Acute Myeloid Leukemia Measurable Residual Disease Research Articles

Analytical Validation of a Duplex Sequencing AML Assay with a Limit of Detection Below 0.01% VAF for SNVs and Indels

Sensitive, specific, precise, and accurate detection of low frequency mutations in acute myeloid leukemia (AML) is critical to assess measurable residual disease (MRD). Next generation sequencing (NGS) assays are powerful tools for this, permitting interrogation of thousands of base positions across genomic regions of interest. However, PCR and sequencing errors in these assays limit accurate mutation detection at variant allele frequencies (VAF) below approximately 1%. Duplex sequencing (DS), an error-corrected NGS (ecNGS) method, greatly reduces such errors by relating original top and bottom DNA strands to make double stranded consensus sequences, thus enabling sensitive, specific, accurate, and precise detection of variants below 0.01% VAF. Here, we report analytical validation of an updated DuplexSeq™ AML assay, a 36-gene panel informed by 2022 European LeukemiaNet (ELN) recommendations combined with kitted library preparation reagents and a cloud-based analysis pipeline. The assay uniformly targets regions that harbor AML-associated mutations: 82% of targeted regions exhibit sequencing depth >80% of the panel-wide mean and >99.5% of targeted regions exhibit depth >20% of the panel-wide mean. These analytical studies also validate an improved “v2 chemistry” version of a DS library preparation kit. This improved chemistry provides an enzymatic fragmentation step that replaces time-consuming mechanical fragmentation methods while increasing the yield of duplex data for a given input mass of DNA sample and eliminating damage that results from mechanical fragmentation. A contrived human genomic DNA sample carrying 26 variants targeted by the panel, DNA extracted from AML-positive peripheral blood (PB) and bone marrow aspirate (BMA) specimens, and DNA extracted from healthy normal PB specimens were used as test samples to execute limit of detection (LoD), limit of blank (LoB), accuracy, linearity, and repeatability & reproducibility studies. In this assay a duplex depth threshold of ≥20,000x is applied; ≥91.8% of the 42,605 genomic base positions targeted by the panel are consistently (in 95% of analyzed libraries) above this threshold. The LoD study assayed samples carrying variants from 0.37% to 0.00055% VAF. The assay demonstrated excellent sensitivity, with variants down to 0.00055% VAF detected. A probit model was used to estimate the VAF at which 95% of variants would be detected, establishing an LoD of 0.008% VAF for single-nucleotide variants (SNVs) and insertions and deletions (indels) (see Figure 1). The LoB study assessed the background detection rate in DNA samples derived from healthy normal specimens. In >95% of sites surveyed, no variants were observed, establishing an assay LoB of 0 (0% VAF). Accuracy of the assay was determined by interrogating PB and BMA samples from AML-positive and -negative donors along with contrived test samples. Results were compared to data acquired via orthogonal methods. For variants above the LoD of 0.008% VAF, accuracy was high, with overall percent agreement (OPA) of 98.3%, positive percent agreement (PPA) of 100.0%, and negative percent agreement (NPA) of 98.3%. Data were linear from 0.0016% VAF to 96.1% VAF with R 2 = 0.95. All 6 expected FLT3-ITD variants, and all 5 expected NPM1 insertions were detected by the assay. Precision study data showed that the assay was highly repeatable, with OPA of 97.5%, PPA of 98.0%, and NPA of 97.3%. Reproducibility across 2 operators, 2 lots of reagents, and 3 independent runs of library preparation was also very high, with OPA of 97.5%, PPA of 98.8%, and NPA of 96.9%. Current ELN guidelines provisionally define NGS-MRD positivity as ≥0.1% VAF, but recent evidence suggests lower frequency variants may be informative. With an LoD of 0.008% VAF for SNVs and indels, and an LoB of 0, this novel AML assay comprising an updated gene panel coupled with improved duplex sequencing chemistry and software represents a highly sensitive, specific, accurate, and precise ecNGS assay for detecting variants associated with AML MRD.

Impact of Hemodilution on Measurable Residual Disease Measured Via Flow-Cytometry in Acute Myeloid Leukemia Analyzed Using Subsequent Pulls

Background: Measurable residual disease (MRD) detection plays a crucial role in assessing remission status and prognosis for acute myeloid leukemia (AML) patients. Multiparameter flow cytometry (MFC) and NPM1 gene mutations reverse transcriptase polymerase chain reaction (RT-PCR) are validated and recommended used methods for MRD measurement after two cycles of high-dose induction chemotherapy. However, the accuracy of MRD assessment can be compromised by hemodilution, a phenomenon that occurs during bone marrow (BM) aspiration when peripheral blood (PB) mixes with the BM sample. Due to the lower presence of MRD in PB, this may lead to false-negative results. Although formulas to quantify hemodilution exist, their validation and adoption remain limited, and the exact impact of hemodilution remains unclear. Aim: This prospective study aimed to investigate the impact of hemodilution on MFC-MRD assessment by aspirating three sequential pulls of 2 ml each, instead of the standard 6 ml BM sample, and comparing them with a PB sample collected on the same day. Additionally, we evaluated the performance of different hemodilution formulas and analyzed changes in ratios/percentages of cell populations across the BM pulls and PB samples. Methods: We included 30 AML patients in complete remission, resulting in 40 samples measured after one or two cycles of induction chemotherapy with 46 leukemia-associated immunophenotypes (LAIPs). The first 2 ml of BM were collected as the “first pull”, followed by a second aspirate of another 2 ml to form the “second pull”. This process was repeated to obtain the “third pull”. Precautions were taken during BM aspiration to prevent aspirate loss between pulls, and the aspiration needle remained stationary throughout the procedure. All samples from one time point were analyzed on the same machine by the same operator. The formulas proposed for hemodilution assessment were evaluated using a newly developed tube containing additional markers (CD10, CD16, CD38, and CD138) not present in the standard MFC-MRD assay. Differences in outcomes from the formulas and cell populations across the specimens were analyzed using the non-parametric Friedman's ANOVA test. Moreover, the ability of individual populations or formulas to differentiate between BM and PB samples was assessed using the area under the receiver operating characteristic curve (ROC-AUC) in a binary classification task. Results: Significant decreases in blasts and median MRD% were observed between different pulls and PB samples. The median MRD% in pull 1 (0.06%) was significantly higher than in pull 2 (0.05%), pull 3 (0.04%), and PB (0.01%) ( P<0.001). Pairwise comparisons, adjusted for multiple testing, revealed significant differences between pull 1 and pull 2 ( P=0.025), and between pull 2 to pull 3 ( P=0.025), indicating the effect of hemodilution ( Figure 1A). In the first pull 18/46 LAIPs were above the 0.1% cut-off, compared to 14/46 in the third pull. This resulted in 9 patients being MRD-positive in the first/second pull, compared to 8 patients in the third pull. The evaluated formulas demonstrated progressively higher quantities of diluted samples from pull 1 to PB. Five parameters exhibited an AUC above 0.9, indicating their ability to differentiate between BM and PB samples. These parameters are CD10 (AUC: 0.956), plasma cells (AUC: 0.949), CD16 dim cells (AUC: 0.940), mast cells (AUC: 0.924), and the PB contamination index formula (AUC: 0.905) ( Figure 1B). Conclusion: Hemodilution occurs even after aspirating the initial milliliters of BM, emphasizing the need to consider hemodilution when assessing MRD in AML to avoid false-negative results. We recommend incorporating a hemodilution detection formula into routine practice for AML patients to further evaluate the effect on clinical choices. The results of this study support the examination of the CD16 dim population or mast cell population (CD117hi) for this purpose. Furthermore, we suggest implementing a practical approach that involves numbering each pull of BM during aspiration and taking this into account when giving the final MRD result, thus providing clarity regarding the specific pull being measured. In cases of doubt (e.g., MFC-MRD between 0.07% and 0.09% in a later pull), repeating the BM aspiration is recommended to ensure reliability.

