scholarly journals Challenges and Experiences Extending the cBioPortal for Cancer Genomics to a Molecular Tumor Board Platform

2021 ◽  
Author(s):  
Niklas Reimer ◽  
Philipp Unberath ◽  
Hauke Busch ◽  
Melanie Börries ◽  
Patrick Metzger ◽  
...  
Keyword(s):  
Decision Making ◽  
Cancer Patients ◽  
Cancer Genomics ◽  
Tumor Board ◽  
Molecular Profile ◽  
Therapy Recommendations ◽  
Tumor Boards ◽  
Research Platform ◽  
Molecular Tumor Board ◽  
Aid Decision

In Molecular Tumor Boards (MTBs), therapy recommendations for cancer patients are discussed. To aid decision-making based on the patient’s molecular profile, the research platform cBioPortal was extended based on users’ requirements. Additionally, a comprehensive dockerized workflow was developed to support the deployment of cBioPortal and connected services. In this work, we present the challenges and experiences of nearly two years of implementing and deploying an MTB platform based on cBioPortal and compare those to findings of a previous study.

The Johns Hopkins Molecular Tumor Board Precision Oncology elective for Medical Oncology fellows.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. 11035-11035
Author(s):  
Kristen Marrone ◽  
Jessica Tao ◽  
Jenna VanLiere Canzoniero ◽  
Paola Ghanem ◽  
Emily Nizialek ◽  
...  
Keyword(s):  
Decision Making ◽  
Precision Medicine ◽  
Clinical Decision Making ◽  
Cancer Genomics ◽  
Medical Oncology ◽  
Clinical Decision ◽  
Tumor Board ◽  
Precision Oncology ◽  
Adaptive Expertise ◽  
Molecular Tumor Board

11035 Background: The accelerated impact of next generation sequencing (NGS) in clinical decision making requires the integration of cancer genomics and precision oncology focused training into medical oncology education. The Johns Hopkins Molecular Tumor Board (JH MTB) is a multi-disciplinary effort focused on integration of NGS findings with critical evidence interpretation to generate personalized recommendations tailored to the genetic footprint of individual patients. Methods: The JH MTB and the Medical Oncology Fellowship Program have developed a 3-month precision oncology elective for fellows in their research years. Commencing fall of 2020, the goals of this elective are to enhance the understanding of NGS platforms and findings, advance the interpretation and characterization of molecular assay outputs by use of mutation annotators and knowledgebases and ultimately master the art of matching NGS findings with available therapies. Fellow integration into the MTB focuses on mentored case-based learning in mutation characterization and ranking by levels of evidence for actionability, with culmination in form of verbal presentations and written summary reports of final MTB recommendations. A mixed methods questionnaire was administered to evaluate progress since elective initiation. Results: Three learners who have participated as of February 2021 were included. Of the two who had completed the MTB elective, each have presented at least 10 cases, with at least 1 scholarly publication planned. All indicated strong agreement that MTB elective had increased their comfort with interpreting clinical NGS reports as well as the use of knowledgebases and variant annotators. Exposure to experts in the field of molecular precision oncology, identification of resources necessary to interpret clinical NGS reports, development of ability to critically assess various NGS platforms, and gained familiarity with computational analyses relevant to clinical decision making were noted as strengths of the MTB elective. Areas of improvement included ongoing initiatives that involve streamlining variant annotation and transcription of information for written reports. Conclusions: A longitudinal elective in the JHU MTB has been found to be preliminarily effective in promoting knowledge mastery and creating academic opportunities related to the clinical application of precision medicine. Future directions will include leveraging of the MTB infrastructure for research projects, learner integration into computational laboratory meetings, and expansion of the MTB curriculum to include different levels of learners from multiple medical education programs. Continued elective participation will be key to understanding how best to facilitate adaptive expertise in assigning clinical relevance to genomic findings, ultimately improving precision medicine delivery in patient care and trial development.

