PMID- 31553307
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20240216
IS  - 2291-9694 (Print)
IS  - 2291-9694 (Electronic)
VI  - 7
IP  - 4
DP  - 2019 Nov 29
TI  - Mapping ICD-10 and ICD-10-CM Codes to Phecodes: Workflow Development and Initial 
      Evaluation.
PG  - e14325
LID - 10.2196/14325 [doi]
LID - e14325
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.
CI  - (c)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. Originally published in JMIR Medical Informatics 
      (http://medinform.jmir.org), 29.11.2019.
FAU - Wu, Patrick
AU  - Wu P
AUID- ORCID: 0000-0002-1437-6688
AD  - Department of Biomedical Informatics, Vanderbilt University Medical Center, 
      Nashville, TN, United States.
AD  - Medical Scientist Training Program, Vanderbilt University School of Medicine, 
      Nashville, TN, United States.
FAU - Gifford, Aliya
AU  - Gifford A
AUID- ORCID: 0000-0001-8931-8362
AD  - Department of Biomedical Informatics, Vanderbilt University Medical Center, 
      Nashville, TN, United States.
FAU - Meng, Xiangrui
AU  - Meng X
AUID- ORCID: 0000-0003-4889-4640
AD  - Centre for Global Health Research, Usher Institute of Population Health Sciences 
      and Informatics, The University of Edinburgh, Edinburgh, United Kingdom.
FAU - Li, Xue
AU  - Li X
AUID- ORCID: 0000-0001-6880-2577
AD  - Centre for Global Health Research, Usher Institute of Population Health Sciences 
      and Informatics, The University of Edinburgh, Edinburgh, United Kingdom.
FAU - Campbell, Harry
AU  - Campbell H
AUID- ORCID: 0000-0002-6169-6262
AD  - Centre for Global Health Research, Usher Institute of Population Health Sciences 
      and Informatics, The University of Edinburgh, Edinburgh, United Kingdom.
FAU - Varley, Tim
AU  - Varley T
AUID- ORCID: 0000-0002-6106-568X
AD  - Public Health and Intelligence Strategic Business Unit, National Services 
      Scotland, Edinburgh, United Kingdom.
FAU - Zhao, Juan
AU  - Zhao J
AUID- ORCID: 0000-0003-1429-0662
AD  - Department of Biomedical Informatics, Vanderbilt University Medical Center, 
      Nashville, TN, United States.
FAU - Carroll, Robert
AU  - Carroll R
AUID- ORCID: 0000-0003-3802-8183
AD  - Department of Biomedical Informatics, Vanderbilt University Medical Center, 
      Nashville, TN, United States.
FAU - Bastarache, Lisa
AU  - Bastarache L
AUID- ORCID: 0000-0003-3020-447X
AD  - Department of Biomedical Informatics, Vanderbilt University Medical Center, 
      Nashville, TN, United States.
FAU - Denny, Joshua C
AU  - Denny JC
AUID- ORCID: 0000-0002-3049-7332
AD  - Department of Biomedical Informatics, Vanderbilt University Medical Center, 
      Nashville, TN, United States.
AD  - Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 
      United States.
FAU - Theodoratou, Evropi
AU  - Theodoratou E
AUID- ORCID: 0000-0001-5887-9132
AD  - Centre for Global Health Research, Usher Institute of Population Health Sciences 
      and Informatics, The University of Edinburgh, Edinburgh, United Kingdom.
AD  - Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, 
      University of Edinburgh, Edinburgh, United Kingdom.
FAU - Wei, Wei-Qi
AU  - Wei WQ
AUID- ORCID: 0000-0003-4985-056X
AD  - Department of Biomedical Informatics, Vanderbilt University Medical Center, 
      Nashville, TN, United States.
LA  - eng
GR  - T15 LM007450/LM/NLM NIH HHS/United States
GR  - R01 LM010685/LM/NLM NIH HHS/United States
GR  - R01 HL133786/HL/NHLBI NIH HHS/United States
GR  - T32 GM007347/GM/NIGMS NIH HHS/United States
GR  - P50 GM115305/GM/NIGMS NIH HHS/United States
GR  - 22804/CRUK_/Cancer Research UK/United Kingdom
PT  - Journal Article
DEP - 20191129
PL  - Canada
TA  - JMIR Med Inform
JT  - JMIR medical informatics
JID - 101645109
PMC - PMC6911227
OTO - NOTNLM
OT  - data science
OT  - electronic health record
OT  - genome-wide association study
OT  - medical informatics applications
OT  - phenome-wide association study
OT  - phenotyping
COIS- Conflicts of Interest: None declared.
EDAT- 2019/09/26 06:00
MHDA- 2019/09/26 06:01
PMCR- 2019/11/29
CRDT- 2019/09/26 06:00
PHST- 2019/04/09 00:00 [received]
PHST- 2019/09/24 00:00 [accepted]
PHST- 2019/08/03 00:00 [revised]
PHST- 2019/09/26 06:00 [pubmed]
PHST- 2019/09/26 06:01 [medline]
PHST- 2019/09/26 06:00 [entrez]
PHST- 2019/11/29 00:00 [pmc-release]
AID - v7i4e14325 [pii]
AID - 10.2196/14325 [doi]
PST - epublish
SO  - JMIR Med Inform. 2019 Nov 29;7(4):e14325. doi: 10.2196/14325.