What if a single test could simultaneously contribute to the diagnosis, characterization, and treatment guidance of childhood cancer–while helping avoid toxic or potentially unnecessary treatments? That's the bold challenge taken on by the Meta-Platform for Integrated Genomics (MPGI), under the scientific leadership of Dr. Vincent-Philippe Lavallée, hematologist and clinician-researcher at CHU Sainte-Justine and professor in the Department of Pediatrics at Université de Montréal. The team is introducing a novel approach to whole-genome sequencing that combines speed, precision, and accessibility.
Using Oxford Nanopore Technologies and adaptive sampling, the team can now detect a wide range of genetic and epigenetic abnormalities in under 24 hours–some even in less than an hour. This platform paves the way for accelerated clinical decision-making in a context where every hour counts to initiate the right treatment.
The challenge of diagnosis in pediatric oncology: lengthy and costly tests
Pediatric cancers, whether leukemias or solid tumors, are often caused by complex genetic alterations: mutations, gene fusions, and even epigenetic modifications such as methylation, which can deactivate certain genes. Diagnosis currently relies on a series of separate tests that are lengthy, costly, and require a significant amount of biological material–such as blood, bone marrow, or tumor tissue–which is difficult and limited to collect in children.
The scientific team proposes an innovative solution: whole-genome sequencing with adaptive sampling. Unlike traditional methods, this approach reads native DNA directly–as it exists in the patient's cells, without being modified or amplified–while targeting in real time the most relevant regions for cancer analysis.
With a single biological sample, the machine "learns" to recognize areas of interest and preferentially sequence them, while maintaining a comprehensive view of the genome. The result: simultaneous detection of all clinically relevant anomalies, including those missed by traditional tests.
Chromosomal abnormalities detected in one hour
Powered by the Azrieli Platform in Pediatric Precision Health, Dr. Lavallée's project was developed within the MPGI, a technological environment dedicated to genomic innovation. The study enabled a complete analysis of the 31 samples studied in less than five days. The results are impressive: 95% of clinically identified gene fusions and 94% of mutations were successfully detected.
"This approach offers great flexibility: you simply train the machine to recognize new genes of interest, without needing to modify the lab protocol," explains Dr. Vincent-Philippe Lavallée.
One of the major advantages of this approach is its ability to generate actionable results at different stages of sequencing. Within the first hour, some anomalies–such as large chromosomal alterations or methylation profiles–can already be detected. Then, gene fusions and clonal mutations become identifiable, enabling faster and potentially more effective therapeutic guidance. This progressive dynamic offers valuable flexibility for clinical teams, who can adapt their decisions in real time.
Although developed for pediatric oncology, this method is transferable to other fields, such as rare diseases or adult cancers. It can be applied to various types of samples (blood, bone marrow, biopsies).
"If the next steps confirm these results, this method could be transferred to clinical settings in the coming years, profoundly transforming diagnostic practices in pediatric oncology–and beyond." concluded Dr. Lavallée.
