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ABL1 Kinase Domain (ABL1-KD) mutations are a common resistance mechanism to tyrosine-kinase inhibitors (TKIs) in Chronic Myeloid Leukemia (CML) and Philadelphia Positive Acute Lymphoblastic Leukemia (ALL). Different ABL1-KD mutations induce different degrees of resistance to different TKIs. The early detection of these resistant mutations helps to adjust patient's treatment. Here we present an Ultra-Deep Sequencing approach to detect and quantify acquired ABL1-KD mutations in genomic DNA (gDNA), aiming to define a robust test to detect such alterations in TKIs exposed Philadelphia-Positive Leukemia Patients with a resolution below 1E-4. Firstly, we defined an ABL1 specific next-generation sequencing (NGS) panel designed to cover all coding regions of ABL1 exons 4-10. The 9 amplicons were designed to cover full exons where possible to detect co-occurring mutations (Figure 1A). A panel was then applied to 3 biological replicates of 3 Healthy control donors (9 NGS data points each with 220ng of gDNA). The average coverage per amplicon in all samples was at least 500,000x. The NGS data was then analyzed applying the NGS-MRD algorithm described elsewhere (Onecha, E et al. Haematologica 2019) to 25 known ABL1-KD hotspots. After applying our error correcting algorithm, we obtained an average of 135,000 (22,000-503,000) refined reads for the 25 hotspots. The limit of detection (LOD) was calculated for every position in the DNA as the mean noise (Variant Read Frequency; VRF) per position in the controls ± 3SD (standard deviation); the limit of quantification (LOQ) being defined as mean ± 10SD. For all the hotspots analyzed, the LOD was below 1E-4 and the LOQ below 3E-4 (Figure 1B), except for p.F311L (c.931T>C; LOD=2.7E-3). The high level of noise in this position, constant in the different control samples sequenced in different sequencing runs, is most likely related to the high number of homopolymers in the region. Ten Philadelphia-Positive Leukemia patients were then screened after TKI treatment (8 CML and 2 ALL). The median BCR-ABL1 defined by quantitative PCR (ratio BCR-ABL1 vs ABL1) in these follow-up samples was 0.6% (0.034% - 95%). All patients were screened in triplicates (220ng gDNA each) and the data-points ± 1SD from the mean were considered outliers (NGS false positives) and excluded from further analysis. Five patients presented a signal above the LOD for p.T315I (c.944C>T). This position is covered by 2 different amplicons in our panel. By bioinformatically demultiplexing the signal, the detection of those five mutations in both amplicons was confirmed (Amp_4; LOD=3E-5, Amp_5; LOD=4E-5). Moreover, aiming to validate this new approach, we applied to paired RNA samples an in-house BCR-ABL1/ABL1 nested PCR + NGS approach designed to quantify those alterations in cDNA. This approach confirmed the presence of 4 out of 5 gDNA detected mutations, with a Pearson correlation of 0.92 (Pval Here we show an Ultra-Deep NGS based test which allows the early detection of TKI resistant emerging clones in genomic DNA samples with a resolution of 1E-4. Despite the facts that in Phi-positive leukemia patients' other techniques such as the nested PCR are available, for most of heme- dyscrasias it is not easy to detect acquired mutations below 1% VRF. Our test can reduce this limit by at least 2 logarithms. The clinical impact of this approach is illustrated by the two LLA patients included, both under dasatinib therapy when the p.T315I mutations were detected. Those 2 patients were changed to ponatinib, reducing BCR-ABL1 levels. An extension of the cohort and the validation of our test at clinical level will be presented at the meeting. Figure Disclosures Heredia: Altum sequencing: Current Employment. Carrillo:Altum sequencing: Current Employment. Rufian:Altum sequencing: Current Employment. Wang:Hosea Precision Medical Technology Co., Ltd: Current Employment. Ribera:Pfizer, Amgen: Research Funding; Pfizer, Amgen, Ariad, Novartis: Consultancy, Speakers Bureau. Martinez-López:Janssen, BMS, Sanofi, Novartis, Incyte, F. Hoffmann-La Roche and Amgen: Honoraria, Other: Advisory boards; Hosea and Altum: Membership on an entity's Board of Directors or advisory committees; Janssen, Novartis, BMS, Incyte: Consultancy.

