Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Wu P

PROVIDER: S-EPMC6911227 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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

Wu Patrick P Gifford Aliya A Meng Xiangrui X Li Xue X Campbell Harry H Varley Tim T Zhao Juan J Carroll Robert R Bastarache Lisa L Denny Joshua C JC Theodoratou Evropi E Wei Wei-Qi WQ

JMIR medical informatics 20191129 4

<h4>Background</h4>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).<h4>Objective</h4>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-1 ...[more]

PMID: 31553307

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Project description:Background:The International Classification of Diseases, Ninth Edition, Clinical Modification (ICD-9-CM) Injury Severity Score (ICISS) is a risk adjustment model when injuries are recorded using ICD-9-CM coding. The trauma mortality prediction model (TMPM-ICD9) provides better calibration and discrimination compared with ICISS and injury severity score (ISS). Though TMPM-ICD9 is statistically rigorous, it is not precise enough mathematically and has the tendency to overestimate injury severity. The purpose of this study is to develop a new ICD-10-CM injury model which estimates injury severities for every injury in the ICD-10-CM lexicon by a combination of rigorous statistical probit models and mathematical properties and improves the prediction accuracy. Methods:We developed an injury mortality prediction (IMP-ICDX) using data of 794,098 patients admitted to 738 hospitals in the National Trauma Data Bank from 2015 to 2016. Empiric measures of severity for each of the trauma ICD-10-CM codes were estimated using a weighted median death probability (WMDP) measurement and then used as the basis for IMP-ICDX. ISS (version 2005) and the single worst injury (SWI) model were re-estimated. The performance of each of these models was compared by using the area under the receiver operating characteristic (AUC), the Hosmer-Lemeshow (HL) statistic, and the Akaike information criterion statistic. Results:IMP-ICDX exhibits significantly better discrimination (AUCIMP-ICDX, 0.893, and 95% confidence interval (CI), 0.887 to 0.898; AUCISS, 0.853, and 95% CI, 0.846 to 0.860; and AUCSWI, 0.886, and 95% CI, 0.881 to 0.892) and calibration (HLIMP-ICDX, 68, and 95% CI, 36 to 98; HLISS, 252, and 95% CI, 191 to 310; and HLSWI, 92, and 95% CI, 53 to 128) compared with ISS and SWI. All models were improved after the extension of age, gender, and injury mechanism, but the augmented IMP-ICDX still dominated ISS and SWI by every performance. Conclusions:The IMP-ICDX has a better discrimination and calibration compared to ISS. Therefore, we believe that IMP-ICDX could be a new viable trauma research assessment method.

Project description:Various assessment methods based on the International Classification of Diseases, Tenth Edition, Clinical Modification (ICD-10-CM), such as ICD-10-CM Injury Severity Score (ICISS), trauma mortality prediction model (TMPM-ICD10), and injury mortality prediction (IMP-ICDX), are purely anatomic trauma assessment, which need to be further improved. Traumatic injury mortality prediction (TRIMP-ICDX) is a comprehensive assessment method based on anatomic injuries and incorporating available information to determine whether it is superior to Trauma and Injury Severity Score (TRISS) and IMP-ICDX in predicting trauma outcomes. This retrospective cohort study was based on data from 704,287 trauma patients admitted to 710 trauma centers in the National Trauma Data Bank of the United States in 2016. The TRIMP-ICDX was established using anatomical injury, physiological reserves, and physiological response indicators. Its performance was compared with the IMP-ICDX and TRISS by examining the area under the receiver operating characteristic curve (AUC), calibration (Hosmer-Lemeshow goodness-of-fit test, HL), and the Akaike information criterion (AIC). The TRIMP-ICDX showed significantly better discrimination (AUCTRIMP-ICDX 0.968; 95% confidence interval (CI), 0.966–0.970, AUCTRISS 0.922; 95% CI, 0.918–0.925, and AUCIMP-ICDX 0.894; 95% CI, 0.890–0.899), better calibration (HLTRIMP-ICDX 5.6; 95% CI, 3.0–8.0, HLTRISS 72.7; 95% CI, 38.4–104.5, and HLIMP-ICDX 53.1; 95% CI, 26.6–77.8), and a lower AIC (AICTRIMP-ICDX 24,774, AICTRISS 30,753, and AICIMP-ICDX 32,780) compared with TRISS and IMP-ICDX. Similar results were found in statistical comparisons among different body regions. As a comprehensive evaluation method based on the ICD-10-CM lexicon TRIMP-ICDX is significantly better than IMP-ICDX and TRISS with respect to both discriminative power and calibration. The TRIMP-ICDX should become a research method for the comprehensive evaluation of trauma severity.

Project description:BackgroundMost current state-of-the-art models for searching the International Classification of Diseases, Tenth Revision Clinical Modification (ICD-10-CM) codes use word embedding technology to capture useful semantic properties. However, they are limited by the quality of initial word embeddings. Word embedding trained by electronic health records (EHRs) is considered the best, but the vocabulary diversity is limited by previous medical records. Thus, we require a word embedding model that maintains the vocabulary diversity of open internet databases and the medical terminology understanding of EHRs. Moreover, we need to consider the particularity of the disease classification, wherein discharge notes present only positive disease descriptions.ObjectiveWe aimed to propose a projection word2vec model and a hybrid sampling method. In addition, we aimed to conduct a series of experiments to validate the effectiveness of these methods.MethodsWe compared the projection word2vec model and traditional word2vec model using two corpora sources: English Wikipedia and PubMed journal abstracts. We used seven published datasets to measure the medical semantic understanding of the word2vec models and used these embeddings to identify the three-character-level ICD-10-CM diagnostic codes in a set of discharge notes. On the basis of embedding technology improvement, we also tried to apply the hybrid sampling method to improve accuracy. The 94,483 labeled discharge notes from the Tri-Service General Hospital of Taipei, Taiwan, from June 1, 2015, to June 30, 2017, were used. To evaluate the model performance, 24,762 discharge notes from July 1, 2017, to December 31, 2017, from the same hospital were used. Moreover, 74,324 additional discharge notes collected from seven other hospitals were tested. The F-measure, which is the major global measure of effectiveness, was adopted.ResultsIn medical semantic understanding, the original EHR embeddings and PubMed embeddings exhibited superior performance to the original Wikipedia embeddings. After projection training technology was applied, the projection Wikipedia embeddings exhibited an obvious improvement but did not reach the level of original EHR embeddings or PubMed embeddings. In the subsequent ICD-10-CM coding experiment, the model that used both projection PubMed and Wikipedia embeddings had the highest testing mean F-measure (0.7362 and 0.6693 in Tri-Service General Hospital and the seven other hospitals, respectively). Moreover, the hybrid sampling method was found to improve the model performance (F-measure=0.7371/0.6698).ConclusionsThe word embeddings trained using EHR and PubMed could understand medical semantics better, and the proposed projection word2vec model improved the ability of medical semantics extraction in Wikipedia embeddings. Although the improvement from the projection word2vec model in the real ICD-10-CM coding task was not substantial, the models could effectively handle emerging diseases. The proposed hybrid sampling method enables the model to behave like a human expert.

Dataset Information

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

Publications

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

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