Developing and Evaluating Mappings of ICD-10 and ICD-10-CM codes to Phecodes

Wu, P.; Gifford, A.; Meng, X.; Li, X.; Campbell, H.; Varley, T.; Zhao, J.; Bastarache, L.; Denny, J. C.; Theodoratou, E.; Wei, W.-Q.

doi:10.1101/462077

bioRxiv · 10.1101/462077

Developing and Evaluating Mappings of ICD-10 and ICD-10-CM codes to Phecodes

Wu, P.·Gifford, A.·Meng, X.·Li, X.·Campbell, H.·Varley, T.·Zhao, J.·Bastarache, L.·Denny, J. C.·Theodoratou, E.·Wei, W.-Q.

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Abstract

BackgroundThe PheCode system was built upon the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) for phenome-wide association studies (PheWAS) in the electronic health record (EHR).\n\nObjectiveHere, we present our work on the development and evaluation of maps from ICD-10 and ICD-10-CM codes to PheCodes.\n\nMethodsWe mapped ICD-10 and ICD-10-CM codes to PheCodes using a number of methods and resources, such as concept relationships and explicit mappings from the Unified Medical Language System (UMLS), Observational Health Data Sciences and Informatics (OHDSI), Systematized Nomenclature of Medicine - Clinical Terms (SNOMED CT), and National Library of Medicine (NLM). We assessed the coverage of the maps in two databases: Vanderbilt University Medical Center (VUMC) using ICD-10-CM and the UK Biobank (UKBB) using ICD-10. We assessed the fidelity of the ICD-10-CM map in comparison to the gold-standard ICD-9-CM[->]PheCode map by investigating phenotype reproducibility and conducting a PheWAS.\n\nResultsWe mapped >75% of ICD-10-CM and ICD-10 codes to PheCodes. Of the unique codes observed in the VUMC (ICD-10-CM) and UKBB (ICD-10) cohorts, >90% were mapped to PheCodes. We observed 70-75% reproducibility for chronic diseases and <10% for an acute disease. A PheWAS with a lipoprotein(a) (LPA) genetic variant, rs10455872, using the ICD-9-CM and ICD-10-CM maps replicated two genotype-phenotype associations with similar effect sizes: coronary atherosclerosis (ICD-9-CM: P < .001, OR = 1.60 vs. ICD-10-CM: P < .001, OR = 1.60) and with chronic ischemic heart disease (ICD-9-CM: P < .001, OR = 1.5 vs. ICD-10-CM: P < .001, OR = 1.47).\n\nConclusionsThis study introduces the initial \"beta\" versions of ICD-10 and ICD-10-CM to PheCode maps that will enable researchers to leverage accumulated ICD-10 and ICD-10-CM data for high-throughput PheWAS in the EHR.

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Wu, P., Gifford, A., Meng, X., Li, X., Campbell, H., Varley, T., Zhao, J., Bastarache, L., Denny, J. C., Theodoratou, E., Wei, W.-Q.. 2018-11-05. Developing and Evaluating Mappings of ICD-10 and ICD-10-CM codes to Phecodes. https://doi.org/10.1101/462077

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