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Rashid R, Copelli S, Silverstein JC, Becich MJ. REDCap and the National Mesothelioma Virtual Bank-a scalable and sustainable model for rare disease biorepositories. J Am Med Inform Assoc 2023; 30:1634-1644. [PMID: 37487555 PMCID: PMC10531116 DOI: 10.1093/jamia/ocad132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/16/2023] [Accepted: 07/10/2023] [Indexed: 07/26/2023] Open
Abstract
OBJECTIVE Rare disease research requires data sharing networks to power translational studies. We describe novel use of Research Electronic Data Capture (REDCap), a web application for managing clinical data, by the National Mesothelioma Virtual Bank, a federated biospecimen, and data sharing network. MATERIALS AND METHODS National Mesothelioma Virtual Bank (NMVB) uses REDCap to integrate honest broker activities, enabling biospecimen and associated clinical data provisioning to investigators. A Web Portal Query tool was developed to source and visualize REDCap data in interactive, faceted search, enabling cohort discovery by public users. An AWS Lambda function behind an API calculates the counts visually presented, while protecting record level data. The user-friendly interface, quick responsiveness, automatic generation from REDCap, and flexibility to new data, was engineered to sustain the NMVB research community. RESULTS NMVB implementations enabled a network of 8 research institutions with over 2000 mesothelioma cases, including clinical annotations and biospecimens, and public users' cohort discovery and summary statistics. NMVB usage and impact is demonstrated by high website visits (>150 unique queries per month), resource use requests (>50 letter of interests), and citations (>900) to papers published using NMVB resources. DISCUSSION NMVB's REDCap implementation and query tool is a framework for implementing federated and integrated rare disease biobanks and registries. Advantages of this framework include being low-cost, modular, scalable, and efficient. Future advances to NVMB's implementations will include incorporation of -omics data and development of downstream analysis tools to advance mesothelioma and rare disease research. CONCLUSION NVMB presents a framework for integrating biobanks and patient registries to enable translational research for rare diseases.
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Affiliation(s)
- Rumana Rashid
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Medical Scientist Training Program, University of Pittsburgh-Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Susan Copelli
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jonathan C Silverstein
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Michael J Becich
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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Palchuk MB, London JW, Perez-Rey D, Drebert ZJ, Winer-Jones JP, Thompson CN, Esposito J, Claerhout B. A global federated real-world data and analytics platform for research. JAMIA Open 2023; 6:ooad035. [PMID: 37193038 PMCID: PMC10182857 DOI: 10.1093/jamiaopen/ooad035] [Citation(s) in RCA: 67] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/09/2023] [Accepted: 05/05/2023] [Indexed: 05/18/2023] Open
Abstract
Objective This article describes a scalable, performant, sustainable global network of electronic health record data for biomedical and clinical research. Materials and Methods TriNetX has created a technology platform characterized by a conservative security and governance model that facilitates collaboration and cooperation between industry participants, such as pharmaceutical companies and contract research organizations, and academic and community-based healthcare organizations (HCOs). HCOs participate on the network in return for access to a suite of analytics capabilities, large networks of de-identified data, and more sponsored trial opportunities. Industry participants provide the financial resources to support, expand, and improve the technology platform in return for access to network data, which provides increased efficiencies in clinical trial design and deployment. Results TriNetX is a growing global network, expanding from 55 HCOs and 7 countries in 2017 to over 220 HCOs and 30 countries in 2022. Over 19 000 sponsored clinical trial opportunities have been initiated through the TriNetX network. There have been over 350 peer-reviewed scientific publications based on the network's data. Conclusions The continued growth of the TriNetX network and its yield of clinical trial collaborations and published studies indicates that this academic-industry structure is a safe, proven, sustainable path for building and maintaining research-centric data networks.
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Affiliation(s)
- Matvey B Palchuk
- Corresponding Author: Matvey B. Palchuk, MD, MS, FAMIA, TriNetX, LLC, 125 Cambridge Park Dr, Suite 500, Cambridge, MA 02140, USA;
| | - Jack W London
- Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - David Perez-Rey
- Biomedical Informatics Group, Artificial Intelligence Department, Universidad Politécnica de Madrid, Madrid, Spain
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Andritsos LA, Anghelina M, Neal J, Blachly JS, Mathur P, Lele O, Dearden C, Iyengar S, Cross M, Zent CS, Rogers KA, Epperla N, Lozanski G, Oakes CC, Kraut E, Ruppert AS, Zhao Q, Bhat SA, Forconi F, Banerji V, Handunnetti S, Tam CS, Seymour JF, Else M, Kreitman RJ, Saven A, Call T, Parikh SA, Ravandi F, Johnston JB, Tiacci E, Troussard X, Tallman MS, Dietrich S, Tadmor T, Gozzetti A, Zinzani PL, Robak T, Quest G, Demeter J, Rai K, Fernandez SA, Grever M. Development of a distributed international patient data registry for hairy cell leukemia. Leuk Lymphoma 2022; 63:3021-3031. [PMID: 36070610 PMCID: PMC9990910 DOI: 10.1080/10428194.2022.2109157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 01/11/2023]
Abstract
Hairy cell leukemia (HCL) is a rare lymphoproliferative disorder, comprising only 2% of all leukemias. The Hairy Cell Leukemia Foundation (HCLF) has developed a patient data registry to enable investigators to better study the clinical features, treatment outcomes, and complications of patients with HCL. This system utilizes a centralized registry architecture. Patients are enrolled at HCL Centers of Excellence (COE) or via a web-based portal. All data are de-identified, which reduces regulatory burden and increases opportunities for data access and re-use. To date, 579 patients have been enrolled in the registry. Efforts are underway to engage additional COE's to expand access to patients across the globe. This international PDR will enable researchers to study outcomes in HCL in ways not previously possible due to the rarity of the disease and will serve as a platform for future prospective research.
