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.

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 Individualized Molecular Profiling for Allocation to Clinical Trials Singapore Study—An Asian Tertiary Cancer Center Experience

2021 ◽  
pp. 859-875
Author(s):  
Amanda O. L. Seet ◽  
Aaron C. Tan ◽  
Tira J. Tan ◽  
Matthew C. H. Ng ◽  
David W. M. Tai ◽  
...  
Keyword(s):  
Clinical Trial ◽  
Clinical Trials ◽  
Tumor Tissue ◽  
Molecular Profiling ◽  
Tumor Board ◽  
Cancer Center ◽  
Precision Oncology ◽  
Molecular Tumor Board ◽  
Tumor Types ◽  
Tertiary Cancer Center

PURPOSE Precision oncology has transformed the management of advanced cancers through implementation of advanced molecular profiling technologies to identify increasingly defined subsets of patients and match them to appropriate therapy. We report outcomes of a prospective molecular profiling study in a high-volume Asian tertiary cancer center. PATIENTS AND METHODS Patients with advanced cancer were enrolled onto a prospective protocol for genomic profiling, the Individualized Molecular Profiling for Allocation to Clinical Trials Singapore study, at the National Cancer Center Singapore. Primary objective was to identify molecular biomarkers in patient's tumors for allocation to clinical trials. The study commenced in February 2012 and is ongoing, with the results of all patients who underwent multiplex next-generation sequencing (NGS) testing until December 2018 presented here. The results were discussed at a molecular tumor board where recommendations for allocation to biomarker-directed trials or targeted therapies were made. RESULTS One thousand fifteen patients were enrolled with a median age of 58 years (range 20-83 years). Most common tumor types were lung adenocarcinoma (26%), colorectal cancer (15%), and breast cancer (12%). A total of 1,064 NGS assays were performed, on fresh tumor tissue for 369 (35%) and archival tumor tissue for 687 (65%) assays. TP53 (39%) alterations were most common, followed by EGFR (21%), KRAS (14%), and PIK3CA (10%). Of 405 NGS assays with potentially actionable alterations, 111 (27%) were allocated to a clinical trial after molecular tumor board and 20 (4.9%) were enrolled on a molecularly matched clinical trial. Gene fusions were detected in 23 of 311 (7%) patients tested, including rare fusions in new tumor types and known fusions in rare tumors. CONCLUSION Individualized Molecular Profiling for Allocation to Clinical Trials Singapore demonstrates the feasibility of a prospective broad molecular profiling program in an Asian tertiary cancer center, with the ability to develop and adapt to a dynamic landscape of precision oncology.

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.

Strategic Physician Communication and Oncology Clinical Trials

1999 ◽  
Vol 17 (10) ◽  
pp. 3324-3332 ◽  
Author(s):  
Terrance L. Albrecht ◽  
Christina Blanchard ◽  
John C. Ruckdeschel ◽  
Michael Coovert ◽  
Rebecca Strongbow
Keyword(s):  
Clinical Trial ◽  
Clinical Trials ◽  
Physician Behavior ◽  
Cancer Center ◽  
Coding System ◽  
Patient Centered ◽  
Number Of Patients ◽  
Oncology Clinical Trials ◽  
Primary Means ◽  
Analysis System

PURPOSE: Clinical trials are the primary means for determining new, effective treatments for cancer patients, yet the number of patients that accrue is relatively limited. The purpose of this study was to explore the relationship between physician behavior and patient accrual to a clinical trial by videotaping the interaction. PATIENTS AND METHODS: Forty-eight patient-physician interactions involving 12 different oncologists were videotaped in several clinics at the H. Lee Moffitt Cancer Center and Research Institute (Tampa, FL). The purpose of each interaction was to present the possibility of a clinical trial to the patient. A coding system, the Moffitt Accrual Analysis System, was developed by the authors to code behaviors that represented both the legal-informational and social influence models of communication behavior. Thirty-two patients agreed to participate in the clinical trial. RESULTS: Videotaping was found to be a viable, valid, and reliable method for studying the interaction. Physicians who were observed to use both models of influence were found to enroll more patients. Thus, patients were more likely to accrue to the trial when their physician verbally presented items normally included in an informed consent document and when they behaved in a reflective, patient-centered, supportive, and responsive manner. Discussion of benefits, side effects, patient concerns and resources to manage the concerns were all associated with accrual. CONCLUSION: This research has implications for modifying physician behavior and, thus, increasing the numbers of patients accruing to oncology clinical trials.

scholarly journals Who Needs What? Perceptions of Patients and Caregivers in Oncology Phase 1 Trials

