Implementation of an NGS‐based sequencing and gene fusion panel for clinical screening of patients with suspected hematologic malignancies

• Published in: European journal of haematology 2019-09, Vol.103 (3), p.178-189
• Main Authors: Levy, Michael A., Santos, Stephanie, Kerkhof, Jennifer, Stuart, Alan, Aref‐Eshghi, Erfan, Guo, Fen, Hedley, Ben, Wong, Henry, Rauh, Michael, Feilotter, Harriet, Berardi, Philip, Semenuk, Laura, Yang, Ping, Knoll, Joan, Ainsworth, Peter, McLachlin, Catherine Meg, Chin‐Yee, Ian, Kovacs, Michael, Deotare, Uday, Lazo‐Langner, Alejandro, Hsia, Cyrus, Keeney, Mike, Xenocostas, Anargyros, Howlett, Christopher, Lin, Hanxin, Sadikovic, Bekim
• Format: Article
• Language: English
• Subjects: Biomarkers, Tumor; clinical validation; Computational Biology - methods; Cytogenetics; Deoxyribonucleic acid; diagnostic testing; DNA; Flow cytometry; Gene fusion; gene panel; Genes; Genetic Predisposition to Disease; Genetic screening; Genetic Testing; Genetic Variation; Genomics - methods; hematologic malignancies; Hematologic Neoplasms - diagnosis; Hematologic Neoplasms - epidemiology; Hematologic Neoplasms - genetics; High-Throughput Nucleotide Sequencing; Humans; Laboratories; Mutation; myeloid; NGS; Oncogene Proteins, Fusion - genetics; Retrospective Studies; Ribonucleic acid; RNA
• ISSN: 0902-4441; 1600-0609
• DOI: 10.1111/ejh.13272

Objectives The diagnosis of hematologic malignancies integrates multiple diagnostic and clinical disciplines. Historically, targeted (single‐analyte) genetic testing has been used as reflex to initial prescreening by other diagnostic modalities including flow cytometry, anatomic pathology, and clinical cytogenetics. Given the wide range of mutations associated with hematologic malignancies a DNA/RNA‐based NGS panel can provide a more effective and economical approach to comprehensive testing of patients as an initial, tier‐1 screen. Methods Using a cohort of 380 patients, we performed clinical validation of a gene panel designed to assess 40 genes (DNA), and 29 fusion driver genes with over 600 gene fusion partners (RNA), including sample exchange data across three clinical laboratories, and correlation with cytogenetic testing results. Results The clinical validation of this technology demonstrated that its accuracy, sensitivity, and specificity are comparable to the majority of targeted single‐gene approaches, while assessment of the initial patient cohort data demonstrated a high diagnostic yield of 50.5%. Conclusions Implementation of a tier‐1 NGS‐based protocol for gene panel screening provides a comprehensive alternative to targeted molecular testing in patients with suspected hematologic malignancies, with increased diagnostic yield, scalability, reproducibility, and cost effectiveness, making it ideally suited for implementation in clinical laboratories.