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Development of an automated method to capture bladder cancer recurrence and progression for epidemiologic research

Funder: National Cancer Institute

Funding period
USD 172 K
Funding amount
Abstract
Project Summary / Abstract: Bladder cancer is the sixth most common cancer in the United States, and non-muscle invasive bladder cancer (NMIBC) accounts for 75-80% of all cases. Tumor recurrence and progression are common among NMIBC patients: over 50% of patients have their tumors recur, most within the first year, and up to 45% of high-risk tumors progress to muscle-invasive disease within 5 years. Patients therefore undergo intensive clinical surveillance and treatment, contributing to bladder cancer being the most expensive cancer to treat on a per patient basis. Large population-based studies have been limited in their ability to study tumor recurrence and progression because these key outcomes are not typically captured in cancer registry or other discretely coded data. To overcome this limitation and facilitate future epidemiologic and outcomes studies on NMIBC, we propose to develop and validate automated algorithms using natural language processing (NLP) to capture bladder cancer recurrence (Aim 1) and progression (Aim 2) from free-text pathology, urology, and imaging notes. We will externally validate the accuracy of the algorithms for extracting tumor characteristics using a national sample of 575 patients from the Veterans Affairs (VA) healthcare system (Aim 3). NLP is a powerful tool that works by segmenting notes into units of related text (e.g., sentences) and applying computational methods to determine meaning and extract data. We will use a novel, internally-developed NLP tool that integrates the best components of several open source NLP packages to efficiently develop, refine, and validate the proposed algorithms. Kaiser Permanente Southern California (KPSC) is an ideal study setting because of its large, diverse population, advanced electronic health record, high-quality cancer registry, and complete capture of care. The initial NLP algorithms will be created based on clinical input and chart reviews of a sample of medical records. The algorithms first will be developed using diagnostic reports, leveraging validated cancer registry data on 6,000 patients; the same clinical procedures are used for initial diagnosis as for recurrence / progression. Then, algorithms will be applied to surveillance reports and iteratively refined based on false positive and negative results vs. study chart reviews (n=100 for each iteration). The final algorithms will be compared to an expert reference standard provided by 2 urologic oncologists and a pathologist in a sample of 200 patients. Algorithm performance will be assessed by sensitivity, specificity, positive predictive value, and negative predictive value. The final algorithms will be applied to 4,000 newly diagnosed NMIBC patients age >18 from 2008-2017 within KPSC. The frequency of recurrence and progression will be described, and characteristics of patients with and without the outcomes will be compared. Successful completion of study aims will produce novel, automated methods that will facilitate large epidemiologic and outcomes studies, whose results may improve care for NMIBC patients.

 
258
Projects
USD 157.3 M
Aggregated funding amount
USD 721 K
Average funding amount
Project list item
Chromatin Modifier Gene Mutation and Enhancer Dysfunction in Bladder Cancer

National Cancer Institute to BYRON H LEE

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Combatting Bladder Cancer by Inducing Epithelial Turnover

National Cancer Institute to SOMAN N ABRAHAM

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Phase 1/2 Study of Modern Immunotherapy in BCG-Relapsing Urothelial Carcinoma of the Bladder - (ADAPT-BLADDER)

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Defining the impact of intra-tumoral morphologic, immune and mutational heterogeneity in urothelial carcinoma

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The role of a new molecular driver in bladder cancer

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Identifying DNA Biomarkers of Bacillus Calmette-Guerin (BCG) Resistance in Non-Muscle-Invasive Bladder Cancer

Canadian Institutes of Health Research to Jack Victor Warren Bacon, Alexander William Wyatt

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Elucidating immunotherapy resistance mechanisms in non-T cell-inflamed bladder cancer

National Cancer Institute to RANDY F. SWEIS

USD 212,669
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Novel recombinant BCG for immunotherapy of bladder cancer

National Cancer Institute to BORIS SHOR

USD 290,014
2018 - 2019
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Modeling bladder cancer metastasis using human patient-derived tumor organoids

Bladder Cancer Advocacy Network to Michael M Shen

USD 300,000
2018 - 2020
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Novel Biomarkers for the Clinical Management of Bladder Cancer

National Cancer Institute to VINATA B LOKESHWAR

USD 466,211
2018 - 2023
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Circulating tumor DNA as a predictive biomarker in metastatic bladder cancer

Canadian Institutes of Health Research to Gillian Rae Vandekerkhove, Alexander William Wyatt

USD 53,221
2018 - 2021
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Intra-operative MRI-guided Robotic System for Photothermal Therapy of Bladder Cancer

University Grants Committee to Kwok Ka Wai, Wong Kenneth Kin Yip, Vardhanabhuti Varut Vince, TEOH Yuen Chun Jeremy

USD 80,682
2018 - 2021
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New Drug and Technology Assessment in Bladder Cancer: Creation of a Novel Canadian Policy Model for Bladder Cancer

Canadian Institutes of Health Research to Murray Dale Krahn, Girish Satish Kulkarni, William Wai Lun Wong, George Andrew Tomlinson, Nathan Perlis, Wassim Kassouf, Peter Colin Black, Shabbir Muhammad Husayn Alibhai

USD 77,161
2018 - 2019
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Role of B-arrestins in bladder cancer progression and response to chemotherapy

United States Department of Veterans Affairs to BAL L LOKESHWAR

 
2018 - 2022
Project list item
Transurethral En Bloc Versus Standard Resection of Bladder Tumour: A Multi-centre Randomised Controlled Trial (EB-StaR study).

University Grants Committee to TEOH Yuen Chun Jeremy

USD 75,274
2018 - 2020
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Deciphering the neoantigen landscape in bladder cancer patients

Swiss National Science Foundation to Laurent Derré, Alexandre Harari, Sylvain Nguyen

USD 639,521
2018 - 2022
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Ty21a immunotherapy of non-muscle-invasive bladder cancer

Swiss National Science Foundation to Denise Nardelli Haefliger, Mathieu Chevalier, Patrice Jichlinski, Lenka Chalupova

USD 436,670
2018 - 2021
Project list item
CISTO: Comparison of Intravesical Therapy and Surgery as Treatment Options for Bladder Cancer

Patient-Centered Outcomes Research Institute to John Gore

USD 8,500,000
2018 - 2022
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