scholarly journals UK phenomics platform for developing and validating electronic health record phenotypes: CALIBER

2019 ◽  
Vol 26 (12) ◽  
pp. 1545-1559 ◽  
Author(s):  
Spiros Denaxas ◽  
Arturo Gonzalez-Izquierdo ◽  
Kenan Direk ◽  
Natalie K Fitzpatrick ◽  
Ghazaleh Fatemifar ◽  
...  
Keyword(s):  
Primary Care ◽  
International Classification Of Diseases ◽  
Population Based ◽  
Source Population ◽  
Snomed Ct ◽  
Lifestyle Risk Factors ◽  
Classification Of Diseases ◽  
Electronic Health ◽  
Lifestyle Risk

AbstractObjectiveElectronic health records (EHRs) are a rich source of information on human diseases, but the information is variably structured, fragmented, curated using different coding systems, and collected for purposes other than medical research. We describe an approach for developing, validating, and sharing reproducible phenotypes from national structured EHR in the United Kingdom with applications for translational research.Materials and MethodsWe implemented a rule-based phenotyping framework, with up to 6 approaches of validation. We applied our framework to a sample of 15 million individuals in a national EHR data source (population-based primary care, all ages) linked to hospitalization and death records in England. Data comprised continuous measurements (for example, blood pressure; medication information; coded diagnoses, symptoms, procedures, and referrals), recorded using 5 controlled clinical terminologies: (1) read (primary care, subset of SNOMED-CT [Systematized Nomenclature of Medicine Clinical Terms]), (2) International Classification of Diseases–Ninth Revision and Tenth Revision (secondary care diagnoses and cause of mortality), (3) Office of Population Censuses and Surveys Classification of Surgical Operations and Procedures, Fourth Revision (hospital surgical procedures), and (4) DM+D prescription codes.ResultsUsing the CALIBER phenotyping framework, we created algorithms for 51 diseases, syndromes, biomarkers, and lifestyle risk factors and provide up to 6 validation approaches. The EHR phenotypes are curated in the open-access CALIBER Portal (https://www.caliberresearch.org/portal) and have been used by 40 national and international research groups in 60 peer-reviewed publications.ConclusionsWe describe a UK EHR phenomics approach within the CALIBER EHR data platform with initial evidence of validity and use, as an important step toward international use of UK EHR data for health research.

scholarly journals UK phenomics platform for developing and validating EHR phenotypes: CALIBER

2019 ◽  
Author(s):  
Spiros Denaxas ◽  
Arturo Gonzalez-Izquierdo ◽  
Kenan Direk ◽  
Natalie Fitzpatrick ◽  
Amitava Banerjee ◽  
...  
Keyword(s):  
Primary Care ◽  
Electronic Health Records ◽  
Population Based ◽  
Source Population ◽  
Snomed Ct ◽  
Health Records ◽  
Lifestyle Risk Factors ◽  
Electronic Health ◽  
Lifestyle Risk ◽  
The Uk

ABSTRACTObjectiveElectronic health records are a rich source of information on human diseases, but the information is variably structured, fragmented, curated using different coding systems and collected for purposes other than medical research. We describe an approach for developing, validating and sharing reproducible phenotypes from national structured Electronic Health Records (EHR) in the UK with applications for translational research.Materials and MethodsWe implemented a rule-based phenotyping framework, with up to six approaches of validation. We applied our framework to a sample of 15 million individuals in a national EHR data source (population based primary care, all ages) linked to hospitalization and death records in England. Data comprised continuous measurements such as blood pressure, medication information and coded diagnoses, symptoms, procedures and referrals, recorded using five controlled clinical terminologies: a) Read (primary care, subset of SNOMED-CT), b) ICD-9, ICD-10 (secondary care diagnoses and cause of mortality), c) OPCS-4 (hospital surgical procedures) and d) Gemscript Drug Codes.ResultsThe open-access CALIBER Portal (https://www.caliberresearch.org/portal) demonstrates phenotyping algorithms for 50 diseases, syndromes, biomarkers and lifestyle risk factors and provides up to six validation layers. These phenotyping algorithms have been used by 40 national/international research groups in 60 peer-reviewed publications.ConclusionHerein, we describe the UK EHR phenomics approach, CALIBER, with initial evidence of validity and use, as an important step towards international use of UK EHR data for health research.