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Affiliation(s)
- Leslie A Andritsos
- Division of Hematology Oncology, University of New Mexico Comprehensive Cancer Center, Albuquerque, NM, USA
| | - Mirela Anghelina
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Jasmine Neal
- Department of Internal Medicine, Division of Hematology, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - James S Blachly
- Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, OH, USA
| | - Puneet Mathur
- Department of Research Information Technology, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Omkar Lele
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | | | | | | | - Clive S Zent
- James P. Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA
| | - Kerry A Rogers
- Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, OH, USA
| | - Narendranath Epperla
- Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, OH, USA
| | - Gerard Lozanski
- Department of Pathology, The Ohio State University Medical Center, Columbus, OH, USA
| | - Christopher C Oakes
- Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, OH, USA
| | - Eric Kraut
- Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, OH, USA
| | - Amy S Ruppert
- Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, OH, USA
| | - Qiuhong Zhao
- Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, OH, USA
| | - Seema A Bhat
- Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, OH, USA
| | - Francesco Forconi
- Cancer Sciences and Haematology Department, University of Southampton Hospital Trust, Southampton, UK
| | - Versha Banerji
- Department of Internal Medicine & Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada
- Research Institute in Oncology and Hematology, Winnipeg, Canada
| | - Sasanka Handunnetti
- Haematology Department, Peter MacCallum Cancer Centre & Royal Melbourne Hospital, University of Melbourne, Melbourne, Australia
| | - Constantine S Tam
- Haematology Department, Peter MacCallum Cancer Centre & Royal Melbourne Hospital, University of Melbourne, Melbourne, Australia
| | - John F Seymour
- Haematology Department, Peter MacCallum Cancer Centre & Royal Melbourne Hospital, University of Melbourne, Melbourne, Australia
| | - Monica Else
- The Institute of Cancer Research, London, UK
| | - Robert J Kreitman
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Alan Saven
- Division of Hematology and Oncology, Scripps Clinic, La Jolla, CA, USA
| | - Timothy Call
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | | | - Farhad Ravandi
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - James B Johnston
- Department of Internal Medicine & Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada
- Research Institute in Oncology and Hematology, Winnipeg, Canada
| | - Enrico Tiacci
- Department of Medicine and Surgery, Institute of Hematology, University and Hospital of Perugia, Perugia, Italy
| | - Xavier Troussard
- Department of Hematology, Centre Hospitalier Universitaire Cote de Nacre, Caen, France
| | - Martin S Tallman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sascha Dietrich
- Department of Hematology, University Hospital of Heidelberg, Heidelberg, Germany
| | - Tamar Tadmor
- Hematology Division, Bnai Zion Medical Center and The Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Alessandro Gozzetti
- Department of Medicine, University of Siena Policlinico S Maria alle Scotte, Siena, Italy
| | - Pier Luigi Zinzani
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale Università degli Studi, IRCCS Azienda Ospedaliero-Universitaria di Bologna and Istituto di Ematologia "Seràgnoli", Bologna, Italy
| | - Tadeusz Robak
- Department of Hematology, Medical University of Lodz, Lodz, Poland
| | - Graeme Quest
- Pathology and Molecular Medicine, Queen's University and Kingston Health Sciences Centre, Kingston, Canada
| | - Judit Demeter
- Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
| | - Kanti Rai
- Zucker School of Medicine at Hofstra/Northwell, New Hyde Park, NY, USA
| | - Soledad A Fernandez
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Michael Grever
- Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, OH, USA
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4
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Wang L, Fu S, Wen A, Ruan X, He H, Liu S, Moon S, Mai M, Riaz IB, Wang N, Yang P, Xu H, Warner JL, Liu H. Assessment of Electronic Health Record for Cancer Research and Patient Care Through a Scoping Review of Cancer Natural Language Processing. JCO Clin Cancer Inform 2022; 6:e2200006. [PMID: 35917480 PMCID: PMC9470142 DOI: 10.1200/cci.22.00006] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/18/2022] [Accepted: 06/15/2022] [Indexed: 11/20/2022] Open
Abstract
PURPOSE The advancement of natural language processing (NLP) has promoted the use of detailed textual data in electronic health records (EHRs) to support cancer research and to facilitate patient care. In this review, we aim to assess EHR for cancer research and patient care by using the Minimal Common Oncology Data Elements (mCODE), which is a community-driven effort to define a minimal set of data elements for cancer research and practice. Specifically, we aim to assess the alignment of NLP-extracted data elements with mCODE and review existing NLP methodologies for extracting said data elements. METHODS Published literature studies were searched to retrieve cancer-related NLP articles that were written in English and published between January 2010 and September 2020 from main literature databases. After the retrieval, articles with EHRs as the data source were manually identified. A charting form was developed for relevant study analysis and used to categorize data including four main topics: metadata, EHR data and targeted cancer types, NLP methodology, and oncology data elements and standards. RESULTS A total of 123 publications were selected finally and included in our analysis. We found that cancer research and patient care require some data elements beyond mCODE as expected. Transparency and reproductivity are not sufficient in NLP methods, and inconsistency in NLP evaluation exists. CONCLUSION We conducted a comprehensive review of cancer NLP for research and patient care using EHRs data. Issues and barriers for wide adoption of cancer NLP were identified and discussed.
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Affiliation(s)
- Liwei Wang
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, MN
| | - Sunyang Fu
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, MN
| | - Andrew Wen
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, MN
| | - Xiaoyang Ruan
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, MN
| | - Huan He
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, MN
| | - Sijia Liu
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, MN
| | - Sungrim Moon
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, MN
| | - Michelle Mai
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, MN
| | - Irbaz B. Riaz
- Department of Hematology/Oncology, Mayo Clinic, Scottsdale, AZ
| | - Nan Wang
- Department of Computer Science and Engineering, College of Science and Engineering, University of Minnesota, Minneapolis, MN
| | - Ping Yang
- Department of Quantitative Health Sciences, Mayo Clinic, Scottsdale, AZ
| | - Hua Xu
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX
| | - Jeremy L. Warner
- Departments of Medicine (Hematology/Oncology), Vanderbilt University, Nashville, TN
- Department Biomedical Informatics, Vanderbilt University, Nashville, TN
| | - Hongfang Liu
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, MN
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Hunger M, Bardenheuer K, Passey A, Schade R, Sharma R, Hague C. The Value of Federated Data Networks in Oncology: What Research Questions Do They Answer? Outcomes From a Systematic Literature Review. VALUE IN HEALTH : THE JOURNAL OF THE INTERNATIONAL SOCIETY FOR PHARMACOECONOMICS AND OUTCOMES RESEARCH 2022; 25:855-868. [PMID: 35249830 DOI: 10.1016/j.jval.2021.11.1357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 10/22/2021] [Accepted: 11/14/2021] [Indexed: 06/14/2023]
Abstract
OBJECTIVES Real-world evidence (RWE) plays an important role in addressing key research questions of interest to healthcare decision makers. Federated data networks (FDNs) apply novel technology to enable the conduct of RWE studies with multiple partners, without the need to share the individual partner's data set. A systematic review of the published literature was performed to determine which types of research questions can best be addressed through FDNs, specifically in the field of oncology. METHODS Systematic searches of MEDLINE and Embase were undertaken to identify the types of research questions that had been addressed in studies using FDNs. Additional information was retrieved about study characteristics, statistical methods, and the FDN itself. RESULTS In total, 40 publications were included where research questions on the following had been addressed (multiple categories possible): disease natural history (58%), safety surveillance (18%), treatment pathways (15%), comparative effectiveness (10%), and cost/resource use studies (3%)-13% of studies had to be left uncategorized. A total of 50% of the studies were run with data partners in networks of ≤5. The size of the networks ranged from 227 patients to >5 million patients. Statistical methods used included distributed learning and distributed regression methods. CONCLUSIONS Further work is needed to raise awareness of the important role that FDNs can play in leveraging readily available RWE to address key research questions of interest in cancer and the benefits to the research community in engaging in federated data initiatives with a long-term perspective.
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Affiliation(s)
- Matthias Hunger
- ICON plc, Global Health Economics, Outcomes Research and Epidemiology, Dublin
| | | | | | - René Schade
- ICON plc, Global Health Economics, Outcomes Research and Epidemiology, Dublin
| | - Ruchika Sharma
- ICON plc, Global Health Economics, Outcomes Research and Epidemiology, Dublin
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Zhang PF, Zheng XH, Li XZ, Sun L, Jia WH. Informatics Management of Tumor Specimens in the Era of Big Data: Challenges and Solutions. Biopreserv Biobank 2021; 19:531-542. [PMID: 34030478 DOI: 10.1089/bio.2020.0084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Biomedical data bear the potential to facilitate personalized diagnosis and precision treatment. In the era of Big Data, high-quality annotation of human specimens has become the primary mission of biobankers, especially for tumor biobanks with large amounts of "omics" and clinical data. However, the lack of agreed-upon standardization and the gap among heterogeneous databases make information application and communication a major challenge. International efforts are underway to develop national projects on informatics management. The aim of this review is to provide references in specimen annotation to regulate and take full advantage of biological and biomedical information. First, critical data categories that are vital for specimen applications, including sample attributes, clinical data, preanalytical variations, and analytical records, are systematically listed for subsequent data mining. Second, current standards and guidelines related to biospecimen information are reviewed, and proper standards for tumor biobanks are recommended. In particular, commonly-used approaches and functionalities of data management are summarized and discussed. This review highlights the importance of informatics management of tumor specimens, defines critical data types, recommends data standards, and presents the methodologies of data harmonization for biobankers to reach high quality annotation of biospecimens.
