Genomic breakpoint specific monitoring of measurable residual disease in pediatric non-standard risk acute myeloid leukemia

Abstract

Pediatric acute myeloid leukemia (pedAML) is a highly heterogeneous disease making standardized measurable residual disease (MRD) assessment challenging. Currently, patient-specific DNA-based assays are only rarely applied for MRD assessment in pedAML. We tested whether quantification of genomic breakpoint specific sequences via quantitative PCR (gDNA-PCR) provides a reliable means of MRD quantification in children with non-standard risk (non- SR) AML and compared its results to those obtained with state-of-the art 10-color flow cytometry (FCM). Breakpoint specific gDNA- PCR assays were established according to the guidelines of the Euro-MRD consortium. FCM-MRD assessment was performed according to the European Leukemia Network (ELN) guidelines with adaptations for pedAML. Of 77 consecutively recruited non-SR pedAML cases 49 (64%) carried a chromosomal translocation potentially suitable for MRD quantification. Genomic breakpoint analysis returned a specific DNA sequence in 100% (41/41) of the cases submitted for investigation. MRD levels were evaluated using gDNA-PCR in 243 follow-up (FUP) samples from 36 patients, achieving a quantitative range (QR) of at least 10-4 in 231/243 (95%) of samples. Comparing gDNA-PCR with FCM-MRD data in 183 bone marrow (BM) FUP samples at various therapy timepoints resulted in a high concordance of 90,2% when considering the cut-off of ≥0,1%. Both methodologies outperformed morphologic assessment. We conclude that MRD monitoring by gDNA-PCR is feasible in pediatric AML with traceable genetic rearrangements and correlates well with FCM-MRD in the currently applied clinically relevant range, while being more sensitive below that. The methodology should be evaluated in larger patient cohorts to pave the way for clinical application.