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Open AccessArticle

Nanopore Targeted Sequencing for Rapid Gene Mutations Detection in Acute Myeloid Leukemia

1
Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, P.zza G. Cesare, 11 70124 Bari, Italy
2
Hematology and Bone Marrow Transplant Unit, University of Milan, 24127 Bergamo, Italy
*
Author to whom correspondence should be addressed.
These authors have contributed equally to this work.
Genes 2019, 10(12), 1026; https://doi.org/10.3390/genes10121026
Received: 12 November 2019 / Revised: 5 December 2019 / Accepted: 5 December 2019 / Published: 9 December 2019
(This article belongs to the Special Issue Genetics and Genomics of Acute Myeloid Leukemia)
Acute myeloid leukemia (AML) clinical settings cannot do without molecular testing to confirm or rule out predictive biomarkers for prognostic stratification, in order to initiate or withhold targeted therapy. Next generation sequencing offers the advantage of the simultaneous investigation of numerous genes, but these methods remain expensive and time consuming. In this context, we present a nanopore-based assay for rapid (24 h) sequencing of six genes (NPM1, FLT3, CEBPA, TP53, IDH1 and IDH2) that are recurrently mutated in AML. The study included 22 AML patients at diagnosis; all data were compared with the results of S5 sequencing, and discordant variants were validated by Sanger sequencing. Nanopore approach showed substantial advantages in terms of speed and low cost. Furthermore, the ability to generate long reads allows a more accurate detection of longer FLT3 internal tandem duplications and phasing double CEBPA mutations. In conclusion, we propose a cheap, rapid workflow that can potentially enable all basic molecular biology laboratories to perform detailed targeted gene sequencing analysis in AML patients, in order to define their prognosis and the appropriate treatment. View Full-Text
Keywords: nanopore targeted sequencing; acute myeloid leukemia; mutational analysis; FLT3 internal tandem duplications; biallelic CEBPA mutations nanopore targeted sequencing; acute myeloid leukemia; mutational analysis; FLT3 internal tandem duplications; biallelic CEBPA mutations
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Cumbo, C.; Minervini, C.F.; Orsini, P.; Anelli, L.; Zagaria, A.; Minervini, A.; Coccaro, N.; Impera, L.; Tota, G.; Parciante, E.; Conserva, M.R.; Spinelli, O.; Rambaldi, A.; Specchia, G.; Albano, F. Nanopore Targeted Sequencing for Rapid Gene Mutations Detection in Acute Myeloid Leukemia. Genes 2019, 10, 1026.

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