2019 ◽  
Vol 7 (1) ◽  
pp. 27-33 ◽  
Author(s):  
Victoria Rezash ◽  
Janice Reed ◽  
Barbara Gedeon ◽  
Eric Parsons ◽  
Sandra Siedlecki ◽  
...  
Keyword(s):  
Clinical Trial ◽  
Clinical Trials ◽  
Phase 1 ◽  
Trial Participation ◽  
Clinical Trial Participation ◽  
Oncology Clinical Trial ◽  
Oncology Clinical Trials ◽  
Vulnerable Patient ◽  
Additional Support

Background: The study design and nature of oncology phase 1 clinical trials create a uniquely vulnerable patient population yet little research has been conducted to identify the added burden these trials create for both cancer patients and their caregiver(s). Objective: Examining the perceptions and needs of patients and their caregivers participating in phase 1 oncology clinical trials, the investigators tested the hypothesis that the caregiver will exhibit a higher level of burden and/or distress than the patient. Method: A mixed-methods exploratory process utilizing patient and caregiver interviews and quality-of-life questionnaires was used to assess the psychosocial burdens associated with oncology clinical trial participation. A qualitative and quantitative analysis of the responses were 8 performed. Result: Both patients and caregivers reported similar themes identifying the burdens and benefits related to phase 1 clinical trial participation. However, the caregivers’ expressed burden exceeded that of the patients’ validating the study’s hypothesis. Conclusion: The need for ongoing additional support services for not only the patient but also the caregiver was identified.

Comparative study of ultrasonographic findings with the operative findings of biliary surgery

2020 ◽  
Vol 22 (1) ◽  
pp. 25-29
Author(s):  
Zubayer Ahmad ◽  
Mohammad Ali ◽  
Kazi lsrat Jahan ◽  
ABM Khurshid Alam ◽  
G M Morshed
Keyword(s):  
Bile Duct ◽  
Common Bile Duct ◽  
Imaging Modality ◽  
False Positive Rate ◽  
Gallstone Disease ◽  
False Negative ◽  
False Negative Rate ◽  
Biliary Disease ◽  
Biliary Surgery ◽  
Operative Findings

Background: Biliary disease is one of the most common surgical problems encountered all over the world. Ultrasound is widely accepted for the diagnosis of biliary system disease. However, it is a highly operator dependent imaging modality and its diagnostic success is also influenced by the situation, such as non-fasting, obesity, intestinal gas. Objective: To compare the ultrasonographic findings with the peroperative findings in biliary surgery. Methods: This prospective study was conducted in General Hospital, comilla between the periods of July 2006 to June 2008 among 300 patients with biliary diseases for which operative treatment is planned. Comparison between sonographic findings with operative findings was performed. Results: Right hypochondriac pain and jaundice were two significant symptoms (93% and 15%). Right hypochondriac tenderness, jaundice and palpable gallbladder were most valuable physical findings (respectively, 40%, 15% and 5%). Out of 252 ultrasonically positive gallbladder, stone were confirmed in 249 cases preoperatively. Sensitivity of USG in diagnosis of gallstone disease was 100%. There was, however, 25% false positive rate detection. Specificity was, however, 75% in this case. USG could demonstrate stone in common bile duct in only 12 out of 30 cases. Sensitivity of the test in diagnosing common bile duct stone was 40%, false negative rate 60%. In the series, ultrasonography sensitivity was 100% in diagnosing stone in cystic duct. USG could detect with relatively good but less sensitivity the presence of chronic cholecystitis (92.3%) and worm inside gallbladder (50%). Conclusion: Ultrasonography is the most important investigation in the diagnosis of biliary disease and a useful test for patients undergoing operative management for planning and anticipating technical difficulties. Journal of Surgical Sciences (2018) Vol. 22 (1): 25-29

scholarly journals Preliminary Results of MyCog, a Brief Assessment for the Detection of Cognitive Impairment in Primary Care

2020 ◽  
Vol 4 (Supplement_1) ◽  
pp. 259-260
Author(s):  
Laura Curtis ◽  
Lauren Opsasnick ◽  
Julia Yoshino Benavente ◽  
Cindy Nowinski ◽  
Rachel O’Conor ◽  
...  
Keyword(s):  
Primary Care ◽  
Cognitive Impairment ◽  
Cognitive Aging ◽  
False Positive ◽  
False Positive Rate ◽  
False Negative ◽  
False Negative Rate ◽  
Self Report ◽  
Card Sorting ◽  
Primary Care Settings

