A comparative study of various methods for detection of IL28B rs12979860 in chronic hepatitis C

References

• Venegas M, Villanueva RA, González K, Brahm J. IL28B polymorphisms associated with therapy response in Chilean chronic hepatitis C patients. World J Gastroenterol 2011;17:3636–9.
   PubMed Web of Science ®Google Scholar
• Sakamoto N, Watanabe M. New therapeutic approaches to hepatitis C virus. J Gastroenterol 2009;44:643–9.
   PubMed Web of Science ®Google Scholar
• Powis J, Peltekian KM, Lee SS, Sherman M, Bain VG, Cooper C, Krajden M, Deschenes M, Balshaw RF, Heathcote EJ, Yoshida EM. Exploring differences in response to treatment with peginterferon alpha 2a (40 kD) and ribavirin in chronic hepatitis C between genotypes 2 and 3. J Viral Hepat 2008;15:52–7.
   PubMed Web of Science ®Google Scholar
• Pawlotsky JM, Aghemo A, Dusheiko G, Forns X, Puoti M, Sarrazin C. EASL Recommendations on Treatment of Hepatitis C 2014. J Hepatol 2014;61:373–95.
   PubMed Web of Science ®Google Scholar
• Sedighimehr P, Irani S, Sakhaee F, Vaziri F, Aghasadeghi M, Sadat SM, Jamnani FR, Fateh A, Siadat SD. IL28B rs12980275 and HLA rs4273729 genotypes as a powerful predictor factor for rapid, early, and sustained virologic response in patients with chronic hepatitis C. Arch Virol 2016;6:1–9.
   Google Scholar
• Hengst J, Falk CS, Schlaphoff V, Deterding K, Manns MP, Cornberg M, Wedemeyer H. Direct-acting antiviral-induced hepatitis C virus clearance does not completely restore the altered cytokine and chemokine milieu in patients with chronic hepatitis C. J Infect Dis 2016;214:1965–74.
   PubMed Web of Science ®Google Scholar
• Fiorina L, Paolucci S, Papadimitriou S, Baldanti F. Comparison of three different methods for the evaluation of IL28 and ITPA polymorphisms in patients infected with HCV. J Virol Methods 2012;184:103–5.
   PubMed Web of Science ®Google Scholar
• Medrano RF, de Oliveira CA. Guidelines for the tetra-primer ARMS-PCR technique development. Mol Biotechnol 2014;54:599–608.
   Google Scholar
• Noir R, Kotera M, Pons B, Remy JS, Behr JP. Oligonucleotide-oligospermine conjugates (Zip Nucleic Acids): a convenient means of finely tuning hybridization temperatures. J Am Chem Soc 2008;130:13500–5.
   PubMed Web of Science ®Google Scholar
• Voirin E, Behr JP, Kotera M. Versatile synthesis of oligodeoxyribonucleotide-oligospermine conjugates. Nat Protoc 2007;2:1360–7.
   PubMed Web of Science ®Google Scholar
• Fateh A, Aghasadeghi MR, Keyvani H, Mollaie HR, Yari S, Hadizade Tasbiti AR, Ghazanfari M, Monavari SH. High resolution melting curve assay for detecting rs12979860 IL28B polymorphisms involved in response of Iranian patients to chronic hepatitis C treatment. APJCP 2015;16:1873–80.
   Google Scholar
• Fateh A, Aghasadeghi M, Siadat SD, Vaziri F, Sadeghi F, Fateh R, Keyvani H, Tasbiti AH, Yari S, Ataei-Pirkooh A, Monavari SH. Comparison of three different methods for detection of IL28 rs12979860 polymorphisms as a predictor of treatment outcome in patients with hepatitis C virus. Osong Public Health Res Perspect 2016;7:83–9.
   PubMedGoogle Scholar
• Barczak W, Suchorska W, Rubiś B, Kulcenty K. Universal real-time PCR-based assay for lentiviral titration. Mol Biotechnol 2015;57:195–200.
   PubMed Web of Science ®Google Scholar
• Kwok PY, Chen X. Detection of single nucleotide polymorphisms. Curr Issues Mol Biol 2003;5:43–60.
   PubMedGoogle Scholar
• Chen X, Sullivan P. Single nucleotide polymorphism genotyping: biochemistry, protocol, cost and throughput. Pharmacogenomics J 2003;3:77–96.
   PubMed Web of Science ®Google Scholar
• Sharafi H, Pouryasin A, Alavian SM, Behnava B, Keshvari M, Mehrnoush L, Salimi SH, Kheradvar O. 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;12:190–5.
   PubMed Web of Science ®Google Scholar
• Pampukha V, Kravchenko S, Moroz L, Livshits LA. IFNλ-3 (IL28B) genotyping by restriction fragment length polymorphism method: detection polymorphism of rs12979860. Biopolym Cell 2011;27:231–4.
