A Clinically Validated Targeted Capture Panel to Identify Translocations, Copy Number Abnormalities, and Mutations in Multiple Myeloma

Introduction: Multiple myeloma (MM) is a genetically heterogeneous disease where risk stratification and outcomes are associated with translocations involving the immunoglobulin (Ig) loci and MYC, copy number abnormalities including gain(1q), del(1p), and del(17p), as well as mutations. Additionally, MM tumors may harbor rare mutations in genes that are targetable in other tumors, such as in IDH1 and IDH2. Therefore, we designed a comprehensive MM targeted sequencing panel to interrogate the common genomic abnormalities in MM and validated it against known standards. Methods: The targeted panel was designed to include the exons of 228 genes which are either frequently mutated, associated with prognosis or risk stratification, clinically actionable, or sites of important copy number abnormalities. Additional targets were added across the genome to identify hyperdiploidy. These targeted regions encompass the mutation detection part of the panel and involve approximately 990 kb. The Ig loci and region surrounding MYC were tiled to capture translocations and copy number changes. In total, this translocation part of the panel involves approximately 4.7 Mb. The mutation and translocation panels are manufactured separately and combined during the assay resulting in a 5:1 sequencing ratio, respectively, which prevents over-sequencing of the large translocation panel. 100 ng DNA extracted from CD138+ bone marrow cells (n=223) and from non-tumor tissue (peripheral blood or saliva) was processed using the HyperCap workflow (KAPA Biosystems). Of the 223, 48 samples were processed in a clinical diagnostic laboratory. Adapter ligated DNA was hybridized with a mixture of the mutation and translocation panel and purified, amplified libraries were sequenced using 75 bp paired end reads. Sequences were aligned to hg19 and mutations and translocations identified using Strelka and Manta. Copy number was determined using the ratio of non-tumor to tumor reads in each targeted region. Data were validated using clinical FISH (translocations, n=116), MLPA (copy number, n=101), known standards (mutations), ddPCR (mutations), and whole genome sequencing (WGS; translocations and copy number, n=122). Results: Canonical IgH translocations were detected in 43.2% of patients by the panel, and all agreed with WGS. FISH detected one additional "variant" t(4;14), but did not detect 4 translocations detected by both sequencing methods. In the remainder of the samples no canonical IgH translocation was detected, agreeing with FISH results. Non-canonical translocations were detected in 14.5% of samples, 43% of which were to the MYC locus. MYC translocations were detected in 37.3% of samples with copy number abnormalities occurring surrounding MYC in 32.7% of samples. Overall, MYC abnormalities were detected in 46.4% of samples. Copy number was determined by panel sequencing and MLPA for 22 regions that were directly comparable between the technologies in 101 patient samples and 13 myeloma cell lines. The copy number concordance between the technologies was 96.9% and 99.6% in patient samples and cell lines, respectively. For the important prognostic regions, the concordance was R 2=0.962 (CDKN2C), R 2=0.986 (CKS1B), and R 2=0.973 (TP53). Panel copy number data were also compared to WGS data and showed complete concordance across the three prognostic regions, which the exception of 2 samples. In these 2 samples a homozygous deletion was detected by the panel but not by WGS. The deletions were 6.2 and 8.0 kb in size, one encompassing the coding sequencing of TP53 and the other exons 1-4 of TP53. A larger homozygous deletion of 36.3 kb was detected by both sequencing methods. Mutation detection validation was performed using Horizon Discovery samples with known variant allele frequencies (VAF) for common mutations. We were able to determine the sequencing VAF for 74 mutations across 5 samples which had a concordance of R 2=0.9849 between the expected and observed frequencies. The minimum detected VAF was 1.3% at an average depth of 891x. We also performed ddPCR on 6 patient samples with the common KRAS, NRAS and BRAF mutations which resulted in a VAF concordance of R 2=0.9983. Conclusion: We have developed a targeted sequencing panel for MM patient samples that is as robust or better than both FISH and WGS. A full protocol for sample processing and analysis is available, and has been used in a clinical diagnostic laboratory. Disclosures Ahsan: Bristol Myers Squibb: Current Employment, Current equity holder in publicly-traded company. Abu Zaid: Pieris: Current equity holder in publicly-traded company; Incyte: Research Funding; Pharamcyclic: Research Funding; Syndax: Consultancy, Research Funding. Ramasamy: Amgen: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel, Conference registration, Research Funding; Janssen: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel, Conference registration, Research Funding; Takeda: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel, Conference registration, Research Funding; Celgene (BMS): Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel, Conference registration, Research Funding; GSK: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Oncopeptides: Honoraria, Membership on an entity's Board of Directors or advisory committees; Adaptive biotech: Honoraria, Membership on an entity's Board of Directors or advisory committees; Karyopharm: Honoraria, Membership on an entity's Board of Directors or advisory committees; Pfizer oncology: Honoraria, Membership on an entity's Board of Directors or advisory committees; Sanofi: Honoraria, Membership on an entity's Board of Directors or advisory committees. Yong: GSK: Honoraria; Amgen: Honoraria; BMS: Research Funding; Sanofi: Honoraria, Research Funding; Takeda: Honoraria; Autolus: Research Funding; Janssen: Honoraria, Research Funding. Morgan: Takeda: Honoraria. Abonour: Celgene-BMS: Membership on an entity's Board of Directors or advisory committees, Research Funding; Takeda: Research Funding; Jensen: Honoraria, Research Funding; GSK: Consultancy, Honoraria, Research Funding. Flynt: Bristol Myers Squibb: Current Employment. Ansari-Pour: Bristol Myers Squibb: Consultancy. Gooding: Bristol Myers Squibb: Research Funding. Thakurta: Bristol Myers Squibb: Current Employment, Current equity holder in publicly-traded company. Walker: Bristol Myers Squibb: Research Funding; Sanofi: Speakers Bureau.

