Tissue is Still the issue for Precision Oncology: A Novel Web-Based Platform for Lesion Selection and Biopsy Specimen Acquisition

PURPOSE Evidence-based somatic and germline sequencing has transformed cancer care and improves patient outcomes. However, patients’ low genetic literacy and misunderstanding of their own genomic results poses a threat to the realization of precision oncology. To optimize patient genomic comprehension, we developed a Web-based, patient-directed, genomic sequencing education and return-of-results tool, HOPE-Genomics. METHODS The HOPE-Genomics prototype included somatic and germline sequencing results, embedded multimedia genomic education, and interactive features (eg, request for genetic counseling). Between January and April 2018, we elicited feedback on tool usability and comprehensiveness through participant surveys, 4 focus groups of patients with cancer and their family members, and 3 provider focus groups (comprising 8 patients, 5 family members, and 19 providers). RESULTS We identified themes in patient/family tool-related responses, including the desire to view a patient-friendly report, a desire to receive multiple types of genomic information (eg, prognostic and uncertain), high acceptability of report content, and interest in tool-enabled access to genetic counseling. Major themes from the clinician focus groups included believing the tool could help patients formulate questions and facilitate patients’ communication of results to family members. However, there were diverse responses from all participants in terms of tool implementation (ie, timing and nature of report release). Some participants preferred report release before meeting with the provider, and others preferred it during the appointment. Additionally, some clinicians were concerned about providing prognostic and treatment information through the tool. CONCLUSION There was high acceptability and interest from patients, family members, and providers in a patient-directed genomics report. Future work will determine whether direct-to-patient reporting of genomic results improves patient knowledge, care engagement, and compliance with genomically guided interventions.

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ProjectFlow: a configurable workflow management application for point of care research

JAMIA Open ◽

10.1093/jamiaopen/ooab074 ◽

2021 ◽

Vol 4 (3) ◽

Author(s):

Rupali Dhond ◽

Danne Elbers ◽

Nilla Majahalme ◽

Svitlana Dipietro ◽

Sergey Goryachev ◽

...

Keyword(s):

Clinical Research ◽

Point Of Care ◽

Workflow Management ◽

The United States ◽

Management Tool ◽

Precision Oncology ◽

Web Based ◽

Care Research ◽

Study Recruitment ◽

Management Application

Abstract Objective To best meet our point-of-care research (POC-R) needs, we developed ProjectFlow, a configurable, clinical research workflow management application. In this article, we describe ProjectFlow and how it is used to manage study processes for the Diuretic Comparison Project (DCP) and the Research Precision Oncology Program (RePOP). Materials and methods The Veterans Health Administration (VHA) is the largest integrated health care system in the United States. ProjectFlow is a flexible web-based workflow management tool specifically created to facilitate conduct of our clinical research initiatives within the VHA. The application was developed using the Grails web framework and allows researchers to create custom workflows using Business Process Model and Notation. Results As of January 2021, ProjectFlow has facilitated management of study recruitment, enrollment, randomization, and drug orders for over 10 000 patients for the DCP clinical trial. It has also helped us evaluate over 3800 patients for recruitment and enroll over 370 of them into RePOP for use in data sharing partnerships and predictive analytics aimed at optimizing cancer treatment in the VHA. Discussion The POC-R study design embeds research processes within day-to-day clinical care and leverages longitudinal electronic health record (EHR) data for study recruitment, monitoring, and outcome reporting. Software that allows flexibility in study workflow creation and integrates with enterprise EHR systems is critical to the success of POC-R. Conclusions We developed a flexible web-based informatics solution called ProjectFlow that supports custom research workflow configuration and has ability to integrate data from existing VHA EHR systems.

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STAMPede: A Precision Oncology Catalogue of Solid Tumors

10.1101/2020.09.18.290635 ◽

2020 ◽

Author(s):

Jessica W. Chen ◽

Haik Kalantarian ◽

Christian A. Kunder ◽

James L. Zehnder ◽

Henning Stehr ◽

...