Introduction: Myeloid malignancies are clonal disorders of hematopoietic stem cells and include acute myeloid leukemia (AML), myelodysplastic syndrome (MDS) and myeloproliferative neoplasm (MPN). Common biological markers have been described in the molecular pathogenesis, including gene mutations in splicing factors, epigenetic modifiers, transcription factors, signal pathways and tumor suppressors. These mechanisms have been associated with MDS and MPN progression to AML. Objectives: The main objective of this study is to identify differences in the mutational landscape of myeloid malignancies and describe mutation frequencies of genes and functional pathways in each neoplasm, as well as determine their clinical impact. Methods: This study involved a retrospective analysis of 430 patients with AML (209), MDS (106) and Philadelphia negative MPN (86) diagnosed in the Hospital Universitario 12 de Octubre (Spain). They were analyzed by a next generation sequencing (NGS)- panel for myeloid malignancies. The panel include 32 genes: CALR, ASXL1, EZH2, PHF6, DNMT3A 2, TET2, IDH1, IDH2, KDM6A, KMT2A, SF1, SF3A1, SF3B1, SRSF2, U2AF1, ZRSR2, PRPF40B, EPOR, FLT3, JAK2, KIT, SH2B3, MPL, CBL, HRAS, NRAS, KRAS, ETV6, RUNX1, VHL, TP53, PTEN. In addition, there were included 29 patients diagnosed with benign pathology that were referred to rule out MPN or congenital polyglobulia. Results: In the analyzed cohort we obtained a larger number of mutations in the more aggressive malignancies, AML and MDS. Mutations in epigenetic modifiers and signal pathways were the most frequent detected (31% and 24% respectively). The epigenetic modifiers were notably affected in AML (78%) and MDS (60.4%), whereas signal pathways were mutated more frequently in MPN (70.9%). Transcription factors, tumor suppressors and splicing factors mutations were more detected in AML and MDS (40%, 32%, 44% and 22%, 13%, 32% respectively). The mutation landscape obtained by genes was: Signal pathways: FLT3, NRAS, KIT, KRAS y SH2B3 were specially detected in AML (25%, 11%, 6%, 5% and 4% respectively). JAK2, CALR and MPL in MPN (38%, 15% and 6% respectively). Transcription factors: RUNX1, ETV6, PHF6, CEBPA and WT1 mutations were regularly observed in AML (21%, 6%, 6%, 6% and 5% respectively), and GATA1 in SMD (3.8%). Tumor suppressors: TP53 was particularly affected in AML (21%) and MDS (11%). Epigenetic modifiers: TET2 was notably mutated in MDS (32%), whereas ASXL1, DNMT3A, IDH2, IDH1 and EZH2 were in AML (21%, 21%, 17% 16% and 8% respectively). Splicing factors: SF3B1 was more frequently detected in MDS (18%) than AML (7%), whereas ZRSR2 presented a similar frequency in both pathologies (around 8%). U2AF1 was most commonly mutated in MPN (9%). SRSF2 was specially mutated in AML (23%). SF3A1 was altered in around 1%, similar in all three malignancies. With regard to survival studies, the presence of mutations in splicing factors (primarily in U2AF1) and its absence in signal pathways conferred an adverse outcome for overall survival (OS) in MPN. In MDS, gene mutations in tumor suppressors (especially TP53), U2AF1 splicing factor and EZH2 epigenetic modifier were associated with poor outcome. In our series of AML, gene mutations in tumor suppressors and TP53 were related to unfavorable prognosis in OS. Conclusion: The largest number of mutations and affected genes observed in AML suggest that leukemic transformation of MDS and MPN is conditioned by acquisition of new mutations. We observed different frequencies of mutations between AML, MDS and MPN that could guide the diagnostic and identify new targets of treatment. Further, some mutations have demonstrated differential prognostic impact. An extension of this study and the design of an algorithm with mutation data to elucidate a more accurate molecular prognosis will be presented at the meeting. This work has been financed thanks to the grant PI16/01225, PI 19/01518 and PI19/00730 from the Instituto de Salud Carlos III (Ministerio de Economia, Industria y Competititvidad) and cofinanced by the European Development Fund. Figure 1. Mutations detected (%) in AML, MDS and MPN classified by function. Table 1. Median overall survival of patients with MPN, MDS and AML according to gene state (mutated or not). Figure Disclosures No relevant conflicts of interest to declare.

