Abstract: To obtain a comprehensive genomic profile of presenting multiple myeloma cases we performed high-resolution single nucleotide polymorphism mapping array analysis in 114 samples alongside 258 samples analyzed by U133 Plus 2.0 expression array (Affymetrix). We examined DNA copy number alterations and loss of heterozygosity (LOH) to define the spectrum of minimally deleted regions in which relevant genes of interest can be found. The most frequent deletions are located at 1p (30%), 6q (33%), 8p (25%), 12p (15%), 13q (59%), 14q (39%), 16q (35%), 17p (7%), 20 (12%), and 22 (18%). In addition, copy number-neutral LOH, or uniparental disomy, was also prevalent on 1q (8%), 16q (9%), and X (20%), and was associated with regions of gain and loss. Based on fluorescence in situ hybridization and expression quartile analysis, genes of prognostic importance were found to be located at 1p (FAF1, CDKN2C), 1q (ANP32E), and 17p (TP53). In addition, we identified common homozygously deleted genes that have functions relevant to myeloma biology. Taken together, these analyses indicate that the crucial pathways in myeloma pathogenesis include the nuclear factor-κB pathway, apoptosis, cell-cycle regulation, Wnt signaling, and histone modifications. This study was registered at http://isrctn.org as ISRCTN68454111.

Abstract: Pegylated interferon (Peg-IFN) increases molecular response rates when used in combination with imatinib (IM) and dasatinib compared with tyrosine kinase inhibitor (TKI) monotherapy in de novo chronic phase chronic myeloid leukemia (CP-CML). (Preudhomme NEJM 2010, Hjorth-Hansen Leukemia 2016). The phase II Pinnacle (ALLG CML 11) study evaluated the tolerability and molecular response rate of nilotinib (NIL) with Peg-IFN alfa-2B (PegIntron, MSD) in CP-CML patients. Co-primary end points were MMR (BCR-ABL1 ≤ 0.1%) at 12 mths and MR4.5 (BCR-ABL1 ≤ 0.0032%) at 24 mths. Key secondary end points were survival and overall molecular response. Patients were screened for cardiac / vascular disease and associated risk factors at baseline (EKG, left ventricular ejection fraction, arterial duplex of carotids and lower limbs, blood HbA1c and lipid profiles). Those with uncontrolled vascular risk factors (diabetes, hypertension, dyslipidemia) or a history of vascular events were excluded. Eligible pts received NIL 300mg BID alone for the first 3 months (mths). PegIntron was then added at 30mcg/week in pts without persistent hematological toxicities, increasing to 50mcg/week as tolerated over the following mth. Combination therapy continued until 24 mths, when pts reverted to TKI monotherapy. Switching to IM 400-600mg QD was allowed for pts with persistent grade II or any grade III/IV toxicity from NIL. Sixty pts were enrolled from 12 Australian centres. Median age was 48.5 years (range 19-72); 45% were female. Sokal risk was low in 43% and high in 18%. Median follow up (FU) was 34 mths (24-60). Data is presented on an intention to treat basis. Eight pts (13%) did not commence Pegintron (2 due to persistent haem toxicities, 4 from GI disturbance, liver/pancreatic enzyme derangements, and 2 from pt preference). Considering Pegintron as a product of protocol assigned dose and duration, adjusted for time from study entry, 21 pts (35%) received 〉 85% of their assigned dose, 13 (22%) received between 50-84% and 18 pts (30%) received 〈 50% (Fig 1A). There was no difference between patients who had 〉 85% of their assigned dose versus those wwho took 〈 85% with respect to age or sex. The median duration of Pegintron exposure was 15 mths (Range 1-21 months). Adverse events (AE) are reported at a similar frequency compared to the interim analysis. Grade III/IV AEs attributed to NIL were increased lipase and neutropenia (each 12%), pancreatitis (6%), thrombocytopenia and rash (each 5%). Grade III/IV AEs attributed to Pegintron were neutropenia (10%), atrial fibrillation (6%), and myalgia, depression and rash (4% each). Three vascular revents occurred: one case each of ischaemic colitis, femoral artery occlusion, coronary artery disease. The former occurred on imaitnib and the latter 2 occurred after 2.5 and 4 years of niloitnib respectively; both patient have since switched to imatinib. Eighteen pts (30%) have withdrawn from study: 2 withdrew consent, 6 due to intolerance (diarrhoea, pancreatitis, GI upset, rash, high amylase and LFT derangements), 4 for failing to consistently achieve BCR-ABL MMR, 2 for loss of response; 4 pts withdrew for other reasons. Fig 1B shows BCR-ABL1 transcript levels over time. At 3 mths, 22 (37%) have achieved MMR, 23 (38%) had BCR-ABL between 0.1-1%, and 6 (10%) had BCR-ABL between 1-10%; 3 have already withdrawn. Six pts (10%) had BCR-ABL1 ≥10%; 3 subsequently achieved and maintained MMR, 1 has BCR-ABL 〈 1% at 24 mos, 1 transformed to AP after study withdrawal, and 1 was refractory to all TKIs and received an allograft. At 12 mths, MMR (BCR-ABL ≤ 0.1%) and MR4.5 (BCR-ABL ≤ 0.0032%) rates were 78.3% (95% CI 65.3-88.2; Fig 1C) and 43.3% (95% CI 30.1-57.3%; Fig 1D), respectively. At 24 mths, MR4.5 was 50% (95% CI 36.6-63.4%). No BCR-ABL mutations were reported on study. Three pts lost MMR - 2 were transient; the other was associated with non-compliance. Current TKI treatment for pts on study is NIL (n=37; 62%) and IM (n=5; 8%). Combination therapy with NIL and Peg-IFN leads to favourable rates of molecular responses that may be superior to NIL monotherapy (Table). While the majority of patients did not durably tolerate full dose Pegintron, there was minimal interference with TKI dose intensity. Such strategies may maximise achievement of deep molecular response, allowing a trial of TKI cessation and the benefit of treatment free remission to an increased number of patients. Disclosures Yeung: BMS: Honoraria, Research Funding; Pfizer: Honoraria; Amgen: Honoraria; Novartis: Honoraria, Research Funding. Shanmuganathan:Gilead: Other: Travel Support; Janssen: Other: Travel Support; Amgen: Other: Travel Support; Bristol-Myers Squibb: Honoraria, Other: Travel Support; Novartis: Honoraria, Other: Travel Support. Grigg:Abbvie: Membership on an entity's Board of Directors or advisory committees; Roche: Other: Travel; Janssen: Membership on an entity's Board of Directors or advisory committees; MSD: Membership on an entity's Board of Directors or advisory committees. Reynolds:AUSTRALASIAN LEUKAEMIA & LYMPHOMA GROUP (ALLG): Consultancy; Novartis AG: Equity Ownership; Novartis Australia: Honoraria; Alfred Health: Employment, Other: Biostatistician for trials funded by the Australian government and Abbvie, Amgen, Celgene, GSK, Janssen-Cilag, Merck, Novartis, Takeda, but sponsored by Alfred Health.. Harrup:Cooperative Trial Group for NeuroOncolog: Other: Collaborative Clinical Trials Group; Cancer Council of Tasmania: Membership on an entity's Board of Directors or advisory committees. Ross:BMS: Honoraria, Membership on an entity's Board of Directors or advisory committees; Celgene: Honoraria, Research Funding; Novartis: Consultancy, Honoraria, Research Funding. Mills:Novartis: Other: Speaker Fees; Specialised Therapeutics: Honoraria; Abbvie: Membership on an entity's Board of Directors or advisory committees; Amgen: Other: Conference Sponsorship; MSD: Membership on an entity's Board of Directors or advisory committees. Yong:BMS: Honoraria, Research Funding; Celgene: Research Funding; Novartis: Honoraria, Research Funding. White:BMS: Honoraria, Research Funding; AMGEN: Honoraria, Speakers Bureau. Branford:Qiagen: Honoraria, Membership on an entity's Board of Directors or advisory committees; Cepheid: Honoraria; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; BMS: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau. Hughes:Novartis, Bristol-Myers Squibb, Celgene: Research Funding; Novartis, Bristol-Myers Squibb: Consultancy, Other: Travel. OffLabel Disclosure: Pegylated interferon is not registered for use in chronic phase CML

