Molecular Stratification Research Articles

Prognostic factors and survival outcomes according to tumor subtype in patients with breast cancer lung metastases.

BackgroundReports on the incidence and prognoses of lung metastases when diagnosing breast cancer patients with different subtypes are limited. Our study investigated the effect of molecular sub-typing stratification on the prognoses of lung metastatic breast caner patients.MethodsPatients with breast cancer and lung metastases were identified from Surveillance, Epidemiology and End Results population-based data between 2010 and 2015. Univariate and multivariate Cox regression analyses were performed to identify risk factors and prognoses, overall survival (OS) and breast cancer-specific survival for patients with breast cancer lung metastases.ResultsWe identified 6,516 patients with lung metastatic breast cancer, representing 1.7% of the entire cohort and 30.4% of the subset with metastatic disease. This included 2,940 hormone receptor (HR)+/HER2− patients, 852 HR+/HER2+ patients, 547 HR−/HER2+ patients and 983 triple-negative patients. The median OS for all lung metastatic patients was 13 months. Multivariate analysis revealed that those lung metastatic breast cancer patients of older age (>80), black race, with poorly differentiated tumors, carcinoma histology, triple-negative subtype, more metastatic sites and no surgery, and no chemotherapy showed significantly poor survival, both overall and breast cancer-specific.ConclusionsOur findings show that molecular sub-type and more metastatic sites might have significant influence on the incidence and prognosis of breast cancer lung metastases. We also identified several prognostic factors that could guide therapy selection in the treatment of lung metastatic patients.

Molecular stratification within triple-negative breast cancer subtypes

Triple-negative breast cancer (TNBC) has been subdivided into six distinct subgroups: basal-like 1 (BL1), basal-like 2 (BL2), mesenchymal (M), mesenchymal stem–like (MSL), immunomodulatory (IM), and luminal androgen receptor (LAR). We recently identified a subgroup of TNBC with loss of the tumor suppressor PTEN and five specific microRNAs that exhibits exceedingly poor clinical outcome and contains TP53 mutation, RB1 loss and high MYC and WNT signalling. Here, show that these PTEN-low/miRNA-low lesions cluster with BL1 TNBC. These tumors exhibited high RhoA signalling and were significantly stratified on the basis of PTEN-low/RhoA-signalling-high with hazard ratios (HRs) of 8.2 (P = 0.0009) and 4.87 (P = 0.033) in training and test cohorts, respectively. For BL2 TNBC, we identified AKT1 copy gain/high mRNA expression as surrogate for poor prognosis (HR = 3.9; P = 0.02 and HR = 6.1; P = 0.0032). In IM, programmed cell death 1 (PD1) was elevated and predictive of poor prognosis (HR = 5.3; P = 0.01 and HR = 3.5; P < 0.004). Additional alterations, albeit without prognostic power, characterized each subtype including high E2F2 and TGFβ signalling and CXCL8 expression in BL2, high IFNα and IFNγ signalling and CTLA4 expression in IM, and high EGFR signalling in MSL, and may be targeted for therapy. This study identified PTEN-low/RhoA-signalling-high, and high AKT1 and PD1 expression as potent prognostications for BL1, BL2 and IM subtypes with survival differences of over 14, 2.75 and 10.5 years, respectively. This intrinsic heterogeneity could be exploited to prioritize patients for precision medicine.

Associations between changes in oxygenation, dead space and driving pressure induced by the first prone position session and mortality in patients with acute respiratory distress syndrome.

Outcome prediction in acute respiratory distress syndrome (ARDS) is challenging, especially in patients with severe hypoxemia. The aim of the current study was to determine the prognostic capacity of changes in PaO2/FiO2, dead space fraction (VD/VT) and respiratory system driving pressure (ΔPRS) induced by the first prone position (PP) session in patients with ARDS. This was a post hoc analysis of the conveniently-sized 'Molecular Diagnosis and Risk Stratification of Sepsis' study (MARS). The current analysis included ARDS patients who were placed in the PP. The primary endpoint was the prognostic capacity of the PP-induced changes in PaO2/FiO2, VD/VT, and ΔPRS for 28-day mortality. PaO2/FiO2, VD/VT, and ΔPRS was calculated using variables obtained in the supine position before and after completion of the first PP session. Receiving operator characteristic curves (ROC) were constructed, and sensitivity, specificity positive and negative predictive value were calculated based on the best cutoffs. Ninety patients were included; 28-day mortality was 46%. PP-induced changes in PaO2/FiO2 and VD/VT were similar between survivors vs. non-survivors [+83 (+24 to +137) vs. +58 (+21 to +113) mmHg, and -0.06 (-0.17 to +0.05) vs. -0.08 (-0.16 to +0.08), respectively]. PP-induced changes in ΔPRS were different between survivors vs. non-survivors [-3 (-7 to 2) vs. 0 (-3 to +3) cmH2O; P=0.03]. The area under the ROC of PP-induced changes in ΔPRS for mortality, however, was low [0.63 (95% confidence interval (CI), 0.50 to 0.75]; PP-induced changes in ΔPRS had a sensitivity and specificity of 76% and 56%, and a positive and negative predictive value of 60% and 73%. Changes in PaO2/FiO2, VD/VT, and ΔPRS induced by the first PP session have poor prognostic capacities for 28-day mortality in ARDS patients.

