Ketterling, Rhett P.

Abstract Background : Momelotinib is a JAK1 and JAK2 inhibitor that is currently being evaluated in phase-3 clinical trials for the treatment of myelofibrosis (MF) (NCT01969838, NCT02101268). In a phase-1/2 clinical trial of patients with MF, the drug was shown to improve anemia, reduce spleen size and alleviate symptoms (Leukemia 2013;27:1322). In the current study, we considered 100 consecutive patients from the Mayo Clinic who received momelotinib therapy, in order to identify molecular and cytogenetic predictors of treatment response and survival from the time of study entry. Methods : The study patients constituted part of a phase-1/2 clinical trial (NCT00935987) using momelotinib in MF. Details of the protocol, including inclusion and exclusion criteria were previously published (Leukemia 2013;27:1322). Response was determined by the 2006 response criteria published by the IWG-MRT. Data analysis and interpretation was carried out independent of any influence from the sponsor. Results : 100 patients with MF (median age 66 years; 58% males) were treated at the Mayo Clinic between 11/20/09 and 11/10/10. MF type was primary in 64% of the patients and post-polycythemia vera/essential thrombocythemia in 36%. DIPSS-plus risk distribution was 63% high, 36% intermediate-2 and 1% intermediate-1. Red cell transfusion dependency was documented in 49% and palpable spleen size of >5 cm (median 19 cm) in 92%. All patients were annotated for JAK2/CALR/MPL mutations with respective frequencies of 73%, 16% and 7%. Frequencies for other mutations included 42% for ASXL1 (84 evaluable) and 18% for SRSF2(78 evaluable). All patients were evaluable for karyotype, which was unfavorable in 17%. Previous treatment included other JAK inhibitors in 21 patients, thalidomide/lenalidomide/pomalidomide in 31 and hydroxyurea or other cytoreductive agents in 55. Momelotinib was initiated at 100 mg/day in 3 patients, 150 mg/day in 21, 150 mg twice-daily in 20, 200 mg/day in 3, 300 mg/day in 47 and 400 mg/day in 6. The maximum momelotinib dose was 150 mg/day in 6 patients, 150 mg twice-daily in 20, 300 mg/day in 68 and 400 mg/day in 6. Treatment duration was <6 months in 12 patients, 6-12 months in 22, 12-24 months in 19 and >24 months in 47. Genetic correlates of response to momelotinib : Overall response rate was 57% and included no complete remissions (0%), one (1%) partial remission and 57 (57%) clinical improvements (CI). Response rates for spleen/liver and anemia were 43% (91 evaluable) and 44% (68 evaluable), respectively. Transfusion independency was achieved in 25 (51%) of 49 evaluable cases. Spleen/liver response rate was significantly affected by JAK2/CALR/MPL mutational status (34% vs 73% vs 60%, respectively, and 50% in triple-negative; p=0.04), CALR mutated vs unmutated status (73% vs 37%; p=0.009), and unmutated vs mutated ASXL1 (53% vs 29%; p=0.035). Furthermore, all 8 (100%) patients who were CALR+/ASXL1- responded vs 6 (25%) of 24 CALR-/ASXL1+ vs 3 (50%) of 6 CALR+/ASXL1+ vs 16 (43%) of 37 CALR-/ASXL1- patients (p=0.003). Spleen/liver response rates were not affected by SRSF2 mutations (p=0.93) or karyotype (p=0.41). Anemia response rate was not affected by JAK2/CALR/MPL (p=0.81), ASXL1 (p=0.16), SRSF2 (p=0.12) or CALR/ASXL1 (p=0.42) mutational status or karyotype (p=0.65). The number of informative cases for EZH2, IDH, SF3B1 and U2AF1mutations were not adequate enough to warrant similar analysis. Genetic correlates of survival from time of protocol entry : Median follow-up after the institution of protocol drug therapy was 35 months (range 1-49). During this period, 57 (57%) deaths and 12 (12%) leukemic transformations were documented. On multivariable analysis, shortened survival was predicted by the presence of ASXL1 (p=0.01; HR 2.1, 95% CI 1.2-3.8) or SRSF2 (0.01; HR 2.4, 95% CI 1.2-4.8) mutations and the absence of CALR mutations (p=0.03; HR 3.2, 95% CI 1.1-8.9). Karyotype was significant on univariate (p=0.01) but not in multivariable (p=0.6) analysis that included the aforementioned mutations. The prognostic relevance of each specific mutation was DIPSS-plus independent. Conclusions : We demonstrate significant associations between CALR and ASXL1 mutational status and spleen response to momelotinib therapy in MF. We also show that momelotinib therapy did not overcome the inferior survival associated with the presence of ASXL1 or SRSF2 mutations or the absence of CALR mutations. Disclosures No relevant conflicts of interest to declare.

