Abstract: Imatinib mesylate is a potent inhibitor of BCR-ABL, the constitutively active tyrosine kinase protein critical for the pathogenesis of chronic myeloid leukemia. Patients and Methods We reviewed 284 patients with late chronic-phase Philadelphia chromosome (Ph) –positive chronic myeloid leukemia treated with imatinib 400 mg daily after interferon-α failure. In a retrospective study, we evaluated the pattern and rapidity of the response to imatinib, comparing the cytogenetic and molecular responses, progression-free and overall survival rates in patients who obtained a complete cytogenetic response within 1 year of treatment (early responders), and in patients where a complete cytogenetic response was detected after 12 months (late responders). Results After 3 or 4 years of treatment, the molecular response of the late cytogenetic responders was similar to that of the early cytogenetic responders. At 36 months of treatment the amount of residual disease measured by standardized quantitative reverse-transcriptase polymerase chain reaction was 0.00047 in late responders versus 0.00022 in early responders, and at 48 months it was 0.00019 versus 0.00026 (median values, P value = nonsignificant). The estimated 4-year progression-free survival rate was 88% for early responders and 100% for late responders, while the estimated 4-year overall survival rates were 92% and 100% for early and late responders, respectively. Conclusion The sensitivity and the response (cytogenic and molecular) to imatinib may require 1 year or more. Long-term follow-up results continue to improve in terms of rates and durability of the complete cytogenetic response, major or complete molecular response, and progession-free and overall survival.

Abstract: Molecular tests are the best way to monitor CML course in patients under treatment with tyrosine kinase inhibitors (TKI). International guidelines indicate the absolute copy number of the control gene ABL1 as reference for the definition of the sensitivity of the analytical method. A general implementation of the International Guidelines (EUTOS) and the moving forward of current technologies towards one-step reactions, that allow direct testing from the patient RNA, require continuous verification of the method performances. Here, as Italian laboratory network for the standardization of CML diagnosis (LabNet), we performed a comparative study across the three reference laboratories in order to evaluate the inclusion of "BCR-ABL P210 ELITe MGB® Kit" (ELITechGroup S.p.A.) one-step assay among the technologies indicated in the Laboratory Recommendations and Indications (R.I.L.) of the Italian Network for CML monitoring. "BCR-ABL P210 ELITe MGB® Kit" is a new assay that allows to perform in a unique reaction the retro-transcription and the amplification of the extracted RNA sample. In this study 30 RNA extracted from whole blood samples of CML patients at different stages of the disease and centrally distributed to the other reference labs have been analyzed. All laboratories tested 300 ng per reaction of each RNA according the one-step approach and the same RNA according each own routine method. Moreover, in the same experiments, the European Reference Material certified plasmid ERM-AD623 has been evaluated. Our results show an increased analytical sensitivity in detection of both genes (BCR/ABL1 and ABL1): the limit of detection of the one-step reaction is as low as 0.001% IS BCR/ABL1. By testing the ERM-AD623 at 1 copy/reaction the rate of PCR positivities is 63%, and the average estimated quantity is 2.5 (SD = ± 1.5) copies/reaction. The linear measurement range of BCR/ABL1 and of the control gene ABL1 evaluated using the ERM-AD623 reference material are linear and equivalent in the range of 102-107 copies/reaction. Quantifications obtained with this kit are aligned to the European Reference Material. Using 7500 Fast Dx Real-Time PCR Instrument or 7900 Real-Time PCR System (Applied Biosystem, Thermo Fisher Scientific), we confirm that the calibrator of the "BCR-ABL