Repository of Research and Investigative Information

Repository of Research and Investigative Information

Ilam University of Medical Sciences

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

Sat Aug 13 17:53:57 2022

(2017) A comparative study of various methods for detection of IL28B rs12979860 in chronic hepatitis C. Scandinavian Journal of Clinical & Laboratory Investigation. pp. 247-252. ISSN 0036-5513

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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/L for the PCR-RFLP, RMC and ARMS-PCR assays; whilst ZNA assay was able to detect 2-3 copies/L. 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.

Item Type: Article
Creators:
CreatorsEmail
Monavari, S. H.UNSPECIFIED
Fateh, R.UNSPECIFIED
Vaziri, F.UNSPECIFIED
Jamnani, F. R.UNSPECIFIED
Anvari, E.UNSPECIFIED
Sadeghi, F.UNSPECIFIED
Afrough, P.UNSPECIFIED
Behrouzi, A.UNSPECIFIED
Sakhaee, F.UNSPECIFIED
Meidaninikjeh, S.UNSPECIFIED
Mollaie, H.UNSPECIFIED
Tasbiti, A. H.UNSPECIFIED
Yari, S.UNSPECIFIED
Sadeghi, M.UNSPECIFIED
Fateh, A.UNSPECIFIED
Siadat, S. D.UNSPECIFIED
Keywords: Amplification refractory mutation system IL28B rs12979860 resolution melting curve restriction fragment length polymorphism zip nucleic acid real-time PCR DNA melting analysis zip nucleic-acids polymorphisms assay pcr Research & Experimental Medicine
Divisions:
Page Range: pp. 247-252
Journal or Publication Title: Scandinavian Journal of Clinical & Laboratory Investigation
Journal Index: ISI
Volume: 77
Number: 4
Identification Number: https://doi.org/10.1080/00365513.2017.1299207
ISSN: 0036-5513
Depositing User: مهندس مهدی شریفی
URI: http://eprints.medilam.ac.ir/id/eprint/389

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