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1.
J Med Internet Res ; 26: e53367, 2024 Apr 04.
Artículo en Inglés | MEDLINE | ID: mdl-38573752

RESUMEN

BACKGROUND: Real-time surveillance of emerging infectious diseases necessitates a dynamically evolving, computable case definition, which frequently incorporates symptom-related criteria. For symptom detection, both population health monitoring platforms and research initiatives primarily depend on structured data extracted from electronic health records. OBJECTIVE: This study sought to validate and test an artificial intelligence (AI)-based natural language processing (NLP) pipeline for detecting COVID-19 symptoms from physician notes in pediatric patients. We specifically study patients presenting to the emergency department (ED) who can be sentinel cases in an outbreak. METHODS: Subjects in this retrospective cohort study are patients who are 21 years of age and younger, who presented to a pediatric ED at a large academic children's hospital between March 1, 2020, and May 31, 2022. The ED notes for all patients were processed with an NLP pipeline tuned to detect the mention of 11 COVID-19 symptoms based on Centers for Disease Control and Prevention (CDC) criteria. For a gold standard, 3 subject matter experts labeled 226 ED notes and had strong agreement (F1-score=0.986; positive predictive value [PPV]=0.972; and sensitivity=1.0). F1-score, PPV, and sensitivity were used to compare the performance of both NLP and the International Classification of Diseases, 10th Revision (ICD-10) coding to the gold standard chart review. As a formative use case, variations in symptom patterns were measured across SARS-CoV-2 variant eras. RESULTS: There were 85,678 ED encounters during the study period, including 4% (n=3420) with patients with COVID-19. NLP was more accurate at identifying encounters with patients that had any of the COVID-19 symptoms (F1-score=0.796) than ICD-10 codes (F1-score =0.451). NLP accuracy was higher for positive symptoms (sensitivity=0.930) than ICD-10 (sensitivity=0.300). However, ICD-10 accuracy was higher for negative symptoms (specificity=0.994) than NLP (specificity=0.917). Congestion or runny nose showed the highest accuracy difference (NLP: F1-score=0.828 and ICD-10: F1-score=0.042). For encounters with patients with COVID-19, prevalence estimates of each NLP symptom differed across variant eras. Patients with COVID-19 were more likely to have each NLP symptom detected than patients without this disease. Effect sizes (odds ratios) varied across pandemic eras. CONCLUSIONS: This study establishes the value of AI-based NLP as a highly effective tool for real-time COVID-19 symptom detection in pediatric patients, outperforming traditional ICD-10 methods. It also reveals the evolving nature of symptom prevalence across different virus variants, underscoring the need for dynamic, technology-driven approaches in infectious disease surveillance.


Asunto(s)
Biovigilancia , COVID-19 , Médicos , SARS-CoV-2 , Estados Unidos , Humanos , Niño , Inteligencia Artificial , Estudios Retrospectivos , COVID-19/diagnóstico , COVID-19/epidemiología
2.
Brief Bioinform ; 22(1): 55-65, 2021 01 18.
Artículo en Inglés | MEDLINE | ID: mdl-32249310

RESUMEN

Precision medicine promises to revolutionize treatment, shifting therapeutic approaches from the classical one-size-fits-all to those more tailored to the patient's individual genomic profile, lifestyle and environmental exposures. Yet, to advance precision medicine's main objective-ensuring the optimum diagnosis, treatment and prognosis for each individual-investigators need access to large-scale clinical and genomic data repositories. Despite the vast proliferation of these datasets, locating and obtaining access to many remains a challenge. We sought to provide an overview of available patient-level datasets that contain both genotypic data, obtained by next-generation sequencing, and phenotypic data-and to create a dynamic, online catalog for consultation, contribution and revision by the research community. Datasets included in this review conform to six specific inclusion parameters that are: (i) contain data from more than 500 human subjects; (ii) contain both genotypic and phenotypic data from the same subjects; (iii) include whole genome sequencing or whole exome sequencing data; (iv) include at least 100 recorded phenotypic variables per subject; (v) accessible through a website or collaboration with investigators and (vi) make access information available in English. Using these criteria, we identified 30 datasets, reviewed them and provided results in the release version of a catalog, which is publicly available through a dynamic Web application and on GitHub. Users can review as well as contribute new datasets for inclusion (Web: https://avillachlab.shinyapps.io/genophenocatalog/; GitHub: https://github.com/hms-dbmi/GenoPheno-CatalogShiny).


