Molecular measurable residual disease (MRD) assessment is not established in approximately 60% of acute myeloid leukemia (AML) patients because of the lack of suitable markers for quantitative real-time polymerase chain reaction. To overcome this limitation, we established an error-corrected next-generation sequencing (NGS) MRD approach that can be applied to any somatic gene mutation. The clinical significance of this approach was evaluated in 116 AML patients undergoing allogeneic hematopoietic cell transplantation (alloHCT) in complete morphologic remission (CR). Targeted resequencing at the time of diagnosis identified a suitable mutation in 93% of the patients, covering 24 different genes. MRD was measured in CR samples from peripheral blood or bone marrow before alloHCT and identified 12 patients with persistence of an ancestral clone (variant allele frequency [VAF] >5%). The remaining 96 patients formed the final cohort of which 45% were MRD (median VAF, 0.33%; range, 0.016%-4.91%). In competing risk analysis, cumulative incidence of relapse (CIR) was higher in MRD than in MRD patients (hazard ratio [HR], 5.58; < .001; 5-year CIR, 66% vs 17%), whereas nonrelapse mortality was not significantly different (HR, 0.60; = .47). In multivariate analysis, MRD positivity was an independent negative predictor of CIR (HR, 5.68; < .001), in addition to - and mutation status at the time of diagnosis, and of overall survival (HR, 3.0; = .004), in addition to conditioning regimen and and mutation status. In conclusion, NGS-based MRD is widely applicable to AML patients, is highly predictive of relapse and survival, and may help refine transplantation and posttransplantation management in AML patients.

Next-generation sequencing (NGS)-based measurable residual disease (MRD) monitoring in patients with acute myeloid leukemia (AML) is widely applicable and prognostic prior to allogeneic hematopoietic cell transplantation (alloHCT). We evaluated the prognostic role of clonal hematopoiesis–associated DNMT3A, TET2, and ASXL1 (DTA) and non-DTA mutations for MRD monitoring post-alloHCT to refine MRD marker selection. Of 154 patients with AML, 138 (90%) had at least one mutation at diagnosis, which were retrospectively monitored by amplicon-based error-corrected NGS on day 90 and/or day 180 post-alloHCT. MRD was detected in 34 patients on day 90 and/or day 180 (25%). The rate of MRD positivity was similar when DTA and non-DTA mutations were considered separately (17.6% vs 19.8%). DTA mutations had no prognostic impact on cumulative incidence of relapse, relapse-free survival, or overall survival in our study and were removed from further analysis. In the remaining 131 patients with at least 1 non-DTA mutation, clinical and transplantation-associated characteristics were similarly distributed between MRD-positive and MRD-negative patients. In multivariate analysis, MRD positivity was an independent adverse predictor of cumulative incidence of relapse, relapse-free survival, and overall survival but not of nonrelapse mortality. The prognostic effect was independent of different cutoffs (above limit of detection, 0.1% and 1% variant allele frequency). MRD log-reduction between diagnosis and post-alloHCT assessment had no prognostic value. MRD status post-alloHCT had the strongest impact in patients who were MRD positive prior to alloHCT. In conclusion, non-DTA mutations are prognostic NGS-MRD markers post-alloHCT, whereas the prognostic role of DTA mutations in the posttransplant setting remains open.

