Measurable Residual Disease Monitoring Research Articles

Immunophenotypic Profile and Measurable Residual Disease Monitoring in Multiple Myeloma: A Prospective Study From a Tertiary Care Centre in Southern India

Immunophenotypic Profile and Measurable Residual Disease Monitoring in Multiple Myeloma: A Prospective Study From a Tertiary Care Centre in Southern India

Comprehensive insights into AML relapse: genetic mutations, clonal evolution, and clinical outcomes.

Acute myeloid leukemia (AML) is a complex hematologic malignancy characterized by uncontrolled proliferation of myeloid precursor cells within bone marrow. Despite advances in understanding of its molecular underpinnings, AML remains a therapeutic challenge due to its high relapse rate and clonal evolution. In this retrospective study, we analyzed data from 24 AML patients diagnosed at a single institution between January 2017 and August 2023. Comprehensive genetic analyses, including chromosomal karyotyping, next-generation sequencing, and gene fusion assays, were performed on bone marrow samples obtained at initial diagnosis and relapse. Clinical data, treatment regimens, and patient outcomes were also documented. Mutations in core genes of FLT3, NPM1, DNMT3A, and IDH2 were frequently discovered in diagnostic sample and remained in relapse sample. FLT3-ITD, TP53, KIT, RUNX1, and WT1 mutation were acquired at relapse in one patient each. Gene fusion assays revealed stable patterns, while chromosomal karyotype analyses indicated a greater diversity of mutations in relapsed patients. Clonal evolution patterns varied, with some cases showing linear or branching evolution and others exhibiting no substantial change in core mutations between diagnosis and relapse. Our study integrates karyotype, gene rearrangements, and gene mutation results to provide a further understanding of AML heterogeneity and evolution. We demonstrate the clinical relevance of specific mutations and clonal evolution patterns, emphasizing the need for personalized therapies and measurable residual disease monitoring in AML management. By bridging the gap between genetics and clinical outcome, we move closer to tailored AML therapies and improved patient prognoses.

Measurable residual disease monitoring by ddPCR in the early posttransplant period complements the traditional MFC method to predict relapse after HSCT in AML/MDS: a multicenter retrospective study

BackgroundDroplet digital PCR (ddPCR) is widely applied to monitor measurable residual disease (MRD). However, there are limited studies on the feasibility of ddPCR-MRD monitoring after allogeneic hematopoietic stem cell transplantation (allo-HSCT), especially targeting multiple molecular markers simultaneously.MethodsOur study collected samples from patients with acute myeloid leukemia (AML) or high-risk myelodysplastic syndrome (MDS) in complete remission after allo-HSCT between January 2018 and August 2021 to evaluate whether posttransplant ddPCR-MRD monitoring can identify patients at high risk of relapse.ResultsOf 152 patients, 58 (38.2%) were MRD positive by ddPCR within 4 months posttransplant, with a median variant allele frequency of 0.198%. The detectable DTA mutations (DNMT3A, TET2, and ASXL1 mutations) after allo-HSCT were not associated with an increased risk of relapse. After excluding DTA mutations, patients with ddPCR-MRD positivity had a significantly higher cumulative incidence of relapse (CIR, 38.7% vs. 9.7%, P < 0.001) and lower rates of relapse-free survival (RFS, 55.5% vs. 83.7%, P < 0.001) and overall survival (OS, 60.5% vs. 90.5%, P < 0.001). In multivariate analysis, ddPCR-MRD positivity of non-DTA genes was an independent adverse predictor for CIR (hazard ratio [HR], 4.02; P < 0.001), RFS (HR, 2.92; P = 0.002) and OS (HR, 3.12; P = 0.007). Moreover, the combination of ddPCR with multiparameter flow cytometry (MFC) can further accurately identify patients at high risk of relapse (F+/M+, HR, 22.44; P < 0.001, F+/M-, HR, 12.46; P < 0.001 and F-/M+, HR, 4.51; P = 0.003).ConclusionddPCR-MRD is a feasible approach to predict relapse after allo-HSCT in AML/MDS patients with non-DTA genes and is more accurate when combined with MFC.Trial registrationClinicalTrials.gov identifier: NCT06000306. Registered 17 August 2023 –Retrospectively registered (https://clinicaltrials.gov/study/NCT06000306?term=NCT06000306&rank=1).

Clonal relapse dynamics in acute myeloid leukemia following allogeneic hematopoietic cell transplantation

AbstractPatients with acute myeloid leukemia (AML) who experience relapse following allogeneic hematopoietic cell transplantation (alloHCT) face unfavorable outcomes regardless of the chosen relapse treatment. Early detection of relapse at the molecular level by measurable residual disease (MRD) assessment enables timely intervention, which may prevent hematological recurrence of the disease. It remains unclear whether molecular MRD assessment can detect MRD before impending relapse and, if so, how long in advance. This study elucidates the molecular architecture and kinetics preceding AML relapse by using error-corrected next-generation sequencing (NGS) in 74 patients with AML relapsing after alloHCT, evaluating 140 samples from peripheral blood collected 0.6 to 14 months before relapse. At least 1 MRD marker became detectable in 10%, 38%, and 64% of patients at 6, 3, and 1 month before relapse, respectively. By translating these proportions into monitoring intervals, 38% of relapses would have been detected through MRD monitoring every 3 months, whereas 64% of relapses would have been detected with monthly intervals. The relapse kinetics after alloHCT are influenced by the functional class of mutations and their stability during molecular progression. Notably, mutations in epigenetic modifier genes exhibited a higher prevalence of MRD positivity and greater stability before relapse, whereas mutations in signaling genes demonstrated a shorter lead time to relapse. Both DTA (DNMT3A, TET2, and ASXL1) and non-DTA mutations displayed similar relapse kinetics during the follow-up period after alloHCT. Our study sets a framework for MRD monitoring after alloHCT by NGS, supporting monthly monitoring from peripheral blood using all variants that are known from diagnosis.

Evaluation of next-generation sequencing for measurable residual disease monitoring in three major fusion transcript subtypes of B-precursor acute lymphoblastic leukaemia

The use of next-generation sequencing (NGS) for monitoring measurable residual disease (MRD) in acute lymphoblastic leukaemia (ALL) has been gaining traction. This study aimed to investigate the utility of NGS in MRD monitoring for the three major fusion transcript (FT) subtypes of B-precursor ALL (B-ALL). The MRD results for 104 bone marrow samples from 56 patients were analysed through NGS and real time quantitative reverse transcription PCR (RT-qPCR) for the three major FTs: BCR::ABL1, TCF3::PBX1, and ETV6::RUNX1. To validate the NGS approach, NGS-MRD was initially compared with allele-specific oligonucleotide-qPCR-MRD, and the coefficient of determination was good (R2=0.8158). A subsequent comparison of NGS-MRD with FT-MRD yielded a good coefficient of determination (R2=0.7690), but the coefficient varied by subtype. Specifically, the R2 was excellent for TCF3::PBX1 ALL (R2=0.9157), good for ETV6::RUNX1 ALL (R2=0.8606), and subpar for BCR::ABL1 ALL (R2=0.5763). The overall concordance between the two methods was 83.7%, and an excellent concordance rate of 95.8% was achieved for TCF3::PBX1 ALL. Major discordance, which was defined as a >1 log difference between discordant NGS-MRD and FT-MRD, occurred in 6.7% of the samples, with all but one sample being BCR::ABL1 ALL. Among the four non-transplanted patients with BCR::ABL1-MRD (+)/NGS-MRD (-), three did not relapse after long-term follow-up. Our finding indicates that NGS-MRD has a better prognostic impact than RT-qPCR-MRD in ETV6::RUNX1 and BCR::ABL1 ALL, whereas in TCF3::PBX1 ALL, both methods exhibit comparable efficacy.

