Minimal residual disease levels assessed by NPM1 mutation–specific RQ-PCR provide important prognostic information in AML

Blood ◽  
2009 ◽  
Vol 114 (11) ◽  
pp. 2220-2231 ◽  
Author(s):  
Susanne Schnittger ◽  
Wolfgang Kern ◽  
Claudia Tschulik ◽  
Tamara Weiss ◽  
Frank Dicker ◽  
...  

Abstract Nucleophosmin (NPM1)–mutated acute myeloid leukemia (AML), which is recognized as a provisional entity in the World Health Organization 2008 classification of myeloid neoplasms, accounts for 30% of AML. We analyzed 1227 diagnostic and follow-up samples in 252 NPM1-mutated AML patients with 17 different NPM1 mutation–specific real-time quantitative polymerase chain reaction (RQ-PCR) assays. Paired diagnostic/relapse samples of 84 patients revealed stable NPM1 mutations in all cases, suggesting that they are pathogenetically early events and thus applicable for minimal residual disease detection. A total of 47 relapses were predictable because of an NPM1 mutation level (%NPM1/ABL1) increase of at least 1 log or in 15 cases because of NPM1 mutation levels not decreasing less than 3 log ranges. A high prognostic value of NPM1 levels was shown for 4 different intervals after therapy was initiated. Furthermore, thresholds of 0.1 and 0.01%NPM1/ABL1 during/after treatment discriminated between prognostic subgroups. Univariate analyses, including age, white blood cell count, blast count, CD34 positivity, FLT3 mutations status, FAB type, karyotype, NPM1 mutation type, and pretreatment NPM1 mutational level, showed that, besides NPM1 mutation level, only age and FLT3-LM mutation status were prognostically significant for EFS. Multivariate analysis, including age, FLT3-LM status, and NPM1 mutation level at different time points, demonstrated that NPM1 level was the most relevant prognostic factor during first-line treatment. Similar results were obtained in patients undergoing second-line chemotherapy or allogeneic stem cell transplantation.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 4672-4672
Author(s):  
Dana Dvorakova ◽  
Zdenek Racil ◽  
Ivo Palasek ◽  
Marketa Protivankova ◽  
Ivana Jeziskova ◽  
...  

Abstract Abstract 4672 Background Mutations within NPM1 gene occurs in about 60% of adult cytogenetic normal AML (CN-AML) and represent the single most frequent molecular aberration in this subgroups of patients. These mutations usually occur at exon 12 and induce most frequently a net insertion of four base pairs. Aims To examine the applicability and sensitivity of DNA-based real-time quantitative polymerase chain reaction (RQ-PCR) with mutation-specific reverse primers and common minor groove binding (MGB) probe and to evaluate whether minimal residual disease levels are of prognostic relevance in CN-AML patients with NPM1 mutations. Methods Patients were treated within different AML trials and follow-up samples of peripheral blood or bone marrow were referred to perform an RQ-PCR. Samples were analysed at diagnosis, during, and after therapy. The NPM1 mutations were A (17 pts), B (1 pt), D (2 pts) and 7 patients with individual rare types. For all cases, levels of minimal residual disease were determined by DNA-based RQ-PCR with mutation-specific reverse primer, one common forward primer and one common MGB probe. The NPM1 mutation value was normalized on the number of albumin gene copies and expressed as the number of NPM1 mutations every 106 genomic equivalents. This assay is highly specific as no wildtype NPM1 could be detected. Maximal reproducible sensitivity was 10 plasmide molecules per reaction. Results A total of 950 samples of bone marrow and/or peripheral blood from 27 patients have been analyzed. Twenty of 27 patients (74%) achieved molecular remission (MR), twenty-six of 27 patients (96%) achieved hematological remission (HR). 6 of 27 (22%) patients achieved HR without MR and one patient failed therapy. 8 of 20 patients (40%) with MR after treatment relapsed at molecular level and except one in all these patients hematological relaps occured (one patient is still in HR with bone marrow blast present, but < 5%). Considering relapsed patients, time from molecular to hematological relapse was 1 to 5 months (median: 3 months). Considering all 14 patients with HR without MR (6 pts) or with molecular relapse (8 pts), in 11 of them hematological relaps occured (79%) and molecular positivity anticipating hematological relaps with median of 3,5 month (1-7 months). 3 of these 14 patients are still in HR. Conclusions Mutations within NPM1 gene are a sensitive marker for monitoring minimal residual disease in CN-AML patients. RQ-PCR using a MGB probe is an efficient approach to long-term follow-up of residual leukemia cells and frequent quantitative monitoring is useful for reliably predicting hematological relapse. Achievement of negativity appears to predict favorable clinical outcome. This work was partially supported by research grant No. MSM0021622430 Disclosures: No relevant conflicts of interest to declare.