   Google Scholar
• Nakamoto S, Kanda T, Imazeki F, Wu S, Arai M, Fujiwara K, Yokosuka O. Simple assay based on restriction fragment length polymorphism associated with IL28B in chronic hepatitis C patients. Scand J Gastroenterol 2011;46:955–61.
   PubMed Web of Science ®Google Scholar
• Rasmussen HB. Restriction fragment length polymorphism analysis of PCR-amplified fragments (PCR-RFLP) and gel electrophoresis-valuable tool for genotyping and genetic fingerprinting. Rijeka, Croatia: INTECH Open Access Publisher; 2012: 356–80.
   Google Scholar
• Li W, Zeng Y, Wang J, Zhou B, Zhang J, Zhang H, Li J, Wu Y, Hamoudi R, Zhou Y. Predicting sustained viral response to hepatitis C using a rapid and simple IL28B rs8099917 genotyping assay. Antiviral Res 2012;94:54–6.
   PubMed Web of Science ®Google Scholar
• Delvaux N, da Costa VD, da Costa MM, Lampe E. Comparison of four methods of genotyping IL28B polymorphisms in chronic hepatitis C patients. J Virol Methods 2015;220:1–4.
   PubMed Web of Science ®Google Scholar
• Galmozzi E, Menico BD, Rametta R, Dongiovanni P, Fracanzani AL, Benedan L, Borroni V, Maggioni P, Fargion S, Valenti L. A tetra‐primer amplification refractory mutation system polymerase chain reaction for the evaluation of rs12979860 IL28B genotype. J Viral Hepat 2011;18:628–30.
   PubMed Web of Science ®Google Scholar
• Poon KS, Ho SY, Tang JWT, Chua CW, Chiu L, Koay ES. Targeting both rs12979860 and rs8099917 polymorphisms with a single-tube high-resolution melting assay for IL28B genotyping. J Clin Microbiol 2012;50:3353–5.
   PubMed Web of Science ®Google Scholar
• Chen J, Wang L, Li Y, Cai B, Fu Y, Liao Y, Zhang J. Association analysis between SNPs in IL-28B gene and the progress of hepatitis B infection in Han Chinese. PloS One 2012;7:e50787.
   PubMed Web of Science ®Google Scholar
• Ito K, Higami K, Masaki N, Sugiyama M, Mukaide M, Saito H, Aoki Y, Sato Y, Imamura M, Murata K, Nomura H, Hige S, Adachi H, Hino K, Yatsuhashi H, Orito E, Kani S, Tanaka Y, Mizokami M. The rs8099917 polymorphism, when determined by a suitable genotyping method, is a better predictor for response to pegylated alpha interferon/ribavirin therapy in Japanese patients than other single nucleotide polymorphisms associated with interleukin-28B. J Clin Microbiol 2011;49:1853–60.
   PubMed Web of Science ®Google Scholar
• Wittwer CT. High-resolution DNA melting analysis: advancements and limitations. Hum Mutat 2009;30:857–9.
   PubMed Web of Science ®Google Scholar
• Montgomery JL, Sanford LN, Wittwer CT. High-resolution DNA melting analysis in clinical research and diagnostics. Expert Rev Mol Diagn 2010;10:219–40.
   PubMed Web of Science ®Google Scholar
• Taylor CF. Mutation scanning using high-resolution melting. Biochem Soc Trans 2009;37:433–7.
   PubMed Web of Science ®Google Scholar
• Moreau V, Voirin E, Paris C, Kotera M, Nothisen M, Rémy JS, Behr JP, Erbacher P, Lenne-Samuel N. Zip nucleic acids: new high affinity oligonucleotides as potent primers for PCR and reverse transcription. Nucleic Acids Res 2009;37:e130.
   PubMed Web of Science ®Google Scholar
• Paris C, Moreau V, Deglane G, Voirin E, Erbacher P, Lenne-Samuel N. Zip nucleic acids are potent hydrolysis probes for quantitative PCR. Nucleic Acids Res. 2010;38:e95.
   PubMed Web of Science ®Google Scholar
• Alvandi E, Koohdani F. Zip nucleic acid: a new reliable method to increase the melting temperature of real-time PCR probes. J Diabetes Metab Disord 2014;13:26–8.
   PubMedGoogle Scholar
• Iranmanesh Z, Mollaie HR, Arabzadeh SA, Zahedi MJ, Fazlalipour M, Ebrahimi S. Evaluation of the frequency of the IL-28 polymorphism (rs8099917) in patients with chronic hepatitis C using Zip nucleic acid probes, Kerman, Southeast of Iran. APJCP 2015;16:1919–24.
   Google Scholar