Asunto(s)
Bases de Datos Genéticas , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Fenotipo , Medicina de Precisión/métodos , Predisposición Genética a la Enfermedad , Humanos , Secuenciación Completa del Genoma/métodos
3.
J Pediatr ; 252: 131-140.e3, 2023 01.
Artículo en Inglés | MEDLINE | ID: mdl-36027975

RESUMEN

OBJECTIVE: To characterize distinct comorbidities, outcomes, and treatment patterns in children with Down syndrome and pulmonary hypertension in a large, multicenter pediatric pulmonary hypertension registry. STUDY DESIGN: We analyzed data from the Pediatric Pulmonary Hypertension Network (PPHNet) Registry, comparing demographic and clinical characteristics of children with Down syndrome and children without Down syndrome. We examined factors associated with pulmonary hypertension resolution and a composite outcome of pulmonary hypertension severity in the cohort with Down syndrome. RESULTS: Of 1475 pediatric patients with pulmonary hypertension, 158 (11%) had Down syndrome. The median age at diagnosis of pulmonary hypertension in patients with Down syndrome was 0.49 year (IQR, 0.21-1.77 years), similar to that in patients without Down syndrome. There was no difference in rates of cardiac catheterization and prescribed pulmonary hypertension medications in children with Down syndrome and those without Down syndrome. Comorbidities in Down syndrome included congenital heart disease (95%; repaired in 68%), sleep apnea (56%), prematurity (49%), recurrent respiratory exacerbations (35%), gastroesophageal reflux (38%), and aspiration (31%). Pulmonary hypertension resolved in 43% after 3 years, associated with a diagnosis of pulmonary hypertension at age <6 months (54% vs 29%; P = .002) and a pretricuspid shunt (65% vs 38%; P = .02). Five-year transplantation-free survival was 88% (95% CI, 80%-97%). Tracheostomy (hazard ratio [HR], 3.29; 95% CI, 1.61-6.69) and reflux medication use (HR, 2.08; 95% CI, 1.11-3.90) were independently associated with a composite outcome of severe pulmonary hypertension. CONCLUSIONS: Despite high rates of cardiac and respiratory comorbidities that influence the severity of pulmonary hypertension, children with Down syndrome-associated pulmonary hypertension generally have a survival rate similar to that of children with non-Down syndrome-associated pulmonary hypertension. Resolution of pulmonary hypertension is common but reduced in children with complicated respiratory comorbidities.


Asunto(s)
Síndrome de Down , Reflujo Gastroesofágico , Cardiopatías Congénitas , Hipertensión Pulmonar , Niño , Humanos , Lactante , Hipertensión Pulmonar/epidemiología , Hipertensión Pulmonar/etiología , Hipertensión Pulmonar/terapia , Estudios Retrospectivos , Síndrome de Down/complicaciones , Cardiopatías Congénitas/cirugía , Sistema de Registros , Reflujo Gastroesofágico/complicaciones
4.
Hum Genomics ; 16(1): 67, 2022 12 08.
Artículo en Inglés | MEDLINE | ID: mdl-36482414