Measurable Residual IDH1 before Allogeneic Transplant for Acute Myeloid Leukemia

Introduction: Detection of measurable residual disease (MRD) prior to allogeneic hematopoietic cell transplant (alloHCT) in patients with acute myeloid leukemia (AML) in remission is associated with increased relapse and inferior survival after transplant. We recently reported that next-generation sequencing (NGS) detection of mutated NPM1 or FLT3-ITD in first complete remission (CR1) blood prior to alloHCT is strongly associated with increased relapse and death (PMID: 36881031). However, the prognostic implications of detecting persistence of other common AML-associated mutations at this treatment landmark remain incompletely defined. Around 20% of patients diagnosed with AML have variants in isocitrate dehydrogenase ( IDH) genes (~7% for IDH1) and clinical outcomes are known to differ due to co-occurrence of other mutations, IDH subtypes, treatment strategies, and patient factors. Studies have examined the relationship between residual IDH1 variants ( IDH1m) in CR and subsequent clinical outcomes, but definitive standardized evidence to inform decision-making for the clinical utility of IDH1m as a target for AML MRD testing was not previously available. Methods: Adult patients undergoing alloHCT for IDH1 mutated AML in CR1 at CIBMTR sites in the USA between 2013-2019 were eligible for the study if remission blood sample collected within 100 days before alloHCT and outcome data were available. Ultrasensitive error-corrected NGS (NGS-MRD) targeting IDH1, NPM1, and FLT3 genes was performed on DNA from pre-conditioning blood to identify residual variants. Detected IDH1m were validated by digital droplet PCR (ddPCR). The day of transplant was considered as day 0. Median follow-up time was calculated for censored patients. Overall survival (OS) was estimated using Kaplan-Meier (log-rank tests) and Cox proportional hazards models (forward selection); cumulative incidence of relapse was examined using Fine-Gray regression models with non-relapse mortality as a competing risk. Results: A total of 148 patients were included in the study, with a median follow-up time of 24 months. Relapse was observed in 37 (25%) patients, with the majority occurring within 1 year after alloHCT (n = 28, 76%). Pre-transplant flow cytometry results were reported by the transplant centers for 97% of patients (n = 144), but no statistically significant differences in clinical outcomes were observed between the positive and negative groups (OS: p = 0.3; relapse: p = 0.07). 53 patients (36%) tested positive for IDH1m persistence in CR1, with a 100% validation rate by ddPCR for variants with an orthogonal assay available. Logistic regression indicated that IDH1m persistence in remission was more likely to occur in patients older than 40 years (OR: 1.02 with every 1-year increase after 40, p = 0.04). Clinical outcomes showed no statistically significant difference between the pre-alloHCT IDH1m positive and negative groups (Figure 1A), and this remained true after further subgroup analysis by age. The variant allele fraction (VAF) of the residual IDH1m ranged from 0.09% to 48.5% (median: 1.5%), and no differences in clinical outcomes were observed when stratifying by high (≥2.5%) or low VAF (<2.5%). Among patients with co-mutated NPM1 and/or FLT3-ITD at baseline (n=69), those with residual mutated NPM1 and/or FLT3-ITD in pre-transplant remission had significantly higher rates of relapse compared to those with residual IDH1m only or NGS-negative groups (p = 0.01, Figure 1B). The cohort excluding patients with co-mutated NPM1 and/or FLT3-ITD did not show any significant clinical outcome differences based on IDH1m persistence. Conditioning intensity did not show an association with clinical outcomes, and multivariable analysis for overall survival and relapse did not identify residual IDH1m as an important marker. Conclusion: Detection of persistent IDH1 variants in the blood of adult patients with AML in CR1 prior to first alloHCT is common, but not associated with increased relapse or death after transplant compared with those testing negative. For those patients with IDH1 mutated AML co-mutated with either NPM1 and/or FLT3-ITD, detection of persistent NPM1 and/or FLT3-ITD was associated with higher rates of relapse. These findings, from the largest study to date, do not support the detection of isolated IDH1 variants in CR1 blood prior to alloHCT as evidence of AML MRD or increased post-transplant relapse risk.

Persistence of FLT3-TKD in Blood Prior to Allogeneic Transplant Is Associated with Increased Relapse and Death in Adults with AML in First Remission

Introduction: Next-generation sequencing (NGS) represents a promising modality for measurable residual disease (MRD) testing in patients with acute myeloid leukemia (AML), but systematic efforts are required to define the appropriate targets, test characteristics, and clinical implications. We recently reported that detection of persistent NPM1 or FLT3 internal tandem duplication (ITD) mutations in adults with AML in first complete remission (CR1) prior to allogeneic hematopoietic cell transplantation (alloHCT) is associated with increased relapse and death compared with those testing negative (JAMA 2023, PMID: 36881031). FLT3 tyrosine kinase domain (TKD) variants are present in 7-10% of adult patients with AML but the utility of this target for AML MRD testing in CR1 prior to alloHCT was previously unknown. Methods: Patients aged 18 or older who underwent alloHCT for AML in CR1 between 2013 and 2019 reported to have a FLT3-TKD variant at diagnosis and a pre-conditioning remission blood sample available in the CIBMTR biorepository were eligible for this study. Single-amplicon NGS (SA-NGS) library generation utilizing UMI-tagged primers targeting the D835 and I836 codons of FLT3 was performed on 400ng genomic DNA sequenced with unique dual indices, with error-corrected variant calling. Primary outcomes were overall survival (OS) and cumulative incidence of relapse (CIR). Secondary outcomes were relapse-free survival (RFS) and non-relapse mortality (NRM), with NRM being considered as a competing risk. Results: A total of351 patients met inclusion criteria for this study, and 342 (97.4%) had sufficient DNA for SA-NGS and were analyzed for clinical outcomes. Of these patients, 81 (23.7%) experienced relapse at a median of 5 months post-alloHCT. Using the current ELN-recommended variant allele fraction (VAF) threshold of 0.1% for NGS-based AML MRD, 14 patients (4.1%) tested positive. Patients with FLT3-TKD MRD VAF≥0.1% experienced higher rates of relapse (73.8% vs. 20.5%, p < 0.0001) and decreased OS (11.4% vs. 66.8%, p < 0.001) compared to VAF<0.1%. The highly sensitive SA-NGS method allowed for exploration to determine if a deeper VAF threshold of 0.01% (previously validated for NPM1 and FLT3-ITD in the Pre-MEASURE study) was prognostic for FLT3-TKD as an MRD target. This led to an additional 20 patients being reclassified as positive (n = 34 with VAF above 0.01%, =9.9%). However, there was no significant difference in CIR (33.6% vs. 19.7%, p = 0.089) or OS (65.2% vs. 66.9%, p = 0.267) between patients with 0.01%≤VAF<0.1% and VAF<0.01% ( Figure). Out of 28 SA-NGS positive calls, 6 could not be validated by orthogonal digital droplet PCR testing, and interestingly, none of those 6 patients experienced relapse. Site-reported pre-transplant remission multiparametric flow cytometry (MFC) was available for 335 patients (98%). Results of MFC were not associated with differences in CIR (HR 1.2, 95% CI 0.52 - 2.76, p = 0.67) or OS (HR 0.78, 95% CI 0.34 - 1.77, p = 0.551).In multivariable analysis, FLT3-TKD NGS-MRD VAF≥0.1% remained prognostic for CIR (HR 6.1, 95% CI 3.1 - 12.0, p < 0.001) and OS (HR 3.2, 95% CI 1.7 - 5.9, p < 0.001). Conclusions: Detectable persistence of FLT3-TKD variants in blood from AML patients in first remission prior to first alloHCT is rare, but at a VAF level of 0.1% was strongly associated with increased relapse and death after transplant compared to those testing negative. In contrast to FLT3-ITD NGS-MRD, no evidence was found to support lowering the NGS-MRD VAF threshold from 0.1% to 0.01% for FLT3-TKD. Alternative methodology may further improve NGS-MRD test performance. Site-reported MFC prior to alloHCT did not stratify for post-transplant relapse or survival. Optimal NGS-MRD testing for patients with AML will likely require a multi-target approach and testing for persistence of FLT3-TKD MRD is shown here to represent an important component of this strategy.