Background: Relapse occurs in 30-40% of AML patients undergoing allogeneic hematopoietic stem cell transplantation (alloHSCT). Detecting molecular relapse before clinical relapse offers the opportunity of early interventions (e.g. donor lymphocyte infusions, reduction of immunosuppression etc.). Next-generation sequencing (NGS)-based error-corrected sequencing approaches have shown promising results in AML patients prior to alloHSCT, which identified MRD in 45% of patients and predicted a cumulative incidence of relapse of 66% versus 17% in MRD negative patients at 5 years. However, NGS-based MRD is not well studied in patients after alloHSCT. Aim: To evaluate the prognostic impact of MRD on day 90 and day 180 after alloHSCT in AML patients in morphologic complete remission (CR) using error-corrected NGS applicable to the majority of AML patients. Patients and Methods: We quantified MRD in 138 patients who underwent myeloablative (MA, n=47) or reduced-intensity conditioned (RIC, n=91) alloHSCT for AML on day 90 and 180 after alloHSCT. All patients had at least one mutation at the time of diagnosis that was identified by NGS with a myeloid panel on the Illumina platform. Amplicon-based error-corrected sequencing and bioinformatics analysis was applied to samples on day 90 (n=133) and day 180 (n=125) after alloHSCT as described previously (Thol et al. Blood 2018). In the first approach we analysed 1-2 diagnostic mutations (=limited marker approach). In the second approach an extended marker set with (2-4) markers was used (=extended marker approach). Genomic DNA from peripheral blood (PB) was used for the majority of analyses (PB n= 394; bone marrow n=17). Cumulative incidence of relapse (CIR) and non-relapse mortality (NRM) were evaluated by competing risk analysis. Results: The median follow up time of the cohort was 5.5 years. The mean limit of detection was a variant allele frequency (VAF) of 0.012% using error correction and 0.071 when using forward/reverse read error correction. MRD positivity on day 90 and/or day 180 was detected in 22 out of 138 patients (16%) with the limited marker approach, while MRD was found in 28 patients (20.3%) with the extended marker approach. Using the limited marker approach, the 5-year CIR was 52% for MRD positive and 30% for MRD negative patients (P=0.001), while NRM was similar between both groups (Figure 1A). Overall survival (OS) was shorter in MRD positive patients compared to MRD negative patients (P=.044, Figure 1B). In multivariate analysis using variables significant in univariate analysis (P&lt;0.1), MRD remained significant for CIR (HR 3.19; CI 1.73-5.89; P&lt;0.001). Using the extended marker approach improved the prognostic power with a 5-year CIR of 58% for MRD positive and 27% for MRD negative patients (P&lt;0.001, Figure 1C) and reduced OS in MRD positive patients (P=0.001 Figure 1D) which remained significant in multivariate analysis for CIR (HR 4.75; CI 2.66-8.50; P=&lt;0.001) and OS (HR 2.56; CI 1.26-5.20; P&lt;0.009). On day 90 after alloHSCT, 26 of 133 (20%) MRD positive patients were identified with the extended marker approach, while only 2 additional MRD positive patients were identified on day 180. 9 of 26 MRD positive patients on day 90 never relapsed during the follow up period. The rate of chronic GvHD was 29% in these patients compared to 43% in MRD negative patients (P=.28). MRD was detected in 17% of patients with acute graft-versus-host-disease (aGvHD) of any grade compared to 25% in patients with no aGvHD (P=0.23). To better understand which markers may be most useful for MRD analysis we sequenced 34 available samples at relapse. In 25 patients (74%), at least one mutation persisted from diagnosis to relapse and at least one mutation was gained at relapse. Eight patients (24%) had no overlapping mutation while only one patient had no change in the molecular profile between diagnosis and relapse. Conclusion: NGS-based MRD monitoring on day 90 and 180 after alloHSCT is predictive for CIR and OS in AML patients. The discriminative power can be further improved when selecting 2-4 markers instead of a limited marker approach with only 1 to 2 markers per patient. Our results suggest that MRD from peripheral blood collected already at day 90 is prognostic for relapse and OS. Thus, day 90 NGS-based MRD monitoring from peripheral blood may become useful as a tool to tailor post-transplant care in AML patients. Figure 1 Disclosures Chaturvedi: Bayer Pharma AG, Berlin, Germany: Research Funding. Paschka:Agios: Membership on an entity's Board of Directors or advisory committees; Sunesis: Membership on an entity's Board of Directors or advisory committees; Amgen: Other: Travel expenses; Pfizer: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Takeda: Other: Travel expenses; BMS: Other: Travel expenses, Speakers Bureau; Abbvie: Other: Travel expenses; Astellas: Membership on an entity's Board of Directors or advisory committees; Astex: Membership on an entity's Board of Directors or advisory committees, Travel expenses; Otsuka: Membership on an entity's Board of Directors or advisory committees; Janssen: Other: Travel expenses; Novartis: Membership on an entity's Board of Directors or advisory committees, Other: Travel expenses, Speakers Bureau; Celgene: Membership on an entity's Board of Directors or advisory committees, Other: Travel expenses, Speakers Bureau; Jazz: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau. Bullinger:Menarini: Honoraria; Novartis: Honoraria; Pfizer: Honoraria; Sanofi: Honoraria; Seattle Genetics: Honoraria; Bayer: Other: Financing of scientific research; Hexal: Honoraria; Janssen: Honoraria; Abbvie: Honoraria; Amgen: Honoraria; Astellas: Honoraria; Bristol-Myers Squibb: Honoraria; Celgene: Honoraria; Daiichi Sankyo: Honoraria; Gilead: Honoraria; Jazz Pharmaceuticals: Honoraria. Fiedler:Amgen, Jazz Pharmaceuticals, Daiichi Sanchyo Oncology, Servier: Other: Support for meeting attendance; Amgen, Pfizer, Abbvie: Other: Support in medical writing; Amgen, Pfizer, Novartis, Jazz Pharmaceuticals, Ariad/Incyte: Membership on an entity's Board of Directors or advisory committees; Amgen: Research Funding. Krauter:Pfizer: Honoraria. Döhner:Daiichi: Honoraria; Jazz: Honoraria; Novartis: Honoraria; Celgene: Honoraria; Janssen: Honoraria; CTI Biopharma: Consultancy, Honoraria. Döhner:AROG, Bristol Myers Squibb, Pfizer: Research Funding; Celgene, Novartis, Sunesis: Honoraria, Research Funding; AbbVie, Agios, Amgen, Astellas, Astex, Celator, Janssen, Jazz, Seattle Genetics: Consultancy, Honoraria. Heuser:Bayer Pharma AG, Berlin: Research Funding; Synimmune: Research Funding.