Abstract Background : The 2016 revision to the World Health Organization classification of myeloid neoplasms has recommended distinction between "proliferative" (WBC ≥ 13 x 10(9)/L) and "dysplastic" (WBC < 13 X 10(9)/L) subtypes of chronic myelomonocytic leukemia (CMML). In addition, CMML is characterized by a spectrum of cytogenetic and molecular abnormalities (Patnaik Leukemia 2014). In the current study, we looked for correlations between gene expression profiles (GEP) and morphologic or molecular categories of previously untreated patients with CMML. Methods : 35 patients with CMML were included in the study. Targeted capture assays were carried out on BM DNA specimens obtained at diagnosis for 28 myeloid-relevant genes (Patnaik Blood C. J.). RNA sequencing (Stranded Total RNA- Illumina, San Diego, CA), was performed on 9 normal BM controls, and 35 CMML samples (25 peripheral blood (PB) and 10 BM). The RNA-Seq data was analyzed using MAPRSeq v.2.0. Normalization and differential expression analysis was performed using edgeR 2.6.2. We selected genes that were differentially expressed with a False Discovery Rate (FDR) <0.1 and a fold change bigger than 2. Pathway enrichment analysis was performed using Ingenuity Pathway Analysis (IPA). Results: Among the 35 study patients, 75% were males and median age was 71 years (range, 55-87). 21 (60%), 9 (25%) and 5 (15%) patients were classified as CMML-0, 1 and 2, respectively. 16 (45%) had a dysplastic while 19 (55%) had a proliferative phenotype. At a median follow-up of 16 months, 5 (14%) deaths and 4 (14%) leukemic transformations were documented. Mutational frequencies included; TET2 45%, ASXL1 45%, SRSF2 40%, NRAS 14%, SETBP1 13%, CBL 10%, JAK2 7%, RUNX1 6%, DNMT3A 6%, U2AF1 6%, SF3B1 5%, ZRSR2 4%, Tp53 4%, and IDH2 4%. Abnormal cytogenetics (n=9, 35%) included; -Y 8%, trisomy 8 6%, monosomy 7 3%, del(13q) 3% and monosomal karyotype 3%. i) Differential GEP in PB samples: 25 PB CMML samples were analyzed. Unsupervised GEP demonstrated two unique clusters (figure one); cluster one was enriched with dysplastic CMML (90%) and cluster two with proliferative CMML (64%). Consistent with the difference in the distribution of morphologic categories, in comparison to cluster one, patients in cluster two had a higher white blood count (p=0.003), higher monocyte count (p=0.02) and higher risk prognostication by the Mayo Model (p=0.016); there was no significant difference between the two clusters in terms of age and gender distribution, hemoglobin level, neutrophil and platelet counts, PB or BM blast content, cytogenetic risk stratification, ASXL1, TET2, RAS, CBL and SETBP1 mutational status. Genes significantly upregulated (FDR<1e-5 and fold change ≥ 16x); in cluster two (proliferative CMML) in comparison to cluster one included; PRG2, CTSG, BEX1, CD34, CRISP2, while those significantly down-regulated included (FDR<1e-15 and fold change ≥ 5x); IL2RB, PRF1, GNLY, PDGFRB. IPA analysis identified the following pathways preferentially expressed in cluster two (proliferative CMML) 1) mitotic roles of polo-like kinase (KIF23, WEE-1, PLK1, PLK4), 2) Cell cycle: G2/M checkpoint regulation (CDC25C, WEE-1, AURKA, CDK1), 3) Cell cycle: chromosomal replication (CDC45, RPA3, MCM2, CDC7), and 4) BRCA1 in DNA damage response (BARD1, RBBP8, PLK1, RAD51). Whereas in the cluster one (dysplastic CMML), preferentially expressed pathways included; 1) T-cell receptor signalling (CD247 PRKCQ, CD4, PLCG1, CD28) and 2) STAT3 signalling (SOCS3, MAP3K9). ii) Differential GEP in BM samples: 10 BM CMML samples were analyzed along with 10 normal controls. Samples and controls clustered separately and within the CMML samples two clusters were identified (figure two). These clusters had equal representations of dysplastic (n=5) and proliferative (n=5) CMML sub-types. Additional samples are being processed. Conclusions: Differential gene expression profiling in patients with CMML identifies two unique clusters, clinically demarcated, at least in PB samples, by "proliferative" and "dysplastic" CMML subtypes. The proliferative cluster is enriched in genes involved in cell cycle regulation and DNA damage response; whereas the dysplastic cluster is enriched in T-cell receptor and STAT3 signalling. The prognostic and therapeutic impact of these gene clusters remains to be assessed in a larger group of informative patients. Figure 1. Figure 1. Figure 2. Figure 2. Disclosures Al-Kali: Novartis: Research Funding; Celgene: Research Funding.