Realizing better doctor-patient dialogue about choices in palliative care and early phase clinical trial participation: towards an online value clarification tool (OnVaCT)

BackgroundPatients with advanced cancer for whom standard systemic treatment is no longer available may be offered participation in early phase clinical trials. In the decision making process, both medical-technical information and patient values and preferences are important. Since patients report decisional conflict after deciding on participation in these trials, improving the decision making process is essential. We aim to develop and evaluate an Online Value Clarification Tool (OnVaCT) to assist patients in clarifying their values around this end-of-life decision. This improved sharing of values is hypothesized to support medical oncologists in tailoring their information to individual patients’ needs and, consequently, to support patients in taking decisions in line with their values and reduce decisional conflict.MethodsIn the first part, patients’ values and preferences and medical oncologists’ views hereupon will be explored in interviews and focus groups to build a first prototype OnVaCT using digital communication (serious gaming). Next, we will test feasibility during think aloud sessions, to deliver a ready-to-implement OnVaCT. In the second part, the OnVaCT, with accompanied training module, will be evaluated in a pre-test (12–18 months before implementation) post-test (12–18 months after implementation) study in three major Dutch cancer centres. We will include 276 patients (> 18 years) with advanced cancer for whom standard systemic therapy is no longer available, and who are referred for participation in early phase clinical trials. The first consultation will be recorded to analyse patient-physician communication regarding the discussion of patients’ values and the decision making process. Three weeks afterwards, decisional conflict will be measured.DiscussionThis project aims to support the discussion of patient values when considering participation in early phase clinical trials. By including patients before their first appointment with the medical oncologist and recording that consultation, we are able to link decisional conflict to the decision making process, e.g. the communication during consultation. The study faces challenges such as timely including patients within the short period between referral and first consultation. Furthermore, with new treatments being developed rapidly, molecular stratification may affect the patient populations included in the pre-test and post-test periods.Trial registrationNetherlands Trial Registry number: NTR7551 (prospective; July 17, 2018).

REVIEW: MR elastography of brain tumors.

MR elastography allows non-invasive quantification of the shear modulus of tissue, i.e. tissue stiffness and viscosity, information that offers the potential to guide presurgical planning for brain tumor resection. Here, we review brain tumor MRE studies with particular attention to clinical applications. Studies that investigated MRE in patients with intracranial tumors, both malignant and benign as well as primary and metastatic, were queried from the Pubmed/Medline database in August 2018. Reported tumor and normal appearing white matter stiffness values were extracted and compared as a function of tumor histopathological diagnosis and MRE vibration frequencies. Because different studies used different elastography hardware, pulse sequences, reconstruction inversion algorithms, and different symmetry assumptions about the mechanical properties of tissue, effort was directed to ensure that similar quantities were used when making inter-study comparisons. In addition, because different methodologies and processing pipelines will necessarily bias the results, when pooling data from different studies, whenever possible, tumor values were compared with the same subject's contralateral normal appearing white matter to minimize any study-dependent bias. The literature search yielded 10 studies with a total of 184 primary and metastatic brain tumor patients. The group mean tumor stiffness, as measured with MRE, correlated with intra-operatively assessed stiffness of meningiomas and pituitary adenomas. Pooled data analysis showed significant overlap between shear modulus values across brain tumor types. When adjusting for the same patient normal appearing white matter shear modulus values, meningiomas were the stiffest tumor-type. MRE is increasingly being examined for potential in brain tumor imaging and might have value for surgical planning. However, significant overlap of shear modulus values between a number of different tumor types limits applicability of MRE for diagnostic purposes. Thus, further rigorous studies are needed to determine specific clinical applications of MRE for surgical planning, disease monitoring and molecular stratification of brain tumors.

Gene Signatures in Cutaneous Malignancies

In this review, we will discuss the recent advances in the identification of landmark gene signatures in cutaneous melanoma and in the discovery of those relevant to cutaneous squamous cell carcinoma (cSCC). Melanoma and cSCC are the most important cutaneous malignancies when considering morbidity and mortality. They are responsible for the greatest number of skin cancer related deaths. Over the past several years, a number of gene signatures have been identified showing great promise in terms of tumor molecular classification and risk stratification of patients to anticipate best therapeutic modalities. These gene signatures have allowed a personalized medicine approach to a comprehensive decision-making process for these patients. Prediction of the prognosis and therapeutic response of patients with melanoma and high-risk cSCC will be aided by the elucidation and utilization of these gene signatures.

