Clonal hematopoiesis of indeterminate potential (CHIP) has been well-characterized in patients receiving chemotherapy and hematopoietic cell transplantation. However, its immunologic relevance and potential role in modulating chimeric antigen receptor T-cell (CAR-T) therapy-related toxicities, inflammation, and clinical outcomes remains incompletely defined. In this exploratory study of 104 CAR-T recipients, we investigated the prognostic impact of pre-existing CHIP clones on toxicity and survival, and examined CHIP-associated inflammatory proteomic signatures leveraging longitudinal serum samples. Overall CHIP status was not associated with inflammatory toxicities, outcomes, or systemic inflammatory profiles. Analysis of clonal dynamics revealed TP53- and ASXL1-mutated clones to be the dominant expanding CHIP clones post-infusion, whereas DNMT3A- and PPM1D-mutated clones showed reduced clonal abundance over time. Notably, TP53-mutated CHIP was linked to lower platelet and hemoglobin levels, a higher baseline CAR-HEMATOTOX score, inferior clinical outcomes, and a distinct inflammatory signature. These findings identify TP53-mutated CHIP in CAR-T-treated patients as a high-risk CHIP genotype compared with other CHIP mutations. Importantly, patients who developed treatment-emergent myeloid neoplasms after CAR T-cell therapy exhibited distinct patterns of clonal expansion and inflammatory profiles. Together, these findings support a risk-adapted approach prioritizing longitudinal monitoring of TP53-mutated CHIP, especially in patients with high CAR-HEMATOTOX scores who develop cytopenias.

Acute myeloid leukemia (AML) is a complex disease characterized by diverse molecular pathogenesis. Genetic alterations, including germline and somatic variants in the DEAD box helicase 41 gene ( DDX41) located on chromosome 5 play an increasingly recognized role. Recent reports indicate that 5% of intensively treated adult AML patients harbor DDX41 germline mutations ( DDX41MutGL), and their precise impact remains incompletely understood. These studies suggest that DDX41MutGL may define a distinct biological subgroup, associated with e.g. older age, male gender, low blast, and low white blood cell count (WBC). To further elucidate the role of DDX41 in AML, we performed a retrospective analysis of 906 unselected adult AML patients from the AML Cooperative Group (AMLCG) registry (2015-2022), by targeted sequencing. As DDX41MutGL are typically “null mutations”, leading to reduced DDX41 expression, we additionally investigated whether DDX41 gene expression correlates or resembles the observed germline phenotype. Our analysis encompassed >1000 independent gene expression profiles (GSE37642, GSE14468, and GSE106291) of intensively treated adult AML patients. We identified a sub-cohort with low DDX41 ( DDX41-low) expression and re-analyzed them with next-generation sequencing to detect DDX41MutGL. Additionally, we correlated gene expression data with 198 DNA methylation profiles (from patients who had undergone both analyses) to identify potential epigenetic mechanisms underlying DDX41-low expression. Among the 906 patients (median age 61 years; range 18-98 years), we identified 11 unrelated individuals with suspected DDX41MutGL (VAF > 40%). Notably, the overall frequency of DDX41MutGL in the German unselected AML patient population was merely 1%, considerably lower than previously reported (p<0.0001 in comparison to Duployez et al. 2022). Characteristically, DDX41MutGL patients in this cohort were mostly male (73%), with a median age of 67 years displaying low WBC (average 1,3G/l) and a normal karyotype (80%) at initial diagnosis. Remarkably, our analysis of independent large gene expression cohorts revealed a pattern of phenotypic association in patients with decreased DDX41 expression ( DDX41-low) closely resembling those with DDX41MutGL. These associations were consistent across different datasets and included e.g. older age, low WBC, and low blast count. Furthermore, DDX41-low patients had poor overall survival. The DDX41-low subgroup constituted almost 10% of all AML patients, surpassing the reported frequencies of DDX41MutGL. In an exploratory pilot study, we screened 48 patients exhibiting the lowest DDX41 gene expression by sequencing the coding regions for DDX41 mutations but found none, suggesting alternative mechanisms, such as copy number changes, non-coding alterations or aberrant DNA methylation patterns that may replicate the phenotypic effects associated with DDX41MutGL. To further elucidate this mechanism, we correlated the gene expression of DDX41 with all DNA methylation loci (CpG sites covered by the EPIC array) on chromosome 5 using Spearman correlation analysis (GSE106291). We plotted the correlations against the sorted chromosome length, identifying a peak at a specific location corresponding to the PCDH (Protocadherin) cluster (Figure). Thus, DDX41-low was associated with reduced methylation at the PCDH loci and linked to higher PCDH gene expression. Across several data sets, we confirmed the association between higher PCDH cluster gene expression and low DDX41 expression. In summary, our study reveals that the frequency of DDX41MutGL in an unselected population of German AML patients is considerably lower than previously reported. Additionally, we found that apart from DDX41MutGL, DDX41-low exhibits a comparable clinical profile and is linked to specific methylation and gene expression patterns, with a notable emphasis on the PCDH complex located on chromosome 5. Understanding the functional implications of PCDH genes and their interaction with DDX41 in AML may significantly advance our knowledge of AML pathogenesis. Gaining insights into DDX41 alterations may open avenues for personalized therapeutic approaches and further prognostic stratification for AML patients with distinct molecular characteristics.