Introduction The 2-year survival for AML patients relapsing after allogeneic hematopoietic cell transplantation (alloHCT) is &lt;20%, independent of the choice of relapse-treatment. Relapse detection in its molecular state enables early interventions and possibly prevention of hematological recurrence of the disease. The role of measurable residual disease (MRD) monitoring for risk stratification has been described for pre and post-alloHCT MRD analyses. Yet, it remains unclear, if and by which lead-time NGS assessment can detect MRD before impending relapse. We hypothesize that the functional class of mutations determines the relapse kinetics in AML after alloHCT. Methods We identified mutations present at AML relapse after alloHCT by Illumina myeloid panel sequencing covering 48 AML associated genes. Peripheral whole blood samples were retrospectively collected before hematological relapse, with a minimum of one sample per patient at three months prior to relapse and if available, additional monthly samples. Amplicon-based NGS and bioinformatics error-correction were performed on those samples as described in Thol et al. 2018. Positive MRD was defined as MRD detectable above the limit of detection. In the last step, we performed polynomic curve interpolation to model relapse dynamics. Results MRD was assessed in 75 AML patients after alloHCT using 203 AML-related mutations present at the time of relapse, corresponding to a median of 2.7 trackable mutations per patient (range 1-7). In total, 305 MRD analyses were performed from peripheral blood (median 1.5 per mutation, range 1-5) prior to relapse. VAFs measured above the limit of detection (median LOD across all targets 0.0315) ranged from 0.0048-26% (median 1.3%). In 45 of 75 patients (60%), we detected MRD in at least one sample and one marker before relapse. Of those, 23 patients (51%) were MRD positive in all markers before relapse and 22 patients (49%) were MRD positive in some, but not all markers before relapse. The majority of MRD-positive patients (30 of 45) were first detected three or fewer months before relapse, whereas 15 (33%) of 45 patients were MRD positive more than 3 months before relapse. The median time to relapse from the first MRD-positive sample to relapse was 2.9 months (range 0.6-10.2). Among the 203 mutations found in relapse, 93 (46%) were detectable by MRD monitoring before relapse while the remaining 110 markers (54%) remained undetectable prior to relapse. Of note, 88 of those 110 markers (80%) were measured only once before relapse, indicating that frequent sampling increases the likelihood of MRD detection. Genes in which mutations were found mostly MRD-positive were TET2 (6 out of 6), ASXL2 (4 out of 5), SF3B1 (4 out of 5), and RUNX1 (7 out of 9). Mutations in WT1 (1 out of 13), NRAS (1 out of 8), FLT3-ITD (9 out of 29), and PTPN11 (1 out of 5) were among the most common MRD negative mutations before relapse. To assess clonal relapse dynamics, pre-relapse samples were assigned to the monthly interval that best matched the sampling time. If MRD was measured positive at one time point, all the following monthly intervals were considered MRD-positive, whether a sample was available for that interval or not. The fraction of positive samples from all samples per time point was plotted against time to relapse and the function was approximated by fifth-order polynomials. The percentage of patients being MRD positive increased markedly with shortened distance to relapse. Thus, 29% of patients were MRD positive at 3 months, 44% at 2 months and 66% 1 month prior to relapse. Summarized by functional gene classes, mutations in tumor suppressor genes and especially signaling genes showed a higher slope and thus a shorter lead-time to relapse than mutations in epigenetic modifier genes (Figure 2). Conclusion In summary, hematologic relapse can be detected in peripheral blood in 29, 44, and 66% of patients at 3, 2, and 1 months before relapse by NGS-MRD analysis, respectively. Mutations in epigenetic modifier genes show a higher fraction of MRD positivity before relapse than other mutations. In contrast, mutations in signaling genes show a shorter lead-time to relapse. Figure 1 Figure 1. Disclosures Ganser: Celgene: Honoraria; Novartis: Honoraria; Jazz Pharmaceuticals: Honoraria. Thol: Abbvie: Honoraria; Astellas: Honoraria; Novartis: Honoraria; Pfizer: Honoraria; Jazz: Honoraria; BMS/Celgene: Honoraria, Research Funding. Heuser: BergenBio: Research Funding; Bayer Pharma AG: Research Funding; AbbVie: Membership on an entity's Board of Directors or advisory committees, Research Funding; BMS/Celgene: Membership on an entity's Board of Directors or advisory committees, Research Funding; Janssen: Honoraria; Novartis: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Pfizer: Membership on an entity's Board of Directors or advisory committees, Research Funding; Daiichi Sankyo: Membership on an entity's Board of Directors or advisory committees, Research Funding; Jazz: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Astellas: Research Funding; Tolremo: Membership on an entity's Board of Directors or advisory committees; Karyopharm: Research Funding; Roche: Membership on an entity's Board of Directors or advisory committees, Research Funding.

