scholarly journals Prospective analysis of 895 patients on a UK Genomics Review Board

ESMO Open ◽  
2019 ◽  
Vol 4 (2) ◽  
pp. e000469 ◽  
Author(s):  
David Allan Moore ◽  
Marina Kushnir ◽  
Gabriel Mak ◽  
Helen Winter ◽  
Teresa Curiel ◽  
...  
Keyword(s):  
Clinical Trial ◽  
Clinical Trials ◽  
Cancer Genetics ◽  
Routine Practice ◽  
Prospective Data ◽  
Expert Review ◽  
Molecular Oncology ◽  
Oncology Clinical Trials ◽  
Uncertain Significance ◽  
Generation Sequencing

BackgroundThe increasing frequency and complexity of cancer genomic profiling represents a challenge for the oncology community. Results from next-generation sequencing–based clinical tests require expert review to determine their clinical relevance and to ensure patients are stratified appropriately to established therapies or clinical trials.MethodsThe Sarah Cannon Research Institute UK/UCL Genomics Review Board (GRB) was established in 2014 and represents a multidisciplinary team with expertise in molecular oncology, clinical trials, clinical cancer genetics and molecular pathology. Prospective data from this board were collated.ResultsTo date, 895 patients have been reviewed by the GRB, of whom 180 (20%) were referred for clinical trial screening and 62 (7%) received trial therapy. For a further 106, a clinical trial recommendation was given.ConclusionsNumerous challenges are faced in implementing a GRB, including the identification of potential germline variants, the interpretation of variants of uncertain significance and consideration of the technical limitations of pathology material when interpreting results. These challenges are likely to be encountered with increasing frequency in routine practice. This GRB experience provides a model for the multidisciplinary review of molecular profiling data and for the linking of molecular analysis to clinical trial networks.

scholarly journals OCTANE: Oncology Clinical Trial Annotation Engine

2019 ◽  
pp. 1-11 ◽  
Author(s):  
Jia Zeng ◽  
Md Abu Shufean ◽  
Yekaterina Khotskaya ◽  
Dong Yang ◽  
Michael Kahle ◽  
...  
Keyword(s):  
Clinical Trial ◽  
Clinical Trials ◽  
False Positive Rate ◽  
False Negative ◽  
False Negative Rate ◽  
Cancer Center ◽  
Precision Oncology ◽  
Expert Review ◽  
Oncology Clinical Trial ◽  
Oncology Clinical Trials

PURPOSE Many targeted therapies are currently available only via clinical trials. Therefore, routine precision oncology using biomarker-based assignment to drug depends on matching patients to clinical trials. A comprehensive and up-to-date trial database is necessary for optimal patient-trial matching. METHODS We describe processes for establishing and maintaining a clinical trial database, focusing on genomically informed trials. Furthermore, we present OCTANE (Oncology Clinical Trial Annotation Engine), an informatics framework supporting these processes in a scalable fashion. To illustrate how the framework can be applied at an institution, we describe how we implemented an instance of OCTANE at a large cancer center. OCTANE consists of three modules. The data aggregation module automates retrieval, aggregation, and update of trial information. The annotation module establishes the database schema, implements data integration necessary for automation, and provides an annotation interface. The update module monitors trial change logs, identifies critical change events, and alerts the annotators when manual intervention may be needed. RESULTS Using OCTANE, we annotated 5,439 oncology clinical trials (4,438 genomically informed trials) that collectively were associated with 1,453 drugs, 779 genes, and 252 cancer types. To date, we have used the database to screen 4,220 patients for trial eligibility. We compared the update module with expert review, and the module achieved 98.5% accuracy, 0% false-negative rate, and 2.3% false-positive rate. CONCLUSION OCTANE is a general informatics framework that can be helpful for establishing and maintaining a comprehensive database necessary for automating patient-trial matching, which facilitates the successful delivery of personalized cancer care on a routine basis. Several OCTANE components are publically available and may be useful to other precision oncology programs.