Analytical Performance Evaluation of a Digital Real-Time PCR for Quantifying Major BCR::ABL1 Transcripts.

Accurate quantification of the BCR::ABL1 transcripts is essential for measurable residual disease (MRD) monitoring in chronic myeloid leukemia (CML) after tyrosine kinase inhibitor (TKI) treatment. This study evaluated the newly developed digital real-time PCR method, Dr. PCR, as an alternative reverse transcription-PCR (qRT-PCR) for MRD detection. The performance of Dr. PCR was assessed using reference and clinical materials. Precision, linearity, and correlation with qRT-PCR were evaluated. MRD levels detected by Dr. PCR were compared with qRT-PCR, and practical advantages were investigated. Dr. PCR detected MRD up to 0.0032%IS (MR4.5) with excellent precision and linearity and showed a strong correlation with qRT-PCR results. Notably, Dr. PCR identified higher levels of MRD in 12.7% (29/229) of patients than qRT-PCR, including six cases of MR4, which is a critical level for TKI discontinuation. Dr. PCR also allowed for sufficient ABL1 copies in all cases, while qRT-PCR necessitated multiple repeat tests in 3.5% (8/229) of cases. Our study provides a body of evidence supporting the clinical application of Dr. PCR as a rapid and efficient method for assessing MRD in patients with CML under the current treatment regimen.

Usefulness of KIT mutant transcript levels for monitoring measurable residual disease in t (8;21) acute myeloid leukemia.

In addition to RUNX1::RUNX1T1 transcript levels, measurable residual disease monitoring using KIT mutant (KITmut ) DNA level is reportedly predictive of relapse in t (8; 21) acute myeloid leukemia (AML). However, the usefulness of KITmut transcript levels remains unknown. A total of 202 bone marrow samples collected at diagnosis and during treatment from 52 t (8; 21) AML patients with KITmut (D816V/H/Y or N822K) were tested for KITmut transcript levels using digital polymerase chain reaction. The individual optimal cutoff values of KITmut were identified by performing receiver operating characteristics curve analysis for relapse at each of the following time points: at diagnosis, after achieving complete remission (CR), and after Course 1 and 2 consolidations. The cutoff values were used to divide the patients into the KITmut -high (KIT_H) group and the KITmut -low (KIT_L) group. The KIT_H patients showed significantly lower relapse-free survival (RFS) and overall survival (OS) rates than the KIT_L patients after Course 1 consolidation (p=0.0040 and 0.021, respectively) and Course 2 consolidation (p=0.018 and 0.011, respectively) but not at diagnosis and CR. The <3-log reduction in the RUNX1::RUNX1T1 transcript levels after Course 2 consolidation was an independent adverse prognostic factor for RFS and OS. After Course 2 consolidation, the KIT_H patients with >3-log reduction in the RUNX1::RUNX1T1 transcript levels (11/45; 24.4%) had similar RFS as that of patients with <3-log reduction in the RUNX1::RUNX1T1 transcript levels. The combination of KITmut and RUNX1::RUNX1T1 transcript levels after Course 2 consolidation may improve risk stratification in t (8; 21) AML patient with KIT mutation.

Flow cytometry-based measurable residual disease (MRD) analysis identifies AML patients who may benefit from allogeneic hematopoietic stem cell transplantation.

Measurable residual disease (MRD) monitoring independently predicts long-term outcomes in patients with acute myeloid leukemia (AML). Of the various modalities available, multiparameter flow cytometry-based MRD analysis is widely used and relevant for patients without molecular targets. In the transplant (HCT) setting, the presence of MRD pre-HCT is associated with adverse outcomes. MRD-negative remission status pre-HCT was also associated with longer overall (OS) and progression-free survival and a lower risk of relapse. We hypothesize that the combination of disease risk and MRD at the time of first complete remission (CR1) could identify patients according to the benefit gained from HCT, especially for intermediate-risk patients. We performed a retrospective analysis comparing the outcomes of HCT versus non-HCT therapies based on MRD status in AML patients who achieved CR1. Time-dependent analysis was applied considering time-to-HCT as a time-dependent covariate and compared HCT versus non-HCT outcomes according to MRD status at CR1. Among 336 patients assessed at CR1, 35.1% were MRD positive (MRDpos) post-induction. MRDpos patients benefitted from HCT with improved OS and relapse-free survival (RFS), while no benefit was observed in MRDneg patients. In adverse-risk patients, HCT improved OS (HR for OS 0.55; p = 0.05). In intermediate-risk patients, HCT benefit was not significant for OS and RFS. Intermediate-risk MRDpos patients were found to have benefit from HCT with improved OS (HR 0.45, p = 0.04), RFS (HR 0.46, p = 0.02), and CIR (HR 0.41, p = 0.02). Our data underscore the benefit of HCT in adverse risk and MRDpos intermediate-risk AML patients.

ZNF384 fusion transcript levels for measurable residual disease monitoring in adult B-cell acute lymphoblastic leukemia.

Zinc finger protein 384 (ZNF384) rearrangement defined a novel subtype of B-cell acute lymphoblastic leukemia (B-ALL). The prognostic significance of ZNF384 fusion transcript levels represented measurable residual disease remains to be explored. ZNF384 fusions were screened out in 57 adult B-ALL patients at diagnosis by real-time quantitative polymerase chain reaction and their transcript levels were serially monitored during treatment. The reduction of ZNF384 fusion transcript levels at the time of achieving complete remission had no significant impact on survival, whereas its ≥2.5-log reduction were significantly associated with higher relapse free survival (RFS) and overall survival (OS) rates after course 1 consolidation (p=0.022 and=0.0083) and course 2 consolidation (p=0.0025 and=0.0008). Compared with chemotherapy alone, allogeneic hematopoietic stem cell transplantation (allo-HSCT) significantly improved RFS and OS of patients with <2.5-log reduction after course 1 consolidation (p<0.0001 and=0.0002) and course 2 consolidation (p=0.0003 and=0.019), whereas exerted no significant effects in patients with ≥2.5-log reduction (all p>0.05). ZNF384 fusion transcript levels after course 1 and course 2 consolidation strongly predict relapse and survival and may guide whether receiving allo-HSCT in adult B-ALL.

