ALBERT

Description: Abstract 2458 The bacterially derived enzyme L-Asparaginase (ASNase) is a key component in the multidrug therapy regimens used worldwide to treat pediatric and adult patients with acute lymphoblastic leukemia (ALL), however little is known about the molecular mechanisms that control the pharmacokinetics of this therapeutic protein. As a result, many patients who receive a standardized dose either exceed or do not reach the desired serum concentration. While elevated serum levels are associated with an increase in treatment related morbidity, underexposure seriously compromises therapeutic benefits. In search of molecular factors that determine ASNase turnover in vivo, we investigated a patient with strongly aberrant clearance kinetics. This 3-year old female diagnosed with common ALL suffered from severe ASNase-induced adverse events upon treatment with ErwiniaSNase as a result of strongly elevated serum ASNase levels. Pharmacokinetics data showed a severely delayed ASNase clearance. As a result, serum ASNase levels accumulated to intolerable levels upon repeated administration of the drug. We isolated DNA from peripheral blood mononuclear cells and buccal cells of this patient and performed targeted sequencing on genes suggested to be involved in ASNase clearance. We identified a novel heterozygous mutation in the gene encoding Cathepsin B in the germline of this patient. The mutant allele shows a deletion of a single codon, leading to a deletion of a lysine residue in the C terminus of the protein. We generated an EBV LCL cell line from this patients which showed a 75% reduction in Cathepsin B activity, relative to controls, indicating that this heterozygous mutation has a profound effect on the total Cathepsin B activity. Cathepsin B is normally synthesized as a 37 kD pre-pro enzyme and is processed in a two step process into a mature 2-chain active form. During this process, the protein is transported to the lysosome where it exerts its primary function. Using a combination of biochemical and imaging experiments we show that the mutant Cathepsin B cannot be processed into the mature form and is retained in the endoplasmatic reticulum. ASNase degradation assays demonstrate that this mutant form of Cathepsin B shows a diminished protease activity towards both E.coli and Erwinia ASNase, consistent with the reduced clearance observed in our patient. Cathepsin B and other cellular proteases are either actively secreted or released into the serum as a result of cell lysis. Although we find a variable low but detectable activity of Cathepin B in serum samples, all tested preparations of ASNase were stable upon prolonged incubation in serum, suggesting that serum components are not contributing to ASNase clearance in vivo. Hence, we propose that cellular uptake and subsequent proteolytic degradation of ASNase is the primary mechanism of clearance. In conclusion, we have identified a mutation in protease Cathepsin B and provide evidence that this mutation results in a loss of protease function towards ASNase, which can explain the strongly delayed clearance of ASNase in the patient. Our data suggest that differences in Cathepsin B activity may contribute to the large inter-patient variability in ASNase pharmacokinetics. Furthermore, given the role of Cathepsin proteases in antigen presentation, Cathepsin B may not only provide a target for predicting or controlling ASNase clearance kinetics but inhibition of Cathepsin may also prevent or delay the formation of inhibitory antibodies. Disclosures: Boos: European Erwinase Providers (EUSAPharm): Speakers Bureau; Medac: Consultancy, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau. Lanvers-Kaminsky:Medac: Speakers Bureau.