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Affiliation(s)
- Pei-Fen Zhang
- State Key Laboratory of Oncology in South China, Tumor Biobank, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P. R. China
| | - Xiao-Hui Zheng
- State Key Laboratory of Oncology in South China, Tumor Biobank, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P. R. China
| | - Xi-Zhao Li
- State Key Laboratory of Oncology in South China, Tumor Biobank, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P. R. China
| | - Lin Sun
- Department of Information, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, P. R. China
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Tumor Biobank, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P. R. China
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7
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Lai H, Jiang W, Zhao J, Dinglin X, Li Y, Li S, Wang Y, Yao H. Global Trend in Research and Development of CDK4/6 Inhibitors for Clinical Cancer Therapy: A Bibliometric Analysis. J Cancer 2021; 12:3539-3547. [PMID: 33995631 PMCID: PMC8120189 DOI: 10.7150/jca.51609] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 03/25/2021] [Indexed: 02/03/2023] Open
Abstract
Background: Cyclin-dependent kinase (CDK) 4/6 inhibitors are frequently used anti-cancer agents in hormone receptor-positive breast cancers. This study assessed the course of research and development (R&D) for CDK4/6 inhibitors in terms of publications over the past two decades. Methods: The Web of Science (WOS) and PubMed databases were searched to identify publications related to research on CDK4/6 inhibitors since 2001. The VOS Viewer software was used to analyze co-occurring keywords to stratify the publication data and collaborations in research. Results: There were 1395 publications related to research on CDK4/6 inhibitors since 2001. Eight of the top 10 institutions originated from the USA and the other two were a Swiss Pharmaceutical Company and French Research Institute. Bardia A, the first author for some of the articles published in the USA, was the most prolific with 25 publications. The journal with the most publications was Cancer Res with 162 publications. Basic research comprised six of the 10 most frequently cited publications and the rest consisted of three reviews and a clinical trial. The most common keywords for publications since 2011 were “palbociclib”, “abemaciclib”, “ribociclib” and “double blind”, indicating the successful development of CDK4/6 inhibitors as anticancer drugs. Conclusions: This study provides a comprehensive review of the CDK4/6 inhibitors R&D history. The data imply that drug development in this field is a decade-long process and clinical trials have been performed before clinical applications. Thereafter, research was conducted on the adverse effects and drug resistance associated with the inhibitors.
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Affiliation(s)
- Hongna Lai
- Guangdong Provincial Key Laboratory of Malignant Tumour Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, SunYat-Sen University, Guangzhou 510120, China.,Breast Tumour Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Wei Jiang
- Department of Pharmacy, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Jianli Zhao
- Guangdong Provincial Key Laboratory of Malignant Tumour Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, SunYat-Sen University, Guangzhou 510120, China.,Breast Tumour Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Xiaoxiao Dinglin
- Guangdong Provincial Key Laboratory of Malignant Tumour Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, SunYat-Sen University, Guangzhou 510120, China.,Breast Tumour Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Yudong Li
- Guangdong Provincial Key Laboratory of Malignant Tumour Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, SunYat-Sen University, Guangzhou 510120, China.,Breast Tumour Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Shunying Li
- Guangdong Provincial Key Laboratory of Malignant Tumour Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, SunYat-Sen University, Guangzhou 510120, China.,Breast Tumour Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Ying Wang
- Guangdong Provincial Key Laboratory of Malignant Tumour Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, SunYat-Sen University, Guangzhou 510120, China.,Breast Tumour Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Herui Yao
- Guangdong Provincial Key Laboratory of Malignant Tumour Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, SunYat-Sen University, Guangzhou 510120, China.,Breast Tumour Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
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Zhang L, Jia W, Ji N, Li D, Xiao D, Shan GL, Wang T, Xiao X. Construction of the National Brain Tumor Registry of China for better management and more efficient use of data: a protocol. BMJ Open 2021; 11:e040055. [PMID: 33455925 PMCID: PMC7813366 DOI: 10.1136/bmjopen-2020-040055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
INTRODUCTION Brain tumours encompass a complex group of intracranial tumours that mostly affect young adults and children, with a high incidence rate and poor prognosis. It remains impossible to systematically collect data on patients with brain tumours in China and difficult to perform in-depth analysis on the status of brain tumours, medical outcomes or other important medical issues through a multicentre clinical study. This study describes the first nation-wide data platform including the entire spectrum of brain tumour entities, which will allow better management and more efficient application of patient data in China. METHODS AND ANALYSIS The National Brain Tumor Registry of China (NBTRC) is a registry of real-word clinical data on brain tumours. It is established and managed by the China National Clinical Research Center for Neurological Diseases and administered by its scientific and executive committees. The 54 participating hospitals of the NBTRC are located in 27 provinces/municipalities, performing more than 40 000 brain tumour surgeries per year. The data consist of in-hospital medical records, images and follow-up information after discharge. Data can be uploaded in three ways: the web portal, remote physical servers and offline software. The data quality control scheme is seven-dimensional. Each participating hospital could focus on a single pathology subtype and public subtypes of brain tumour for which they expect to conduct related multicentre clinical research. The standardised workflow to conduct clinical research is based on the benefit-sharing mechanism. Data collection will be conducted continuously from 1 February 2019 to 31 January 2024. ETHICS AND DISSEMINATION Informed consent will be obtained from all participants. Consent for the adolescents' participation will be also obtained from their guardians via written consent. The results will be published in professional journals, in both Chinese and English. TRIAL REGISTRATION NUMBER Chinese Clinical Trial Registry (ChiCTR1900021096).
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Affiliation(s)
- Liwei Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Beijing, China
| | - Wang Jia
- Department of Neurosurgery, Beijing Tiantan Hospital, Beijing, China
| | - Nan Ji
- Department of Neurosurgery, Beijing Tiantan Hospital, Beijing, China
| | - Deling Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Beijing, China
| | - Dan Xiao
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Guang-Liang Shan
- Department of Epidemiology and Statistics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Tao Wang
- Information Center, Beijing Tiantan Hospital, Beijing, China
| | - Xiong Xiao
- Department of Neurosurgery, Beijing Tiantan Hospital, Beijing, China
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9
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MYC Targets Scores Are Associated with Cancer Aggressiveness and Poor Survival in ER-Positive Primary and Metastatic Breast Cancer. Int J Mol Sci 2020; 21:ijms21218127. [PMID: 33143224 PMCID: PMC7663719 DOI: 10.3390/ijms21218127] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/25/2020] [Accepted: 10/29/2020] [Indexed: 12/18/2022] Open
Abstract
MYC is one of the most studied oncogenes that is known to promote cell proliferation. We utilized MYC targets v1 and MYC targets v2 scores of gene set variation analysis and hypothesized that these scores correlate with tumor aggressiveness and survival outcomes. We examined a total of 3109 breast cancer patients from TCGA, METABRIC, and GSE124647 cohorts. In each cohort, the patients were divided into high- and low-score groups using the upper third value as the cut off. As expected, higher scores were related to increased cell proliferation and worse clinical and pathologic features. High MYC targets scores were associated with worse survival, specifically in primary ER-positive breast cancer, consistently in both TCGA and METABRIC cohorts. In ER-positive breast cancer, high MYC targets v1, but not v2 score, was associated with high mutation load, and high MYC targets v1 and v2 scores were both associated with increased infiltration of pro- and anti-cancerous immune cells. We found that high MYC scores were associated with worse survival in metastatic breast cancer. Our findings show that the MYC targets v1 and v2 scores are associated with tumor aggressiveness and poor prognosis in ER-positive primary tumors, as well as in metastatic breast cancer.
