NEW YORK – A trio of European partners has set out to develop a new informatics tool that will enable better use of clinical cancer sequencing data by helping to cancel so-called "genomic noise."
Euformatics, Oncompass Medicine, and Institut Curie early this month received €1 million ($1.1 million) through Eurostars to fund the effort, which will run through 2026. Eurostars is a European R&D funding program subsidized in part by the EU and focuses on supporting small- and medium-sized businesses.
Espoo, Finland-based Euformatics and Budapest, Hungary-based Oncompass are already partners on several other projects. In February, they partnered with ViennaLab Diagnostics and eight European medical centers to develop a liquid biopsy platform for molecular profiling in cancer patients. Last year, Euformatics and Oncompass partnered with BC Platforms and seven Central European hospitals to create standardized next-generation sequencing workflows in oncology.
According to Euformatics CEO Tommi Kaasalainen, these projects inspired in part the new Eurostars-backed endeavor with Oncompass and Institut Curie, which will commence Jan. 1.
Kaasalainen said that the proposed genomic noise-canceling tool will sit on top of Euformatics' existing Genomics Hub platform for clinical genomic analysis, which is paired with Oncompass' software for improving therapeutic decisions in precision oncology. France's Institut Curie will provide clinical research data to support the new project.
"Our Genomics Hub starts from the raw sequence data and ends with the clinically relevant variants that get reported from the sample in the context of the disease," Kaasalainen said. "Oncompass takes that and applies it for precision medicine and clinical decision-making" to help determine optimized patient treatments, he said.
There are also plans to commercialize and obtain CE-IVDR certification for the resulting platform so that it can be used clinically in Europe, but this will take place after the project concludes in 2026, Kaasalainen said. All three parties will jointly hold any new intellectual property, but Euformatics and Oncompass will be responsible for commercialization.
Founded in 2010, Euformatics employs about 15 staffers from its offices in Espoo, a suburb of Helsinki. Kaasalainen said that the company's main clients are clinical labs and hospitals that use next-generation sequencing data to inform the treatment of cancers and rare diseases. The company has for years worked with the genomic quality assessment bodies EMQN and Genomics Quality Assessment (GenQA), where its software has been used to carry out quality assurance of participating labs' data.
"Through these collaborations, we have learned a lot about NGS data quality," remarked Kaasalainen, "and now we are applying that learning in this project."
Kaasalainen said that Euformatics has drawn up a conceptual framework for resolving genomic noise issues. Part of it involves flagging artifacts or variants that are filtered out during initial analyses should they actually be relevant for the cancer being assessed. "We can see if any of those variants should be rescued," he said, "and, if so, it becomes part of the resulting dataset."
Kaasalainen likened the approach to the way that noise-canceling headphones filter out background noise. "We take a genomic region [of interest] and do the noise canceling on that specific region and identify the specific variants we think are important," he said. Kaasalainen noted that every cancer has variants that are relevant to it, and so the tool that Euformatics is building has to be constructed in a disease-specific way.
He added that the new tool will be developed and validated using short-read next-generation sequencing data generated on platforms sold by vendors like Illumina, Thermo Fisher Scientific, and Element Biosciences. "Our bioinformatics tools also work for long-read NGS data from Oxford Nanopore or Pacific Biosciences, but those are not in the scope of this project," he said.
Kaasalainen said that Euformatics will benefit from developing such a tool, as its customers will be able to better identify variants from noisy and hard-to-sequence regions. "Hospitals and labs can produce better results from a patient care perspective," he said. "That naturally helps everyone."
Founded in 2003, Oncompass Medicine focuses on precision oncology. It began to work with NGS 15 years ago, and it introduced the first version of its informatics platform for assessing molecular diagnostics results and guiding effective treatment selection in 2016.
According to Barbara Vodicska, head of translational science for the Hungarian company, its software system relies on a "rules-based knowledge engine" to personalize targeted treatment selection by ranking associated drugs based on the individual molecular profile of the tumor. As part of its AI-supported diagnostic and decision support workflow, it also includes a virtual molecular tumor board as a service to oncologists. Vodicska noted that Oncompass' tools have been developed in-house.
"Using this method, we can generate predictive scores for each drug associated with the full molecular profile," she said, "and we can standardize personalized treatment decisions."
With regards to the new project with Euformatics and Institut Curie, Vodicska said that Oncompass Medicine's goal is to be able to "produce the optimal output" with the new genomic noise-canceling tool. "We would like to have the best possible bioinformatic filtering setup, to be able to maximally predict response," she said.
Vodicska also said that Oncompass will help to improve the genomic noise-canceling tool by comparing the outputs of different settings, and will also serve as an alpha customer, providing feedback to Euformatics on its usability.