Background: Kinase domain (KD) mutations is a common resistance mechanism, secondary to the tyrosine-kinase inhibitors (ITKs) treatment in the case of chronic myeloid leukemia (CML) and Philadelphia (Ph)-positive acute lymphoblastic leukemia (ALL) patients. Sanger sequencing is the gold standard technique and already the currently recommended method for BCR-ABL1 KD mutation detection. However, Sanger sequencing has limited sensitivity and cannot firmly identify populations with variant allele frequencies (VAF) < 15-20%. Next-generation sequencing (NGS) allow us the screening of mutations in the whole KD with variants with a VAF greater than 1%. The aim of this study is to evaluate the clinical and prognostic implications of CML and Ph-positive ALL patients who have been studied for mutations in BCR-ABL1 by NGS. Methods: Seventy CML and Ph-pos ALL patients have been studied for BCR-ABL1 mutations between years 2015-2017. The study reason was warning or failure according to European Leukemia Net recommendations in the case of CML patients, and diagnostic or relapse in the case of ALL patients. Clinical characteristics of the patients are depicted on Table 1. Categorical variables are described as frequency, and quantitative variables as medians. Contingency tables were used to analyze associations between categorical variables (χ2). Median test was used to compare medians of continuous variables between groups. Overall survival (OS) was estimated using the Kaplan-Meier method and compared between patients using the log-rank test. Results: We have found 37 patients with mutations (51%), the most frequent being p.T315I, p.L248V and p.L387M. 28 out of 59 were found in CML (47%) vs 9 out of 13 (69%) in ALL. Of the 37 patients with mutations, double mutations have been found 10 times (27%). In the 72 analyses performed, 62 mutations were found in total, 41 of them were variants of uncertain significance (VUS) and 21 were well-known mutation. The median levels of BCR-ABL1 (IS) at the time of analysis were 3.00 (0.01-196.18) %. Regarding CML patients, we have found 12 and 16 cases with pathogenic mutations and VUS, respectively. The mean survival for CML and ALL were 75.2 months (CI 95%, 65.7-84.6) and 24.7 months (13.3-36.2), respectively. There are significant differences between the overall survival curves for patients with CML who have mutations in BCR-ABL1 compared to those who have VUS or do not (p-value = 0.024, n=59), suggesting a second role of the VUS variants in the resistance of the patients to the TKI. These two groups have no significant differences in ALL patients (p-value= 0.32, n=13). Overall survival at 10 years from the date of diagnosis is 74% for CML patients with mutations and 90% for CML patients without mutations. Data dropped significantly for ALL patients, but the number of cases is too low. Conclusions: - Mutations have been identified in 47% of CML patients studied in the case of failure or warning and 69% of the patients of ALL at diagnosis or relapse moments. - The identification of pathogenic variants has poor prognosis in patients with CML (p = 0.024), however no differences were observed in ALL. - The identification of VUS is not associated to poor prognosis and these variants could not confer resistance to ITK. Disclosures Sevilla: Rocket Pharmaceuticals, Inc.: Honoraria, Patents & Royalties: Inventor on patents on lentiviral vectors filled by CIEMAT, CIBERER and F.J.D and may be entitled to receive financial benefits from the licensing of such patents; NOVARTIS: Honoraria, Membership on an entity's Board of Directors or advisory committees; Rocket: Membership on an entity's Board of Directors or advisory committees; Amgen: Honoraria, Membership on an entity's Board of Directors or advisory committees; Sobi: Membership on an entity's Board of Directors or advisory committees; Miltenyi Biotech: Honoraria. Steegmann:Incyte: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Pfizer: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; BMS: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding. García Gutiérrez:Novartis: Honoraria, Research Funding; BMS: Honoraria, Research Funding; Pfizer: Honoraria, Research Funding; Incyte: Honoraria, Research Funding.