Abstract Background: Momelotinib is a JAK 1/2 inhibitor that is active in the treatment of myelofibrosis (MF); a previous phase 1/2 study included 100 consecutive patients from the Mayo Clinic (Leukemia. 2015;29:741). In the current long-term study of these 100 patients, we provide a cumulative account of short and long term efficacy and toxicity data, as well as survival analysis. Methods: The current study represents sponsor-independent analysis. The study patients are part of a larger (n=166) phase-1/2 momelotinib study (NCT00935987), which was conducted in two dose-escalation (100 mg-400 mg daily doses) and dose-confirmation (300 mg daily dose) phases. Adverse events (AEs) were monitored by Common Terminology Criteria for Adverse Events (Version 4.03) and responses by the International Working Group criteria (Blood. 2013;122:1395). All statistical analyses considered clinical and laboratory parameters obtained at the time of entry to study. Results: Baseline data: 100 patients with MF (median age 66 years; 58% males) were treated between 11/20/09 and 11/10/10; 64 patients had primary MF, 22 post-polycythemia vera MF and 14 post-essential thrombocythemia MF. 73 (73%) patients harbored JAK2 mutations, 16 (16%) CALR, 7 MPL and 4 were "triple-negative"; among the 16 CALR-mutated cases, 13 were classified as "type 1/type 1-like". DIPSS-plus risk distribution (JCO 2011;29:392) was 63% high, 36% intermediate-2 and 1% intermediate-1; 49% displayed red cell transfusion-dependency, 58% constitutional symptoms, 87% palpable splenomegaly >5 cm and 50% abnormal karyotype. 94 patients were screened for ASXL1 mutations with 41 (44%) mutated and 78 for SRSF2 mutations with 14 (18%) mutated. 21 (21%) patients were previously treated with another JAK inhibitor. Current disposition: All information was updated in July 2016. To-date, after a median follow-up of 3.2 years, 88 drug discontinuations, 70 deaths and 14 leukemic transformations have been documented; median follow-up for living patients was 5.7 years (range 5.1-6.4). Among the 30 patients who are currently alive, 12 remain on study and another 5 have received stem cell transplant. Toxicity data: After a median treatment duration of 1.7 years, "momelotinib related" grade 3 or 4 AEs included thrombocytopenia (34%), neutropenia (9%), anemia (5%), increased lipase (7%), increased ALT (4%), increased AST (2%), increased ALP (2%) and headaches (2%). In addition, noteworthy grade 1 or 2 AEs included peripheral neuropathy (PN) 47%, increased lipase (14%), increased amylase (17%), increased bilirubin (13%), increased AST (21%), increased ALT (19%), increased APTT (17%), headaches (13%), dizziness (22%), nausea (23%) and diarrhea (20%). Most of the AEs, except PN, were reversible. Efficacy data and predictors of response and relapse-free survival: Clinical improvement (CI) was documented in 57% of patients, anemia response in 44%, and spleen response in 43%. 51% of transfusion-dependent patients became transfusion independent. The majority of patients also had marked improvement in their symptoms. 46 (81%) of the 57 responding patients discontinued treatment after a median treatment duration of 2.3 years. ASXL1 mutations predicted inferior CI (p=0.03) whereas relapse-free survival was adversely affected by absence of type 1/type 1-like CALR (p=0.03) or presence of unfavorable karyotype (p=0.002); among the 11 responding patients currently still receiving the drug, all had favorable karyotype and 5 had type 1/type 1-like CALR mutations. Survival analysis and risk factors : Median survival, calculated from the time of study entry, was 3.2 years with 5-year survival rate of 32%. In multivariable analysis of genetic markers, absence of type 1/type 1-like CALR (HR 2.9, 95% CI 1.1-7.2) or presence of SRSF2 (2.9, 1.5-5.4) or ASXL1 (1.8, 1.1-3.2) mutations were independently predictive of shortened survival (Figure). Conclusions: Momelotinib therapy in MF provides effective palliation in terms of anemia, splenomegaly and constitutional symptoms. However, less than 20% of treated patients enjoy durable long-term benefit and almost half experience drug-related and mostly irreversible peripheral neuropathy. Long-term survival and durability of response were superior in patients with type 1/type 1-like CALR mutations and inferior in those with ASXL1/SRSF2 mutations or unfavorable karyotype. Figure Figure. Disclosures Al-Kali: Onconova Therapeutics, Inc.: Research Funding; Celgene: Research Funding.

Abstract Background: Cytogenetic evaluation using fluorescence in situ hybridization (FISH) at the time of diagnosis is essential for initial risk stratification in multiple myeloma. The presence of specific cytogenetic abnormalities is known to confer a poor prognosis, less is known about the cumulative effect of multiple cytogenetic high-risk abnormalities. We aimed to evaluate the prognostic implications of the presence of multiple cytogenetic high-risk abnormalities at the time of diagnosis. Methods: We studied 226 patients who were diagnosed with multiple myeloma between July 2004 and July 2014 at Mayo Clinic Rochester, underwent FISH evaluation within six months of diagnosis, and presented with cytogenetic high-risk abnormalities. High-risk cytogenetics were defined as t(4;14), t(14;16), t(14;20), del(17p), or gain(1q). Bone marrow aspirates were evaluated for deletions, monosomies, trisomies, and tetrasomies using chromosome- or centromere-specific FISH probes. IGH rearrangements were evaluated using an IGH break-apart probe and evaluating up to five potential partners (FGFR3, CCND1, CCND3, MAF, and MAFB). Kaplan-Meier overall survival estimates were calculated and the log-rank test was used to compare overall survival in patients with single and multiple cytogenetic high-risk abnormalities. A multivariable-adjusted Cox regression model was used to assess the effect of multiple cytogenetic high-risk abnormalities on overall survival adjusting for age, sex, and Revised International Staging System (R-ISS) stage. P-values below 0.05 were considered statistically significant. Results: The median age at diagnosis was 65 years (32 - 90), 129 (57%) of the patients were male. The median overall