Dedicated clinical trial tissue tracking database to improve turn-around time at high-volume center.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. 1543-1543
Author(s):  
Peter Blankenship ◽  
David DeLaRosa ◽  
Marc Burris ◽  
Steven Cusson ◽  
Kayla Hendricks ◽  
...  
Keyword(s):  
Clinical Trial ◽  
Clinical Trials ◽  
Tissue Sample ◽  
High Volume ◽  
Trial Participation ◽  
Fresh Tissue ◽  
Oncology Clinical Trials ◽  
The Status ◽  
Unique Source

1543 Background: Tissue requirements in oncology clinical trials are increasingly complex due to prescreening protocols for patient selection and serial biopsies to understand molecular-level treatment effects. Novel solutions for tissue processing are necessary for timely tissue procurement. Based on these needs, we developed a Tissue Tracker (TT), a comprehensive database for study-related tissue tasks at our high-volume clinical trial center. Methods: In this Microsoft Access database, patients are assigned an ID within the TT that is associated with their name, medical record number, and study that follows their request to external users: pathology departments, clinical trial coordinators and data team members. To complete tasks in the TT, relevant information is required to update the status. Due to the high number of archival tissue requests from unique pathology labs, the TT has a “Follow-Up Dashboard” that organizes information needed to conduct follow-up on all archival samples with the status “Requested”. This results in an autogenerated email and pdf report sent to necessary teams. The TT also includes a kit inventory system and a real-time read only version formatted for interdepartmental communication, metric reporting, and other data-driven efforts. The primary outcome in this study was to evaluate our average turnaround time (ATAT: average time from request to shipment) for archival and fresh tissue samples before and after TT development. Results: Before implementing the TT, between March 2016 and March 2018, we processed 2676 archival requests from 235 unique source labs resulting in 2040 shipments with an ATAT of 19.29 days. We also processed 1099 fresh biopsies resulting in 944 shipments with an ATAT of 7.72 days. After TT implementation, between April 2018 and April 2020, we processed 2664 archival requests from 204 unique source labs resulting in 2506 shipments (+28.0%) with an ATAT of 14.78 days (-23.4%). During that same period, we processed 1795 fresh biopsies (+63.3%) resulting in 2006 shipments (+112.5%) with an ATAT of 6.85 days (-11.3%). Conclusions: Oncology clinical trials continue to evolve toward more extensive tissue requirements for prescreening and scientific exploration of on-treatment molecular profiling. Timely results are required to optimize patient trial participation. During the intervention period, our tissue sample volume and shipments increased, but the development and implementation of an automated tracking system allowed improvement in ATAT of both archival and fresh tissue. This automation not only improves end-user expectations and experiences for patients and trial sponsors but this allows our team to adapt to the increasing interest in tissue exploration.

scholarly journals PATH-03. CLINICAL UTILITY OF NEXT GENERATION SEQUENCING IN IDH-WILDTYPE GLIOBLASTOMA: THE DANA-FARBER CANCER INSTITUTE EXPERIENCE

2020 ◽  
Vol 22 (Supplement_2) ◽  
pp. ii164-ii164
Author(s):  
Mary Jane Lim-Fat ◽  
Gilbert Youssef ◽  
Mehdi Touat ◽  
Bryan Iorgulescu ◽  
Eleanor Woodward ◽  
...  
Keyword(s):  
Clinical Trial ◽  
Clinical Trials ◽  
Next Generation Sequencing ◽  
Immune Checkpoint Blockade ◽  
Next Generation ◽  
Single Nucleotide Variants ◽  
Dana Farber Cancer Institute ◽  
Clinical Records ◽  
Ngs Data ◽  
Generation Sequencing