Introduction Selinexor is an exportin-1 (XPO1) inhibitor which forces the nuclear retention and functional activation of tumor suppressor proteins, inducing apoptosis in cancer cells. Overexpression of XPO-1 is common in many tumors, including acute myeloid leukemia (AML). A phase II study, "SAIL", of selinexor with cytarabine and idarubicin in patients with relapsed/refractory AML was conducted by Fiedler et al. showing a high remission rate. To identify molecular predictors of response and survival we evaluated the molecular mutations and their course in selinexor treated patients. Methods All 42 patients treated in the SAIL trial were eligible to participate in this translational study. The main criterion for inclusion in the present study was availability of DNA from bone marrow or peripheral blood at 3 time points: initial AML diagnosis, screening for the SAIL trial and first response assessment on day 28 of cycle 1. A custom TruSight myeloid sequencing panel was used to identify molecular mutations at diagnosis. Molecular response was defined as variant-allele frequency (VAF) &lt;1% in the follow-up sample after SAIL treatment independent of morphologic remission. Minimal residual disease (MRD) under selinexor maintenance treatment was quantified by error-corrected NGS with a limit of detection of 0.02%. Results Eighteen patients were included for whom DNA was available for all three time points. The median age was 47.5 years (29-72), median prior therapies was 3 (1-9). 13 patients had de novo and 5 secondary/therapy-related AML. ELN risk at first diagnosis was favorable in eight, intermediate in five and adverse in three patients. Only one course of SAIL treatment was administered to all patients. 8 patients achieved morphologic complete remission (CR) or CR with incomplete hematologic recovery (CRi). 13 patients proceeded to allogeneic hematopoietic cell transplantation (alloHCT) or donor lymphocyte infusion. The median overall survival was 0.69 years. The molecular profile showed a predominance of secondary AML-type mutations. No clear pattern was found between mutation status and morphologic CR or CRi (Figure 1). Molecular response to the SAIL induction treatment was found in 6 of 14 patients who had a molecular marker. Mutations in FLT3 (FLT3-TKD=1, FLT3-ITD=2), SF3B1 and TP53 were associated with molecular response, whereas mutations in GATA2, CUX1, TET2, BCOR, DNMT3A, RAD21, ASXL1, SRSF2, and WT1 were associated with resistance. When comparing the molecular characteristics of patients achieving CR/CRi (n=8) and all other patients (n=10), a trend to achieve CR was observed among patients with NPM1 mutations (P=0.094), whereas mutations in ASXL1 (P=0.09) and SRSF2 (P=0.09) were associated with refractoriness. One of the responding patients received selinexor as maintenance therapy for four years. The patient was diagnosed with de novo AML with normal cytogenetics, with SF3B1 and SRSF2 mutations. The patient received an HLA-identical transplant after myeloablative conditioning, but relapsed 6 years after alloHCT. One cycle of selinexor/chemotherapy was administered and the patient achieved CR. The patient continued selinexor maintenance treatment with 60 mg selinexor twice a week. SF3B1 and SRSF2 mutations were still present at the time of relapse and declined under SAIL treatment (Figure 2). The patient received one course of DLI (1x10 7CD3 +), which was tolerated well without signs of GvHD. MRD remained detectable 17 days after DLI. At 30 days after DLI treatment both MRD markers were negative. Under continued selinexor maintenance treatment MRD remained negative until last follow-up at 4.9 years after SAIL treatment. The patient tolerated selinexor well with short-term nausea and dysgeusia after selinexor intake. Selinexor maintenance treatment was stopped 4 years after SAIL treatment and the patient remains in CR 14 months after the end of maintenance. Conclusion In this small series, we found a correlation between FLT3, TP53 and