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331 Reusing EHR Phenotyping Algorithms in Practice: Developing the Colorado Diabetes EHR Research Repository (CODER)
OBJECTIVES/GOALS: The rates of computational phenotyping algorithm reuse across health systems are low, leading to a proliferation of algorithms for the same trait. We propose a framework for reusing computational phenotyping algorithms and describe the real-world deployment of this framework for th...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Cambridge University Press
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10129663/ http://dx.doi.org/10.1017/cts.2023.378 |
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author | Wilson, Melissa P. Mayer, David A. Rasmussen, Luke V. Khanal, Pramod Nuriyeva, Maryam McRae, Michael Raghavan, Sridharan Wiley, Laura K. |
author_facet | Wilson, Melissa P. Mayer, David A. Rasmussen, Luke V. Khanal, Pramod Nuriyeva, Maryam McRae, Michael Raghavan, Sridharan Wiley, Laura K. |
author_sort | Wilson, Melissa P. |
collection | PubMed |
description | OBJECTIVES/GOALS: The rates of computational phenotyping algorithm reuse across health systems are low, leading to a proliferation of algorithms for the same trait. We propose a framework for reusing computational phenotyping algorithms and describe the real-world deployment of this framework for the development of the Colorado Diabetes EHR Research Repository. METHODS/STUDY POPULATION: The novel phenotype reuse framework consists of 4 steps: select algorithms that are appropriate for reuse by assessing whether they are fit for purpose; extend the algorithm to account for changes in data and care practice standards; localize the algorithm to use local database standards and terminologies; optimize the algorithm by applying a data driven approach to achieve the desired local performance. To identify individuals with type 1 diabetes (T1D) or type 2 diabetes (T2D), we selected and implemented T2D algorithms in a cohort of adults with any diabetes or pre-diabetes related diagnosis code, medication, or abnormal glucose-related laboratory test in the clinical data warehouse for UCHealth and the University of Colorado. RESULTS/ANTICIPATED RESULTS: We included a total of 926,290 patients who were identified by initial filters. Patients were more likely to be female (53%), identify as non-Hispanic white (69%) and had a median age of 58 years (IQR: 41, 70). Implementation, extension, localization, & optimization through iterative chart review prioritized high sensitivity for all-cause diabetes and high specificity for T1D and T2D. Of the original cohort, 252,946 (27%) were identified by the all-cause diabetes algorithm. Of these 11,688 were identified as T1D and 135,588 as T2D. After optimization the all-cause diabetes algorithm had 88% sensitivity, 90% specificity, 74% positive predictive value (PPV), and 96% negative predictive value (NPV). Our algorithms for T1D and T2D had high specificity (100% and 99%, respectively) and PPV (100 and 96% respectively). DISCUSSION/SIGNIFICANCE: Developing computational phenotyping algorithms is expensive and time consuming, yet algorithm reuse is low due to a lack of practical approaches for reusing algorithms. We demonstrate application of a novel framework for algorithm reuse, yielding good alignment of algorithm performance with study goals for identifying individuals with diabetes. |
format | Online Article Text |
id | pubmed-10129663 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Cambridge University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-101296632023-04-26 331 Reusing EHR Phenotyping Algorithms in Practice: Developing the Colorado Diabetes EHR Research Repository (CODER) Wilson, Melissa P. Mayer, David A. Rasmussen, Luke V. Khanal, Pramod Nuriyeva, Maryam McRae, Michael Raghavan, Sridharan Wiley, Laura K. J Clin Transl Sci Precision Medicine/Health OBJECTIVES/GOALS: The rates of computational phenotyping algorithm reuse across health systems are low, leading to a proliferation of algorithms for the same trait. We propose a framework for reusing computational phenotyping algorithms and describe the real-world deployment of this framework for the development of the Colorado Diabetes EHR Research Repository. METHODS/STUDY POPULATION: The novel phenotype reuse framework consists of 4 steps: select algorithms that are appropriate for reuse by assessing whether they are fit for purpose; extend the algorithm to account for changes in data and care practice standards; localize the algorithm to use local database standards and terminologies; optimize the algorithm by applying a data driven approach to achieve the desired local performance. To identify individuals with type 1 diabetes (T1D) or type 2 diabetes (T2D), we selected and implemented T2D algorithms in a cohort of adults with any diabetes or pre-diabetes related diagnosis code, medication, or abnormal glucose-related laboratory test in the clinical data warehouse for UCHealth and the University of Colorado. RESULTS/ANTICIPATED RESULTS: We included a total of 926,290 patients who were identified by initial filters. Patients were more likely to be female (53%), identify as non-Hispanic white (69%) and had a median age of 58 years (IQR: 41, 70). Implementation, extension, localization, & optimization through iterative chart review prioritized high sensitivity for all-cause diabetes and high specificity for T1D and T2D. Of the original cohort, 252,946 (27%) were identified by the all-cause diabetes algorithm. Of these 11,688 were identified as T1D and 135,588 as T2D. After optimization the all-cause diabetes algorithm had 88% sensitivity, 90% specificity, 74% positive predictive value (PPV), and 96% negative predictive value (NPV). Our algorithms for T1D and T2D had high specificity (100% and 99%, respectively) and PPV (100 and 96% respectively). DISCUSSION/SIGNIFICANCE: Developing computational phenotyping algorithms is expensive and time consuming, yet algorithm reuse is low due to a lack of practical approaches for reusing algorithms. We demonstrate application of a novel framework for algorithm reuse, yielding good alignment of algorithm performance with study goals for identifying individuals with diabetes. Cambridge University Press 2023-04-24 /pmc/articles/PMC10129663/ http://dx.doi.org/10.1017/cts.2023.378 Text en © The Association for Clinical and Translational Science 2023 https://creativecommons.org/licenses/by-nc-nd/4.0/This is an Open Access article, distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives licence (https://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is unaltered and is properly cited. The written permission of Cambridge University Press must be obtained for commercial re-use or in order to create a derivative work. |
spellingShingle | Precision Medicine/Health Wilson, Melissa P. Mayer, David A. Rasmussen, Luke V. Khanal, Pramod Nuriyeva, Maryam McRae, Michael Raghavan, Sridharan Wiley, Laura K. 331 Reusing EHR Phenotyping Algorithms in Practice: Developing the Colorado Diabetes EHR Research Repository (CODER) |
title | 331 Reusing EHR Phenotyping Algorithms in Practice: Developing the Colorado Diabetes EHR Research Repository (CODER) |
title_full | 331 Reusing EHR Phenotyping Algorithms in Practice: Developing the Colorado Diabetes EHR Research Repository (CODER) |
title_fullStr | 331 Reusing EHR Phenotyping Algorithms in Practice: Developing the Colorado Diabetes EHR Research Repository (CODER) |
title_full_unstemmed | 331 Reusing EHR Phenotyping Algorithms in Practice: Developing the Colorado Diabetes EHR Research Repository (CODER) |
title_short | 331 Reusing EHR Phenotyping Algorithms in Practice: Developing the Colorado Diabetes EHR Research Repository (CODER) |
title_sort | 331 reusing ehr phenotyping algorithms in practice: developing the colorado diabetes ehr research repository (coder) |
topic | Precision Medicine/Health |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10129663/ http://dx.doi.org/10.1017/cts.2023.378 |
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