Abstract AP09: COPY-NUMBER SIGNATURES AND MUTATIONAL PROCESSES IN HIGH GRADE SEROUS OVARIAN CARCINOMA

Abstract BACKGROUND: The genomic complexity of profound copy-number aberration has prevented effective molecular stratification of high grade serous ovarian carcinoma (HGSOC). Recent algorithmic advances have enabled interpretation of complex genomic changes by identifying mutational signatures—genomic patterns that are the imprint of mutagenic processes accumulated over the lifetime of a cancer cell. We hypothesized that specific features of copy-number (CN) abnormalities could represent the imprints of distinct mutational processes, and developed methods to identify signatures from copy-number features in HGSOC. METHODS: We derived copy-number signatures from absolute copy number profiles from 253 primary and relapsed HGSOC samples from 132 patients in the BriTROC-1 cohort using low-cost shallow whole-genome sequencing (sWGS; 0.1×). A subset of 56 of these cases had deep whole-genome sequencing (dWGS) performed for mutation analysis and comparison with sWGS data. Independent validation was performed using 112 dWGS HGSOC cases from PCAWG and 415 HGSOC cases with SNP array and whole exome sequence from TCGA. CN signature exposures were correlated with mutation data, SNV signatures, and other measures derived from deep WGS and exome sequencing to identify statistically significant genomic associations using a false discovery rate &amp;lt;0.05. RESULTS: We identified 7 CN signatures that provided a molecular framework to rederive the major defining elements of HGSOC genomes, including defective homologous recombination (HRD), tandem duplication, amplification of CCNE1 and amplification-associated fold-back inversions. Almost all patients with HGSOC demonstrated a mixture of signatures indicative of combinations of mutational processes, including those with early driver events such as BRCA2 mutation (in addition to HRD signatures). High exposure to CN signature 3, characterised by BRCA1/2-related HRD, was associated with improved overall survival. Conversely, high exposure to signature 1, which was characterised by oncogenic RAS signaling (including NF1, KRAS and NRAS mutation), predicted platinum-resistant relapse and poor survival. CONCLUSIONS: HGSOC lacks clinically-relevant patient stratification, which is reflected in poor survival and is a significant barrier to precision medicine. Copy-number signature exposures at diagnosis predict both overall survival and the probability of platinum-resistant relapse. Our results suggest that early TP53 mutation, the ubiquitous initiating event in HGSOC, may permit multiple mutational processes to co-evolve, potentially simultaneously and that additional signature exposures may alter the risk of developing therapeutic resistance. Thus, our results suggest that HGSOC is a continuum of genomes. We derived signatures using inexpensive sWGS of DNA from core biopsies. These approaches are rapid and cost effective, thus providing a clear path to clinical implementation. By dissecting the mutational forces shaping HGSOC genomes, our study paves the way to understanding extreme genomic complexity, as well as revealing the evolution of tumors as they relapse and acquire resistance to therapy. Citation Format: Geoff Macintyre, Teodora E. Goranova, Dilrini De Silva, Darren Ennis, Anna M. Piskorz, Matthew Eldridge, Daoud Sie, Liz-Anne Lewsley, Aishah Hanif, Cheryl Wilson, Suzanne Dowson, Rosalind M. Glasspool, Michelle Lockley, Elly Brockbank, Ana Montes, Axel Walther, Sudha Sundar, Richard Edmondson, Geoff D. Hall, Andrew Clamp, Charlie Gourley, Marcia Hall, Christina Fotopoulou, Hani Gabra, James Paul, Anna Supernat, David Millan, Aoisha Hoyle, Gareth Bryson, Craig Nourse, Laura Mincarelli, Luis Navarro Sanchez, Bauke Ylstra, Mercedes Jimenez-Linan, Luiza Moore, Oliver Hofmann, Florian Markowetz, Iain A. McNeish, James D. Brenton. COPY-NUMBER SIGNATURES AND MUTATIONAL PROCESSES IN HIGH GRADE SEROUS OVARIAN CARCINOMA [abstract]. In: Proceedings of the 12th Biennial Ovarian Cancer Research Symposium; Sep 13-15, 2018; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2019;25(22 Suppl):Abstract nr AP09.

Comparative Study of Tumor Biopsy and Ctdna to Support Patient Selection in Phase I Trials: The Gustave Roussy Single Center Experience in Aggressive B-Cell Lymphomas

Patient's selection in early phase clinical trials is guided by stringent clinical criteria and can be supported or improved by precise tumor characterization and/or molecular stratification. Most of the precision medicine data are generated using historical tumor biopsies often collected before anticancer drugs treatment, which may thus only partially reflect the tumor's molecular landscape at inclusion in early phase clinical trials. The gold standard fresh tumor biopsy is not always feasible without risk for the patient. For this reason, ctDNA could be a simple, safe and attractive technique for obtaining critical information on the tumor genomic landscape. This study was designed to explore if whether NGS results obtained with from ctDNA could replace fresh tumor biopsies in patients (pts) at inclusion in early phase clinical trials. Data generated on both tissue samples collected in a short period of time in 52 pts treated for a B-cell aggressive lymphoma in the DITEP department at Gustave Roussy prior to inclusion were compared (18/52 pts had one course of chemotherapy between the 2 tissue samples). Characteristics at sampling were: mean age = 66 y.o., male/female: 32/20, Ann Arbor staging: 1/2/3/4 = 4 (7.7%), 5 (9.6%), 8 (15.4%) and 35 (67.3%) pts. The median number of prior chemotherapy was 2 (Min=1; Max=7). NGS tests were done using a panel of 39 genes and more recently 44 genes. 34 genes were found mutated in at least one pt. 150 mutations of pathologic significance were identified and 105 mutations out of 150 (70.0%) were concordant between the fresh biopsy and the blood (95%CI=62.0%; 77.2%). No patient had a mutation detected in the ctDNA analysis that was not found in the fresh tumor biopsy. In 8/52(15%) patients, no mutation was detected in both tumor biopsy and blood. Of the 44-remaining pts, 10 had no mutation detected in the blood and 34 pts (77.3%) carried at least one mutation detectable in both the tumor and blood. In 25/44patients (56.8%) all mutations identified in the tumor could be also detected in the blood (95%CI=41.0%; 71.7%), which are "informative ctDNA patients" if we consider that tumor biopsy is the "gold standard" as it is in clinical trials. Among the 44 pts that have at least one mutation detected in the tumor, the median VAF detection in the tumor biopsy was 41% (range 2-98%) and in the blood it was 7% (range 0-83%), but if we focus on the 105 mutations detected in both the biopsy and in the blood, the median VAF observed is 43% in the tumor (range 2-98%) and 14% in the blood (range 1-83%). Our results suggest that 85% of the pts included in phase I trials have at least one detectable mutation in the tumor biopsy, but approximately 50% of the pts have concordant mutations found in both ctDNA and fresh tumor samples. These results also suggest that ctDNA could be a useful tool in those "informative ctDNA" pts for residual disease assessment without sequential biopsies. Disclosures Ribrag: MSD: Membership on an entity's Board of Directors or advisory committees; Nanostring: Membership on an entity's Board of Directors or advisory committees; Gilead: Membership on an entity's Board of Directors or advisory committees; Incyte: Membership on an entity's Board of Directors or advisory committees; Infinity: Membership on an entity's Board of Directors or advisory committees; Roche: Other: Travel, accommodations, and expenses ; BMS: Membership on an entity's Board of Directors or advisory committees, Other: Travel, accommodations, and expenses ; Servier: Consultancy, Membership on an entity's Board of Directors or advisory committees; AZ: Membership on an entity's Board of Directors or advisory committees; ArgenX: Research Funding; Epizyme: Consultancy, Research Funding.

