Development and Validation of a Simple, Rapid and Inexpensive PCR-RFLP Method for Genotyping of Common IL28B Polymorphisms: A Useful Pharmacogenetic Tool for Prediction of Hepatitis C Treatment Response

authors:

avatar Heidar Sharafi 1 , avatar Ali Pouryasin 2 , * , avatar Seyed Moayed Alavian 1 , avatar Bita Behnava 1 , avatar Maryam Keshvari 1 , avatar Leila Mehrnoush 1 , avatar Shima Salimi 1 , avatar Osveh Kheradvar 1

1) Armin Pathobiology Laboratory, 2) Tehran Hepatitis Cohort (THC) Study, IR Iran
1) Armin Pathobiology Laboratory, 2) Tehran Hepatitis Cohort (THC) Study, 3) Department of Genetics, Islamic Azad University-Arsanjan branch, pouryasin@iaua.ac.ir, IR Iran
Hepatitis Monthly: Vol.12, issue 3; 190-195
article type: Research Article
received: January 9, 2012
accepted: March 2, 2012
DOI: https://doi.org/10.5812/hepatmon.849

how to cite: Sharafi H, Pouryasin A, Alavian S, Behnava B, Keshvari M, et al. Development and Validation of a Simple, Rapid and Inexpensive PCR-RFLP Method for Genotyping of Common IL28B Polymorphisms: A Useful Pharmacogenetic Tool for Prediction of Hepatitis C Treatment Response. Hepat Mon. 2012;12(3): 190-195. https://doi.org/10.5812/hepatmon.849.

Abstract

Background: In 2009, 3 genome-wide association studies implicated IL28B single-nucleotide polymorphisms (SNPs) as the strongest genetic pretreatment predictor of sustained virological response (SVR) in hepatitis C infection. Recently, the American Association for the Study of Liver Diseases (AASLD) and the European Association for the Study of the Liver (EASL) included IL28B testing in their guidelines.
Objectives: The main aim of this study was to develop and validate a simple, rapid, and inexpensive polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method for genotyping of common IL28B polymorphisms (rs12979860 and rs8099917).
Patients and Methods: Two methods were developed to genotype common IL28B polymorphisms: 1) PCR-sequencing as a reference method and 2) PCR-RFLP as a rapid and inexpensive method. Both polymorphisms were genotyped in 104 Iranian hepatitis C patients by both methods simultaneously. To validate the PCR-RFLP method, the PCR-RFLP genotyping results should be 100% concordant with the PCR-sequencing results.
Results: Genotyping of rs12979860 and rs8099917 by PCR-RFLP was concordant with PCR-sequencing in 104 (100%) individuals. The analytical sensitivity and specificity of the PCR-RFLP method for genotyping of both SNPs are 100%. Among these 104 patients with chronic hepatitis C, the frequency of the rs12979860 CC, CT and TT genotypes were 40.4%, 47.1% and 12.5% and the frequency of the rs8099917 TT, GT and GG genotypes were 59.6%, 35.6% and 4.8%, respectively. Also, three IL28B haplotypes (rs12979860-rs8099917) were found among our patients including C-T, T-G and T-T with 63.9%, 22.6% and 13.5% frequency, respectively. C-G haplotype was absent in all of our patients.
Conclusions: We have developed a validated, fast, and simple PCR-RFLP method for genotyping of common IL28B SNPs that is more cost-effective than sequencing.

  • Implication for health policy/practice/research/medical education:
    This article focuses on development of a simple method for genotyping of IL28B polymorphisms. This study is recommended to researchers in the field of viral hepatitis.
  • Please cite this paper as:
    Sharafi H, Pouryasin A, Alavian SM, Behnava B, Keshvari M, Mehrnoush L, et al. Development and Validation of a Simple, Rapid and Inexpensive PCR-RFLP Method for Genotyping of Common IL28B Polymorphisms: A Useful Pharmacogenetic Tool for Prediction of Hepatitis C Treatment Response. Hepat Mon. 2012;12(3):190-5. DOI: 10.5812/hepatmon.849

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