2021 ◽  
Vol 16 (3) ◽  
pp. 16-25
Author(s):  
L. Yu. Grivtsova ◽  
T. Yu. Mushkarina ◽  
V. V. Lunin ◽  
P. A. Zeynalova

The article considers the features and possibilities of flow cytometric diagnostics of plasma cell neoplasms, taking into account the classification of lymphoid and hematopoietic tissue tumors of the World Health Organization, revision of 2017 and the NCCN clinical recommendations, 2021. Standardized flow cytometric protocols (the Euro-Flow conception) and algorithms for both the diagnosis of plasma cell tumors and the detection of minimal residual disease in plasma cell myeloma are described.


Blood ◽  
2006 ◽  
Vol 107 (3) ◽  
pp. 1116-1123 ◽  
Author(s):  
Monika Brüggemann ◽  
Thorsten Raff ◽  
Thomas Flohr ◽  
Nicola Gökbuget ◽  
Makoto Nakao ◽  
...  

AbstractAdult patients with acute lymphoblastic leukemia (ALL) who are stratified into the standard-risk (SR) group due to the absence of adverse prognostic factors relapse in 40% to 55% of the cases. To identify complementary markers suitable for further treatment stratification in SR ALL, we evaluated the predictive value of minimal residual disease (MRD) and prospectively monitored MRD in 196 strictly defined SR ALL patients at up to 9 time points in the first year of treatment by quantitative polymerase chain reaction (PCR). Frequency of MRD positivity decreased from 88% during early induction to 13% at week 52. MRD was predictive for relapse at various follow-up time points. Combined MRD information from different time points allowed definition of 3 risk groups (P < .001): 10% of patients with a rapid MRD decline to lower than 10-4 or below detection limit at day 11 and day 24 were classified as low risk and had a 3-year relapse rate (RR) of 0%. A subset of 23% with an MRD of 10-4 or higher until week 16 formed the high-risk group, with a 3-year RR of 94% (95% confidence interval [CI] 83%-100%). The remaining patients whose RR was 47% (31%-63%) represented the intermediate-risk group. Thus, MRD quantification during treatment identified prognostic subgroups within the otherwise homogeneous SR ALL population who may benefit from individualized treatment.


2011 ◽  
Vol 29 (19) ◽  
pp. 2709-2716 ◽  
Author(s):  
Jan Krönke ◽  
Richard F. Schlenk ◽  
Kai-Ole Jensen ◽  
Florian Tschürtz ◽  
Andrea Corbacioglu ◽  
...  

Purpose To evaluate the prognostic value of minimal residual disease (MRD) in patients with acute myeloid leukemia (AML) with NPM1 mutation (NPM1mut). Patients and Method RNA-based real-time quantitative polymerase chain reaction (RQ-PCR) specific for the detection of six different NPM1mut types was applied to 1,682 samples (bone marrow, n = 1,272; blood, n = 410) serially obtained from 245 intensively treated younger adult patients who were 16 to 60 years old. Results NPM1mut transcript levels as a continuous variable were significantly associated with prognosis after each treatment cycle. Achievement of RQ-PCR negativity after double induction therapy identified patients with a low cumulative incidence of relapse (CIR; 6.5% after 4 years) compared with RQ-PCR–positive patients (53.0%; P < .001); this translated into significant differences in overall survival (90% v 51%, respectively; P = .001). After completion of therapy, CIR was 15.7% in RQ-PCR–negative patients compared with 66.5% in RQ-PCR–positive patients (P < .001). Multivariable analyses after double induction and after completion of consolidation therapy revealed higher NPM1mut transcript levels as a significant factor for a higher risk of relapse and death. Serial post-treatment assessment of MRD allowed early detection of relapse in patients exceeding more than 200 NPM1mut/104 ABL copies. Conclusion We defined clinically relevant time points for NPM1mut MRD assessment that allow for the identification of patients with AML who are at high risk of relapse. Monitoring of NPM1mut transcript levels should be incorporated in future clinical trials to guide therapeutic decisions.


Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 289-289
Author(s):  
Jorge Sierra ◽  
Ana Garrido ◽  
Marina Diaz Beya ◽  
Montserrat Hoyos ◽  
Marisa Calabuig ◽  
...  

BACKGROUND: AML risk classification is based on genetics (cytogenetics and molecular features) and more recently also on minimal residual disease (MRD) after chemotherapy. These two aspects allow predicting relapse and supporting or not the most anti-leukemia treatment that remains allogeneic hematopoietic cell transplantation (HCT). We prospectively investigated the combined use of the two predictive markers to allocate post-remission therapy with or without HCT. Objectives of the study were testing: a) if this approach was feasible in a multicenter setting; b) the proportion of patients who were allocated to an allogeneic HCT and finally received the procedure; c) the final distribution into the risk categories and their outcome; d) to analyze the outcome of patients with favorable or intermediate genetics moved to the high risk category because of positive MRD. METHODS: Adult patients with primary AML treated at 15 academic hospitals were included between February 2012 and December 2018. Induction chemotherapy consisted of idarubicin 12 mg/m2 days 1-2-3 and cytarabine 200 mg/m2 days 1 to 7. Consolidation courses were high-dose cytarabine (3 g/m2 or 1.5 g/m2 if ≥60 y/o). The number of consolidation courses was based on genetic risk: 3 in favorable genetics category (FGC) (CBF, NPM1mut/FLT3-ITDwild or ratio&lt;0.5, and CEBPA biallelic mutation); and one in the intermediate genetics category (IGC), including intermediate cytogenetics without favorable or unfavorable (FLT3-ITD, MLL, EVI1) molecular features, as well as in adverse genetics category (AGC). Following, the mandatory option was allogeneic HCT in the AGC and in the other genetic categories when MRD was positive. In the IGC without MRD autologous or HLA preferentially matched allogeneic HCT was a center decision. MRD was assessed by flow (positive &gt;0.1%) and/or quantitative PCR of the specific transcripts (RUNX1/RUNX1T1, CBFβ/MYH11 and NPM1). RESULTS: Seven hundred forty-five patients (median age: 55, range18-70 y/o, 51% male) were enrolled. Cytogenetics according the revised MRC classification in 707 informative cases was: CBF AML 12%, intermediate 65% (75% of them normal karyotype), and adverse 23%. FLT3-ITD was detected in 28% of patients with intermediate risk cytogenetics and NPM1 mutation in the same group was present in the 48%. Complete remission (CR) was achieved in 81% (n=603) of patients, 82% and 80% in patients up to and above 60 yrs, respectively. Induction death occurred in 9% of patients, 7% and 11% the two age groups, and 10% of patients had refractory leukemia; 542 (90%) of the 603 CR patients completed the consolidation phase and were risk allocated taking into account genetics and MRD. The remaining CR patients were not allocated because of early relapse (n=22), death in CR (n=5), severe toxicity (n=22) or others (n=12). After risk allocation, 208 (38%) patients were in the genetics-MRD combined favorable group (CFG), 103 (19%) in combined intermediate group (CIG) and 231 (43%) in the combined adverse group (CAG). In the latter, 185 (80%) of patients received an allogeneic HCT in first CR. Fifty-seven patients (11%) moved from the genetically FGC or IGC to the CAG because of high MRD at the end of consolidations. Median follow-up in survivors was 25 months. Overall 4-years survival (OS) of the whole series is 48±2%; event-free survival (EFS) is 77+3% in the CFG group, 45+6% in the CIG and 34+4% in the CAG (p&lt;0.001) due to difference in the cumulative relapse incidence (19%, 38% and 45%, respectively, p&lt;0.001 ). In the 57 patients who were MRD positive at the end of consolidation (FGC and IGC) had an OS of 53±8% and EFS of 45±7% at 4 years. CONCLUSION Risk adapted therapy for primary AML based on genetics and MRD is feasible in a cooperative group setting. The proportion of CR was high (&gt;80%) even in patients older than 60 y/o. MRD assessment at the end of consolidation moved 57 patients with favorable or intermediate genetics to the CAG. Avoiding HCT in first CR in the FGC patients associated to EFS above 75% at 4 years. Allogeneic transplantation feasibility was 80% when this was the intended treatment because of adverse genetics and/or MRD positivity. Risk assessment based on genetics and MRD continues separating three groups of patients with different outcomes. Since relapses remain frequent when adverse AML features are present, further approaches after transplantation, such as targeted agents and immune therapies deserve investigation. Disclosures Sierra: Astellas: Honoraria; Pfizer: Honoraria; Daiichi-Sankyo: Honoraria, Speakers Bureau; Abbvie: Honoraria, Speakers Bureau; Roche: Honoraria; Jazz Pharmaceuticals: Honoraria; Novartis: Honoraria, Research Funding, Speakers Bureau. Salamero:Daichii Sankyo: Honoraria; Pfizer: Honoraria; Celgene: Honoraria; Novartis: Honoraria. Esteve:Jazz Pharmaceuticals: Consultancy; Celgene: Consultancy, Speakers Bureau; Novartis: Consultancy, Research Funding, Speakers Bureau; Amgen: Consultancy; Daiichi Sankyo: Consultancy; Roche: Consultancy; Astellas: Consultancy, Speakers Bureau; Pfizer: Consultancy.


Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 3295-3295
Author(s):  
Enrico Gottardi ◽  
Daniela Cilloni ◽  
Sarah Daly ◽  
S. Green ◽  
Niels Pallisgaard ◽  
...  

Abstract Detection of minimal residual disease (MRD) has proven to provide independent prognostic information for treatment stratification in several types of leukemia. In acute myeloid leukemia (AML), the reliability of real-time quantitative PCR (RQ-PCR) and its potential clinical value for MRD studies using fusion gene (FG) transcripts as PCR targets such as PML-RARa, AML1-ETO and CBFb- MYH11 has been demonstrated, but these markers are present only in a minority of cases. In order to overcome this problem several groups looked for alternative markers and growing evidence has suggested that the high expression of WT1 in a significant proportion of acute leukemia cases provides a suitable target for therapy as well as for monitoring of MRD. However, heterogeneity of molecular approaches resulted in a lack of comparability between different MRD studies. This has been solved using RQ-PCR in a network of 9 laboratories within the European LeukemiaNet. Overall 8 primer/probe sets were evaluated including published and “in-house” sets. The assays analyzed differed significantly in terms of efficiency and sensitivity. Three assays with superior performance were identified, achieving sensitivities of at least 1 in 10,000 in serial dilutions of HL60 cells (WT1 positive). Subsequent analysis of two of the primer/probe sets, which amplify ex. 6/7 and 7/8 of WT1 respectively, revealed the potential for false negative results, following documentation of deletions of the WT1 gene in this region in primary AML samples. In two of these cases, different deletions of sequences corresponding to part of WT1 ex.8 were documented by WT1 RNA sequencing. Therefore, a primer/probe set amplifying ex. 1/2 of WT1 has been subject to further analysis in a QC round involving 9 labs. The analysis of 33 normal BM, 32 normal PB and 12 CD34 enriched PBMNCs gave the following results: BM, mean 70,32 WT1 copies/104 ABL copies (range 8,99–209,82); PB, mean 3,30 WT1 copies/104 ABL copies (range 0–13,55); CD34 enriched PBMNCs, mean 8,16 WT1 copies/104 ABL copies (range 1,55–26,16). Overall, these analyses underline the importance of standardization in the development of RQ-PCR assays for MRD detection in leukemia. There is increasing interest in identification of genes that are over-expressed in leukemia as potential MRD targets. However, it is clear that incorporation of such MRD targets into risk-directed treatment protocols is critically dependent upon establishing thresholds of expression in normal blood and marrow on regeneration following myeloablative therapy.


Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 698-698 ◽  
Author(s):  
Susanne Schnittger ◽  
Wolfgang Kern ◽  
Tamara Weiss ◽  
Claudia Tschulik ◽  
Frank Dicker ◽  
...  

Abstract The aim of this study was to further evaluate the impact of minimal residual disease (MRD) in NPM1 mutated AML in comparison to other factors like FAB, cytogenetics, FLT3 mutations, NPM1 mutation type and age. In total 1002 samples of 219 NPM1 mutated (NPM1mut) patients (pts) were analysed at diagnosis, during, and after therapy. Pts were treated within different AML trials, and follow-up samples were referred to perform an NPM1 specific RQ-PCR for MRD. The cohort was comprised of 112 females and 107 males, median age was 58.8 years (range: 20–79 years). 207 had de novo AML (M0: n=5; M1: n=49; M2: n=55; M4=57; M5: n=28, M5: n=6; M7: n=1, nd: n=6), 4 s-AML and 5 t-AML. Cytogenetic data was available in 215 pts: 178 with normal (NK) and 37 with aberrant karyotypes (+4: n=4; +8: n=7; +21: n=2, two or more trisomies: n=4; -Y: n=4; del(7q): n=2; del(9q): n=3; del(20q): n=2; rare translocations: n=9). At diagnosis 87/219 pts (39.7%) had FLT3-ITDs in addition to the NPM1mut. FLT3-TKD status was available in 206 cases (14 mutated (6.7%) and 192 WT). The NPM1 mutation types were A (n=174), B (n=13), D (n=14), I: (n=4), L: (n=2), R: (n=4) and 8 with individual rare types. Univariate analysis for overall survival (OS) revealed unfavourable impact for age (p=0.049), and for FLT3-ITD (p=0.002), favourable impact for FLT3-TKD (p=0.046), and no impact for FAB, chromosomal aberrations or NPM1 mutation type. For MRD assessment for all 14 different NPM1 mutation types mRNA based RQ-PCR assays were established with sensitivities of 10,000–1,000,000. For each patient 2–17 samples (spls) were analyzed (median: 4) spanning a median follow up time of 252 days (range: 18–2347 days). Paired samples of diagnosis and relapse were available in 71 pts, in 8 pts also from second relapse. At relapse all cases had high NPM1 levels comparable to those at diagnosis. The FLT3-ITD status was mutated (+/+) at both time points in 25 pts and −/− in another 25 pts. 10 pts gained FLT3-ITD at relapse and 3 lost it. For 48 paired samples cytogenetics was available for both time points. A normal karyotype (NK) at both time points was detected in 36 pts, 7 cases showed a normal or aberrant karyotype (AK) at diagnosis and and AK at relapse (two of these gained additional aberrations at relapse), 2 different AK at both time points in were detected in 3 cases and a regression from AK to NK in 2 cases. These data show that NPM1 seems to be the primary genetic aberration in these cases and detection of NPM1 is more reliable to detect relapse than cytogenetics. To analyse the impact of NPM1 mutation levels on prognosis four different follow-up intervals were defined: interval 1: days 21–60 after start of therapy; interval 2: days 61–120; interval 3: days 121–365, 4: >365 days. First a set of 605 samples referred for analysis during first line treatment were analysed. Using Cox regression analysis a significant impact of MRD levels (as continuous variable) on EFS was detected for interval 2 (128 spls, p=0.008), interval 3 (214 spl; p<0.001), interval 4 (171 spls; p<0.001) but not for the early interval up to day 60 showing that early molecular response is not relevant for long time outcome. A multivariate analysis showed that MRD was the most significant prognostic parameter (p<0.001) (p-values for interval 3), followed by age (p=0.003), and pretreatment FLT3-ITD status (p=0.065). The same analysis was performed for a second set of 183 spls taken from 50 pts during salvage therapy after relapse. The most relevant interval for this group was between days 30–60 (26 spls; p=0.003). In a third set 87 spls from 28 pts after allogeneic bone marrow transplantation were analyzed. A prognostic impact of MRD could be shown for interval 2 (17 spls; p=0.005) and 3 (23 spls; p=0.006) (no samples from later intervals available). Of the total cohort 325 spls were analysed in parallel with RQ-PCR for NPM1 and genescan for the FLT3-ITD. A high correlation of both follow up markers was observed (r=0.807, p<0.001). Although the method for NPM1 detection is 3–4 log ranges more sensitive our data suggest parallel assessment for FLT3-ITD for high risk patients as many of them aquired FLT3-ITD as additional marker during progression. In conclusion, MRD is the most relevant prognostic marker in NPM1 mutated AML and it is a very useful tool to assess therapy response and to guide therapy.


Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 1723-1723 ◽  
Author(s):  
Daniela Sauter ◽  
Katharina Ringel ◽  
Jan Braess ◽  
Wolfgang Hiddemann ◽  
Karsten Spiekermann ◽  
...  

Abstract Abstract 1723 Background: Quantification of minimal residual disease (MRD) by multiparameter flowcytometry (MFC) in patients with acute myeloid leukemia (AML) provides significant prognostic information. Previous analyses have shown that positivity of leukemia-associated aberrant immunophenotype (LAIP) after induction and consolidation therapy is a risk factor concerning relapse and reflects over-all survival and relapse-free survival. Albeit molecular MRD monitoring has translated into therapeutic strategies in certain AML subgroups, e.g. APL, flowcytometric MRD assessment is still not integrated into therapeutic strategies. Methods: We performed a retrospective analysis of flowcytometric MRD data of 201 adult patients with AML. Patients were treated within the clinical study of the German AML cooperation group (AMLCG99 or sHAM); patients with APL were excluded. 165 patients were in the intermediate risk group according to karyotype; NPM1 and Flt3 positivity was present in 80 and 59 patients, respectively. 51% of patients relapsed in the course of disease, the median overall survival (OS) and relapse-free survival (RFS) were 518 and 292 days, respectively. MRD assessment by 3-color-flowcytometry was performed at initial diagnosis, during bone marrow aplasia (day 16 – 18 of induction therapy), after induction, after consolidation and at time of relapse. MRD flow was compared to molecular MRD assessment in patients with mutated NPM1. Results: Data on flowcytometric MRD assessment were available in 99% of patients at initial diagnosis, 74% on day16 of induction therapy, 80% post-induction, 42% post-consolidation and 62% at time of relapse. MRD positivity was defined as percentage of LAIP positive cells > 0,15%. In addition, the post-therapeutic degree of LAIP reduction compared to initial diagnosis was assessed: an indequate degree of LAIP reduction was set at a log difference (initial diagnosis/ day16) < 2. We could confirm that flowcytometric MRD predicts OS and RFS. The absolute level of MRD as well as the relative degree of MRD reduction on day16 of induction therapy defined significantly distinct risk groups concerning OS and RFS (OS: p = 0,03, RFS: p = 0,002). Discriminating the different types of LAIPs, we could demonstrate that cross-lineage phenotypes have the best sensitivity and specificity for predicting relapse (sensitivity 64%, specificity 88% on day16). The course of LAIP and NPM1 as assessed by rtPCR, highly correlates on day16 (correlation coefficient 0,84). Conclusion: Flowcytometric MRD assessment provides significant prognostic information at a very early point in induction therapy. In a subpopulation of NPM1+ AML patients we found a strong correleation of flowcytometric MRD and molecular MRD assessment. LAIP reduction on day 16 post-induction could therefore be integrated into prognostic models and can improve risk stratification especially in the absence of molecular MRD markers. Disclosures: No relevant conflicts of interest to declare.


Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 3548-3548
Author(s):  
Felicitas Thol ◽  
Frederik Damm ◽  
Katharina Wagner ◽  
Katarina Reinhardt ◽  
Jan-Henning Klusmann ◽  
...  

