Next generation sequencing analysis of IKZF1, CDKN2A, CDKN2B and PAX5 alterations in acute lymphoblastic leukemia

Acute lymphoblastic leukemia (ALL) is the most frequent cancer in children, mainly driven by gene alterations such as fusions and mutations. In this study transcriptomic analysis carried out to examine gene fusions, single nucleotide variants and other molecular changes in B-cell ALL (B-ALL) patients from a regional cohort in Iraq. Samples of peripheral blood RNA from B-ALL pediatric patients before and after treatment, and healthy individuals were analysed using NGS enrichment panel targeting 114 hematologic genes. Data was quality checked, aligned to GRCh37/hg19 reference genome and examined for altered expression, sequence variants and gene fusions. Gene expression analysis demonstrated that key oncogenes such as MYCN , ERG , CDKN2A were significantly upregulated, while immune-related genes involving IL7R , BCL11B were markedly downregulated. Variant analysis revealed mutations in NOTCH1 , TP53BP1 and JAK1 . Gene fusion analysis identified diverse rearrangements, with a higher burden before treatment. The results also show prominent transcriptional dysregulation of CDKN2A , substantial intronic variation in IKZF1 and PAX5 , and minimal alteration in CDKN2B . In this cohort, pediatric B-ALL samples showed changes in gene expression, sequence variants and gene fusions, some of which persisted after treatment. These findings suggest that targeted RNA sequencing may enhance early diagnosis and identify potential biomarkers for B-ALL monitoring and risk stratification.