Secondary use of clinical data
Ioana Danciu,James D. Cowan,Melissa A. Basford,Xiaoming Wang,Alexander Saip,Susan Osgood,Jana K. Shirey-Rice,Jacqueline Kirby,Paul A. Harris +8 more
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TLDR
This work provides a summary of the Vanderbilt research data warehouse framework's approach in the secondary use of clinical data for research domain, including a description of key components and a list of lessons learned, designed to assist others assembling similar services and infrastructure.About:
This article is published in Journal of Biomedical Informatics.The article was published on 2014-12-01 and is currently open access. It has received 205 citations till now. The article focuses on the topics: Spatial data infrastructure & Data access layer.read more
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PRSice-2: Polygenic Risk Score software for biobank-scale data.
TL;DR: PRSice-2 is introduced, an efficient and scalable software program for automating and simplifying PRS analyses on large-scale data, and its combination of efficiency and power will be increasingly important as data sizes grow and as the applications of PRS become more sophisticated, e.g., when incorporated into high-dimensional or gene set–based analyses.
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Precision medicine in cardiology
TL;DR: The cardiovascular research and clinical communities are ideally positioned to address the epidemic of noncommunicable causes of death, as well as advance the understanding of human health and disease, through the development and implementation of precision medicine.
Journal ArticleDOI
Penetrance and Pleiotropy of Polygenic Risk Scores for Schizophrenia in 106,160 Patients Across Four Health Care Systems
Amanda B Zheutlin,Amanda B Zheutlin,Jessica Dennis,Richard Karlsson Linnér,Arden Moscati,Nicole Restrepo,Peter Straub,Douglas M. Ruderfer,Victor M. Castro,Chia-Yen Chen,Chia-Yen Chen,Tian Ge,Laura M. Huckins,Alexander W. Charney,H. Lester Kirchner,Eli A. Stahl,Eli A. Stahl,Christopher F. Chabris,Lea K. Davis,Jordan W. Smoller,Jordan W. Smoller +20 more
TL;DR: The study demonstrates that an available measure of genetic risk for schizophrenia is robustly associated with schizophrenia in health care settings and has pleiotropic effects on related psychiatric disorders as well as other medical syndromes.
Journal ArticleDOI
SMART on FHIR Genomics: Facilitating standardized clinico-genomic apps
Gil Alterovitz,Jeremy L. Warner,Peijin Zhang,Yishen Chen,Mollie Ullman-Cullere,David A. Kreda,Isaac S. Kohane +6 more
TL;DR: This prototyping work suggests that an entirely data (and web) standards-based approach could prove both effective and efficient for advancing personalized medicine.
Journal ArticleDOI
A clinician friendly data warehouse oriented toward narrative reports: Dr. Warehouse.
Nicolas Garcelon,Antoine Neuraz,Rémi Salomon,Hassan Faour,Vincent Benoit,Arthur Delapalme,Arnold Munnich,Anita Burgun,Bastien Rance +8 more
TL;DR: Dr. Warehouse is dedicated to translational research with cohort recruitment capabilities, high throughput phenotyping and patient centric views (including similarity metrics among patients), and features leverage Natural Language Processing based on the extraction of UMLS® concepts, as well as negation and family history detection.
References
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Research electronic data capture (REDCap)-A metadata-driven methodology and workflow process for providing translational research informatics support
Paul A. Harris,Robert W. Taylor,Robert J. Thielke,Jonathon Payne,Nathaniel Gonzalez,José G. Conde +5 more
TL;DR: Research electronic data capture (REDCap) is a novel workflow methodology and software solution designed for rapid development and deployment of electronic data Capture tools to support clinical and translational research.
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STRIDE--An integrated standards-based translational research informatics platform.
TL;DR: STRIDE's semantic model uses standardized terminologies, such as SNOMED, RxNorm, ICD and CPT, to represent important biomedical concepts and their relationships to create a standards-based informatics platform supporting clinical and translational research.
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PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations.
Joshua C. Denny,Marylyn D. Ritchie,Melissa A. Basford,Jill M. Pulley,Lisa Bastarache,Kristin Brown-Gentry,Deede Wang,Daniel R. Masys,Dan M. Roden,Dana C. Crawford +9 more
TL;DR: A novel method to scan phenomic data for genetic associations using International Classification of Disease billing codes, which are available in most EMR systems, and develops a code translation table to automatically define 776 different disease populations and their controls using prevalent ICD9 codes derived from EMR data.
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Development of a large-scale de-identified DNA biobank to enable personalized medicine.
Dan M. Roden,Jill M. Pulley,Melissa A. Basford,Gordon R. Bernard,Ellen Wright Clayton,Jeffrey R. Balser,Masys +6 more
TL;DR: A “opt‐out” model was implemented after significant review and revision to develop a DNA biobank linked to phenotypic data derived from an electronic medical record (EMR) system.
Journal ArticleDOI
The use of receiver operating characteristic curves in biomedical informatics
TL;DR: The basic concepts of ROC analysis are reviewed, their use with sample calculations, make recommendations drawn from the literature, and list readily available software are made.
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