RNA-Seq Can Help Identify IGH Disease Clones for MRD Monitoring in Childhood B-Lymphoblastic Leukemia

Background As a single platform, RNA sequencing (RNA-Seq) can accurately identify majority of oncogenic driver fusion genes and aneuploidy. This provides refined molecular subtyping and risk stratification; RNA-Seq is increasing used upfront for genetic subtype assignment in on-going contemporary ALL trials. The IGH gene is highly expressed in our diagnostic ALL samples using RNA-Seq. We investigated the usefulness of RNA-Seq in identifying IGH disease sequences for MRD monitoring in 258 childhood B-lymphoblastic leukemia (B-LL) samples. Methods RNA-seq was performed on a total of 259 diagnostic bone marrow or peripheral blood samples from children with B-LL treated in the Ma-Spore ALL 2003 and ALL 2010 studies. The reads were aligned to germline IGH gene V, D and J segments, and reads covered IGH VHDJH or DJH junctional regions are clustered into clones. Overall, the distribution of read count of the IGH background clones follows Zipf's law, i.e. the read count of the IGH background clones is negative linearly correlated with the number of IGH clones with that read count in the log-log scale (Figure 1A). IGH disease clones are outliers with exceedingly high read count. For each sample, a linear model is fitted between log transformed read count (using only read count ≤10) and log transformed number of IGH clones. The expected number of IGH clones (E-value) of a read count can be predicted by the fitted linear model. A clone with E-value &amp;lt;0.01 is defined as a disease clone (Figure 1B). Disease clones identified by RNA-Seq are compared with conventional Sanger sequencing. Results In 90.3% of the patients, 497 IGH disease clones (median 2, range 0-7 clones/patient) are identified. The number of IGH disease clones significantly correlated with genetic subtype (P=1.9×10-8; Table 1). Specifically, high hyperdiploid patients have the most IGH disease clones (median 3) with 67% (22/33) have &amp;gt;2 IGH disease clones, due to the gain of chromosome 14. In contrast, DUX4 high expressers have the least (median 1) IGH disease clones with 19% (8/43) have no IGH disease clone, due to the rearrangements involving one of the IGH locus. Of the 348 IGH disease clones identified by Sanger sequencing, 90.8% are also identified by RNA-Seq; and in the 199 Sanger sequences that yielded sensitive markers, 191 (96.0%) are also defined as IGH disease clones by RNA-Seq. In addition, RNA-Seq identified 43% more IGH disease clones. In 69 patients lacking sensitive IGH targets by Sanger sequencing, the disease clones identified by RNA-Seq were used collectively for MRD monitoring by targeted deep sequencing of IGH (IGH-Seq) and showed high correlation with conventional RQ-PCR MRD using non-IGH targets (R=0.93; P=1.3x10-14;Figure 1C). In addition, IGH-Seq showed improved sensitivity with quantifiable MRD in 20% more samples compared to RQ-PCR (78% vs 58%; Figure 1C). In the samples that are positive below sensitivity or negative by RQ-PCR, IGH-Seq obtained quantifiable MRD for 60% (9/15) or 25% (5/20) of the samples (Figure 1C). Conclusion In conclusion, IGH disease clone sequences are highly expressed and can be distinctly identified from whole transcriptome RNA-Seq in &amp;gt;90% of children with B-LL. These can be used for molecular MRD monitoring using RQ-PCR or NGS-based IGH-Seq. In addition to identifying the constellation of oncogene fusions and chromosomal aneuploidies that drive B-LL and RNA-Seq can identify IGH MRD sequences for molecular MRD monitoring. Disclosures No relevant conflicts of interest to declare.

Molecular Treatment Stratification for Newly Diagnosed High-Risk Myeloma, Including Plasma Cell Leukemia - Feasibility Results of the Ukmra Optimum: MUK9 Trial (NCT03188172)