The impact of clinical decision making in a molecular tumor board at a tertiary care center.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. 3128-3128
Author(s):  
Meena Sadaps ◽  
Kathryn Demski ◽  
Ying Ni ◽  
Vicky Konig ◽  
Brandie Leach ◽  
...  
Keyword(s):  
Decision Making ◽  
Clinical Decision Making ◽  
Clinical Decision ◽  
Genetic Counselors ◽  
Tumor Board ◽  
Treatment Recommendation ◽  
Precision Oncology ◽  
Off Label ◽  
Tumor Boards ◽  
Molecular Tumor Board

3128 Background: Multidisciplinary molecular tumor boards were first established with the onset of precision oncology (PO), as many clinicians were unfamiliar with the interpretation and incorporation of the information into clinical practice. PO has since rapidly evolved and integrated itself into standard of care practices for most cancer patients, yet molecular tumor boards have not grown accordingly and in fact some have been discontinued. There remains a paucity of data in regards to the value and impact of molecular tumor board discussions themselves. We previously reported on our longitudinal experiences in PO ( Sadaps et al, 2018), focusing on the therapeutic impact of matched therapy. Here, we report on the utility of our molecular tumor board in clinical decision making. Methods: We conducted a retrospective review of patients seen at Cleveland Clinic with a solid tumor malignancy who had large panel, next-generation-sequencing (NGS) performed via any commercial platform from November 2019-January 2021. Cases were filtered through a local therapeutic algorithm and then reviewed individually. Initial review was performed by a core genomics committee comprised of 2 oncologists and 2 genetic counselors. Interesting and/or complex cases were flagged for discussion at our bimonthly molecular tumor board, which is regularly attended by medical oncologists, pathologists, genetic counselors, bioinformaticians, and patient care coordinators. Data analyzed included categorization of treatment recommendations and the percentage of cases for which initial recommendations were changed based on tumor board discussion. Results: Of 782 total cases, 575 (73.5%) had a clinically relevant genomics tumor board (GTB) recommendation as compared to 51.7% from our previously reported study. 16.7% of patients had on label recommendation(s) and 86.4% had off label/ clinical trial recommendation(s). 179 (22.9%) patients were recommended for genetic counseling (GC). During our bimonthly GTB, we discussed 173 (22.1%) of these cases. Of the discussed cases, the most common tumor types were hepatobiliary (18.5%), lower gastrointestinal (17.3%), and breast (16.2%). Topics of discussion at GTB included such things as pathologic/histologic/molecular testing, prioritization of available trials, appropriateness of an off label therapy, and need for a genetics consult. Discussion at GTB resulted in a change in treatment recommendation in 63 (36.4%) cases. Conclusions: Discussions from multidisciplinary molecular tumor board impacted treatment decisions for our patients. Referral to GC was also common and should be considered an integral part of somatic sequencing review. Molecular tumor boards remain a crucial platform for treatment guidance and clinical management, especially given the increase in “actionability” over the years due to newly discovered targets and targeted therapies in this rapidly evolving field.

Virtual Clinical and Precision Medicine Tumor Boards: A Cloud-based Platform-mediated Implementation of Multidisciplinary Reviews among Oncology Centers in the Covid-19 Era. (Preprint)

2020 ◽  
Author(s):  
Livio Blasi ◽  
Roberto Bordonaro ◽  
Vincenzo Serretta ◽  
Dario Piazza ◽  
Alberto Firenze ◽  
...  
Keyword(s):  
Decision Making ◽  
Health Professionals ◽  
Clinical Pathways ◽  
Prospective Trial ◽  
Banking System ◽  
Outcome Data ◽  
Tumor Board ◽  
Time Saving ◽  
Tumor Boards ◽  
Multidisciplinary Tumor Board

