Use of the Ion PGM and the GeneReader NGS Systems in Daily Routine Practice for Advanced Lung Adenocarcinoma Patients: A Practical Point of View Reporting a Comparative Study and Assessment of 90 Patients

Abstract

Background: With the integration of various targeted therapies into the clinical management of patients with advanced lung adenocarcinoma, next-generation sequencing (NGS) has become the technology of choice and has led to an increase in simultaneously interrogated genes. However, the broader adoption of NGS for routine clinical practice is still hampered by sophisticated workflows, complex bioinformatics analysis and medical interpretation. Therefore, the performance of the novel QIAGEN GeneReader NGS system was compared to an in-house ISO-15189 certified Ion PGM NGS platform. Methods: Clinical samples from 90 patients (60 Retrospectively and 30 Prospectively) with lung adenocarcinoma were sequenced with both systems. Mutations were analyzed and EGFR, KRAS, BRAF, NRAS, ALK, PIK3CA and ERBB2 genes were compared and sampling time and suitability for clinical testing were assessed. Results: Both sequencing systems showed perfect concordance for the overlapping genes. Correlation of allele frequency was r2 = 0.93 for the retrospective patients and r2 = 0.81 for the prospective patients. Hands-on time and total run time were shorter using the PGM system, while the GeneReader platform provided good traceability and up-to-date interpretation of the results. Conclusion: We demonstrated the suitability of the GeneReader NGS system in routine practice in a clinical pathology laboratory setting.

Prospective evaluation of NGS-based liquid biopsy in untreated late stage non-squamous lung carcinoma in a single institution

“…Briefly, one tissue Section (5 µm) was analyzed for EGFR evaluation using the Idylla system [9], and 4 tissue Sections (3 µm each) were used for ALK (D5F3, Ventana, Tucson, AZ, USA), ROS1 (D4D6, Cell Signaling, Danvers, MA, USA), BRAF (VE1, Ventana) and PD-L1 (22C3, Dako, Santa Clara, CA, USA) immunohistochemistry for status assessment. NGS analysis from DNA extracted from formalin-fixed and paraffin-embedded (FFPE) tissue was conducted using the AmpliSeq Hotspot V2 Panel (Thermo Fisher Scientific) as described previously [10]. Genes covered by the respective panels are summarized in Additional file 1: Figure S1.…”

Current status of ctDNA in precision oncology for hepatocellular carcinoma

“…The European Consortium Cancer ID (https:// www.cancer-id.eu) and the United States Working Groups Blood Profiling Atlas in Cancer (BloodPAC [https://www.bloodpac.org/]) published best-practice protocols when implementing liquid biopsies [53]. Additionally, before NGS-based technologies are applied, full validation, cyclic testing, and external quality assessment should be done according to ISO 15189 [54].…”

The OncoAge Consortium: Linking Aging and Oncology from Bench to Bedside and Back Again

“…Since 2015, OncoAge has been associated with the publication of 86 scientific articles referenced in NCBI PubMed (the “FHU OncoAge” was listed with the author’s affiliation). For example, some publications are related to epidemiological, clinical, and translational research projects made in lung cancer and COPD, such as lung cancer screening and assessment of biomarkers [37,38,39,40,41,42,43,44,45,46]. Recently, a new project was accomplished by physicians from the Nice University Hospital and researchers belonging to the “Institut National de Recherche en Informatique et en Automatique” (Inria) who aimed to develop a lung cancer screening program based on the integration of three signatures: clinical data (leading to better risk factor assessment), chest low dose CT scan (by using computer-aided diagnosis), and biological blood signatures [47].…”