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Oshi M, Asaoka M, Tokumaru Y, Yan L, Matsuyama R, Ishikawa T, Endo I, Takabe K. CD8 T Cell Score as a Prognostic Biomarker for Triple Negative Breast Cancer. Int J Mol Sci 2020; 21:E6968. [PMID: 32971948 PMCID: PMC7555570 DOI: 10.3390/ijms21186968] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 12/24/2022] Open
Abstract
CD8 T cell is an essential component of tumor-infiltrating lymphocytes (TIL) and tumor immune microenvironment (TIME). Using the xCell CD8 T cell score of whole tumor gene expression data, we estimated these cells in total of 3837 breast cancer patients from TCGA, METABRIC and various GEO cohorts. The CD8 score correlated strongly with expression of CD8 genes. The score was highest for triple-negative breast cancer (TNBC), and a high score was associated with high tumor immune cytolytic activity and better survival in TNBC but not other breast cancer subtypes. In TNBC, tumors with a high CD8 score had enriched expression of interferon (IFN)-α and IFN-γ response and allograft rejection gene sets, and greater infiltration of anti-cancerous immune cells. The score strongly correlated with CD4 memory T cells in TNBC, and tumors with both a high CD8 score and high CD4 memory T cell abundance had significantly better survival. Finally, a high CD8 score was significantly associated with high expression of multiple immune checkpoint molecules. In conclusion, a high CD8 T cell score is associated with better survival in TNBC, particularly when tumor CD4 memory T cells were elevated. Our findings also suggest a possible use of the score as a predictive biomarker for response to immune checkpoint therapy.
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Affiliation(s)
- Masanori Oshi
- Breast Surgery, Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (M.O.); (M.A.); (Y.T.)
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan; (R.M.); (I.E.)
| | - Mariko Asaoka
- Breast Surgery, Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (M.O.); (M.A.); (Y.T.)
- Department of Breast Surgery and Oncology, Tokyo Medical University, Tokyo 160-8402, Japan;
| | - Yoshihisa Tokumaru
- Breast Surgery, Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (M.O.); (M.A.); (Y.T.)
- Department of Surgical Oncology, Graduate School of Medicine, Gifu University, 1-1 Yanagido, Gifu 501-1194, Japan
| | - Li Yan
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA;
| | - Ryusei Matsuyama
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan; (R.M.); (I.E.)
| | - Takashi Ishikawa
- Department of Breast Surgery and Oncology, Tokyo Medical University, Tokyo 160-8402, Japan;
| | - Itaru Endo
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan; (R.M.); (I.E.)
| | - Kazuaki Takabe
- Breast Surgery, Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (M.O.); (M.A.); (Y.T.)
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan; (R.M.); (I.E.)
- Department of Breast Surgery and Oncology, Tokyo Medical University, Tokyo 160-8402, Japan;
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8520, Japan
- Department of Breast Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
- Department of Surgery, Jacobs School of Medicine and Biomedical Sciences, State University of New York, Buffalo, NY 14263, USA
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11
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Oshi M, Takahashi H, Tokumaru Y, Yan L, Rashid OM, Nagahashi M, Matsuyama R, Endo I, Takabe K. The E2F Pathway Score as a Predictive Biomarker of Response to Neoadjuvant Therapy in ER+/HER2- Breast Cancer. Cells 2020; 9:E1643. [PMID: 32650578 PMCID: PMC7407968 DOI: 10.3390/cells9071643] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/28/2020] [Accepted: 07/07/2020] [Indexed: 12/20/2022] Open
Abstract
E2F transcription factors play critical roles in the cell cycle. Therefore, their activity is expected to reflect tumor aggressiveness and responsiveness to therapy. We scored 3905 tumors of nine breast cancer cohorts for this activity based on their gene expression for the Hallmark E2F targets gene set. As expected, tumors with a high score had an increased expression of cell proliferation-related genes. A high score was significantly associated with shorter patient survival, greater MKI67 expression, histological grade, stage, and genomic aberrations. Furthermore, metastatic tumors had higher E2F scores than the primary tumors from which they arose. Although tumors with a high score had greater infiltration by both pro- and anti-cancerous immune cells, they had an increased expression of immune checkpoint genes. Estrogen receptor (ER)-positive/human epidermal growth factor receptor 2 (HER2)-negative cancer with a high E2F score achieved a significantly higher pathological complete response (pCR) rate to neoadjuvant chemotherapy. The E2F score was significantly associated with the expression of cyclin-dependent kinase (CDK)-related genes and strongly correlated with sensitivity to CDK inhibition in cell lines. In conclusion, the E2F score is a marker of breast cancer aggressiveness and predicts the responsiveness of ER-positive/HER2-negative patients to neoadjuvant chemotherapy and possibly to CDK and immune checkpoint inhibitors.
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Affiliation(s)
- Masanori Oshi
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (M.O.); (H.T.); (Y.T.)
- Department of Gastroenterological Surgery, Yokohama City University School of Medicine, Yokohama 2360004, Japan; (R.M.); (I.E.)
| | - Hideo Takahashi
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (M.O.); (H.T.); (Y.T.)
| | - Yoshihisa Tokumaru
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (M.O.); (H.T.); (Y.T.)
- Department of Surgical Oncology, Graduate School of Medicine, Gifu University, Gifu 501-1194, Japan
| | - Li Yan
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA;
| | - Omar M. Rashid
- Department of Surgery, Holy Cross Hospital, Michael and Dianne Bienes Comprehensive Cancer Center, Fort Lauderdale, FL 33308, USA;
- Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Masayuki Nagahashi
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata 9518520, Japan;
| | - Ryusei Matsuyama
- Department of Gastroenterological Surgery, Yokohama City University School of Medicine, Yokohama 2360004, Japan; (R.M.); (I.E.)
| | - Itaru Endo
- Department of Gastroenterological Surgery, Yokohama City University School of Medicine, Yokohama 2360004, Japan; (R.M.); (I.E.)
| | - Kazuaki Takabe
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (M.O.); (H.T.); (Y.T.)
- Department of Gastroenterological Surgery, Yokohama City University School of Medicine, Yokohama 2360004, Japan; (R.M.); (I.E.)
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima 9601295, Japan
- Department of Surgery, Jacobs School of Medicine and Biomedical Sciences, State University of New York, Buffalo, NY 14263, USA
- Department of Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata 9518510, Japan
- Department of Breast Surgery and Oncology, Tokyo Medical University, Tokyo 1608402, Japan
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12
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Blohmer M, Zhu L, Atkinson JM, Beriwal S, Rodríguez-López JL, Rosenzweig M, Brufsky AM, Tseng G, Lucas PC, Lee AV, Oesterreich S, Jankowitz RC. Patient treatment and outcome after breast cancer orbital and periorbital metastases: a comprehensive case series including analysis of lobular versus ductal tumor histology. Breast Cancer Res 2020; 22:70. [PMID: 32586354 PMCID: PMC7318761 DOI: 10.1186/s13058-020-01309-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 06/10/2020] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Breast cancer is the most common malignancy to spread to the orbit and periorbit, and the invasive lobular carcinoma (ILC) histologic subtype of breast cancer has been reported to form these ophthalmic metastases (OM) more frequently than invasive ductal carcinomas (IDC). We herein report our single academic institution experience with breast cancer OM with respect to anatomical presentation, histology (lobular vs. ductal), treatment, and survival. METHODS We employed the natural language processing platform, TIES (Text Information Extraction System), to search 2.3 million de-identified patient pathology and radiology records at our institution in order to identify patients with OM secondary to breast cancer. We then compared the resultant cohort, the "OM cohort," to two other representative metastatic breast cancer patient (MBC) databases from our institution. Histological analysis of selected patients was performed. RESULTS Our TIES search and manual refinement ultimately identified 28 patients who were diagnosed with breast cancer between 1995 and 2016 that subsequently developed OM. Median age at diagnosis was 54 (range 28-77) years of age. ER, PR, and HER2 status from the 28 patients with OM did not differ from other patients with MBC from our institution. The relative proportion of patients with ILC was significantly higher in the OM cohort (32.1%) than in other MBC patients in our institution (11.3%, p = 0.007). Median time to first OM in the OM cohort was 46.7 months, and OM were the second most frequent first metastases after bony metastases. After diagnosis of the first distant metastasis of any kind, median survival of patients with ILC (21.4 months) was significantly shorter than that of patients with IDC (55.3 months, p = 0.03). Nine patients developed bilateral OM. We observed a significant co-occurrence of OM and central nervous system metastases (p = 0.0053). The histological analysis revealed an interesting case in which the primary tumor was of a mixed ILC/IDC subtype, while only ILC was present in the OM. CONCLUSIONS OM from breast cancer are illustrative of the difference in metastatic behavior of ILC versus IDC and should be considered when treating patients with ILC, especially in those with complaints of visual acuity changes.