Description: In B cell neoplasia, many transcription factors known to be involved in B cell differentiation and commitment, like E2A, EBF1 and PAX5, are frequently targeted by focal deletions, mutations or chromosomal aberrations. Recent studies have shown that the human genes BTG1 and BTG2 are commonly affected by gene alterations in different B cell malignancies, but their role in normal B cell development has not been established. BTG1 and BTG2 can act as transcriptional cofactors through recruitment of the protein arginine N-methyltransferase PRMT1, which mediates arginine methylation of transcription factors, like RUNX1, and on histone 4 arginine 3 (H4R3). Here we report that Btg1 and Btg2 display unique and overlapping functions during mouse B cell development. We observed a reduction in the fraction of B220+ progenitor cells in the bone marrow compartment of the different knockout animals, ranging from a 10% decrease in the Btg2-/-, 20% in Btg1-/- , and 40% in the Btg1-/-;Btg2-/- mice relative to wild-type controls. Deficiency for Btg1, but not Btg2, resulted in reduced outgrowth of IL-7 dependent lymphoid progenitors in methylcellulose, which correlated with a higher fraction of apoptotic cells. Btg2-/- mice showed impaired differentiation at the pre-pro-B, pro-B and pre-B cell stage, while Btg1-deficiency mainly affected later stages of B cell differentiation with reduced numbers of immature B cells. Btg1-/-;Btg2-/- mice displayed additive effects with more significant reduction of B220+ cells predominantly at the pre-B and immature B cell stage. Expression analysis revealed no reduction in the mRNA levels of master regulators E2a, Foxo1, Ebf1 and Pax5 in the absence of Btg1 and Btg2. However, higher expression levels of T cell-specific genes were observed in Btg1-/-;Btg2-/- progenitor B cells, e.g. Cd4, Ikzf2 and Tcf7 (Figure 1), some of which are known to be transcriptional repressed by Ebf1, such as Id2, Gata3, Dtx3l and Notch1. Flow cytometric analyses confirmed increased expression of CD3, CD4 and CD8 markers on CD19+ bone marrow cells lacking Btg1 and Btg2 function. Additionally, we detected enhanced levels of DC, NK and myeloid markers on Btg1-/-;Btg2-/- CD19+ BM cells, indicating that Btg1 and Btg2 repress alternative cell fates during B cell lineage specification, and are required for the maintenance of B cell identity. Biochemical studies showed evidence for a physical association between Ebf1, Btg1/Btg2 and PRMT1. We propose a model in which Btg1 and Btg2 affect the function of the critical B cell transcription factor Ebf1 by recruitment of PRMT1. Figure 1. Aberrant T-lineage expression in progenitor B cells deficient for Btg1 and Btg2. Relative expression levels of Cd4, Runx1, Ikzf2, Tcf7, Id2, Gata3, Notch1 and Dtx3l were determined on cDNA generated from B220+ BM cells of wild-type (WT), Btg1-/-, Btg2-/- and Btg1-/-;Btg2-/- mice by quantitative real-time PCR and normalized to the expression of the housekeeping gene TATA box binding protein (TBP). Data represent the mean and SEM of three independent experiments containing cDNA derived from 2 different biological samples. *, P〈 0.05, **, P〈 0.01, ***, P〈 0.001. Figure 1. Aberrant T-lineage expression in progenitor B cells deficient for Btg1 and Btg2. Relative expression levels of Cd4, Runx1, Ikzf2, Tcf7, Id2, Gata3, Notch1 and Dtx3l were determined on cDNA generated from B220+ BM cells of wild-type (WT), Btg1-/-, Btg2-/- and Btg1-/-;Btg2-/- mice by quantitative real-time PCR and normalized to the expression of the housekeeping gene TATA box binding protein (TBP). Data represent the mean and SEM of three independent experiments containing cDNA derived from 2 different biological samples. *, P〈 0.05, **, P〈 0.01, ***, P〈 0.001. Disclosures No relevant conflicts of interest to declare.

Description: Translocation t(12;21) (p13;q22), giving rise to the ETV6-RUNX1 fusion gene, is the most common genetic abnormality in childhood B-cell precursor acute lymphoblastic leukemia (BCP-ALL). The ETV6-RUNX1 translocation arises in utero, but its expression is insufficient to induce leukemia and requires other cooperating genetic lesions for BCP-ALL to develop. Deletions affecting the transcriptional coregulator BTG1 are commonly observed in BCP-ALL (9%), but are significantly enriched in ETV6-RUNX1-positive leukemia (25%). The BTG1 protein displays no intrinsic enzymatic activity but may act by recruiting effector molecules like protein arginine methyltransferase 1 (PRMT1) to specific transcription factors. Here, we show that ETV6-RUNX1 interacts both with BTG1 and PRMT1, and this interaction is lost in c-Kit+Ter-119-Btg1-/- fetal