survival was 3.5 years (3.1 - 4.9) for the entire cohort (n = 226), 4.0 years (3.3 - 5.1) for those with one cytogenetic high-risk abnormality (n = 182, 80%), and 2.6 years (1.7 - 3.1) for those with two cytogenetic high-risk abnormalities (n = 44, 20%). There were no patients with more than two cytogenetic high-risk abnormalities. Ninety-eight patients (45%) had a high-risk translocation, 77 (35%) had del(17p), 39 (18%) had a high-risk translocation plus del(17p), and 5 (2%) had gain(1q) plus either a high-risk translocation or del(17p). Figure 1 shows the Kaplan-Meier overall survival estimates stratified by the number of cytogenetic high-risk abnormalities (n = 226). The presence of two cytogenetic high-risk abnormalities (compared to one) was of prognostic significance after adjusting for age, sex, and R-ISS stage (HR 2.01, 95% CI 1.27 - 3.19, p = 0.003, n = 205). Conclusions: Approximately one in five patients with newly diagnosed high-risk multiple myeloma presented with two high-risk abnormalities at the time of diagnosis. These patients experienced inferior overall survival suggesting a cumulative effect of multiple cytogenetic high-risk abnormalities. The relatively low number of observed gain(1q) was likely related to the fact that not all patients were evaluated for that abnormality. Therefore the presented hazard ratio represents a conservative effect estimate and may underestimate the true effect. Figure 1 Figure 1. Disclosures Dispenzieri: GSK: Membership on an entity's Board of Directors or advisory committees; Jannsen: Research Funding; Alnylam: Research Funding; Celgene: Research Funding; Takeda: Membership on an entity's Board of Directors or advisory committees, Research Funding; Prothena: Membership on an entity's Board of Directors or advisory committees; pfizer: Research Funding. Kapoor:Takeda: Research Funding; Celgene: Research Funding; Amgen: Research Funding. Kumar:Janssen: Consultancy, Research Funding; BMS: Consultancy; AbbVie: Research Funding; Millennium: Consultancy, Research Funding; Onyx: Consultancy, Research Funding; Celgene: Consultancy, Research Funding; Sanofi: Consultancy, Research Funding; Skyline: Honoraria, Membership on an entity's Board of Directors or advisory committees; Array BioPharma: Consultancy, Research Funding; Noxxon Pharma: Consultancy, Research Funding; Kesios: Consultancy; Glycomimetics: Consultancy.

Background: Small lymphocytic lymphoma/chronic lymphocytic leukemia (SLL/CLL) is a lymphoproliferative disorder of small mature B-cells, most commonly presenting with peripheral blood and bone marrow involvement. Tumoral lesions are variably encountered, resulting from either lymph node involvement or, less commonly, infiltration into virtually any extramedullary site. The prognostic assessment of patients with SLL/CLL relies strongly on the identification of recurrent chromosomal abnormalities, which are routinely tested by fluorescence in situ hybridization (FISH) on peripheral blood or bone marrow specimens. However, the incidence of such recurrent chromosomal abnormalities on tumoral lesions has only been studied on small series, and its concordance with peripheral blood and/or bone marrow testing remains unknown. We hereby report a large series of chromosomal abnormalities detected on tumoral SLL/CLL lesions, based on a validated FISH panel for formalin-fixed/paraffin-embedded (FFPE) biopsy sections. Methods: FISH was performed at Mayo Clinic on FFPE tissue sections from biopsies obtained from May 2014 to November 2018, as clinically indicated. Pathology reports and H&E-stained sections were reviewed and were consistent with a diagnosis of SLL/CLL in all cases. Probes were validated to detect previously described chromosomal abnormalities in SLL/CLL, including trisomy 12 (+12) and deletions of 6q23 (6q-), 11q22.3 (11q-), 13q14.3 (13q-) and 17p13.1 (17p-). Available FISH results performed on peripheral blood or bone marrow samples from these patients were also reviewed for comparison. Results: Tissue biopsies involved by SLL/CLL from 346 patients were evaluated by FISH. The majority of specimens were either lymph nodes (65%) or soft tissue masses (29%). The median age was 66.9 years (range: 36 to 91), and the male to female ratio was 2.1:1. FISH abnormalities were identified in 60% of evaluated tissue sections. The most frequently detected aberration was +12 (35%), followed by 13q- (24%), 11q- (15%), 17p- (6%) and 6q- (2%) (Figure A). In particular, the incidence of +12 was significantly higher, and the incidence of 13q- significantly lower compared to frequencies previously reported on peripheral blood or bone marrow specimens (p<0.01 for both abnormalities, in comparison to a recently published cohort of 1585 patients: Br J Haematol 2016;173:105). Most cases had 1 abnormality (55%), with fewer patients having 2 abnormalities (13%), and only 1 case showing 3 abnormalities. Of 47 patients with 2 or more chromosomal aberrations, most (72%) had 13q- in combination with either 11q- (7 cases), +12 (10 cases) or 17p- (7 cases) (Figure 1B). Of 29 patients with positive blood or bone marrow FISH results within 12 months of tissue biopsy, 7 patients (24%) had discrepant results, all of which were limited to discordant +12 and/or 13q- detection. In 14 additional patients with positive blood or bone marrow FISH results more than 12 months before or after tissue biopsy, discordant results were found in 3 cases (21%), all of which indicated gains of 17p- (2 cases) or 11q- (1 case) on the follow-up analysis. Conclusions: We hereby report the largest documented series (to the best of our knowledge) of FISH results performed on tumoral lesions of SLL/CLL. Trisomy 12 was overrepresented in tumoral lesions, as compared to the reported predominance of 13q- in leukemic involvement. Discrepant results between concurrent tumoral and leukemic FISH testing were limited to differences in +12 and 13q- in our series. We also document the acquisition of aberrancies of unfavorable prognosis (17p- and 11q-) on follow up FISH analysis in a small subset of patients, which should be taken into account when considering repeat FISH studies. Figure Disclosures Horna: MorphoSys AG: Research Funding.

