The combination of improved genomic analysis methods, decreasing genotyping costs, and increasing computing resources has led to an explosion of clinical genomic knowledge in the last decade. Similarly, healthcare systems are increasingly adopting robust electronic health record (EHR) systems that not only can improve health care, but also contain a vast repository of disease and treatment data that could be mined for genomic research. Indeed, institutions are creating EHR-linked DNA biobanks to enable genomic and pharmacogenomic research, using EHR data for phenotypic information. However, EHRs are designed primarily for clinical care, not research, so reuse of clinical EHR data for research purposes can be challenging. Difficulties in use of EHR data include: data availability, missing data, incorrect data, and vast quantities of unstructured narrative text data. Structured information includes billing codes, most laboratory reports, and other variables such as physiologic measurements and demographic information. Significant information, however, remains locked within EHR narrative text documents, including clinical notes and certain categories of test results, such as pathology and radiology reports. For relatively rare obs...Continue Reading
A new method of classifying prognostic comorbidity in longitudinal studies: development and validation
Evaluation of a deidentification (De-Id) software engine to share pathology reports and clinical documents for research
Accuracy of Medicare claims-based diagnosis of acute myocardial infarction: estimating positive predictive value on the basis of review of hospital records
Collecting information on the quality of prescribing in primary care using semi-automatic data extraction from GPs' electronic medical records
Re: combination of intraneural injection and high-injection pressure leads to fasicular injury and neurologic deficits in dogs
Transition to the new race/ethnicity data collection standards in the Department of Veterans Affairs
Extracting principal diagnosis, co-morbidity and smoking status for asthma research: evaluation of a natural language processing system
Using regular expressions to abstract blood pressure and treatment intensification information from the text of physician notes
Informed consent and subject motivation to participate in a large, population-based genomics study: the Marshfield Clinic Personalized Medicine Research Project
A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants
Automated identification of acute hepatitis B using electronic medical record data to facilitate public health surveillance
Association of chromosome 9p21 SNPs with cardiovascular phenotypes in morbid obesity using electronic health record data
Characterization of low-density lipoprotein cholesterol-lowering efficacy for atorvastatin in a population-based DNA biorepository
Association of three genetic loci with uric acid concentration and risk of gout: a genome-wide association study
Collaborative genome-wide association studies of diverse diseases: programs of the NHGRI's office of population genomics
Active computerized pharmacovigilance using natural language processing, statistics, and electronic health records: a feasibility study
Potential etiologic and functional implications of genome-wide association loci for human diseases and traits
Opportunities and challenges for the NIH--an interview with Francis Collins. Interview by Robert Steinbrook
Follow-up of 1715 SNPs from the Wellcome Trust Case Control Consortium genome-wide association study in type I diabetes families
Robust replication of genotype-phenotype associations across multiple diseases in an electronic medical record
Applying active learning to high-throughput phenotyping algorithms for electronic health records data
Combining structured and unstructured data to identify a cohort of ICU patients who received dialysis
Effectively processing medical term queries on the UMLS Metathesaurus by layered dynamic programming
Design patterns for the development of electronic health record-driven phenotype extraction algorithms
A systematic comparison of feature space effects on disease classifier performance for phenotype identification of five diseases.
Evaluation of matched control algorithms in EHR-based phenotyping studies: a case study of inflammatory bowel disease comorbidities
Engaging Māori in biobanking and genomic research: a model for biobanks to guide culturally informed governance, operational, and community engagement activities
Review and evaluation of electronic health records-driven phenotype algorithm authoring tools for clinical and translational research
The tip of the iceberg: challenges of accessing hospital electronic health record data for biological data mining
Validating drug repurposing signals using electronic health records: a case study of metformin associated with reduced cancer mortality
Evaluating phecodes, clinical classification software, and ICD-9-CM codes for phenome-wide association studies in the electronic health record
Design and anticipated outcomes of the eMERGE-PGx project: a multicenter pilot for preemptive pharmacogenomics in electronic health record systems
Phenome-wide association study of TTR and RBP4 genes in 361,194 individuals reveals novel insights in the genetics of hereditary and wildtype transthyretin amyloidoses
Phenotype-genotype comorbidity analysis of patients with rare disorders provides insight into their pathological and molecular bases.
Improving a full-text search engine: the importance of negation detection and family history context to identify cases in a biomedical data warehouse
A case study evaluating the portability of an executable computable phenotype algorithm across multiple institutions and electronic health record environments
Automatic identification of methotrexate-induced liver toxicity in patients with rheumatoid arthritis from the electronic medical record
TEPAPA: a novel in silico feature learning pipeline for mining prognostic and associative factors from text-based electronic medical records
A study paradigm integrating prospective epidemiologic cohorts and electronic health records to identify disease biomarkers
Linking glycemic dysregulation in diabetes to symptoms, comorbidities, and genetics through EHR data mining
Assessing the role of a medication-indication resource in the treatment relation extraction from clinical text
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