Dataset Information

Mapping the Read2/CTV3 controlled clinical terminologies to Phecodes in UK Biobank primary care electronic health records: implementation and evaluation.

ABSTRACT: Objective: To establish and validate mappings between primary care clinical terminologies (Read Version 2, Clinical Terms Version 3) and Phecodes. Methods: We processed 123,662,421 primary care events from 230,096 UK Biobank (UKB) participants. We assessed the validity of the primary care-derived Phecodes by conducting PheWAS analyses for seven pre-selected SNPs in the UKB and compared with estimates from BioVU. Results: We mapped 92% of Read2 (n=10,834) and 91% of CTV3 (n=21,988) to 1,449 and 1,490 Phecodes. UKB PheWAS using Phecodes from primary care EHR and hospitalizations replicated all (n=22) previously-reported genotype-phenotype associations. When limiting Phecodes to primary care EHR, replication was 81% (n=18). Conclusion: We introduced a first version of mappings from Read2/CTV3 to Phecodes. The reference list of diseases provided by Phecodes can be extended, enabling researchers to leverage primary care EHR for high-throughput discovery research.

SUBMITTER: Denaxas S

PROVIDER: S-EPMC8861677 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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Mapping the Read2/CTV3 controlled clinical terminologies to Phecodes in UK Biobank primary care electronic health records: implementation and evaluation.

Denaxas Spiros S Liu Ge G Feng Qiping Q Fatemifar Ghazaleh G Bastarache Lisa L Kerchberger Eric V EV Hingorani Aroon D AD Lumbers Tom T Peterson Josh F JF Wei Wei-Qi WQ Hemingway Harry H

AMIA ... Annual Symposium proceedings. AMIA Symposium 20210101

Objective: To establish and validate mappings between primary care clinical terminologies (Read Version 2, Clinical Terms Version 3) and Phecodes. Methods: We processed 123,662,421 primary care events from 230,096 UK Biobank (UKB) participants. We assessed the validity of the primary care-derived Phecodes by conducting PheWAS analyses for seven pre-selected SNPs in the UKB and compared with estimates from BioVU. Results: We mapped 92% of Read2 (n=10,834) and 91% of CTV3 (n=2 ...[more]

PMID: 35308936

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Project description:BackgroundThe 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).ObjectiveThe 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.MethodsWe 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.ResultsWe 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]).ConclusionsThis 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.

Project description:ObjectiveTo determine common patterns of recorded primary care for osteoarthritis (OA), and patient and provider characteristics associated with the quality of recorded care.DesignAn observational study nested within a cluster-randomised controlled trial.SettingEight UK general practices who were part of the Management of Osteoarthritis in Consultations study.ParticipantsPatients recorded as consulting within the eight general practices for clinical OA.Primary outcomesAchievement of seven quality indicators of care (pain/function assessment, information provision, exercise/weight advice, analgesics, physiotherapy), recorded through an electronic template or routinely recorded in the electronic healthcare records, was identified for patients aged ≥45 years consulting over a 6-month period with clinical OA. Latent class analysis was used to cluster patients based on care received. Clusters were compared on patient and clinician-level characteristics.Results1724 patients (median by practice 183) consulted with clinical OA. Common patterns of recorded quality care were: cluster 1 (38%, High) received most quality indicators of care; cluster 2 (11%, Moderate) had pain and function assessment, and received or were considered for other indicators; cluster 3 (17%, Low) had pain and function assessment, and received or were considered for paracetamol or topical non-steroidal anti-inflammatory drugs; cluster 4 (35%, None) had no recorded quality indicators. Patients with higher levels of recorded care consulted a clinician who saw more patients with OA, consulted multiple times and had less morbidity. Those in the High cluster were more likely to have recorded diagnosed OA and have knee/hip OA.ConclusionsPatterns of recorded care for OA fell into four natural clusters. Appropriate delivery of core interventions and relatively safe pharmacological options for OA are still not consistently recorded as provided in primary care. Further research to understand clinical recording behaviours and determine potential barriers to quality care alongside effective training for clinicians is needed.Trial registration numberISRCTN06984617; Results.

Dataset Information

Mapping the Read2/CTV3 controlled clinical terminologies to Phecodes in UK Biobank primary care electronic health records: implementation and evaluation.

Publications

Mapping the Read2/CTV3 controlled clinical terminologies to Phecodes in UK Biobank primary care electronic health records: implementation and evaluation.

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