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

Autor:	Abolfazl Fateh, Farzam Vaziri, Parviz Afrough, Shamsi Yari, Enayat Anvari, Fatemeh Rahimi Jamnani, Hamid Reza Mollaie, Roohollah Fateh, Seyed Davar Siadat, Ava Behrouzi, Seyed Hamidreza Monavari, Farzin Sadeghi, Alireza Hadizadeh Tasbiti, Maryam Sadeghi, Sepideh Meidaninikjeh, Fatemeh Sakhaee
Rok vydání:	2017
Předmět:	0301 basic medicine Genotype Hepatitis C virus Clinical Biochemistry Single-nucleotide polymorphism Biology medicine.disease_cause Real-Time Polymerase Chain Reaction Polymorphism Single Nucleotide Melting curve analysis 03 medical and health sciences 0302 clinical medicine Limit of Detection medicine Humans Genotyping Interleukins General Medicine Hepatitis C Chronic DNA extraction Molecular biology Hepatitis C 030104 developmental biology Real-time polymerase chain reaction 030211 gastroenterology & hepatology Interferons Restriction fragment length polymorphism Polymorphism Restriction Fragment Length
Zdroj:	Scandinavian journal of clinical and laboratory investigation. 77(4)
ISSN:	1502-7686
Popis:	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.
Databáze:	OpenAIRE
Externí odkaz:	https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0c5a9a624aacd89495916b372babe569 https://pubmed.ncbi.nlm.nih.gov/28281380 Zobrazit plný text záznamu Plný text ve formátu PDF Plný text ve formátu HTML
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