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

• Published in: PloS one 2017-09, Vol.12 (9), p.e0183084-e0183084
• Main Authors: Duffy, Darragh, Mottez, Estelle, Ainsworth, Shaun, Buivan, Tan-Phuc, Baudin, Aurelie, Vray, Muriel, Reed, Ben, Fontanet, Arnaud, Rohel, Alexandra, Petrov-Sanchez, Ventzislava, Abel, Laurent, Theodorou, Ioannis, Miele, Gino, Pol, Stanislas, Albert, Matthew L
• Format: Article
• Language: English
• Subjects: Adult; Aged; Aged, 80 and over; Analysis; Antiviral agents; Assaying; Biology and Life Sciences; Biomarkers; Chronic infection; Clinical outcomes; Cytokines; Demography; Dendritic cells; Diagnostic systems; Epidemiology; Female; Genetic aspects; Genomes; Genomics; Genotype & phenotype; Genotyping; Health aspects; Heating and cooling; Hepatitis; Hepatitis C; Hepatitis C, Chronic - diagnosis; Hepatitis C, Chronic - genetics; Humans; Immunology; In vitro methods and tests; Infections; Infectious diseases; Interferon; Interferons; Interleukins - genetics; Laboratories; Life Sciences; Liver cancer; Male; Medical diagnosis; Medicine and Health Sciences; Melting; Middle Aged; Patients; Physical Sciences; Physiological aspects; Point-of-Care Systems; Polymorphism, Single Nucleotide - genetics; Precision medicine; Reproducibility of Results; Research and Analysis Methods; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Tuberculosis; Young Adult
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0183084

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.