A Multiomic, Single-Cell Measurable Residual Disease (scMRD) Assay for Phasing DNA Mutations and Surface Immunophenotypes

The small population of cancerous cells that remain following treatment, known as measurable residual disease (MRD), is the major cause of relapse in acute myeloid leukemia (AML). Usually, these refractory cells have gained additional resistance mutations or changed their surface immunophenotypes in ways that preclude detection and phasing by current gold standard flow cytometry or bulk next-generation sequencing assays. For this reason, a multiomic single-cell MRD (scMRD) assay could offer a more comprehensive indicator of relapse and the potential for faster response. Here, we present a new scMRD assay with a 0.01% limit of detection that provides single-cell clonal architecture and immunophenotyping to not only identify residual leukemia cells, but also identify putative DNA or protein targets for salvage therapy. The assay enables rare-cell detection on a standard Mission Bio Tapestri run by adding (i) an upfront bead-based protocol to enrich for blast cells, (ii) a DNA and protein panel specifically designed for AML MRD diagnosis and treatment, and (iii) a new, automated analysis pipeline to evaluate single-cell multiomics output. By utilizing Mission Bio's single-molecule DNA sensitivity for single cells, this pipeline can identify and correlate co-occurring de novo variants, thereby reducing false positive rates over bulk assays that do not correlate variants. It furthermore can create phylogenetic trees of the detected MRD cells and present their surface protein signature and arm-level copy number. In addition, the multiplexing of up to three patient samples combined in one run via germline identification further reduces per sample costs and increases throughput. To demonstrate these features on 0.01% MRD, samples were constructed by titrating diseased cells into healthy bone marrow cells before processing them with the scMRD assay. We detected 0.01% spike-in (CD34+) and 0.1% spike-in (CD117+) in 6 of 6 samples, with an average enrichment of 41x and 13x, respectively. Further testing detected CD34+ 0.1% spike-ins in 10 of 10 samples (32x average enrichment). We applied the scMRD assay to banked bone marrow aspirate samples from 3 AML patients. The scMRD assay resolved the clonal architecture identifying multiple leukemic clones with co-occurring mutations. The assay readily distinguished pre-leukemic from leukemic clones thereby increasing the specificity of MRD results. The integration of genotype and immunophenotypic further enhanced MRD detection by identifying genotype-specific protein expression patterns. By combining high sensitivity with multiomics, this assay offers a potential scalable solution for comprehensive MRD detection that guides therapeutic decision-making.

Molecular Measurable Residual Disease in Patients with Newly Diagnosed m IDH1 Acute Myeloid Leukemia Treated with Ivosidenib + Azacitidine

Background: Ivosidenib (IVO) + azacitidine (AZA) improved complete remission (CR) rates and overall survival (OS) relative to placebo (PBO) + AZA in patients (pts) with newly diagnosed mutant isocitrate dehydrogenase 1 (m IDH1) acute myeloid leukemia (AML) in the pivotal AGILE study (Montesinos et al. NEJM 2022). Prior analyses showed clinical responses to IVO+AZA were associated with deep clearance of m IDH1 (limit of detection [LOD]: 0.02-0.04% variant allele frequency [VAF]), as well as clearance of baseline co-mutations below the threshold of conventional next-generation sequencing (NGS) (LOD: 2.0% VAF) (Döhner et al. Blood 2022; Daigle et al. Blood 2021). Measurable residual disease (MRD), a negative prognostic marker, following chemotherapy is often detected via multiparametric flow cytometry or quantitative polymerase chain reaction although both techniques have their limitations. (Heuser et al. Blood 2021). NGS can detect a wide range of AML mutations and studies show that NGS-assessed MRD is highly predictive of both relapse and survival (Thol et al. Blood 2018; Tsai et al. Blood Adv 2021). However, a limitation of NGS is difficulty in distinguishing between somatic leukemia-associated mutations and clonal hematopoiesis of indeterminate potential (CHIP) (Bacher et al. Blood Cancer J 2018). We aimed to perform an NGS analysis of MRD responses in the AGILE study. Methods: All AGILE pts who had a best overall response (BOR) of CR, CR with incomplete count recovery, or CR with incomplete platelet recovery, and had ≥1 on-treatment bone marrow mononuclear cell (BMMC) sample available were included. Suggested timepoints for MRD testing included day 1 of treatment cycles 3, 5, 7, 9, 11, 14, 20, 26, and 32. Baseline and on-treatment BMMC DNA samples were analyzed using a diagnostic 51-gene myeloid NGS panel (LOD: 3% VAF) and a 26-gene AML MRD panel, respectively. For variants detected at baseline, the LOD was 0.1% VAF; for variants not detected at baseline (either emerging mutations or if baseline samples were unavailable), the LOD was 0.5% VAF. All variants above the applicable LOD with known or potential clinical significance were considered evidence of positive MRD, aside from DNMT3A, TET2 and ASXL1 (“DTA”) mutations to reduce the risk of false-positive MRD due to CHIP. Results: The analysis set comprised 173 samples from 33 IVO+AZA-treated pts and 10 PBO+AZA-treated pts (Fig. 1). Clinical response data were based on a March 18, 2021 primary analysis data cut; OS data were based on an updated June 30, 2022 data cut. The median number of baseline mutations was 4 (range: 1-10) per patient, median number of MRD assessments was 3 (range: 1-9) and median follow-up period was 189 days (range: 49-875). Ten (30.3%) IVO+AZA-treated pts became MRD-negative (MRD neg), compared with 2 (20.0%) PBO+AZA-treated pts. All pts attaining an MRD neg response had a BOR of CR (10 [34.5%] of 29 IVO+AZA-treated pts in CR; 2 [22.2%] of 9 PBO+AZA-treated pts in CR). Seven (70.0%) of the 10 MRD neg IVO+AZA-treated responding pts converted to an MRD neg response by day 1 of cycle 7 (C7D1). Fewer pts with an MRD neg response had an Adverse risk at baseline according to European LeukemiaNet 2022 genetic risk classification versus those pts with an MRD-positive (MRD pos) response (26.3% vs 73.7%) (Table 1). In the IVO+AZA arm, rates of event-free survival at 12 months and OS at 24 months were numerically higher in MRD neg vs MRD pos responders (80.0% vs 60.6% and 88.9% vs 72.3%, respectively) but did not reach statistical significance. All 5 (15.2%) IVO+AZA-treated pts with confirmed relapses had detectable MRD at the last completed assessment prior to relapse. One pt converted from an MRD neg to an MRD pos response (“MRD relapse”) 169 days prior to overt clinical relapse. Among the 23 IVO+AZA-treated pts without an MRD neg response, 16 were alive as of the updated data cut; OS duration ranged from 20.3-48.9 months. Conclusions: IVO+AZA induced molecular MRD negativity in approximately one third of responding pts with newly diagnosed m IDH1 AML; MRD neg responses were most often observed on or before C7D1. Interestingly, several pts had durable clinical responses and OS despite ongoing MRD positivity, potentially due to persistent CHIP rather than true MRD, illustrating the complexity of interpreting NGS MRD data. Additional analyses, including associations between specific molecular alterations, MRD response, and OS are ongoing and will be presented.