REALM (OP-RW001): Comparing the Characteristics and Clinical Outcomes of Patients with Relapsed/Refractory Multiple Myeloma in the Real World to Patients Receiving Melflufen in the Horizon Study

Introduction: Melphalan flufenamide (melflufen) is a first-in-class peptide-drug conjugate that targets aminopeptidases and rapidly releases alkylating agents into tumor cells. The single-arm, open-label, Phase 2 HORIZON study (NCT02963493), conducted in Europe and the USA, demonstrated in patients with heavily pre-treated relapsed/refractory multiple myeloma (RRMM), including those with triple-class-refractory and extramedullary disease, that melflufen in combination with dexamethasone showed clinically meaningful efficacy and a manageable safety profile (Richardson PG, et al. J Clin Oncol. 2021;39:757-767). Comparative trials between all regimens/agents are not feasible, and hence, real-world datasets may be valuable to allow the comparison of patient outcomes in single-arm clinical trials with similar patient populations in the real world. The objective of the REAL-world Myeloma (REALM) study was to compare clinical outcomes between patients in the COTA database and those of patients in the HORIZON study in order to compare routine care with melflufen. Methods: REALM is a retrospective, observational study using real-world data from 605 patients with RRMM collected in the COTA database, a USA-based real-world evidence database comprising longitudinal, Health Insurance Portability and Accountability Act (HIPAA)-compliant data on the diagnosis, clinical management, and outcomes of patients with cancer. Patients in REALM met the main HORIZON eligibility criteria (aged ≥18 years; ≥2 lines of prior therapy [including an immunomodulatory drug and a proteasome inhibitor]; refractory to pomalidomide and/or daratumumab on or after January 1, 2015; and received a line of therapy after meeting the inclusion criteria). Propensity score (PS) matching is a commonly used approach for comparing the effectiveness of 2 treatment options across different studies where individual patient data are available for both treatments. This abstract presents adjusted clinical outcome results based on 1:1 PS matching of patients in the COTA and HORIZON datasets for 12 covariates (COTA PS and HORIZON PS, Table 1). These covariates were considered important because they reflect patient characteristics that impact clinical outcomes and were validated in a feasibility study, and by independent experts. The primary endpoint of the HORIZON study was overall response rate. The primary endpoints of the REALM study were time to treatment discontinuation (TTD) and time to next treatment (TTNT), to mitigate against missing treatment response data in the COTA database identified in the feasibility study. Results: Selected patient demographic and clinical characteristics were generally well matched (Table 1) between patients from COTA PS (n=110) and HORIZON PS (n=110), except for the Eastern Cooperative Oncology Group performance status, which was better in the COTA PS dataset than in the HORIZON PS dataset. Patients in both the COTA PS and the HORIZON PS datasets were predominantly male and White. Patients had a median age of 67 years in the COTA PS dataset and 64 years in the HORIZON PS dataset, with a median of 4 and 5 prior lines of therapy, respectively. The median time since first diagnosis to index data was 60.19 months in the COTA PS dataset and 72.56 months in the HORIZON PS dataset. The median TTNT (95% confidence interval [CI]) in the COTA PS dataset versus the HORIZON PS dataset was 4.6 (3.7-6.9) months and 5.9 (4.7-7.7) months, respectively (p=0.949). The median TTD (95% CI) in the COTA PS dataset versus the HORIZON PS dataset was 3.2 (2.6-3.9) months and 3.9 (3.0-4.6) months, respectively (p=0.642). Conclusions: Pharmacoepidemiologic methods using individual patient data play an important role in evaluating the effectiveness of treatments in the absence of randomized controlled trial data. Patients with RRMM receiving melflufen in combination with dexamethasone noted a trend toward improved TTNT and TTD compared with corresponding real-world treatment approaches. This benefit may be clinically meaningful especially in the triple-class-refractory patient population, which remains an unmet need in RRMM. Figure 1 Figure 1. Disclosures Ailawadhi: Karyopharm: Consultancy; AbbVie: Consultancy; Genentech: Consultancy; Takeda: Consultancy; GSK: Consultancy, Research Funding; Xencor: Research Funding; Cellectar: Research Funding; Medimmune: Research Funding; Ascentage: Research Funding; Pharmacyclics: Consultancy, Research Funding; Amgen: Consultancy, Research Funding; Janssen: Consultancy, Research Funding; Bristol Myers Squibb: Consultancy, Research Funding; BeiGene, Ltd.: Consultancy; Sanofi: Consultancy; Oncopeptides: Consultancy. Wang: COTA, Inc.: Current Employment, Other: Equity ownership. Belli: COTA, Inc.: Current Employment, Other: Equity ownership. Jansson Blixt: Oncopeptides: Current Employment, Current holder of individual stocks in a privately-held company, Current holder of stock options in a privately-held company. Cripps: Oncopeptides: Other: Independent consultant. Zavisic: Oncopeptides: Current Employment, Current holder of stock options in a privately-held company. Ramasamy: Amgen: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel, Conference registration, Research Funding; Janssen: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel, Conference registration, Research Funding; Takeda: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel, Conference registration, Research Funding; Celgene (BMS): Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel, Conference registration, Research Funding; GSK: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Oncopeptides: Honoraria, Membership on an entity's Board of Directors or advisory committees; Adaptive biotech: Honoraria, Membership on an entity's Board of Directors or advisory committees; Karyopharm: Honoraria, Membership on an entity's Board of Directors or advisory committees; Pfizer oncology: Honoraria, Membership on an entity's Board of Directors or advisory committees; Sanofi: Honoraria, Membership on an entity's Board of Directors or advisory committees.

