Research Projects
Sycomia develops applied research projects centered on ctDNA bioinformatics pipeline design, at the intersection of genomics and artificial intelligence for precision oncology
Multi-platform ctDNA analysis pipeline for precision oncology
Cancer remains one of the most pressing public health challenges of our time. While therapies continue to advance, diagnosis and therapeutic monitoring still fall short: too invasive, too late, and insufficiently informative at the molecular level. Conventional methods such as tumor biopsy or medical imaging, cannot identify minimal residual disease, the small population of surviving tumor cells that signal an impending relapse.
Liquid biopsy changes the equation. By analyzing circulating tumor DNA (ctDNA) from a simple blood draw, it becomes possible to detect cancer at an earlier stage, monitor treatment response in real time, and anticipate relapse before it becomes clinically apparent. Sycomia is developing a multi-platform bioinformatics pipeline that unlocks the full potential of this technology, natively integrating the three major sequencing technologies and an artificial intelligence layer to transform raw data into clinically actionable results.
Our ctDNA bioinformatics pipeline
Our ctDNA bioinformatics pipeline integrates three complementary sequencing technologies: short-read sequencing (Illumina) with Unique Molecular Identifiers for ultra-sensitive detection of point mutations, and long-read sequencing (Oxford Nanopore and PacBio HiFi) for the direct detection of structural variants, gene fusions, and chromosomal rearrangements. Long-read technologies also enable native reading of epigenetic modifications such as DNA methylation, providing simultaneous genomic and epigenomic information from the same molecules, a capability out of reach for current single-technology approaches.
Artificial intelligence is embedded at every stage of the analysis. It enables multimodal signal fusion, improved signal-to-noise discrimination in complex genomic regions, cancer classification with enhanced sensitivity, tissue-of-origin prediction, and treatment efficacy assessment. The result is a modular, containerized pipeline compatible with multiple sequencing platforms, capable of delivering structured clinical reports within 48 to 72 hours.
What sets us apart
Current ctDNA solutions on the market rely exclusively on short-read Illumina sequencing and proprietary gene panels limited to a few dozen targets. Sycomia takes a fundamentally different approach: platform-agnostic, multi-technology, and open to any sequencing data regardless of its origin.
This positioning allows us to work alongside existing sequencing laboratories rather than competing with them. Our ctDNA bioinformatics pipeline is designed to be open to any sequencing data regardless of its origin, establishing partnerships across the entire ecosystem: hospitals, academic research centers, CROs, and biotechnology companies.
Sycomia is currently in the active development phase of the pipeline, with a six-month roadmap structured in three stages: technical proof of concept on public reference datasets, validation on 20 to 30 pilot samples, and integration of AI models for multimodal analysis and automated report generation.
The pipeline targets a variant allele frequency detection sensitivity of 0.01%, with false positive rates below 0.1% and a total result turnaround of 48 to 72 hours.