Measurable residual disease monitoring in patients with acute myeloid leukemia treated with lower-intensity therapy: Roadmap from an ELN-DAVID expert panel.

With the availability of effective targeted agents, significant changes have occurred in the management of patients with acute myeloid leukemia (AML) over the past several years, particularly for those considered unfit for intensive chemotherapy. While testing for measurable residual disease (MRD) is now routinely performed in patients treated with intensive chemotherapy to refine prognosis and, possibly, inform treatment decision-making, its value in the context of lower-intensity regimens is unclear. As such regimens have gained in popularity and can be associated with higher response rates, the need to better define the role of MRD assessment and the appropriate time points and assays used for this purpose has increased. This report outlines a roadmap for MRD testing in patients with AML treated with lower-intensity regimens. Experts from the European LeukemiaNet (ELN)-DAVID AML MRD working group reviewed all available data to propose a framework for MRD testing in future trials and clinical practice. A Delphi poll served to optimize consensus. Establishment of uniform standards for MRD assessments in lower-intensity regimens used in treating patients with AML is clinically relevant and important for optimizing testing and, ultimately, improving treatment outcomes of these patients.

Biomarker subpanel customization for different use cases in acute myeloid leukemia research.

e19026 Background: Treatment guidance and decision making according to modified RECIST guidelines often depends on characterization of these biomarkers in patients with cancer. Although panels with larger breadths of coverage are useful for initial detection of these biomarkers for evaluation of disease burden and prognosis, their cost-effectiveness decreases as treatment and disease progress; smaller subpanels may yield equally valuable information into disease progress and guide treatment in a more cost-effective manner, potentially leading to more datapoints in decision making in comparison to larger panels. Methods: QBDA is an NGS enrichment research technology that allows the enrichment of rare variants, reducing the sequencing cost while maximizing the sensitivity. Here we introduce a new capability of our platform that allows tailoring sequencing panel breath to the disease stage needs. We demonstrate the ability to generate a 384-plex NGS subpanel from a 2400-plex acute myeloid-leukemia (AML) measurable residual disease (MRD) targeting research panel. Both panels were tested on both wild-type and 0.1% variant allele frequency (VAF) AML MRD contrived samples. Results: Without any optimization of the subpanel itself, the subpanel exhibited similar or better performance to the main panel. The main panel had a ~80% uniformity of coverage whereas the subpanel had a uniformity of coverage exceeding 75%. The subpanel covers fewer genes of interest and requires fewer overall reads. Both panels had a bulk LoD of below 0.1% VAF. Conclusions: This data represents proof-of-concept for the design of small custom panels from large-scale multiplex panels for different use cases, potentially increasing cost-effectiveness.

Novel Tools for Diagnosis and Monitoring of AML.

In recent years, major advances in the understanding of acute myeloid leukemia (AML) pathogenesis, together with technological progress, have led us into a new era in the diagnosis and follow-up of patients with AML. A combination of immunophenotyping, cytogenetic and molecular studies are required for AML diagnosis, including the use of next-generation sequencing (NGS) gene panels to screen all genetic alterations with diagnostic, prognostic and/or therapeutic value. Regarding AML monitoring, multiparametric flow cytometry and quantitative PCR/RT-PCR are currently the most implemented methodologies for measurable residual disease (MRD) evaluation. Given the limitations of these techniques, there is an urgent need to incorporate new tools for MRD monitoring, such as NGS and digital PCR. This review aims to provide an overview of the different technologies used for AML diagnosis and MRD monitoring and to highlight the limitations and challenges of current versus emerging tools.

Molecular MRD Assessment in Acute Myeloid Leukemias

AbstractDetection of measurable residual disease (MRD) is of significant value in the management of acute myeloid leukemia (AML) patients. Along with multicolor flowcytometry (MFC), molecular techniques form an integral tool in AML MRD detection. Multiple studies have reiterated the role of molecular MRD evaluation in AML at defined timepoints during the course of therapy, helping in risk stratification, prediction of relapse, and as guide for pre-emptive therapy. The latest World Health Organization (WHO) classification (WHO-HEME5) has refined the classification of AML bringing forth newer entities defined by molecular abnormalities, especially fusions. AML is a clonally heterogeneous disease characterized by a spectrum of multiple molecular abnormalities including gene mutations and fusions. Accordingly, the molecular methods employed are also diverse and need robust technical standardization in clinical laboratories. Real-time quantitative polymerase chain reaction (PCR), digital PCR, and next-generation sequencing (NGS) are the major molecular platforms for AML MRD. The European LeukemiaNet (ELN) MRD Working Party consensus document recently updated in 2021 for the first time has reflected on the technical recommendations for NGS MRD in AML and stressed the value of an integrated approach. It is, therefore, desirable for physicians, scientists, and pathologists alike to thoroughly understand these molecular methods for appropriate utilization and interpretation. In this article, we discuss the various facets of molecular methods for MRD detection in AML including technical requirements, advantages, drawbacks, and applications.

Targeting Measurable Residual Disease (MRD) in Acute Myeloid Leukemia (AML): Moving beyond Prognostication.

Measurable residual disease (MRD) assessment in acute myeloid leukemia (AML) has an established role in disease prognostication, particularly in guiding decisions for hematopoietic cell transplantation in first remission. Serial MRD assessment is now routinely recommended in the evaluation of treatment response and monitoring in AML by the European LeukemiaNet. The key question remains, however, if MRD in AML is clinically actionable or "does MRD merely portend fate"? With a series of new drug approvals since 2017, we now have more targeted and less toxic therapeutic options for the potential application of MRD-directed therapy. Recent approval of NPM1 MRD as a regulatory endpoint is also foreseen to drastically transform the clinical trial landscape such as biomarker-driven adaptive design. In this article, we will review (1) the emerging molecular MRD markers (such as non-DTA mutations, IDH1/2, and FLT3-ITD); (2) the impact of novel therapeutics on MRD endpoints; and (3) how MRD might be used as a predictive biomarker to guide therapy in AML beyond its prognostic role, which is the focus of two large collaborative trials: AMLM26 INTERCEPT (ACTRN12621000439842) and MyeloMATCH (NCT05564390).

Achieving MRD negativity in AML: how important is this and how do we get there?