Introduction: Clonal hematopoiesis of indeterminate potential (CHiP) represents a myeloid precursor lesion described by the presence of clonal hematopoiesis without signs of neoplasia and cytopenia. Previous studies have highlighted its high frequency in lymphoma and multiple myeloma (MM) patients treated with chimeric antigen receptor T-cell (CAR-T) therapy – with a reported CHiP prevalence of 33-56% before treatment initiation. CHiP has been extensively studied in the context of chemotherapy and hematopoietic cell transplantation (HCT). However, its immunologic impact and potential influence on CAR-T-associated toxicities, inflammation, and treatment outcomes remain poorly defined. Methods: This observational study aimed (i) to investigate the impact of pre-existing CHiP clones on CAR-T-associated toxicity and treatment outcomes, and (ii) to explore correlations between CHiP mutations and the inflammatory serum proteome that drives immune-related toxicities. Outcome data and toxicity were analyzed from 65 large B-cell lymphoma, 13 mantle-cell lymphoma, 19 MM, and 2 follicular lymphoma patients treated with CD19- or BCMA CAR-T constructs. Peripheral blood mononuclear cells (PBMCs) and serum samples were collected before and after CAR-T infusion. Targeted next-generation sequencing for CHiP mutations was performed on 99 PBMC samples. Proteomic profiling was conducted using the 92-plex proximity extension assay on the Olink® platform (Immuno-Oncology Panel); serum samples were collected from 80 patients on days 0, 4, 14, 28, 90, 180, 360 post-infusion, censoring at disease progression. Results: The median age of the patient cohort was 64 years (range: 19-85) and the median follow up was 23.3 months (mo). Patients had received a median of three prior treatment lines (IQR=2-4), including 36.4% who had undergone autologous HCT. Sequencing of the total cohort identified CHiP-related mutations in 37 patients (37.4%, VAF≥1%) prior to CAR-T cell infusion. The most frequently mutated gene was DNMT3A (n=18), followed by TP53 and ASXL1 (n=7), PPM1D (n=5), TET2 and SF3B1 (n=2), and NRAS and BRAF (n=1). Among CHiP patients, 28 had a single mutation, 8 had two mutations, and 1 patient had three mutations. The incidence of grade ≥3 CRS and ICANS was comparable between CHiP and non-CHiP patients (CRS: 14% vs 15%, p>0.9; ICANS: 14% vs 13%, p>0.9). Early and late grade ≥3 ICAHT occurred in 22% vs 23% (p>0.9) and 24% vs 37% (p=0.27) of CHiP vs non-CHiP patients. Neutrophil recovery phenotypes were similar between groups, with an aplastic phenotype observed in 19% of CHiP and 18% of non-CHiP patients (p>0.9). Progression-free survival (PFS) and overall survival (OS) did not differ significantly between the two groups (median PFS: 6.4 vs 5.0 mo, p=0.58; median OS: 18.1 vs 21.9 mo, p>0.9). Longitudinal inflammatory profile of CHiP (n=30) and non-CHiP (n=50) patients was performed by Olink®. Importantly, the CHiP cohort was not characterized by a distinct immune dysregulation signature compared to the non-CHiP cohort. Accordingly, not a single serum protein differed significantly across the patient cohorts (corrected p>0.05). On subgroup analysis, patients with a TP53 CHiP mutation (n=7) were characterized at baseline by lower platelets (Plt) and hemoglobin (Hb) counts compared to all other patients independent of CHiP status (median Plt: 124 vs 178.5 e9/L, p=0.03; median Hb: 8.6 vs 10.3 g/dL, p=0.01). A baseline inflammatory signature was detected in the TP53 CHiP patients characterized by higher levels of C-reactive protein (CRP) and ferritin compared to the non-TP53 CHiP group (median CRP: 2.3 vs 0.6 mg/L, p=0.04; median ferritin: 1450 vs 331 mg/L, p=0.001). Interestingly, the Olink® analysis confirmed an inflammatory profile showing upregulation of IL-6, IL-18, PGF, Gal-9, MIC-A/B and HO-1 between days 0 and 28. Notably, one patient in the TP53 CHiP group subsequently developed a therapy related myeloid neoplasm. Conclusions: In this exploratory analysis of 99 CAR-T recipients, CHiP status was not associated with toxicity, outcomes, or systemic inflammatory profiles. These findings challenge the clinical relevance of CHiP as a biomarker for toxicity in the CAR-T setting. Notably, TP53 CHiP mutations were linked to lower platelet and hemoglobin levels and a distinct inflammatory signature, warranting further investigation. Ongoing studies aim to characterize CHiP clonal dynamics and their potential link to secondary malignancies post-CAR-T.

