Projects

A Groundbreaking Stand-Alone Diagnostic Kit to Predict Human Papilloma Virus Infections Evolving into Cervical Cancer

PROJECT OUTCOMES

1) a highly sensitive hrHPV screening IVD assay able to accurately detect all women infected with one or more of all 14 hrHPV types (full-genotyping hrHPV test) at risk of developing disease, including an internal control for sample cellularity to identify false negatives resulting from an inadequate number of cells in the collected sample.

2) a highly specific triage hrHPV-RNA IVD assay (E6/E7 mRNA) for reflex testing of HPV-positive samples, aimed at discriminating those hrHPV infections at increased risk of disease progression. Highly multiplexed, full-genotyping hrHPV assay. Multiplex real-time PCR testing, combining in one tube primers and probes for the detection and differentiation of all hrHPV types by means of Gene- First’s patented MPA technology, to determine the presence, type, viral load and oncogenic transcripts of hrHPV.

3) a highly specific triage hrHPV-DNA IVD assay (quantitative and normalized) for reflex testing of HPV-positive samples, aimed at discriminating those hrHPV infections at increased risk of disease progression.

Stand-alone tests vs the need for additional testing
All the above competing solutions have a good sensitivity for high-grade CIN lesions, but all of them also detect irrelevant/transient hrHPV infections and therefore cannot be used as a stand-alone test. They can be used as a primary test but must be combined with additional triage testing of HPV positive samples, such as direct cytological analysis or cytological staining, methods that are operator dependant and require the preparation of slides and/or methylation analysis with bisulphite treatment.

Sample adequacy assessment
Accurate cellularity quantification allows sample adequacy assessment, not available in any of the competing solutions. This is particularly important for the implementation of screening on self-col- lected samples, to avoid false negative results of at-risk patients that have apparently negative test results due to inadequate sampling.

HPV full-genotyping assay
The competing solutions have different abilities regarding HPV genotyping: either unavailable (do not distinguish between HPV types at all) or able to genotype HPV16 and HPV18 only (restri- cted-genotyping methods), 5 to 8 hrHPV types (limited-genotyping methods), all 14 high-risk HPV types (full-genotyping assays), or discriminating 28 or more types (including low-risk HPV types). Although HPV16 and HPV18 are the most common hrHPV types and require different clinical ma- nagement, other hrHPV types are also clinically relevant and are the cause of 20% of current col- poscopy referrals. Following the recent uptake of HPV vaccination protocols (covering HPV16 and HPV18) in many European countries, the frequency of cancer associated with other hrHPV types is expected to increase in the future, encouraging the use of limited or full-genotyping methods.

High-throughput
The ability to screen and triage a single patient sample, using high-throughput molecular methods with reduced ’hands-on’ and ’turn around times’ (TATs).

Versatility (renders self-sampling possible and reliable)
HPV OncoPredict is able to carry out both screening and follow up triage testing from just one pa- tient sample. The combination of normalised viral load and the expression of viral oncogenes make the proposed HPV OncoPredict test of high value in the reflex testing of hrHPV-positive subjects, replacing cytology in patient triage. This is of particular advantage when dealing with self-collected samples as it is not possible to carry out cytology triage on self-collected samples [24]. Recently pu- blished data from a meta-analysis [17] have clearly demonstrated that the accuracy of HPV testing performed on self-collected samples is comparable to that on clinician-collected samples only if the diagnostic test is based on nucleic acid amplification methods (NAATs), such as HPV Oncopredict. This offers a further major commercial advantage over the major competitor assay (HC2).

Innovative method for SARS-Cov-2 rapid and low-cost search in respiratory samples: validation with multiple diagnostics and process automation.

PROJECT OUTCOMES

1) a clinically validated rapid extraction system of nucleic acids in both symptomatic and asympto- matic subjects, in combination with the diagnostic systems currently in use and a new quantitative diagnostic kit developed as part of the project;

2) a new clinically validated quantitative diagnostic kit for the analytical phase of the diagnostic process. The kit includes the use of unique enhancer solutions, specifically formulated to facilitate direct amplification of viral RNA in the presence of various types of PCR inhibitors, generally present in clinical samples. Integration with an existing analytical assay, which can assess the quality and efficiency of all phases of the diagnostic process, from sampling to amplification of viral genes, avoid false negative results and accurate quantitative evaluation of the viral load;

3) a clinically validated integrated diagnostic platform, with hardware and software implementation, to optimize the efficiency, reliability and high throughput of the pre-analytic and analytical process for the research of SARS-Cov-2, capable of processing up to 2000 samples per day, while ensuring optimal levels of diagnostic sensitivity and safety for operators.