Background High-risk myeloma patients have unsatisfactory outcomes with current treatments and are in urgent need of improved diagnostic and therapeutic strategies. We have recently validated specific markers predicting high-risk disease in newly diagnosed MM (NDMM), in particular double-hit with presence of ≥2 consensus high-risk markers t(4;14), t(14;16), t(14;20), del(1p), gain(1q), del(17p) (Shah V, et al., Leukemia 2018) and diagnostic GEP SKY92 high risk signature (Sherborne A, et al., IMW 2017). Diagnostic tests for these markers were implemented in the UK multi-center OPTIMUM: MUK9 trial to prospectively stratify therapy for high-risk NDMM. Trial design OPTIMUM: MUK9 is a phase 2 trial for transplant eligible NDMM, consisting of two inter-related protocols: a molecular screening protocol (MUK9A) and an interventional trial (MUK9B) for high-risk MM identified in MUK9A. Patients with suspected or confirmed MM fit for intensive therapy enrolled in MUK9A have central molecular profiling at ICR, London, of CD138-selected BM MM cells for translocations, copy number aberrations (qRT-PCR; MLPA P425, MRC Holland) and SKY92 signature status (MMprofiler; SkylineDx). If clinically indicated SOC therapy (VTD, max. 2 cycles) can be given whilst central results are generated. Patients found to have high-risk MM by double-hit and/or SKY92 are offered enrolment into MUK9B. All other patients receive SOC (VTD, HD-MEL+ASCT) for which clinical data is collected. Patients diagnosed with plasma cell leukemia (PCL) can be enrolled directly in MUK9B. MUK9B treatment consists of quintuplet daratumumab, cyclophosphamide, bortezomib, lenalidomide, dexamethasone (Dara-CVRd) induction (up to 6 cycles), bortezomib-augmented single HD-MEL+ASCT, Dara-VRd consolidation 1 (6 cycles), Dara-VR consolidation 2 (12 cycles) and Dara-R maintenance (until PD). Dose adjustments are permitted in order to maximize tolerability of long-term therapy. Patient reported outcomes (PRO) are recorded at baseline and throughout treatment. Response and MRD are centrally assessed (Birmingham, Leeds). Primary endpoint for MUK9A is feasibility of central molecular testing within 56 days turnaround time, which we report on here. Primary endpoint of MUK9B is treatment efficacy, comparing MUK9B PFS to near-concurrent molecularly matched high-risk patient outcomes from UK NCRI Myeloma XI using a Bayesian design. Secondary endpoints include safety, PFS2, MRD and OS and study of molecular evolution in high-risk disease. Results The protocol recruited 29/Sep/17 - 31/Jul/19 at 39 UK sites, achieving the recruitment target of 105 high-risk patients treated on MUK9B ahead of projections. At the time of analysis (12/Jul/19), 430 patients with suspected or confirmed NDMM have been recruited to MUK9A across 39 UK NHS hospitals. Of these, 376 (87%) patients were confirmed to have symptomatic MM (60.9% male; median age 61y (range 29-79)) as per updated IMWG diagnostic criteria (2014), including 9 (2%) PCL patients, with the remainder diagnosed as SMM/MGUS (31; 7%) or other (14; 3%). For 371 of the 376 symptomatic MM patients BM was received by the central laboratory and was of sufficient quality for profiling in 331 (89%) patients. Repeat samples were requested for all others and a sufficient sample received for 20/45 (44%). Central results were successfully reported within the pre-specified 56 day interval for all patients (median 17 days; IQR 13-22). Of 346 patients with a reported result, 128 (37.0%) have high-risk MM, with molecular characteristics mirroring Myeloma XI patients (Figure 1). PCL patients show expected characteristics as listed in Table 1. Basic demographics were not different between high-risk vs. non-high-risk. 101 high-risk patients have or are planning to enter MUK9B, 10 pending decision; 17 high-risk patients did not enter MUK9B, the majority due to ineligibility. 92 patients have started Dara-CVRD therapy. There are currently no safety concerns, the majority of patients are completing induction successfully; 1 patient stopped induction therapy due to adverse events. Updated results will be presented. Discussion Our data demonstrate feasibility of multi-center molecular stratified trial delivery for high-risk NDMM patients. These early trial results strongly support accelerated trial strategies for MM patient groups with high unmet need and rational drug development specifically for high-risk MM. Disclosures Jenner: Abbvie, Amgen, Celgene, Novartis, Janssen, Sanofi Genzyme, Takeda: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau. Hall:Celgene, Amgen, Janssen, Karyopharm: Other: Research funding to Institution. Walker:Janssen, Celgene: Other: Research funding to Institution. Croft:Celgene: Other: Travel expenses. Jackson:Celgene, Amgen, Roche, Janssen, Sanofi: Honoraria. Flanagan:Amgen, Celgene, Janssen, Karyopharm: Other: Research funding to Institution. Drayson:Abingdon Health: Consultancy, Equity Ownership. Owen:Celgene, Janssen: Consultancy; Celgene: Research Funding; Janssen: Other: Travel expenses; Celgene, Janssen: Honoraria. Pratt:Binding Site, Amgen, Takeda, Janssen, Gilead: Consultancy, Honoraria, Other: Travel support. Cook:Celgene, Janssen-Cilag, Takeda: Honoraria, Research Funding; Janssen, Takeda, Sanofi, Karyopharm, Celgene: Consultancy, Honoraria, Speakers Bureau; Amgen, Bristol-Myers Squib, GlycoMimetics, Seattle Genetics, Sanofi: Honoraria. Brown:Amgen, Celgene, Janssen, Karyopharm: Other: Research funding to Institution. Kaiser:Celgene, Janssen: Research Funding; Abbvie, Celgene, Takeda, Janssen, Amgen, Abbvie, Karyopharm: Consultancy; Takeda, Janssen, Celgene, Amgen: Honoraria, Other: Travel Expenses.