Abstract BACKGROUND Comprehensive next generation sequencing (NGS) is available through many academic institutions and commercial entities, and is incorporated in practice guidelines for glioblastoma (GBM). We retrospective evaluated the practice patterns and utility of incorporating NGS data into routine care of GBM patients at a clinical trials-focused academic center. METHODS We identified 1,011 consecutive adult patients with histologically confirmed GBM with OncoPanel testing, a targeted exome NGS platform of 447 cancer-associated genes at Dana Farber Cancer Institute (DFCI), from 2013-2019. We selected and retrospectively reviewed clinical records of all IDH-wildtype GBM patients treated at DFCI. RESULTS We identified 557 GBM IDH-wildtype patients, of which 227 were male (40.7%). OncoPanel testing revealed 833 single nucleotide variants and indels in 44 therapeutically relevant genes (Tier 1 or 2 mutations) including PIK3CA (n=51), BRAF (n=9), FGFR1 (n=8), MSH2 (n=4), MSH6 (n=2) and MLH1 (n=1). Copy number analysis revealed 509 alterations in 18 therapeutically relevant genes including EGFR amplification (n= 186), PDGFRA amplification (N=39) and CDKN2A/2B homozygous loss (N=223). Median overall survival was 17.5 months for the whole cohort. Seventy-four therapeutic clinical trials accrued 144 patients in the upfront setting (25.9%) and 203 patients (36.4%) at recurrence. Altogether, NGS data for 107 patients (19.2%) were utilized for clinical trial enrollment or targeted therapy indications. High mutational burden (>17mutations/Mb) was identified in 11/464 samples (2.4%); of whom 3/11 received immune checkpoint blockade. Four patients received compassionate use therapy targeting EGFRvIII (rindopepimut, n=2), CKD4/6 (abemaciclib, n=1) and BRAFV600E (dabrafenib/trametinib, n=1). CONCLUSION While NGS has greatly improved diagnosis and molecular classification, we highlight that NGS remains underutilized in selecting therapy in GBM, even in a setting where clinical trials and off-label therapies are relatively accessible. Continued efforts to develop better targeted therapies and efficient clinical trial design are required to maximize the potential benefits of genomically-stratified data.

Abstract WP257: Accuracy of Pre-enrollment Last Known Well Time in a Large Prehospital Stroke Clinical Trial

Stroke ◽  
2017 ◽  
Vol 48 (suppl_1) ◽  
Author(s):  
Nerses Sanossian ◽  
Emma Balouzian ◽  
Lucas Ramirez ◽  
David S Liebeskind ◽  
Sidney Starkman ◽  
...  
Keyword(s):  
Clinical Trial ◽  
Clinical Trials ◽  
Routine Practice ◽  
Stroke Therapy ◽  
Screening Criteria ◽  
Intervention Evaluation ◽  
Treatment Start ◽  
Tiered System ◽  
Telephone Screening ◽  
Entry Window

Background: Clinical trials of stroke therapies require accurate documentation of last known well time (LKWT) to account for injury accumulation prior to treatment start. For prehospital studies, this requirement is particularly challenging, as paramedic-determined and final-determined LKWTs in routine practice are concordant (within 15 mins) in only half of cases. We sought to determine the accuracy of LKWT obtained in the field by a two-tier enrollment system of study-trained paramedics and cellphone-connected physician-investigators. Methods: Paramedics screened consecutive transports for participation in the NIH Field Administration of Stroke Therapy-Magnesium (FAST-MAG) clinical trial. Paramedic screening criteria included LKWT <2 hours. Physician-investigators by cellphone confirmed or refined the LKWT after conversation with paramedics and patients or legally authorized representative. Prehospital LKWT was compared with post-arrival LKWT determined by trained study nurses after ED arrival by speaking with patients, family and other sources. We describe the number of enrollment calls with inaccurate LKWT at the paramedic-screening level and at the post paramedic plus physician-investigator telephone screening level. Results: A total of 4458 post-screening enrollment calls were made by paramedics from January 2005 to December 2012 of which 539 (12%) were determined by physician-instigators to have inaccurate LKWT leading to non-enrollment. Of the remaining 3919 calls, 1700 led to enrollments in the study and 2219 were not enrolled for a reason other than inaccurate LKWT. Among enrolled cases, exact congruence between prehospital and post-arrival LKWTs occurred 72% (n=1220), concordance within 15 minutes in 87%, within 30 minutes in 93%, and within 1 hour in 97%. Among enrolled cases, final-determined LKWT was within the study entry window of 2h in 96.3%. Conclusions: A 2-tiered system of paramedic screening followed by physician-investigator cellphone assessment led to high congruence between prehospital-determined and post-arrival-determined of LKWT. This system can be used in future trials of prehospital, paramedic-in initiated stroke therapy when accuracy of LKWT is important for intervention evaluation.

scholarly journals Clinical Trial Accrual Targeting Genomic Alterations After Next-Generation Sequencing at a Non-National Cancer Institute–Designated Cancer Program