liver (FL) derived hematopoietic progenitors (HPCs). Moreover, targeted deletion of Btg1 enhanced the proliferative capacity of ETV6-RUNX1 in FL-HPCs as measured by enhanced colony-forming and serial replating capacity (Figure 1). The combined loss of Btg1 function and ETV6-RUNX1 expression correlated with strong upregulation of the proto-oncogene Bcl6 and downregulation of BCL6 target genes, such as p19Arf and Tp53 (Figure 2). Similarly, ectopic expression of BCL6 promoted both proliferation and replating capacity of FL-derived progenitor cells in the presence of SCF, FLT3L and IL-7. This phenotype correlated with a fivefold suppression of p19Arf and a twofold suppression of Tp53 expression. Inhibition of BCL6 in a variety of human BCP-ALL cell lines by the peptide inhibitor RI-BPI resulted in decreased proliferation and induction of apoptosis as measured by Annexin-V staining. These included the ETV6-RUNX1-positive cell lines UOC-B6, AT-2 and REH, the BCR-ABL1-positive cell line SD1, as well as Nalm6. Together our results point to a novel role for BCL6 in promoting cell proliferation of primitive progenitor B cells and suggest that targeted inhibition of BCL6 may be effective in the treatment of various BCP-ALL subtypes. Figure 1. Btg1-deficiency enhances the proliferative capacity of early FL-HPCs expressing ETV6-RUNX1. FL-derived hematopoietic progenitor cells (FL-HPCs) (cKit+Ter119-) were isolated from wild-type and Btg1-/- embryos at day 13.5dpc and transduced with control and ETV6-RUNX1 virus. Control and ETV6-RUNX1 transduced FL-HPCs (1x104 cells) were added 48 hours after transduction in B cell specific methylcellulose in the presence of FLT-3L, IL-7 and SCF. Serial replating was performed under identical conditions. Mean colony counts (and SEM) were determined (〉30 cells/colony) after 6-10 days of culture. Data is a representative of 2 independent experiments. *, P〈 0.05, **, P〈 0.01. Figure 1. Btg1-deficiency enhances the proliferative capacity of early FL-HPCs expressing ETV6-RUNX1. FL-derived hematopoietic progenitor cells (FL-HPCs) (cKit+Ter119-) were isolated from wild-type and Btg1-/- embryos at day 13.5dpc and transduced with control and ETV6-RUNX1 virus. Control and ETV6-RUNX1 transduced FL-HPCs (1x104 cells) were added 48 hours after transduction in B cell specific methylcellulose in the presence of FLT-3L, IL-7 and SCF. Serial replating was performed under identical conditions. Mean colony counts (and SEM) were determined (〉30 cells/colony) after 6-10 days of culture. Data is a representative of 2 independent experiments. *, P〈 0.05, **, P〈 0.01. Figure 2. Targeted deletion of Btg1 cooperates with ETV6-RUNX1 in regulating critical effector pathways implicated in leukemia. Relative expression levels of Bcl6, Tp53 and p19arf in empty control (Ctrl) and ETV6-RUNX1 transduced wild-type and Btg1-deficient fetal liver-derived hematopoietic progenitor cells by real-time PCR and normalized to the expression of the housekeeping gene TATA box binding protein (TBP). Data represent the mean and SEM of three independent experiments. *, P〈 0.05, **, P〈 0.01, ***, P〈 0.001. Figure 2. Targeted deletion of Btg1 cooperates with ETV6-RUNX1 in regulating critical effector pathways implicated in leukemia. Relative expression levels of Bcl6, Tp53 and p19arf in empty control (Ctrl) and ETV6-RUNX1 transduced wild-type and Btg1-deficient fetal liver-derived hematopoietic progenitor cells by real-time PCR and normalized to the expression of the housekeeping gene TATA box binding protein (TBP). Data represent the mean and SEM of three independent experiments. *, P〈 0.05, **, P〈 0.01, ***, P〈 0.001. Disclosures No relevant conflicts of interest to declare.

Description: Abstract 1303 B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is the most common form of cancer in children, characterized by genetic aberrations affecting master regulators of lymphoid differentiation, such as RUNX1, IKZF1, TCF3, and PAX5, as well as tumor suppressor genes that control the cell cycle, including RB1 and CDKN2A. Another gene frequently altered in BCP-ALL is BTG1, which displays highly clustered mono-allelic deletions in childhood BCP-ALL (9%) and adult ALL (6%). The frequency of BTG1 deletions is two- to three-fold higher in ETV6-RUNX1- and BCR-ABL1-positive leukemias. BTG1, and its close homologue BTG2 regulate gene expression, for instance by associating with protein arginine methyltransferase 1 (PRMT1), affecting the activity of a variety of transcription factors, including several nuclear hormone receptors and HoxB9. In addition, BTG1 and BTG2 have been implicated in regulating mRNA stability by