A Phase I/II Study of Ibrutinib and Ixazomib in Relapsed/Refractory Mantle Cell Lymphoma: PrE0404

A Phase I/II Study of Ibrutinib and Ixazomib in Relapsed/Refractory Mantle Cell Lymphoma: PrE0404

CBMT-03. EVALUATION OF PET TRACERS TO DIFFERENTIATE IDH1 MUTANT GBM

Abstract OBJECTIVE PET/CT offers the unique potential to noninvasively evaluate biomarker expression and aberrant metabolism. 18F-FDG has driven PET/CT to the forefront of cancer imaging, as altered glucose metabolism is a hallmark of oncogenesis. However, 18F-FDG is suboptimal for GBM due to high physiologic uptake in normal brain. The development of alternative tracers has reignited the field of PET/CT in GBM and offers hope for diagnosis and molecular staging in GBM. We hypothesize that fundamental differences in metabolism and oncogene expression present in IDH1 mutatant gliomas can be shown using PET imaging, as has been suggested in some correlative clinical studies. Our objective was therefore to establish a causal link between IDH1 mutation in GBM and uptake of targeted PET tracers in a unique proneural GBM transgenic model characterized by p53, IDH1 mutations and PDGF expression. METHODS We examined the uptake of 3 blood-brain-barrier (BBB) penetrant tracers that have been used in GBM: (a) 18F-FDG, a surrogate for increased glycolysis; (b) 18F-Fluciclovine, an amino acid derivative transported into cells through the energy-independent L-type amino acid transporter (LAT) system and is approved by the FDA for prostate cancer; and (c) 11C-ER176, a tracer that binds the TSPO receptor that is generally expressed on activated microglia as well as GBM. RESULTS We did not observe significant differences in 18F-FDG uptake between wt and IDH mutant GBM cells. However, we found that IDH mutant GBM cells demonstrated significantly increased 18F-Fluciclovine (47%) and 11C-ER176 (53%) versus IDH wt cells. CONCLUSION We have established a causal link between IDH mutation status and uptake of (a) 18F-Fluciclovine, a promising FDA approved PET tracer and (b) 11C-ER176, a second generation TSPO ligand. Thus, we are performing further studies in orthotopic syngeneic GBM models to determine if PET imaging can non-invasively demonstrate molecular characterization and therapeutic stratification in glioma.

RBTT-06. TESSA JOWELL BRAIN MATRIX STUDY: A BRITISH FEASIBILITY STUDY OF MOLECULAR STRATIFICATION AND TARGETED THERAPY TO OPTIMIZE THE CLINICAL MANAGEMENT OF PATIENTS WITH GLIOMA

Abstract In 2016 there were 5250 brain cancer deaths in the UK. Standard treatment is surgical resection followed by chemo-radiotherapy. In most cases of diffuse glioma, complete tumour resection is not feasible. Many chemotherapy drugs have untested penetration through the blood brain barrier, potentially leading to sub-therapeutic concentrations in the tumour. There is need to refine current treatment strategies in relation to the understanding of tumour biology, and rapidly introduce and evaluate novel therapeutic approaches and agents through delivering rigorous clinical trials. The TESSA JOWELL BRAIN MATRIX Study will evaluate the feasibility of delivering precision medicine for brain cancer patients within the NHS. A multicentre, platform feasibility study of 1200 patients with diffuse glioma will build on the 100,000 genome project to develop and evaluate an infrastructure to collect and integrate: 1) real time comprehensive integrated molecular analysis, including whole genome sequencing and epigenetic classification; 2) serial sampling and annotation of tumours; 3) collection of matched clinical data; 4) assessment of patient quality of life; 5) centralised radiological review and response assessment as per RANO criteria. Once developed this will allow rapid introduction of therapeutic trials to specific patient groups. Secondary objectives include: understanding the association between extent of resection and molecular stratification to refine the role of surgery; optimisation and harmonisation of protocols to best collect, manage and store tissue, clinical data, and radiological images in order to provide a resource for researchers, both within and outside of the study. Improve patient recruitment by identifying and removing recruitment barriers and improve the information and consent processes for patients. Promote the development of a national network with expertise in brain cancer. Enrolment of the first patient is expected in late 2019. For further information, please contact the Brain Matrix Trial Office BrainMatrix@trials.bham.ac.uk.

Optimization of in silico tools for predicting genetic variants: individualizing for genes with molecular sub-regional stratification.

Genes are unique in functional role and differ in their sensitivities to genetic defects, but with difficulties in pathogenicity prediction. This study attempted to improve the performance of existing in silico algorithms and find a common solution based on individualization strategy. We initiated the individualization with the epilepsy-related SCN1A variants by sub-regional stratification. SCN1A missense variants related to epilepsy were retrieved from mutation databases, and benign missense variants were collected from ExAC database. Predictions were performed by using 10 traditional tools with stepwise optimizations. Model predictive ability was evaluated using the five-fold cross-validations on variants of SCN1A, SCN2A, and KCNQ2. Additional validation was performed in SCN1A variants of damage-confirmed/familial epilepsy. The performance of commonly used predictors was less satisfactory for SCN1A with accuracy less than 80% and varied dramatically by functional domains of Nav1.1. Multistep individualized optimizations, including cutoff resetting, domain-based stratification, and combination of predicting algorithms, significantly increased predictive performance. Similar improvements were obtained for variants in SCN2A and KCNQ2. The predictive performance of the recently developed ensemble tools, such as Mendelian clinically applicable pathogenicity, combined annotation-dependent depletion and Eigen, was also improved dramatically by application of the strategy with molecular sub-regional stratification. The prediction scores of SCN1A variants showed linear correlations with the degree of functional defects and the severity of clinical phenotypes. This study highlights the need of individualized optimization with molecular sub-regional stratification for each gene in practice.