Introduction: Abnormal metaphase cytogenetics are associated with inferior survival in newly diagnosed multiple myeloma (MM). These abnormalities are only detected in one third of cases due to the low proliferative rate of plasma cells. It is unknown if metaphase cytogenetics improve risk stratification when using contemporary prognostic models such as the revised international staging system (R-ISS), which incorporates interphase fluorescence in situ hybridization (FISH). Aims: The aims of this study were to 1) characterize the association between abnormalities on metaphase cytogenetics and overall survival (OS) in newly diagnosed MM treated with novel agents and 2) evaluate whether the addition of metaphase cytogenetics to R-ISS, age, and plasma cell labeling index (PCLI) improves model discrimination with respect to OS. Methods: We analyzed a retrospective cohort of 483 newly diagnosed MM patients treated with proteasome inhibitors (PI) and/or immunomodulators (IMID) who had metaphase cytogenetics performed prior to initiation of therapy. Abnormal metaphase cytogenetics were defined as MM specific abnormalities, while normal metaphase cytogenetics included constitutional cytogenetic variants, age-related Y chromosome loss, and normal metaphase karyotypes. Multivariable adjusted proportional hazards regression models were fit for the association between known prognostic factors and OS. Covariates associated with inferior OS on multivariable analysis included R-ISS stage, age ≥ 70, PCLI ≥ 2, and abnormal metaphase cytogenetics. We devised a risk scoring system weighted by their respective hazard ratios (R-ISS II +1, R-ISS III + 2, age ≥ 70 +2, PCLI ≥ 2 +1, metaphase cytogenetic abnormalities + 1). Low (LR), intermediate (IR), and high risk (HR) groups were established based on risk scores of 0-1, 2-3, and 4-5 in modeling without metaphase cytogenetics, and scores of 0-1, 2-3, and 4-6 in modeling incorporating metaphase cytogenetics, respectively. Survival estimates were calculated using the Kaplan-Meier method. Survival analysis was stratified by LR, IR, and HR groups in models 1) excluding metaphase cytogenetics 2) including metaphase cytogenetics and 3) including metaphase cytogenetics, with IR stratified by presence and absence of metaphase cytogenetic abnormalities. Survival estimates were compared between groups using the log-rank test. Harrell's C was used to compare the predictive power of risk modeling with and without metaphase cytogenetics. Results: Median age at diagnosis was 66 (31-95), 281 patients (58%) were men, median follow up was 5.5 years (0.04-14.4), and median OS was 6.4 years (95% CI 5.7-6.8). Ninety-seven patients (20%) were R-ISS stage I, 318 (66%) stage II, and 68 (14%) stage III. One-hundred and fourteen patients (24%) had high-risk abnormalities by FISH, and 115 (24%) had abnormal metaphase cytogenetics. Three-hundred and thirteen patients (65%) received an IMID, 119 (25%) a PI, 51 (10%) received IMID and PI, and 137 (28%) underwent upfront autologous hematopoietic stem cell transplantation (ASCT). On multivariable analysis, R-ISS (HR 1.59, 95% CI 1.29-1.97, p < 0.001), age ≥ 70 (HR 2.32, 95% CI 1.83-2.93, p < 0.001), PCLI ≥ 2, (HR 1.52, 95% CI 1.16-2.00, p=0.002) and abnormalities on metaphase cytogenetics (HR 1.35, 95% CI 1.05-1.75, p=0.019) were associated with inferior OS. IR and HR groups experienced significantly worse survival compared to LR groups in models excluding (Figure 1A) and including (Figure 1B) the effect of metaphase cytogenetics (p < 0.001 for all comparisons). However, the inclusion of metaphase cytogenetics did not improve discrimination. Likewise, subgroup analysis of IR patients by the presence or absence of metaphase cytogenetic abnormalities did not improve risk stratification (Figure 1C) (p < 0.001). The addition of metaphase cytogenetics to risk modeling with R-ISS stage, age ≥ 70, and PCLI ≥ 2 did not improve prognostic performance when evaluated by Harrell's C (c=0.636 without cytogenetics, c=0.642 with cytogenetics, absolute difference 0.005, 95% CI 0.002-0.012, p=0.142). Conclusions: Abnormalities on metaphase cytogenetics at diagnosis are associated with inferior OS in MM when accounting for the effects of R-ISS, age, and PCLI. However, the addition of metaphase cytogenetics to prognostic modeling incorporating these covariates did not significantly improve risk stratification. Disclosures Lacy: Celgene: Research Funding. Dispenzieri:Akcea: Consultancy; Intellia: Consultancy; Alnylam: Research Funding; Celgene: Research Funding; Janssen: Consultancy; Pfizer: Research Funding; Takeda: Research Funding. Kapoor:Celgene: Honoraria; Sanofi: Consultancy, Research Funding; Janssen: Research Funding; Cellectar: Consultancy; Takeda: Honoraria, Research Funding; Amgen: Research Funding; Glaxo Smith Kline: Research Funding. Leung:Prothena: Membership on an entity's Board of Directors or advisory committees; Takeda: Research Funding; Omeros: Research Funding; Aduro: Membership on an entity's Board of Directors or advisory committees. Kumar:Celgene: Consultancy, Research Funding; Janssen: Consultancy, Research Funding; Takeda: Research Funding.

