Cytogenetic landscape in pediatric acute lymphoblastic leukemia: Insights from a regional center

Dear Editor,

Acute lymphoblastic leukemia (ALL), the most common childhood malignancy, is driven by specific chromosomal abnormalities that play a crucial role in diagnosis, prognosis, and therapy selection. Among these, the Breakpoint cluster region-Abelson murine leukemia viral oncogene homolog 1 (BCR-ABL1) fusion gene stands apart not only as a defining cytogenetic subtype but also as the only therapeutically actionable target with approved treatment options such as tyrosine kinase inhibitors (TKIs). This contrasts with other common translocations (ETV6-RUNX1, TCF3-PBX1, KMT2A rearrangements), which serve primarily prognostic roles.

Both the World Health Organization (WHO) 2016 and WHO-HAEM5 classifications acknowledge these cytogenetic changes as defining criteria for B-cell ALL (B-ALL) subtypes. In clinical practice, cytogenetic profiling aids in risk stratification, typically alongside age, total leukocyte count, and minimal residual disease. However, in resource-limited settings, performing full-spectrum cytogenetic testing for all patients may not be feasible. An algorithmic approach, where BCR-ABL1 is screened first due to its treatment implications, is therefore both cost-effective and clinically prudent.

We evaluated 27 pediatric ALL patients (aged 1–10 years). Diagnosis was based on peripheral blood/bone marrow morphology, cytochemistry, and immunophenotyping through flow cytometry (Beckman Coulter Cytomics FC 500). Reverse transcription-polymerase chain reaction (RT-PCR) screening was done for key fusions: BCR-ABL1, ETS variant transcription factor 6-Runt-related transcription factor 1 [ETV6-RUNX1] (TEL-AML1), Transcription Factor 3-Pre-B-cell Leukemia Homeobox 1 (TCF3-PBX1 (E2A-PBX1), and MLL rearrangements Mixed Lineage Leukemia-ALL1-fused gene from chromosome 4q21, Mixed Lineage Leukemia-ALL1-fused gene from chromosome 9p22 and Mixed Lineage Leukemia-Eleven-nineteen Leukemia gene (MLL-AF4, MLL-AF9, and MLL-ENL).

Of the 27 pediatric patients analyzed, the most common presenting feature was pallor (18/24), followed by splenomegaly (16/24) and lymphadenopathy (15/24). All cases demonstrated an immunophenotype consistent with B-ALL. RT-PCR identified fusion transcripts in 10 out of 27 cases, all of which were mutually exclusive. Table 1 mentions the frequencies. Among the BCR-ABL1-positive patients, two exhibited the major transcript (p210) and three had the minor transcript (p190); no microvariant (p230) was detected. Chromosomal abnormalities are observed in approximately 80–90% of pediatric ALL cases and often carry prognostic significance.^[1] The BCRABL1 fusion gene, derived from t(9;22)(q34;q11), is typically associated with chronic myeloid leukemia (CML), but it also occurs in approximately 5% of pediatric and 20% of adult ALL patients. It is considered an adverse prognostic marker in pediatric populations.^[2] Indian studies have reported a higher incidence of BCR-ABL1 in ALL (ranging from 10% to 25%) compared to Western cohorts (10–15%), reflecting possible regional biological differences.^[3] In our cohort, the prevalence was 18.5%. The three BCR-ABL1 transcript variants – p190, p210, and p230 – are associated with distinct disease profiles: p190 is most common in ALL, p210 in CML, and p230 in chronic neutrophilic leukemia.^[4] Approximately 70% of BCR-ABL1-positive ALL cases harbor the minor breakpoint (e1a2; p190), while 30% exhibit major transcripts (e13a2/e14a2; p210).^[4] The mutually exclusive nature of BCR-ABL1 and other major ALL translocations (e.g., ETV6-RUNX1, TCF3-PBX1, and KMT2A) supports the rationale for a sequential testing strategy. ETV6-RUNX1, caused by t(12;21)(p13;q22), is one of the most common fusions in pediatric ALL (20– 25%) and generally confers a favorable prognosis, although variability has been observed in different populations.^[5] One patient in our cohort exhibited MLL-ENL, linked to KMT2A rearrangements, which occur in ~5% of pediatric and ~10% of adult ALL cases.^[5]

All patients had a B-ALL immunophenotype Fusion transcripts were identified in 10 of 27 cases (37%) Only BCR-ABL1 (18.5%) had actionable therapeutic relevance. Fusion mutations were mutually exclusive in all cases No Transcription Factor 3 (TCF3-HLF )or IGH-IL3 was detected.

In resource-constrained settings, strategic use of molecular diagnostics is essential to balance cost-efficiency with clinical value. Among all structural cytogenetic abnormalities in pediatric ALL, BCR-ABL1 stands out as the only mutation with direct therapeutic implications, targetable with TKIs. Its detection influences treatment decisions immediately, unlike other recurrent fusions such as ETV6-RUNX1, TCF3-PBX1, and KMT2A rearrangements, which primarily serve prognostic roles.

Given the mutual exclusivity of major cytogenetic translocations in ALL, we propose an algorithmic approach where RT-PCR screening for BCR-ABL1 is conducted as the first-line test. If BCR-ABL1 is negative, secondary testing for prognostic markers can then be pursued. This structured algorithm allows for rational resource utilization, ensures timely identification of patients who may benefit from TKI therapy, and provides essential risk stratification where resources permit extended analysis.

Our findings underscore the high prevalence (18.5%) of BCRABL1 in pediatric ALL in our region, higher than Western counterparts, and reaffirm its role as the first-line molecular test. Implementation of a BCR-ABL1 – the first algorithm for cytogenetic screening in ALL – is recommended in settings with limited resources. This model ensures timely treatment decisions while maintaining molecular diagnostic value.