Once upon a time at ViennaLab… – a short story of recent developments
This story goes back to December 2022 just before Christmas, when Oncompass Medicine from Hungary (HU) and Euformatics from Finland (FI) partnered together with ViennaLab Diagnostics (AT) under the HUFIAT Cancer Liquidation Consortium and was awarded to start phase 1 of the OncNGS project. The aim is to develop a cutting-edge technology for liquid biopsy pan-cancer profiling, together with bioinformatic analysis and clinical reporting for precision oncology. Liquid biopsies offer new possibilities in cancer diagnostics as they are less invasive for a patient than regular tissue biopsies. cfDNA collected from these biopsies represents tumor heterogeneity therefore its analysis constitutes a non-invasive source of valuable information for early cancer detection and treatment. For more details about phase 1 please follow this link.
Phased-approach to allow the Suppliers to benefit from feedback from external experts
The Buyers Group coordinated by Sciensano, consisting of leading European Oncology Centers from Belgium, Spain, France, Italy, and Germany, identified the unmet need for non-invasive pan-cancer profiling. In order to bridge gaps in cancer diagnostics and stimulate the development of state-of-the-art cfDNA liquid biopsy for oncology NGS solution, they initiated the call for tender. This pre-commercial procurement comprises 3 phases: solution design (phase 1), prototype development and analytical testing (phase 2), and clinical validation (phase 3)**. The phased approach was planned to allow the successful Suppliers to learn and improve their designs based on feedback received from the Buyers Group. While progressing through the phases, the finest solutions are identified and the best teams advance further.
Phase 1 lasted 4 months and required the preparation of a written proposal. During this phase, participants needed to develop the whole design concept and plan the experimental steps required in the next phase. The design of two panels was requested by the Buyers Group: Pan-Cancer oncNGS panel covering at least 158 genes and a hemato/lymphoma oncNGS panel targeting at least 50 genes. The solutions should comprise library preparation, bioinformatic analysis, and molecular and clinical interpretation with the results available within 7 days.
Each team was asked to highlight its approach in great detail to demonstrate its feasibility to target the requested genes and fulfil all the requirements set up by the Buyers Group. Four teams submitted their applications by mid-July where they presented their concepts. The HUFIAT team members coordinated their efforts to meet the deadline and deliver a strong proposal. The anticipation for a decision was growing with every day since only 3 teams would advance to the next phase while 1 was to be eliminated.
HUFIAT’s expertise appreciated as funding for phase 2 was granted
After a few weeks of fervently waiting, the news came at the end of August 2023 that our expertise was recognized again and we secured funding for the next phase! The funding of phase 2 covers prototyping, sequencing, and computing as well as brain power. This means that we now have 12 months to test our approach and develop the prototype of the assay. We are very excited about this phase as we will be able to do a significant amount of wet lab work and apply our broad knowledge of cfDNA analysis and NGS technologies to prove that our concept is feasible and can work robustly and reliably. The analytical validation will be performed to assess the assay’s specificity, precision, and accuracy as requested by the Buyers Group. The tenderers will have the opportunity to demonstrate the prototype during an on-site visit and its performance will be evaluated. The most promising and innovative solutions, which present the best value for money, will be chosen to proceed to the next phase. Only 2 tenderers will remain.
Challenge breeds advancement and HUFIAT members are driven to deliver a state-of-the-art solution
Challenging as it sounds and with the clock ticking, we are excited to enter this unexplored territory of cancer diagnostics Our expertise will definitely bring many benefits and lay the groundwork, invaluable also for future projects.
ViennaLab’s part of the project is supervised by Adrian Stütz, PhD, Head of the NGS team and expert in cfDNA genomics, and Johanna Trupke, PhD, Head of R&D. Paola Caruso, MSc, an NGS scientist at ViennaLab and one of the members involved in the development of the wet lab part of the assay says: "cfDNA input amount for library preparation is usually very limited and circulating tumor DNA (ctDNA) constitutes only a small fraction of the total cfDNA. Our chemistry allows to uniquely tag and effectively capture those molecules in order to detect variants at extremely low allele frequencies."
NGS technology is a powerful method that certainly provides an enormous amount of information. However, this also means that expertise is needed to manage these overwhelming quantities of data, for an accurate and appropriate prediction for decision making about patients’ treatment and consequently their future. Luis Enrique Cabrera Quio, PhD, an NGS scientist and bioinformatic expert at ViennaLab thinks: "Our biggest challenge will be to implement a system flexible and robust enough to deal with the vast amount of data that will be generated and doing so in the most time-efficient manner. In addition, identifying the true causing variant from the rest (noise) will also be a topic that we need to accurately address."
Phase 2 of oncNGS will require a high level of organization between partners. Once ViennaLab generates data, Euformatics and Oncompass Medicine will apply their expertise to design automated QC and sequencing data analysis and produce AI-based medical reporting. Together, we aim to improve therapeutic decisions in precision oncology.
Diversity empowers innovation as three experts partnered together
ViennaLab is pleased to be able to work with its partners – leading experts in bioinformatics (Euformatics) and artificial intelligence-mediated medical reporting (Oncompass Medicine). Together, we possess all the means to develop a state-of-the-art solution and overcome the limits of cancer detection. The diversity we represent coming from multiple cultural and scientific backgrounds fuels stimulating and groundbreaking discussion. According to Martin Zeppetzauer, M.Res., the CEO of ViennaLab: "The product will be used by medical professionals and scientists in multiple countries, health care systems and medical institutions. The range and extent of knowledge, formal training and acquired experience of this truly multinational and multidisciplinary project team will ensure that our solution captures the needs of these users with a sophisticated and multifarious solution."
ViennaLab, brace yourself for a busy Autumn and months ahead
Twelve months. For some, it might sound like a long time. For HUFIAT team members, they will pass by in the blink of an eye. Since the countdown has started, ViennaLab is not wasting any minute.
It is not the first time that ViennaLab Diagnostics needs to act under pressure and time constraints. When the COVID pandemic hit, our team members put hard work into designing a sensitive and robust diagnostic test contributing to the control of the global outbreak. As ViennaLab has a long history of developing products for in vitro diagnostics and extensive expertise in NGS technology, variants detection, and cfDNA analysis, we are confident that we are a strong player in this tender. Our customer-oriented approach with user-friendly assays and easy-to-follow protocols has already been appreciated for more than 30 years.
Surely, these will be exciting 12 months for ViennaLab and our partners. We are glad that our expertise was recognized again as we were given this opportunity. We are perfectly equipped for this challenge and ready to test where our limits lie.
As ViennaLab is about to start the first experiments, please keep your fingers crossed for ViennaLab and its partners and wish us luck with prototype development!
For more information, please follow the link.
Please stay tuned for future announcements as this story continues…
*The OncPCP Consortium consists of the following members: Sciensano and Institut Jules Bordet from Belgium, Alleanza Contro il Cancro from Italy, Institut Curie and Hospices Civils de Lyon from France, Institut Catala d’Oncologia from Spain, Ludwig-Maximilians-Universitaet Muenchen and Charite - Universitaetsmedizin Berlin from Germany.
**This pre-commercial procurement is part of a project funded by the European Union under Grant Agreement number 874467.