interacting with the Ccr4-Not complex. Recent studies have also identified missense point mutations in BTG1 and BTG2 in about 20% of non-Hodgkin lymphomas, arguing that altered function of these genes contributes to B cell malignancies. To investigate a role of BTG1 and BTG2 in B cell development, we studied the phenotype of Btg1 and Btg2 single knockout (KO) and Btg1;Btg2 double KO mice. Animals deficient for either BTG1 or BTG2 displayed a mild B cell phenotype with a moderate reduction of ∼20% in the total amount of B220+ progenitor B cells in bone marrow, while splenic B cells were present at normal frequencies. More detailed analyses revealed that Btg1−/− and Btg2−/− mice both showed a partial block at the pre-pro-B cell stage (Hardy fraction A). Methylcellulose colony assays in the presence of interleukin-7 (IL-7) demonstrated 30% fewer colonies using bone marrow from Btg2−/− mice, whereas 70% fewer colonies were obtained using bone marrow derived from Btg1−/− mice. To assess whether BTG1 and BTG2 fulfill redundant functions during B cell development, we analyzed the phenotype of Btg1−/−;Btg2−/− mice. Hence we observed that the combined loss of BTG1 and BTG2 led to a much stronger block in B cell differentiation, with the majority of progenitor B cells arrested at the pre-pro-B cell stage. In the spleens of these double knockout mice we observed a roughly 50% reduction in B220+ IgM+ B cells, suggesting that these genes act to modify the activity of B lineage transcription factors rather than to fully block their activities. This is consistent with a role for these genes as modifiers of transcriptional activity. Current studies are aimed at defining the molecular targets regulated by BTG1 and BTG2 during early B cell development using RNA sequencing and protein interaction experiments. In conclusion, our data demonstrate that BTG1 and BTG2 act as important regulators of normal B cell differentiation, and that this function might be critical for their role as tumor suppressors in (early) B cell malignancies. Disclosures: No relevant conflicts of interest to declare.

Description: Abstract 126 Relapse is the major cause of treatment failure in pediatric acute lymphoblastic leukemia (ALL). Recent studies have shown a complex, dynamic architecture of clonal diversity in ALL and other leukemia subtypes, both at diagnosis and relapse. This multiclonal diversity follows a Darwinian model of evolution, and likely contributes to the selective outgrowth of therapy-resistant leukemic cells during or after chemotherapy treatment, resulting in relapse. In order to gain more insight into the multiclonal architecture of ALL, we selected two cytogenetically normal B-cell precursor ALL patients treated according to the DCOG-ALL9 protocol who, based on a previous study (Kuiper et al, Leukemia 2010, 24:1258–64), developed relapses with only minor genomic alterations as compared to diagnosis. Patient 1 had an IKZF1 deletion (exons 4 to 8) and a 23-nt insertion in IKZF1 exon 4 at diagnosis and developed a relapse after 12 months, whereas patient 2 was IKZF1 wild-type, and developed two relapses at 32 months and 4.5 years after diagnosis, respectively. Comparison of clonal rearrangements in the Ig and TCR genes between diagnosis and relapse(s) revealed that both leukemias were genomically stable. Copy number analysis revealed an acquired intragenic PAX5 deletion at relapse in patient 1 and two acquired copy number changes in the second relapse of patient 2 (Kuiper et al., 2010). In the current study, we performed whole exome sequencing on diagnosis, remission and relapse samples of both patients, and identified and confirmed 21 and 7 somatic missense, frameshift or splicesite mutations in the diagnosis and/or relapse samples, respectively. These variants were subsequently selected for amplicon-based ultra-deep sequencing (IonTorrent PGM with 318 chip, Applied Biosystems), using 15 ng of genomic DNA (corresponding to 2,200 haploid genome copies), reaching an average read-depth of 15,000x. All amplicons were mixed at equimolar levels and barcoded per patient sample. In patient 1, 19 mutations, including the 23-nt insertion in IKZF1 exon 4, were detected in 44–52% of the reads at both diagnosis and relapse, thus confirming that this leukemia was genomically stable. Two mutations were present at subclonal levels both at diagnosis and relapse, of which one (FMN1) was detected at 4-fold higher levels in relapse (Table 1). The second patient showed substantially more subclonal variability, revealing a mutation in GHR at diagnosis that was lost at relapse, and three mutations that appeared as novel mutations in the