Analyzing the cost of medical student virtual conference registration by specialty during the COVID-19 pandemic

Context Medical student involvement in research is an important metric used by residency programs across most specialties to better assess the candidates’ commitment to advancing medicine as well as their specialty of interest. One strategy is presentation of research work at national conferences in the specialty of interest; another is simply attending these events for networking purposes with program directors. However, attending these conferences carries cost. Objectives To investigate the cost incurred by medical students to attend the premier annual scientific meeting of each major medical specialty in 2020, during the novel coronavirus 2019 (COVID-19) pandemic, and to evaluate whether “research intensive” specialties carried greater conference registration costs. Methods Potential medical specialties to which students can apply upon graduation were identified in the National Residency Match Program (NRMP). “Research intensive” specialties were defined as those with a mean number of abstracts, presentations, or publications ≥10 per matched applicant in the 2020 NRMP. The premier conference for each specialty was determined by membership in the American Medical Association House of Delegates in the NRMP. The cost to be a member of each conference’s parent organization and attend the annual meeting were determined by internet search. Subgroup analysis was conducted to compare cost between research intensive and non research intensive specialties. Results The registration cost of 19 virtual conferences held in 2020 were analyzed in this study. The average cost to attend as a medical student member of the hosting organization for all conferences was $49.82 (range, $0–$331; SD±$92.18), while the average cost to attend as a nonmember across all conferences was $188.16 (range, $0–$595; SD±$176.35; p<0.001). Seven of 19 (36.8%) meetings had free registration for medical students who are members of the hosting organization. The premier meetings affiliated with the seven research intensive specialties had a significantly higher mean cost for medical students who were members of the parent organization than the meetings of the other specialties ($125.60 vs. $49.20; p=0.031). There was no significant difference in mean registration cost between research intensive and non research intensive specialty conference registration for nonmember medical students (p=0.85). Vascular surgery, radiation oncology, and emergency medicine were the three specialties with the most expensive medical student member registration fees overall ($331, $200, and $195, respectively). Conclusions Medical student attendance and presentation at national scientific meetings was found to be significantly more costly for research intensive specialties, although all meetings were held in an online format due to the COVID-19 pandemic. Overall, this reflects an increased financial burden to an already indebted medical student population and compounds the stresses brought on by the pandemic. More national medical societies might consider free meeting registration to reflect support for medical students and encourage their continued participation in research to advance their specialty of interest.