RESUMEN

BACKGROUND: The human exposome is composed of diverse metabolites and small chemical compounds originated from endogenous and exogenous sources, respectively. Genetic and environmental factors influence metabolite levels, while the extent of genetic contributions across metabolic pathways is not yet known. Untargeted profiling of human metabolome using high-resolution mass spectrometry (HRMS) combined with genome-wide genotyping allows comprehensive identification of genetically influenced metabolites. As such previous studies of adults discovered and replicated genotype-metabotype associations. However, these associations have not been characterized in children. RESULTS: We conducted the largest genome by metabolome-wide association study to date of children (N = 441) using 619,688 common genetic variants and 14,342 features measured by HRMS. Narrow-sense heritability (h2) estimates of plasma metabolite concentrations using genomic relatedness matrix restricted maximum likelihood (GREML) method showed a bimodal distribution with high h2 (> 0.8) for 15.9% of features and low h2 (< 0.2) for most of features (62.0%). The features with high h2 were enriched for amino acid and nucleic acid metabolism, while carbohydrate and lipid concentrations showed low h2. For each feature, a metabolite quantitative trait loci (mQTL) analysis was performed to identify genetic variants that were potentially associated with plasma levels. Fifty-four associations among 29 features and 43 genetic variants were identified at a genome-wide significance threshold p < 3.5 × 10-12 (= 5 × 10-8/14,342 features). Previously reported associations such as UGT1A1 and bilirubin; PYROXD2 and methyl lysine; and ACADS and butyrylcarnitine were successfully replicated in our pediatric cohort. We found potential candidates for novel associations including CSMD1 and a monostearyl alcohol triglyceride (m/z 781.7483, retention time (RT) 89.3 s); CALN1 and Tridecanol (m/z 283.2741, RT 27.6). A gene-level enrichment analysis using MAGMA revealed highly interconnected modules for dADP biosynthesis, sterol synthesis, and long-chain fatty acid transport in the gene-feature network. CONCLUSION: Comprehensive profiling of plasma metabolome across age groups combined with genome-wide genotyping revealed a wide range of genetic influence on diverse chemical species and metabolic pathways. The developmental trajectory of a biological system is shaped by gene-environment interaction especially in early life. Therefore, continuous efforts on generating metabolomics data in diverse human tissue types across age groups are required to understand gene-environment interaction toward healthy aging trajectories.


Asunto(s)
Genómica , Metabolómica , Humanos , Niño
5.
J Med Internet Res ; 24(11): e41750, 2022 11 04.
Artículo en Inglés | MEDLINE | ID: mdl-36331535

RESUMEN

The federal Trusted Exchange Framework and Common Agreement (TEFCA) aims to reduce fragmentation of patient records by expanding query-based health information exchange with nationwide connectivity for diverse purposes. TEFCA provides a common agreement and security framework allowing clinicians, and possibly insurance company staff, public health officials, and other authorized users, to query for health information about hundreds of millions of patients. TEFCA presents an opportunity to weave information exchange into the fabric of our national health information economy. We define 3 principles to promote patient autonomy and control within TEFCA: (1) patients can query for data about themselves, (2) patients can know when their data are queried and shared, and (3) patients can configure what is shared about them. We believe TEFCA should address these principles by the time it launches. While health information exchange already occurs on a large scale today, the launch of TEFCA introduces a major, new, and cohesive component of 21st-century US health care information infrastructure. We strongly advocate for a substantive role for the patient in TEFCA, one that will be a model for other systems and policies.


Asunto(s)
Intercambio de Información en Salud , Health Insurance Portability and Accountability Act , Estados Unidos , Humanos , Privacidad , Confidencialidad , Seguridad Computacional
6.
BMC Bioinformatics ; 22(1): 259, 2021 May 20.
Artículo en Inglés | MEDLINE | ID: mdl-34016036

RESUMEN

BACKGROUND: Whole exome sequencing (WES) is widely adopted in clinical and research settings; however, one of the practical concerns is the potential false negatives due to incomplete breadth and depth of coverage for several exons in clinically implicated genes. In some cases, a targeted gene panel testing may be a dependable option to ascertain true negatives for genomic variants in known disease-associated genes. We developed a web-based tool to quickly gauge whether all genes of interest would be reliably covered by WES or whether targeted gene panel testing should be considered instead to minimize false negatives in candidate genes. RESULTS: WEScover is a novel web application that provides an intuitive user interface for discovering breadth and depth of coverage across population-scale WES datasets, searching either by phenotype, by targeted gene panel(s) or by gene(s). Moreover, the application shows metrics from the Genome Aggregation Database to provide gene-centric view on breadth of coverage. CONCLUSIONS: WEScover allows users to efficiently query genes and phenotypes for the coverage of associated exons by WES and recommends use of panel tests for the genes with potential incomplete coverage by WES.