P210 ELITe MGB® Kit" is aligned to the ERM-AD623 DNA international standard and we demonstrated the inter-laboratory low variability and good linearity of the method by processing the secondary reference material aligned to WHO primary reference material. By analysis of 30 RNA of CML patients we observed high results reproducibility among laboratories (figure 1). In addition, at comparison with the individual routine methods (ipsogen BCR-ABL1 Mbcr IS-MMR DX, P210 PHILADELPHIA Q-PCR Alert kit. and an home-made assay) we report up to 97.4% correlation of BCR-ABL P210 ELITe MGB® kit results. In conclusion, our data demonstrate that "BCR-ABL P210 ELITe MGB® Kit" is a rapid, reproducible assay, aligned and calibrated towards the current goal standards BCR/ABL1 assays. It allows direct testing from RNA samples while maintaining the desired sensitivity. By requiring reduced hands on time of the operators and by allowing direct testing of RNA, "BCR-ABL P210 ELITe MGB® kit" will provide a significant improvement in the standardization of the molecular approach to CML monitoring. Figure 1 BCR-ABL P210 ELITe MGB® Kit reproducibility with clinical samples. Data of the individual laboratory were plotted against the mean assigned value. The regression fit of all data is R-Sq=96.8%. Figure 1. BCR-ABL P210 ELITe MGB® Kit reproducibility with clinical samples. Data of the individual laboratory were plotted against the mean assigned value. The regression fit of all data is R-Sq=96.8%. Disclosures Castagnetti: Bristol-Myers Squibb: Consultancy, Honoraria; Novartis: Consultancy, Honoraria; Pfizer: Consultancy, Honoraria; ARIAD Pharmaceuticals: Consultancy, Honoraria. Martinelli:ARIAD: Consultancy; Genentech: Consultancy; Roche: Consultancy; Amgen: Consultancy; MSD: Consultancy; Pfizer: Consultancy, Speakers Bureau; BMS: Speakers Bureau; Genentech: Consultancy; Amgen: Consultancy; Novartis: Speakers Bureau; MSD: Consultancy; Roche: Consultancy; ARIAD: Consultancy; Pfizer: Consultancy, Speakers Bureau. Saglio:Novartis: Consultancy, Honoraria; BMS: Consultancy, Honoraria; ARIAD: Consultancy, Honoraria; Pfizer: Consultancy, Honoraria; Roche: Consultancy, Honoraria.

Abstract: Background: The European LeukemiaNet (ELN) response criteria are widely used to decide, at given time points, when the treatment with tyrosine-kinase inhibitors (TKIs) of CML patients should be continued (optimal response, OR), when a careful monitoring is required (warning, W) or when the therapy should be changed (failure, F). The 2013 ELN response criteria are the same for all chronic phase CML patients, irrespective of the prescribed TKI, but the time to response is influenced by the first-line TKI. Despite faster responses, a clear survival advantage of 2nd generation TKIs over imatinib (IM) has not been demonstrated yet. A validation of the 2013 ELN response definitions and an analysis of their prognostic impact in IM-treated patients may provide important information. Aims: The aim of our study was to assess the significance of 2013 ELN response criteria in CML patients treated frontline with IM, investigating whether or not optimal responders, warnings or failures at 3, at 6 and at 12 months have a different long-term outcome. Methods: 559 patients enrolled within 3 prospective clinical trials (NCT00514488, NCT00510926, observational trial CML/023) were analyzed (ITT population of each study). The 3-month response according to 2013 ELN criteria was not fully evaluable due to missing cytogenetic analysis in 452/559 patients, so we focused on the early molecular response (EMR, BCR-ABL 〈 10% at 3 months), corresponding to OR. The responses at 6 and 12 months were retrospectively defined according to 2013 ELN criteria: F, BCR-ABL 〉 10% and/or Ph+ 〉 35% at 6 months, BCR-ABL 〉 1% and/or Ph+ 〉 0 at 12 months; OR, BCR-ABL 〈 1% and/or Ph+ 0 at 6 months, BCR-ABL 〈 0.1% at 12 months; W: intermediate conditions. As the ELN criteria changed over time, not all the failures switched to alternative treatment. Progression: transformation to advanced