Multiple studies have demonstrated that patients with acute myeloid leukemia (AML) who have measurable residual disease (MRD) detected during or after treatment have higher relapse rates and worse survival than similar patients testing negative. Updated response criteria for AML reflect the understanding that achievement of complete remission (CR) with no detectable MRD using high-sensitivity tests represents a superior response over conventional cytomorphological CR alone. Potential use cases for AML MRD testing are diverse and include patient selection for clinical trials and therapeutic assignment, early relapse detection and intervention during sequential monitoring, and drug development, including deep quantification for antileukemia efficacy and as a surrogate endpoint for overall survival in regulatory approvals. Testing for AML MRD has not, however, been harmonized, and many technical and clinical questions remain. The implications of MRD test results for specific therapeutic combinations, molecular subsets, test types, treatment time points, sample types, and patient characteristics remain incompletely defined. No perfect AML MRD test or testing strategy currently exists, and the evidence basis for clinical recommendations in this rare disease is sparse but growing. It is unproven whether conversion of an MRD test result from positive to negative by additional therapeutic intervention improves relapse risk and survival. Several national- and international-level consortia have recently been initiated to advance the generation and collection of evidence to support the use of AML MRD testing in clinical practice, drug development, and regulatory approvals.

Evaluation of High-Dose Cytarabine Induction Therapy and Flow Cytometric Measurable Residual Disease Monitoring for Children with De Novo Acute Myeloid Leukemia: A Report from the JPLSG-AML-12 Trial

Background: High-dose cytarabine (HDAC) in initial induction therapy has been tested in several clinical trials both in children and adults with acute myeloid leukemia (AML), however, the trial results are conflicting. In addition, there is growing evidence on significance of measurable residual disease (MRD) monitoring to predict subsequent relapse, but MRD in AML is still challenging in terms of methodology and quality control. In the nationwide clinical trial AML-12 by the Japanese Pediatric Leukemia/Lymphoma Study Group (JPLSG), the hematological malignancy subgroup of the Japan Children's Cancer Group (JCCG), a role of HDAC in initial induction and feasibility and efficacy of central reference laboratory-based flow cytometric MRD (FCM-MRD) monitoring were evaluated in children with AML. Patients & Methods: JPLSG-AML-12 trial (registered as jRCTs041180128) was designed as a seamless phase II/III trial; because of a safety concern in HDAC induction, children (0-18 years old) with newly diagnosed de novo AML (excluding acute promyelocytic leukemia and AML in Down syndrome patients) registered in selected institutions were randomized to receive either standard ECM (etoposide, standard-dose cytarabine, and mitoxantrone) or experimental HD-ECM (etoposide, HDAC, and mitoxantrone) induction, while patients registered in non-selected institutions were non-randomly allocated to receive standard ECM; in the following phase III part, all the patients were randomized. FCM-MRD were measured at two time points [end of Induction-1 (EOI-1) and end of Induction-2 (EOI-2)] at either of the two central reference laboratories (Mie University or Kyoto University) but was not used to guide subsequent therapies. Following complete remission (CR) evaluation at EOI-2, patients achieving CR were allocated to either of the 3 risk groups and received post-remission chemotherapies; core-binding-factor standard risk (CBF SR), non-CBF SR, or high risk (HR) group. Only HR patients were allocated to receive allogeneic hematopoietic stem cell transplantation in first CR. Primary endpoints of the trial were 3-year EFS and positive FCM-MRD (≥0.1%) rate at EOI-1. Results: Total 359 eligible patients were registered at 102 institutions between 2014-2018. CR, 3-year EFS, and 3-year OS rates of all patients were 94.0%, 63.1% (95%CI, 57.9-67.9%), and 80.3% (95%CI, 75.8-84.1%), respectively. Among all, 324 patients were randomized (ECM, n=168; HD-ECM, n=156). Median follow-up period of these patients was 50.9 months (range, 0.2 - 84.7 months). No significant difference in outcomes were observed between the 2 arms; CR rates were 94.2% vs. 93.8% (p=0.998), 3-year EFS rates were 64.3% (95%CI, 56.5-71.0%) vs. 61.2% (53.1-68.4%) (p=0.551), 3-year OS rates were 84.4% (95%CI, 78.0-89.1%) vs. 75.3% (95%CI, 67.7-81.4%) (p=0.053), 3-year cumulative incidence of relapse were 28.6% (95%CI, 21.5-36.0%) vs. 30.9% (95%CI, 23.3-38.8%) (p=0.585), and 3-year non-relapse mortality rates were 0.9% (95%CI, 0.1-6.4%) vs. 1.8% (95%CI, 0.4-7.1%) (p=0.832). These outcome parameters were not different within each risk groups as well. FCM-MRD at EOI-1 was evaluated in 135 patients (80.4%) in the ECM arm and 127 patients (81.4%) in the HD-ECM arm; the positive FCM-MRD rates were 21.5% vs. 25.2% (p=0.575). Regarding grade 3 or higher adverse events (AEs) evaluated by CTCAE version 4 during Induction-1, disseminated intravascular coagulation was more frequent in the HD-ECM arm (1.8% vs. 6.4%, p=0.046), but no significant difference was observed for other AEs. Univariable Cox regression analysis for baseline characteristics revealed that the intermediate-risk cytogenetics and positive FLT3-ITD were significantly associated with decreased EFS rate. However, in multivariable analyses for EFS after EOI-1 and EOI-2, FCM-MRD was the sole poor prognostic factor; hazard ratios were 5.24 (95%CI, 3.19-8.63) (p<0.001) at EOI-1 and 5.56 (95%CI, 2.93-10.54) (p<0.001) at EOI-2. Conclusions: Although HDAC in initial induction did not improve the outcome of children with AML, overall outcomes were comparable to the recently completed pediatric AML trials worldwide. Central reference laboratory-based FCM-MRD measurement was feasible and MRD at both EOI-1 and EOI-2 were the most powerful prognostic factors to predict outcome of children with AML. Therefore, FCM-MRD should be included in future risk stratification for children with AML. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Post-Remission Outcomes in Patients with Acute Myeloid Leukemia (AML) Are Similar between Hypomethylating Agent/Venetoclax Therapy and Intensive Chemotherapy after Accounting for Measurable Residual Disease (MRD) Status