Steps toward preregistration of research on research integrity

Background A proposal to encourage the preregistration of research on research integrity was developed and adopted as the Amsterdam Agenda at the 5th World Conference on Research Integrity (Amsterdam, 2017). This paper reports on the degree to which abstracts of the 6th World Conference in Research Integrity (Hong Kong, 2019) reported on preregistered research. Methods Conference registration data on participants presenting a paper or a poster at 6th WCRI were made available to the research team. Because the data set was too small for inferential statistics this report is limited to a basic description of results and some recommendations that should be considered when taking further steps to improve preregistration. Results 19% of the 308 presenters preregistered their research. Of the 56 usable cases, less than half provided information on the six key elements of the Amsterdam Agenda. Others provided information that invalidated their data, such as an uninformative URL. There was no discernable difference between qualitative and quantitative research. Conclusions Some presenters at the WCRI have preregistered their research on research integrity, but further steps are needed to increase frequency and completeness of preregistration. One approach to increase preregistration would be to make it a requirement for research presented at the World Conferences on Research Integrity.

Innovations in Text Analysis: Review of the International Conference MAXDAYS2

The article analyzes the conference held online by the German company VERBI Software GmbH - a developer of the well-known MAXQDA software designed for computerized content analysis of texts. Over the past decade Russian undergraduate and graduate students have been actively using this program in their research work as evidenced by a number of publications including in the "Istoricheskaya Informatika" journal. The author focuses on the dynamics of topics of the annual 2019-2021 conferences and characterizes the latest online conference. The author draws attention to the fact that the online status of the conference resulted in a sharp increase in the number of participants in comparison with previous traditional conferences. The novelty of this study is the fact that the author compares the reports of three conferences focusing on the range of methodological and methodical issues of computerized text analysis, constant update of research tools, new trends in the provision of educational materials to program users including open access to Maxqda Press publications. The article provides useful links to conference materials posted both on the developer's website and on YouTube. The author pays attention to those tools (platforms for online conferences) which are used by software developers to attract the maximum number of participants: free conference registration, user-friendly interface and international aware work (9 languages).

Design Approach in Document Management System: The Development of EZDESK Dashboard

Document Management System is a concept of planning and managing a document in various activities simultaneously, which one of common activity is publication from before the conference starts to after the conference finished. Pre-conference activities include the process of registering a conference, the admin process of verifying the registered conference, until the conference has been published. In this case, user experience (UX) orientation and paradigm was investigated through the simplified RMS (Recognize, Materialize and Scrutinize) design approach by generating the prototype with the usability criteria and aspects to comply with the user demand as the critical factors and trigger for comprehensive execution. The EzDesk application is an application designed to assist users in registering conferences and verifying conference registration documents. There are 2 actors, primarily in this module, which are chair as the conference organizer and the admin plays a role in conference verification. To verify a conference to be held, the admin must check the required documents for holding a conference. After going through the verification stage, a conference can be distributed via visualization on the main page of document management system application.

Creative Decisions Foundation Sponsors AHP/ANP Presentations at 2019MCDM Conference

The 2019 Multi-Criteria Decision Making (MCDM) Conference took place at Istanbul Technical University (ITU) in Istanbul from June 17 - 21. Grants that covered the conference registration fee were awarded by the Creative Decisions Foundation (CDF) to selected teachers, researchers with recent PhD degrees, and students studying for their PhD.

Eating Your Own Dog Food

XML and markup technologies are a wonderful thing, but only lately has the author had the confidence to really and truly eat his own dog food, trusting entirely on the technologies familiar to him. He's learned to ignore the calls for real programmers while discovering how to copy and paste from Stack Overflow and the like in moderation. XForms, XQuery, XSLT, XSL-FO, and a proper XML database might just be all you need, at least if you know how to Google and ask for help. This, then, is nominally about building a conference registration application ensuring that we get paid for every delegate, but really all about the fact that we can now rule the world without bothering with the programmers.