BACKGROUND Multidisciplinary tumor boards play a pivotal role in the patients -centered clinical management and in the decision-making process to provide best evidence -based, diagnostic and therapeutic care to cancer patients. Among the barriers to achieve an efficient multidisciplinary tumor board, lack of time and geographical distance play a major role. Therefore the elaboration of an efficient virtual multidisciplinary tumor board (VMTB) is a key-point to reach a successful oncology team and implement a network among health professionals and institutions. This need is stronger than ever in a Covid-19 pandemic scenario. OBJECTIVE This paper presents a research protocol for an observational study focused on exploring the structuring process and the implementation of a multi-institutional VMTB in Sicily. Other endpoints include analysis of cooperation between participants, adherence to guidelines, patients’ outcomes, and patients satisfaction METHODS This protocol encompasses a pragmatic, observational, multicenter, non-interventional, prospective trial. The study's programmed duration is five years, with a half-yearly analysis of the primary and secondary objectives' measurements. Oncology care health-professionals from various oncology subspecialties at oncology departments in multiple hospitals (academic and general hospitals as well as tertiary centers and community hospitals) are involved in a non-hierarchic fashion. VMTB employ an innovative, virtual, cloud-based platform to share anonymized medical data which are discussed via a videoconferencing system both satisfying security criteria and HIPAA compliance. RESULTS The protocol is part of a larger research project on communication and multidisciplinary collaboration in oncology units and departments spread in the Sicily region in Italy. Results of this study will particularly focus on the organization of VMTB involving oncology units present in different hospitals spread in the area and create a network to allow best patients care pathways and a hub and spoke relationship. Results will also include data concerning organization skills and pitfalls, barriers, efficiency, number and type con clinical cases, and customers’ satisfaction. CONCLUSIONS VMTB represents a unique opportunity to optimize patient’s management in a patient centered approach. An efficient virtualization and data banking system is potentially time-saving, a source for outcome data, and a detector of possible holes in the hull of clinical pathways. The observations and results from this VMTB study may hopefully useful to design nonclinical and organizational interventions that enhance multidisciplinary decision-making in oncology.

scholarly journals Personalized Medicine in the Oncology Clinic: Implementation and Outcomes of the Johns Hopkins Molecular Tumor Board

2017 ◽  
pp. 1-19 ◽  
Author(s):  
W. Brian Dalton ◽  
Patrick M. Forde ◽  
Hyunseok Kang ◽  
Roisin M. Connolly ◽  
Vered Stearns ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Targeted Therapy ◽  
Targeted Therapies ◽  
Progression Free Survival ◽  
Molecular Profiling ◽  
Tumor Board ◽  
Free Survival ◽  
Off Label ◽  
Tumor Boards ◽  
Molecular Tumor Board

Purpose Tumor genomic profiling for personalized oncology therapy is being widely applied in clinical practice even as it is being evaluated more formally in clinical trials. Given the complexities of genomic data and its application to clinical use, molecular tumor boards with diverse expertise can provide guidance to oncologists and patients seeking to implement personalized genetically targeted therapy in practice. Methods A multidisciplinary molecular tumor board reviewed tumor molecular profiling reports from consecutive referrals at the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins over a 3-year period. The tumor board weighed evidence for actionability of genomic alterations identified by molecular profiling and provided recommendations including US Food and Drug Administration–approved drug therapy, clinical trials of matched targeted therapy, off-label use of such therapy, and additional tumor or germline genetic testing. Results One hundred fifty-five patients were reviewed. Actionable genomic alterations were identified in 132 patients (85%). Off-label therapies were recommended in 37 patients (24%). Eleven patients were treated off-label, and 13 patients were enrolled onto clinical trials of matched targeted therapies. Median progression-free survival of patients treated with matched therapies was 5 months ( 95% CI, 2.9 months to not reached), and the progression-free survival probability at 6 months was 43% (95% CI, 26% to 71%). Lack of locally available clinical trials was the major limitation on clinical actionability of tumor profiling reports. Conclusion The molecular tumor board recommended off-label targeted therapies for a quarter of all patients reviewed. Outcomes were heterogeneous, although 43% of patients receiving genomically matched therapy derived clinical benefit lasting at least 6 months. Until more data become available from precision oncology trials, molecular tumor boards can help guide appropriate use of tumor molecular testing to direct therapy.

scholarly journals A virtual molecular tumor board to improve efficiency and scalability of delivering precision oncology to physicians and their patients

