A Simple PCR-RFLP Method for Genotyping of<i>IFNL4</i>rs368234815 Polymorphism in Patients With Chronic Hepatitis C

Pouryasin, Mohammad; Sharafi, Heidar; Behnava, Bita; Alavian, Seyed Moayed; Keshvari, Maryam; Pouryasin, Ali

doi:10.1093/labmed/lmw060

Cited by 11 publications

(14 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In the study of Sharafi et al on IL28B polymorphism to evaluate the response to hepatitis C treatment, they showed that the PCR‐RFLP technique was convenient to use and inexpensive. However, the method of sequencing is a standard and validated, but it is expensive and requires experienced technician …”

Section: Discussionmentioning

confidence: 99%

A facile PCR‐RFLP method for genotyping of ITPA rs1127354 and rs7270101 polymorphisms

Alavian

Sharafi

Shirmast

et al. 2018

Clinical Laboratory Analysis

Self Cite

View full text Add to dashboard Cite

show abstract

Section: Discussionmentioning

confidence: 99%

A facile PCR‐RFLP method for genotyping of ITPA rs1127354 and rs7270101 polymorphisms

Alavian

Sharafi

Shirmast

et al. 2018

Clinical Laboratory Analysis

Self Cite

View full text Add to dashboard Cite

show abstract

“…In this study, we applied the PCR_RFLP method for genotyping of rs368234815 polymorphism which was recently described by Pouryasin et al [25]. Among Iranian non-uremic patients with chronic HCV infection tested with this method, the rs368234815 ΔG/ΔG frequency was 17.3% [25]. Caucasian HD patients of Polish origin with persistently positive testing for HCV RNA revealed a similar frequency of the ΔG/ΔG genotype (16.1%).…”

Section: Discussionmentioning

confidence: 88%

“…Our paper for the first time describes associations between IFNL4 rs368234815 polymorphism and spontaneous HCV clearance in HD patients who substantially differ from the general population due to persistent uremic status and altered immune competence [34]. In this study, we applied the PCR_RFLP method for genotyping of rs368234815 polymorphism which was recently described by Pouryasin et al [25]. Among Iranian non-uremic patients with chronic HCV infection tested with this method, the rs368234815 ΔG/ΔG frequency was 17.3% [25].…”

Section: Discussionmentioning

confidence: 94%

“…IFNL4 rs368234815 polymorphism (TT/TT, ΔG/TT, ΔG/ΔG) was genotyped by a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method as recently described by Pouryasin et al [25]. Genotyping of rs4803217, rs12980275, rs8099917, and rs12979860 polymorphisms was carried out by a high-resolution melting curve analysis (HRM) as in our previous studies [20,22].…”

Section: Genotypingmentioning

confidence: 99%

See 1 more Smart Citation

Polymorphism rs368234815 of Interferon Lambda 4 Gene and Spontaneous Clearance of Hepatitis C Virus in Haemodialysis Patients: A Case Control Study

