A Comparative Study of RT-PCR, FISH, and Karyotyping for T(9;22) Positive Leukemias, and Their Outcomes in Pediatric Patients in a Low Middle-Income Country (LMIC)

Objectives: Various diagnostic tests are available for detecting t(9;22) transcripts in acute and chronic leukemia. This study aims to determine the most effective and cost-efficient testing strategy. Additionally, we analyzed the outcomes of Ph+ leukemias in our population. Methods: Retrospective cohort study was conducted at a tertiary care center in a LMIC. Online and paper charts from January 2011 till December 2022, of patients <18 years of age were reviewed. The sensitivity (SS), specificity (SP), positive predictive value (PPV), and negative predictive value (NPV) of RT-PCR, FISH, and karyotyping were compared. Survival analysis was performed using the Kaplan-Meier method. Results: The cohort consisted of 13 ALL and 10 CML. The median time and cost for RT-PCR results were 7 days (IQR: 7-9) and $93, respectively. All patients were positive on RT-PCR. Three patients initially categorized as ALL were re-categorized as CML after transcript variant verification by RT-PCR. The SS, SP, PPV, and NPV of RT-PCR relative to FISH were 100%, 0%, 82.6%, and 0%, respectively. Compared to cytogenetics, these values were 100%, 0%, 73.9%, and 0%, respectively. The median time and cost for cytogenetics results were 14 days (IQR: 12-15) and $48, respectively. The SS, SP, PPV, and NPV of cytogenetics relative to RT-PCR were 73.9%, 0%, 100%, and 0%, respectively. For FISH, these values were 84.2%, 78%, 94%, and 50%, respectively. The median time and cost for FISH results were 10 days (IQR: 9-12) and $57, respectively. The SS, SP, PPV, and NPV of FISH relative to RT-PCR were 82.6%, 0%, 100%, and 0%, respectively, while for cytogenetics, these values were 94%, 50%, 84.2%, and 75%, respectively. The median survival rate for ALL and CML patients was 44.4% and 78% respectively. A significant survival difference was observed between those who received TKI and those who did not (68.8% vs. 0%; P=0.001). Conclusions: Qualitative RT-PCR was found to be the most effective and cost-friendly tool for the accurate and timely diagnosis of Ph+ leukemias, in low resource setting. The outcomes in our patients can be improved by timely diagnosis, early initiation of TKIs, treatment compliance, and preventing infections.