JAMIA Open ◽  
2019 ◽  
Vol 2 (4) ◽  
pp. 505-515 ◽  
Author(s):  
Michael J Pishvaian ◽  
Edik M Blais ◽  
R Joseph Bender ◽  
Shruti Rao ◽  
Simina M Boca ◽  
...  
Keyword(s):  
Treatment Plan ◽  
Critical Role ◽  
Tumor Board ◽  
Care Process ◽  
Molecular Profile ◽  
Molecular Testing ◽  
Precision Oncology ◽  
Therapy Options ◽  
Scoring Model ◽  
Molecular Tumor Board

Abstract Objectives Scalable informatics solutions that provide molecularly tailored treatment recommendations to clinicians are needed to streamline precision oncology in care settings. Materials and Methods We developed a cloud-based virtual molecular tumor board (VMTB) platform that included a knowledgebase, scoring model, rules engine, an asynchronous virtual chat room and a reporting tool that generated a treatment plan for each of the 1725 patients based on their molecular profile, previous treatment history, structured trial eligibility criteria, clinically relevant cancer gene-variant assertions, biomarker-treatment associations, and current treatment guidelines. The VMTB systematically allows clinician users to combine expert-curated data and structured data from clinical charts along with molecular testing data to develop consensus on treatments, especially those that require off-label and clinical trial considerations. Results The VMTB was used as part of the cancer care process for a focused subset of 1725 patients referred by advocacy organizations wherein resultant personalized reports were successfully delivered to treating oncologists. Median turnaround time from data receipt to report delivery decreased from 14 days to 4 days over 4 years while the volume of cases increased nearly 2-fold each year. Using a novel scoring model for ranking therapy options, oncologists chose to implement the VMTB-derived therapies over others, except when pursuing immunotherapy options without molecular support. Discussion VMTBs will play an increasingly critical role in precision oncology as the compendium of biomarkers and associated therapy options available to a patient continues to expand. Conclusion Further development of such clinical augmentation tools that systematically combine patient-derived molecular data, real-world evidence from electronic health records and expert curated knowledgebases on biomarkers with computational tools for ranking best treatments can support care pathways at point of care.

Patient attendance at molecular tumor board: A new means of shared decision making?

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e18001-e18001
Author(s):  
Timothy Lewis Cannon ◽  
Donald L. Trump ◽  
Laura Knopp ◽  
Hongkun Wang ◽  
Tiffani DeMarco ◽  
...  
Keyword(s):  
Decision Making ◽  
Shared Decision Making ◽  
Medical Decision Making ◽  
Medical Decision ◽  
Tumor Board ◽  
Shared Decision ◽  
Treatment Team ◽  
Level Of Satisfaction ◽  
Holistic Method ◽  
Molecular Tumor Board

e18001 Background: Patient engagement in medical decision-making improves patient related outcomes through compliance and patient satisfaction. The Inova Schar Cancer Institute (ISCI) has a weekly molecular tumor board (MTB) to match comprehensive genomic sequencing results with targeted therapies for patients. The ISCI MTB invites patients to attend and engage in the MTB discussion. We performed a pilot study to investigate the feasibility and satisfaction in patients who attended MTB. Methods: During the time of this study, August 2017 through October 2018, 139 patients were presented and all 20 who were able to attend MTB completed pre-and post- MTB surveys. Patients who did not attend were either not invited by their primary oncologist, unable to attend, or chose not to attend. The survey included six questions related to comprehension, engagement, and satisfaction with the treatment team. Results: There was a statistically significant change for the question “I am satisfied with how well informed I am about targeted therapy” with p = 0.016. All 20 patients answered positively that it was beneficial for them to attend. Many patients expressed concerns about their difficulty understanding the technical aspects of the meeting. Conclusions: Patients who attended MTB reported a higher level of satisfaction after MTB attendance as compared to before MTB. This may reflect a sense of engagement in shared decision making rather than comprehension of genomic information. A more holistic method of studying this practice would include sampling a larger patient population and a formal evaluation of the physicians’ experience with patients attending. Supported by philanthropic funds from the Inova Schar Cancer Institute.