Background: Intensive chemotherapy regimens (IC; e.g., 7+3 or CPX-351) broadly target leukemic blast populations in acute myeloid leukemia (AML) by interfering with DNA replication, whereas hypomethylating agent/venetoclax therapy (HMA/ven) takes advantage of metabolic vulnerabilities in leukemic stem cells via inhibition of anti-apoptotic pathways. IC regimens are often targeted to 'fit', younger patients, while HMA/ven is typically used in patients who are older or who have significant comorbidities. Both therapeutic paradigms can induce morphologic remission, with resultant measurable residual disease (MRD) status remaining a prognostically significant factor. Here, we aim to determine whether post-remission outcomes in AML patients depend mainly on MRD status or are further modified by chosen induction (IC vs HMA/ven). Methods: Retrospective chart review was performed on adult (age 18 years and older) patients newly diagnosed with AML and treated at Johns Hopkins Hospital, Baltimore, MD between September 2014 and June 2021. Patients were excluded if they had promyelocytic or mixed phenotype leukemia. Complete remission (CR) was defined by <5% medullary blasts with no extramedullary disease and count recovery. Primary covariates of interest included age in years, performance status (PS; ECOG 0-1 for good vs 2-4 for poor), European LeukemiaNet (ELN) 2022 risk group, number of HMA/ven cycles to best response, hematopoietic stem cell transplantation (HCT) status, chemotherapy type (IC vs HMA/ven), and MRD status by multiparametric flow cytometry (MFC). Groups were compared using Wilcoxon rank sum, Kruskal-Wallis, and Fisher's exact tests. Laplace regression models were used to estimate subgroup median overall survivals (OS) in order to compare them using the Wald test. Associations between OS and the above covariates were examined in Cox models; one multivariable model included an interaction term for therapy type and MRD status. Analyses were performed using Stata version 17. Results: Of the 388 patients initially reviewed, 214 (55%) achieved a CR or CR with incomplete count recovery and were included in further analysis. Most (103 of 159) IC patients received 7+3; 20 received CPX-351 and 36 received a high-dose cytarabine-based regimen. Fifty-five patients received HMA/ven. The HMA/ven patients were significantly older than those receiving IC regardless of MRD status (median age 72 vs 58 years, respectively, P<0.001). MRD negative (MRD-) remission was achieved in 134 (84.3%) patients after IC and 44 (80.0%) patients after HMA/ven. Patients who achieved MRD- CRs after IC were more likely to undergo HCT than those with identical MRD status after HMA/ven (77.6% vs 40.9%, P<0.001) and were younger (median age 60 vs 73 years, P<0.001). Univariate analysis showed significantly decreased hazard of death in patients with favorable ELN 2022 risk score, MRD- status in first CR, and HCT (Table 1). Kaplan-Meier curves showed patients with MRD- remissions had superior survival to those with MRD positive (MRD+) remissions (median OS not reached vs. 21.9 months, P<0.05), whereas there was no statistically significant difference in median OS between therapies (36.1 months HMA/ven vs. 61.2 months IC). Patients in the IC, MRD- group and HMA/ven, MRD- group had similar outcomes (median OS not reached for both); both groups had superior survival to MRD+ groups (P<0.05; Figure 1). Multivariable analysis showed decreased hazards of death for ELN favorable risk patients (hazard ratio [HR] 0.49, 95% confidence interval [CI] 0.28-0.85) and those MRD- in first CR (HR 0.47, 95% CI 0.28-0.77) after adjusting for age, PS, therapy type, and cycles. In a subsequent model, an interaction term between therapy type and MRD status was not significant (HR=0.96, suggesting no difference in impact of MRD between therapy types). Conclusions: In this retrospective study evaluating outcomes in patients with AML, chemotherapy type does not appear to differentially impact survival by MRD status in those achieving remission. MRD status as measured by MFC significantly impacts survival when adjusting for relevant baseline covariates. These results suggest that obtaining deep, MRD- remissions matters regardless of whether these are achieved with HMA/venetoclax or intensive therapy. Ultimately, randomized controlled trials are needed to better determine the value of MRD in AML after different induction strategies. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Single-Cell Immune Landscape of Measurable Residual Disease in AML after Allogeneic Hematopoietic Stem Cell Transplantation

Measurable residual disease (MRD) is the most important prognostic marker for relapse after allogeneic hematopoietic stem cell transplantation (allo-HSCT) in acute myeloid leukemia (AML). Unfortunately, our understanding of critical immune cell clusters in bone marrow (BM) which contribute to MRD occurrence is limited. Thus, we generated 184,231 single-cell transcriptomes to compare the BM immune cell landscape between MRD positive and negative patients. KLRG1-CD8+ T cell and KLRG1+CD8+ T cell clusters were prevalent in MRD positive and negative patients, respectively, demonstrating significantly different gene expression profiles (particularly cytotoxicity genes). KLRG1+CD8+ T cells showed a stronger cytotoxicity to leukemia cells compared with KLRG1-CD8+ T cells in vitro. Exhausted CD8+ T cell clusters were similar between MRD positive and negative patients. In addition, IGHG1+ B cells, IFITM3+ monocytes, and HSP90AB1+ erythrocytes were associated with MRD occurrence. MRD clearance by immunotherapies was accompanied with the increase of KLRG1+CD8+ T cell clusters and decrease of KLRG1-CD8+ T cell, IGHG1+ B cell, IFITM3+ monocyte, and HSP90AB1+ erythrocyte clusters, and vice versa. An independent cohort showed that the decrease of immune cell clusters which were prevalent in MRD positive patients was associated with MRD achieving negative after allo-HSCT. Macrophage migration inhibitory factor pathway might be the critical pathway among these immune cell populations, and it was weakened in MRD patients who showed response to immunotherapy. We firstly provided a complete landscape on BM immune cells in MRD stage which will facilitate a better understanding of the immune mechanisms for MRD occurrence in AML. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Measurable Residual Disease Conversion Rate with Consolidation Chemotherapy in Acute Myeloid Leukemia

Background Patients with acute myeloid leukemia (AML) who achieve complete remission (CR) following induction therapy but continue to have measurable residual disease (MRD) have inferior outcomes following allogeneic hematopoietic cell transplant (alloHCT). Determining the historical rate of MRD clearance in response to standard consolidative therapy is needed as an initial step in developing a new therapeutic strategy to clear MRD prior to alloHCT. Methods A multi-institution retrospective analysis was performed on consecutively treated AML patients in morphologic CR with detectable MRD post-induction therapy who received standard chemotherapy consolidation from January 2016 to December 2021. MRD was measured by multiparametric flow cytometry (MPFC, sensitivity 0.01-0.1%), next generation sequencing (NGS, sensitivity 1-5%), real-time quantitative PCR (qPCR, sensitivity 1:100,000-0.5%), and/or fluorescence in situ hybridization (FISH)/karyotype (sensitivity 1-5%). Any detectable disease-related abnormalities were considered to be evidence of MRD for the purpose of this study. Results Eighty-three patients met inclusion criteria for this analysis, with a median age at diagnosis of 51 years (IQR 43-63). Adverse-risk disease by ELN 2017 criteria was observed in 36 patients (43%). The majority received induction therapy with "7+3" (cytarabine + idarubicin or daunorubicin, 77 patients, 93%), and most (71 patients, 86%) required only 1 line of therapy to achieve CR. At the time of CR following induction therapy, 35 patients (42%) had MRD detected by MPFC, 38 patients (46%) had MRD detected by NGS, 10 patients (12%) had MRD detected by qPCR, and 32 patients (39%) were found to have an abnormal FISH or karyotype. Twenty-eight patients had MRD detected by more than 1 method. Consolidation therapy consisted of intermediate-dose cytarabine (defined as <3 g/m2, 41 patients, 49%) or high-dose cytarabine (defined as 3 g/m2, 39 patients, 47%) in all patients, except for 3 who received daunorubicin and cytarabine (liposomal) consolidation. The number of cycles of cytarabine consolidation were 1 cycle (36 patients, 43%), 2 cycles (23 patients, 28%), 3 cycles (15 patients, 18%), and 4 cycles (9 patients, 11%), respectively. Sixteen patients received cytarabine consolidation in combination with another agent including sorafenib (1 patient), midostaurin (10 patients), gilteritinib (1 patient), enasidenib (1 patient), and gemtuzumab (3 patients). In response to consolidation therapy, 27 of the 83 patients with measurable disease converted to MRD-negative (33%) after all given cycles of consolidation cytarabine. Of the 35 patients whose AML had MRD detected by MPFC prior to consolidation, 17 converted to MRD-negative (49%). Of the 38 patients whose AML had MRD detected by NGS prior to consolidation, 6 converted to MRD-negative (16%). Of the 10 patients whose AML had MRD detected by qPCR prior to consolidation, 6 converted to MRD-negative (60%). Of the 32 patients whose AML had MRD detected by FISH or karyotype prior to consolidation, 13 converted to MRD-negative (41%). Of note, 22 patients developed progressive disease following consolidation therapy (and therefore also did not achieve MRD-negativity). Multivariable logistic regression was performed to assess potential associations with MRD conversion during consolidation chemotherapy. Older age decreased the odds of conversion of AML to MRD-negative (OR = 0.96, 95% CI 0.92-1.00, p = 0.04). Higher ELN risk category, higher dose of cytarabine, and more cycles of consolidation did not affect the likelihood of conversion of AML to MRD-negative. Fifty-five patients received alloHCT following consolidation therapy. Thirty-one of these patients had AML with MRD detected post-consolidation, of whom 14 had MRD measured by MPFC. With a median follow-up time of 437 days post-transplant (IQR 151-914), two-year progression-free survival post-transplant was 57% in AML patients with MRD detected post-consolidation compared to 71% in AML patients with no MRD (p = 0.28). Conclusions The rate of MRD eradication with standard consolidation chemotherapy in AML is suboptimal. Combined with the known poor outcomes after alloHCT in patients with AML and detectable MRD pre-transplant, this demonstrates an unmet need to develop a new therapeutic strategy for eradicating MRD after induction therapy. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Trial in Progress: Tagraxofusp-Based Therapy to Eradicate Measurable Residual Disease of Acute Myelogenous Leukemia Prior to Allogeneic Hematopoietic Cell Transplantation

