Assessment of the clinical utility of four NGS panels in myeloid malignancies. Suggestions for NGS panel choice or design

• Published in: PloS one 2020-01, Vol.15 (1), p.e0227986-e0227986
• Main Authors: Aguilera-Diaz, Almudena, Vazquez, Iria, Ariceta, Beñat, Mañú, Amagoia, Blasco-Iturri, Zuriñe, Palomino-Echeverría, Sara, Larrayoz, María José, García-Sanz, Ramón, Prieto-Conde, María Isabel, Del Carmen Chillón, María, Alfonso-Pierola, Ana, Prosper, Felipe, Fernandez-Mercado, Marta, Calasanz, María José
• Format: Article
• Language: English
• Subjects: Biology and life sciences; Bone marrow; Cancer; Data analysis; Deoxyribonucleic acid; Diagnosis; Disease; Disease control; DNA; Genes; Genes, Neoplasm; Genetics; Genomes; Genomics; Hematology; High-Throughput Nucleotide Sequencing - methods; Hospitals; Humans; Information management; Laboratories; Leukemia; Leukemia, Myeloid - genetics; Medical diagnosis; Medical prognosis; Medical research; Medicine and Health Sciences; Mutation; Mutation - genetics; Neoplasms; Next-generation sequencing; Oncology; Panels; Patients; Research and analysis methods; Tumors
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0227986

The diagnosis of myeloid neoplasms (MN) has significantly evolved through the last few decades. Next Generation Sequencing (NGS) is gradually becoming an essential tool to help clinicians with disease management. To this end, most specialized genetic laboratories have implemented NGS panels targeting a number of different genes relevant to MN. The aim of the present study is to evaluate the performance of four different targeted NGS gene panels based on their technical features and clinical utility. A total of 32 patient bone marrow samples were accrued and sequenced with 3 commercially available panels and 1 custom panel. Variants were classified by two geneticists based on their clinical relevance in MN. There was a difference in panel's depth of coverage. We found 11 discordant clinically relevant variants between panels, with a trend to miss long insertions. Our data show that there is a high risk of finding different mutations depending on the panel of choice, due both to the panel design and the data analysis method. Of note, CEBPA, CALR and FLT3 genes, remains challenging the use of NGS for diagnosis of MN in compliance with current guidelines. Therefore, conventional molecular testing might need to be kept in place for the correct diagnosis of MN for now.