Abstract: Alfa Interferon, commonly used in chronic phase chronic myeloid leukemia (CML-CP) in the pre-imatinib era, was able to induce a cytogenetic response in a minority of patients (pts). Pegylated interferon (Peg-IFN) is better tolerated than IFN, and increases molecular response rates when used in combination with imatinib (IM) compared with IM monotherapy (Preudhomme NEJM 2010). The phase II Pinnacle (ALLG CML 11) study evaluated the tolerability and molecular response rate of nilotinib (NIL) with Peg-IFN alfa-2B (PegIntron, MSD) in de novo CML-CP. Pts were screened for cardiac / vascular disease and associated risk factors at baseline (EKG, left ventricular ejection fraction, arterial duplex of carotids and lower limbs, blood HbA1c and lipid profiles). Those with uncontrolled vascular risk factors (diabetes, hypertension, dyslipidemia) or a history of vascular events were excluded. Eligible pts received NIL 300mg BID alone for the first 3 months (mths). PegIntron was then added at 30mcg/week in pts without persistent hematological toxicities, increasing to 50mcg/week as tolerated over the following mth. Combination therapy continued until 24 mths, when pts reverted to TKI monotherapy. Switching to IM 400-600mg QD was allowed for pts with persistent grade II or any grade III/IV toxicity from NIL.. Sixty pts were enrolled from 12 Australian centres. Median age was 48.5 years (range 19-72); 45% were female. Sokal risk was low in 43% and high in 18%. Median follow up (FU) was 28 mths (16-51). Data is presented on an intention to treat basis. Figure 1a shows BCR-ABL1 transcript levels over time. The co-primary end points are MMR (BCR-ABL1 ≤0.1% IS) AT 12 mths and MR4.5 (BCR-ABL1 ≤0.0032% IS) at 24 mths. At 12 mths, MMR and MR4.5 rates were 76.7% (95% CI 63.4-87%). and 43.4% (95% CI 30.1-57.3%), respectively. In 40 evaluable pts at 24 mths, MR4.5 was 50% (95% CI 29.9-70.1%). The median time to MMR and MR4.5 was 5.8 mths and 18 mths respectively for pts achieving these responses (Figs 1B & C). Six pts (10%) had BCR-ABL1 ≥10% at 3 mths - 2 of whom had multiple dose interruptions due to toxicity; 3/6 have since achieved MMR, 1 has BCR-ABL 〈 1%, 2 withdrew of which 1 transformed to AP off study. No BCR-ABL mutation was reported on study. Dose intensities of NIL were assessed in 3 mth blocks. Median and lower quartile NIL dose intensity was 600mg/d for all 3 mth blocks up to mth 24, except for the lower quartile NIL dose of 567mg for the first 3 mths. Eight pts (13%) did not commence Pegintron (2 due to persistent haem toxicities, 4 from GI disturbance, liver/pancreatic enzyme derangements, and 2 from pt preference). Considering Pegintron as a product of protocol assigned dose and duration, adjusted for time from study entry, 22 pts (37%) received 〉 90% of their assigned dose, 13 (22%) received between 50-90% and 25 pts (41%) received 〈 50% of assigned Peg-IFN (Fig 1D). The median duration of Pegintron exposure was 15 mths. Grade III/IV adverse events (AE) attributed to NIL were increased lipase and neutropenia (each 12%), pancreatitis (6%), thrombocytopenia and rash (each 5%). Three thrombotic events occurred: ischemic colitis in a patient on IM monotherapy, femoral artery thrombosis in a 56yo man after 2.5 yrs of NIL, and coronary disease in a 51yo man after 4 yrs of NIL. Grade III/IV AEs attributed to Pegintron were neutropenia (10%), and myalgia, depression and rash (4% each); other common AEs included fatigue (35%), myalgia (23%), flu-like symptoms (21%) and depression (17%). Ten pts (13%) have withdrawn from study: 2 withdrew consent, 5 due to toxicity (pancreatitis, GI upset, rash, high amylase and fatigue), and 3 for failing to consistently achieve BCR-ABL 〈 10% beyond 6 mths. No death occured on study. Three pts lost MMR - 2 were transient; the other was associated with non-compliance. Current TKI treatment for pts on study: 41 on NIL (68%), 9 on IM (15%). Of the 40 pts with 24 mth FU, 15 (38%) received 〉 90% of assigned NIL/IM and Pegintron doses. This interim analysis suggests that combination therapy with NIL and Peg-IFN leads to favourable rates of molecular responses when compared with with NIL monotherapy (Table 1). While the majority of patients did not durably tolerate full dose Pegintron, there was minimal interference with TKI dose intensity. Longer term results, and impact upon treatment free remission outcome of this combination is awaited. Disclosures Yeung: Pfizer: Honoraria; BMS: Honoraria, Research Funding; Novartis: Honoraria, Research Funding; Specialised Therapeutics Australia: Honoraria; Amgen: Honoraria. Grigg:Takeda: Membership on an entity's Board of Directors or advisory committees; Roche: Membership on an entity's Board of Directors or advisory committees; BMS: Membership on an entity's Board of Directors or advisory committees; Gilead: Membership on an entity's Board of Directors or advisory committees. Shanmuganathan:Janssen: Honoraria; Royal Adelaide Hospital Research Fund: Other: Scholarship; Novartis: Honoraria, Other: Travel sponsorship; Bristol-Myers Squibb: Honoraria, Other: Travel sponsorship. Reynolds:Novartis: Equity Ownership, Other: former employee of Novartis AG and holds stock in the company. . Ross:BMS: Honoraria; Novartis: Consultancy, Honoraria, Research Funding, Speakers Bureau; Celgene: Research Funding. Yong:Celgene: Research Funding; Novartis: Honoraria, Research Funding; BMS: Honoraria, Research Funding. White:Novartis: Honoraria, Research Funding; BMS: Research Funding. Branford:Qiagen: Honoraria, Membership on an entity's Board of Directors or advisory committees; Cepheid: Honoraria; BMS: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau. Hughes:BMS: Honoraria, Membership on an entity's Board of Directors or advisory committees; Incyte: Honoraria, Membership on an entity's Board of Directors or advisory committees; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees.

Abstract: Myeloid neoplasms and acute leukemias derive from the clonal expansion of hematopoietic cells driven by somatic gene mutations. Although assessment of morphology plays a crucial role in the diagnostic evaluation of patients with these malignancies, genomic characterization has become increasingly important for accurate diagnosis, risk assessment, and therapeutic decision making. Conventional cytogenetics, a comprehensive and unbiased method for assessing chromosomal abnormalities, has been the mainstay of genomic testing over the past several decades and remains relevant today. However, more recent advances in sequencing technology have increased our ability to detect somatic mutations through the use of targeted gene panels, whole-exome sequencing, whole-genome sequencing, and whole-transcriptome sequencing or RNA sequencing. In patients with myeloid neoplasms, whole-genome sequencing represents a potential replacement for both conventional cytogenetic and sequencing approaches, providing rapid and accurate comprehensive genomic profiling. DNA sequencing methods are used not only for detecting somatically acquired gene mutations but also for identifying germline gene mutations associated with inherited predisposition to hematologic neoplasms. The 2022 International Consensus Classification of myeloid neoplasms and acute leukemias makes extensive use of genomic data. The aim of this report is to help physicians and laboratorians implement genomic testing for diagnosis, risk stratification, and clinical decision making and illustrates the potential of genomic profiling for enabling personalized medicine in patients with hematologic neoplasms.

Abstract: Next-generation sequencing revealed variants in cancer-associated genes at diagnosis of CML more frequently in patients with poor outcomes. All patients at BC had mutated cancer genes, including fusions, that predated BCR-ABL1 kinase domain mutations in a majority.