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MESH Headings
- Adult
- Aged
- Breast Neoplasms/metabolism
- Breast Neoplasms/pathology
- Breast Neoplasms/radiotherapy
- Carcinoma, Ductal, Breast/metabolism
- Carcinoma, Ductal, Breast/pathology
- Carcinoma, Ductal, Breast/radiotherapy
- Carcinoma, Lobular/metabolism
- Carcinoma, Lobular/mortality
- Carcinoma, Lobular/pathology
- Carcinoma, Lobular/radiotherapy
- Female
- Follow-Up Studies
- Humans
- Lymphatic Metastasis
- Middle Aged
- Orbital Neoplasms/metabolism
- Orbital Neoplasms/radiotherapy
- Orbital Neoplasms/secondary
- Prognosis
- Radiotherapy, Intensity-Modulated
- Receptor, ErbB-2/metabolism
- Receptors, Estrogen/metabolism
- Receptors, Progesterone/metabolism
- Retrospective Studies
- Survival Rate
- Treatment Outcome
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Affiliation(s)
- Martin Blohmer
- Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
- Charité - Universitätsmedizin Berlin, Berlin, Germany
- Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee Women's Research Institute, Pittsburgh, PA, USA
| | - Li Zhu
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jennifer M Atkinson
- Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
- Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee Women's Research Institute, Pittsburgh, PA, USA
| | - Sushil Beriwal
- University of Pittsburgh School of Medicine, Department of Radiation Oncology, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Joshua L Rodríguez-López
- University of Pittsburgh School of Medicine, Department of Radiation Oncology, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Margaret Rosenzweig
- Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee Women's Research Institute, Pittsburgh, PA, USA
- School of Nursing, University of Pittsburgh, Pittsburgh, PA, USA
| | - Adam M Brufsky
- University of Pittsburgh School of Medicine, Department of Medicine, Division of Hematology/Oncology, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - George Tseng
- Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee Women's Research Institute, Pittsburgh, PA, USA
- University of Pittsburgh School of Medicine, Department of Medicine, Division of Hematology/Oncology, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Peter C Lucas
- Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee Women's Research Institute, Pittsburgh, PA, USA
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Adrian V Lee
- Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
- Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee Women's Research Institute, Pittsburgh, PA, USA
| | - Steffi Oesterreich
- Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
- Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee Women's Research Institute, Pittsburgh, PA, USA
| | - Rachel C Jankowitz
- University of Pittsburgh School of Medicine, Department of Medicine, Division of Hematology/Oncology, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
- Department of Medicine, Division of Hematology/Oncology, Perelman School of Medicine, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA.
- Rena Rowan Breast Center, Perelman Center for Advanced Medicine and the Abramson Cancer Center, 3rd Floor, West Pavilion, 3400 Civic Center Boulevard, Philadelphia, PA, 19104, USA.
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13
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Takahashi H, Oshi M, Asaoka M, Yan L, Endo I, Takabe K. Molecular Biological Features of Nottingham Histological Grade 3 Breast Cancers. Ann Surg Oncol 2020; 27:4475-4485. [PMID: 32436191 DOI: 10.1245/s10434-020-08608-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Cancer biology dominates the behavior and prognosis of a tumor. Although Nottingham histological grade is a subjective pathological determination, it has been accepted as a surrogate model for cancer biology. As such, histologic grade was incorporated into the latest 8th edition of the American Joint Committee on Cancer breast cancer staging system. In this study, we hypothesized that grade 3 breast cancers demonstrate aggressive molecular biological profiles, reflecting worse biology and possible underlying immunogenicity. METHODS Transcriptomic and clinical data were obtained from the Molecular Taxonomy of Breast Cancer International Consortium, and the findings were validated by The Cancer Genome Atlas breast cancer cohort and GSE25066. RESULTS Overall, 2876 patients were analyzed in this study. Grade 3 tumors were more common in estrogen receptor (ER)-negative, advanced-stage patients, and were associated with human epidermal growth factor receptor 2 and basal subtypes by the PAM50 classifier, as well as with increased MKI67 expression (all p <0.001). Disease-free survival was significantly worse in grade 3 tumors (all cohorts). Gene set enrichment analysis demonstrated that grade 3 tumors were significantly enriched with not only cell proliferation and cell cycle-related gene sets but also immune activity-related gene sets. CIBERSORT confirmed that grade 3 tumors were infiltrated with macrophage M1, follicular helper T cells, and activated natural killer cells (all p <0.001). Furthermore, grade 3 tumors were associated with more diverse T cell receptors (p =0.001) and increased cytolytic activity (p <0.001). Lastly, major T-cell exhaustion markers were significantly elevated in grade 3 breast cancers (p <0.001). CONCLUSION Grade 3 breast cancers demonstrated aggressive transcriptomic features with enhanced immunogenicity and elevated T-cell exhaustion markers.
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Affiliation(s)
- Hideo Takahashi
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Masanori Oshi
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.,Department of Surgery, Yokohama City University, Yokohama, Japan
| | - Mariko Asaoka
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.,Department of Breast Surgery and Oncology, Tokyo Medical University, Tokyo, Japan
| | - Li Yan
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Itaru Endo
- Department of Surgery, Yokohama City University, Yokohama, Japan
| | - Kazuaki Takabe
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA. .,Department of Breast Surgery and Oncology, Tokyo Medical University, Tokyo, Japan. .,Department of Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan. .,Department of Surgery, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, The State University of New York, Buffalo, NY, USA. .,Department of Surgery, Yokohama City University, Yokohama, Japan.
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14
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G2M Cell Cycle Pathway Score as a Prognostic Biomarker of Metastasis in Estrogen Receptor (ER)-Positive Breast Cancer. Int J Mol Sci 2020; 21:ijms21082921. [PMID: 32331421 PMCID: PMC7215898 DOI: 10.3390/ijms21082921] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/20/2020] [Accepted: 04/20/2020] [Indexed: 12/20/2022] Open
Abstract
The vast majority of breast cancer death is a result of metastasis. Thus, accurate identification of patients who are likely to have metastasis is expected to improve survival. The G2M checkpoint plays a critical role in cell cycle. We hypothesized that breast cancer tumors with high activity of G2M pathway genes are more aggressive and likely to metastasize. To test this, we used the single-sample gene set variation analysis method to calculate the score for the Hallmark G2M checkpoint pathway using gene expression data of a total of 4626 samples from 12 human breast cancer cohorts. As expected, a high G2M pathway score correlated with enriched tumor expression of other cell proliferation-related gene sets. The score was significantly associated with clinical aggressive features of tumors and patient survival in estrogen receptor (ER)-positive/human epidermal growth factor receptor 2 (HER2)-negative breast cancer. Interestingly, a high G2M score of metastasis tumors was also significantly associated with worse survival. In primary as well as metastasis tumors with high scores, the infiltration of both pro- and anti-cancerous immune cells increased. Tumor G2M score was also associated with treatment response to systemic chemotherapy in ER-positive/HER2-negative cancer, and was predictive of response to cyclin-dependent kinase inhibition therapy.