second relapse. These latter mutations thus may have been induced during treatment of the first relapse. Three mutations were detected at subclonal levels already at diagnosis, albeit in very low amounts for RANBP17 (Table 1). Based on these findings, we conclude that i) using paired whole-exome sequencing of diagnosis, remission and relapse samples we have identified novel somatic mutations in childhood ALL, ii) amplicon-based ultra-deep sequencing allows the sensitive detection of relapse-prone subclones at diagnosis, iii) this sequencing effort provides insight into the complex dynamic architecture of clonal diversity in childhood ALL. Table 1. Subclonal mutations in relapsed childhood ALL patients patient gene mutation status at relapse mean read depth per sample % variant reads diagnosis (1st) relapse 2nd relapse 1 FMN1 subclonal outgrowth 20,292 8% 34% - 1 NAT8 preserved subclone 4,249 24% 27% - 2 GHR lost 14,530 38% 0% 0% 2 ARHGEF1 acquired 14,370 0% 0% 44% 2 PNPLA8 acquired 19,301 0% 0% 44% 2 IQGAP1 acquired 19,811 0% 0% 46% 2 RANBP17 subclonal outgrowth 30,260

Description: Background: Osteonecrosis (ON) and decline of bone mineral density (BMD) are serious side effects during and after treatment of childhood acute lymphoblastic leukemia (ALL). It is unknown whether ON and low BMD co-occur in the same patients, and whether these two osteogenic side effects can influence each other’s development during pediatric ALL treatment. Methods: BMD and the incidence of symptomatic ON were prospectively assessed in 466 patients with ALL (4-18 years of age) treated according to the dexamethasone-based Dutch Child Oncology Group-ALL9 protocol. Symptomatic ON was defined as persistent pain in arms or legs not caused by vincristine administration, and confirmed by magnetic resonance imaging. Bone mineral density of the lumbar spine (BMDLS) (n=466) and of the total body (BMDTB) (n=106) were measured by dual X-ray absorptiometry at ALL diagnosis, after 32 weeks of treatment, at cessation of treatment (109 weeks) and 1 year after cessation of treatment. BMD was expressed as age-matched and gender-matched standard deviation scores (SDS; Z-score). Multivariate linear mixed models were adjusted for age at diagnosis. Results: Thirty patients (6.4%) suffered from ON. At cessation of treatment, mean BMDLS was -1.28 SDS (SD: 1.27, n=332; p

Description: Background: Body mass index (BMI: kg/m2) and change in BMI during treatment might influence treatment outcome of pediatric patients with acute lymphoblastic leukemia (ALL). However, previous studies in pediatric acute lymphoblastic leukemia reported contradictory results. Therefore, we studiedthe influence of (change in) BMI on treatment outcome in pediatric ALL patients who were treated according to a dexamethasone-based protocol (Dutch Childhood Oncology Group [DCOG] ALL-9). Patients and Methods: Data on body composition were prospectively collected from a cohort of newly diagnosed Dutch pediatric ALL patients (N=762, age 2-17 years), treated from 1997-2004. BMI at diagnosis was expressed as standard deviation scores (SDS) and categorized into underweight (≤–1.8SDS), or normal weight and overweight (〉–1.8SDS). BMI loss was defined after 32 weeks of treatment. Dual X-ray absorptiometry scans were performed in a nested single center cohort (n=106) to assess the contribution of %fat and lean body mass to BMI. Multivariate analyses were corrected for age at diagnosis and risk treatment grpup. Results: Multivariate analyses showed that patients with underweight (8%) had an increased risk of relapse (Hazard Ratio (HR) 1.79, 95% CI: [1.04-3.10], and a similar overall survival (HR 1.10 [0.57-2.10]). BMI loss during the first 32 weeks of treatment was associated with a decreased overall survival (HR 2.10 [1.14-3.87]), and a similar risk of relapse (HR 1.27 [0.70-2.30]) compared to patients without BMI loss. Dual X-ray absorptiometry revealed that BMI loss mainly consisted of a loss of lean body mass and gain in %fat. Conclusion: Underweight at diagnosis is associated with an increased risk of relapse and a BMI loss early during treatment is associated with an increased mortality. This suggests that these patients might benefit from exercise interventions and a high-quality nutrient diet during therapy. Disclosures No relevant conflicts of interest to declare.

Description: Key Points Chromosomal abnormalities predict outcome after relapse in BCP-ALL, and high-risk cytogenetics takes precedence over clinical risk factors. Patients with mutations or deletions targeting TP53, NR3C1, BTG1, and NRAS were associated with clinical high risk and an inferior outcome.

