Proceedings of Oncobiology Symposiums
Proceedings of XIV Oncobiology Symposium

INTRODUCTION AND OBJECTIVES: Because IKZF1 deletions (ΔIKZF1) are associated with an increased risk of relapse in patients with B-cell precursor acute lymphoblastic leukemia (B-ALL), the development of methods for rapid and accurate detection of this alteration has a great clinical impact. Although multiplex ligation-dependent probe amplification (MLPA) has been widely used for the evaluation of ΔIKZF1, the method presents certain limitations and high cost. Therefore, a multiplex (M)-PCR has been established for the detection of recurrent intragenic ΔIKZF1 (Δ2-3, Δ2-7, Δ2-8, Δ4-7, Δ4-8). Since the M-PCR is not able to detect all types of ΔIKZF1, the present study aims to evaluate the breakpoint map of non-recurrent ΔIKZF1 to update the M-PCR for the diagnosis of this genetic alteration. MATERIAL AND METHODS: This study included pediatric and adult patients with B-ALL. Copy-number alterations (CNAs) within IKZF1 locus were screened using SALSA MLPA P335. Suspicious ΔIKZF1 were confirmed with SALSA MLPA P202 and/or M-PCR. Recurrent ΔIKZF1 encompassed Δ1-8, Δ2-3, Δ2-7, Δ2-8, Δ4-7, Δ4-8, while non-recurrent deletions included the remaining alterations. First, we determined IKZF1 status in a discovery cohort. After the identification of non-recurrent alterations, we collected B-ALL samples to validate and provide a detailed description of rare deletions. Mapping the breakpoints of such deletions will allow us to update the M-PCR for diagnosis of ΔIKZF1. RESULTS AND CONCLUSION: First, we verified IKZF1 status in 113 patients with B-ALL using the SALSA MLPA P335. Thirty-five (31%) patients had suspicious ΔIKZF1, which were classified as recurrent (n=21) and non-recurrent (n=14) ΔIKZF1. Considering the rarity of the latter group, we performed an international and multicenter collaboration to collect suspicious non-recurrent deletions. IKZF1 status was further investigated in 1,474 B-ALL samples, and 16% presented ΔIKZF1 overall. Non-recurrent deletions were associated with 9% of ΔIKZF1, and comprised miscellaneous alterations: Δ1, Δ1-2, Δ1-3, Δ1-4, Δ1-5, Δ4-6, Δ5, and Δ6-8. Validation analyses led to redefinition of the status of non-recurrent ΔIKZF1 in 67% of cases; 42% had no ΔIKZF1 at all. Although MLPA (P335) is an important method for the determination of this genetic alteration, our data highlight the importance of confirmatory methods (MLPA P202 and M-PCR) for the determination of IKZF1 status, especially regarding non-recurrent deletions. Indeed, MLPA screening using a broad panel (P335) provides evidence for other CNAs, which are important for risk stratification based on the UKALL–CNA or IKZF1plus classifiers.