Background Numerous studies convincingly demonstrate that measurable residual disease (MRD) in AML at time of allogeneic cell transplantation (alloHCT) is a powerful, independent predictor of subsequent relapse. Attempts to eradicate AML MRD pre-transplant with consolidation chemotherapy have been unsuccessful, with reported MRD conversion rates as low as 20% (Appelbaum et al., Blood 2019). Tagraxofusp is an IL-3 truncated diphtheria toxin recombinant protein that binds CD123 with high affinity. Preliminary data using tagraxofusp as consolidation therapy in AML patients has demonstrated good tolerability (Lane et al., Blood 2017). Pathways of resistance to tagraxofusp have been identified preclinically as loss of the intracellular target for diphtheria toxin, diphthamide, through methylation of an enzyme involved in diphthamide synthesis. Treatment with a hypomethylating agent has the potential to restore expression of diphthamide and increase tagraxofusp sensitivity in AML cells (Togami et al., J Clin Invest 2019). Design This is a single-arm, open-label, multi-center phase Ib/II clinical trial to evaluate the safety and effectiveness of tagraxofusp +/- azacitidine in AML patients who are in first or second remission with detectable MRD and are planned to undergo alloHCT. MRD will be measured by multi-dimensional flow cytometry with sensitivity of 0.02% (Hematologics). Patients will be enrolled in a modified 3+3 dose escalation design with two cohorts: cohort A) tagraxofusp 12 mcg/kg IV qday on days 1-5; and cohort B) azacitidine 75 mg/m2 subq qday on days 1-5 plus tagraxofusp 12 mcg/kg qday on days 8-12. Patients achieving MRD-negativity after cycle 1 will proceed to alloHCT. If a patient remains MRD-positive, an additional cycle of investigational therapy will be administered. All patients will proceed to alloHCT after no more than 2 cycles of investigational therapy. Both cohorts contain a dose escalation and a dose expansion phase. Cohort B will open if cohort A is not efficacious. Up to 44 participants will be enrolled in this trial at University of California Los Angeles and University of California San Francisco (two constituent sites of the University of California Hematologic Malignancies Consortium). Objectives The primary objective is to estimate the rate of conversion from MRD-positive pre-investigational therapy to MRD-negative after 1 or 2 cycles of investigational therapy. Key secondary objectives include to determine the safety of tagraxofusp +/- azacitidine in this patient population and to evaluate if adverse effects of this investigational therapy lead to delays in alloHCT. Exploratory objectives will involve use of single cell RNA sequencing to investigate if response to investigational therapy is predicted by leukemia-specific biomarkers and to evaluate if putative cell surface markers (inferred from RNA detection) are associated with MRD persistence. Main Outcomes The primary endpoint is MRD status after 1 or 2 cycles of investigational therapy. Key secondary endpoints include dose-limiting toxicities (any grade 4 or 5 non-hematologic toxicity or any grade 3 or greater hematologic toxicity at day 42) and number of days between investigational therapy and alloHCT. Conclusions There is an unmet need to improve outcomes in AML with detectable MRD pre-transplant. The strategy in this study is to employ tagraxofusp as an alternative mechanism of action to eradicate chemo-resistant AML cells responsible for subsequent relapse. In order to mitigate any potential resistance the residual leukemia population may have against tagraxofusp, azacitidine will be added to optimize the likelihood for MRD negativity and the possibility for improved outcomes after alloHCT. This study was sponsored by the ASH CRTI. References Appelbaum J, Loeb A, Gardner K, et al. Additional Cytotoxic Chemotherapy Is Unlikely to Eliminate Measurable Residual Acute Myeloid Leukemia (AML). Blood. 2019;134(Supplement_1):260-260. Lane AA, Sweet KL, Wang ES, et al. Results from Ongoing Phase 1/2 Trial of SL-401 As Consolidation Therapy in Patients with Acute Myeloid Leukemia (AML) in Remission with Minimal Residual Disease (MRD). Blood. 2017;130(Supplement 1):2583-2583. Togami K, Pastika T, Stephansky J, et al. DNA methyltransferase inhibition overcomes diphthamide pathway deficiencies underlying CD123-targeted treatment resistance. J Clin Invest. 2019;129(11):5005-5019. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Development of a 27-color panel for the detection of measurable residual disease in patients diagnosed with acute myeloid leukemia.

Acute myeloid leukemia (AML) measurable residual disease (MRD) evaluated by multiparametric flow cytometry (MFC) is a surrogate for progression-free and overall survival in clinical trials and patient management. Due to the limited number of detection channels available in conventional flow cytometers, panels used for assessing AML MRD are typically split into multiple tubes. This cripples the simultaneous and correlated assessment of all myeloblast measurements. In response, we prototyped a single-tube 27-color MFC assay for the evaluation of AML MRD, incorporating all recommended markers. Marrow aspirates from 22 patients were processed for analysis using full spectrum flow cytometry (FSFC). The signal resolution of each marker was compared between samples stained with single antibody vs. the fully stained panel. The analytical accuracy for quantifying hematopoietic cells between our established 8-color assay and the new 27-color method were compared. Variations within an operator and between separate operators were assessed to evaluate the assays reproducibility. The limited of blank (LOB), limit of detection (LOD), and lower limit of quantification (LLOQ) of the 27-color method were empirically determined using limiting dilution experiments. The stability of antibody cocktails over a period of 120 h was also studied using cryopreserved marrow cells. The stain indices for all antibodies were lower in the fully stained panel compared to cells stained with one antibody but clear separations between negative and positive signals were achieved for all antibodies. Our results demonstrated a high concordance between the established 8-color method and the new 27-color assay for enumerating myeloblasts and MRD interpretation within and between operators. The data further showed that the single-tube 27-color assay easily achieved the minimum required detection sensitivity of 0.1%. When antibodies were combined, however, expression intensity of some antigens deteriorated significantly when stored. Our single-tube 27-color panel is a suitable, high sensitivity flow cytometric approach that can be used for AML MRD testing, which improves the correlation of aberrant antigens and detection of asynchronous differentiation patterns. Based on the stability study, we recommend the full panel be made prior to staining.