Asunto(s)
Exoma , Genómica , Exoma/genética , Secuenciación de Nucleótidos de Alto Rendimiento , Fenotipo , Secuenciación del Exoma
7.
Genet Med ; 23(4): 782-786, 2021 04.
Artículo en Inglés | MEDLINE | ID: mdl-33420348

RESUMEN

PURPOSE: Pharmacogenomic biomarkers are increasingly listed on medication labels and authoritative guidelines but pharmacogenomic-guided prescribing is not yet common. Our objective was to assess the potential for incorporating knowledge of patients' genomic characteristics into prescribing practices. METHODS: We performed a retrospective analysis of claims data for 2,096,971 beneficiaries with pharmacy coverage from a national, commercial health insurance plan between January 2017 and December 2019. Children between 0 and 17 years comprised 21% of the cohort. Adults were age 18 to 64. Medications with actionable pharmacogenomic biomarkers (MAPBs) were identified using public information from the US Food and Drug Administration (FDA), Clinical Pharmacogenomics Implementation Consortium (CPIC), and PharmGKB. RESULTS: MAPBs were dispensed to 63% of the adults and 29% of the children in the cohort. Most frequently dispensed were ibuprofen, ondansetron, codeine, and oxycodone. Most common were medications with CYP2D6, G6PD, or CYPC19 pharmacogenomic biomarkers. Ten percent of the cohort were codispensed more than one MAPB for at least 30 days. CONCLUSION: The number of people who might benefit from pharmacogenomic-guided prescribing is substantial. Future work should address obstacles to integrating genomic data into prescriber workflows, complex factors contributing to the magnitude of benefit, and the clinical availability of reliable on-demand or pre-emptive pharmacogenomic testing.


Asunto(s)
Farmacogenética , Pruebas de Farmacogenómica , Adolescente , Adulto , Biomarcadores , Niño , Etiquetado de Medicamentos , Humanos , Persona de Mediana Edad , Estudios Retrospectivos , Adulto Joven
8.
J Med Internet Res ; 23(3): e22219, 2021 03 02.
Artículo en Inglés | MEDLINE | ID: mdl-33600347

RESUMEN

Coincident with the tsunami of COVID-19-related publications, there has been a surge of studies using real-world data, including those obtained from the electronic health record (EHR). Unfortunately, several of these high-profile publications were retracted because of concerns regarding the soundness and quality of the studies and the EHR data they purported to analyze. These retractions highlight that although a small community of EHR informatics experts can readily identify strengths and flaws in EHR-derived studies, many medical editorial teams and otherwise sophisticated medical readers lack the framework to fully critically appraise these studies. In addition, conventional statistical analyses cannot overcome the need for an understanding of the opportunities and limitations of EHR-derived studies. We distill here from the broader informatics literature six key considerations that are crucial for appraising studies utilizing EHR data: data completeness, data collection and handling (eg, transformation), data type (ie, codified, textual), robustness of methods against EHR variability (within and across institutions, countries, and time), transparency of data and analytic code, and the multidisciplinary approach. These considerations will inform researchers, clinicians, and other stakeholders as to the recommended best practices in reviewing manuscripts, grants, and other outputs from EHR-data derived studies, and thereby promote and foster rigor, quality, and reliability of this rapidly growing field.


