An in vitro diagnostic certified point of care single nucleotide test for IL28B polymorphisms

Darragh Duffy, Estelle Mottez, Shaun Ainsworth, Tan-Phuc Buivan, Aurelie Baudin, Muriel Vray, Ben Reed, Arnaud Fontanet, Alexandra Rohel, Ventzislava Petrov-Sanchez, Laurent Abel, Ioannis Theodorou, Gino Miele, Stanislas Pol, Matthew L Albert, Darragh Duffy, Estelle Mottez, Shaun Ainsworth, Tan-Phuc Buivan, Aurelie Baudin, Muriel Vray, Ben Reed, Arnaud Fontanet, Alexandra Rohel, Ventzislava Petrov-Sanchez, Laurent Abel, Ioannis Theodorou, Gino Miele, Stanislas Pol, Matthew L Albert

Abstract

Numerous genetic polymorphisms have been identified as associated with disease or treatment outcome, but the routine implementation of genotyping into actionable medical care remains limited. Point-of-care (PoC) technologies enable rapid and real-time treatment decisions, with great potential for extending molecular diagnostic approaches to settings with limited medical infrastructure (e.g., CLIA certified diagnostic laboratories). With respect to resource-limited settings, there is a need for simple devices to implement biomarker guided treatment strategies. One relevant example is chronic hepatitis C infection, for which several treatment options are now approved. Single nucleotide polymorphisms (SNPs) in the IL-28B / IFNL3 locus have been well described to predict both spontaneous clearance and response to interferon based therapies. We utilized the Genedrive® platform to develop an assay for the SNP rs12979860 variants (CC, CT and TT). The assay utilizes a hybrid thermal engine, permitting rapid heating and cooling, enabling an amplification based assay with genetic variants reported using endpoint differential melting cure analysis in less than 60 minutes. We validated this assay using non-invasive buccal swab sampling in a prospective study of 246 chronic HCV patients, achieving 100% sensitivity and 100% specificity (95% exact CI: 98.8-100%)) in 50 minutes as compared to conventional lab based PCR testing. Our results provide proof of concept that precision medicine is feasible in resource-limited settings, offering the first CE-IVD (in vitro diagnostics) validated PoC SNP test. We propose that IL-28B genotyping may be useful for directing patients towards lower cost therapies, and rationing use of costly direct antivirals for use in those individuals showing genetic risk.

Conflict of interest statement

Competing Interests: The Genedrive SNP test for IL28B is commercialized and marketed by Genedrive PLC. Shaun Ainsworth, Ben Reed, and Gino Miele are employees of Genedrive PLC. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

Figures

Fig 1. Comparison of Genedrive ® and…
Fig 1. Comparison of Genedrive® and Taqman assays.
(A) Melt Curve Analysis for detection of SNP and template control. (B) Results of Genedrive assay on initial test samples. (C) Results of Taqman assay on initial test samples. (D) Summary of initial Beta test results in run, remelts, and retests prior to and after assay optimization.
Fig 2. Clinical study validation of 246…
Fig 2. Clinical study validation of 246 HCV patients.
(A) Workflow and Layout of Assay. (B) Contingency table for sensitivity and specificity to detect CC genotype. (C) Contingency table for sensitivity and specificity to discriminate CC, CT, and TT genotypes.

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Source: PubMed

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