Keyword(s):

Healthcare Providers ◽

Genetic Data ◽

Molecular Profiling ◽

Precision Oncology ◽

Summary Statistics ◽

Sequencing Data ◽

Web Based ◽

Cancer Types ◽

Tumor Sequencing ◽

Insight Into

ABSTRACTMolecular profiling of tumor specimens is a key contributor in the application of precision medicine toward patient care in oncology. The presence of genetic mutational data may provide insight into the etiology of the cancer and inform about the available therapeutic options for patients diagnosed with various cancer types. However, the ability to centrally organize, structure, and visualize this genetic data can be hindered by the lack of necessary computational infrastructure. Here we present a somatic tumor data visualization portal titled STAMPede that utilizes tumor sequencing data from an in-house solid tumor oncology sequencing panel at Stanford Health Care. STAMPede is intended to provide Stanford healthcare providers and clinical researchers an easy to navigate web-based portal to query and display gene-, variant-, and cancer-level summary statistics.

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Precision Trial Drawer, a Computational Tool to Assist Planning of Genomics-Driven Trials in Oncology

JCO Precision Oncology ◽

10.1200/po.18.00015 ◽

2018 ◽

pp. 1-16 ◽

Cited By ~ 1

Author(s):

Giorgio E.M. Melloni ◽

Alessandro Guida ◽

Giuseppe Curigliano ◽

Edoardo Botteri ◽

Angela Esposito ◽

...

Keyword(s):

Specific Treatment ◽

Real Data ◽

Genetic Alterations ◽

The Cancer Genome Atlas ◽

Allocation Rule ◽

Precision Oncology ◽

Cancer Trial ◽

Web Based ◽

Number Of Patients ◽

Optimized Allocation

Purpose Trials that accrue participants on the basis of genetic biomarkers are a powerful means of testing targeted drugs, but they are often complicated by the rarity of the biomarker-positive population. Umbrella trials circumvent this by testing multiple hypotheses to maximize accrual. However, bigger trials have higher chances of conflicting treatment allocations because of the coexistence of multiple actionable alterations; allocation strategies greatly affect the efficiency of enrollment and should be carefully planned on the basis of relative mutation frequencies, leveraging information from large sequencing projects. Methods We developed software named Precision Trial Drawer (PTD) to estimate parameters that are useful for designing precision trials, most importantly, the number of patients needed to molecularly screen (NNMS) and the allocation rule that maximizes patient accrual on the basis of mutation frequency, systematically assigning patients with conflicting allocations to the drug associated with the rarer mutation. We used data from The Cancer Genome Atlas to show their potential in a 10-arm imaginary trial of multiple cancers on the basis of genetic alterations suggested by the past Molecular Analysis for Personalised Therapy (MAP) conference. We validated PTD predictions versus real data from the SHIVA (A Randomized Phase II Trial Comparing Therapy Based on Tumor Molecular Profiling Versus Conventional Therapy in Patients With Refractory Cancer) trial. Results In the MAP imaginary trial, PTD-optimized allocation reduces number of patients needed to molecularly screen by up to 71.8% (3.5 times) compared with nonoptimal trial designs. In the SHIVA trial, PTD correctly predicted the fraction of patients with actionable alterations (33.51% [95% CI, 29.4% to 37.6%] in imaginary v 32.92% [95% CI, 28.2% to 37.6%] expected) and allocation to specific treatment groups (RAS/MEK, PI3K/mTOR, or both). Conclusion PTD correctly predicts crucial parameters for the design of multiarm genetic biomarker-driven trials. PTD is available as a package in the R programming language and as an open-access Web-based app. It represents a useful resource for the community of precision oncology trialists. The Web-based app is available at https://gmelloni.github.io/ptd/shinyapp.html .

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Ultrastructure of NPC/HK1 cells heterotransplanted in athymic nude mice

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010005384x ◽

1982 ◽

Vol 40 ◽

pp. 236-237

Author(s):

E.C. Chew ◽

C.L. Li ◽

D.P. Huang ◽

H.C. Ho ◽

L.S. Mak ◽

...

