High-throughput detection of clinically targetable alterations using next-generation sequencing

Julie A Vendrell (1) , David Grand (2) , Isabelle Rouquette (2) , Valérie Costes (1, 3) , Samira Icher (2) , Janick Selves (2) , Marion Larrieux (1) , Aurore Barbe (2) , Pierre Brousset (2, 4) , Jérôme Solassol (1, 5)

1 Service de Biopathologie [CHRU Montpellier]
2 IUCT Oncopole - UMR 1037 - Institut Universitaire du Cancer de Toulouse - Oncopole
3 Pathogénèse et contrôle des infections chroniques (PCCI)
4 UM - Université de Montpellier
5 IRCM - U1194 Inserm - UM - Institut de Recherche en Cancérologie de Montpellier

Next-generation sequencing (NGS) has revolutionized the therapeutic care of patients by allowing high-throughput and parallel sequencing of large numbers of genes in a single run. However, most of available commercialized cancer panels target a large number of mutations that do not have direct therapeutic implications and that are not fully adapted to low quality formalin-fixed, paraffin-embedded (FFPE) samples. Here, we designed an amplicon-based NGS panel assay of 16 currently actionable genes according to the most recent recommendations of the French National Cancer Institute (NCI). We developed a panel of short amplicons (<150 bp) using dual-strand library preparation. The clinical validation of this panel was performed on well-characterized controls and 140 routine diagnostic samples, including highly degraded and cross-linked genomic DNA extracted from FFPE tumor samples. All mutations were detected with elevated inter-laboratory and inter-run reproducibility. Importantly, we could detect clinically actionable alterations in FFPE samples with variant allele frequencies as low as 1%. In addition, the overall molecular diagnosis rate was increased from 40.7% with conventional techniques to 59.2% with our NGS panel, including 41 novel actionable alterations normally not explored by conventional techniques. Taken together, we believe that this new actionable target panel represents a relevant, highly scalable and robust tool that is easy to implement and is fully adapted to daily clinical practice in hospital and academic laboratories.

Mots clés: routine practice; molecular diagnosis; targeted therapies; NGS cancer panel

Domaines: Cancer; Biologie cellulaire

Julie A Vendrell, David Grand, Isabelle Rouquette, Valérie Costes, Samira Icher, et al.. High-throughput detection of clinically targetable alterations using next-generation sequencing. Oncotarget, 2017, 8 (25), pp.40345-40358. ⟨10.18632/oncotarget.15875⟩. ⟨hal-01762917⟩