Description: Abstract 272 The response to therapy as determined by minimal residual disease (MRD) is currently used for stratification in treatment protocols for pediatric acute lymphoblastic leukemia (ALL). Even though MRD classification clearly identifies patients at low or at high risk for relapse, it also results in a large intermediate group (50 to 60% of patients), which still contains approximately half of all relapse cases. To improve risk stratification, we evaluated the added value of the IKZF1 alteration status, recently identified as a prognostic factor, in precursor-B-ALL patients. In an unbiased cohort of 131 uniformly treated precursor-B-ALL patients, we determined MRD levels at 42 and 84 days after treatment initiation using RQ-PCR analysis of Ig/TCR rearrangements. Based on these levels, patients were divided into three groups: MRD-Low (MRD-L), MRD-Medium (MRD-M) and MRD-High (MRD-H). IKZF1 alterations at diagnosis were determined using multiplex ligation-dependent probe amplification and genomic sequencing. We confirmed the strong prognostic significance of MRD classification, which was independent of IKZF1 status. Importantly, in the large MRD-M group (n=81; 62% of patients) containing 46% of the relapsed patients, IKZF1 alteration status identified 8 out of 11 relapsed patients (72%). The 9 year relapse-free survival (RFS) for IKZF1 mutated patients in this MRD-M group was 27% compared to 96% for patients wild-type for IKZF1 (P

Description: Current risk assessments for treatment of children with B-cell precursor acute lymphoblastic leukemia (BCP-ALL) are based on several clinical and biological criteria, including genomic alterations. Genomic profiling of BCP-ALL in the last few years has substantially extended the number of risk factors that can be used for risk stratification, including a novel entity known as BCR-ABL1 -like or Ph-like ALL. This subgroup of BCR-ABL1-like cases is characterized by the high recurrence of a diverse repertoire of novel gene fusions and mutations which frequently result in enhanced tyrosine kinase and cytokine receptor signaling [Roberts et al., NEJM 2014;371:1005-15]. Leukemia's with these alterations could potentially be targeted with appropriate tyrosine kinase inhibitors. Clinical trials with newly-diagnosed patients carrying these alterations are therefore required, but the large genomic diversity within this group of patients currently provides a major bottleneck. Here, we describe the use of Targeted Locus Amplification (TLA), combined with deep-sequencing to detect fusion genes and sequence mutations relevant for stratification of BCP-ALL. TLA involves a strategy to selectively amplify and sequence regions 〉100 kb around a preselected primer pair by crosslinking of physically proximal genomic sequences [de Vree et al., Nat Biotechnol. 2014;32:1019-25]. Since TLA results in the amplification of all sequences at either end of the primer pair, TLA is highly effective in picking up structural variations including novel fusion partners. Furthermore, breakpoints can be identified from the TLA sequencing data from which targets for detection of minimal residual disease can be directly designed. A total of 31 primer sets targeting 19 recurrently affected genes were designed and multiplexed, including the 'classical' players MLL, RUNX1, TCF3, and IKZF1, the tyrosine kinase genes ABL1, ABL2, PDGFRB, CSF1R, JAK1, JAK2, JAK3, FLT3, and TYK2, and the cytokine signaling genes CRLF2, EPOR, IL7R, TSLP, SH2B3, and IL2RB. Primer sets were chosen such that the most relevant regions were sufficiently covered. As a pilot, viable cells from 46 selected BCP-ALL samples were analysed, including 26 cases with a BCR-ABL1 -like expression profile [Den Boer et al., Lancet Oncol. 2009;10:125-34], of which 6 had a known kinase fusion. 7 Gb of aligned sequence data was obtained for each patient sample. All 21 rearrangements known to be present in these samples were detected by TLA, including rearrangements in ETV6-RUNX1 (n=5), MLL (n=4), TCF3-PBX1 (n=3), CRLF2 (n=4), EBF1-PDGFRB (n=2), BCR-ABL1 (n=1), RCSD1-ABL2 (n=1), and SSBP2 -CSF1R (n=1). For 10 of the fusions sequencing depth was sufficient to extract breakpoint-spanning sequences directly. For two cases with known JAK2 fusions with an unknown partner, the fusion gene was identified (TERF2 and BCR), as was the case for an unknown ABL1 fusion (FOXP1). New fusions were identified in 9 cases, including previously described IGH@-EPOR and TCF3-ZNF384 fusions, and novel kinase activating fusions of MAP3K19-TSLP and HDAC9-FLT3. In addition we identified deletion breakpoint fusions in IKZF1, and sequence mutations in JAK1, JAK3,and IL7R. In total, we detected gene fusions or sequence mutations affecting tyrosine kinase or cytokine receptor signaling in 16 of the 26 cases with a BCR-ABL1 -like expression profile. We conclude that TLA is an effective method for the reliable detection of sequence mutations and structural variations that are relevant for disease prognosis and/or could be targeted by approved kinase inhibiton. Disclosures Simonis: Cergentis BV: Employment. Klous:Cergentis BV: Employment. Yilmaz:Cergentis BV: Employment. Splinter:Cergentis BV: Employment.