Development and Validation of a One-Step RT-qPCR Assay for Identifying Common Fusion Gene Transcripts Associated with the Prognosis of Mexican Children with B-Lineage Acute Lymphoblastic Leukemia

Abstract

The aims of the present study were to optimize the detection of common fusion gene transcripts associated with childhood B-ALL prognosis through the development and validation of a one-step RT-qPCR assay and to identify the prevalence of these genes in a cohort of pediatric patients attended in public hospitals in Mexico City. The one-step RT-qPCR assay was sensitive, specific, easy to use, fast and cost efficient. The standard curves were linear, with amplification efficiencies between 97-107%; coefficients of variation were 2.1-3.0% in reproducibility and 2.6-3.8% in repeatability, with agreement between two different laboratories. The prevalence of fusion gene transcripts was ETV6-RUNX1, 10.3%; TCF3-PBX1, 7.5%; BCR-ABL1p190, 3.6%; and KMT2A-AFF1, 2.8%. The prevalence of the ETV6-RUNX1 fusion was low, consistent with the findings in Hispanics. The KMT2A-AFF1 fusion was not exclusively present in infants, as we also found it in patients 4-16 years of age, in whom it was related to a poor prognosis. TCF3-PBX1 patients were associated with an intermediate outcome. The present study highlights the importance of the detection of common genetic fusions in Mexican children with ALL, taking into account that some have molecular subtypes associated with a poor prognosis.