phases (2013 ELN definitions) at any time, including after treatment discontinuation. Overall survival (OS): all the deaths at any time (in-study or off-study) were included. Leukemia-unrelated death: known cause of death, no progression, CCyR and/or MMR 〈 6 months prior to death; all other deaths were classified as leukemia-related (LRD). The cumulative incidence of LRD was estimated considering the competing risk of leukemia-unrelated death. Results: The median follow-up was 76 months (66-99 months). The patients with OR at 3 months were 82%; the patients with OR-W-F at 6 months were 76%, 14% and 10%, respectively; the patients with OR-W-F at 12 months were 65%, 20% and 14%, respectively. The OS, the progression-free survival (PFS) and the cumulative incidence of LRD according to the presence-absence of EMR were 87-81% (p=0.015), 85-81% (p=0.035) and 11-5% (p=0.019), respectively. Combining the Sokal score and the EMR, the patients were divided into 4 groups, low and intermediate risk/responders, low and intermediate risk/not responders, high risk/responders, high risk/not responders: the OS and the cumulative incidence of LRD across the 4 groups were 88%, 84%, 86% and 70% (p=0.005, Figure 1) and 3%, 9%, 10% and 20% (p 〈 0.001), respectively. The OS according to the 6-month ELN response (OR-W-F) was 88%, 88% and 70% (p 〈 0.001, Figure 2), the PFS was 88%, 86% and 64% (p 〈 0.001), while the cumulative incidence of LRD was 2%, 5% and 28% (p 〈 0.001), respectively. The patients subsequently remaining on IM treatment according to the ELN response at 6 months (OR-W-F) were 77%, 52% and 26%, respectively. The OS, the PFS and the cumulative incidence of LRD according to ELN response criteria at 12 months (OR-W-F) were 89%, 93% and 78% (p 〈 0.001, Figure 3), 89%, 93% and 77% (p 〈 0.001), and 1%, 1% and 16% (p 〈 0.001), respectively. The patients subsequently remaining on IM according to the response at 12 months (OR-W-F) were 80%, 72% and 35%, respectively. Conclusions: The patients without OR at 3 months (particularly high Sokal score patients) had a significantly poorer outcome compared to patients with OR. The warnings at 6 and 12 months had a similar outcome to optimal responders at the same time points; both had a significantly better outcome than the failures. Compared to optimal responders, a larger proportion of patients classified as warnings was subsequently switched to alternative treatment; the subsequent treatment may explain, at least in part, the absence of outcome differences between these 2 groups. Disclosures Castagnetti: Novartis: Consultancy, Honoraria; BMS: Consultancy, Honoraria; Pfizer: Consultancy, Honoraria; ARIAD: Consultancy, Honoraria. Gugliotta:BMS: Honoraria; Novartis: Honoraria. Abruzzese:BMS, Novartis, Pfizer, Ariad: Consultancy. Tiribelli:Ariad Pharmaceuticals: Consultancy, Speakers Bureau; Bristol Myers Squibb: Consultancy, Speakers Bureau; Novartis Farma: Consultancy, Speakers Bureau. Soverini:Novartis, Briston-Myers Squibb, ARIAD: Consultancy. Cavo:Jansenn: Consultancy, Honoraria; Sanofi: Consultancy, Honoraria; BMS: Honoraria; Millenium Pharmaceuticals: Honoraria; Onyx: Honoraria; Celgene: Consultancy, Honoraria; Novartis: Consultancy, Honoraria. Martinelli:MSD: Consultancy; Roche: Consultancy; ARIAD: Consultancy; Pfizer: Consultancy, Speakers Bureau; BMS: Speakers Bureau; Novartis: Speakers Bureau. Saglio:Novartis: Consultancy, Honoraria; BMS: Consultancy. Baccarani:BMS: Honoraria, Speakers Bureau; Novartis: Honoraria, Other: Consulting or Advisory Role, Speakers Bureau; Pfizer: Honoraria, Other: Consulting or Advisory Role, Speakers Bureau; ARAID Pharmaceutical Inc.: Other: Consulting or Advisory Role, Speakers Bureau; Novartis: Other: Travel, Accommodations, Expenses; BMS: Other: Travel, Accommodations, Expenses; Pfizer: Other: Travel, Accommodations, Expenses; ARIAD Pharmaceutical Inc.: Other: Travel, Accommodations, Expenses. Rosti:Bristol Myers Squibb: Honoraria, Research Funding, Speakers Bureau; Novartis: Honoraria, Research Funding, Speakers Bureau.