Background: A variety of risk factors have been described in multiple myeloma and current risk assessment incorporates ISS stage with specific FISH results and serum LDH (R-ISS). However, this model does not include all the current abnormalities described as prognostic for survival in multiple myeloma. Importantly, the impact of many of these high-risk abnormalities are not uniform. We examined if we can better integrate FISH results into a risk assessment tool to better predict the outcomes of newly diagnosed MM. Patients and methods: We studied a cohort of 1316 patients with FISH done within 6 months of diagnosis of MM, in whom results for commonly observed abnormalities were available. We specifically examined the individual impact of common translocations involving chromosome 14, MYC rearrangements, chromosome 1q gain (single or multiple duplication) and del13q/monosomy 13. A risk assessment system was developed, weighting each abnormality according to their Risk Ratio and integrating ISS stage and serum LDH into the final model construction. Overall survival was calculated from diagnosis, with those alive at last follow up being censored. Results: We first examined the impact of each of the above FISH abnormalities: 1) high risk translocations [t(4;14), t(14;16), or t(14,20)], 2) trisomies, 3) t(11;14), 4) MYCrearrangements, 5) del13q/monosomy 13, and 6) 1q gain . Each of the abnormalities, except for t(11;14), was prognostic for survival (Table 1 with the risk ratios). For 1q gain, the median OS was NR, 105 mos and 79 mos respectively for no abnormality, duplication of 1 copy and duplication of multiple copies, (p<0.001). On multivariate analysis, t(11;14) and trisomies were no longer prognostic for overall survival (Table 1). The cumulative impact of abnormalities demonstrated worsening survival in the presence of increasing numbers of abnormalities (Figure 1). Including ISS stage 3 and LDH > ULN as additional variables for prognostication indicated both were individually prognostic for OS. In a multivariate analysis, including these two and FISH abnormalities, 1q gain and LDH were not independently prognostic. The final model consisted of HR translocations, MYCrearrangements, del17p/monosomy 17, del13q/monosomy 13, and ISS stage 3. Each of these variables was weighted using their risk ratio and a composite score was developed using 998 patients for whom all variables were available (range: 0-7.9; median 1.8). Three patient groups were characterized: group 1 (0; 32%), group 2 (1-4; 58%) and group 3 (>4; 10%) with a median OS of 53 mos, 106 mos, and NR, respectively, p <0.001 (Figure 2). Conclusion: Using the most relevant FISH and laboratory factors, in a large cohort of patients, we refined the current system to develop a risk stratification system that predicts survival in patients with newly diagnosed MM treated with contemporary treatment regimens. This needs validation in future studies. Disclosures Kumar: Janssen: Consultancy, Research Funding; Takeda: Research Funding; Celgene: Consultancy, Research Funding. Gertz:International Waldenstrom Foundation: Research Funding; Annexon: Consultancy; Medscape: Consultancy, Speakers Bureau; Amyloidosis Foundation: Research Funding; Abbvie: Other: personal fees for Data Safety Monitoring board; i3Health: Other: Development of educational programs and materials; Springer Publishing: Patents & Royalties; Physicians Education Resource: Consultancy; Pharmacyclics: Membership on an entity's Board of Directors or advisory committees; Proclara: Membership on an entity's Board of Directors or advisory committees; Ionis/Akcea: Consultancy; Alnylam: Consultancy; Prothena Biosciences Inc: Consultancy; Celgene: Consultancy; Janssen: Consultancy; Spectrum: Consultancy, Research Funding; Appellis: Consultancy; Research to Practice: Consultancy; Teva: Speakers Bureau; Johnson and Johnson: Speakers Bureau; DAVA oncology: Speakers Bureau; Amgen: Consultancy. Dispenzieri:Akcea: Consultancy; Janssen: Consultancy; Intellia: Consultancy; Pfizer: Research Funding; Takeda: Research Funding; Celgene: Research Funding; Alnylam: Research Funding. Lacy:Celgene: Research Funding. Dingli:alexion: Consultancy; Janssen: Consultancy; Millenium: Consultancy; Rigel: Consultancy; Karyopharm: Research Funding. Kapoor:Celgene: Honoraria; Janssen: Research Funding; Sanofi: Consultancy, Research Funding; Glaxo Smith Kline: Research Funding; Takeda: Honoraria, Research Funding; Amgen: Research Funding; Cellectar: Consultancy. Leung:Prothena: Membership on an entity's Board of Directors or advisory committees; Takeda: Research Funding; Omeros: Research Funding; Aduro: Membership on an entity's Board of Directors or advisory committees. Bergsagel:Celgene: Consultancy; Ionis Pharmaceuticals: Consultancy; Janssen Pharmaceuticals: Consultancy.