SF3B1 mutation status and molecular response to selinexor/chemotherapy (SAIL). NPM1 mutations were associated with morphologic response to SAIL by trend. Finally, selinexor maintenance may have contributed to long-term disease control in a patient with relapsed AML, and long term therapy with selinexor is feasible. Figure 1 Figure 1. Disclosures Fiedler: Servier: Consultancy, Other: Meeting attendance, Preparation of information material; Stemline: Consultancy; Daiichi Sanyko: Consultancy, Other: Meeting attendance, Preparation of information material; Pfizer: Consultancy, Honoraria, Research Funding; Novartis: Honoraria; MorphoSys: Consultancy, Honoraria; Jazz: Consultancy, Honoraria, Other: Meeting attendance, Preparation of information material; Celgene: Consultancy, Honoraria; Ariad/Incyte: Honoraria; Amgen: Consultancy, Honoraria, Other: Meeting attendance, Preparation of information material, Patents & Royalties, Research Funding; Abbvie: Consultancy, Honoraria, Other: Meeting attendance, Preparation of information material. Modemann: Servier: Honoraria, Other: Travel accomodation; Incyte: Other: Travel accomodation; Gilead: Other: Travel accomodation; Jazz Pharmaceuticals: Other: Travel accomodation; Novartis: Other: Travel accomodation; Teva: Other: Travel accomodation; Pfizer: Other: Travel accomodation; Amgen: Other: Travel accomodation; Daiichi Sankyo: Research Funding; Abbvie: Honoraria, Other: Travel accomodation. Bokemeyer: Merck KGaA: Honoraria; Sanofi: Consultancy, Honoraria, Other: Travel accomodation; Roche: Honoraria, Research Funding; Bayer: Honoraria, Research Funding; BMS: Honoraria, Other: Travel accomodation, Research Funding; AstraZeneca: Honoraria, Research Funding; Merck Sharp Dohme: Consultancy, Honoraria; Lilly/ImClone: Consultancy; Merck Serono: Consultancy, Other: Travel accomodation ; Bayer Schering Pharma: Consultancy; GSO: Consultancy; AOK Health insurance: Consultancy; Abbvie: Research Funding; ADC Therapeutics: Research Funding; Agile Therapeutics: Research Funding; Alexion Pharmaceuticals: Research Funding; Amgen: Research Funding; Apellis Pharmaceuticals: Research Funding; Astellas: Research Funding; BerGenBio: Research Funding; Blueprint Medicine: Research Funding; Boehringer Ingelheim: Research Funding; Celgene: Research Funding; Daiichi Sankyo: Research Funding; Eisai: Research Funding; Gilead Sciences: Research Funding; Gylcotope GmbH: Research Funding; GlaxoSmithKline: Research Funding; Inside: Research Funding; IO Biotech: Research Funding; Isofol Medical: Research Funding; Janssen-Cilag: Research Funding; Karyopharm Therapeutics: Research Funding; Lilly: Research Funding; Millenium: Research Funding; MSD: Research Funding; Nektar: Research Funding; Rafael Pharmaceuticals: Research Funding; Springworks Therapeutics: Research Funding; Taiho Pharmaceutical: Research Funding; Pfizer: Other. Ganser: Celgene: Honoraria; Novartis: Honoraria; Jazz Pharmaceuticals: Honoraria. Thol: Astellas: Honoraria; Jazz: Honoraria; Novartis: Honoraria; Pfizer: Honoraria; BMS/Celgene: Honoraria, Research Funding; Abbvie: Honoraria. Heuser: Karyopharm: Research Funding; AbbVie: Membership on an entity's Board of Directors or advisory committees, Research Funding; Astellas: Research Funding; Roche: Membership on an entity's Board of Directors or advisory committees, Research Funding; Pfizer: Membership on an entity's Board of Directors or advisory committees, Research Funding; Tolremo: Membership on an entity's Board of Directors or advisory committees; Jazz: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Janssen: Honoraria; Novartis: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Bayer Pharma AG: Research Funding; BMS/Celgene: Membership on an entity's Board of Directors or advisory committees, Research Funding; BergenBio: Research Funding; Daiichi Sankyo: Membership on an entity's Board of Directors or advisory committees, Research Funding. OffLabel Disclosure: Selinexor in patients with relapsed or refractory AML