&lt;p&gt;Poor Prognosis With Coexistence Of &lt;em&gt;EGFR&lt;/em&gt; T790M Mutation And Common &lt;em&gt;EGFR&lt;/em&gt;-Activating Mutation In Non- Small Cell Lung Cancer&lt;/p&gt;

PurposePrevious studies have shown that the presence of EGFR T790M mutation may reduce the treatment efficacy of tyrosine kinase inhibitors (TKIs) in EGFR-mutant lung cancer. However, little is known about the clinical features and outcomes of EGFR T790M mutation in pretreated patients with NSCLC.Patients and methodsThe clinical features of EGFR-activating and T790M mutations were assessed in a large cohort of patients with EGFR-TKI-naïve NSCLC (all/EGFR mutations, n=16,347/7,687). The correlation between the pretreatment T790M mutation status and clinical outcomes was evaluated using univariate and multivariate analyses.ResultsPretreatment T790M mutation was reported in 1.39% of the patients and coexisted with an EGFR-activating or uncommon mutation. The dual EGFR T790M and common EGFR-activating mutations were more likely to be detected in lung adenocarcinoma, whereas single T790M mutation was more prevalent in non-adenocarcinomas. The presence of de novo T790M mutation correlated with reduced recurrence-free survival (RFS) in patients with NSCLC (odds ratio [OR] 3.37, 95% confidence interval [CI] 1.67–6.79, P = 0.001). After molecular stratification, T790M mutation was shown to exert adverse effects on the RFS of EGFR 19-del group (OR 2.89, 95% CI 1.10–7.91, P = 0.028) and EGFR L858R group (OR 3.43, 95% CI 1.33–8.88, P = 0.013). Furthermore, pretreatment T790M mutation promoted tumor metastasis to different sites.ConclusionT790M-positive tumors presented special clinical features, and the coexistence of T790M and common EGFR-activating mutations was associated with poor prognosis in patients with NSCLC.

Combination of mTOR inhibition and paclitaxel as a personalised strategy in the context of MYC-amplified high-grade serous ovarian cancer

Abstract Background The extreme genomic heterogeneity of high-grade serous ovarian carcinoma (HGSOC) is a major barrier to precision medicine approaches. We have developed mutational signature analysis from shallow whole genome sequencing (sWGS) for molecular stratification and therapeutic prediction. PARP inhibitor therapy has significant survival advantage for women with germline BRCA1/2 mutations, but treatments and predictive biomarkers for women without homologous recombination deficiency have not been developed. MYC amplification is the most common driver in HGSOC, present in 42% of the TCGA cases. The best responder from the phase 1 trial of AZD2014 (dual m-TORC1/2 inhibitor) and paclitaxel in HGSOC had a mutation in MYC and we have hypothesised that biosynthetic effects of MYC are mediated through the mTOR pathway and blocked by AZD2014 perturbation. Methods Primary ovarian cancer spheroids were purified from 28 human ascites and profiled with sWGS. Ex-vivo therapeutic response was measured to four standard of care chemotherapeutic agents and eight inhibitors targeting nodal points of the PI3K and DNA damage repair pathways. RNA seq data from the TCGA HGSOC cohort was used to establish the genes whose expression was highly correlated with the expression of MYC. Results Ex-vivo assays were predictive of first-line clinical response to chemotherapy agents (P Conclusions Our results suggest that therapeutic strategies combining paclitaxel and inhibition of mTOR pathway can be used as personalised treatment in the context of MYC-amplified HGSOC. We are currently examining gene expression after AZD2014 pertubation in HGSOC models and performing the genomic analysis of cases from the phase 1 trial of AZD2014 and paclitaxel. Legal entity responsible for the study The authors. Funding Academy of Medical Sciences, Addenbrookes Charitable Trust, Cancer Research UK, University of Cambridge. Disclosure F.C. Martins: Research grant / Funding (self), The Clinical Lectureship from the Experimental Medicine Initiative is partly funded by AstraZeneca: AstraZeneca. All other authors have declared no conflicts of interest.

Using next generation sequencing technology to analyze gene mutations in patients with acute myeloid leukemia and the impact on prognosis

Objective: To analyze the distribution of gene mutations in newly diagnosed acute myeloid leukemia (AML) patients, based on next generation sequencing technology (NGS) and to evaluate their value in AML risk stratification. Methods: The study analyzed 453 newly diagnosed AML(excluded acute promyelocytic leukemia, APL) patients from seven hospitals in Shanghai, from January 1st 2014 to December 31th 2017. RNA and DNA were extracted from pretreatment bone marrow mononuclear cells and targeted sequencing of AML genes were performed. The data of different groups was compared. Results: A total of 453 newly diagnosed AML patients were enrolled in the study, including 247 males and 206 females with a median age of 49.5 (range,11-85) years. A total of 540 mutations/fusion genes were detected in 289 patients, 29.1% (132/259) of whom with two or more mutations/fusion genes. In all patients, NPM1 was the most common mutation(12.8%), followed by ETO and TET2 mutation (11.92% and 11.04%, respectively) . And WT1 over-expression accounted for 10.6%. Patients over the age of 50 were with a higher frequency of mutations associated with epigenetic modification, 11.93% for ASXL1, 13.99% for DMNT3A, 6.58% for IDH1/IDH2, and 13.17% for TET2. The frequency of DMNT3A mutations was three times higher than that of patients under 50 years of age (P=0.017). In this study, a relatively low proportion of genetic mutations was observed in low-risk karyotype group. In the medium-risk karyotype group, the relatively high mutation frequencies were observed in NPM1, TET2, FLT3-ITD, DNMT3A, ASXL1, and CEBPA genes. In the poor-risk karyotype group, the mutation frequencies of ASXL1, TET2, DNMT3A and PHF6 genes were more than 10%, especially ASXL1 and PHF6 mutation frequencies were significantly higher than other molecular risk stratification groups (P<0.05). Of the 254 patients (56%) with normal karyotype AML (NK-AML), 56 patients were detected to have gene mutations about epigenetic modification. The median OS of this group was worse than that of patients without related mutations, while the median LFS had no significant difference. In patients with NK-AML older than 50 years, the OS and LFS of patients with epigenetic modification related gene mutations was 12 months and 10 months, versus 18 months and 12 months of patients without mutations. Conclusions: The gene mutations frequencies in AML patients with different age and molecular risk stratification groups are different. Epigenetics gene mutation frequencies, such as DNMT3A, ASXL1, IDH1/IDH2 and TET2,are higher in patients older than 50 years. A shorter OS can be observed in older patients(>50 years) with epigenetics gene mutation.