Quantification of Measurable Residual Disease Detection by Next-Generation Sequencing–Based Clonality Testing in B-Cell and Plasma Cell Neoplasms

Next generation sequencing (NGS)-based measurable residual disease (MRD) monitoring in post-treatment settings can be crucial for relapse risk stratification in patients with B-cell and plasma cell neoplasms. Prior studies have focused on validation of various technical aspects of the MRD assays, but more studies are warranted to establish the performance characteristics and enable standardization and broad utilization in routine clinical practice. Here, we describe our approach and clinical experience with an NGS-based IGH MRD quantification assay, incorporating a spike-in calibrator for monitoring B-cell and plasma cell neoplasms based on their unique IGH rearrangement status. Comparison of MRD status (positive or undetectable) by NGS and flow cytometry (FC) assays showed high concordance (91%, 471/519 cases) and overall good linear correlation in MRD quantitation, particularly for chronic lymphocytic leukemia and B-lymphoblastic leukemia/lymphoma (R=0.85). Quantitative correlation was lower for plasma cell neoplasms, where underestimation by FC is a known limitation. No significant effects on sequencing efficiency by the spike-in calibrator were observed, with excellent inter- and intra-assay reproducibility within our laboratory, and in comparison to an external laboratory, using the same assay and protocols. Assays performed both at internal and external laboratories showed highly concordant MRD detection (100%) and quantitation (R=0.97). Overall, this NGS-based MRD assay showed highly reproducible results with quantitation that correlated well with FC MRD assessment, particularly for B-cell neoplasms.

Panel-based RNA fusion sequencing improves diagnostics of pediatric acute myeloid leukemia

New methods like panel-based RNA fusion sequencing (RNA-FS) promise improved diagnostics in various malignancies. We here analyzed the impact of RNA-FS on the initial diagnostics of 241 cases with pediatric acute myeloid leukemia (AML). We show that, compared to classical cytogenetics (CCG), RNA-FS reliably detected risk-relevant fusion genes in pediatric AML. In addition, RNA-FS strongly improved the detection of cryptic fusion genes like NUP98::NSD1, KMT2A::MLLT10 and CBFA2T3::GLIS2 and thereby resulted in an improved risk stratification in 25 patients (10.4%). Validation of additionally detected non-risk-relevant high confidence fusion calls identified PIM3::BRD1, C22orf34::BRD1, PSPC1::ZMYM2 and ARHGAP26::NR3C1 as common genetic variants and MYB::GATA1 as recurrent aberration, which we here describe in AML subtypes M0 and M7 for the first time. However, it failed to detect rare cytogenetically confirmed fusion events like MNX1::ETV6 and other chromosome 12p-abnormalities. As add-on benefit, the proportion of patients for whom measurable residual disease (MRD) monitoring became possible was increased by RNA-FS from 44.4 to 75.5% as the information on the fusion transcripts’ sequence allowed the design of new MRD assays.

Parallel Monitoring of Measurable Residual Disease and Chimerism By NGS in Myelodysplastic Syndrome after Allogenic STEM Cell Transplant

Background: Minimal Residual Disease (MRD) and chimerism monitoring in patients with Myelodysplastic Syndrome (MDS) is essential to track and quantify the proportion of donor and recipient cells to assess engraftment and treatment efficacy. Next Generation Sequencing (NGS) is rapidly evolving, can identify several somatic mutations simultaneously, quantifies allele burden, and is a suitable technology for this task. Traditionally its main limitations have been high single base error rates, which limited the sensibility to 0.1-1% Variant Allele Frequency (VAF). However, sensitivities up to 10 -4 VAF can be achieved by applying novel ultrasensitive personalized sequencing techniques. Aims: This study explores the applicability of PhasedSNP, a deep sequencing approach that quantifies chimerism in parallel to MRD in MDS patients after Allogenic Stem Cell Transplantation (ASCT). Methods: We included 24 patients older than 18 years who underwent ASCT between 2015 and 2022 at four third-level hospitals. We excluded patients with missing follow-up due to procedure-related mortality or relapse before day 100 and patients with unavailable samples. Fifty-three post-transplant samples were sequenced (six at day +30; two at +60; 21 at +100; 21 at +180, and three at day +360). Seven additional pre-transplant samples were included to confirm the donor and receptor signal switch. The genomic DNA of the donor and receptor was sequenced with an in-house PhasedSNP panel that covers 58 regions with paired polymorphisms in less than 15bp. Receptor DNA was also sequenced with a 42-gene panel (Ion Torrent TM) to identify somatic mutations used as biomarkers in follow-up samples to quantify MRD as previously described in ( Onecha E. et al. Haematologica 2019). Briefly, an amplicon-multiplexed mini-panel was defined for every patient to detect the selected MRD biomarkers and donor/receptor phased SNPs identified at diagnosis. The mini-panel included molecular-tagged primer pairs to amplify every selected marker (PhasedSNPs and somatic mutations) in three biological replicates. Final libraries were sequenced on the Ion S5 System platform with a median coverage of 211,190 reads per amplicon. A median of 558 ng of genomic DNA (range 73.44 - 858.6 ng) was sequenced in follow-up cases. Results: After excluding potential CHIP and Germline mutations, the most frequently mutated genes in the cohort were STAG2 (21%), SETBP1TP53RUNX1 andETV6 (16% each one). The baseline genotyping permitted to identify at least one somatic MRD biomarker in 79% of the patients (19/24), and 50% (12/24) presented more than one somatic mutation. MRD could be calculated for 42 of 53 samples. Thirteen patients presented sample at day +180 and clinical information. Four of them progressed, being three of them MRD positive. At this time-point the sensitivity of the test was 75% and the negative predictive value of 86%. The baseline PhasedSNP panel identified chimerism biomarkers (donor and receptor) for all patients. The PhasedSNP chimerism test presented a dynamic detection range below 10 -5 in serial dilutions. The test was positive for 48/53 samples using a threshold of 10 -4, with an average signal of 7·10 -3 (range 2·10 -5 to 4·10 -2). The correlation between PhasedSNP chimerism and MRD was high (R=0.921, p&amp;lt;0.001). However, the chimerism signal was consistently above the MRD signal, most likely due to the detection of healthy receptor cells with the PhasedSNP test. This can be seen in the two examples presented in the figure, with one patient ( MDS7, Figure, top) with an equivalent signal of chimerism at days +30, +100, and +180, but with MRD negativity at day +420 and two logarithms reduction in chimerism compared the highest value (day 100). Regarding the other patient, MDS13 ( Figure, bottom), chimerism and MRD dynamics evolve parallel but with more than two logarithmic differences between both values. This patient was MRD negative at day +100, but positive at day +180, and relapses one year later. Summary/Conclusion: NGS-based parallel detection of chimerism and MRD in MDS is feasible and has high applicability and sensitivity, with several advantages compared to traditional methods. Nevertheless, further research and a larger cohort is necessary to draw meaningful conclusions.