Grzegorzewska

Mostowska

Świderska

et al. 2019

Preprint

View full text Add to dashboard Cite

BackgroundIn non-uremic subjects, IFNL4 rs368234815 predicts the HCV clearance. We investigated whether rs368234815 is associated with spontaneous HCV clearance in haemodialysis patients and whether it is a stronger predictor of HCV resolution than the IFNL polymorphisms already associated with HCV clearance in haemodialysis subjects. An association of rs368234815 with survival and alterations in transcription factor binding sites (TFBS) caused by IFNL polymorphisms were also evaluated. MethodsAmong 161 haemodialysis patients with positive anti-HCV antibodies, 68 (42.2%) spontaneously resolved HCV infection, whereas 93 remained HCV RNA positive. Patients were tested for near IFNL3 rs12980275, IFNL3 rs4803217, IFNL4 rs12979860, IFNL4 rs368234815, and near IFNL4 rs8099917. IFNL4 rs368234815 polymorphism (TT/TT, ΔG/TT, ΔG/ΔG) was genotyped by restriction fragment length polymorphism analysis; other IFNL polymorphisms - by high resolution melting curve analysis. The Kaplan-Meier method with the log-rank test was used for survival analysis. In silico analysis included the use of ENCODE TFBS ChIP-seq data, HOCOMOCO, JASPAR CORE, and CIS-BP databases, and FIMO software. Results: The probability (OR, 95%CI, P) of spontaneous HCV clearance for rs368234815 TT/TT patients was higher than for the ΔG allele carriers (2.63, 1.38–5.04, 0.003). This probability for other major homozygotes varied between 2.80, 1.45–5.43, 0.002 for rs12980275 and 2.44, 1.27–4.69, 0.007 for rs12979860. In the additive model, rs368234815 TT/TT was the strongest predictor of HCV clearance (6.38, 1.69–24.2, 0.003). Survival analysis suggested an association of the ΔG allele with mortality due to neoplasms (log-rank P = 0.005). The rs368234815 ∆G allele caused TFBS removal for PLAGL1. ConclusionsIn haemodialysis patients, the association of rs368234815 with the spontaneous HCV clearance is better than that documented for other IFNL3/IFNL4 polymorphisms only in the additive mode of inheritance. However, an identification of the homozygosity in the variant ∆G allele of rs368234815 means a more potent prediction of persistent HCV infection in haemodialysis subjects that it is observed in the case of the variant homozygosity of other tested IFNL3/IFNL4 polymorphisms. Removal of PLAGL1 TFBS in subjects harboring the rs368234815 ∆G allele may contribute to cancer susceptibility. The association of rs368234815 with cancer-related mortality needs further studies in HCV-exposed subjects.

show abstract

“…Furthermore, both techniques have been used to differentiate many organisms to species level by the amplification of a conserved region of the mitochondrial D-loop, 11,12 ribosomal regions, 13,14 or other genetic loci. 15,16 However, although PCR-SSCP can be applied to any gene in any organism, PCR-RFLP has less spectrum superiority. Nevertheless, PCR-RFLP has attracted researchers' attention worldwide because of its low costs and does not require advanced instruments.…”

Section: Introductionmentioning

confidence: 99%

Exploring the Potential and Limitations of PCR-RFLP and PCR-SSCP for SNP Detection: A Review

Hashim

Al-Shuhaib

2019

J Apple Biotechnol Rep

View full text Add to dashboard Cite

Polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) and PCR-restriction fragment length polymorphism (PCR-RFLP) are two independent methods used in the post-amplification genotyping of DNA variations. Both techniques are used in a wide range of screening applications to characterize single nucleotide polymorphisms (SNPs). The PCR-SSCP enables the identification of a potentially causative unknown SNP that could not be identified by PCR-RFLP. However, because complicated steps are not required to perform PCR-RFLP, it is used in many applications. On the other hand, PCR-RFLP is easier to process in terms of time and handover experience, the detection of a particular unknown SNP by PCR-SSCP has further chances. The simplicity of PCR-RFLP does not mean that it is better than PCR-SSCP. The reason is the limited ability of PCR-RFLP to detect nucleotide variations, which often go undetected because each restriction enzyme (RE) scans only a few recognition sequences, and other sequences are ignored. Furthermore, the efficacy of PCR-SSCP is sometimes hindered by many optimizations and also lack of experience. As PCR-SSCP allows other sequences within an amplicon to be separated and characterized, the choice between PCR-RFLP and PCR-SSCP is largely dependent on the reason for each genotyping experiment. This review provides a useful guide for comparing PCR-RFLP and PCR-SSCP in terms of their concepts, efficiency, ease of use, interpretation, and sensitivity as well as several other parameters. The comparison is extended to the practical applications of both techniques in terms of their utilization in molecular diagnostics and related applications.

show abstract

A Simple PCR-RFLP Method for Genotyping ofIFNL4rs368234815 Polymorphism in Patients With Chronic Hepatitis C

Abstract: The PCR-RFLP method that we developed is accurate, rapid, inexpensive, and easy to perform for genotyping of the IFNL4 rs368234815 polymorphism. This method can be used for clinical and research work.

Cited by 11 publications

References 34 publications

A facile PCR‐RFLP method for genotyping of ITPA rs1127354 and rs7270101 polymorphisms

A facile PCR‐RFLP method for genotyping of ITPA rs1127354 and rs7270101 polymorphisms

Polymorphism rs368234815 of Interferon Lambda 4 Gene and Spontaneous Clearance of Hepatitis C Virus in Haemodialysis Patients: A Case Control Study

Exploring the Potential and Limitations of PCR-RFLP and PCR-SSCP for SNP Detection: A Review

Contact Info

Product

Resources

About