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A major challenge in human genetics is to devise a systematic strategy to integrate disease-associated variants with diverse genomic and biological data sets to provide insight into disease pathogenesis and guide drug discovery for complex traits such as rheumatoid arthritis (RA). Here we performed a genome-wide association study meta-analysis in a total of(More)
Medication information is one of the most important types of clinical data in electronic medical records. It is critical for healthcare safety and quality, as well as for clinical research that uses electronic medical record data. However, medication data are often recorded in clinical notes as free-text. As such, they are not accessible to other(More)
Candidate gene and genome-wide association studies (GWAS) have identified genetic variants that modulate risk for human disease; many of these associations require further study to replicate the results. Here we report the first large-scale application of the phenome-wide association study (PheWAS) paradigm within electronic medical records (EMRs), an(More)
Genome-wide association studies (GWAS) have identified thousands of variants robustly associated with complex traits. However, the biological mechanisms underlying these associations are, in general, not well understood. We propose a gene-based association method called PrediXcan that directly tests the molecular mechanisms through which genetic variation(More)
We repurposed existing genotypes in DNA biobanks across the Electronic Medical Records and Genomics network to perform a genome-wide association study for primary hypothyroidism, the most common thyroid disease. Electronic selection algorithms incorporating billing codes, laboratory values, text queries, and medication records identified 1317 cases and 5053(More)
The erythrocyte sedimentation rate (ESR), a commonly performed test of the acute phase response, is the rate at which erythrocytes sediment in vitro in 1 hr. The molecular basis of erythrocyte sedimentation is unknown. To identify genetic variants associated with ESR, we carried out a genome-wide association study of 7607 patients in the Electronic Medical(More)
Clinical documentation is central to patient care. The success of electronic health record system adoption may depend on how well such systems support clinical documentation. A major goal of integrating clinical documentation into electronic heath record systems is to generate reusable data. As a result, there has been an emphasis on deploying(More)
OBJECTIVE Clinical notes, typically written in natural language, often contain substructure that divides them into sections, such as "History of Present Illness" or "Family Medical History." The authors designed and evaluated an algorithm ("SecTag") to identify both labeled and unlabeled (implied) note section headers in "history and physical examination"(More)
Clinical Natural Language Processing (NLP) systems extract clinical information from narrative clinical texts in many settings. Previous research mentions the challenges of handling abbreviations in clinical texts, but provides little insight into how well current NLP systems correctly recognize and interpret abbreviations. In this paper, we compared(More)
Variants in ABCB1 and CYP2C19 have been identified as predictors of cardiac events during clopidogrel therapy initiated after myocardial infarction (MI) or percutaneous coronary intervention (PCI). In addition, PON1 has recently been associated with stent thrombosis. The reported effects of these variants have not yet been replicated in a real-world(More)