Asunto(s)
COVID-19/epidemiología , Recolección de Datos/métodos , Registros Electrónicos de Salud , Recolección de Datos/normas , Humanos , Revisión de la Investigación por Pares/normas , Edición/normas , Reproducibilidad de los Resultados , SARS-CoV-2/aislamiento & purificación
9.
Hum Mutat ; 41(2): 387-396, 2020 02.
Artículo en Inglés | MEDLINE | ID: mdl-31691385

RESUMEN

Genome sequencing is positioned as a routine clinical work-up for diverse clinical conditions. A commonly used approach to highlight candidate variants with potential clinical implication is to search over locus- and gene-centric knowledge databases. Most web-based applications allow a federated query across diverse databases for a single variant; however, sifting through a large number of genomic variants with combination of filtering criteria is a substantial challenge. Here we describe the Clinical Genome and Ancestry Report (CGAR), an interactive web application developed to follow clinical interpretation workflows by organizing variants into seven categories: (1) reported disease-associated variants, (2) rare- and high-impact variants in putative disease-associated genes, (3) secondary findings that the American College of Medical Genetics and Genomics recommends reporting back to patients, (4) actionable pharmacogenomic variants, (5) focused reports for candidate genes, (6) de novo variant candidates for trio analysis, and (7) germline and somatic variants implicated in cancer risk, diagnosis, treatment and prognosis. For each variant, a comprehensive list of external links to variant-centric and phenotype databases are provided. Furthermore, genotype-derived ancestral composition is used to highlight allele frequencies from a matched population since some disease-associated variants show a wide variation between populations. CGAR is an open-source software and is available at https://tom.tch.harvard.edu/apps/cgar/.


Asunto(s)
Biología Computacional/métodos , Bases de Datos Genéticas , Genoma Humano , Genómica/métodos , Programas Informáticos , Navegador Web , Estudios de Asociación Genética/métodos , Predisposición Genética a la Enfermedad , Variación Genética , Humanos , Anotación de Secuencia Molecular , Interfaz Usuario-Computador
10.
Genet Med ; 22(2): 371-380, 2020 02.
Artículo en Inglés | MEDLINE | ID: mdl-31481752

RESUMEN

PURPOSE: Clinicians and researchers must contextualize a patient's genetic variants against population-based references with detailed phenotyping. We sought to establish globally scalable technology, policy, and procedures for sharing biosamples and associated genomic and phenotypic data on broadly consented cohorts, across sites of care. METHODS: Three of the nation's leading children's hospitals launched the Genomic Research and Innovation Network (GRIN), with federated information technology infrastructure, harmonized biobanking protocols, and material transfer agreements. Pilot studies in epilepsy and short stature were completed to design and test the collaboration model. RESULTS: Harmonized, broadly consented institutional review board (IRB) protocols were approved and used for biobank enrollment, creating ever-expanding, compatible biobanks. An open source federated query infrastructure was established over genotype-phenotype databases at the three hospitals. Investigators securely access the GRIN platform for prep to research queries, receiving aggregate counts of patients with particular phenotypes or genotypes in each biobank. With proper approvals, de-identified data is exported to a shared analytic workspace. Investigators at all sites enthusiastically collaborated on the pilot studies, resulting in multiple publications. Investigators have also begun to successfully utilize the infrastructure for grant applications. CONCLUSIONS: The GRIN collaboration establishes the technology, policy, and procedures for a scalable genomic research network.


Asunto(s)
Manejo de Datos/métodos , Procesamiento Automatizado de Datos/métodos , Almacenamiento y Recuperación de la Información/métodos , Bancos de Muestras Biológicas/normas , Investigación Biomédica/métodos , Bases de Datos Factuales , Bases de Datos Genéticas , Comités de Ética en Investigación , Genómica/métodos , Humanos , Difusión de la Información , Investigadores
12.
J Pediatr ; 220: 132-138.e2, 2020 05.
Artículo en Inglés | MEDLINE | ID: mdl-32067779

