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

• Published in: Journal of virological methods Vol. 184; no. 1-2; pp. 103 - 105
• Main Authors: Fiorina, Loretta, Paolucci, Stefania, Papadimitriou, Stavros, Baldanti, Fausto
• Format: Journal Article
• Language: English
• Published: Kidlington Elsevier B.V 01-09-2012; Elsevier
• Subjects: Antiviral Agents - administration & dosage; Biological and medical sciences; chronic hepatitis C; DHPLC; DNA; Fundamental and applied biological sciences. Psychology; genes; hemolytic anemia; Hepatitis C virus; Hepatitis C, Chronic - drug therapy; high performance liquid chromatography; Humans; IL 28-B; Interferons - administration & dosage; Interleukins - genetics; ITPA; Leukocytes, Mononuclear; Microbiology; mononuclear leukocytes; patients; Polymorphism, Single Nucleotide; Pyrophosphatases - genetics; Ribavirin - administration & dosage; screening; sequence analysis; single nucleotide polymorphism; Techniques used in virology; therapeutics; Treatment Outcome; Virology; Virology - methods; IL 28-B; DHPLC; Hepatitis C virus; ITPA; Virus; Human; Method; Flaviviridae; Hepacivirus; Polymorphism
• ISSN: 0166-0934; 1879-0984
• DOI: 10.1016/j.jviromet.2012.05.006

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.