Prevalence and Incidence of Heart Failure Among Urban Patients in China: A National Population-Based Analysis

2021 ◽  
Author(s):  
Hua Wang ◽  
Ke Chai ◽  
Minghui Du ◽  
Shengfeng Wang ◽  
Jian-Ping Cai ◽  
...  
Keyword(s):  
Heart Failure ◽  
Large Scale ◽  
International Classification Of Diseases ◽  
Population Based ◽  
Unique Identifier ◽  
Classification Of Diseases ◽  
Per Capita ◽  
Mean Cost ◽  
Incident Cases

Background: Large-scale and population-based studies of heart failure (HF) incidence and prevalence are scarce in China. The study sought to estimate the prevalence, incidence, and cost of HF in China. Methods: We conducted a population-based study using records of 50.0 million individuals ≥25 years old from the national urban employee basic medical insurance from 6 provinces in China in 2017. Incident cases were individuals with a diagnosis of HF (International Classification of Diseases code, and text of diagnosis) in 2017 with a 4-year disease-free period (2013–2016). We calculated standardized rates by applying age standardization to the 2010 Chinese census population. Results: The age-standardized prevalence and incidence were 1.10% (1.10% among men and women) and 275 per 100 000 person-years (287 among men and 261 among women), respectively, accounting for 12.1 million patients with HF and 3.0 million patients with incident HF ≥25 years old. Both prevalence and incidence increased with increasing age (0.57%, 3.86%, and 7.55% for prevalence and 158, 892, and 1655 per 100 000 person-years for incidence among persons who were 25–64, 65–79, and ≥80 years of age, respectively). The inpatient mean cost per-capita was $4406.8 and the proportion with ≥3 hospitalizations among those hospitalized was 40.5%. The outpatient mean cost per-capita was $892.3. Conclusions: HF has placed a considerable burden on health systems in China, and strategies aimed at the prevention and treatment of HF are needed. Registration: URL: https://www.clinicaltrials.gov ; Unique identifier: ChiCTR2000029094.

Readmission after Adult Uvulopalatopharyngoplasty: A Population-Based Inpatient Cohort Study in Taiwan

2018 ◽  
Vol 160 (3) ◽  
pp. 559-566 ◽  
Author(s):  
Ying-Shuo Hsu ◽  
Wei-Chung Hsu ◽  
Jenq-Yuh Ko ◽  
Te-Huei Yeh ◽  
Chia-Hsuan Lee ◽  
...  
Keyword(s):  
Odds Ratio ◽  
International Classification Of Diseases ◽  
Population Based ◽  
Factors Associated ◽  
Risk Of Bleeding ◽  
Increased Risk ◽  
Classification Of Diseases ◽  
Insurance Database ◽  
Population Based Survey

Objective To investigate readmissions among adult inpatients who underwent uvulopalatopharyngoplasty (UPPP) in Taiwan. Design Population-based survey. Setting Retrospective study with the National Health Insurance Database. Methods All cases of inpatient adult UPPP (age >20 years) from 1997 to 2012 were identified through International Classification of Diseases, Ninth Revision, Clinical Modification. Factors associated with readmission within 30 days after surgery were analyzed. Results A total of 38,839 adults with UPPP were identified (mean age, 39.3 years; men, 73.7%). The incidence of UPPP was 14.6 per 100 000 adults, which increased from 1997 to 2012 (6.7 to 16.7 per 100,000, Ptrend < .001). The rates of readmission for any reason, readmission for bleeding, reoperation for bleeding, and 30-day mortality were 4.2%, 1.7%, 1.0%, and 0.14%, respectively. Young age increased the risk of reoperation for bleeding, and old age increased the risk of readmission for any reason and mortality. Men had an increased risk of readmission and reoperation. Hypertension was associated with an increased risk of readmission for any reason (odds ratio [OR], 1.29; 95% CI, 1.10-1.51), bleeding-related readmission (OR, 1.89; 95% CI, 1.52-2.36), and reoperation (OR, 2.47; 95% CI, 1.84-3.30). Concurrent hypopharyngeal surgery was associated with an increased risk of readmission for any reason (OR, 1.34; 95% CI, 1.07-1.66) and bleeding-related readmission (OR, 1.69; 95% CI, 1.25-2.27). Finally, the use of steroids was associated with an increased risk of bleeding-related readmission and reoperation. Conclusions The incidence of adult UPPP increased from 1997 to 2012 in Taiwan. Age, sex, comorbidity, concurrent hypopharyngeal surgery, and drug administration were associated with readmission after inpatient UPPP.

