DP029 | HIGH-RESOLUTION dMLPA-ALL PROFILING OF COPY NUMBER ALTERATIONS AND RELEVANT GENETIC LESIONS IN A LARGE COHORT OF ADULT ACUTE LYMPHOBLASTIC LEUKEMIA PATIENTS

Background: Acute lymphoblastic leukemia (ALL) shows recurrent genetic alterations relevant to risk and patient (pt) outcomes. Specific deletions or amplifications, such as IKZF1/IKZF1plus, are linked to poor prognosis. We used a new digitalMLPA (dMLPA) tool, designed for ALL, to detect CNAs and ploidy, including in pts with non-evaluable karyotypes. Its targeted probes can also reveal del/amp-driven fusions (e.g. PAX5–ZCCHC7) or help identify recurrent ALL fusions. We also explored whether intrachromosomal dels involving neighboring genes cause only CNAs or also generate fusion transcripts. Methods: We sequenced with dMLPA-ALL Probemix assay (MRC-Holland; 52 genes covered and 249 karyotyping probes) 216 B/T-ALL adult patients. dMLPA data were compared with standard cytogenetic and molecular results (karyotyping, MLPA, SNP array, IKZF1-PCR), when available. In 171 cases, RNA-seq and fusion analysis were done using a 4-tool in-house pipeline. Results: 25 samples were excluded (data issues/failed analysis); updated probemix testing is ongoing at MRC-Holland. Notably, 11/25 showed hyper/hypodiploidies. In the remaining 191 cases (177 B-ALL, 9 T-ALL, 3 MPAL, 1 AUL), CNAs were found in 92.7%. Whole chromosome dels occurred in 5.8%, mainly chrs 7 and 15, while hyperdiploidy was seen in 17.3% (chrs X, 21, 10, 14, and 6). A wide range of gene alterations was identified. IKZF1 dels were found in 40.8% (78/191) of cases, including 39 with an IKZF1plus profile. MTAP, a prognostic marker linked to PRMT5i response, was co-deleted with CDKN2A/B in 64 pos cases. ETV6, BTG1, and RB1 were dels in 16.2, 15.7, and 9.9% respectively. BTLA and CD200 were deleted in 18 and 17 cases, only 3 cases lacked co-del. NR3C1 dels, tied to glucocorticoid resistance, were found in 5.1% of diagnoses and 18.8% of relapses, suggesting a strong link with relapse (p=0.0067). Moreover, comparison between dMLPA and RNA-seq revealed that the mechanism underlying the frequent fusions involving the PAR1 region (e.g. CRLF2-CSF2RA, P2RY8-CD99), despite commonly affected by del/amp, is not driven by copy number alterations. PAX5-ZCCHC7 del was detected in 19 pts. The del was retained at relapse in all 6 paired cases (diagnosis/relapse). Furthermore, in 3 cases, it was confirmed that this deletion generates a fusion. dMLPA shows promise for comprehensive CNA profiling in ALL, aiding in high-risk profiles and personalized treatment strategies. Supported by the Italian MoH within PNRR-POC-2022-12375862