Molecular stratification of idiopathic nephrotic syndrome.

Idiopathic nephrotic syndrome (INS) describes a group of pathologies of the renal glomerulus that result in the classic triad of heavy proteinuria, oedema and hypoalbuminaemia. The disease has historically been defined by evidence of distinctive histological changes in the absence of clinical evidence of a distinct pathological driver. However, the current classification is not based on any systematic mechanistic understanding of biological processes, and therefore current treatment regimens are broad, iterative and nonspecific. Over the past 20 years delineation of the underlying biology of the target cell in INS - the glomerular podocyte - has transformed our understanding of the mechanisms that contribute to breakdown of the glomerular filtration barrier and the development of INS. It is increasingly clear that nephrotic syndrome caused by monogenic mutations is distinct from immune-driven disease, which in some cases is mediated by circulating factors that target the podocyte. The combination of systems biology and bioinformatics approaches, together with powerful laboratory models and ever-growing patient registries has potential to identify disease 'signatures' that reflect the underlying molecular mechanism of INS on an individual basis. Understanding of such processes could lead to the development oftargeted therapies.

Observation after surgery for low grade glioma: long-term outcome in the light of the 2016 WHO classification.

To provide detailed long-term data after initial observation for patients after histological confirmation of low grade (WHO II) gliomas according to molecular stratification. A series of 110 patients with watchful waiting strategy after initial surgery for LGG and re-surgery at tumor progression were analyzed. Progression-free survival, time to malignant transformation, post-recurrence survival, and overall survival were estimated with the Kaplan-Meier method. Prognostic factors were identified by the Log Rank test and Cox multivariate proportional hazards model. The cohort comprised 18 IDH wild type (IDHwt) and 53 IDH mutated (IDHmut) astrocytomas, and 39 IDH mutated and 1p 19q co-deleted (IDHmut/codel) patients. The median follow-up was 126 (95% CI 109-143) months. Surgery was gross total resection in 58, subtotal resection in 28, and biopsy in 24 patients. Progression-free survival rates at 5, 10 and 15 years was 38% 18% and 1%. The corresponding malignant transformation rates were 17%, 39% and 71%. The initial extent of resection influenced progression-free survival, time to malignant transformation and overall survival. Molecular subtype IDHmut/codel was the strongest prognostic factor for overall survival and for time to malignant transformation. The strongest determinant of the patients' course after initial watchful waiting was the molecular tumor status. Extensive resection may increase time to progression and malignant transformation. Observation may be justified in selected patients.

Relevance of calcification and contrast enhancement pattern for molecular diagnosis and survival prediction of gliomas based on the 2016 World Health Organization Classification

ObjectivesThe significance of conventional neuroimaging features for predicting molecular diagnosis and patient survival based on the updated World Health Organization (WHO) classification remains uncertain. We assessed the relevance of neuroimaging features (ring enhancement [RE], non-ring enhancement [non-RE], overall gadolinium enhancement [GdE], and intratumoral calcification [IC]) for molecular diagnosis and survival in glioma patients. Patients and methodsWe evaluated 234 glioma patients according to the updated WHO classification. Isocitrate dehydrogenase (IDH), H3F3A, BRAF hotspot mutations, TERT promotor mutation, and chromosome 1p/19q co-deletion were examined. RE, non-RE, GdE, and IC were evaluated as significant neuroimaging findings. Kaplan-Meier analyses were performed to evaluate overall survival (OS) and the correlations of prognostic factors were evaluated by log-rank tests. Univariate and multivariate analyses were performed to detect prognostic factors for OS. ResultsA total of 207 patients were eligible. In 110 patients presenting RE, 102 (93%) were glioblastoma (GBM), IDH-wild type. In 97 patients without RE, presence of GdE or IC were not significantly different between IDH-mutant and -wild type tumors, whereas presence of GdE was a significant indicator of higher WHO grades. IC was the only significant finding for 1p/19q co-deleted tumors. TERT promoter mutation was observed in 7/17 patients with diffuse astrocytic glioma, IDH-wild type; recently-defined as “molecular GBM.” IC, RE, and GdE were observed with lower prevalence in molecular GBMs. While presence of RE, GdE, and absence of IC were significant factors of OS in overall cohort, presence of GdE was not significant in OS in cases without RE, and IDH-mutant tumors. IC was a significant predictor of favorable OS in cases without RE and IDH-wild type tumors. Multivariate analysis also validated these findings. ConclusionGdE alone is not a significant predictor of IDH mutation status, but the pattern of enhancement is a significant predictor with RE demonstrating high sensitivity and specificity for GBM, IDH-wild type. Predicting “molecular GBM” by conventional neuroimaging is difficult. Moreover, GdE is not a significant factor of survival analyzed with pattern of enhancement or molecular stratifications. IC is an important radiographic finding for predicting molecular diagnosis and survival in glioma patients.