Abstract: The e13a2 and the e14a2 are the most frequent BCR-ABL1 transcripts in chronic myeloid leukemia (CML) patients. The aim of the present study was to assess the prognostic value of the e13a2 (b2a2) or the e14a2 (b3a2) fusion transcripts on the long-term outcome of early chronic phase (ECP) CML patients treated frontline with imatinib mesylate (IM). Few studies, mostly based on a small number of patients or with a relatively short observation, have been published, particularly in ECP setting. Due to partially conflicting data, the transcript type is not actually considered an established baseline prognostic factor. To our knowledge, this is the first long-term analysis conducted in the context of large prospective studies. Methods A retrospective analysis of 3 GIMEMA CML WP prospective clinical studies (NCT00514488, NCT00510926, observational study CML/023) was performed. All the 559 enrolled patients were analyzed. A qualitative RT-PCR for BCR-ABL1 transcript was routinely performed at enrollment. Patients expressing rare transcripts or with both e13a2-e14a2 transcripts were excluded: 493 out of 559 patients were included, 203 (41%) with e13a2 transcript and 290 with e14a2 transcript (59%). Definitions. Major molecular response (MMR): BCR-ABL1IS ratio 〈 0.1%. Deep molecular response (MR4.0): detectable disease ≤ 0.01% BCR-ABL1IS or undetectable disease with ≥10,000 ABL1 transcripts. Progression: transformation to accelerated or blastic phase. Failure: according to 2013 ELN recommendations. Event: failure or permanent discontinuation for any reasons. All the deaths, at any time and for any reasons, were included. Results The median follow-up was 76 months; 95% of the patients had at least a 5-year observation. The 2 groups were comparable for demographic and hematologic characteristics, except for the proportion of male patients, that was higher in the e13a2 group (p = 0.05), and for the baseline percentages of eosinophils, that was lower in the e13a2 group (p = 0.009). The Sokal, Hasford and EUTOS risk score distributions and the proportion of patients with CCA in Ph+ cells were comparable. The complete cytogenetic response (CCyR) rate at 12 month was not significantly different (75% and 79% in e13a2 e14a2 patients, respectively, p=0.274), but the MMR rate at 18 months and the MR4.0 at 36 months were significantly lower in e13a2 patients (52% and 67%, p = 0.001; 20% and 30%, p = 0.013, respectively). As far as the rapidity of response, the time to MMR and the time to MR4 were significantly slower for patients with e13a2 transcript (12 and 6 months; 54 and 37 months, respectively), with an inferior overall estimated probability of MMR (85% and 92%, p 〈 0.001) and MR4 (57% and 71%, p = 0.002). The overall survival (83% and 86%, p = 0.023), the progression-free survival (81% and 86%, p = 0.007), the failure-free survival (54% and 71%, p 〈 0.001) and the event-free survival (46% and 61%, p = 0.003) were significantly lower in patients with e13a2 transcript (figure 1). In a multivariate analysis (Cox model), the transcript type retained its prognostic significance, when adjusted for other relevant variables. Analyzing separately the patients treated with IM 400 mg (n = 371; e13a2 and e14a2 transcript: 208 and 163 patients, respectively) or IM 800 mg (n = 122; e13a2 and e14a2 transcript: 82 and 40 patients, respectively), all the above mentioned response and outcome differences were confirmed, with one exception: in the high-dose IM group the overall survival probability was inferior for the e13a2 patients, but, probably due to the small number of patients, the difference was not statistically significant (83% and 86%, p = 0.268). Conclusions A long-term analysis in a large cohort of CML patients suggests that the e13a2 transcript is an adverse prognostic factor in ECP CML patients treated frontline with IM. An independent evaluation is required for confirmation. Acknowledgments University of Bologna, BolognaAIL, COFIN, Fondazione Carisbo. Disclosures: Castagnetti: Novartis: Consultancy, Honoraria; Bristol Myers Squibb: Consultancy, Honoraria. Gugliotta:Novartis: Consultancy, Honoraria; Bristol-Myers Squibb: Consultancy, Honoraria. Abruzzese:BMS, Novartis: Consultancy.