Secret sauce in collaborative tumor boards: Team-based characteristics that optimize tumor board functionality.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. e23015-e23015
Author(s):  
Barbara Oureilidis-DeVivo
Keyword(s):  
Decision Making ◽  
Best Practices ◽  
Organizational Behavior ◽  
Treatment Decision ◽  
The United States ◽  
Interdisciplinary Teams ◽  
Tumor Board ◽  
Treatment Decision Making ◽  
Tumor Boards ◽  
Decision Making Processes

e23015 Background: Interdisciplinary teams are an indispensable characteristic of modern organizations, particularly in healthcare settings that require specialists to work together to solve multifaceted patient care problems. Multidisciplinary tumor boards (TBs) aim to coordinate multidisciplinary perspectives to help the oncology team devise the best treatment program for the patient. Yet, while this is their purpose, studies have found that TBs do not always achieve that goal effectively. Why are some tumor board (TB) teams more effective than others? This study shed light on key characteristics found among highly effective TBs. It provides a theoretical explanation of their organizational behaviors and structures and their effect on cancer treatment decision-making. The research is grounded in organizational behavior theories that have historical prominence in group decision-making, social hierarchy, and interdisciplinary collaboration, and are used to explain the phenomenon under investigation best. Methods: Qualitative research was used in the study. Data from 44 different TB observations and 18 interviews were gathered over four years at seven research hospitals in the United States and United Kingdom. The data were then coded, analyzed and synthesized with organizational behavior theory to explain the social phenomena under investigation. Results: The study revealed that certain TBs practice strong collaboration displaying high levels of partnership, cooperation, equality, and interdependency, which was incorporated explicitly into their meeting systems to achieve their common goal. Team-based characteristics such as members’ consistent shared preferences and identity, coordinated interactions, a collective learning process, and shared power and partnership are key markers found within these teams that positively influenced treatment decision-making processes and outcomes, earmarking best practices in TB groups. Conclusions: Organizational theory that suggests that for a collaborative process to be effective, team-based mechanisms need to be adopted in which each member respects, trusts, and acknowledges the skills and expertise of other disciplines in the organization, shares team values, decision-making processes, responsibilities, and planning, relies mutually upon other team members, and works outside normal professional boundaries openly and willingly. In an egalitarian structure like that of the TBs reviewed in this study, where preferences and identities are consistent and groups are collaborative, treatment decisions are less biased and incorporate multidisciplinary perspectives. Thus, this study suggests that by possessing both team- and task-based characteristics and practices, TBs engage in best practices, and thereby optimize their functionality.

scholarly journals Support systems to guide clinical decision-making in precision oncology: The Cancer Core Europe Molecular Tumor Board Portal

2020 ◽  
Vol 26 (7) ◽  
pp. 992-994 ◽  
Author(s):  
David Tamborero ◽  
◽  
Rodrigo Dienstmann ◽  
Maan Haj Rachid ◽  
Jorrit Boekel ◽  
...  
Keyword(s):  
Decision Making ◽  
Clinical Decision Making ◽  
Support Systems ◽  
Clinical Decision ◽  
Tumor Board ◽  
Precision Oncology ◽  
Molecular Tumor Board

scholarly journals cbpManager: a web application to streamline the integration of clinical and genomic data in cBioPortal to support the Molecular Tumor Board

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Arsenij Ustjanzew ◽  
Alexander Desuki ◽  
Christoph Ritzel ◽  
Alina Corinna Dolezilek ◽  
Daniel-Christoph Wagner ◽  
...  
Keyword(s):  
Clinical Data ◽  
Web Application ◽  
Cancer Biology ◽  
Data Privacy ◽  
Large Scale ◽  
Cancer Genomics ◽  
Tumor Board ◽  
Data Formats ◽  
Tumor Boards ◽  
Data Files

