Analysis of Somatic Mutations in Epigenetic Genes in Major Leukemia Subtypes

Aim: To investigate presence of somatic mutations in DNMT3A, TET1, TET2, IDH1, IDH2, ASXL1, and SETBP1 genes playing a role in epigenetic regulation by NGS analysis of bone marrow samples of 13 ALL, 19 AML, 14 CLL, and 15 CML patients. Methods: DNA was isolated from bone marrow samples of 13 ALL, 19 AML, 14 CLL, and 15 CML patients, and Kapa NGS DNA extraction kit was used. Purity and concentration of DNA were measured by Qubit fluorometer, and NadPrep DNA Universal Library Preparation Kit was used for high-quality library preparation. Bioinformatic analyses were performed through the portal provided by Roche Diagnostics for NGS solutions. The pathogenicity status of the variants detected in the relevant genes was determined under the ACMG classification. Results: Variations in at least one gene were found in all but one of the 13 patients diagnosed with ALL. Among seven genes, most distinct variant was detected in TET3 gene, and all of them were VUS variants according to ACMG classification. In 19 patients diagnosed with AML, the gene with highest number of distinct variants was TET3, and all variants were in the VUS class, followed by TET2 and ASXL1 genes, respectively. Variants were detected in at least one gene in all but four AML patients. No variant was detected in four of 14 patients diagnosed with CLL. Variants were detected in at least one of the related genes in the remaining patients. The genes with the highest number of distinct variants in CML patients were TET3, ASXL1, and SETBP1, respectively. Conclusions: At least one variant of related genes was detected in all leukaemia subtypes. The c.856-2A>T variant in the DNMT3A gene was detected in at least one patient with major leukaemia subtypes, suggesting this variant may play an important role in haematopoietic stem cell processes.