Clonal hematopoiesis (CH) is common in the general population and associated with various health risks, but its prevalence and clinical implications in acute myeloid leukemia (AML) long-term survivors (LTS; ≥5-year survival) are unknown. We analyzed CH in 373 AML-LTS with a median 11.6-year follow-up from diagnosis using a sensitive targeted sequencing assay based on single-molecule molecular inversion probes. CH variants were detected in 61.9% of survivors, with 26% having small-clone CH (SC-CH, variant allele frequency (VAF) < 2%) and 35.9% CH of indeterminate potential (≥2% VAF). CH was more prevalent in survivors treated with chemotherapy only (75.7%) compared to those who received allogeneic stem cell transplantation (alloSCT, 54.0%) and to age group-matched healthy controls. In chemotherapy-treated survivors, CH prevalence increased with age, whereas in alloSCT recipients, it most closely associated with hematopoietic age (i.e., the sum of donor age and time since transplantation). The variant spectrum also differed by treatment, with TP53 and PPM1D variants being more common in the chemotherapy group. CH variants ≥10% VAF associated with increased risks of diabetes in alloSCT recipients and secondary neoplasms in chemotherapy-treated survivors. This study provides insights into the high prevalence and potential clinical relevance of CH in AML-LTS.

Whether patients with acute myeloid leukemia (AML) harboring Nucleophosmin mutations (NPM1mut) with measurable residual disease (MRD) should undergo allogeneic stem cell transplantation (alloSCT) in complete remission (CR) remains subject of debate. This study aimed to assess whether the presence of bone marrow (BM) NPM1mut MRD, detected using a RT-qPCR assay with a sensitivity of 10-5, could influence the benefit derived from alloSCT. Data from four German transplantation centers were analyzed including 174 AML NPM1mut patients who underwent a first alloSCT between 2011-2022. Among 122 patients transplanted in complete remission (CR), pre-alloSCT MRD was positive in 54%. After alloSCT, the cumulative rate of BM MRD negativity increased from 65% by day +30 to 73% by day +100, with FLT3-ITD and ELN risk profile significantly impacting on MRD conversion rate at day +30. No significant difference in leukemia-free survival (LFS) and overall survival (OS) based on pre-transplant MRD status (3y LFS MRD+ 60% vs MRD- 74%, HR 1.5, p=0.28; 3y OS MRD+ 68% vs MRD- 78%, HR 1.42, p=0.39) was observed. Outcomes between MRD persistence and molecular relapse did not differ (p=0.8). Whereas adverse molecular risk features (HR 4.69, p=0.003) and relapsed/refractory disease (HR 2.83/3.59, p=0.005/0.001) were associated with unfavorable prognosis, administration of post-transplant maintenance improved survival in multivariable analysis (HR 0.48, p=0.06). Our findings suggest that in patients with NPM1mut AML MRD positivity as assessed per qPCR at time of transplant does not impact posttransplant outcomes of NPM1mut AML.