Purpose: B-cell acute lymphoblastic leukemia/lymphoma (B-ALL/LBL) represents the most common childhood malignancy. Classification of recurrent genetic abnormalities in B-ALL/LBL is essential for risk stratification and patient management. Observed in approximately 5% of B-ALL/LBL cases, hypodiploidy is considered a poor prognostic finding and can be further characterized as near-haploidy (24-31 chromosomes), low hypodiploidy (32-39 chromosomes) and high hypodiploidy (40-43 chromosomes). Importantly, masked hypodiploid clones that have undergone endoreduplication can be mischaracterized as hyperdiploidy, a favorable prognostic finding in B-ALL/LBL. These "doubled" hypodiploid clones are termed pseudo-hyperdiploid and their accurate detection is critical. Mate-pair sequencing (MPseq) is a next-generation sequencing (NGS) technology designed to sequence larger DNA fragments (2000-5000bp) than paired-end sequencing. This allows for the detection of large genetic rearrangements (e.g. translocations, inversions, etc.) and copy number variants (CNVs) at a high resolution with low base coverage. It has demonstrated particular clinical utility for genetic characterization of hematologic malignancies. To expand the role of MPseq in the evaluation of hematologic neoplasms, we aimed to improve the analysis of MPseq results to allow for the detection of copy-neutral loss of heterozygosity (cnLOH) that would enable the differentiation between hyperdiploid and pseudo-hyperdiploid clones. Methods: A new algorithm was applied that statistically analyzes common SNP locations in MPseq data in order to detect both cnLOH regions, and provides global heterozygosity levels at a resolution that allows for the detection of hypodiploidy. This method accounts for the low base-coverage of MPseq data (<10x) in order to provide the highest possible accuracy and precision without increasing cost by requiring changes to the input or sequencing requirements. The algorithm was applied to 17 B-ALL samples classified by conventional chromosome analysis, FISH, and/or chromosomal microarray as either pseudo-hyperdiploidy (n=8) or hyperdiploidy (n=9). The cases were sequenced using MPseq with 101bp read lengths across a range of base coverages (1-10x; 30-135 million fragments) and tumor percentages (50-100%). Results: We demonstrate the method's ability to differentiate between hyperdiploidy and pseudo-hyperdiploidy in all cases without any changes to the MPseq input or sequencing requirements. We detected an average of 11.5 whole-chromosome cnLOH (range 8-20) in the pseudo-hyperdiploidy cases, compared to an average of 0.67 whole-chromosome cnLOH (range 0-2) in the hyperdiploidy cases. Additionally, the method allows for the detection of cnLOH regions across the genome. For example, we observed a recurrent cnLOH of chromosome 9 in the hyperdiploid subtype (3/9 hyperdiploid cases), which is a recurrent abnormality in the disease. The method provides an easy to read visual output that compares favorably to the output of chromosomal microarray, increasing its utility for clinical application. Conclusions: This advancement in the analysis of low-coverage sequencing data makes MPseq available for the genetic characterization of B-ALL/LBL, where hypodiploidy is a primary cytogenetic abnormality and is sometimes missed by conventional cytogenetic techniques. Additionally, the algorithm allows for the detection of cnLOH regions across the genome, which is important across many disease types for diagnosis, prognosis, and the detection of potential therapeutic targets. The addition of the algorithm to the MPseq analysis pipeline makes it a more complete genetic characterization tool and brings it closer to its promise as a potential single assay replacement for conventional cytogenetic techniques. Disclosures No relevant conflicts of interest to declare.

Abstract Background: We previously demonstrated that putative clinical epidemiologic exposures associated with leukemia risk are prevalent among AML patients, and some are associated with unique cytogenetic risk group and with clinical phenotype (Finn, Cancer Epidemiol, 2015). Herein, we studied genome-wide DNA methylation in a cohort of AML patients to evaluate the association of individual hyper- and hypo-methylated CpG sites with epidemiologic exposures and overall survival. Methods: The Mayo Clinic AML Epidemiology Cohort is a highly annotated retrospective case series of 295 consecutive patients (pts) with AML diagnosed and treated at Mayo Clinic Florida and Arizona, with central cytogenetics performed in all cases. The prevalence of clinical epidemiologic exposures, past medical and family history as well as medication use and lifestyle was systematically obtained. After IRB approval, we interrogated the cytogenetic database and successfully obtained leukemia DNA from available remnant diagnostic cytogenetic cell pellets in a cohort of 148 AML patients in the Mayo epidemiology case series and performed an assessment of genome-wide DNA methylation using the Infinium HumanMethylation450K BeadChip. Samples were processed using the R Bioconductor package 'minfi' using Subset Within Array Quantile Normalization (PMID: 22703947). Individual CpGs that did not reach a detection p-value of <0.05 were filtered out. An internal control was included on each array to control for significant batch effects. To determine differential methylation status of 473,864 individual CpG sites (after exclusion of 11,648 that did not pass detection p-value QC), CpG sites with low interpatient variability, a standard deviation <0.05 of methylation values, and an interquartile range <0.05 of methylation values and X/Y chromosome probes were excluded from analysis. Epidemiologic and important clinical variables occurring in at least 10 pts or previously-identified as of unique interest but in fewer than 10 pts were evaluated, including sex, BMI, performance status and comorbidities, tobacco and alcohol use, family history of hematologic malignancy, medications of interest, history of toxin exposure, and history of immunosuppression and/or solid organ transplant or of secondary and therapy-related AML (t-AML). Associations of differential hypo or hypermethylation at 281,259 CpG sites with epidemiologic exposures/clinical variables were evaluated using Spearman's test of correlation (continuous or ordinal exposures), a Wilcoxon rank sum test (dichotomous exposures), or a Kruskal-Wallis rank sum test (multi-category exposures). A Bonferroni correction was applied for multiple testing, after which p <1.8 x 10-7 was considered as significant. To reduce the likelihood of false-negative findings, we additionally considered p <5 x 10-6 as indicating suggestive evidence of an association. CpG sites and associated gene and function was determined using Illumina manifest file & www.ncbi.nlm.nih.gov/gene. Results: Statistically significant associations (p <1.8 x 10-7) with individual epidemiologic and clinical exposures were identified for 109 unique CpG sites, corresponding to differential methylation in the genes listed in Table. Specifically, obesity (predominantly hypomethylation), specific cytogenetic lesions and risk group, and gender were highly significantly associated with unique CpG methylation status, but not smoking, toxin exposure, family history, comorbidity or performance status, secondary or t-AML, immunosuppression, medication use, of family history in the analysis. A further 353 unique CpG sites had defined suggestive associations (ongoing analysis). We also identified 8 additional CpG sites where differential methylation was associated with overall survival (p <5 x 10-6, Table). Conclusion: Obesity, cytogenetic lesions, and sex are associated with differential methylation of unique CpG sites at AML diagnosis, using stringent univariate statistical criteria. Significant CpG sites were identified in genes previously linked to AML biology and prognosis (DOCK6, HOXB3, MIR10A, FOXN3/CHES1, GPX1, MYST2/KAT7, PTPRD), but some represent novel findings in AML. These preliminary results suggest an association of some AML risk factors and clinical variables with unique gene methylation and will undergo validation in a prospective AML epidemiology dataset. Disclosures Cerhan: Jannsen: Other: Scientific Advisory Board; Nanostring: Research Funding; Celgene: Research Funding. Foran:Agios: Research Funding; Xencor, Inc.: Research Funding.