Abstract Abstract 3548 Minimal Residual Disease (MRD) monitoring has become an important tool for risk and treatment stratification in hematological malignancies. MRD monitoring in FLT3 mutated patients has been difficult in the past as FLT3-ITDs vary from patient to patient and individual primer/probe sets would be required to assess MRD over time. In the present study we evaluated next-generation sequencing (NGS) as a new tool for MRD monitoring in patients with FLT3-ITD and NPM1 mutations. Five pediatric and 5 adult AML patients with FLT3-ITD and 10 adult patients with NPM1 mutations were analyzed by NGS with a target coverage of 10,000 reads per amplicon. Pediatric samples were collected at diagnosis, day 22 and after consolidation chemotherapy while adult samples were collected at different time points (average 4 timepoints per patient). Samples were sequenced unidirectionally on eight-lane PicoTiterPlates on a GS FLX sequencing system. In total, 2,563,550 sequencing reads were generated, corresponding to a total of 1,176,171 high-quality sequencing reads. NPM1 mutations were analyzed by quantitative RT-PCR using the MutaQuant kit from Ipsogen (Ispogen, Marseille, France). Allelic ratios of FLT3-ITDs were determined by fragment analysis on a DNA sequencer using GeneMapper software 4.0. First, the sensitivity of NGS to detect mutated alleles was evaluated by sequencing serial dilutions of a patient sample that had 46.3 percent mutated FLT3-ITD alleles at diagnosis. With a target coverage of 10,000 sequences and an allelic ratio of 46.3 percent the theoretical detection sensitivity was at most 1 in 4630 sequences. In fact, the allelic ratio in the sequenced samples linearly decreased in the tested dilutions down to the 5×10-4 dilution (Pearson correlation R2=.996). Samples from healthy volunteers were tested negative for both FLT3-ITD and NPM1 mutations (n=3). Allelic ratios from three diagnostic specimens of FLT3-ITD mutated patients were highly reproducible when determined in two independent NGS runs. As proof of principle we analyzed NPM1 mutated patients by NGS and quantitative RT-PCR in parallel. The mean allelic ratio of NPM1 mutants at diagnosis was 0.37 (range 0.29–0.46). An allelic ratio of 0.37 and 0.4 was measured in peripheral blood of two patients, and thus was similar to ratios in bone marrow. Concordant results between NGS and qRT-PCR were found in 38 samples (95%), whereas in two samples one method did not detect the mutation while the other did (NGS and RT-PCR were negative once each). We analyzed relapse samples in four patients. The NPM1 mutation was detected consistently by both methods in three patients at allelic ratios of 0.013, 0.19, and 0.32, while one patient had lost the mutation at relapse. One patient had an atypical NPM1 mutation for which no RT-PCR kit was available. NGS allowed quantification of the allelic ratio in this patient, which was 0.37 at diagnosis, 0.06 after one cycle of induction therapy, and 0 after the second cycle of induction therapy. In FLT3-ITD mutated patients we could determine insertion site, insertion length, number of individual clones, and allelic ratio from NGS data. The mean allelic ratio in diagnostic samples was 0.27 as measured by NGS and 0.4 as measured by fragment analysis. Three follow up samples were negative by fragment analysis, while a small clone could still be detected with NGS in these samples (allelic ratio 0.0004 to 0.001). All other samples were concordant between fragment analysis and NGS. NGS was used to determine MRD status in 5 patients with childhood AML harboring mutated FLT3. A reduction of 2–3 orders of magnitude was achieved during induction chemotherapy. During consolidation a further decrease or disappearance of mutated alleles was achieved in 3 patients, who remained in remission. However, allelic burden increased in 2 patients after first consolidation treatment (HAM) by 9- and 735-fold compared to the allelic ratio after induction therapy, and they relapsed 74 and 303 days later. Thus, accurate determination of the FLT3-ITD allelic ratio by NGS may become useful to identify patients before overt relapse. In summary, we show that NGS can be used for minimal residual disease assessment in FLT3-ITD mutated AML patients. The sensitivity of the method is scalable depending on the read depth, however, an adequate sensitivity level for efficient MRD detection still needs to be determined. Disclosures: No relevant conflicts of interest to declare.


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