We performed a questionnaire-based cross-sectional study to analyze Acute Myeloid Leukemia (AML) long-term survivor (LTS) outcomes, including psychosocial well-being and somatic health status. Four-hundred-twenty-seven former AML patients participated (response rate, 63%) ≥5 years[y] and up to 18.6 y past their leukemia diagnosis (median, 11.3 y). Median age at study participation was 61 y (range 28y–93y), 23% had experienced disease relapse, and 63% had received allogeneic hematopoietic stem cell transplantation (alloHSCT). Overall, quality of life (QoL) and general life satisfaction (gLS) summary scores were higher in AML LTS (p < 0.001) compared to age-/sex-matched reference cohorts, although differences were small and likely not clinically relevant. However, we identified subgroups of survivors reporting impaired QoL (27%), gLS (13%) and health-related life satisfaction (hrLS; 17%). Using multivariable regression models, we identified predisposing and protective factors for each of these outcomes. Treatment with alloHSCT did not adversely impact QoL, gLS, or hrLS. In summary, global QoL and LS in AML LTS are comparable to the general population, irrespective of treatment modality, although some survivors report clinically significant impairment of global QoL and/or in specific domains. We identified factors associated with impaired outcomes (e.g., comorbidity and fatigue), delineating a subgroup of survivors with unmet needs ≥5 y after their AML diagnosis.

Preclinical cancer research requires robust model systems, especially for poor prognosis entities like acute myeloid leukemia (AML), a highly aggressive blood cancer. Here, primary tumor cells from 137 AML patients of all age groups were transplanted into immune compromised mice to generate patient-derived xenografts (PDX). From these, 23 models enable robust, virtually endless serial re-transplantation and are amenable to lentiviral genetic engineering (*PDX AML models). These models primarily originate from patients with highly aggressive, relapsed disease. Comprehensive genomic, transcriptomic, and epigenomic analyses confirmed that they replicate primary AML biology more faithfully than conventional cell lines. Notably, *PDX AML models include AML subgroups that are underrepresented or absent in existing model systems, such as cytogenetically normal or IDH1/2 -mutant AML. They withstand freeze-thaw cycles, making them suitable for broad distribution and reproducibility across research institutions. Luciferase-based in vivo imaging enables real-time monitoring of tumor progression and treatment responses in preclinical trials. Surprisingly, long-term treatment, including repeated cytarabine therapy over a period of one year, showed a gradual reduction in leukemia cell proliferation, which decreased continuously after each treatment block. Collectively, our *PDX models represent a robust, versatile, and relevant platform that holds great promise to accelerate translational research for the benefit of cancer patients. ![Figure][1] Key Points ### Competing Interest Statement TH: Travel support: Jazz Pharmaceuticals; Participation on Advisory Board: Servier and Jazz Pharmaceuticals; honoraria for speakers: Astellas Pharma. All other authors declare no competing interest. European Research Council, https://ror.org/0472cxd90, 681524 Deutsche Forschungsgemeinschaft, https://ror.org/018mejw64, 537701335, SFB 1709/1 2025 - 533056198 German Cancer Aid, https://ror.org/01wxdd722, Mildred Scheel Professorship Deutsche José Carreras Leukämie-Stiftung, https://ror.org/00826gz80, DJCLS 15 R/2021, DJCLS 02 R/2023 Bettina Bräu Stiftung Dr. Helmut Legerlotz Stiftung [1]: pending:yes