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15
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Asaoka M, Patnaik SK, Zhang F, Ishikawa T, Takabe K. Lymphovascular invasion in breast cancer is associated with gene expression signatures of cell proliferation but not lymphangiogenesis or immune response. Breast Cancer Res Treat 2020; 181:309-322. [PMID: 32285241 DOI: 10.1007/s10549-020-05630-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/04/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND While the prognostic relevance of lymphovascular invasion (LVI) in breast cancer is well known, its molecular biology is poorly understood. We hypothesized that pathologically determined LVI reflects molecular features of tumors and can be discerned from their genomic and transcriptomic profiles. METHODS LVI status and Nottingham histological scores of primary breast tumors of The Cancer Genome Atlas (TCGA) project were assessed from pathology reports; other clinical and molecular data were obtained from TCGA data portals and publications. Two independent datasets (GSE5460 and GSE7849) were combined and used for validation. RESULTS LVI status was determinable for 639 and 196 cases of the TCGA and validation cohorts, among whom LVI incidence was 37.8% and 37.2%, respectively. LVI was associated with high tumor Ki67 expression, advanced pathologic stage, and high Nottingham scores. LVI-positive cases had worse overall and progression-free survival regardless of cancer subtype. Surprisingly, in both cohorts, LVI was not associated with lymphangiogenesis or lymphatic vessel density as estimated from tumor expression of lymphatic endothelium-associated genes. LVI-positive tumors had higher genome copy number aberrations, aneuploidy, and homologous recombination defects, but not single-nucleotide variations or intra-tumor genome heterogeneity. Tumor immune cell composition and cytolytic activity was not associated with LVI status. On the other hand, expression of cell proliferation-related genes was significantly increased in LVI-positive tumors. CONCLUSION Our study suggests that breast cancer with LVI is a highly proliferative cancer, and it does not correlate with gene expression markers for lymphangiogenesis or immune response.
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Affiliation(s)
- Mariko Asaoka
- Department of Breast Surgery, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.,Department of Breast Surgery and Oncology, Tokyo Medical University, Tokyo, Japan
| | - Santosh K Patnaik
- Department of Thoracic Surgery, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Frank Zhang
- Giesel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Takashi Ishikawa
- Department of Breast Surgery and Oncology, Tokyo Medical University, Tokyo, Japan
| | - Kazuaki Takabe
- Department of Breast Surgery, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA. .,Department of Breast Surgery and Oncology, Tokyo Medical University, Tokyo, Japan. .,Department of Surgery, Jacobs School of Medicine and Biomedical Sciences, State University of New York, Buffalo, NY, USA. .,Department of Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan. .,Department of Surgery, Yokohama City University, Yokohama, Japan.
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16
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Cummings KJ, Becich MJ, Blackley DJ, Deapen D, Harrison R, Hassan R, Henley SJ, Hesdorffer M, Horton DK, Mazurek JM, Pass HI, Taioli E, Wu XC, Zauderer MG, Weissman DN. Workshop summary: Potential usefulness and feasibility of a US National Mesothelioma Registry. Am J Ind Med 2020; 63:105-114. [PMID: 31743489 PMCID: PMC7427840 DOI: 10.1002/ajim.23062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/10/2019] [Accepted: 10/10/2019] [Indexed: 01/29/2023]
Abstract
The burden and prognosis of malignant mesothelioma in the United States have remained largely unchanged for decades, with approximately 3200 new cases and 2400 deaths reported annually. To address care and research gaps contributing to poor outcomes, in March of 2019 the Mesothelioma Applied Research Foundation convened a workshop on the potential usefulness and feasibility of a national mesothelioma registry. The workshop included formal presentations by subject matter experts and a moderated group discussion. Workshop participants identified top priorities for a registry to be (a) connecting patients with high-quality care and clinical trials soon after diagnosis, and (b) making useful data and biospecimens available to researchers in a timely manner. Existing databases that capture mesothelioma cases are limited by factors such as delays in reporting, deidentification, and lack of exposure information critical to understanding as yet unrecognized causes of disease. National disease registries for amyotrophic lateral sclerosis (ALS) in the United States and for mesothelioma in other countries, provide examples of how a registry could be structured to meet the needs of patients and the scientific community. Small-scale pilot initiatives should be undertaken to validate methods for rapid case identification, develop procedures to facilitate patient access to guidelines-based standard care and investigational therapies, and explore approaches to data sharing with researchers. Ultimately, federal coordination and funding will be critical to the success of a National Mesothelioma Registry in improving mesothelioma outcomes and preventing future cases of this devastating disease.
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Affiliation(s)
- Kristin J. Cummings
- Respiratory Health Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, West Virginia
| | - Michael J. Becich
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - David J. Blackley
- Respiratory Health Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, West Virginia
| | - Dennis Deapen
- Los Angeles Cancer Surveillance Program, Department of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, California
| | - Robert Harrison
- Occupational Health Branch, California Department of Public Health, Richmond, California
| | - Raffit Hassan
- Thoracic and GI Malignancies Branch, National Cancer Institute, Bethesda, Maryland
| | - S. Jane Henley
- Division of Cancer Prevention and Control, National Center for Chronic Disease Prevention and Health Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Mary Hesdorffer
- Mesothelioma Applied Research Foundation, Washington, District of Columbia
| | - D. Kevin Horton
- Division of Toxicology and Human Health Sciences, Agency for Toxic Substances and Disease Registry, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Jacek M. Mazurek
- Respiratory Health Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, West Virginia
| | - Harvey I. Pass
- Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York
| | - Emanuela Taioli
- Institute for Translational Epidemiology and Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Xiao-Cheng Wu
- Louisiana Tumor Registry, Department of Epidemiology, School of Public Health, Louisiana State University Health Sciences Center, New Orleans, Louisiana
| | - Marjorie G. Zauderer
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David N. Weissman
- Respiratory Health Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, West Virginia
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17
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Mudaranthakam DP, Shergina E, Park M, Thompson J, Streeter D, Hu J, Wick J, Gajewski B, Koestler DC, Godwin AK, Jensen RA, Mayo MS. Optimizing Retrieval of Biospecimens Using the Curated Cancer Clinical Outcomes Database (C3OD). Cancer Inform 2019; 18:1176935119886831. [PMID: 31798300 PMCID: PMC6864036 DOI: 10.1177/1176935119886831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 10/15/2019] [Indexed: 11/16/2022] Open
Abstract
To fully support their role in translational and personalized medicine, biorepositories and biobanks must continue to advance the annotation of their biospecimens with robust clinical and laboratory data. Translational research and personalized medicine require well-documented and up-to-date information, but the infrastructure used to support biorepositories and biobanks can easily be out of sync with the host institution. To assist researchers and provide them with accurate pathological, epidemiological, and bio-molecular data, the Biospecimen Repository Core Facility (BRCF) at the University of Kansas Medical Center (KUMC) merges data from medical records, the tumor registry, and pathology reports using the Curated Cancer Clinical Outcomes Database (C3OD). In this report, we describe the utilization of C3OD to optimally retrieve and dispense biospecimen samples using these 3 data sources and demonstrate how C3OD greatly increases the efficiency of obtaining biospecimen samples for the researchers.
