TY  - JOUR
AU  - Wu, Patrick
AU  - Gifford, Aliya
AU  - Meng, Xiangrui
AU  - Li, Xue
AU  - Campbell, Harry
AU  - Varley, Tim
AU  - Zhao, Juan
AU  - Carroll, Robert
AU  - Bastarache, Lisa
AU  - Denny, Joshua C
AU  - Theodoratou, Evropi
AU  - Wei, Wei-Qi
PY  - 2019
DA  - 2019/11/29
TI  - Mapping ICD-10 and ICD-10-CM Codes to Phecodes: Workflow Development and Initial Evaluation
JO  - JMIR Med Inform
SP  - e14325
VL  - 7
IS  - 4
KW  - electronic health record
KW  - genome-wide association study
KW  - phenome-wide association study
KW  - phenotyping
KW  - medical informatics applications
KW  - data science
AB  - 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) using the electronic health record (EHR). Objective: The goal of this paper was to develop and perform an initial evaluation of maps from the International Classification of Diseases, 10th Revision (ICD-10) and the International Classification of Diseases, 10th Revision, Clinical Modification (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 Centers for Medicare & Medicaid Services, the Unified Medical Language System, Observational Health Data Sciences and Informatics, Systematized Nomenclature of Medicine-Clinical Terms, and the National Library of Medicine. 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 and ICD-10-CM codes to phecodes. Of the unique codes observed in the UKBB (ICD-10) and VUMC (ICD-10-CM) cohorts, >90% were mapped to phecodes. We observed 70-75% reproducibility for chronic diseases and <10% for an acute disease for phenotypes sourced from the ICD-10-CM phecode map. Using the ICD-9-CM and ICD-10-CM maps, we conducted a PheWAS with a Lipoprotein(a) genetic variant, rs10455872, which replicated two known genotype-phenotype associations with similar effect sizes: coronary atherosclerosis (ICD-9-CM: P<.001; odds ratio (OR) 1.60 [95% CI 1.43-1.80] vs ICD-10-CM: P<.001; OR 1.60 [95% CI 1.43-1.80]) and chronic ischemic heart disease (ICD-9-CM: P<.001; OR 1.56 [95% CI 1.35-1.79] vs ICD-10-CM: P<.001; OR 1.47 [95% CI 1.22-1.77]). Conclusions: This study introduces the beta versions of ICD-10 and ICD-10-CM to phecode maps that enable researchers to leverage accumulated ICD-10 and ICD-10-CM data for PheWAS in the EHR. 
SN  - 2291-9694
UR  - http://medinform.jmir.org/2019/4/e14325/
UR  - https://doi.org/10.2196/14325
UR  - http://www.ncbi.nlm.nih.gov/pubmed/31553307
DO  - 10.2196/14325
ID  - info:doi/10.2196/14325
ER  -