Abstract Background Extensive sequencing of tumor tissues has greatly improved our understanding of cancer biology over the past years. The integration of genomic and clinical data is increasingly used to select personalized therapies in dedicated tumor boards (Molecular Tumor Boards) or to identify patients for basket studies. Genomic alterations and clinical information can be stored, integrated and visualized in the open-access resource cBioPortal for Cancer Genomics. cBioPortal can be run as a local instance enabling storage and analysis of patient data in single institutions, in the respect of data privacy. However, uploading clinical input data and genetic aberrations requires the elaboration of multiple data files and specific data formats, which makes it difficult to integrate this system into clinical practice. To solve this problem, we developed cbpManager. Results cbpManager is an R package providing a web-based interactive graphical user interface intended to facilitate the maintenance of mutations data and clinical data, including patient and sample information, as well as timeline data. cbpManager enables a large spectrum of researchers and physicians, regardless of their informatics skills to intuitively create data files ready for upload in cBioPortal for Cancer Genomics on a daily basis or in batch. Due to its modular structure based on R Shiny, further data formats such as copy number and fusion data can be covered in future versions. Further, we provide cbpManager as a containerized solution, enabling a straightforward large-scale deployment in clinical systems and secure access in combination with ShinyProxy. cbpManager is freely available via the Bioconductor project at https://bioconductor.org/packages/cbpManager/ under the AGPL-3 license. It is already used at six University Hospitals in Germany (Mainz, Gießen, Lübeck, Halle, Freiburg, and Marburg). Conclusion In summary, our package cbpManager is currently a unique software solution in the workflow with cBioPortal for Cancer Genomics, to assist the user in the interactive generation and management of study files suited for the later upload in cBioPortal.

Effect of a multidisciplinary cancer conference for thoracic malignancies on patient care management.

2014 ◽  
Vol 32 (3_suppl) ◽  
pp. 112-112
Author(s):  
Henner M. Schmidt ◽  
John M. Roberts ◽  
Artur M. Bodnar ◽  
Steven H. Kirtland ◽  
Sonia H. Kunz ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Decision Making ◽  
Esophageal Cancer ◽  
Cancer Patients ◽  
Treatment Plan ◽  
Treatment Decision ◽  
Primary Treatment ◽  
Prior Treatment ◽  
Tumor Board ◽  
Treatment Decision Making

112 Background: Treatment of thoracic cancers frequently involve multiple subspecialties thus treatment decisions are typically best facilitated in multidisciplinary tumor boards (MTB). This approach should facilitate and improve treatment decision making, standardize staging and therapeutic decisions and improve outcomes. In this study we analyze the evolution in staging and treatment decision making associated with presentation at MTB. Methods: Retrospective review of all patients with lung or esophageal cancer presented at our weekly MTB from June 1, 2010 to September 30, 2012. All providers submitting patients to tumor board recorded their current treatment plan prior to presentation. The physician’s plan was then compared to the tumor board’s final recommendation. Changes made were graded according to degree of magnitude as minor, moderate or major change. Minor changes included changes in diagnostic imaging. Moderate changes involved modifications in the type of invasive staging or biopsy procedures. Major changes were defined as changes to final therapeutic plans such as surgery, chemotherapy, or radiation therapy. Results: 435 patients with esophageal or lung cancer were discussed in the MTB. 86 patients having no prior treatment plan available were excluded. In the remaining 347 patients there were 163 patients with esophageal cancer (47%) and 184 patients with lung cancer (53%). In the esophageal cancer patients a change to the physician’s prior treatment plan was recommended in 33 cases (21%). For lung cancer patients a change in the treatment plan was recommended in 50 cases (27%). Overall a recommendation for change in treatment occurred in 83 cases (24 %). Changes were major 13%, moderate 6% and minor 5%. Follow-up in 249 patients confirmed that MTB recommendations were followed in 97% of cases. Conclusions: MTB recommendations frequently differs from the physician’s primary treatment plan. MTB reviews have previously been documented to improve patient’s outcome. The study demonstrates that in one quarter of patients MTB recommendation will be different from the primary treatment plan. Complex cancer patients should be considered for presentation at MTB whenever feasible.

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