Phenotype Phebruary 2025 Office Hours Phebruary 12th 2025
Youtube https://youtu.be/17UXeDIJWos
Full details OHDSI Phenotype Phebruary and workgroup updates - #73 by Gowtham_Rao
Executive Summary:
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Type 2 Diabetes Phenotype Development:
The group debated whether to define type 2 diabetes using diagnosis codes alone or by incorporating lab values and medication data. Emphasis was placed on balancing sensitivity (to capture as many cases as possible) with specificity (to avoid misclassification), particularly in relation to insulin use and alternate entry criteria. Multiple phenotype variants will be developed and compared using cohort diagnostics to determine the optimal approach. -
Diabetic Retinopathy Screening Cohort Design:
Discussion centered on designing a cohort that reflects the recurrent nature of diabetic retinopathy screening (typically recommended annually). The team weighed the benefits of indexing on the earliest screening event versus capturing all screening events over time. Key challenges include managing variable provider specialty data, reliance on specific CPT codes, and the potential need for custom SQL to integrate washout periods effectively. -
Antipsychotic Treatment Cohort and Censoring Strategy:
Strategies were discussed to isolate a monotherapy cohort by excluding patients with prior exposure to other antipsychotics and censoring those who switch treatments post-index. Although this approach helps maintain a clean cohort, concerns were raised about the risk of informative censoring, where treatment changes driven by clinical factors could bias the results. -
Technical Implementation in Atlas and Query Logic:
The technical discussion emphasized using the visit start date as the index for cohort entry, with conditions required to occur within the visit window. Given that condition end dates are often missing, the query logic defaults to using the condition start date. The group acknowledged that while standard Atlas functionality covers most needs, complex scenarios may require custom SQL adjustments. -
Naming Conventions and Infrastructure for the Phenotype Library:
To enhance consistency and discoverability, the group proposed standard naming conventions (e.g., prefixes like PP25 or F-25) for phenotype definitions. Integration with the Odyssey forums and GitHub was recommended to ensure clear clinical descriptions, facilitate collaboration, and maintain version control across the phenotype library. -
Project Coordination, Communication, and Next Steps:
The meeting concluded with plans for robust progress tracking through scheduled office hours and proactive outreach to study leads. Emphasis was placed on volunteer engagement, standardization of outputs, and ensuring that phenotype definitions are well-documented and aligned with the established infrastructure.
Overall, the workgroup’s collaborative effort aims to refine phenotype development by testing multiple definitions, addressing technical challenges, and ensuring clear communication and coordination among study leads and volunteers.