Improve Pediatric Leukemia Patient Care with Next Generation Sequencing

Minimal residual disease (MRD) status in pediatric patients who have been recently diagnosed with acute lymphoblastic leukemia (ALL) have risk stratification which may be improved by using next generation sequencing (NGS). A multi-center study that was presented at the American Society of Hematology (ASH) 2021 annual meeting showed that the unique genetic sequence employed in NGS detects MRD at levels as low as 12 leukemic cells out of 1 million cells, providing earlier detection of the disease. Patients are considered to have high MRD when they have over 1 leukemic cell per 10,000 body cells.

NGS vs. FCM Testing in Pediatric ALL

The study includes a total of 317 children who were being treated using the Dana-Farber Cancer Institute ALL protocol. Current assays being used such as flow cytometry (FCM) require higher levels for detection.  In this study, when compared to FCM, next generation sequencing allowed researchers to identify a higher portion of cases that had a higher MRD status, with the bulk of the cases that were not detected by FCM falling just beyond the limits of detection for the technology.

For this study, next generation sequencing was leveraged as the primary MRD-based method for determining risk, with FCM used as a backup to ensure that nobody was overlooked in the process. To record the changes in the patients, an initial bone marrow evaluation was completed both at the time of the diagnosis as well as four weeks following induction therapy, which was identified as the patient’s first time point (TP1). Patients who were found to have a high MRD were provided with an intensified therapy routine as well as additional MRD assessments following 10 and 20 weeks of treatment.

Qualifications for the study included patients between one year and 21 years of age who had B- or T-cell ALL, with 84% having B-cell ALL and 67% being under 10 years old. Based on age, baseline leukocyte count, immunophenotype, disease biology and central nervous system leukemia status, 52% of the subjects were determined to be low risk, 31% were high risk and 17% at very high risk.

There were 70 patients with both high MRD and B-ALL, in which 43% were high by next generation sequencing while the FCM was either low or undetectable. An estimated 90% of the discrepancies between the testing methods fell between the thresholds of detection for FCM and NGS. By comparison, among the 28 T-ALL patients that had a high TP1 MRD, 74% were high only by NGS, with no detectable FCM readings, with 67% being at the baseline for the technology and the remaining 33% below it. This knowledge makes NGS a far better choice for suspected T-ALL cases as well as for borderline B-ALL cases where FCM testing is inconclusive.

Relevance of NGS Testing in Prognostic Processes

Though the study wasn’t designed to determine clinical treatment courses based on the MRD status, the relevance of low MRD levels as a prognostic tool is being evaluated for future use. Given the more sensitive MRD status assessment both at baseline as well as following induction therapy, treatment intensification can provide better results, making NGS a feasible tool for oncologists.

Though the study isn’t the only effort to add NGS as a standard of care for pediatric patients with risk stratification, with another multicenter study of pediatric ALL and NGS evaluation already in operation at the Children’s Oncology Group, its results provide hope for earlier detection and higher standards of customized care to optimize pediatric leukemia patient care and outcomes, improving lifespans and quality of life following treatment.