title: A comparative study of various methods for detection of IL28B rs12979860 in chronic hepatitis C.
abstract: Interleukin-28B (IL28B) single-nucleotide polymorphisms (SNPs) constitute important host-related factors influencing the response rate to Hepatitis C virus (HCV) standard antiviral therapy. In the last few years, several new technologies for SNP detection have been developed. However, the sensitivity and specificity of various methods are different and needs evaluation. Five different methods (resolution melting curve [RMC], polymerase chain reaction-restriction fragment length polymorphism [PCR-RFLP], PCR-sequencing analysis, amplification refractory mutation system [ARMS], and zip nucleic acid probe-based real-time PCR [ZNA]) were developed for genotyping rs12979860 associated with IL28B. In this study, limit of detection (LD), costs and turnaround time of these methods were compared in 350 subjects. As for IL28B rs12979860 polymorphisms, 348/350 (99.4%) samples were consistent among the five methods, while results for 2/350 (0.57%) samples were concordant by ZNAs and PCR-sequencing, and discordant by other methods. Without considering the cost of DNA extraction, the price of each reaction for ARMS-PCR, RMC, PCR-RFLP, ZNA and PCR-sequencing were respectively: US$3.10, US$5.0, US$5.50, US$8.50 and US$17.0. RMC was the fastest method, while the ZNA method was easy to use, reliable and effective. Lower LD was determined to be 50-60 copies/μL for the PCR-RFLP, RMC and ARMS-PCR assays; whilst ZNA assay was able to detect 2-3 copies/μL. In conclusion, in the current study, all four methods are suitable for IL28B rs12979860 genotyping, but the ZNA assay can be a reliable tool. Due to its lower LD for SNP identification, this method is better than others for detecting this type of polymorphism.
authors.affiliation: a Department of Virology , Iran University of Medical Sciences , Tehran , Iran.
authors.forename: Seyed Hamidreza
authors.initials: SH
authors.lastname: Monavari
authors.affiliation: b Department of Microbiology and Immunology, Faculty of Medicine , Qom University of Medical Sciences , Qom , Iran.
authors.forename: Roohollah
authors.initials: R
authors.lastname: Fateh
authors.affiliation: c Department of Mycobacteriology and Pulmonary Research , Pasteur Institute of Iran , Tehran , Iran.|d Microbiology Research Center (MRC) , Pasteur Institute of Iran , Tehran , Iran.
authors.forename: Farzam
authors.initials: F
authors.lastname: Vaziri
authors.affiliation: c Department of Mycobacteriology and Pulmonary Research , Pasteur Institute of Iran , Tehran , Iran.|d Microbiology Research Center (MRC) , Pasteur Institute of Iran , Tehran , Iran.
authors.forename: Fatemeh
authors.initials: F
authors.lastname: Rahimi Jamnani
authors.affiliation: e Department of Physiology, Faculty of Medicine , Ilam University of Medical Sciences , Ilam , Iran.
authors.forename: Enayat
authors.initials: E
authors.lastname: Anvari
authors.affiliation: f Department of Immunology and Microbiology , Babol University of Medical Sciences, School of Medicine , Babol , Iran.
authors.forename: Farzin
authors.initials: F
authors.lastname: Sadeghi
authors.affiliation: c Department of Mycobacteriology and Pulmonary Research , Pasteur Institute of Iran , Tehran , Iran.|d Microbiology Research Center (MRC) , Pasteur Institute of Iran , Tehran , Iran.
authors.forename: Parviz
authors.initials: P
authors.lastname: Afrough
authors.affiliation: c Department of Mycobacteriology and Pulmonary Research , Pasteur Institute of Iran , Tehran , Iran.
authors.forename: Ava
authors.initials: A
authors.lastname: Behrouzi
authors.affiliation: c Department of Mycobacteriology and Pulmonary Research , Pasteur Institute of Iran , Tehran , Iran.
authors.forename: Fatemeh
authors.initials: F
authors.lastname: Sakhaee
authors.affiliation: c Department of Mycobacteriology and Pulmonary Research , Pasteur Institute of Iran , Tehran , Iran.
authors.forename: Sepideh
authors.initials: S
authors.lastname: Meidaninikjeh
authors.affiliation: g Department of Medical Virology , Kerman University of Medical Sciences , Kerman , Iran.
authors.forename: Hamidreza
authors.initials: H
authors.lastname: Mollaie
authors.affiliation: c Department of Mycobacteriology and Pulmonary Research , Pasteur Institute of Iran , Tehran , Iran.
authors.forename: Alireza
authors.initials: A
authors.lastname: Hadizadeh Tasbiti
authors.affiliation: c Department of Mycobacteriology and Pulmonary Research , Pasteur Institute of Iran , Tehran , Iran.
authors.forename: Shamsi
authors.initials: S
authors.lastname: Yari
authors.affiliation: h Department of English , Mahshahr Branch, Islamic Azad University , Mahshahr , Iran.
authors.forename: Maryam
authors.initials: M
authors.lastname: Sadeghi
authors.affiliation: c Department of Mycobacteriology and Pulmonary Research , Pasteur Institute of Iran , Tehran , Iran.|d Microbiology Research Center (MRC) , Pasteur Institute of Iran , Tehran , Iran.
authors.forename: Abolfazl
authors.initials: A
authors.lastname: Fateh
authors.affiliation: c Department of Mycobacteriology and Pulmonary Research , Pasteur Institute of Iran , Tehran , Iran.|d Microbiology Research Center (MRC) , Pasteur Institute of Iran , Tehran , Iran.
authors.forename: Seyed Davar
authors.initials: SD
authors.lastname: Siadat
mesh_terms: D005838:Genotype; D006526:Hepatitis C / Q000235:genetics; D019698:Hepatitis C, Chronic / Q000235:genetics*; D006801:Humans; D007372:Interferons; D007378:Interleukins / Q000235:genetics*; D057230:Limit of Detection; D012150:Polymorphism, Restriction Fragment Length; D020641:Polymorphism, Single Nucleotide; D060888:Real-Time Polymerase Chain Reaction / Q000191:economics; D000095022:Interferon Lambda
chemical_list: D007372:Interferons; D007378:Interleukins; C000624353:interferon-lambda, human; D000095022:Interferon Lambda
keywords: Amplification refractory mutation system; IL28B rs12979860; resolution melting curve; restriction fragment length polymorphism; zip nucleic acid real-time PCR