RESUMEN

OBJECTIVES: To determine the prevalence of features of viral illness in a national sample of visits involving children tested for group A Streptococcus pharyngitis. Additionally, we sought to derive a decision rule to identify patients with features of viral illness who were at low risk of having group A Streptococcus and for whom laboratory testing might be avoided. STUDY DESIGN: Retrospective validation study using data from electronic health records of patients 3-21 years old evaluated for sore throat in a national network of retail health clinics (n = 67 127). We determined the prevalence of features of viral illness in patients tested for group A Streptococcus and developed a decision tree algorithm to identify patients with features of viral illness at low risk (<15%) of having group A Streptococcus. RESULTS: Overall, 54% of patients had features of viral illness. Among patients with features of viral illness, those without tonsillar exudates who were 11 years or older and either lacked cervical adenopathy or had cervical adenopathy and lacked fever were identified as at low risk for group A Streptococcus according to the decision rule. This group comprised 34% of patients with features of viral illness, or 19% of all patients tested for group A Streptococcus infection. CONCLUSIONS: Our findings provide an objective way to identify patients with features of viral illness who are at low risk of having group A Streptococcus. Improved identification such patients at low risk of group A Streptococcus could improve appropriate testing and antibiotic prescribing for pharyngitis.


Asunto(s)
Faringitis/epidemiología , Faringitis/microbiología , Infecciones Estreptocócicas/epidemiología , Streptococcus pyogenes , Adolescente , Niño , Preescolar , Femenino , Humanos , Masculino , Prevalencia , Estudios Retrospectivos , Medición de Riesgo , Adulto Joven
13.
Am J Public Health ; 110(S3): S319-S325, 2020 10.
Artículo en Inglés | MEDLINE | ID: mdl-33001719

RESUMEN

Objectives. To examine the role that bots play in spreading vaccine information on Twitter by measuring exposure and engagement among active users from the United States.Methods. We sampled 53 188 US Twitter users and examined who they follow and retweet across 21 million vaccine-related tweets (January 12, 2017-December 3, 2019). Our analyses compared bots to human-operated accounts and vaccine-critical tweets to other vaccine-related tweets.Results. The median number of potential exposures to vaccine-related tweets per user was 757 (interquartile range [IQR] = 168-4435), of which 27 (IQR = 6-169) were vaccine critical, and 0 (IQR = 0-12) originated from bots. We found that 36.7% of users retweeted vaccine-related content, 4.5% retweeted vaccine-critical content, and 2.1% retweeted vaccine content from bots. Compared with other users, the 5.8% for whom vaccine-critical tweets made up most exposures more often retweeted vaccine content (62.9%; odds ratio [OR] = 2.9; 95% confidence interval [CI] = 2.7, 3.1), vaccine-critical content (35.0%; OR = 19.0; 95% CI = 17.3, 20.9), and bots (8.8%; OR = 5.4; 95% CI = 4.7, 6.3).Conclusions. A small proportion of vaccine-critical information that reaches active US Twitter users comes from bots.


Asunto(s)
Comunicación , Difusión de la Información , Medios de Comunicación Sociales , Vacunas , Humanos , Estados Unidos , Vacunación/tendencias
14.
J Med Internet Res ; 22(12): e24824, 2020 12 11.
Artículo en Inglés | MEDLINE | ID: mdl-33306034

RESUMEN

The 21st Century Cures Act and the recently published "final rule" define standardized methods for obtaining electronic copies of electronic health record (EHR) data through application programming interfaces. The rule is meant to create an ecosystem of reusable, substitutable apps that can be built once but run at any hospital system "without special effort." Yet, despite numerous provisions around information blocking in the final rule, there is concern that the business practices that govern EHR vendors and health care organizations in the United States could still stifle innovation. We describe potential app ecosystems that may form. We caution that misaligned incentives may result in anticompetitive behavior and purposefully limited functionality. Closed proprietary ecosystems may result, limiting the value derived from interoperability. The 21st Century Cures Act and final rule are an exciting step in the direction of improved interoperability. However, realizing the vision of a truly interoperable app ecosystem is not predetermined.