Abstract: Abstract 2196 Poster Board II-173 BACKGROUND: Imatinib (IM) 400 mg daily is the standard treatment for Chronic Myeloid Leukemia (CML) in early chronic phase (ECP). The European LeukemiaNet (ELN) recommendations were designed to help identify ECP CML patients responding poorly to front-line IM, suggesting, at given time points, when the treatment strategy should be changed (”failure”), or when “the long-term outcome of the treatment would not likely be as favourable” (“suboptimal response”). Suboptimal response is a “grey zone”: the patient may still have substantial benefit from continuing IM, but other therapies should be considered. AIM: To assess the outcome of “failure” and “suboptimal responders” Philadelphia-positive (Ph+) CML patients in a large multicentric, nationwide experience. METHODS: Between January 2004 and April 2007, 559 patients were enrolled in an observational study and in 2 independent intervention studies of the GIMEMA CML WP (Clin Trials Gov. NCT00514488 and NCT00510926). Response monitoring was based on conventional cytogenetic examination of bone marrow cell metaphases every 6 months and RT Q-PCR evaluations of blood cells after 3, 6, 12 months, and every 6 months thereafter. Definitions: major molecular response (MMR): BCR-ABL/ABL ratio 〈 0,1%IS; failure (according to ELN criteria): no hematologic response (HR) at 3 months, no complete HR (CHR) at 6 months, no cytogenetic response (CgR) at 6 months, no partial CgR (PCgR) at 1 year, no complete CgR (CCgR) at 18 months, loss CHR or CCgR, progression or death; suboptimal response (according to ELN criteria): no CHR at 3 months, no PCgR at 6 months, no CCgR at 12 months, no MMR at 18 months ; optimal response: non-suboptimal and non-failure at each time-point; event: failure or treatment discontinuation for any reason. All the calculations have been made according to the intention-to-treat principle. RESULTS: The patients who fitted the ELN criteria for failure had a significantly lower probability of subsequently achieving a CCgR and a MMR, and had a significantly lower overall survival (OS), failure-free survival (FFS) and event-free survival (EFS). The patients who fitted the ELN definitions of suboptimal response at 6 months (data not shown) and at 12 months (figure 1) had a significantly lower probability than “optimal” responders of subsequently achieving a CCgR and a MMR, and a significantly poorer FFS and EFS (figure 1), while the OS was not different in the two groups (90% and 95%, p= 0.35). CONCLUSIONS Our data confirms that suboptimal responders at 6 and at 12 months have a poorer outcome with respect to “optimal” responders, comparable to the outcome of failure patients. Acknowledgments: European LeukemiaNet, COFIN, University of Bologna and BolognAIL. Disclosures: No relevant conflicts of interest to declare.