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Affiliation(s)
- Dinesh Pal Mudaranthakam
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS, USA.,University of Kansas Cancer Center, Kansas City, KS, USA
| | - Elena Shergina
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS, USA
| | - Michele Park
- University of Kansas Cancer Center, Kansas City, KS, USA
| | - Jeffrey Thompson
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS, USA.,University of Kansas Cancer Center, Kansas City, KS, USA
| | - David Streeter
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS, USA.,University of Kansas Cancer Center, Kansas City, KS, USA
| | - Jinxiang Hu
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS, USA.,University of Kansas Cancer Center, Kansas City, KS, USA
| | - Jo Wick
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS, USA.,University of Kansas Cancer Center, Kansas City, KS, USA
| | - Byron Gajewski
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS, USA.,University of Kansas Cancer Center, Kansas City, KS, USA
| | - Devin C Koestler
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS, USA.,University of Kansas Cancer Center, Kansas City, KS, USA
| | | | - Roy A Jensen
- University of Kansas Cancer Center, Kansas City, KS, USA
| | - Matthew S Mayo
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS, USA.,University of Kansas Cancer Center, Kansas City, KS, USA
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Asaoka M, Ishikawa T, Takabe K, Patnaik SK. APOBEC3-Mediated RNA Editing in Breast Cancer is Associated with Heightened Immune Activity and Improved Survival. Int J Mol Sci 2019; 20:E5621. [PMID: 31717692 PMCID: PMC6888598 DOI: 10.3390/ijms20225621] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 11/07/2019] [Accepted: 11/08/2019] [Indexed: 12/15/2022] Open
Abstract
APOBEC3 enzymes contribute significantly to DNA mutagenesis in cancer. These enzymes are also capable of converting C bases at specific positions of RNAs to U. However, the prevalence and significance of this C-to-U RNA editing in any cancer is currently unknown. We developed a bioinformatics workflow to determine RNA editing levels at known APOBEC3-mediated RNA editing sites using exome and mRNA sequencing data of 1040 breast cancer tumors. Although reliable editing determinations were limited due to sequencing depth, editing was observed in both tumor and adjacent normal tissues. For 440 sites (411 genes), editing was determinable for ≥5 tumors, with editing occurring in 0.6%-100% of tumors (mean 20%, SD 14%) at an average level of 0.6%-20% (mean 7%, SD 4%). Compared to tumors with low RNA editing, editing-high tumors had enriched expression of immune-related gene sets, and higher T cell and M1 macrophage infiltration, B and T cell receptor diversity, and immune cytolytic activity. Concordant with this, patients with increased RNA editing in tumors had better disease- and progression-free survivals (hazard ratio = 1.67-1.75, p < 0.05). Our study identifies that APOBEC3-mediated RNA editing occurs in breast cancer tumors and is positively associated with elevated immune activity and improved survival.
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Affiliation(s)
- Mariko Asaoka
- Department of Breast Surgery, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
- Department of Breast Surgery and Oncology, Tokyo Medical University, Tokyo 160-8402, Japan
| | - Takashi Ishikawa
- Department of Breast Surgery and Oncology, Tokyo Medical University, Tokyo 160-8402, Japan
| | - Kazuaki Takabe
- Department of Breast Surgery, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
- Department of Breast Surgery and Oncology, Tokyo Medical University, Tokyo 160-8402, Japan
- Department of Surgery, Jacobs School of Medicine and Biomedical Sciences, State University of New York, Buffalo, NY 14263, USA
- Department of Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
- Department of Surgery, Yokohama City University, Yokohama 236-0004, Japan
| | - Santosh K. Patnaik
- Department of Surgery, Jacobs School of Medicine and Biomedical Sciences, State University of New York, Buffalo, NY 14263, USA
- Department of Thoracic Surgery, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
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19
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Linkov F, Silverstein JC, Davis M, Crocker B, Hao D, Schneider A, Schwenk M, Winters S, Zelnis J, Lee AV, Becich MJ. Integration of Cancer Registry Data into the Text Information Extraction System: Leveraging the Structured Data Import Tool. J Pathol Inform 2018; 9:47. [PMID: 30662793 PMCID: PMC6319041 DOI: 10.4103/jpi.jpi_38_18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/26/2018] [Indexed: 01/18/2023] Open
Abstract
Introduction/Background Cancer registries in the US collect timely and systematic data on new cancer cases, extent of disease, staging, biomarker status, treatment, survival, and mortality of cancer cases. Existing methodologies for accessing local cancer registry data for research are time-consuming and often rely on the manual merging of data by staff registrars. In addition, existing registries do not provide direct access to these data nor do they routinely provide linkage to discrete electronic health record (EHR) data, reports, or imaging data. Automation of such linkage can provide an impressive data resource and make valuable data available for translational cancer research. Methods The UPMC Network Cancer Registry collects highly structured, longitudinal data on all reportable cancer patients, from the point of the diagnosis throughout treatment and follow-up/outcomes. Using commercial registry software, we collect data in compliance with standards governed by the North American Association of Central Cancer Registries. This standardization ensures that the data are highly structured with standard coding and collection methods, which support data exchange among central cancer registries and the Centers for Disease Control and Prevention. Results At the UPMC Hillman Cancer Center and University of Pittsburgh, we explored the feasibility of linking this well-curated, structured cancer registry data with unstructured text (i.e., pathology and radiology reports), using the Text Information Extraction System (TIES). We used the TIES platform to integrate breast cancer cases from the UPMC Network Cancer Registry system and then combine these data with other EHR data as a pilot use case that can be replicated for other cancers. Conclusions As a result of this integration, we now have a single searchable repository of information for breast cancer patients from the UPMC registry, combined with their pathology and radiology reports. The system that we developed is easily scalable to other health systems and cancer centers.
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Affiliation(s)
- Faina Linkov
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jonathan C Silverstein
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Michael Davis
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Brenda Crocker
- UPMC Hillman Cancer Center Information Services, Pittsburgh, Pennsylvania, USA
| | - Degan Hao
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | | | - Melissa Schwenk
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Sharon Winters
- UPMC Network Cancer Registry, Pittsburgh, Pennsylvania, USA
| | - Joyce Zelnis
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Adrian V Lee
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, The Institute for Precision Medicine, Pittsburgh, Pennsylvania, USA
| | - Michael J Becich
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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Xie F, Lee J, Munoz-Plaza CE, Hahn EE, Chen W. Application of Text Information Extraction System for Real-Time Cancer Case Identification in an Integrated Healthcare Organization. J Pathol Inform 2017; 8:48. [PMID: 29416911 PMCID: PMC5760847 DOI: 10.4103/jpi.jpi_55_17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/01/2017] [Indexed: 12/29/2022] Open
Abstract
Background: Surgical pathology reports (SPR) contain rich clinical diagnosis information. The text information extraction system (TIES) is an end-to-end application leveraging natural language processing technologies and focused on the processing of pathology and/or radiology reports. Methods: We deployed the TIES system and integrated SPRs into the TIES system on a daily basis at Kaiser Permanente Southern California. The breast cancer cases diagnosed in December 2013 from the Cancer Registry (CANREG) were used to validate the performance of the TIES system. The National Cancer Institute Metathesaurus (NCIM) concept terms and codes to describe breast cancer were identified through the Unified Medical Language System Terminology Service (UTS) application. The identified NCIM codes were used to search for the coded SPRs in the back-end datastore directly. The identified cases were then compared with the breast cancer patients pulled from CANREG. Results: A total of 437 breast cancer concept terms and 14 combinations of “breast“and “cancer“ terms were identified from the UTS application. A total of 249 breast cancer cases diagnosed in December 2013 was pulled from CANREG. Out of these 249 cases, 241 were successfully identified by the TIES system from a total of 457 reports. The TIES system also identified an additional 277 cases that were not part of the validation sample. Out of the 277 cases, 11% were determined as highly likely to be cases after manual examinations, and 86% were in CANREG but were diagnosed in months other than December of 2013. Conclusions: The study demonstrated that the TIES system can effectively identify potential breast cancer cases in our care setting. Identified potential cases can be easily confirmed by reviewing the corresponding annotated reports through the front-end visualization interface. The TIES system is a great tool for identifying potential various cancer cases in a timely manner and on a regular basis in support of clinical research studies.