Prospective Evaluation of Measurable Residual Disease (MRD) and Sustainability of the Response in Patients with Systemic AL Amyloidosis Treated with Daratumumab

Background: Daratumumab can provide deep hematologic responses for patients with light chain (AL) amyloidosis, both through its direct anti-clonal activity and immunomodulatory effects on other cell populations in the bone marrow (BM) microenvironment. Promising efficacy in the frontline setting when combined with CyBorD (per the ANDROMEDA trial), as well as in the relapsed/refractory setting as monotherapy, has led to daratumumab becoming the first FDA-approved therapy for AL amyloidosis. Though it is administered for up to 24 cycles, the optimal duration of treatment is unclear. Dynamic monitoring of measurable residual disease (MRD) may provide insights into changes in the aberrant plasma cell (PC) clone and sustainability of the hematologic response in relation to daratumumab therapy. Aims: We sought to evaluate the rates of MRD clearance and resurgence both during and after daratumumab therapy for AL amyloidosis. Methods: MRD status was assessed for patients followed at the Boston University Amyloidosis Center, who were treated with a daratumumab-based regimen and achieved a hematologic very good partial response (hemVGPR) or complete response (hemCR) according to consensus criteria (Palladini, 2012). MRD assessments were performed by multiparametric 10-color flow cytometry of BM aspirates (sensitivity level of ≤10 -5) and repeated at 12-month intervals during follow-up. Clonal progression was defined as growth in the aberrant PC clone size of &amp;gt;1-log. Results: Between 2019 and 2023, a total of 66 patients achieved ≥hemVGPR and were tested for MRD; 43 (65%) received daratumumab monotherapy in the relapsed/refractory setting and 23 (35%) in combination with CyBorD as frontline therapy. Collectively, 48 (73%) achieved a hemCR and 18 (27%) a hemVGPR. The median age at diagnosis was 60 years (range 35-78); 19 (29%) patients were female; and 11 (17%) identified as non-white race. MRD assessment was performed once, twice or ≥3 times for 33, 18 and 15 patients, respectively. The first MRD evaluation occurred while still receiving daratumumab for 33 patients (at median 12 cycles, range 6-23); the remaining patients had their first MRD evaluation after therapy completion (median one month after, range 0-25). Of the entire cohort, 28 (42%) patients achieved MRD negativity and 38 (58%) MRD positivity (median estimated aberrant PC clone size 1.5 x 10 -4, range 1.4 x 10 -5 to 1.1 x 10 -2, representing 46.9% ± 32.8% of total PCs) at first evaluation. All but one patient with a hemVGPR had detectable MRD. Of the 23 patients who received frontline daratumumab-CyBorD (18 hemCR and 5 hemVGPR), 8 (35%) achieved MRD negativity at first evaluation; whereas 20 (47%) of the 43 patients who received daratumumab as monotherapy (30 hemCR and 13 hemVGPR) achieved MRD negativity. We surveyed MRD profiles based on the number of daratumumab treatment cycles received (Table 1) and found no apparent patterns with increasing cycles. Serial MRD monitoring was performed for 33 patients (Figure 1). Of 10 patients who continued to receive daratumumab between MRD assessments (group 1), 6 had sustained MRD negativity; 2 had persistent MRD positivity (of whom one had clonal progression); and 2 had MRD clearance (conversion from positive to negative). Of 23 patients who underwent serial MRD assessments after completing daratumumab (group 2), 9 (39%) had sustained MRD negativity; 10 (43%) had persistent MRD positivity; 2 (9%) had MRD clearance; and 2 (9%) had MRD resurgence (conversion from negative to positive), which occurred 17 and 26 months after daratumumab cessation. Clonal progression was observed in 5 of the 10 patients with persistent positivity, of whom 3 experienced a hematologic relapse. Conclusions: Our findings show that patients with AL amyloidosis can attain deep responses with daratumumab-based treatments, even to the depth of undetectable MRD. Clearance of MRD was frequent not only during treatment with daratumumab but also after completion of therapy, suggesting continuing effects on the plasma cell clone. Clonal progression after daratumumab completion was often associated with hematologic relapse. Prospective studies are needed to investigate whether daratumumab may be stopped early for those with undetectable MRD, or whether those with persistent detectable disease may benefit from extending daratumumab treatment beyond 24 cycles.

Detection of Isolated Extramedullary AML Using Next-Generation Sequencing of Cell-Free DNA

Introduction Isolated extramedullary (IEM) manifestation of AML is a recurrent event especially after allogenic hematopoietic cell transplantation (alloHCT). To date, measurable residual disease (MRD) assessment for early detection and monitoring of this difficult-to-treat patient cohort has not been established. Using cell-free DNA (cfDNA) from plasma or serum for MRD measurement shows comparable sensitivity to bone marrow mononuclear cells (BMMCs) and improved sensitivity over peripheral blood mononuclear cells (PBMCs) in medullary AML (Nakamura et al., Blood, 2019). Here, we evaluate next-generation sequencing (NGS) for MRD assessment of cfDNA in a cohort of patients with IEM AML. Methods We retrospectively collected tumor tissue and matched BMMC/PBMCs and cfDNA serum or plasma samples from IEM AML patients at our institution. BMMC/PBMCs and IEM tumor tissue were sequenced with 35- to 48-gene panels at diagnosis and relapse. Amplicon-based NGS-MRD (sensitivity 0.01%) of matched cfDNA and BMMC/PBMCs was quantified at time of IEM manifestation and in all available samples collected up to 12 months before IEM manifestation using the known mutations from IEM AML tissue. Amplicon-based NGS and bioinformatic error-correction was conducted and analyzed as previously described (Thol et al., Blood, 2018). Results We identified a cohort of 15 IEM AML patients at our institution. One patient was diagnosed with IEM AML at first diagnosis, 14 patients suffered from IEM relapse. For three patients, matched BMMC/PBMCs and cfDNA samples were collected from a second IEM AML relapse during the disease course. 15 of 18 IEM AML episodes (83%) occurred as relapse after alloHCT. 42 AML-related mutations were identified in the IEM AML tissue with a median of three mutations per patient (range 1-5). 33 of 39 mutations (85%) found in IEM relapse tissue had been already present at first diagnosis. All mutations were then evaluated in cfDNA and BMMCs at the time of the IEM manifestation by sensitive NGS-MRD analysis for all 18 IEM AML episodes. For two IEM episodes, BMMCs were not available and PBMCs were used instead. 17 of 18 (94%) cfDNA samples were NGS-MRD positive at the time of IEM manifestation, while only 8 of 18 (44%) BMMC/PBMC samples were positive. 20 of 53 mutations (38%) at first and second IEM episode could only be detected using cfDNA, 15 mutations (28%) were detected in both cfDNA and BMMC/PBMCs and only one mutation was solely found in BMMCs. 17 mutations (32%) could not be detected by either method (Figure 1). The variant allele frequency (VAF) of mutations detected by both methods was significantly higher using cfDNA with a median VAF of 2.45% (range 0.12 - 24%) compared to BMMC/PBMCs with a median VAF of 0.048% (range 0.13 - 10%; p &amp;lt; 0.01). Median VAF of mutations that were only found in cfDNA was 0.63% (range 0.017 - 39.6) and did not significantly differ from the cfDNA VAF of mutations that were found by both methods (p=0.43), indicating that these mutations represented the major clone. However, no correlation was found between IEM tumor VAF and cfDNA VAF (r=0.01; p=0.95). For ten IEM episodes from nine patients at least one cfDNA sample was available within 12 months before IEM relapse. In six IEM episodes (60%) cfDNA samples were MRD positive, one at 6 months, one at 5 months, two at 3 months and two at 2 months before IEM relapse. In four IEM episodes (40%) cfDNA samples were MRD negative, one at 10 months, one at 5 months and two at 2 months before IEM relapse. Conclusion In summary, cfDNA analysis from serum or plasma of AML patients can identify the molecular characteristics of a large proportion of patients with IEM AML. More than one third of clinically relevant mutations could only be detected using cfDNA and were missed by NGS-MRD of BMMC/PBMCs. Our data suggest that MRD monitoring from cfDNA detects IEM relapse earlier than routine monitoring from PB or BM in a significant proportion of patients.