Prevalence and incidence of doctor-diagnosed Dupuytren’s disease: a population-based study

2017 ◽  
Vol 42 (7) ◽  
pp. 673-677 ◽  
Author(s):  
J. Nordenskjöld ◽  
M. Englund ◽  
C. Zhou ◽  
I. Atroshi
Keyword(s):  
General Population ◽  
International Classification Of Diseases ◽  
Population Based ◽  
Dupuytren’S Disease ◽  
Level Of Evidence ◽  
Dupuytren's Disease ◽  
Population Based Study ◽  
Classification Of Diseases ◽  
First Time

The prevalence and incidence of doctor-diagnosed Dupuytren’s disease in the general population is unknown. From the healthcare register for Skåne region (population 1.3 million) in southern Sweden, we identified all residents aged ⩾20 years (on 31 December 2013), who 1998 to 2013 had consulted a doctor and received the diagnosis Dupuytren’s disease (International Classification of Diseases 10th Revision code M720). During the 16 years, 7207 current residents (72% men) had been diagnosed with Dupuytren’s disease; the prevalence among men was 1.35% and among women 0.5%. Of all people diagnosed, 56% had received treatment (87% fasciectomy). In 2013, the incidence of first-time doctor-diagnosed Dupuytren’s disease among men was 14 and among women five per 10,000. The annual incidence among men aged ⩾50 years was 27 per 10,000. Clinically important Dupuytren’s disease is common in the general population. Level of evidence: III

scholarly journals Progress of Diabetic Severity and Risk of Dementia

2015 ◽  
Vol 100 (8) ◽  
pp. 2899-2908 ◽  
Author(s):  
Wei-Che Chiu ◽  
Wen-Chao Ho ◽  
Ding-Lieh Liao ◽  
Meng-Hung Lin ◽  
Chih-Chiang Chiu ◽  
...  
Keyword(s):  
Severity Index ◽  
International Classification Of Diseases ◽  
Population Based ◽  
International Classification ◽  
Diabetic Patients ◽  
Research Database ◽  
Classification Of Diseases ◽  
New Onset

Context: Diabetes is a risk factor for dementia, but the effects of diabetic severity on dementia are unclear. Objective: The purpose of this study was to investigate the association between the severity and progress of diabetes and the risk of dementia. Design and Setting: We conducted a 12-year population-based cohort study of new-onset diabetic patients from the Taiwan National Health Insurance Research Database. The diabetic severity was evaluated by the adapted Diabetes Complications Severity Index (aDCSI) from the prediabetic period to the end of follow-up. Cox proportional hazard regressions were used to calculate the hazard ratios (HRs) of the scores and change in the aDCSI. Participants: Participants were 431,178 new-onset diabetic patients who were older than 50 years and had to receive antidiabetic medications. Main Outcome: Dementia cases were identified by International Classification of Diseases, ninth revision, code (International Classification of Diseases, ninth revision, codes 290.0, 290.1, 290.2, 290.3, 290.4, 294.1, 331.0), and the date of the initial dementia diagnosis was used as the index date. Results: The scores and change in the aDCSI were associated with the risk of dementia when adjusting for patient factors, comorbidity, antidiabetic drugs, and drug adherence. At the end of the follow-up, the risks for dementia were 1.04, 1.40, 1.54, and 1.70 (P &lt; .001 for trend) in patients with an aDCSI score of 1, 2, 3, and greater than 3, respectively. Compared with the mildly progressive patients, the adjusted HRs increased as the aDCSI increased (2 y HRs: 1.30, 1.53, and 1.97; final HRs: 2.38, 6.95, and 24.0 with the change in the aDCSI score per year: 0.51–1.00, 1.01–2.00, and &gt; 2.00 vs &lt; 0.50 with P &lt; .001 for trend). Conclusions: The diabetic severity and progression reflected the risk of dementia, and the early change in the aDCSI could predict the risk of dementia in new-onset diabetic patients.

scholarly journals Association of Gestational Age with Postpartum Hemorrhage

2021 ◽  
Author(s):  
Alexander J. Butwick ◽  
Can Liu ◽  
Nan Guo ◽  
Jason Bentley ◽  
Elliot K. Main ◽  
...  
Keyword(s):  
Gestational Age ◽  
Postpartum Hemorrhage ◽  
International Classification Of Diseases ◽  
Population Based ◽  
International Classification ◽  
Sensitivity Analyses ◽  
Multiple Gestation ◽  
Classification Of Diseases ◽  
Gestational Age At Delivery