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Affiliation(s)
- Fagen Xie
- Department of Research and Evaluation, Kaiser Permanente Southern California Medical Group, Pasadena, CA, USA
| | - Janet Lee
- Department of Research and Evaluation, Kaiser Permanente Southern California Medical Group, Pasadena, CA, USA
| | - Corrine E Munoz-Plaza
- Department of Research and Evaluation, Kaiser Permanente Southern California Medical Group, Pasadena, CA, USA
| | - Erin E Hahn
- Department of Research and Evaluation, Kaiser Permanente Southern California Medical Group, Pasadena, CA, USA
| | - Wansu Chen
- Department of Research and Evaluation, Kaiser Permanente Southern California Medical Group, Pasadena, CA, USA
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21
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Kelly SM, Wiehagen LT, Schumacher PE, Dhir R. Methods to Improve Sustainability of a Large Academic Biorepository. Biopreserv Biobank 2016; 15:31-36. [PMID: 27860489 DOI: 10.1089/bio.2016.0076] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This article discusses the evolution of the University of Pittsburgh (UPitt) Health Sciences Tissue Bank (HSTB) operation and how it has successfully positioned itself, manages to sustain its value, and remains viable in today's research landscape. We describe the various components of our biobanking operation, which are valued by our researchers, thus leading to sustainability for our biorepository. Operating within the infrastructure of a large academic university, we have access to the most cutting-edge database resources for collecting, tracking, and annotating thousands of specimens. We are constantly improving upon our ability to provide real-time longitudinal follow-up data for our collections, thus providing researchers with valuable, highly annotated research specimens. We believe the combination of all that is described within this article helps to create a biobank that will remain sustainable well into the future.
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Affiliation(s)
- Susan M Kelly
- 1 Health Sciences Tissue Bank, University of Pittsburgh Schools of the Health Sciences , Pittsburgh, Pennsylvania
| | - Luke T Wiehagen
- 1 Health Sciences Tissue Bank, University of Pittsburgh Schools of the Health Sciences , Pittsburgh, Pennsylvania
| | - Philip E Schumacher
- 1 Health Sciences Tissue Bank, University of Pittsburgh Schools of the Health Sciences , Pittsburgh, Pennsylvania
| | - Rajiv Dhir
- 2 Department of Pathology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania
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Hochheiser H, Castine M, Harris D, Savova G, Jacobson RS. An information model for computable cancer phenotypes. BMC Med Inform Decis Mak 2016; 16:121. [PMID: 27629872 PMCID: PMC5024416 DOI: 10.1186/s12911-016-0358-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 09/01/2016] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Standards, methods, and tools supporting the integration of clinical data and genomic information are an area of significant need and rapid growth in biomedical informatics. Integration of cancer clinical data and cancer genomic information poses unique challenges, because of the high volume and complexity of clinical data, as well as the heterogeneity and instability of cancer genome data when compared with germline data. Current information models of clinical and genomic data are not sufficiently expressive to represent individual observations and to aggregate those observations into longitudinal summaries over the course of cancer care. These models are acutely needed to support the development of systems and tools for generating the so called clinical "deep phenotype" of individual cancer patients, a process which remains almost entirely manual in cancer research and precision medicine. METHODS Reviews of existing ontologies and interviews with cancer researchers were used to inform iterative development of a cancer phenotype information model. We translated a subset of the Fast Healthcare Interoperability Resources (FHIR) models into the OWL 2 Description Logic (DL) representation, and added extensions as needed for modeling cancer phenotypes with terms derived from the NCI Thesaurus. Models were validated with domain experts and evaluated against competency questions. RESULTS The DeepPhe Information model represents cancer phenotype data at increasing levels of abstraction from mention level in clinical documents to summaries of key events and findings. We describe the model using breast cancer as an example, depicting methods to represent phenotypic features of cancers, tumors, treatment regimens, and specific biologic behaviors that span the entire course of a patient's disease. CONCLUSIONS We present a multi-scale information model for representing individual document mentions, document level classifications, episodes along a disease course, and phenotype summarization, linking individual observations to high-level summaries in support of subsequent integration and analysis.
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Affiliation(s)
- Harry Hochheiser
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, 5607 Baum Boulevard, Rm 523, Pittsburgh, 15206-3701, PA, USA. .,Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Melissa Castine
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, 5607 Baum Boulevard, Rm 523, Pittsburgh, 15206-3701, PA, USA
| | - David Harris
- Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Guergana Savova
- Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Rebecca S Jacobson
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, 5607 Baum Boulevard, Rm 523, Pittsburgh, 15206-3701, PA, USA.,Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA, USA.,University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
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23
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Rosenstein BS, Capala J, Efstathiou JA, Hammerbacher J, Kerns SL, Kong FMS, Ostrer H, Prior FW, Vikram B, Wong J, Xiao Y. How Will Big Data Improve Clinical and Basic Research in Radiation Therapy? Int J Radiat Oncol Biol Phys 2016; 95:895-904. [PMID: 26797542 PMCID: PMC4864183 DOI: 10.1016/j.ijrobp.2015.11.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 11/03/2015] [Accepted: 11/04/2015] [Indexed: 12/25/2022]
Abstract
Historically, basic scientists and clinical researchers have transduced reality into data so that they might explain or predict the world. Because data are fundamental to their craft, these investigators have been on the front lines of the Big Data deluge in recent years. Radiotherapy data are complex and longitudinal data sets are frequently collected to track both tumor and normal tissue response to therapy. As basic, translational and clinical investigators explore with increasingly greater depth the complexity of underlying disease processes and treatment outcomes, larger sample populations are required for research studies and greater quantities of data are being generated. In addition, well-curated research and trial data are being pooled in public data repositories to support large-scale analyses. Thus, the tremendous quantity of information produced in both basic and clinical research in radiation therapy can now be considered as having entered the realm of Big Data.
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Affiliation(s)
- Barry S Rosenstein
- Departments of Radiation Oncology, Genetics and Genomic Sciences, Dermatology and Preventive Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Radiation Oncology, New York University School of Medicine, New York, New York.
| | - Jacek Capala
- Clinical Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Jason A Efstathiou
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jeff Hammerbacher
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Sarah L Kerns
- Department of Radiation Oncology, University of Rochester Medical Center, Rochester, New York
| | - Feng-Ming Spring Kong
- Department of Radiation Oncology, GRU Cancer Center and Medical College of Georgia, Georgia Regents University, Augusta, Georgia
| | - Harry Ostrer
- Departments of Pathology and Pediatrics, Albert Einstein College of Medicine, Bronx, New York
| | - Fred W Prior
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Bhadrasain Vikram
- Clinical Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - John Wong
- Department of Radiation Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ying Xiao
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, Pennsylvania
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