Abstract: Idiopathic hypereosinophilic syndrome (HES) is an infrequent hematological disorder characterized by persistent eosinophilia with organ involvement, often presenting to other medical specialists. We studied 89 primary HES defined as a peripheral blood eosinophilia greater than 1,500 cells/μL for longer than 6 months, absence of other apparent aetiologies for eosinophilia and symptoms of organ involvement. All patients were negative by molecular analysis for TEL-PDGFRB, and/or BCR-ABL transcripts, frequently associated with HES/CMML/MDS syndromes. We also sought for the recently reported involvement of PDGFRalpha, cryptically fused with FIP1L1 in some HES patients responsive to Imatinib therapy: 34 patients were positive for the FIP1L1-PDGFRA rearrangement and all of them showed previously unreported, abnormal-sized fusion transcripts. A specific RT-PCR assay has been set up for this analysis and a quantitative Q-RT-PCR Taqman assay is in development. Of note, all FIP1L1-PDGFRA positive patients were male. 56 out of 89 (62%) primary HES patients, including 31/34 FIP1L1-PDGFRA positive, were sensitive to imatinib mesylate (100 to 400 mg/daily). Median follow up of treatment was 10 months (range 2–28). Rapid and complete haematological responses (CHR) to imatinib therapy were recorded in all FIP1L1-PDGFRA positive patients (91%) after one month of therapy and partial response in nine cases with HES but without FIP1L1-PDGFRA fusion transcript. Complete molecular response without evidence of FIP1L1-PDGFRA transcript by qualitative RT-PCR was also recorded in the majority of responding patients after median 2 months of therapy, however in few cases the complete molecular response could be recognised only after more than 18 months of imatinib therapy. We conclude that FIP1L1-PDGFRA rearrangement is a useful molecular marker of myeloproliferative HES, a predictor of imatinib-responsiveness and as a means to follow therapy in this subgroup of patients.

Abstract: The median age of chronic myeloid leukemia (CML) patients is ∼ 60 years, and age is still considered an important prognostic factor, included in Sokal and EURO risk scores. However, few data are available about the long-term outcome of older patients treated with imatinib (IM) frontline. We analyzed the relationship between age and outcome in 559 early chronic-phase CML patients enrolled in 3 prospective clinical trials of Gruppo Italiano Malattie Ematologiche dell'Adulto CML Working Party, treated frontline with IM, with a median follow-up of 60 months. There were 115 older patients (≥ 65 years; 21%). The complete cytogenetic and major molecular response rates were similar in the 2 age groups. In older patients, event-free survival (55% vs 67%), failure-free survival (78% vs 92%), progression-free survival (62% vs 78%), and overall survival (75% vs 89%) were significantly inferior (all P 〈 .01) because of a higher proportion of deaths that occurred in complete hematologic response, therefore unrelated to CML progression (15% vs 3%, P 〈 .0001). The outcome was similar once those deaths were censored. These data show that response to IM was not affected by age and that the mortality rate linked to CML is similar in both age groups. This trial was registered at www.clinicaltrials.gov as #NCT00514488 and #NCT00510926.

Abstract: Imatinib is a tyrosine-kinase inhibitor that binds to ABL proteins and induces cytogenetic remissions in patients with chronic myeloid leukemia (CML). In these patients measuring response by molecular techniques is clearly required. We determined the cytogenetic and molecular response (CgR, MR) to imatinib in 191 patients with late chronic-phase Philadelphia-positive (Ph+) CML, previously treated with interferon α. MR was assessed with real-time quantitative (TaqMan) reverse transcription–polymerase chain reaction and was expressed as the ratio between BCR/ABL and β2-microglobulin × 100, the lowest level of detectability of the method being 0.00001. A complete CgR (CCgR) was achieved in 85 (44%) of 191 patients and was maintained for 2 years in 67 (79%) of 85 patients. A reduction of the transcript level of more than 2 logs was achieved in all but 9 patients with CCgR versus none of 23 with partial CgR. In the CCgRs the median value of the MR was 0.0008 after 12 months and 0.0001 after 24 months, with the transcript level undetectable in 22 cases. We conclude that in CCgRs the degree of MR may vary from 2 to more than 4 logs, and that there is a progressive decrease of transcript level by time. Only 1 of 22 negative cases has had a relapse as yet.

