Measurable Residual FLT3 Internal Tandem Duplication Before Allogeneic Transplant for Acute Myeloid Leukemia

Abstract

Importance: Persistence of FLT3 internal tandem duplication (ITD) in adults with acute myeloid leukemia (AML) in first complete remission (CR) prior to allogeneic hematopoietic cell transplant (HCT) is associated with increased relapse and death after transplant, but the association between the level of measurable residual disease (MRD) detected and clinical outcome is unknown.

Objective: To examine the association between pre-allogeneic HCT MRD level with relapse and death posttransplant in adults with AML in first CR.

Design, setting, and participants: In this cohort study, DNA sequencing was performed on first CR blood from patients with FLT3-ITD AML transplanted from March 2013 to February 2019. Clinical follow-up was through May 2022. Data were analyzed from October 2022 to December 2023.

Exposure: Centralized DNA sequencing for FLT3-ITD in pre-allogeneic HCT first CR blood using a commercially available kit.

Main outcomes and measures: The primary outcomes were overall survival and cumulative incidence of relapse, with non-relapse-associated mortality as a competing risk post-allogeneic HCT. Kaplan-Meier estimations (log-rank tests), Cox proportional hazards models, and Fine-Gray models were used to estimate the end points.

Results: Of 537 included patients with FLT3-ITD AML from the Pre-MEASURE study, 296 (55.1%) were female, and the median (IQR) age was 55.6 (42.9-64.1) years. Using the variant allele fraction (VAF) threshold of 0.01% or greater for MRD positivity, the results closely aligned with those previously reported. With no VAF threshold applied (VAF greater than 0%), 263 FLT3-ITD variants (median [range] VAF, 0.005% [0.0002%-44%]), and 177 patients (33.0%) with positive findings were identified. Multivariable analyses showed that residual FLT3-ITD was the variable most associated with relapse and overall survival, with a dose-dependent correlation. Patients receiving reduced-intensity conditioning without melphalan or nonmyeloablative conditioning had increased risk of relapse and death at any given level of MRD compared with those receiving reduced-intensity conditioning with melphalan or myeloablative conditioning.

Conclusions and relevance: This study provides generalizable and clinically applicable evidence that the detection of residual FLT3-ITD in the blood of adults in first CR from AML prior to allogeneic HCT is associated with an increased risk of relapse and death, particularly for those with a VAF of 0.01% or greater. While transplant conditioning intensification, an intervention not available to all, may help mitigate some of this risk, alternative approaches will be necessary for this high-risk population of patients who are underserved by the current standard of care.

Figure 1.. Residual FLT3 Internal Tandem Duplication (ITD) Variants in Patients With Acute Myeloid Leukemia (AML) Prior to Allogeneic Hematopoietic Cell Transplant

A, Comparison of variant allele fraction (VAF) and length of residual FLT3-ITD variants detected in pretransplant blood at a VAF of 0.01% or greater as detected by next-generation sequencing using the Invivoscribe (IVS) FLT3-ITD measurable residual disease (MRD) assay or an anchored multiple polymerase chain reaction–based (AMP) assay. The Pearson correlation is shown in the graph, and the value of equivalence line is displayed as a dashed line. B, Cumulative incidence of relapse and overall survival are shown for patients with FLT3-ITD variants based on the presence (MRD positive) or absence (MRD negative) of residual FLT3-ITD variants, with the positive group defined by a VAF of 0.01% or greater in the pre–allogeneic hematopoietic cell transplant blood. Bp indicates base pairs.

Figure 2.. Association of FLT3 Internal Tandem Duplication (ITD) Residual Disease Burden Level and Clinical Outcomes

A, Cumulative incidence of relapse and overall survival are shown for patients with FLT3-ITD variants based on the presence (measurable residual disease [MRD] positive) or absence (MRD negative) of residual FLT3-ITD variants as detected by next-generation sequencing using the Invivoscribe (IVS) FLT3-ITD MRD assay, with positive patients grouped by residual disease burden level. B, Multivariable competing-risks regression for relapse and Cox regression analysis for overall survival for residual FLT3-ITD variants as detected by the IVS assay grouped by residual disease burden level. Models were selected stepwise using MRD status and baseline clinical characteristics. NMA indicates nonmyeloablative conditioning; RIC, reduced-intensity conditioning without melphalan; VAF, variant allele fraction.

Figure 3.. Evaluation of Potential Factors Modifying the Association of Residual FLT3 Internal Tandem Duplication (ITD) and Clinical Outcomes

A, Cumulative incidence of relapse and overall survival for patients with FLT3-ITD variants based on the presence (measurable residual disease [MRD] positive) or absence (MRD negative) of residual FLT3-ITD variants, variant allele fraction (VAF) ranges, and conditioning regimen received. B, Heatmap illustrating patients who were FLT3-ITD MRD negative pretransplant and experienced relapse within the first year after allogeneic hematopoietic cell transplant and their relapse month, age group, conditioning regimen, and residual variant status for variants in genes other than FLT3-ITD. Patients were ordered by their time to relapse from the shortest to the longest. Residual variant status is denoted as high or unclear based on relevance of the residually mutated gene. Variants in signaling pathways or escape genes are more likely associated with the leukemia clone, while variants in genes such as TP53 and CBL are frequently observed after chemotherapy^,, and could be associated with clonal hematopoiesis unrelated to the leukemic clone. MAC indicates myeloablative conditioning; Mel, reduced-intensity conditioning with melphalan; NMA, nonmyeloablative conditioning; RIC, reduced-intensity conditioning without melphalan.