Final Results of the AIEOP (Associazione Italiana Ematologia/Oncologia Pediatrica) AML 2013 Prospective Randomized Trial in Childhood Acute Myeloid Leukemia (AML)

Background: Treatment of children with newly diagnosed AML is based on induction therapy, followed by consolidation approaches which differ according to the group of risk patients (pts) are allocated to. In this respect, most treatment protocols stratify pts into 3 risk groups, namely standard (SR), intermediate (IR) and high-risk (HR), mainly based on the molecular/cytogenetic characterization and values of measurable residual disease (MRD) at the end of induction therapy. We report the outcomes of 371 pts with de novo AML other than acute promyelocytic leukemia (aged 0-18) enrolled in the randomized trial AIEOP AML 2013 (EudraCT:2014-000652-28). Patients and methods: pts were diagnosed and enrolled in the trial from 06/2015 to 06/2022 at 33 Centers affiliated to the AIEOP group. Main pt characteristics and criteria used for stratification are shown in Table 1. A marker of recurrent molecular lesions was detected at diagnosis for 247 cases out of the 371 enrolled (67%). Monitoring of flow-cytometry MRD at the end of the 1 st and 2 nd induction course was centrally performed in all pts but 7. The 1 st induction course was common for all pts (ICE scheme), while, then, SR pts were treated with 4 additional chemotherapy courses, all including high-dose cytarabine (HD-Ara-C). IR and HR pts were randomized to receive either a 2 nd ICE or the FLA-Liposomal Doxorubicin (L-Doxo) scheme as 2 nd induction course. IR pts were given 3 additional consolidation courses including HD-Ara-C with other agents or, in the presence of an HLA-compatible sibling, 1 consolidation course followed by allogeneic hematopoietic stem cell transplantation (HSCT). Pts of the HR group were consolidated with 2 courses of HD-Ara-C combined with other cytotoxic agents and, then, had an indication to receive HSCT from either a donor compatible for &amp;gt; 9/10 HLA loci or from an HLA-partially matched relative. Data cut-off for the analysis was March 31, 2023. Results: The proportion of pts allocated to the SR, IR and HR groups were 19% (72 pts), 23% (81 pts) and 58% (218 pts), respectively. Overall, 92% of pts obtained morphological complete remission (CR) at the end of the 2 induction courses [as compared to 87% of the previous AIEOP AML 2002 study (Pession et al. Blood 2012), p&amp;lt;0.05]. Twenty-five pts (7%) experienced a primary induction failure. Only 3 pts died during or after the 2 induction courses, while the subsequent cumulative incidence of 3-yr non-relapse mortality in continuous CR was 6.8%. Leukemia recurrence occurred in 63 pts, this leading to a 3-yr cumulative incidence of relapse of 18.9%. With a median follow-up of 4.5 yrs (range 0.8-8), the 3-yr probabilities of overall (OS) and event-free survival (EFS) were 83.9% and 68.5% (Figure 1), respectively, both values being significantly better (p&amp;lt;0.01) than those of the AIEOP AML 2002 study. The 3-yr OS of SR, IR and HR pts were 99.2%, 84.2% and 79.4%, respectively (p=0.01). The 3-yr estimate of disease-free survival (DFS) was 74.3%, with no difference among the 3 risk groups. The EFS did not differ in IR and HR randomized to receive either a 2 nd ICE or the FLA-L-Doxo scheme as second induction course. Levels of flow-cytometry MRD after the 2 nd induction course strongly influenced the probability of EFS which was 76% and 48% in pts with an MRD value &amp;lt; or &amp;gt;0.1%, respectively (p&amp;lt;0.01). Allogeneic HSCT was performed in 160 pts; in these pts, the 3-yr probabilities of OS and DFS were 87.7% and 85.1%, respectively, with no difference according to the type of donor employed. The DFS of the 10 IR pts given HSCT was 100% as compared to 72.1% of the 71 not transplanted (p=0.07). The outcome of infants treated in this study was particularly good, since their 3-yr probability of EFS was 78.3%. The 3-yr EFS of the 35 pts with FLT3-ITD and of the 75 with KMT2-A rearrangements were 57.1% and 64.7%, respectively. Conclusions: These results indicate that in children enrolled in the trial AIEOP AML 2013 the 3-yr OS and EFS overcomes 80% and approaches 70%, respectively, with a significant improvement as compared to the previous AIEOP protocol. Disease recurrence/primary resistance were the main cause of treatment failure, while the probability of DFS did not differ among the 3 different risk groups, this finding indicating that tailoring of consolidation therapy according to the risk profile was successful in improving the outcome of pts with worse prognostic characteristics. The use of FLA-L-Doxodid not offer any advantage over repeating a 2 nd ICE.

Venetoclax and Azacitidine for Molecular Relapse during First Line Intensive Chemotherapy in Patients with NPM1 Mutated or Core Binding Factor (CBF) AML. a Study from the Dataml Registry

