Comparison of three different methods for the evaluation of IL28 and ITPA polymorphisms in patients infected with HCV

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.