Clinical impacts of copy number variations in B-cell differentiation and cell cycle control genes in pediatric B-cell acute lymphoblastic leukemia: a single centre experience.

Background: gene deletions have been identified as a poor prognostic factor in pediatric B-cell acute lymphoblastic leukemia (B-ALL), especially in the presence of co-occurring deletions ( profile). This study aimed to determine the frequency of deletions and deletions in other B-cell differentiation and cell cycle control genes, and their prognostic impact in Slovenian pediatric B-ALL patients.

Patients And Methods: We studied a cohort of 99 patients diagnosed with B-ALL from January 2012 to December 2020 and treated according to the ALL IC-BFM 2009 protocol. Eighty-eight bone marrow or peripheral blood samples were analysed for copy number variations (CNVs) using the SALSA MLPA P335 ALL-IKZF1 probemix.

Results: At least one CNV was detected in more than 65% of analysed samples. The most frequently altered genes were and (30.7%, 26.1%, and 25.0%, respectively). Deletions in were present in 18.2% of analysed samples and were associated with an inferior 5-year event-free survival (EFS; 54.8% . 85.9%, p = 0.016). The profile was identified in 12.5% of the analysed samples, and these patients had an inferior 5-year EFS than those with deletions in only and those without deletions (50.8% . 75.0% . 85.9%, respectively, p = 0.049). Overall survival (OS) was also worse in patients with the profile than those with deletions in only and those without deletions (5-year OS 76.2% . 100% . 93.0%, respectively). However, the difference between the groups was not statistically significant.

Conclusions: Our results are in concordance with the results obtained in larger cooperative clinical trials. Copy number variations analysis using the SALSA MLPA kit is a reliable tool for initial diagnostic approach in children with B-ALL, even in smaller institutions in low- and middle-income countries.