Introduction: Molecular follow-up (FU) for AML patients (pts) with NPM1 mutation, RUNX1::RUNX1T1 or CBFB::MYH11 fusion transcripts has been established over the last ten years. Real-time quantitative PCR (qPCR) is the gold standard for the evaluation of measurable residual disease (MRD) in pts undergoing intensive chemotherapy (IC). Failure to achieve a deep molecular response is a strong predictive factor of relapse and survival and may guide post remission therapy (Ivey A, NEJM 2016). Moreover, the ELN MRD working party recommended a schedule for molecular FU and recently established a definition of molecular relapse (Heuser M, Blood 2021). However, there is no therapeutic consensus for pts with molecular relapse before overt clinical relapse. Frontline allogeneic hematopoietic cell transplantation (alloHCT), salvage IC or even waiting for morphological relapse in order to screen molecular characteristics of the relapsing disease or propose a clinical trial, may be discussed with pts. Venetoclax with azacitidine (VEN/AZA) was recently approved in unfit AML pts and demonstrated a particular efficacy in NPM1-mutated AML. In this study, we thought to describe the safety and efficacy of VEN/AZA in pts with NPM1 mutated or CBF AML in molecular relapse after first line IC. Methods: Pts of the DATAML registry with the following criteria were included in this study : AML with NPM1 mutation, RUNX1::RUNX1T1 or CBFB::MYH11 transcripts, first line IC, morphological complete remission (CR), no alloHCT in first line, regular monitoring of MRD by qPCR in bone marrow (BM) and/or blood, molecular relapse defined according to ELN2021 guidelines on two successive samples, at least one cycle of VEN/AZA. Pts with molecular relapse followed by morphological relapse before VEN/AZA or those who relapsed after alloHCT were not included. Treatment: First line IC was cytarabine 200 mg/m² d1-7 with idarubicin 9mg/m²/d1-5 or daunorubicin 90mg/m²/d1-3 in pts 18-60y or cytarabine 100 mg/m² d1-7 with idarubicin 8mg/m²/d1-5 and lomustine 200 mg/m²/d1 in pts &amp;gt; 60y. Post remission therapy was intermediate or high dose cytarabine or mini-consolidations according to age and performance status. Midostaurin was added in FLT3-mutated pts. At time of molecular relapse, pts received off label venetoclax 400 mg/d (d1-14, d1-21 or d1-28 according to centers) with no ramp-up and azacitidine 75 mg/m²/d subcutaneously (d1-5, d8-9). Antifungal/antibiotic prophylaxis and G-CSF use were not systematically recommended. Results: Twenty-two pts treated with VEN/AZAfrom 21/09/2020 to30/03/2023 were included. Their characteristics at diagnosis were: female (n= 14), median age 55y (range 27-71), de novo AML (n=21), median WBC (68 giga/L, range 2.32-339.7), NPM1 mutation (n=20), CBFB::MYH11 (n=2), FLT3 mutation (n=13). All pts achieved first CR after one cycle of induction chemotherapy. Pts received a median of three consolidation cycles. All but three pts had negative MRD or low level MRD (LL-MRD) in blood and/or BM at the end of consolidation. The median time between CR1 and molecular relapse was 9.5 months (range, 1-50). The median time between molecular relapse and first VEN/AZA cycle was 51 days. During first cycle of VEN/AZA, 12, 5 and 5 pts received 14, 21 or 28 days venetoclax, respectively; 19 were treated as out-pts, 4 received posaconazole and GCSF was used in 11 pts. 12 and 3 pts had grade 3-4 neutropenia or febrile neutropenia (FN), respectively. Only 3 pts (14%) were hospitalized for FN. The median number of VEN/AZA cycles was 2 (range 1-12). After C1+/-C2, 10 (45%) and 11 pts (55%) had undetectable or LL MRD in blood, respectively (Fig1). 20 pts were bridged to alloHCT in morphological CR after a median of 2 cycles (range, 1-4). Only one pt had a molecular progression before transplantation after 2 cycles. Two pts died, one had a molecular relapse after 7 cycles and progress rapidly to frank relapse, the other one died of post-transplant complication while in CR with undetectable MRD. All other pts remained in CR at date of last news. With a median FU from D1C1 of 13.5 months, median OS wat not reached and 1y-OS was 86% (Fig2). Conclusion: In the setting of molecular relapse, VEN/AZA is safe, prevent overt relapse, and induce a high rate of molecular response before alloHCT. Molecular relapse becomes a major therapeutic challenge. Clinical trial endpoints should include the treatment of molecular relapse as an event for RFS and EFS estimation.

Using Peripheral Blood (PB) Measurable Residual Disease (MRD) Levels to Predict &amp;lt;0.01% Bone Marrow Disease (BM uMRD4): Identification of Effective PB Targets for CLL Treatment Cessation in the Ibrutinib+Venetoclax Arm of the FLAIR Trial

CONCLUSIONS Time-limited treatments for CLL are under investigation but the optimal target for treatment cessation is not fully clear. Bone marrow (BM) measurable residual disease (MRD) is usually the most sensitive measure but would be too invasive to guide treatment in a routine setting. The iwCLL threshold of BM uMRD4 (&amp;lt;0.01%) has been demonstrated to be a powerful indicator of improved outcomes across multiple different trials and the aim of this analysis is to determine the feasibility of using PB MRD analysis to identify patients who have attained BM uMRD4. FLAIR (ISRCTN01844152) is an open-label, randomised, controlled, phase 3 trial comparing ibrutinib plus rituximab (IR) with fludarabine, cyclophosphamide and rituximab (FCR), subsequently amended to compare ibrutinib plus venetoclax (I+V) and ibrutinib alone (I) with FCR. Paired PB &amp; BM samples were scheduled at: (1) response assessment 9 months after randomization in all arms (n=1086); (2) end of treatment after 72 months in the ibrutinib-containing arms (n=137, most I/I+V participants have not reached this timepoint yet); and (3) confirmation of BM uMRD4 for initiation of planned stopping rules in participants with sustained PB uMRD4 defined as &amp;lt;0.01% PB MRD at 3 timepoints over 6 months (n=188 in the I+V arm). MRD analysis was performed using an ERIC-compliant 8-colour flow cytometry assay targeting acquisition of 2.2 million events (detection limit MRD5/0.001%). As the target could not always be met due to sample/laboratory limitations, stringent uMRD4 assessing 500 thousand leucocytes (detection limit 0.005%) was also evaluated. Table 1 shows the BM vs. PB MRD levels for different treatment arms and timepoints. The greatest discrepancy was observed in participants receiving FCR with a median 0.8log higher disease in the BM vs. PB. Participants receiving ibrutinib monotherapy had similar PB and BM MRD levels while the addition of either rituximab or venetoclax was associated with slightly higher (median &amp;lt;0.1 log) BM vs. PB MRD levels for both IR and I+V arms. The difference did not persist in the IR arm but remained during I+V treatment in some cases, with median &amp;gt;0.59 log higher BM vs. PB MRD levels in 29/182 participants achieving PB uMRD4 but with detectable BM MRD. Table 1 also shows the proportion of cases that attain BM uMRD4 according to different PB MRD thresholds. For participants with rituximab exposure in the past 3 months, BM uMRD4 was attained in 75-88% of participants with PB uMRD5, and only 43-76% of participants with stringent uMRD4. For participants with PB dMRD5 (0.001-0.01% MRD), only 14-52% achieved BM uMRD4. However, participants on I+V with either PB uMRD5 or stringent uMRD4 attained BM uMRD4 in 94-96% of cases. Planned cessation of treatment in the FLAIR trial was guided by sustained PB uMRD4, defined as 3 successive results with &amp;lt;0.01% PB disease over six months with confirmation of BM uMRD4 at the final time point. This strategy in the I+V arm is highly effective in achieving improved progression-free and overall survival compared to FCR [see related abstract]. Sustained PB uMRD4 led to BM assessments in 188 participants of which 173/188 (92%) attained BM uMRD4. High sensitivity PB MRD gave concordant results to BM MRD4 analysis in 91% of participants (172/188), while 9/188 (5%) had PB dMRD5 / BM uMRD4 (7/9 had detectable BM MRD in the range 0.002-0.007% and 2/9 had BM uMRD5/&amp;lt;0.001%) and 7/188 (4%) had PB uMRD5/stringent uMRD4 but with persistent BM dMRD4 (median 0.02% BM MRD, range 0.01-0.055%). PB MRD level correlates closely with BM MRD level but there is lower concordance at the 0.01%/MRD4 threshold after recent cessation of therapeutic antibody. PB uMRD4 is not a suitable target for treatment cessation as the majority of patients with 0.001%-0.01% PB MRD have &amp;gt;0.01% BM disease. For the identification of people attaining BM uMRD4 (&amp;lt;0.01%) on I+V treatment, sustained PB uMRD4 was &amp;gt;90% effective. For translation into MRD-guided treatment in future routine clinical practice, BM assessment may be replaced with PB MRD monitoring if the 0.001%/MRD5 threshold is applied.