2016 ◽  
Vol 12 (4) ◽  
pp. e396-e404 ◽  
Author(s):  
Kalyan C. Mantripragada ◽  
Adam J. Olszewski ◽  
Andrew Schumacher ◽  
Kimberly Perez ◽  
Ariel Birnbaum ◽  
...  
Keyword(s):  
Clinical Trial ◽  
Clinical Trials ◽  
Next Generation Sequencing ◽  
National Cancer Institute ◽  
Next Generation ◽  
Genomic Alterations ◽  
Cancer Centers ◽  
Cancer Program ◽  
Clinical Trial Accrual ◽  
Generation Sequencing

Purpose: Successful clinical trial accrual targeting uncommon genomic alterations will require broad national participation from both National Cancer Institute (NCI)–designated comprehensive cancer centers and community cancer programs. This report describes the initial experience with clinical trial accrual after next-generation sequencing (NGS) from three affiliated non–NCI-designated cancer programs. Materials and Methods: Clinical trial participation was reviewed after enrollment of the first 200 patients undergoing comprehensive genomic profiling by NGS as part of an institutional intuitional review board–approved protocol at three affiliated hospitals in Rhode Island and was compared with published experience from NCI-designated cancer centers. Results: Patient characteristics included a median age of 64 years, a median of two lines of prior therapy, and a predominance of GI carcinomas (58%). One hundred sixty-four of 200 patients (82%) had adequate tumor for NGS, 95% had genomic alterations identified, and 100% had variants of unknown significance. Fifteen of 164 patients (9.2%) enrolled in genotype-directed clinical trials, and three patients (1.8%) received commercially available targeted agents off clinical trials. The reasons for nonreceipt of NGS-directed therapy were no locally available matching trial (48.6%), ineligibility (33.6%) because of comorbidities or interim clinical deterioration, physician's choice of a different therapy (6.8%), or stable disease (11%). Conclusion: This experience demonstrates that a program enrolling patients in specific targeted agent clinical trials after NGS can be implemented successfully outside of the NCI-designated cancer program network, with comparable accrual rates. This is important because targetable genes have rare mutation rates and clinical trial accrual after NGS is low.

No-cost next generation sequencing of advanced cancer patients within the Strata Precision Oncology Network supports clinical trial enrollment.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. 3073-3073
Author(s):  
Marc Ryan Matrana ◽  
Scott A. Tomlins ◽  
Kat Kwiatkowski ◽  
Khalis Mitchell ◽  
Jennifer Marie Suga ◽  
...  
Keyword(s):  
Clinical Trial ◽  
Clinical Trials ◽  
Next Generation Sequencing ◽  
Clinical Samples ◽  
Precision Oncology ◽  
Cancer Type ◽  
Next Generation ◽  
Match Trial ◽  
The Impact ◽  
Generation Sequencing

3073 Background: Widespread integration of systematized next generation sequencing (NGS)-based precision oncology is hindered by numerous barriers. Hence, we developed the Strata trial (NCT03061305), a screening protocol to determine the impact of scaled precision oncology. Methods: We implemented no-cost NGS on formalin fixed paraffin embedded (FFPE) clinical samples for all patients with advanced tumors, a common portfolio of partnered therapeutic clinical trials, and robust infrastructure development across the Strata Precision Oncology Network. Results: Across the network of 17 centers, specimens from 8673/9222 (94%) patients were successfully tested in the Strata CLIA/CAP/NCI-MATCH accredited laboratory using comprehensive amplicon-based DNA and RNA NGS. Patients were tested with one of three StrataNGS test versions; the most recent panel assesses all classes of actionable alterations (mutations, copy number alterations, gene fusions, microsatellite instability, tumor mutation burden and PD-L1 expression). Median surface area of received FFPE tumor samples was 25mm2 (interquartile range 9-95mm2), and the median turnaround time from sample receipt to report was 6 business days. 2577 (27.9%) patients had highly actionable alterations, defined as alterations associated with within-cancer type FDA approved or NCCN guideline recommended therapies (1072 patients), NCI-MATCH trial arms (1467 patients), Strata-partnered therapeutic trials (327 patients), or specific alteration-matched FDA approved therapies in patients with cancers of unknown primary (71 patients). Of the 1467 patients matched to an NCI-MATCH trial arm, 15 enrolled. Of the 327 patients matched to one of nine Strata-partnered clinical trials, 77 (24%) were screen failures, while 250 (76%) have either enrolled or are being actively followed for enrollment upon progression. Conclusions: Through streamlined consent methods, electronic medical record queries, and high throughput laboratory testing at no cost to patients, we demonstrate that scaled precision oncology is feasible across a diverse network of healthcare systems when paired with access to relevant clinical trials. Clinical trial information: NCT03061305.

