Biocartis (Belgium)

e20519 Background: Current molecular testing for mutations and indels in EGFRexons 18, 19, 20 and 21 is still laborious and often requires > 5 days in specialized labs. Multiple slices of FFPE tissue are often needed. Lack of experience, time or tissue for molecular testing are among the reasons why patients are often deprived of the proper targeted therapies. Therefore, a fast and fully automated assay with minimal hands-on time which can handle small samples should allow laboratories to quickly generate EGFR testing results as part of their precision medicine report. Methods: Idylla is a fully integrated MDx platform that combines speed and ease of use with high sensitivity and high multiplexing capabilities. For EGFR testing, it overcomes the current problem of lack of tissue and the time-consuming step of processing FFPE tissue samples. After insertion of a single 5 µm FFPE slice containing ≥10% neoplastic cells into the cartridge, the complete process of liquefication, extraction, rtPCR, data analysis and reporting is fully automated and takes < 2.5 hours. The Idylla EGFR Mutation Assay (RUO) allows the sensitive detection of 50+ mutations including indels in exons 18, 19, 20 and 21. Results: The Idylla EGFR Mutation Assay (RUO) was tested with single FFPE slices from 280 clinical NSCLC samples with known mutations as analyzed by NGS and digital droplet PCR. It demonstrated excellent specificity and sensitivity with an overall percentage agreement of > 96% and a positive and negative percentage agreement of > 97% and > 95%, respectively. Analytical sensitivity was assessed using cell line derived materials embedded in paraffin containing defined ratios of mutants and dilutions thereof in a WT background. Allelic frequencies ranging from 1 to 10% were tested in 6-fold and showed analytical sensitivities of 1% for all except one target which showed a sensitivity of 5%. Turnaround time of a run was < 2.5 hours and hands-on time was < 2 min. Conclusions:The new and fully automated Idylla EGFR Mutation Assay (RUO) demonstrates excellent specificity, high sensitivity, ease of use combined with a fast turnaround time for complete testing of more than 50 relevant EGFR mutations on FFPE samples from NSCLC patients.

Personalised health care is an evolution, moving away from a disease-focused model of care, translating scientific and technological advances into benefits for patients, and placing them at the centre of the patients' health and care. Companion diagnostics emerge as a very specific and special group of in vitro diagnostics among the different technologies shaping the personalised health care spectrum. Companion diagnostics provide highly valuable information, allowing patients, health practitioners and payers to decide with a higher level of certainty on the potential benefits of a treatment or care pathway. Decreasing uncertainty may result in a more efficient selection of treatments and care, targeted at subpopulations that are most likely to benefit. Companion diagnostics account for a minimal portion of the already small expenditure on in vitro diagnostics (far less than 1% of total health care expenditure), and yet they provide the means to limit inefficient use of health care resources while optimising patient outcomes. It is clear that equal access to personalised health care is still an issue across the EU. One of the most common perceived barriers is affordability. The investment in companion diagnostics can provide long-term value for patients and health care systems, shifting resources to areas of need. Health systems do not fully recognise yet the value that companion diagnostics bring to make personalised health care more affordable across the EU. This inhibits patient access to personalised treatments and care, preventing improved outcomes. In many countries, market access frameworks for diagnostic tests are fragmented and not aligned with specific funding and reimbursement mechanisms, discouraging the use of these tests. Emerging evidence shows that patients are missing out on the appropriate tests and treatments while a reduction in the inefficient use of health care resources is not realised. This article outlines some of these market access barriers for companion diagnostics in the EU, including reimbursement challenges specific to some member states (Germany, the UK, and France). Furthermore, proposals addressing barriers and increasing timely patient access to companion diagnostics in the EU are presented.

The recent development of multimedia applications on mobile terminals raised the need for flexible and scalable computing platforms that are capable of providing considerable (application specific) computational performance within a low cost and a low energy budget. The MPSoC with multi-disciplinary approach, resolving application mapping, platform architecture and runtime management issues, provides such multiple heterogeneous, flexible processing elements. In MPSoC, the run-time manager takes the design time exploration information as an input and selects an active Pareto point based on quality requirement and available platform resources, where a Pareto point corresponds to a particular parallelization possibility of the target application. To use system's scalability at best and enhance application's flexibility a step further, the resource management and Pareto point selection decisions need to be adjustable at run-time. This research work experiment run-time Pareto point switching for the MPEG-4 encoder. The work involves design time exploration and then embedding of two parallelization possibilities of the MPEG-4 encoder into one single component and enabling run-time switching between these parallelizations, to give run-time control over adjusting performance-cost criteria and allocation deallocation of hardware resources at run-time. The new system has the capability to encode each video frame with different parallelization. The obtained results offer a number of operating points on the Pareto curve in between the previous ones at sequence encoding level. The run-time manager can improve application performance up to 50 % or can save memory bandwidth up to 15 %, according to quality request.

The human immunodeficiency virus type 1 (HIV-1) initiates infection through sequential interactions with CD4 and chemokine coreceptors unmasking the gp41 subunit of the viral envelope protein. Consequently, the N-terminal heptad repeats of gp41 form a trimeric coiled-coil groove in which the C-terminal heptad repeats collapse, generating a stable six-helix bundle. This brings the viral and cell membrane in close proximity enabling fusion and the release of viral genome in the cytosol of the host cell. In this chapter, we describe a homogeneous time-resolved fluorescence assay to identify inhibitors of HIV-1 fusion, based on the ability of soluble peptides, derived from the N- and C-terminal domains of gp41, to form a stable six-helix bundle in vitro. Labeling of the peptides with allophycocyanin and the lanthanide europium results in a Föster resonance energy transfer (FRET) signal upon formation of the six-helix bundle. Compounds interfering with the six-helix bundle formation inhibit the HIV-1 fusion process and suppress the FRET signal.

Dengue, a mosquito-borne virus of the Flaviviridae family, is reemerging as one of the most important human pathogens in tropical and subtropical regions of the world. It is estimated that 2.5 billion people live in areas at risk for transmission of dengue virus (DENV). Furthermore, it causes significant morbidity and mortality with 50-100 million infections per year. Currently, there are no vaccines commercially available and no effective antiviral drugs for treatment of DENV infections. In this chapter, we describe a plaque reduction assay and a cell-based high-throughput antiviral assay for identifying inhibitors against DENV. The latter is a homogeneous high-throughput assay that has been fully validated according to the Food and Drug Administration (FDA) guidelines for assay validation and can be used for screening compound libraries.