Validity of Targeted Next-Generation Sequencing in Routine Care for Identifying Clinically Relevant Molecular Profiles in Non–Small-Cell Lung Cancer
Menée à partir d'échantillons tumoraux prélevés sur 1 343 patients atteints d'un cancer du poumon non à petites cellules, cette étude française analyse la possibilité d'utiliser en routine les techniques de séquençage ciblé de nouvelle génération pour identifier des profils moléculaires ayant un intérêt clinique
Theranostic assays are based on single gene testing but the ability of next-generation sequencing (NGS) to interrogate numerous genetic alterations will progressively replace single gene assays. Although NGS was evaluated to screen for theranostic mutations, its usefulness in clinical practice on large series of samples remains to be demonstrated. NGS performance was assessed following guidelines. TaqMan probes and NGS were compared for their ability to detect EGFR and KRAS mutations and NGS mutation profiles were analyzed on a large series of NSCLC (n=1,343). The R2 correlation between expected and measured allelic ratio, using commercial samples, was >0.96. Mutation detection threshold was 2% for 10ng of DNA input. Kappa-scores for TaqMan versus NGS were 0.99 [0.97-1.00]95%CI for EGFR and 0.98 [0.97-1.00]95%CI for KRAS after exclusion of rare EGFR (n=40) and KRAS (n=60) mutations. NGS identified 693 and 292 mutations in validated and potential oncogenic drivers, respectively. Significant associations were found between EGFR and PI3KCA or CTNNB1 and between KRAS and STK11. Potential oncogenic driver mutations or gene amplifications were more frequent in validated oncogenic driver non-mutated samples. This work is a proof of concept that targeted NGS is accessible in routine including large screening at reasonable cost. Clinical data should be collected and implemented in specific databases to make molecular data meaningful for direct patients? benefit.
The Journal of Molecular Diagnostics , résumé, 2017