Evaluation of adverse prognostic gene alterations & MRD positivity in BCR::ABL1-like B-lineage acute lymphoblastic leukaemia patients, in a resource-constrained setting

Background Early detection of BCR::ABL1 -like ALL could impact treatment management and improve the overall survival/outcome. BCR::ABL1 -like ALL cases are characterised by diverse genetic alterations activating cytokine receptors and kinase signalling. Its detection is still an unmet need in low–middle-income countries due to the unavailability of a patented TLDA assay. Methods This study’s rationale is to identify BCR::ABL1 -like ALLs using the PHi-RACE classifier, followed by the characterisation of underlying adverse genetic alterations in recurrent gene abnormalities negative ( RGA neg ) B- ALLs ( n = 108). Results We identified 34.25% (37/108) BCR::ABL1 -like ALLs using PHi-RACE classifier, characterised by TSLPR/CRLF2 expression (11.58%), IKZF1 (Δ4–7) deletion (18.9%) and chimeric gene fusions (34.61%). In overexpressed TSLPR/CRLF2 BCR::ABL1 -like ALLs, we identified 33.33% (1/3 ) CRLF2::IGH and 33.33% (1/3) EPOR::IGH rearrangements with concomitant JAK2 mutation R683S (50%). We identified 18.91% CD13 ( P = 0.02) and 27.02% CD33 ( P = 0.05) aberrant myeloid markers positivity, which was significantly higher in BCR::ABL1 -like ALLs compared to non- BCR::ABL1 -like ALLs. MRD positivity was considerably higher (40% in BCR::ABL1 -like vs. 19.29% in non- BCR::ABL1 -like ALLs). Conclusions With this practical approach, we reported a high incidence of BCR::ABL1 -like ALLs, and a lower frequency of CRLF2 alteration & associated CGFs. Recognising this entity, early at diagnosis is crucial to optimise personalised treatment strategies.