Abstract: Background: For patients with chronic-phase chronic myeloid leukemia (CML), treatment-free remission (TFR) is increasingly becoming a goal of therapy. While the safety of TFR has been established [Mahon, Lancet Oncol 2010; Ross, Blood 2013], the ability to predict success following attempted TFR remains limited. Recent publication of Euro-Ski [Saussele, Lancet Oncol 2018] , the largest tyrosine kinase inhibitor (TKI) cessation study to date, demonstrated that duration of MR4 (BCR-ABL1 〈 0.01% IS) prior to attempted TFR was the main factor predicting TFR success. Aim: To identify the predictors of TFR in a single academic centre. Methods: We performed a retrospective analysis of adult CML patients receiving their primary CML management at the Royal Adelaide Hospital between January 2008 and March 2018, reviewing both clinical and molecular data. Criteria for qualifying for a TFR attempt included a minimum of 3 years (yrs) of TKI therapy and 2 yrs of deep molecular response (DMR: BCR-ABL1 〈 0.0032% IS; MR4.5). History of blast crisis, allogeneic stem cell transplantation and non-quantifiable atypical BCR-ABL1 transcripts precluded TFR qualification. Patients were monitored with monthly BCR-ABL1 qRT-PCRs for at least the first 12 months of the TFR attempt. In the event of molecular recurrence, defined as loss of major molecular response (MMR; BCR-ABL1 ≥ 0.1% IS) on a single test, TKI was recommenced. Our population also included 20 patients enrolled in the Australian CML8 (TWISTER) study where restart criteria was more stringent, requiring TKI restart in the event of BCR-ABL1 becoming detectable on 2 consecutive tests. Results: A total of 298 patients were treated at our institution within the defined time frame and 280 patients qualified for inclusion into our retrospective analysis. TFR eligibility was attained in 114 patients and 96 (84%) attempted TFR. Table 1 details patient characteristics of patients attempting TFR. Of the 82 patients with 〉 12 months of follow-up, 52% (n=43) remain off TKI at 12 months in MMR. Variables were assessed by univariate Cox proportional hazards regresssion analysis for their association with TFR. The most significant finding was that patients attempting TFR with e14a2 BCR-ABL1 transcripts were more likely to remain in TFR at 12 months (65%; n=24/37) in comparison to the e13a2 transcript (34%; n=10/29), p = 0.008. This advantage also translated to patients with both e14a2 and e13a2 transcripts when grouped with the e14a2 cohort and compared with e13a2 alone, p = 0.006. The negative effect of the e13a2 transcript was further confirmed on multivariate analysis (Figure 1a) as patients with either e14a2 or both transcript types were 2.24 times more likely to remain in TFR at 12 months compared with the e13a2 transcript, p=0.032. Patients with sustained MR4.5 〉 3.4 yrs prior to cessation were more likely to remain in TFR at 12 months (42 vs. 64%, p = 0.014). We postulated that the higher rate of TFR in patients with e14a2 might be due in part to the longer time in MR4.5 prior to cessation. The median duration of MR4.5 prior to stopping in the e14a2 cohort was 4.1 yrs (2.05 - 10.76) compared to 3.01 yrs (2 - 10.41) in the e13a2 group (Table 2). Cumulative incidence curves of all 280 patients in our analysis demonstrated that by 6 yrs of TKI therapy, 70% of patients with e14a2 transcripts achieved MR4.5 whereas only 52% of patients with e13a2 transcripts attained MR4.5; confirming that patients with e14a2 transcripts are more likely to achieve DMR earlier (Figure 1b). Furthermore by 8 yrs, 48% of patients with e14a2 transcripts became eligible for a TFR attempt compared with only 32% of e13a2 transcripts (Figure 1c). While patients with e13a2 transcripts eventually achieve the same frequency of MR4.5 as the e14a2 group, the earlier achievement of MR4.5 in e14a2 patients may have contributed to the difference in TFR success. Conclusion: The factors that we identified as most predictive for TFR success were duration of MR4.5 and the presence of the e14a2 transcript, which has not been described previously. We also observed earlier achievement of MR4.5 in the e14a2 cohort, consistent with other studies [Jain, Blood 2016]. These observations, taken together, raise important questions about the impact of transcript type on disease biology, drug sensitivity, and immunological response which warrant further investigation. Disclosures Shanmuganathan: Novartis: Honoraria, Other: Travel sponsorship; Janssen: Honoraria; Royal Adelaide Hospital Research Fund: Other: Scholarship; Bristol-Myers Squibb: Honoraria, Other: Travel sponsorship. Branford:Qiagen: Honoraria, Membership on an entity's Board of Directors or advisory committees; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Cepheid: Honoraria; BMS: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau. Yong:BMS: Honoraria, Research Funding; Novartis: Honoraria, Research Funding; Celgene: Research Funding. Hiwase:Celgene: Research Funding; Novartis: Research Funding. Yeung:Novartis: Honoraria, Research Funding; BMS: Honoraria, Research Funding; Pfizer: Honoraria; Amgen: Honoraria; Specialised Therapeutics Australia: Honoraria. Ross:BMS: Honoraria; Novartis: Consultancy, Honoraria, Research Funding, Speakers Bureau; Celgene: Research Funding. Hughes:BMS: Honoraria, Research Funding; Novartis: Honoraria, Research Funding; Takeda: Honoraria.