Asunto(s)
Innovación Organizacional , Registros Electrónicos de Salud , Historia del Siglo XXI , Humanos , Aplicaciones Móviles
17.
J Pediatr ; 211: 63-71.e6, 2019 08.
Artículo en Inglés | MEDLINE | ID: mdl-31176455

RESUMEN

OBJECTIVE: To investigate racial and ethnic differences in pulmonary hypertension subtypes and survival differences in a pediatric population. STUDY DESIGN: This was a retrospective analysis of a cohort of patients with pulmonary hypertension (aged ≤18 years) enrolled in the Pediatric Pulmonary Hypertension Network registry between 2014 and 2018, comprising patients at eight Pediatric Centers throughout North America (n = 1417). RESULTS: Among children diagnosed after the neonatal period, pulmonary arterial hypertension was more prevalent among Asians (OR, 1.83; 95% CI, 1.21-2.79; P = .0045), lung disease-associated pulmonary hypertension among blacks (OR, 2.09; 95% CI, 1.48-2.95; P < .0001), idiopathic pulmonary arterial hypertension among whites (OR, 1.58; 95% CI, 1.06-2.41; P = .0289), and pulmonary veno-occlusive disease among Hispanics (OR, 6.11; 95% CI, 1.34-31.3; P = .0184). Among neonates, persistent pulmonary hypertension of the newborn (OR, 4.07; 95% CI, 1.54-10.0; P = .0029) and bronchopulmonary dysplasia (OR, 8.11; 95% CI, 3.28-19.8; P < .0001) were more prevalent among blacks, and congenital diaphragmatic hernia was more prevalent among whites (OR, 2.29; 95% CI, 1.25-4.18; P = .0070). An increased mortality risk was observed among blacks (HR, 1.99; 95% CI, 1.03-3.84; P = .0396), driven primarily by the heightened mortality risk among those with lung disease-associated pulmonary hypertension (HR, 2.84; 95% CI, 1.15-7.04; P = .0241). CONCLUSIONS: We found significant racial variability in the prevalence of pulmonary hypertension subtypes and survival outcomes among children with pulmonary hypertension. Given the substantial burden of this disease, further studies to validate phenotypic differences and to understand the underlying causes of survival disparities between racial and ethnic groups are warranted.


Asunto(s)
Pediatría/métodos , Hipertensión Arterial Pulmonar/etnología , Sistema de Registros , Adolescente , Negro o Afroamericano , Niño , Preescolar , Etnicidad , Femenino , Hispánicos o Latinos , Humanos , Lactante , Recién Nacido , Masculino , América del Norte/epidemiología , Prevalencia , Hipertensión Arterial Pulmonar/diagnóstico , Hipertensión Arterial Pulmonar/mortalidad , Grupos Raciales , Análisis de Regresión , Reproducibilidad de los Resultados , Estudios Retrospectivos , Análisis de Supervivencia , Resultado del Tratamiento , Población Blanca
18.
Circ Res ; 121(4): 341-353, 2017 Aug 04.
Artículo en Inglés | MEDLINE | ID: mdl-28611076

RESUMEN

RATIONALE: Pediatric pulmonary hypertension (PH) is a heterogeneous condition with varying natural history and therapeutic response. Precise classification of PH subtypes is, therefore, crucial for individualizing care. However, gaps remain in our understanding of the spectrum of PH in children. OBJECTIVE: We seek to study the manifestations of PH in children and to assess the feasibility of applying a network-based approach to discern disease subtypes from comorbidity data recorded in longitudinal data sets. METHODS AND RESULTS: A retrospective cohort study comprising 6 943 263 children (<18 years of age) enrolled in a commercial health insurance plan in the United States, between January 2010 and May 2013. A total of 1583 (0.02%) children met the criteria for PH. We identified comorbidities significantly associated with PH compared with the general population of children without PH. A Bayesian comorbidity network was constructed to model the interdependencies of these comorbidities, and network-clustering analysis was applied to derive disease subtypes comprising subgraphs of highly connected comorbid conditions. A total of 186 comorbidities were found to be significantly associated with PH. Network analysis of comorbidity patterns captured most of the major PH subtypes with known pathological basis defined by the World Health Organization and Panama classifications. The analysis further identified many subtypes documented in only a few case studies, including rare subtypes associated with several well-described genetic syndromes. CONCLUSIONS: Application of network science to model comorbidity patterns recorded in longitudinal data sets can facilitate the discovery of disease subtypes. Our analysis relearned established subtypes, thus validating the approach, and identified rare subtypes that are difficult to discern through clinical observations, providing impetus for deeper investigation of the disease subtypes that will enrich current disease classifications.