scholarly journals Early Impact of COVID-19 on the Conduct of Oncology Clinical Trials and Long-Term Opportunities for Transformation: Findings From an American Society of Clinical Oncology Survey

2020 ◽  
Vol 16 (7) ◽  
pp. 417-421 ◽  
Author(s):  
David M. Waterhouse ◽  
R. Donald Harvey ◽  
Patricia Hurley ◽  
Laura A. Levit ◽  
Edward S. Kim ◽  
...  
Keyword(s):  
Clinical Trial ◽  
Clinical Trials ◽  
Clinical Care ◽  
Research Committee ◽  
Community Based Programs ◽  
Oncology Clinical Trials ◽  
Community Forum ◽  
American Society ◽  
Remote Patient

The coronavirus disease 2019 (COVID-19) pandemic has disrupted all aspects of clinical care, including cancer clinical trials. In March 2020, ASCO launched a survey of clinical programs represented on its Cancer Research Committee and Research Community Forum Steering Group and taskforces to learn about the types of changes and challenges that clinical trial programs were experiencing early in the pandemic. There were 32 survey respondents; 14 represented academic programs, and 18 represented community-based programs. Respondents indicated that COVID-19 is leading programs to halt or prioritize screening and/or enrollment for certain clinical trials and cease research-only visits. Most reported conducting remote patient care where possible and remote visits and monitoring with sponsors and/or contract research organizations (CROs); respondents viewed this shift positively. Numerous challenges with conducting clinical trials were reported, including enrollment and protocol adherence difficulties with decreased patient visits, staffing constraints, and limited availability of ancillary services. Interactions with sponsors and CROs about modifying trial procedures were also challenging. The changes in clinical trial procedures identified by the survey could serve as strategies for other programs attempting to maintain their clinical trial portfolios during the COVID-19 pandemic. Additionally, many of the adaptations to trials made during the pandemic provide a long-term opportunity to improve and transform the clinical trial system. Specific improvements could be expanded use of more pragmatic or streamlined trial designs, fewer clinical trial–related patient visits, and minimized sponsor and CRO visits to trial programs.

A novel patient-centric approach between sites, CRO, and sponsor to accelerate FPI and drive more patients into oncology protocols.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. 6573-6573
Author(s):  
Krystyna Kowalczyk ◽  
Rhonda U. Henry ◽  
Bellinda Conte
Keyword(s):  
Clinical Trial ◽  
Clinical Trials ◽  
Field Research ◽  
Just In Time ◽  
On Demand ◽  
Oncology Clinical Trial ◽  
Local Access ◽  
Oncology Clinical Trials ◽  
A Site ◽  
New Compounds

6573 Background: According to the Journal of Clinical Oncology, 50% of sites performing clinical trials never enroll a patient. And on top of that, it can take several months to activate a site for an oncology clinical trial; precious time that patients cannot afford when they’ve had a cancer diagnosis and precious time sponsors need when developing new compounds for market. While many patients are interested in participating in trials, they are limited in their opportunities because they do not live near a research site or work with a physician performing clinical trials. So with this crisis in the oncology field, research needs to be more efficient and inclusive. Methods: A combined partnership of sites, physicians, CRO and sponsor leveraging Just-in-Time enrollment methodology helped expedite clinical trial enrollment and diversify trial access driving faster first patient enrolled and expanding the potential patient denominator. Results: This on-demand methodology augmented existing sites that had access to oncology patients by providing broader access, faster, and with no quality loss. Strong partnerships between CRO and sponsor then facilitated two-week site activation allowing every identified patient to be converted to a study subject. This methodology was repeated across seven protocols driving patents on trials within six weeks of trial available. Conclusions: The benefits of this Just-in-Time methodology touch all areas of clinical trials: Patients have greater clinical trial access: A larger denominator of patients across broader geographies have local access to portfolios of clinical trials; Trials start to enroll faster: Patients can be randomized into oncology clinical trials within two weeks of study start up driving trial time to completion; Sites have more trial options to consider: Sites have a broader portfolio of trials to access on demand without added administrative burden; Trials complete faster: Sponsors accrue patients faster driving expedited timelines and accelerating drug development.

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