Abstract Background: Current prognostication in primary myelofibrosis (PMF) utilizes MIPSS70 (mutation-enhanced international prognostic scoring system for transplant-age patients), MIPSS70+ version 2.0 (karyotype-enhanced MIPSS70) and GIPSS (genetically-inspired prognostic scoring system, which is based on mutations and karyotype) (JCO 2018;36:310; JCO doi: 10.1200/JCO.2018.78.9867; Leukemia. 2018;doi:10.1038/s41375-018-0107). These contemporary models are inter-complimentary and highly efficient in predicting overall survival. However, specific risk factors for very long survival (e.g. 20+ years) and short-term mortality (i.e. death within 5 years of diagnosis) have not been systematically looked into. Methods: Study patients were recruited from the Mayo Clinic, Rochester, MN, USA. Diagnoses were according to the 2016 World Health Organization criteria (Blood. 2016;127:2391). Logistic regression statistics was used to identify predictors of 20-year survival and 5-year mortality. Variables evaluated in the logistic model included those that are currently listed in MIPSS70, MIPSS70+ version 2.0 and GIPSS, as well as age (≤70 vs >70 years) and sex. Receiver operating characteristic (ROC) curves and area under the curve (AUC) were used to estimate predictive accuracy. The JMP® Pro 13.0.0 software from SAS Institute, Cary, NC, USA, was used for all calculations. Results: A total of 1,282 consecutive patients with PMF (median age 65 years, range 19-92; 63% males) were used to identify 26 (2%) patients (median age 51 years, range 28-71; 38% males) who survived their disease for at least 20 years (very long-lived patients) and 626 (49%) patients (median age 68 years, range 27-92; 66% males) who died within 5 years of their diagnosis. Clinically-derived information, including the clinical variables used in MIPSS70 and MIPSS70+ version 2.0, with the exception of fibrosis grade (information available in 60%), was available in 99% of the study population; cytogenetic information was available in 94%, driver mutational status in 71% and the full profile of high molecular risk (HMR) mutations, including ASXL1, SRSF2, U2AF1 Q157, EZH2, IDH1 and IDH2, in 42%. MIPSS70+ version 2.0 risk distribution for the entire study population (n=1,282) was 4% very low risk, 16% low risk, 19% intermediate risk, 40% high risk and 21% very high risk; the corresponding percentages for the 26 very long-lived patients were 14%, 29%, 14%, 43% and 0% and for the 626 short-term survivors were 0%, 4%, 10%, 47% and 39% (p<0.001). Cytogenetic, driver mutation and HMR mutation information was available in 100%, 58% and 27% of the 26 long-term survivors, respectively, and 98%, 63% and 39% of the 626 short-term survivors. Multivariable logistic regression analysis of 20-year survival identified the following seven variables as being favorable: age ≤70 years (p=0.002); female sex (p=0.03); hemoglobin level ≥10 g/dl for women and ≥11 g/dl for men (p=0.03), leukocyte count ≤25 x 109/l (p=0.009), platelet count ≥100 x 109/l (p=0.002), circulating blasts ≤1% (p=0.03) and absence of constitutional symptoms (p=0.04). The particular phenotypic profile exhibited a high degree of predictive accuracy with an estimated AUC of 0.90 (Figure 1a); karyotype and mutations did not retain significance in this particular analysis; in fact, 5 (71%) of the 7 long-term survivors who were informative harbored at least one HMR mutation. A similar analysis for 5-year mortality identified the following risk factors: high molecular risk mutations (p<0.001); unfavorable or very high risk karyotype (p<0.001); absence of type 1/like CALR mutations (p<0.001); age >70 years (p<0.001); constitutional symptoms (p<0.001); hemoglobin level <10 g/dl for women and <11 g/dl for men (p<0.001); leukocyte count >25 x 109/l (p=0.004); and circulating blasts >1% (p=0.001); predictive accuracy was estimated at AUC 0.87 (Figure 1b). Conclusions: The phenotypic profile of long-lived patients in PMF includes young age (≤70 years old), female sex, asymptomatic disease (i.e. no constitutional symptoms) and absence of moderate to severe anemia, thrombocytopenia or leukocytosis and ≤1% circulating blasts; each one of these parameters, with the exception of female sex, were present in ≥80% of long-term survivors. Karyotype and mutations were more relevant in predicting short-term mortality. Disclosures No relevant conflicts of interest to declare.