Holman, Matthew J.

Introduction: NPM1 mutations, seen in up to 30% of adults with acute myeloid leukemia (AML), often co-occur with FLT3 internal tandem duplication (FLT3-ITD). Measurable residual disease (MRD) testing before allogeneic hematopoietic cell transplant (alloHCT) for persistence of mutated NPM1 and/or FLT3-ITD can identify patients with AML in complete remission (CR) at highest risk of relapse and death. Quantitative RT-PCR assays are currently recommended for NPM1 MRD testing, while FLT3-ITD MRD testing is DNA-based using next generation sequencing (NGS). DNA-based NGS assays for mutated NPM1 MRD testing may have several advantages but require validation. We performed NPM1 MRD detection in blood collected from patients with AML during first CR (CR1) prior to alloHCT on a subset of patients from the Pre-MEASURE study (PMID: 36881031) using a highly-sensitive, commercially available DNA-based NPM1 NGS MRD assay. Methods: Of the 531 patients aged 18 or older from the Pre-MEASURE study who received an alloHCT for NPM1mutated AML during CR1 at a CIBMTR reporting site in the USA between the years of 2013-2019, a subset of 190 were randomly selected to be included in this analysis. A commercially available research testing kit (IVS, Invivoscribe, San Diego, CA), which can detect DNA-based NPM1 MRD, was used to establish a workflow following clinical testing standards and validated to detect NPM1 insertion variants down to a variant allele fraction (VAF) of at least 0.005%. Results were compared to those previously reported using an anchored multiplex PCR-based (AMP) targeted NGS assay (detection limit 0.01%) and FLT3-ITD MRD results, where applicable. Overall survival (OS) and cumulative incidence of relapse were estimated with the day of transplant as time 0 using Kaplan-Meier estimation (log-rank tests), Fine and Gray model, and Cox proportional hazards models. Results: NPM1 NGS MRD testing was successful for 186 (98%) patients, of which 48 (26%) relapsed (median: 4.0 months; range: 0.7-52.5) and 64 (34%) died (median: 9.7 months; range: 0.4-58.9) post-alloHCT. The IVS assay detected NPM1 insertion variants in 71 patients with a median VAF of 0.0026% (range:0.0002-2.1%). Using a VAF threshold of ≥0.01% for MRD positivity, the IVS test showed that 24 patients tested positive for NPM1 MRD pre-alloHCT, which was associated with significantly increased rates of relapse (52% vs 20% at 3yrs; HR=4.3; P<0.001) and decreased OS (34% vs 71% at 3yrs; HR=3.6; P<0.001) compared to testing negative, in close alignment with those previously reported using the AMP assay. After removing the VAF threshold, an additional 47 patients were classified as NPM1 MRD positive, which remained associated with increased rates of relapse (40% vs 15% at 3yrs; HR=3.4; P<0.001) and decreased OS (50% vs 75% at 3yrs; HR=2.9; P<0.001). In multivariable analysis, residual NPM1 MRD burden prior to alloHCT was associated with risk of relapse and death in a dose-dependent manner. Patients were further subdivided based on their reported FLT3-ITD mutational status at baseline. Increased risk of relapse was seen for NPM1 MRD positive patients regardless of baseline FLT3-ITD. 123 (66%) patients were co-mutated for FLT3-ITD at baseline and previously tested for FLT3-ITD MRD using the IVS assay (PMID: 38696205). Defining MRD based on the presence of NPM1 vs NPM1 and/or FLT3-ITD revealed equivalent levels of relapse (45% vs 44%) and OS (45% vs 46%) at 3 years, with NPM1 MRD evaluation identifying 5 additional relapses. These results were confirmed in the full Pre-MEASURE cohort (n=317) using the AMP assay. NPM1 MRD positive patients receiving nonmyeloablative conditioning or reduced-intensity conditioning (RIC) without melphalan (mel) had increased risk of relapse or death compared to patients receiving myeloablative conditioning or RIC with mel, regardless of FLT3-ITD co-mutational status (3yrs: relapse 87% vs 55%, P=0.006; OS 15% vs 42%, P=0.013). Conclusions: In patients with NPM1 mutated AML from the Pre-MEASURE study, we show that detection of residual NPM1 variants in pre-transplant blood during CR1 using a highly sensitive DNA-based assay is associated in a dose-dependent manner with a significantly increased risk of relapse and death after allo-HCT, which can be mitigated in part by conditioning regimen. In patients co-mutated for both FLT3-ITD and NPM1 at diagnosis, NPM1 should be prioritized as a target for NGS-MRD if only one test is available.

