Evaluating the impact of alternative phenotype definitions on incidence rates across a global data network

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  • dc.contributor.author Makadia, Rupa
  • dc.contributor.author Shoaibi, Azza
  • dc.contributor.author Rao, Gowtham A.
  • dc.contributor.author Ostropolets, Anna
  • dc.contributor.author Rijnbeek, Peter
  • dc.contributor.author Voss, Erica A.
  • dc.contributor.author Duarte Salles, Talita, 1985-
  • dc.contributor.author Ramírez Anguita, Juan Manuel
  • dc.contributor.author Mayer, Miguel Ángel, 1960-
  • dc.contributor.author Maljkovic, Filip
  • dc.contributor.author Denaxas, Spiros
  • dc.contributor.author Nyberg, Fredrik
  • dc.contributor.author Papez, Vaclav
  • dc.contributor.author Sena, Anthony G.
  • dc.contributor.author Alshammari, Thamir M.
  • dc.contributor.author Lai, Lana Y. H.
  • dc.contributor.author Haynes, Kevin
  • dc.contributor.author Suchard, Marc A.
  • dc.contributor.author Hripcsak, George
  • dc.contributor.author Ryan, Patrick B.
  • dc.date.accessioned 2024-10-22T06:23:04Z
  • dc.date.available 2024-10-22T06:23:04Z
  • dc.date.issued 2023
  • dc.description.abstract Objective: Developing accurate phenotype definitions is critical in obtaining reliable and reproducible background rates in safety research. This study aims to illustrate the differences in background incidence rates by comparing definitions for a given outcome. Materials and methods: We used 16 data sources to systematically generate and evaluate outcomes for 13 adverse events and their overall background rates. We examined the effect of different modifications (inpatient setting, standardization of code set, and code set changes) to the computable phenotype on background incidence rates. Results: Rate ratios (RRs) of the incidence rates from each computable phenotype definition varied across outcomes, with inpatient restriction showing the highest variation from 1 to 11.93. Standardization of code set RRs ranges from 1 to 1.64, and code set changes range from 1 to 2.52. Discussion: The modification that has the highest impact is requiring inpatient place of service, leading to at least a 2-fold higher incidence rate in the base definition. Standardization showed almost no change when using source code variations. The strength of the effect in the inpatient restriction is highly dependent on the outcome. Changing definitions from broad to narrow showed the most variability by age/gender/database across phenotypes and less than a 2-fold increase in rate compared to the base definition. Conclusion: Characterization of outcomes across a network of databases yields insights into sensitivity and specificity trade-offs when definitions are altered. Outcomes should be thoroughly evaluated prior to use for background rates for their plausibility for use across a global network.
  • dc.description.sponsorship This research was funded by the European Union’s Horizon 2020 research and innovation programme and EFPIA, European Health Data & Evidence Network (EHDEN) grant agreement number 806968. T.D.-S. acknowledges receiving financial support from the Instituto de Salud Carlos III (ISCIII; Miguel Servet 2021: CP21/00023).
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Makadia R, Shoaibi A, Rao GA, Ostropolets A, Rijnbeek PR, Voss EA, et al. Evaluating the impact of alternative phenotype definitions on incidence rates across a global data network. JAMIA Open. 2023 Nov 21;6(4):ooad096. DOI: 10.1093/jamiaopen/ooad096
  • dc.identifier.doi http://dx.doi.org/10.1093/jamiaopen/ooad096
  • dc.identifier.issn 2574-2531
  • dc.identifier.uri http://hdl.handle.net/10230/68283
  • dc.language.iso eng
  • dc.publisher Oxford University Press
  • dc.relation.ispartof JAMIA Open. 2023 Nov 21;6(4):ooad096
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/806968
  • dc.rights © The Author(s) 2023. Published by Oxford University Press on behalf of the American Medical Informatics Association. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by/4.0/
  • dc.subject.keyword Algorithms
  • dc.subject.keyword Electronic health record
  • dc.subject.keyword Incidence study
  • dc.subject.keyword Phenotype
  • dc.title Evaluating the impact of alternative phenotype definitions on incidence rates across a global data network
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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