Comprehensive NGS Panel Validation for the Identification of Actionable Alterations in Adult Solid Tumors.

Paula Martínez-Fernández,Juan José Ríos-Martín,Alberto Palmeiro-Uriach,Pablo Gargallo,Patricia Pose,Marta Izquierdo-García,Inmaculada Trigo-Sánchez,Marián Lázaro,Enrique Rodríguez-Zarco,Inés Calabria,Paula Carbonell,Ibon Barba,Mjose Garcia-Ruiz,Carlos Méndez Méndez ,A García ,Jerónimo Forteza‐Vila ,Carlos Alberto Ruíz ,Jennifer Valero-García ,Raquel Dolz Gaitón ,N Camarasa-Lillo

doi:10.3390/jpm11050360

Abstract

The increasing identification of driver oncogenic alterations and progress of targeted therapies addresses the need of comprehensive alternatives to standard molecular methods. The translation into clinical practice of next-generation sequencing (NGS) panels is actually challenged by the compliance of high quality standards for clinical accreditation. Herein, we present the analytical and clinical feasibility study of a hybridization capture-based NGS panel (Action OncoKitDx) for the analysis of somatic mutations, copy number variants (CNVs), fusions, pharmacogenetic SNPs and Microsatellite Instability (MSI) determination in formalin-fixed paraffin-embedded (FFPE) tumor samples. A total of 64 samples were submitted to extensive analytical validation for the identification of previously known variants. An additional set of 166 tumor and patient-matched normal samples were sequenced to assess the clinical utility of the assay across different tumor types. The panel demonstrated good specificity, sensitivity, reproducibility, and repeatability for the identification of all biomarkers analyzed and the 5% limit of detection set was validated. Among the clinical cohorts, the assay revealed pathogenic genomic alterations in 97% of patient cases, and in 82.7%, at least one clinically relevant variant was detected. The validation of accuracy and robustness of this assay supports the Action OncoKitDx’s utility in adult solid tumors.

Highlights

Cancer can rely on different genetic aberrations, including point mutations, focal or complete chromosomal copy number variants, rearrangements or structural variants. some of them are well understood, the growing knowledge on less frequent 4.0/).pathogenic variants constituting driver events in tumorigenesis, together with the rapid development of targeted therapies, urges clinical testing to provide broader strategies [1].Traditional molecular diagnosis based on low-throughput techniques for the detection of single nucleotide or small deletions and insertions is being replaced by the pressing need of personalized medicine
2021), it interrogates many other genes related to tumorigenesis and potential targets for therapies being tested in clinical trials or susceptible to be developed in the future
The mean Q30 value of the sequencing runs was 90.7%, and 88.4% the average percentage of clusters passing filter, always within the density range recommended by the manufacturer of the sequencing equipment used

Summary

Introduction

Traditional molecular diagnosis based on low-throughput techniques for the detection of single nucleotide or small deletions and insertions is being replaced by the pressing need of personalized medicine. Given the heterogeneity and genetic complexity that many tumors present, the integration of clinical, pathological, and molecular data provides key information to outline a specific biological profile that could be crucial in clinical decision-making. The current availability and cost-effectiveness of massively parallel next-generation sequencing (NGS) and the improvement of bioinformatic data analysis programs have enabled the implementation to the clinical practice of high-throughput, sensitive, and accurate tumor profiling [2]. We present the analytical validation and clinical utility of the Action OncoKitDx, a hybrid capture NGS-based panel indicated in the study of adult solid tumors.

Methods

Results

Conclusion