Background: In the past year, multiple studies have demonstrated the drastically increased risk of relapse and death in patients with Acute Myeloid Leukemia (AML) who have persistent FLT3 internal tandem duplication (ITD) mutations detectable in clinical remission by next generation sequencing (NGS). Translating this evidence into a change in clinical practice requires both widely available testing and a clear understanding of the clinical implications of FLT3-ITD detection at defined threshold levels. In the largest of the recent studies (Pre-MEASURE, PMID: 36881031), we performed FLT3-ITD MRD detection in blood DNA collected from 608 patients at the time of first remission (CR1) prior to allogeneic hematopoietic cell transplant (alloHCT). To evaluate cross-assay comparability and the impact of residual disease burden levels, we performed analysis on this cohort using a commercially available FLT3-ITD MRD NGS assay. Methods: Of the 608 patients aged 18 or older from the Pre-MEASURE study who received an alloHCT for FLT3-ITD mutated AML during CR1 at a CIBMTR reporting site in the USA between the years of 2013-2019, patients not experiencing non-relapse mortality and with sufficient DNA from pretransplant blood available were included in this analysis. A commercially available testing kit (IVS, Invivoscribe, San Diego, CA), which can detect FLT3-ITD MRD by NGS for up to 21 patients on one Illumina MiSeq flow cell, was used to establish a workflow following clinical testing standards and validated to detect ITDs down to a variant allele fraction (VAF) of at least 0.005%. Results were compared to those previously reported using an anchored multiplex PCR-based (AMP) targeted NGS assay. Overall survival (OS) and cumulative incidence of relapse were estimated with the day of transplant as time 0 using Kaplan-Meier estimation (log-rank tests) and Cox proportional hazards models. Results: A total of 451 patients were included in this study, of which 173 (38%) experienced relapse (median: 5.2 months; range 0.7-52.1) and 133 (29%) died (median: 10.7 months; range 2-53.8) post-alloHCT. The IVS assay identified 232 FLT3-ITD variants with a median VAF of 0.005% (range 0.0002-44%) and length of 51bp (range 5-228). IVS positive patients had a median of 1 FLT3-ITD variant (range 1-15) and median maximum VAF of 0.01% (range 0.0003-44%). Utilizing the same VAF cutoff of 0.01% for MRD positivity for the IVS test as used in the Pre-MEASURE study, patients testing positive prior to alloHCT exhibited higher rates of relapse (79% vs 31%, p<0.0001) and decreased survival (29% vs 77%, p<0.0001) at 3 years compared to testing negative. These results closely align with those previously reported using the AMP assay (Figure A). The IVS test has a superior limit of detection compared with the AMP test, allowing investigation of alternative VAF thresholds. In total, 151 patients (33.5%) were FLT3-ITD MRD positive by IVS of which only 75 (17%) had VAF ≥0.01%. A threshold-free approach for the IVS test improved the ability to identify patients at risk of relapse, predicting 63% of relapses within 6 months of transplant compared to 43% with the 0.01% cutoff, but resulted in decreased specificity as 42% of all positive patients relapsed within 6 months vs. 57% with the 0.01% VAF cutoff. In multivariable analysis, IVS FLT3-ITD MRD status was associated with both relapse and overall survival (Figure B). Additionally, stratifying patients by their level of residual FLT3-ITD disease burden prior to alloHCT revealed a dose-dependent increase in risk for death (Figure B) and relapse. Any detectable level of residual FLT3-ITD over 0.001% VAF exhibited increased risk, with VAFs ≥0.01% being the highest. Conclusions: In this analysis of patients with AML from the Pre-MEASURE study, we show cross-assay evidence that the detection of residual FLT3-ITD variants in pre-transplant blood during CR1 is associated with significantly increased risk of relapse and death after alloHCT. The highly sensitive assay used in this study could identify ~2/3 of patients who relapsed within 6 months and demonstrated that a dose-dependent correlation between residual FLT3-ITD level and adverse clinical outcomes exists, with VAF ≥0.01% representing the highest risk. This evidence provides strong justification for NGS-based AML MRD clinical testing for persistent FLT3-ITD prior to alloHCT to identify patients at high risk of post-transplant relapse and death.