Background: Acute myeloid leukemia (AML) is a heterogenous malignancy and efficient treatment strategies for high-risk patients are still lacking. To facilitate preclinical and translational leukemia research, e.g. to test novel therapeutics in vivo, we generate patient-derived xenograft (PDX) samples. We had transplanted more than 100 primary adult AML samples into immune-compromised NSG mice. Furthermore, we received PDX samples primografted in other labs of pediatric and adult patients. However, only around 20% of primary samples (i.e. “high score samples”) show a robust and reliable serial engraftment and can be genetically modified, facilitating repetitive, reproducible and convenient in vivo experiments. Aims: (i) Identifying factors influencing reliable serial engraftment; (ii) Characterizing high score samples functionally and genetically; (iii) Performing in vivo (therapy) trials. Methods: We generated 23 high score AML PDX samples characterized by (i) a serial, fast, reliable and systemic engraftment, and (ii) the capacity to be genetically engineered. These samples were characterized by DNA panel sequencing (seq), whole exome seq, low coverage whole genome seq, RNA seq, methylation profiling, karyotyping, and immunophenotyping. Furthermore, samples were transplanted repetitively, and capacity for serial engraftment was analyzed. Last, samples were used for diverse in vivo trials, e.g. long-term chemotherapy trials. Results: High score samples originated mainly from relapsed AML cases (18/23, p<0.05). Overall survival (OS) of patients whose cells yielded high score samples was dramatically lower compared to OS of patients whose cells did not engraft or meet the criteria of high score samples (p<0.01). Analysis of AML-related mutations, gene fusions, translocations, copy number alterations and immunophenotype revealed that high score AML PDX samples resembled primary patient cells of both, initial diagnosis and relapsed disease, and - in contrast to established AML cell lines - covered many different genetic and genomic alterations. Within the WHO classification of 2022, most samples belonged to one of the three groups “AML with NPM1 mutation” (n=8), “AML with KMT2A rearrangement” (n=7), or “AML, myelodysplasia-related” (n=6). High score samples were serially transplanted into recipient mice, with up to fifteen repetitive transplantations. Importantly, we did not lose a sample in serial re-transplantations, indicating that leukemia initiating cells proliferated within the murine niche for many months (median 412 days). On the contrary, under in vitro conditions, cells could be kept for some days to weeks, but ultimately died. With every engraftment, PDX cells can be amplified by a factor 30-fold or higher, depending on the sample, allowing the production of indefinite numbers of PDX cells. Engraftment capacity and engraftment time were influenced by several factors; thawed PDX cells and injection of cell numbers below 500,000 cells had a reduced engraftment rate and a longer passaging time compared to freshly isolated cells or higher cells numbers. Serial re-passaging or expression of transgenes did, however, not influence engraftment. While murine gender influenced engraftment capacity of some samples, with male mice being less supportive, mouse age did not, and even older mice with more than 20 weeks of age allowed reliable engraftment. High score AML PDX samples were further used in preclinical in vivo therapy trials. Stable luciferase expression allowed sensitive disease monitoring, facilitating real-time analysis of drug effects and of growth kinetics before and after treatment. Bioluminescence imaging revealed that azacitidine, in contrast to cytarabine, had a delayed effect on tumor burden. Both drugs, however, showed a sustained effect on the cells even after stop of long-term therapy, indicated by a reduced growth rate after treatment. Conclusion and Outlook: High score AML PDX models represent highly aggressive primary patients' cells. By serial engraftment and genetic engineering, we can produce indefinite numbers of these cells, which represent a valuable and unique tool for sophisticated molecular and functional studies. Our well characterized AML PDX cohort allows repetitive and reproducible preclinical trials, and luciferase expression facilitates reliable monitoring of long-term therapy trials.

The outcome of patients with acute myeloid leukemia (AML) worsens with increasing age. Dichotomization into “younger” and “older” patients is clinically routine and often dictates treatment options. We aimed to delineate whether molecular genetic features and/or outcome measures support assorting patient populations by age, including division into “younger” and “older” groups. We analyzed 2823 adult AML patients enrolled onto frontline chemotherapy-based clinical protocols of two cooperative study groups from USA and Germany who were profiled molecularly via targeted sequencing platforms. Frequencies of gene mutations and cytogenetic findings were depicted in 5-year age increments. Clinical outcomes of 2756 AML patients were analyzed with respect to molecular features, genetic-risk groups and age. Age-associated distributions of gene mutations and cytogenetic abnormalities were similar in both cohorts. There was almost linear shortening of overall survival with increasing age among all patients (P < 0.001) and within 2022 European LeukemiaNet-defined genetic-risk groups, with survival decreasing as age increased (favorable-risk, P < 0.001; intermediate-risk, P < 0.001; adverse-risk, P < 0.001). Although mutational profiles and outcomes of the youngest patients differed from those of older patients, there was no age cut-off identifying “younger” and “older” patients. These findings support more age-associated flexibility for drug approval and trial eligibility.