Asunto(s)
Teorema de Bayes , Hipertensión Pulmonar/clasificación , Hipertensión Pulmonar/epidemiología , Seguro de Salud/clasificación , Niño , Preescolar , Clasificación , Estudios de Cohortes , Comorbilidad , Humanos , Hipertensión Pulmonar/diagnóstico , Seguro de Salud/estadística & datos numéricos , Estudios Retrospectivos
19.
J Biomed Inform ; 91: 103122, 2019 03.
Artículo en Inglés | MEDLINE | ID: mdl-30738949

RESUMEN

OBJECTIVE: Phenotyping algorithms can efficiently and accurately identify patients with a specific disease phenotype and construct electronic health records (EHR)-based cohorts for subsequent clinical or genomic studies. Previous studies have introduced unsupervised EHR-based feature selection methods that yielded algorithms with high accuracy. However, those selection methods still require expert intervention to tweak the parameter settings according to the EHR data distribution for each phenotype. To further accelerate the development of phenotyping algorithms, we propose a fully automated and robust unsupervised feature selection method that leverages only publicly available medical knowledge sources, instead of EHR data. METHODS: SEmantics-Driven Feature Extraction (SEDFE) collects medical concepts from online knowledge sources as candidate features and gives them vector-form distributional semantic representations derived with neural word embedding and the Unified Medical Language System Metathesaurus. A number of features that are semantically closest and that sufficiently characterize the target phenotype are determined by a linear decomposition criterion and are selected for the final classification algorithm. RESULTS: SEDFE was compared with the EHR-based SAFE algorithm and domain experts on feature selection for the classification of five phenotypes including coronary artery disease, rheumatoid arthritis, Crohn's disease, ulcerative colitis, and pediatric pulmonary arterial hypertension using both supervised and unsupervised approaches. Algorithms yielded by SEDFE achieved comparable accuracy to those yielded by SAFE and expert-curated features. SEDFE is also robust to the input semantic vectors. CONCLUSION: SEDFE attains satisfying performance in unsupervised feature selection for EHR phenotyping. Both fully automated and EHR-independent, this method promises efficiency and accuracy in developing algorithms for high-throughput phenotyping.


Asunto(s)
Registros Electrónicos de Salud , Fenotipo , Semántica , Algoritmos , Humanos
20.
J Med Internet Res ; 21(2): e12902, 2019 02 01.
Artículo en Inglés | MEDLINE | ID: mdl-30707097

RESUMEN

The Substitutable Medical Apps and Reusable Technology (SMART) Health IT project launched in 2010 to facilitate the development of medical apps that are scalable and substitutable. SMART defines an open application programming interface (API) specification that enables apps to connect to electronic health record systems and data warehouses without custom integration efforts. The SMART-enabled version of the Meducation app, developed by Polyglot, has been implemented at scores of hospitals and clinics in the United States, nation-wide. After expanding their product's reach by relying on a universal, open API for integrations, the team estimates that one project manager can handle up to 20 simultaneous implementations. The app is made available through the SMART App Gallery, an open app store that supports discovery of apps and, because the apps are substitutable, market competition. This case illustrates how a universal open API for patient and clinician-facing health IT systems supported and accelerated commercial success for a start-up company. Giving end users a wide and ever-growing choice of apps that leverage data generated by the health care system and patients at home through a universal, open API is a promising and generalizable approach for rapid diffusion of innovation across health systems.


Asunto(s)
Registros Electrónicos de Salud/normas , Programas Informáticos/normas , Humanos , Aplicaciones Móviles
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