Background Risk factors for postpartum hemorrhage, such as chorioamnionitis and multiple gestation, have been identified in previous epidemiologic studies. However, existing data describing the association between gestational age at delivery and postpartum hemorrhage are conflicting. The aim of this study was to assess the association between gestational age at delivery and postpartum hemorrhage. Methods The authors conducted a population-based retrospective cohort study of women who underwent live birth delivery in Sweden between 2014 and 2017 and in California between 2011 and 2015. The primary exposure was gestational age at delivery. The primary outcome was postpartum hemorrhage, classified using International Classification of Diseases, Ninth Revision—Clinical Modification codes for California births and a blood loss greater than 1,000 ml for Swedish births. The authors accounted for demographic and obstetric factors as potential confounders in the analyses. Results The incidences of postpartum hemorrhage in Sweden (23,323/328,729; 7.1%) and in California (66,583/2,079,637; 3.2%) were not comparable. In Sweden and California, the incidence of postpartum hemorrhage was highest for deliveries between 41 and 42 weeks’ gestation (7,186/75,539 [9.5%] and 8,921/160,267 [5.6%], respectively). Compared to deliveries between 37 and 38 weeks, deliveries between 41 and 42 weeks had the highest adjusted odds of postpartum hemorrhage (1.62 [95% CI, 1.56 to 1.69] in Sweden and 2.04 [95% CI, 1.98 to 2.09] in California). In both cohorts, the authors observed a nonlinear (J-shaped) association between gestational age and postpartum hemorrhage risk, with 39 weeks as the nadir. In the sensitivity analyses, similar findings were observed among cesarean deliveries only, when postpartum hemorrhage was classified only by International Classification of Diseases, Tenth Revision—Clinical Modification codes, and after excluding women with abnormal placentation disorders. Conclusions The postpartum hemorrhage incidence in Sweden and California was not comparable. When assessing a woman’s risk for postpartum hemorrhage, clinicians should be aware of the heightened odds in women who deliver between 41 and 42 weeks’ gestation. Editor’s Perspective What We Already Know about This Topic What This Article Tells Us That Is New

scholarly journals Developing and Evaluating Mappings of ICD-10 and ICD-10-CM Codes to PheCodes

2018 ◽  
Author(s):  
Patrick Wu ◽  
Aliya Gifford ◽  
Xiangrui Meng ◽  
Xue Li ◽  
Harry Campbell ◽  
...  
Keyword(s):  
Medical Center ◽  
Association Studies ◽  
International Classification Of Diseases ◽  
Snomed Ct ◽  
Unified Medical Language System ◽  
Classification Of Diseases ◽  
Icd 10 ◽  
The Uk ◽  
Systematized Nomenclature Of Medicine

AbstractBackgroundThe 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).ObjectiveHere, we present our work on the development and evaluation of maps from ICD-10 and 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 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.ResultsWe 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).ConclusionsThis 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.

Incremental Costs for Psoriasis and Psoriatic Arthritis in a Population-based Cohort in Southern Sweden: Is It All Psoriasis-attributable Morbidity?

2016 ◽  
Vol 43 (3) ◽  
pp. 640-647 ◽  
Author(s):  
Sofia Löfvendahl ◽  
Ingemar F. Petersson ◽  
Elke Theander ◽  
Åke Svensson ◽  
Caddie Zhou ◽  
...  
Keyword(s):  
Psoriatic Arthritis ◽  
Productivity Loss ◽  
International Classification Of Diseases ◽  
Population Based ◽  
Drug Costs ◽  
Productivity Losses ◽  
Classification Of Diseases ◽  
A Minor ◽  
The Cost

Objective.To estimate incremental costs for patients with psoriasis/psoriatic arthritis (PsO/PsA) compared to population-based referents free from PsO/PsA and estimate costs attributable specifically to PsO/PsA.Methods.Patients were identified by International Classification of Diseases, 10th ed., codes for PsO/PsA using information from 1998 to 2007 in the Skåne Healthcare Register, covering healthcare use for the population of the Skåne region of Sweden. For each patient, 3 population-based referents were selected. Data were retrieved from Swedish registers on healthcare, drugs, and productivity loss. The human capital method was used to value productivity losses. Mean annual costs for 2008 to 2011 were assessed from a societal perspective.Results.We identified 15,283 patients fulfilling the inclusion criteria for PsO [n = 12,562, 50% women, mean age (SD) 52 (21) yrs] or PsA [n = 2721, 56% women, mean age 54 (16) yrs] and included 45,849 referents. Mean annual cost per patient with PsO/PsA was 55% higher compared to referents: €10,500 vs €6700. The cost was 97% higher for PsA compared to PsO. Costs due to productivity losses represented the largest share of total costs, ranging from 52% for PsO to 60% for PsA. Biological drug costs represented 10% of the costs for PsA and 1.6% for PsO. The proportion of cost identified as attributable to PsO/PsA problems was greatest among the patients with PsA (drug costs 71% and healthcare costs 31%).Conclusion.Annual mean incremental societal cost per patient was highest for PsA, mainly because of productivity losses and biological treatment. A minor fraction of the costs were identified as attributable to PsO/PsA specifically, indicating an increased morbidity in these patients that needs to be further investigated.

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