A team of researchers from France developed a capture-based next‑generation sequencing panel that can help molecularly diagnose patients with cancer including gastrointestinal stromal tumors (GISTs) and published their results in the International Journal of Molecular Medicine.
The panel focuses on 10 genes that harbor genetic variations, which can be targeted by approved drugs. The genes are ALK, BRAF, EGFR, ERBB2, KIT, KRAS, MAP2K1, MET, NRAS, and PDGFRA. Of these, KIT and PDGFRA are known to be involved in the development of GIST.
The team led by Romain Boidot, PhD, reported “very favorable analytical performances” from their panel for both solid and liquid biopsies. For solid biopsies, the researchers reported a genotype detection accuracy of 100% even with a low read depth.
They said that their method met all the requirements for the ISO15189 certification, and added that clinical reports could be ready in less than 5 days from the day the samples were received. The panel was routinely used for 3 years to analyze close to 2300 samples from patients with cancer. Of these, 42 were GIST samples.
Read more about the etiology of GIST
The panel detected more gain‑of‑function variants than what was described in the literature, the researchers said. Moreover, it detected loss‑of‑function variants in some genes. When they analyzed data obtained from liquid biopsies, they found that there was a statistically significant difference in the frequency of mutated alleles between the different types of tumors, mutated genes, and gene variants.
“In conclusion, the use of our capture‑based [next‑generation sequencing] panel is perfectly adapted to perform relevant molecular diagnosis in a time frame compatible with patient care,” the researchers wrote.
Other cancer types that the researchers analyzed included lung and colorectal cancers and melanomas. They said that this type of method should be developed for the routine diagnosis of other types of cancer.
Chevrier S, Brasselet A, Carnet M, et al. Custom multi‑tumor next‑generation sequencing panel for routine molecular diagnosis of solid tumors: validation and results from three‑year clinical use. Int J Mol Med. 2022;49:57. doi:10.3892/ijmm.2022.5113