P1356: PATIENT-SPECIFIC DIGITAL DROPLET PCR ASSAYS FOR MINIMAL RESIDUAL DISEASE DETECTION OF RUNX1 MUTATIONS IN ACUTE MYELOID LEUKEMIA PATIENTS UNDERGOING ALLOGENEIC STEM CELL TRANSPLANTATION

Background: The persistence of non-clonal-hematopoiesis mutations (mut) in remission prior to a consolidating allogeneic stem cell transplantation (HSCT) in acute myeloid leukemia (AML) patients (pts) has been associated with a higher relapse probability. RUNX1 mut are frequent in AML and associate with adverse outcomes, often indicating the need for an allogeneic HSCT. They may also represent suitable targets for measurable residual disease (MRD) detection, but have not yet been evaluated for this purpose separately. Aims: To develop patient-specific digital droplet PCR (ddPCR) assays for sensitive RUNX1 mut detection and evaluate their applicability for predicting relapse in AML pts undergoing allogeneic HSCT. Methods: We retrospectively analyzed 171 AML pts consolidated by allogeneic HSCT (non-myeloablative 64%, 24% reduced-intensity, or myeloablative 12%) for their diagnostic RUNX1 mut status. At diagnosis, cytogenetics, and additional 53 recurrently mutated genes in AML were analyzed. Adequate material at and/or following HSCT was available for 22 RUNX1mut pts (up to 28 days prior to HSCT [n=19], during post-HSCT follow up [61 samples in 11 pts] and at relapse [n=3]). For these, patient-specific ddPCR assays were developed using a competitive probe approach to reach MRD levels of at least 0.01% VAF. Median follow up after HSCT was 1.5 years. Results: At diagnosis, 22 pts had one and 4 pts had two RUNX1 mut (16%, median VAF 36.5, range 3.8-95.1%), 10 were frameshift, 12 were missense, and 8 were nonsense. Most frequent co-mut were found in ASXL1 (31%), DNMT3A (29%), and NRAS (26%). One patient was transplanted with active AML and had a RUNX1 VAF of 30.4% at HSCT. For all 19 measurable pts in morphologic remission at HSCT, RUNX1 mut had decreased compared to VAFs at diagnosis (median VAF at HSCT 2.3, range 0.06-10.9%), but persisted in 11 (58%) of the pts. Noteworthy, 7/8 RUNX1 MRDneg, but only 2/11 RUNX1 MRDpos pts were female (P=.005). There were no other characteristics or mutated genes at diagnosis that associated with RUNX1 MRDpos at HSCT (Figure 1A). RUNX1 MRDpos pts at HSCT had a higher cumulative incidence of relapse (P=.05) and by trend shorter overall survival (P=.07, Figure 1B,C). At day 28 after HSCT, all 11 pts with material available were MRDneg, 3 of them relapsed. In 2 of those pts, RUNX1 MRD predicted relapse at VAFs of 0.09% and 0.04% 10 and 5.5 months earlier, respectively, while in the third patient the last MRD sample taken 4 months prior to relapse remained RUNX1 MRDneg. All 3 pts with relapse material available relapsed with the RUNX1 mut present at diagnosis (at VAFs of 37%, 8.7%, and 36.2%). All 8 pts with material available that remained in remission had no detectable RUNX1 mut at any time during post-HSCT follow up. Image:Summary/Conclusion:RUNX1-mut based patient-specific ddPCR assays could be developed for all RUNX1 mut AML pts. MRD determination by these assays is a feasible tool to determine AML MRD with a relatively short turn-around time during disease course at high sensitivity and relatively low cost. RUNX1 MRDpos at HSCT associated with high relapse risk. Within 28 days after HSCT, all pts became RUNX1 MRDneg, identifying this timepoint as least meaningful for MRD assessment in our cohort. In sequential analyses after HSCT RUNX1-mut based MRD was a stable marker allowing for a reliable and clinically meaningful MRD detection, as they predicted relapse when rising as well as persisting remissions when remaining undetectable in the majority of analyzed AML pts.

Pre-MEASURE: Multicenter evaluation of the prognostic significance of measurable residual disease testing prior to allogeneic transplantation for adult patients with AML in first remission.

7006 Background: Measurable residual disease (MRD) prior to allogeneic hematopoietic cell transplantation (alloHCT) is associated with increased relapse and death in patients with acute myeloid leukemia (AML) in cytomorphological complete remission (CR). We recently demonstrated AML MRD detected in pre-alloHCT blood by DNA-sequencing was associated with increased relapse and decreased overall survival in patients randomized to reduced intensity conditioning (RIC) versus myeloablative conditioning (MAC). The clinical utility of such ultra-deep next-generation sequencing (NGS-MRD) had not yet been reported in a large multi-center cohort. Methods: Patients aged 18 or older who underwent first alloHCT between 2013-2017 for AML in first CR (CR1), reported to be FLT3, NPM1, IDH1, IDH2 and/or Kit mutated at diagnosis, with a pre-conditioning remission blood sample available in the CIBMTR biobank were eligible for this study. Ultra-deep anchored multiplex PCR-based NGS-MRD for the above mutations was performed on 500ng gDNA with error-corrected variant calling as previously described. The pre-specified statistical analysis plan was registered on OSF. Results: Of 457 patients with a sample available, 448 had sufficient clinical annotation and DNA for analysis. 147 of these 448 patients (33%) experienced relapse at a median of 5.6 months post-alloHCT. NGS-MRD was positive in 129 pre-alloHCT patient samples (29%), averaging 1.35 mutation(s)/patient (range: 1-4). 173 mutations were detected with a median VAF of 0.18% (range: 0.0054-62%), most frequently FLT3-ITD (n = 43 patients), NPM1 (n = 48), and IDH2 (n = 46). Testing positive by NGS-MRD prior to alloHCT was associated with a 3yr RFS of 36% (95% CI: 28-45%) compared with 56% (51-62%) in those testing negative (p &lt; 0.001). Detection of NPM1 and/or FLT3-ITD mutations prior to alloHCT was associated with a 3yr relapse probability of 55% (43-67%) and RFS of 26% (16-37%). NGS-MRD impact was modified by conditioning intensity: positive patients receiving RIC/NMA had the highest relapse of 57% at 3yr, testing negative followed by RIC/NMA had the same relapse rate at 3yr (35%) as those who tested positive but received MAC (p &lt; 0.001). At three years, those positive for FLT3-ITD and/or NPM1 mutations prior to RIC/NMA alloHCT had a relapse probability of 67% (50-83%) with a RFS of 19% (8-33%). HR for relapse if NGS-MRD positive pre-alloHCT in CR1 was 2.3 (p &lt; 0.001, 95% CI 1.6-3.1) when adjusting for conditioning intensity and age group. Conclusions: In this largest cohort of NGS-MRD testing prior to alloHCT for AML reported to date, we confirm the ability to identify patients in CR1 but at high-risk of subsequent relapse. This evidence provides the foundation for future precision medicine approaches to reduce post-transplant AML relapse.