Keyword(s):

Cell Line ◽

Nude Mice ◽

Biopsy Specimen ◽

Epithelial Cell Line ◽

Present Communication ◽

Recurrent Tumour ◽

Athymic Nude Mice ◽

Cell Line Establishment ◽

Fine Structures ◽

Well Differentiated

An epithelial cell line, NPC/HK1, has recently been established from a biopsy specimen of a recurrent tumour of the nasopharynx which was histologically diagnosed as a moderately to well differentiated squamous cell carcinoma. A definite decrease in the amount of tonofilaments and desmosomes in the NPC/HK1 cells during the cell line establishment was observed. The present communication reports on the fine structures of the NPC/HK1 cells heterotraneplanted in athymic nude mice.

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Ultrastructure of two neoplasms in culture compared with original biopsies

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100110623 ◽

1984 ◽

Vol 42 ◽

pp. 50-51

Author(s):

Joseph M. Harb ◽

James T. Casper ◽

Vlcki Piaskowski

Keyword(s):

Electron Microscopy ◽

Tissue Culture ◽

Biopsy Specimen ◽

Cultured Cells ◽

Light And Electron Microscopy ◽

Human Tumor ◽

Soft Agar ◽

Human Tumor Cells ◽

Morphological Distinction ◽

Tumor Types

The application of tissue culture and the newer methodologies of direct cloning and colony formation of human tumor cells in soft agar hold promise as valuable modalities for a variety of diagnostic studies, which include morphological distinction between tumor types by electron microscopy (EM). We present here two cases in which cells in culture expressed distinct morphological features not apparent in the original biopsy specimen. Evaluation of the original biopsies by light and electron microscopy indicated both neoplasms to be undifferentiated sarcomas. Colonies of cells propagated in soft agar displayed features of rhabdomyoblasts in one case, and cultured cells of the second biopsy expressed features of Ewing's sarcoma.

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The PBL-Evaluator: a web-based tool for assessment in tutorials

Journal of Dental Education ◽

10.1002/j.0022-0337.1998.62.9.tb03231.x ◽

1998 ◽

Vol 62 (9) ◽

pp. 671-674

Author(s):

JF Chaves ◽

JA Chaves ◽

MS Lantz

Keyword(s):

Web Based

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Using Popular Mobile Devices in Voice Therapy

Perspectives on Voice and Voice Disorders ◽

10.1044/vvd23.3.82 ◽

2013 ◽

Vol 23 (3) ◽

pp. 82-87 ◽

Cited By ~ 1

Author(s):

Eva van Leer

Keyword(s):

Exercise Behavior ◽

Voice Therapy ◽

Pure Oxygen ◽

Mobile Platforms ◽

Self Monitoring ◽

Web Based ◽

Motivational Messages ◽

Related Information ◽

Health Related ◽

Tailored Approach

Mobile tools are increasingly available to help individuals monitor their progress toward health behavior goals. Commonly known commercial products for health and fitness self-monitoring include wearable devices such as the Fitbit© and Nike + Pedometer© that work independently or in conjunction with mobile platforms (e.g., smartphones, media players) as well as web-based interfaces. These tools track and graph exercise behavior, provide motivational messages, offer health-related information, and allow users to share their accomplishments via social media. Approximately 2 million software programs or “apps” have been designed for mobile platforms (Pure Oxygen Mobile, 2013), many of which are health-related. The development of mobile health devices and applications is advancing so quickly that the Food and Drug Administration issued a Guidance statement with the purpose of defining mobile medical applications and describing a tailored approach to their regulation.

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A Simple Technique for Obtaining a Colon Biopsy Specimen per Rectum

Gastroenterology ◽

10.1016/s0016-5085(62)80097-3 ◽

1962 ◽

Vol 42 (2) ◽

pp. 157-159 ◽

Cited By ~ 3

Author(s):

Eugene J. Gangarosa ◽

William R. Beisel

Keyword(s):

Biopsy Specimen ◽

Simple Technique ◽

Colon Biopsy

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