Next-Generation Sequencing Improves Diagnosis, Prognosis and Clinical Management of Myeloid Neoplasms

Abstract

Molecular diagnosis of myeloid neoplasms (MN) is based on the detection of multiple genetic alterations using various techniques. Next-generation sequencing (NGS) has been proved as a useful method for analyzing many genes simultaneously. In this context, we analyzed diagnostic samples from 121 patients affected by MN and ten relapse samples from a subset of acute myeloid leukemia patients using two enrichment-capture NGS gene panels. Pathogenicity classification of variants was enhanced by the development and application of a custom onco-hematology score. A total of 278 pathogenic variants were detected in 84% of patients. For structural alterations, 82% of those identified by cytogenetics were detected by NGS, 25 of 31 copy number variants and three out of three translocations. The detection of variants using NGS changed the diagnosis of seven patients and the prognosis of 15 patients and enabled us to identify 44 suitable candidates for clinical trials. Regarding AML, six of the ten relapsed patients lost or gained variants, comparing with diagnostic samples. In conclusion, the use of NGS panels in MN improves genetic characterization of the disease compared with conventional methods, thus demonstrating its potential clinical utility in routine clinical testing. This approach leads to better-adjusted treatments for each patient.

Analytical validation and performance characteristics of a 48-gene next-generation sequencing panel for detecting potentially actionable genomic alterations in myeloid neoplasms

“…RNA splicing (SF3B1, SRSF2, U2AF1, and ZRSR2), and transcription factor (CEBPA, ETV6, GATA1, GATA2, IKZF1, KMT2A, PHF6, RUNX1, SETBP1, and WT1) accounted for 27% (n=574/2,053), 22% (n=444/2,053), and 13% (n=272/2,053) of patients, respectively. These findings are consistent with the mutational frequency of gene groups in myeloid neoplasms as reported in literature [22][23][24][25][26].…”

Assessing acquired resistance to IDH1 inhibitor therapy by full-exon IDH1 sequencing and structural modeling

“…Molecular characterization of acute myeloid leukemia (AML) yielded greater understanding of leukemogenesis, revolutionized disease diagnosis and prognosis, and led to the development of new biomarkers and novel targeted therapies (King and Bagg 2017;Carbonell et al 2019;Winer and Stone 2019;DiNardo and Wei 2020). Somatic mutations in two isoforms of isocitrate dehydrogenase gene (IDH1/2) characterize 20%-25% of AML cases Nassereddine et al 2017;Yoshimi et al 2019).…”

Analytical validation and performance characteristics of a 48-gene next-generation sequencing panel for detecting potentially actionable genomic alterations in myeloid neoplasms

“…In recent years, various NGS based myeloid neoplasm panels developed in-house and commercially have been integrated into routine clinical practice [10][11][12][13]. Panels developed inhouse can differ substantially between laboratories in many aspects including gene content, the analysis of genes in a panel, sequencing library preparation chemistry, sequencing platform, and variant types detected [14][15][16][17][18][19][20].…”