Mapping ICD-10 and ICD-10-CM Codes to Phecodes: Workflow Development and Initial Evaluation

Patrick Wu, Aliya Gifford, Xiangrui Meng, Xue Li, Harry Campbell, Tim Varley, Juan Zhao, Robert Carroll, Lisa Bastarache, Joshua C Denny, Evropi Theodoratou, Wei-Qi Wei

Research output: Contribution to journalArticlepeer-review


BACKGROUND: The 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).

OBJECTIVE: Here, we present our work on the development and evaluation of maps from ICD-10 and ICD-10-CM codes to PheCodes.

METHODS: We 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.

RESULTS: We 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).

CONCLUSIONS: This 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.

Original languageEnglish
JournalJMIR Medical Informatics
Issue number4
Early online dateSep 2019
Publication statusE-pub ahead of print - Sep 2019

Fingerprint Dive into the research topics of 'Mapping ICD-10 and ICD-10-CM Codes to Phecodes: Workflow Development and Initial Evaluation'. Together they form a unique fingerprint.

Cite this