Abstract Early detection of Cognitive impairment (CI) is imperative to identify potentially treatable underlying conditions or provide supportive services when due to progressive conditions such as Alzheimer’s Disease. While primary care settings are ideal for identifying CI, it frequently goes undetected. We developed ‘MyCog’, a brief technology-enabled, 2-step assessment to detect CI and dementia in primary care settings. We piloted MyCog in 80 participants 65 and older recruited from an ongoing cognitive aging study. Cases were identified either by a documented diagnosis of dementia or mild cognitive impairment (MCI) or based on a comprehensive cognitive battery. Administered via an iPad, Step 1 consists of a single self-report item indicating concern about memory or other thinking problems and Step 2 includes two cognitive assessments from the NIH Toolbox: Picture Sequence Memory (PSM) and Dimensional Change Card Sorting (DCCS). 39%(31/80) participants were considered cognitively impaired. Those who expressed concern in Step 1 (n=52, 66%) resulted in a 37% false positive and 3% false negative rate. With the addition of the PSM and DCCS assessments in Step 2, the paradigm demonstrated 91% sensitivity, 75% specificity and an area under the ROC curve (AUC)=0.82. Steps 1 and 2 had an average administration time of <7 minutes. We continue to optimize MyCog by 1) examining additional items for Step 1 to reduce the false positive rate and 2) creating a self-administered version to optimize use in clinical settings. With further validation, MyCog offers a practical, scalable paradigm for the routine detection of cognitive impairment and dementia.

scholarly journals Ultrasound guided needle biopsy of axilla to evaluate nodal metastasis after preoperative systemic therapy in cohort of 106 breast cancers enriched with BRCA1/2 pathogenic variant carriers

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Baiba Līcīte ◽  
Arvīds Irmejs ◽  
Jeļena Maksimenko ◽  
Pēteris Loža ◽  
Genādijs Trofimovičs ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Systemic Therapy ◽  
False Positive Rate ◽  
False Negative ◽  
False Negative Rate ◽  
Axillary Node ◽  
Pathogenic Variant ◽  
Axillary Lymph ◽  
Ultrasound Guided ◽  
Node Positive

Abstract Background Aim of the study is to evaluate the role of ultrasound guided fine needle aspiration cytology (FNAC) in the restaging of node positive breast cancer after preoperative systemic therapy (PST). Methods From January 2016 – October 2020 106 node positive stage IIA-IIIC breast cancer cases undergoing PST were included in the study. 18 (17 %) were carriers of pathogenic variant in BRCA1/2. After PST restaging of axilla was performed with ultrasound and FNAC of the marked and/or the most suspicious axillary node. In 72/106 cases axilla conserving surgery and in 34/106 cases axillary lymph node dissection (ALND) was performed. Results False Positive Rate (FPR) of FNAC after PST in whole cohort and BRCA1/2 positive subgroup is 8 and 0 % and False Negative Rate (FNR) – 43 and 18 % respectively. Overall Sensitivity − 55 %, specificity- 93 %, accuracy 70 %. Conclusion FNAC after PST has low FPR and is useful to predict residual axillary disease and to streamline surgical decision making regarding ALND both in BRCA1/2 positive and negative subgroups. FNR is high in overall cohort and FNAC alone are not able to predict ypCR and omission of further axillary surgery. However, FNAC performance in BRCA1/2 positive subgroup is more promising and further research with larger number of cases is necessary to confirm the results.

scholarly journals A Method of Segmenting Apples Based on Gray-Centered RGB Color Space

2021 ◽  
Vol 13 (6) ◽  
pp. 1211
Author(s):  
Pan Fan ◽  
Guodong Lang ◽  
Bin Yan ◽  
Xiaoyan Lei ◽  
Pengju Guo ◽  
...  
Keyword(s):  
Vision System ◽  
False Positive Rate ◽  
Clustering Algorithms ◽  
False Negative ◽  
Color Space ◽  
False Negative Rate ◽  
Feature Selection Method ◽  
Image Features ◽  
Accurate Identification ◽  
Rgb Color Space

In recent years, many agriculture-related problems have been evaluated with the integration of artificial intelligence techniques and remote sensing systems. The rapid and accurate identification of apple targets in an illuminated and unstructured natural orchard is still a key challenge for the picking robot’s vision system. In this paper, by combining local image features and color information, we propose a pixel patch segmentation method based on gray-centered red–green–blue (RGB) color space to address this issue. Different from the existing methods, this method presents a novel color feature selection method that accounts for the influence of illumination and shadow in apple images. By exploring both color features and local variation in apple images, the proposed method could effectively distinguish the apple fruit pixels from other pixels. Compared with the classical segmentation methods and conventional clustering algorithms as well as the popular deep-learning segmentation algorithms, the proposed method can segment apple images more accurately and effectively. The proposed method was tested on 180 apple images. It offered an average accuracy rate of 99.26%, recall rate of 98.69%, false positive rate of 0.06%, and false negative rate of 1.44%. Experimental results demonstrate the outstanding performance of the proposed method.

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