Reshaping MRD Detection Strategies: Next-Generation Sequencing and High DNA Input Identify Previously Missed Measurable Residual Disease in Peripheral Blood of B-Cell Precursor Acute Lmyphoblastic Leukemia

Background: In acute lymphoblastic leukemia (ALL), measurable residual disease (MRD) is the most important prognostic factor. MRD is traditionally quantified in bone marrow aspirates (BM) using real-time quantitative polymerase chain reaction (RQ-PCR) according to EuroMRD standards. Since the emergence of modern molecular methods, it has been a continuous effort to enable MRD assessment from peripheral blood (PB). The less invasive material collection would allow closer MRD monitoring and solve technical challenges of BM aspiration, such as skewed or non-representative MRD values due to hemodilution and unequal distribution of leukemic cells. While several studies demonstrated comparable MRD values of BM and PB in T-ALL, in B-cell precursor ALL (BCP-ALL) MRD determination from PB is still a challenge. Mean MRD levels in PB are considerably lower than in BM and frequently escape detection. Additionally, paired samples show a highly variable MRD level ratio in both pediatric and adult cases (Kotrova et al, Leukemia 2020). Objective: BCP-ALL cases with known MRD positivity in the BM likely also harbor MRD positive cells in the PB, even when missed by traditional methods. With more sensitive assays, either by increased DNA input or by application of amplicon-based next generation sequencing (NGS), MRD detection from PB may improve in these cases. Methods: We retrospectively selected PB - BM sample pairs of 74 BCP-ALL patients with BM MRD positivity (43 with quantifiable MRD positivity and 31 with positivity below quantitative range) and sufficient leftover DNA from a cohort of patients treated according to GMALL protocols, where conventional RQ-PCR of clonal immunoglobuline heavy chain (IGH) VJ/DJ gene rearrangements failed to detect PB MRD. MRD had been determined by standard RQ-PCR with 1.5 µg DNA in BM and PB, respectively, according to the EuroMRD guidelines (van der Velden et al, Leukemia 2007). PB samples were re-tested for MRD with high DNA input RQ-PCR using 6.6 µg DNA and amplicon-based NGS, each using 6.6 µg DNA, as well as standard input NGS. NGS analyses of corresponding PB and BM samples were performed with the EuroClonality amplicon-based NGS assay (Brüggemann et al, Leukemia 2019). Identification and quantification of leukemia-derived clonotypes was done using ARResT/Interrogate. Results: In total, 74 BCP-ALL patients with pre/c-B-ALL (n=60) and pro-B-ALL (n=14) were included. Patient age ranged from 19 - 71 years with a median of 44.5. In all included samples (56 in first-line therapy and 18 salvage treatment), BM was MRD positive and PB was MRD negative in standard RQ-PCR at a sensitivity of at least 10 -4. To assess the effect of high DNA input alone, RQ-PCR was repeated in PB with high DNA input for 59 patients and 63 IGH VJ/DJ markers. At least one positive signal was detected in 19/59 patients (32%) and 20/63 markers (32%) (FIGURE 1A). NGS was performed for 73 PB samples and 84 markers using standard and high DNA input. With standard DNA input, MRD could be detected for 19/73 patients (26%) and 21/84 markers (25%) (FIGURE 1A). In the high input approach, MRD was detected in 36/73 patients (49%) and 40/84 markers (48%) (FIGURE 1A). A quantifiable MRD value was identified in 17 patients and 19 markers. All markers with quantifiable NGS MRD positivity in PB showed higher MRD values in the corresponding BM sample and MRD values below 10 -4 (FIGURE 1B). No correlation of MRD in paired samples could be demonstrated (Pearson correlation coefficient: 0.09) (FIGURE 1B). Conclusion: In BCP-ALL, MRD detection from PB is challenging with conventional methods. Increased DNA input and amplicon-based NGS allowed detection of MRD in a subset of PB samples that were negative in standard RQ-PCR. With identical DNA input, NGS showed a higher sensitivity than RQ-PCR and best results were achieved when high DNA input and NGS were combined, identifying MRD in nearly half of the PB samples. These results demonstrate that PB can be a valuable tool for early MRD detection in BCP-ALL when adjusting traditional MRD assessment strategies. However, in half of the samples, MRD was still missed by high input NGS. Even with assays improved for sensitivity, PB therefore cannot fully replace BM for MRD assessment in BCP-ALL yet and should rather be considered to complement BM analyses or in cases where BM is not accessible.

Flowrna in the Diagnosis of EBV-Related Lymphoproliferative Disease

Introduction Epstein-Barr (EBV) viraemia is frequently encountered in the context of haemophagocytic lymphohistiocytosis (HLH), systemic inflammation and lymphoproliferative disease (LPD). Although EBV typically infects B lymphocytes triggering both polyclonal proliferation and lymphoma, EBV can also infect T and NK cells. Understanding the phenotype of EBV-infected cells can help identify the underlying diagnosis and guide the use of appropriate targeted therapy. We have developed an EBV FlowRNA assay combining the detection of EBV-encoded small RNA (EBER) with multicolour flow cytometry (Collins, Blood, 2020). Here we present a larger case series illustrating how this assay can be used in diagnostic workup. Methods Anticoagulated blood samples were received from patients with EBV viraemia and either HLH or confirmed or suspected LPD within 36 hours of collection. Mononuclear cells were isolated by density centrifugation and one to three million cells were stained with a fixable viability marker and conjugated antibodies to cell surface markers for lymphocyte immunophenotyping. FlowRNA staining was then performed as per manufacturers' instructions (PrimeFlow RNA, Thermo Fisher), using target probe sets (Thermo Fisher) for EBER 1/2 and Beta-2-microglobulin (B2M). The sample was then acquired on a LSRFortessa X-20 cytometer and subsequent analysis performed in FlowJo version 10. Results Between February 2021 and June 2023, we received 23 adequate samples from 19 patients. A definitive EBV+ population was identified in single lymphocyte subsets from 15 samples. Significant EBV-infected subsets were identified; CD19+ B cells from 4 patients, CD56+ NK cells from 6 patients, CD4+ T cells from 1 patient and CD8+ T cells from 4 patients. All patients with EBV-infected T/NK cells had an underlying lymphoma. The frequency of infected cells detected ranged from 0.017% in a case of nodal CD8+ T cell lymphoma (figure A) to 22% in a patient with relapsed extra-nodal NK T lymphoma (ENKTL) with heavy marrow infiltration and an EBV viral load of 1x10 6 copies per ml (figure B). In 5 samples no EBER+ cells were identified despite EBV DNAemia of up 2x10 6 copies per ml. Although a small number of EBER+ events could be detected in a further two samples, the very low frequency of EBV+ cells made it impossible to confirm this was a genuine population. Discussion FlowRNA can be used to give useful clinical information with a short turnaround time. In two patients with suspected relapse of ENKTL, CD56+EBER+ cells could be detected in the peripheral blood despite no lesions being visible with imaging. The diagnosis was only later confirmed by bone marrow biopsy. Importantly, FlowRNA enables the distinction between EBV positivity in circulating tumour cells from bystander B cell reactivation. In one patient with known T cell lymphoma and EBV DNAemia, the B cells were EBER+ but tumour cells were negative confirming bystander infection. Conversely, in another patient with CD8+ nodal lymphoma, EBER+ T cells were identifiable pre and post-treatment. This technique can therefore be used to monitor therapy and has the potential to identify measurable residual disease (MRD). Clonality of EBER+ B cells can be confirmed by Kappa/Lambda staining; in two cases of EBV-related HLH, EBER detection in polyclonal B lymphocytes helped confirm EBV-related lymphoproliferation rather than underlying lymphoma. The assay can be highly sensitive, detecting very small lymphocyte populations. However, to achieve this at least 100,000 lymphocytes must be analysed. Measuring sufficient cell numbers can be challenging in the context of post-treatment lymphopenia, although using up to 50 ml of blood can increase the cell yield. Additionally, this technique can only detect EBER+ cells when present in the peripheral blood. We have noted negative FlowRNA with high EBV viral load in conditions previously associated with cell-free viral DNA including ENKTL and Hodgkin lymphoma, which represented 3/5 negative samples. FlowRNA has several significant strengths, it is highly sensitive, reproducible, has a short turnaround time and by its nature as a blood test, samples can be easily obtained. The ability to monitor low-frequency tumour cells in the blood gives potential for MRD monitoring. We are now working to validate this test for routine diagnostic use.