Abstract: Purpose: Most patients with chronic-phase chronic myeloid leukemia (CML) who receive imatinib achieve a complete cytogenetic remission (CCgR) and low levels of BCR-ABL transcripts. CCgR is durable in the majority of patients but relapse occurs in a subset. Experimental Design: To determine the potential of quantitative reverse transcription-PCR of BCR-ABL to predict cytogenetic relapse, we serially monitored residual disease in 97 CML patients with an imatinib-induced CCgR. Patients with late chronic phase CML after IFN-α failure were treated with imatinib (400 mg daily). Results: During the imatinib median follow-up time of 36 months (range, 12-54 months), disease monitoring occurred by cytogenetics and quantitative PCR. Twenty percent of patients experienced cytogenetic relapse at a median of 18 months after CCgR and a median of 24 months after starting imatinib. None of the possible prognostic factors studied in univariate and multivariate analyses seemed to predict for loss of cytogenetic response but the reduction of BCR-ABL transcript levels at the time of CCgR is an important prognostic factor. Conclusions: In our study, we showed not only that achieving a major molecular remission at 12 months is predictive of a durable cytogenetic remission but also that patients who achieved a major molecular remission (expressed both as the BCR-ABL/β2 microglobulin ratio % & lt;0.0005 and as a 3-log reduction from median baseline value) already at the time of first achieving a CCgR have significantly longer cytogenetic remission durations than those without this magnitude of molecular response (P & lt; 0.05).

Abstract: Background: Although the pathogenesis of BCR-ABL1+ ALL is mainly related to the expression of BCR-ABL1, additional genetic lesions are supposed to be involved in its development and progression. Aim: In order to define the full repertoire of leukemia-related mutations, changes in expression profiles and alternative splicing (AS) events, the leukemia transcriptome of a BCR-ABL1+ ALL patient at diagnosis and relapse was sequenced using a Whole Transcriptome Sequencing (RNA-Seq) approach. Methods: Poly(A) RNA from blast cells was used to prepare cDNA libraries for Illumina/Solexa Genome Analyzer. Obtained sequence reads were mapped to the human genome reference sequence (UCSC hg18) to identify single nucleotide variants (SNVs). Reads that showed no match were mapped to a dataset of all possible splice junctions created in silico to identify AS events. The number of reads corresponding to RNA from known exons was also estimated and a normalized measure of gene expression level (RPKM) was computed. Results: RNA-seq analysis generated 13.9 and 15.8 million reads from de novo and relapsed ALL samples, respectively, detecting transcripts from 62% and 64% of human annotated genes. Low RPKM estimates (0.01 & lt;RPKM & lt; 10) were computed for the great majority of genes (78% at diagnosis and 73% at relapse), whereas a moderate expression (10 & lt;RPKM & lt; 100) was observed for 20% − 24% of active genes and only 2% − 3% of transcripts had high RPKM values (100 & lt;RPKM & lt; 8000). Moreover, 4,334 and 3,651 primary ALL and relapse isoforms with at least one AS event were identified. An average of 1.5 and 1.3 AS per isoform was estimated. The well-known alternatively spliced IKZF1 gene was also detected. Finally, 2,011 and 2,103 SNVs were found at diagnosis and relapse respectively, about 94% of which have been already reported in the dbSNP. As potential ALL-related mutations, 124 and 114 not annotated SNVs were found at diagnosis and relapse, respectively. Of these, 43 affected both samples, while 81 and 71 resulted private variants. The analysis was focused on the coding sequences of annotated genes, finding 12 non-synonymous changes: 1 affecting the PLXNB2 gene on both samples, 6 affecting genes involved in metabolic processes (PDE4DIP, EIF2S3, DPEP1, ZC3H12D, TMEM46) and transport (MVP) at diagnosis and 3 affecting genes involved in cell cycle regulation (CDC2L1) and catalytic activity (CTSZ, CXorf21) at relapse. Furthermore, the T315I mutation in the Bcr-Abl kinase domain was also identified. Conclusions: Discovery of novel missense mutations, as well as exhaustive alternative splicing and gene expression profiles were achieved for the first time for a BCR-ABL1+ positive ALL patient demonstrating that RNA-Seq is a suitable approach for identifying a wide spectrum of genetic alterations. Supported: AIL, AIRC, FIRB, European LeukemiaNet. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 651.