Identification of Genetic Variants Using Next-Generation Sequencing in Pediatric Myelodysplastic Syndrome: From Disease Biology to Clinical Applications

Abstract

This study aimed to identify genetic variants using a customized next-generation sequencing (NGS) panel for pediatric myelodysplastic syndrome (pMDS) and to explore their associations with cytogenetic and clinical characteristics. Cytogenetic analyses were conducted using G-banding and fluorescence in situ hybridization. NGS was performed with the Ion Torrent Personal Genome Machine for the following genes: GATA2, RUNX1, CEBPA, ANKRD26, ETV6, SAMD9, SAMD9L, PTPN11, NRAS, SETBP1, DDX41, TP53, FLT3, SRP72, and JAK3. Analyses were performed with Ion Reporter 5.20.8.0 software. Genetic variants were classified using the dbSNP, 1000 Genomes, COSMIC, and Varsome databases. We analyzed 25 cases of pMDS; 15 presented abnormal karyotypes, and 19 showed genetic variants. Among the 29 variants identified across 12/15 genes, 27% were pathogenic and 14% were likely pathogenic, with NRAS and GATA2 most frequently associated with disease progression. A new somatic variant of uncertain significance in SETBP1 was detected in seven patients showing heterogeneous clinical outcomes. Genetic variants were found in 7/10 patients with normal karyotypes, indicating that submicroscopic alterations can shed light on disease biology. Our results highlight the critical role of a targeted NGS panel in identifying molecular alterations associated with pMDS pathogenesis, thereby enhancing diagnostic precision, prognosis, and aiding in treatment selection.

Keywords: genetic variants; pediatric myelodysplastic syndrome; targeted NGS panel.

Figure 1

Overall clinical, cytogenetic, and genetic spectrum of pMDS patients. (A) The corresponding color coding is defined in the legend. P: pathogenic; LP: likely pathogenic; VUS: variant of uncertain significance; BM: bone marrow; RCC: refractory cytopenia of childhood; AML: acute myeloid leukemia; MDS-EB: myelodysplastic syndrome with excess of blasts. (B) The ribbon plot was created using Flourish [https://flourish.studio/ (accessed on 31 March 2025)], which shows the associations between cytogenetic profiles and genetic variants observed in the present study.