Clinical impact of panel-based error-corrected next generation sequencing versus flow cytometry to detect measurable residual disease (MRD) in acute myeloid leukemia (AML)

Abstract

We accrued 201 patients of adult AML treated with conventional therapy, in morphological remission, and evaluated MRD using sensitive error-corrected next generation sequencing (NGS-MRD) and multiparameter flow cytometry (FCM-MRD) at the end of induction (PI) and consolidation (PC). Nearly 71% of patients were PI NGS-MRD⁺ and 40.9% PC NGS-MRD⁺ (median VAF 0.76%). NGS-MRD⁺ patients had a significantly higher cumulative incidence of relapse (p = 0.003), inferior overall survival (p = 0.001) and relapse free survival (p < 0.001) as compared to NGS-MRD^- patients. NGS-MRD was predictive of inferior outcome in intermediate cytogenetic risk and demonstrated potential in favorable cytogenetic risk AML. PI NGS-MRD^- patients had a significantly improved survival as compared to patients who became NGS-MRD^- subsequently indicating that kinetics of NGS-MRD clearance was of paramount importance. NGS-MRD identified over 80% of cases identified by flow cytometry at PI time point whereas FCM identified 49.3% identified by NGS. Only a fraction of cases were NGS-MRD^- but FCM-MRD⁺. NGS-MRD provided additional information of the risk of relapse when compared to FCM-MRD. We demonstrate a widely applicable, scalable NGS-MRD approach that is clinically informative and synergistic to FCM-MRD in AML treated with conventional therapies. Maximum clinical utility may be leveraged by combining FCM and NGS-MRD modalities.

Fig. 1. Somatic mutations in AML detected at diagnosis and during therapy.

A The interaction of mutations at baseline is demonstrated here using Fisher’s exact test. Co-occurrence is indicated in gray color and mutual exclusivity is indicated in red. B The total number of mutations detected per patient and the number of such patients in the cohort is displayed. The total number of mutations in DNMT3A-TET2-ASXL1 genes is indicated here as a fraction. C Variant allele frequencies of mutations detected at MRD time points for patients of AML in morphological remission. The bars indicate median values with interquartile ranges.

Fig. 2. Clinical relevance of error-corrected NGS-MRD.

Presence of NGS-MRD at post induction (A) and post consolidation time points (B) is associated with a higher cumulative incidence of relapse (CIR). Kaplan–Meyer plots indicate the clinical relevance of NGS-MRD with respect to OS and RFS at post induction (C, E) and post consolidation time points (D, F).

Fig. 3. Comparison between FCM and NGS-MRD.

The clinical relevance detection of MRD during complete remission when measured by FCM or error-corrected NGS at post induction (A, B) and post consolidation time points (C, D).