Clinical outcome of patients with acute myeloid leukemia (AML) is associated with demographic and genetic features. Although the associations of acquired genetic alterations with patients’ sex have been recently analyzed, their impact on outcome of female and male patients has not yet been comprehensively assessed. We performed mutational profiling, cytogenetic and outcome analyses in 1726 adults with AML (749 female and 977 male) treated on frontline Alliance for Clinical Trials in Oncology protocols. A validation cohort comprised 465 women and 489 men treated on frontline protocols of the German AML Cooperative Group. Compared with men, women more often had normal karyotype, FLT3 -ITD, DNMT3A , NPM1 and WT1 mutations and less often complex karyotype, ASXL1 , SRSF2 , U2AF1 , RUNX1 , or KIT mutations. More women were in the 2022 European LeukemiaNet intermediate-risk group and more men in adverse-risk group. We found sex differences in co-occurring mutation patterns and prognostic impact of select genetic alterations. The mutation-associated splicing events and gene-expression profiles also differed between sexes. In patients aged <60 years, SF3B1 mutations were male-specific adverse outcome prognosticators. We conclude that sex differences in AML-associated genetic alterations and mutation-specific differential splicing events highlight the importance of patients’ sex in analyses of AML biology and prognostication.

Despite recent refinements in the diagnostic and prognostic assessment of CEBPA mutations in AML, several questions remain open, i.e. implications of different types of basic region leucin zipper (bZIP) mutations, the role of co-mutations and the allelic state. Using pooled primary data analysis on 1010 CEBPA-mutant adult AML patients, a comparison was performed taking into account the type of mutation (bZIP: either typical in-frame insertion/deletion (InDel) mutations (bZIPInDel), frameshift InDel or nonsense mutations inducing translational stop (bZIPSTOP) or single base-pair missense alterations (bZIPms), and transcription activation domain (TAD) mutations) and the allelic state (single (smCEBPA) vs. double mutant (dmCEBPA)). Only bZIPInDel patients had significantly higher rates of complete remission and longer relapse free and overall survival (OS) compared with all other CEBPA-mutant subgroups. Moreover, co-mutations in bZIPInDel patients (e.g. GATA2, FLT3, WT1 as well as ELN2022 adverse risk aberrations) had no independent impact on OS, whereas in non-bZIPInDel patients, grouping according to ELN2022 recommendations added significant prognostic information. In conclusion, these results demonstrate bZIPInDel mutations to be the major independent determinant of outcome in CEBPA-mutant AML, thereby refining current classifications according to WHO (including all dmCEBPA and smCEBPA bZIP) as well as ELN2022 and ICC recommendations (including CEBPA bZIPms).

The revised 2022 European LeukemiaNet (ELN) AML risk stratification system requires validation in large, homogeneously treated cohorts. We studied 1118 newly diagnosed AML patients (median age, 58 years; range, 18–86 years) who received cytarabine-based induction chemotherapy between 1999 and 2012 and compared ELN-2022 to the previous ELN-2017 risk classification. Key findings were validated in a cohort of 1160 mostly younger patients. ELN-2022 reclassified 15% of patients, 3% into more favorable, and 12% into more adverse risk groups. This was mainly driven by patients reclassified from intermediate- to adverse-risk based on additional myelodysplasia-related mutations being included as adverse-risk markers. These patients ( n = 79) had significantly better outcomes than patients with other adverse-risk genotypes (5-year OS, 26% vs. 12%) and resembled the remaining intermediate-risk group. Overall, time-dependent ROC curves and Harrel’s C-index controlling for age, sex, and AML type (de novo vs. sAML/tAML) show slightly worse prognostic discrimination of ELN-2022 compared to ELN-2017 for OS. Further refinement of ELN-2022 without including additional genetic markers is possible, in particular by recognizing TP53 -mutated patients with complex karyotypes as “very adverse”. In summary, the ELN-2022 risk classification identifies a larger group of adverse-risk patients at the cost of slightly reduced prognostic accuracy compared to ELN-2017.

Monitoring disease response after intensive chemotherapy for acute myeloid leukemia (AML) currently requires invasive bone marrow biopsies, imposing a significant burden on patients. In contrast, cell-free tumor DNA (ctDNA) in peripheral blood, carrying tumor-specific mutations, offers a less-invasive assessment of residual disease. However, the relationship between ctDNA levels and bone marrow blast kinetics remains unclear. We explored this in 10 AML patients with NPM1 and IDH2 mutations undergoing initial chemotherapy. Comparison of mathematical mixed-effect models showed that (1) inclusion of blast cell death in the bone marrow, (2) transition of ctDNA to peripheral blood, and (3) ctDNA decay in peripheral blood describes kinetics of blast cells and ctDNA best. The fitted model allows prediction of residual bone marrow blast content from ctDNA, and its scaling factor, representing clonal heterogeneity, correlates with relapse risk. Our study provides precise insights into blast and ctDNA kinetics, offering novel avenues for AML disease monitoring.