Next-generation phenotyping: introducing phecodeX for enhanced discovery research in medical phenomics
Megan M. Shuey, William W. Stead, Ida Aka, April Barnado, Julie A. Bastarache, Elly Brokamp, Meredith S. Campbell, Robert J. Carroll, Jeffrey A Goldstein, Adam Lewis, Beth A. Malow, Jonathan D. Mosley, Travis Osterman, Dolly Ann Padovani-Claudio, Andrea H. Ramirez, Dan M. Roden, Bryce Schuler, Edward D. Siew, Jennifer M. S. Sucre, Isaac Thomsen, Rory J. Tinker, Sara L. Van Driest, Colin G. Walsh, Jeremy L. Warner, Quinn S. Wells, Lee Wheless, Lisa Bastarache
Abstract
MOTIVATION: Phecodes are widely used and easily adapted phenotypes based on International Classification of Diseases codes. The current version of phecodes (v1.2) was designed primarily to study common/complex diseases diagnosed in adults; however, there are numerous limitations in the codes and their structure. RESULTS: 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 https://github.com/PheWAS/phecodeX.