Interaction between Presenting Features, Co-Occurring Mutations, MRD and Induction Treatment Influences Outcome in Adults with NPM1 Mutated AML - an Analysis of 1357 Patients in the UK NCRI AML17 and AML19 Studies

Background NPM1 mutated (mut) AML is considered favourable risk unless associated with FLT3 internal tandem duplication (ITD) or adverse karyotype. However many other genetic and clinical risk factors have been identified, including high white cell count (WCC), secondary disease, co-mutations and presence of a “triple hit” genotype ( NPM1mut, FLT3 ITD and DNMT3Amut). Although alternative classification systems have been proposed, few studies have been large enough to robustly evaluate clinical and molecular subgroups within NPM1mut, and none have incorporated the effects of measurable residual disease (MRD) status or treatment intensity. Therefore, clinical decision making remains challenging and inconsistent. Here, we performed comprehensive genotyping and molecular MRD assessment in two consecutive prospective randomised studies to clarify these issues. Methods NCRI AML17 (2009-2014) and AML19 (2015-2020) were large randomised trials for younger adults with newly diagnosed AML. Induction regimens included DA +/- etoposide (ADE) and FLAG-IDA, with or without Gemtuzumab. Patients underwent sequential MRD assessment by RT-qPCR, and diagnostic DNA samples were analysed by targeted NGS. Overall survival (OS) was calculated with the Kaplan-Meier method, while cumulative incidence of relapse (CIR) considered death as a competing risk. Relapse events included MRD relapse. All reported hazard/odds ratios are from multivariable analyses including age, prior haematological malignancy, prior chemo/radiotherapy, WCC (log transformed), cytogenetic risk and mutation profile ( FLT3 ITD, DNMT3A, PTPN11, N/KRAS, TET2, IDH1, IDH2, WT1, TP53 MDS-related genes). Results 1357 patients with NPM1mutAML were identified, 888 in AML17 and 469 in AML19. 1100 patients had DNA available for panel sequencing, and 981 underwent MRD monitoring of whom 737 had an evaluable post course 2 (PC2) peripheral blood (PB) sample. Morphological remission (CR+CRi) was achieved in 1264/1357 patients (93%) and PC2 PB MRD negativity in 594/737 (81%). We confirmed the adverse impact of PB PC2 MRD positivity: 3y CIR was 65% vs 29% in those MRD- (p&amp;lt;0.001), and 3yr OS was 40% vs 79% (p&amp;lt;0.001). For PB PC2 MRD+ patients, CIR was &amp;gt;50% in all subgroups. There was a lower rate of PC2 PB MRD negativity in patients with high presenting WCC (OR 1.14, p=0.05), FLT3 ITD (OR 2.58, p&amp;lt;0.001), DNMT3Amut (OR 2.2, p&amp;lt;0.001) and WT1mut (HR 2.04, p=0.02). There was no effect of FLT3 allelic ratio, while patients with both FLT3 ITD and DNMT3A mutations had the lowest rate of MRD- (64%, Figure A). Of the 594 PC2 MRD- patients, we observed higher 3y CIR in patients with high WCC (HR 1.14, p=0.01), DNMT3Amut (HR 1.83, p=0.001), WT1mut(HR 1.96, p=0.01) and IDH1mut (HR 1.9, p=0.002), and lower CIR in patients with N/KRASmut(HR 0.53, p=0.01). Although presence of FLT3 ITD alone was not associated with CIR (HR 0.88, p=0.7), patients with both FLT3 ITD and DNMT3A mutations had 3y CIR from MRD- of 40% (HR 1.74, p=0.03). MDS-related gene mutations had no impact on achieving MRD-, nor relapse from MRD-. Considering all patients, OS was poorer with increasing age (HR 1.03, p&amp;lt;0.001), WCC (HR 1.07, p&amp;lt;0.001), adverse karyotype (HR 2.48, p=0.01), FLT3 ITD (HR 1.34, p=0.01), DNMT3Amut (HR 1.56, p&amp;lt;0.001) and WT1mut(HR 1.71, p&amp;lt;0.001). 3y OS was 52% in patients with both FLT3 ITD and DNMT3Amut, 63% with FLT3 ITD only, 67% with DNMT3A only and 75% with neither. Considering MRD- patients, only age (HR 1.02, p=0.04), DNMT3Amut(HR 1.75, p=0.007) and WT1mut (HR 1.8, p=0.048) remained associated with OS. There was no benefit to CR1 allogeneic transplant in MRD- patients (HR 0.83, 95%CI 0.51-1.34, p=0.4), including in any subgroups (heterogeneity p=0.9). Compared with other treatments, FLAG-Ida increased MRD- (87% vs 79%, p=0.009), reduced relapse from MRD- (16% vs 34%, p&amp;lt;0.001) and improved 3y OS (79% vs 63%, HR 0.52, p&amp;lt;0.001). The OS benefit of FLAG-Ida was greatest in patients with at least one of the features associated with failure to achieve MRD- and relapse from MRD- (high WCC, triple hit or WT1mut, HR 0.39 95%CI 0.26-0.58, heterogeneity p&amp;lt;0.01). Conclusion The “triple hit” ( NPM1, DNMT3A and FLT3 ITD) genotype, WT1mut and high WCC were associated with poor outcomes, due to a lower probability of achieving MRD-, and a higher relapse risk from MRD- remission. Survival was improved for patients receiving intensified induction with FLAG-Ida including patients in these high-risk groups.