Next-Generation Phenotyping: Introducing PhecodeX for Enhanced Discovery Research in Medical Phenomics

Summary Phecodes are widely-used and easily adapted phenotypes based on International Classification of Diseases (ICD) codes. The current version of phecodes (v1.2) was designed primarily to study common/complex diseases diagnosed in adults. Here we present phecodeX, an expanded version of phecodes with a revised structure and 1,761 new codes. PhecodeX adds granularity to phenotypes in key disease domains that are under-represented in the current phecode structure-including infectious disease, pregnancy, congenital anomalies, and neonatology- and is a more robust representation of the medical phenome for global use in discovery research. Availability and implementation phecodeX is available at . Contact lisa.bastarache{at}vumc.org Supplementary information Supplemental Tables 1-4, Bastarache\_bioRxiv\_20220907.pdf WC-1999 ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work was supported by the National Library of Medicine (R01LM010685) and the National Human Genome Research Institute (R01HG012657). MMS was supported by National Institutes of Health (K12HD043483) ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes The presented software is available at: https://github.com/PheWAS/phecodeX.