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Identifying Cases of Spinal Cord Injury/Disorder in an Ontario Primary Care Electronic Medical Record Database

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Identifying Cases of Spinal Cord Injury/Disorder in an Ontario Primary Care Electronic Medical Record Database Identifying Cases of Spinal Cord Injury/Disorder in an Ontario Primary Care Electronic Medical Record Database by John Dean Shepherd A thesis submitted in conformity with the requirements for the degree of Master of Science Rehabilitation Sciences Institute University of Toronto © Copyright by John Shepherd 2020 Identifying Cases of Spinal Cord Injury/Disorder in an Ontario Primary Care Electronic Medical Record Database John Shepherd Master of Science Rehabilitation Sciences Institute University of Toronto 2020 Abstract Currently, little health system information exists on the longitudinal course of spinal cord injury (SCI). The increasing availability of information from electronic medical records (EMR) offers an opportunity to fill this gap. An initial keyword search of all eligible records in a database of primary care EMR in Ontario, Canada, was conducted to identify possible cases of SCI. A random sample of possible cases was selected (n=803) and reviewed using a structured chart review process. 126 validated cases of SCI were identified and this reference standard cohort was used to develop and test potential algorithms. The optimal algorithm uses a combination of free-text keywords and ICD-9 codes, with a sensitivity of 70.6%, a positive predictive value of 89.9%, and an F-score of 79.1%. This cohort can be linked with administrative data to study longitudinally the health status and health care utilization of this population. ii Acknowledgments The analysis documented in this thesis was the work of many people and I am grateful to all those who gave me support and guidance, and from whom I have learned so much. First and foremost, I owe a tremendous debt of gratitude to my supervisor, Dr. Susan Jaglal. She has been unfailing in her support at all times and without peer as a mentor. She has always encouraged me to follow my research interests and has equipped me with the tools to do so effectively. My committee members, Drs. Cathy Craven, Rahim Moineddin, and Karen Tu, have been extremely generous with their time and guidance, and provided many insightful suggestions and comments. I was fortunate to be able to build on the strong foundation of their prior work and the methods they shared with me. My work at ICES was supported by a very welcoming and helpful team including Jin Park, Bogdan Pinzaru, and Dinah Thorpe. I am particularly grateful to Senior Analyst Jacqueline Young, who skillfully and patiently guided me through the analytical process, and whose work is evident particularly in the results section of this thesis. I am also fortunate to have extremely supportive labmates and colleagues; I want to recognize in particular Drs. Sonya Allin, Leslie Carlin, and Sarah Munce, who each gave very generously of their time and expertise to provide feedback and suggestions on my drafts and to encourage me through the writing process. Finally, I want to thank my family: my parents Glen and Eleanor, my sister Elizabeth and her husband Johan, and my nieces Sanna and Alma; they have been, since long before the beginning of this project right through to the end, a source of encouragement, support, and joy. iii Table of Contents Acknowledgments .......................................................................................................................... iii Table of Contents ........................................................................................................................... iv List of Tables ................................................................................................................................ vii List of Figures ................................................................................................................................ ix List of Appendices ...........................................................................................................................x Introduction .................................................................................................................................1 Background .................................................................................................................................3 2.1 Spinal Cord Injury as a Diagnostic Entity ...........................................................................3 2.1.1 Overview ..................................................................................................................3 2.1.2 Definition of SCI ......................................................................................................4 2.1.3 Traumatic and Non-traumatic SCI ...........................................................................6 2.1.4 Classification of SCI ................................................................................................8 2.2 Frequency of Spinal Cord Injury .........................................................................................8 2.2.1 Recent Studies of TSCI Incidence .........................................................................10 2.2.2 Prevalence of SCI ..................................................................................................10 2.2.3 Canadian Estimates of SCI Incidence and Prevalence ..........................................12 2.3 Longitudinal Patterns of Chronic SCI ................................................................................13 2.3.1 Individual Burden and Healthcare System Impact of Chronic SCI .......................13 2.3.2 Longitudinal Datasets in Chronic SCI ...................................................................14 2.3.3 Administrative Data Studies of SCI .......................................................................16 2.4 Using EMR Data for Research ..........................................................................................17 2.4.1 Primary Care EMR Databases ...............................................................................17 2.4.2 Issues with Case Finding in EMRs ........................................................................18 2.4.3 Problem List Use and Reliability ...........................................................................19 2.4.4 Case Finding in EMRALD ....................................................................................20 iv 2.4.5 Case Finding in SCI ...............................................................................................21 2.4.6 Case Finding Criteria in NTSCI ............................................................................22 2.5 Thesis Objectives ...............................................................................................................22 Methods .....................................................................................................................................24 3.1 Overview ............................................................................................................................24 3.1.1 Three-stage Case Identification/Algorithm Development Process ........................24 3.1.2 EMRALD Overview ..............................................................................................25 3.1.3 EMRALD Composition and Representativeness ...................................................25 3.1.4 Overview of EMRALD Charts ..............................................................................26 3.1.5 ICES Policies and Working Arrangements ............................................................27 3.1.6 Inclusion and Exclusion Criteria ............................................................................28 3.2 Stage 1—Keyword Search Strategy Development ............................................................28 3.2.1 Preliminary Chart Review: Round 1 ......................................................................29 3.2.2 Preliminary Chart Review: Round 2 ......................................................................29 3.2.3 Preliminary Chart Review: Round 3 ......................................................................30 3.2.4 Addition of NTSCI-Related Keywords from Literature ........................................31 3.3 Stage 2—Chart Review and Case Identification ...............................................................33 3.3.1 Considerations for Identification of Chronic SCI Cases ........................................33 3.3.2 Case Definition of Chronic SCI .............................................................................33 3.3.3 Chart Entries Used for Case Identification ............................................................35 3.3.4 Hierarchy of Evidence ...........................................................................................35 3.3.5 Developing a Reference Standard: Chart Review Process ....................................37 3.4 Stage 3—Algorithm Development ....................................................................................40 3.4.1 Keyword Analysis and Keyword Lists ..................................................................41 3.4.2 Other Algorithm Components Considered ............................................................43 3.4.3 Evaluating Algorithms ...........................................................................................44 v Results .......................................................................................................................................46 4.1 Stage 1—Keyword Search Strategy Development ............................................................46 4.1.1 Round 1 ..................................................................................................................46
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