High-throughput framework for genetic analyses of adverse drug reactions using electronic health records

Zheng, Neil S.; Stone, Cosby A.; Jiang, Lan; Shaffer, Christian M.; Kerchberger, V.E.; Chung, Cecilia P.; Feng, QiPing; Cox, Nancy J.; Stein, C. Michael; Roden, Dan M.; Denny, Joshua C.

doi:10.1371/journal.pgen.1009593

Cited by 7 publications

(2 citation statements)

References 38 publications

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“…Thus, we suggest starting with semi-structured clinical notes (e.g. problem/medication lists): for example, recent studies have demonstrated the benefits of using allergy lists for clinical studies 50 , 51 .…”

Section: Discussionmentioning

confidence: 99%

Evaluation of the portability of computable phenotypes with natural language processing in the eMERGE network

Pacheco

Rasmussen

Wiley

et al. 2023

Sci Rep

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The electronic Medical Records and Genomics (eMERGE) Network assessed the feasibility of deploying portable phenotype rule-based algorithms with natural language processing (NLP) components added to improve performance of existing algorithms using electronic health records (EHRs). Based on scientific merit and predicted difficulty, eMERGE selected six existing phenotypes to enhance with NLP. We assessed performance, portability, and ease of use. We summarized lessons learned by: (1) challenges; (2) best practices to address challenges based on existing evidence and/or eMERGE experience; and (3) opportunities for future research. Adding NLP resulted in improved, or the same, precision and/or recall for all but one algorithm. Portability, phenotyping workflow/process, and technology were major themes. With NLP, development and validation took longer. Besides portability of NLP technology and algorithm replicability, factors to ensure success include privacy protection, technical infrastructure setup, intellectual property agreement, and efficient communication. Workflow improvements can improve communication and reduce implementation time. NLP performance varied mainly due to clinical document heterogeneity; therefore, we suggest using semi-structured notes, comprehensive documentation, and customization options. NLP portability is possible with improved phenotype algorithm performance, but careful planning and architecture of the algorithms is essential to support local customizations.

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Section: Discussionmentioning

confidence: 99%

Evaluation of the portability of computable phenotypes with natural language processing in the eMERGE network

Pacheco

Rasmussen

Wiley

et al. 2023

Sci Rep

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“…These are the 2 most common gene loci influencing majority drugs used in perioperative settings. 24 Such integrative studies, deriving phenotypes from the EHR and matching up with genomic testing, are increasing and gaining traction as an efficient means to identify selected patients, reduce costs, speed up diagnosis, and improve care. 25 Futurists and advocates of PM opine that the best way to assimilate the vastness of the field into clinical utility is by open-science and open-resource tools.…”

Section: Implementation Science and Societal Acceptancementioning

confidence: 99%

Future of Perioperative Precision Medicine: Integration of Molecular Science, Dynamic Health Care Informatics, and Implementation of Predictive Pathways in Real Time

Pal

Kertai

2022

Anesthesia &Amp; Analgesia

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Conceptually, precision medicine is a deep dive to discover disease origin at the molecular or genetic level, thus providing insights that allow clinicians to design corresponding individualized patient therapies. We know that a disease state is created by not only certain molecular derangements but also a biologic milieu promoting the expression of such derangements. These factors together lead to manifested symptoms. At the level of molecular definition, every average, “similar” individual stands to be “dissimilar.” Hence, there is the need for customized therapy, moving away from therapy based on aggregate statistics. The perioperative state is a mix of several, simultaneously active molecular mechanisms, surgical insult, drugs, severe inflammatory response, and the body’s continuous adaptation to maintain a state of homeostasis. Postoperative outcomes are a net result of several of those rapid genetic and molecular transformations that do or do not ensue. With the advent and advances of artificial intelligence, the translation from identifying these intricate mechanisms to implementing them in clinical practice has made a huge leap. Precision medicine is gaining ground with the help of personalized health recorders and personal devices that identify disease mechanics, patient-reported outcomes, adverse drug reactions, and drug-drug interaction at the individual level in a closed-loop feedback system. This phenomenon is especially true given increasing surgeries in older adults, many of whom are on multiple medications and varyingly frail. In this era of precision medicine, to provide a comprehensive remedy, the perioperative surgical home must expand, incorporating not only clinicians but also basic science experts and data scientists.

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The Use of Electronic Health Records to Study Drug-Induced Hypersensitivity Reactions from 2000 to 2021

Bassir

Varghese

Wang

et al. 2022

Immunology and Allergy Clinics of North America

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High-throughput framework for genetic analyses of adverse drug reactions using electronic health records

Cited by 7 publications

References 38 publications

Evaluation of the portability of computable phenotypes with natural language processing in the eMERGE network

Evaluation of the portability of computable phenotypes with natural language processing in the eMERGE network

Future of Perioperative Precision Medicine: Integration of Molecular Science, Dynamic Health Care Informatics, and Implementation of Predictive Pathways in Real Time

The Use of Electronic Health Records to Study Drug-Induced Hypersensitivity Reactions from 2000 to 2021

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