausto
authors.initials: F
authors.lastname: Baldanti
mesh_terms: D000998:Antiviral Agents / Q000008:administration & dosage*; D019698:Hepatitis C, Chronic / Q000188:drug therapy*; D006801:Humans; D007372:Interferons / Q000008:administration & dosage; D007378:Interleukins / Q000235:genetics*; D007963:Leukocytes, Mononuclear; D020641:Polymorphism, Single Nucleotide; D011755:Pyrophosphatases / Q000235:genetics*; D012254:Ribavirin / Q000008:administration & dosage; D016896:Treatment Outcome; D014773:Virology / Q000379:methods*; D000095022:Interferon Lambda; D000097630:Inosine Triphosphatase
chemical_list: D000998:Antiviral Agents; D007372:Interferons; D007378:Interleukins; D011755:Pyrophosphatases; D012254:Ribavirin; C000624353:interferon-lambda, human; D000095022:Interferon Lambda; C511829:ITPA protein, human; D000097630:Inosine Triphosphatase