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Interferon λ 3 and 4 Genotyping Using High-Resolution Melt Curve Analysis Suitable for Multiple Clinical Sample Types
François M J Lamoury1, Sofia Bartlett1, Brendan Jacka1
1Viral Hepatitis Clinical Research Program, The Kirby Institute, University of New South Wales Australia, Sydney, Australia.
The Journal of Molecular Diagnostics : JMD
|July 8, 2015
Summary
A new, rapid genotyping method for IFNL3 and IFNL4 single-nucleotide polymorphisms (SNPs) is available. This affordable test can guide hepatitis C virus (HCV) treatment decisions until direct-acting antivirals (DAAs) are widely accessible.
Area of Science:
- Genetics
- Hepatology
- Molecular Diagnostics
Background:
- Hepatitis C virus (HCV) treatment often relies on interferon-based regimens.
- Direct-acting antivirals (DAAs) offer better outcomes but face cost and access barriers.
- Host genetic factors, specifically IFNL3 and IFNL4 single-nucleotide polymorphisms (SNPs), influence spontaneous HCV clearance and treatment response.
Purpose of the Study:
- To develop and validate a simple, rapid, and affordable genotyping assay for key IFNL3 and IFNL4 SNPs (rs12979860, rs8099917, rs368234815).
- To assess the utility of this assay across various clinical sample types.
- To evaluate the prevalence of favorable IFNL genotypes in a cohort with recent HCV infection.
Main Methods:
- High-resolution melting (HRM) analysis was employed for genotyping IFNL SNPs.
- DNA was extracted from diverse sample types including whole blood, buffy coat, plasma, serum, and dried blood spots using the automated easyMAG platform.
- Genotyping results were validated against sequenced amplicons.
Main Results:
- The developed HRM assay accurately genotyped all three target IFNL polymorphisms (rs12979860, rs8099917, rs368234815) across all tested sample types.
- Prevalence of favorable genotypes in 126 participants with recent HCV infection: rs8099917 TT (62%), rs12979860 CC (51%), and rs368234815 TT/TT (45%).
Conclusions:
- The described genotyping assay is a rapid, cost-effective method for IFNL3 and IFNL4 genotyping from various clinical samples.
- This assay can aid in identifying individuals with higher likelihood of spontaneous HCV clearance, potentially delaying treatment.
- IFNL genotyping can help prioritize direct-acting antiviral (DAA) therapy for patients less likely to respond to interferon-based regimens, improving treatment strategies until universal DAA access is achieved.
