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Introduction: Pharmacovigilance programs protect patient health and safety by identifying adverse event signals through postmarketing surveillance of claims data and spontaneous reports. Electronic health records (EHRs) provide new opportunities to address limitations of traditional approaches and promote discovery-oriented pharmacovigilance., Methods: To evaluate the current state of EHR-based medication safety signal identification, we conducted a scoping literature review of studies aimed at identifying safety signals from routinely collected patient-level EHR data. We extracted information on study design, EHR data elements utilized, analytic methods employed, drugs and outcomes evaluated, and key statistical and data analysis choices., Results: We identified 81 eligible studies. Disproportionality methods were the predominant analytic approach, followed by data mining and regression. Variability in study design makes direct comparisons difficult. Studies varied widely in terms of data, confounding adjustment, and statistical considerations., Conclusion: Despite broad interest in utilizing EHRs for safety signal identification, current efforts fail to leverage the full breadth and depth of available data or to rigorously control for confounding. The development of best practices and application of common data models would promote the expansion of EHR-based pharmacovigilance., (© 2023. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

Objective: Improving mechanisms to detect adverse drug reactions (ADRs) is key to strengthening post-marketing drug safety surveillance. Signal detection is presently unimodal, relying on a single information source. Multimodal signal detection is based on jointly analyzing multiple information sources. Building on, and expanding the work done in prior studies, the aim of the article is to further research on multimodal signal detection, explore its potential benefits, and propose methods for its construction and evaluation., Material and Methods: Four data sources are investigated; FDA's adverse event reporting system, insurance claims, the MEDLINE citation database, and the logs of major Web search engines. Published methods are used to generate and combine signals from each data source. Two distinct reference benchmarks corresponding to well-established and recently labeled ADRs respectively are used to evaluate the performance of multimodal signal detection in terms of area under the ROC curve (AUC) and lead-time-to-detection, with the latter relative to labeling revision dates., Results: Limited to our reference benchmarks, multimodal signal detection provides AUC improvements ranging from 0.04 to 0.09 based on a widely used evaluation benchmark, and a comparative added lead-time of 7-22 months relative to labeling revision dates from a time-indexed benchmark., Conclusions: The results support the notion that utilizing and jointly analyzing multiple data sources may lead to improved signal detection. Given certain data and benchmark limitations, the early stage of development, and the complexity of ADRs, it is currently not possible to make definitive statements about the ultimate utility of the concept. Continued development of multimodal signal detection requires a deeper understanding the data sources used, additional benchmarks, and further research on methods to generate and synthesize signals., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Identification of adverse drug reactions (ADRs) during the post-marketing phase is one of the most important goals of drug safety surveillance. Spontaneous reporting systems (SRS) data, which are the mainstay of traditional drug safety surveillance, are used for hypothesis generation and to validate the newer approaches. The publicly available US Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS) data requires substantial curation before they can be used appropriately, and applying different strategies for data cleaning and normalization can have material impact on analysis results. We provide a curated and standardized version of FAERS removing duplicate case records, applying standardized vocabularies with drug names mapped to RxNorm concepts and outcomes mapped to SNOMED-CT concepts, and pre-computed summary statistics about drug-outcome relationships for general consumption. This publicly available resource, along with the source code, will accelerate drug safety research by reducing the amount of time spent performing data management on the source FAERS reports, improving the quality of the underlying data, and enabling standardized analyses using common vocabularies.

Big Data holds the promise of fundamentally transforming the manner in which adverse drug reactions can be identified and evaluated. This commentary discusses new data sources that are envisioned to form a Big Data-enabled pharmacovigilance system and the role of these data in powering the future of adverse drug reactions detection., (© 2015 ASCPT.)

Background and Objective: Several studies have demonstrated the ability to detect adverse events potentially related to multiple drug exposure via data mining. However, the number of putative associations produced by such computational approaches is typically large, making experimental validation difficult. We theorized that those potential associations for which there is evidence from multiple complementary sources are more likely to be true, and explored this idea using a published database of drug-drug-adverse event associations derived from electronic health records (EHRs)., Methods: We prioritized drug-drug-event associations derived from EHRs using four sources of information: (1) public databases, (2) sources of spontaneous reports, (3) literature, and (4) non-EHR drug-drug interaction (DDI) prediction methods. After pre-filtering the associations by removing those found in public databases, we devised a ranking for associations based on the support from the remaining sources, and evaluated the results of this rank-based prioritization., Results: We collected information for 5983 putative EHR-derived drug-drug-event associations involving 345 drugs and ten adverse events from four data sources and four prediction methods. Only seven drug-drug-event associations (<0.5 %) had support from the majority of evidence sources, and about one third (1777) had support from at least one of the evidence sources., Conclusions: Our proof-of-concept method for scoring putative drug-drug-event associations from EHRs offers a systematic and reproducible way of prioritizing associations for further study. Our findings also quantify the agreement (or lack thereof) among complementary sources of evidence for drug-drug-event associations and highlight the challenges of developing a robust approach for prioritizing signals of these associations.

Post-market drug safety surveillance is hugely important and is a significant challenge despite the existence of adverse event (AE) reporting systems. Here we describe a preliminary analysis of search logs from healthcare professionals as a source for detecting adverse drug events. We annotate search log query terms with biomedical terminologies for drugs and events, and then perform a statistical analysis to identify associations among drugs and events within search sessions. We evaluate our approach using two different types of reference standards consisting of known adverse drug events (ADEs) and negative controls. Our approach achieves a discrimination accuracy of 0.85 in terms of the area under the receiver operator curve (AUC) for the reference set of well-established ADEs and an AUC of 0.68 for the reference set of recently labeled ADEs. We also find that the majority of associations in the reference sets have support in the search log data. Despite these promising results additional research is required to better understand users' search behavior, biasing factors, and the overall utility of analyzing healthcare professional search logs for drug safety surveillance.

Undetected adverse drug reactions (ADRs) pose a major burden on the health system. Data mining methodologies designed to identify signals of novel ADRs are of deep importance for drug safety surveillance. The development and evaluation of these methodologies requires proper reference benchmarks. While progress has recently been made in developing such benchmarks, our understanding of the performance characteristics of the data mining methodologies is limited because existing benchmarks do not support prospective performance evaluations. We address this shortcoming by providing a reference standard to support prospective performance evaluations. The reference standard was systematically curated from drug labeling revisions, such as new warnings, which were issued and communicated by the US Food and Drug Administration in 2013. The reference standard includes 62 positive test cases and 75 negative controls, and covers 44 drugs and 38 events. We provide usage guidance and empirical support for the reference standard by applying it to analyze two data sources commonly mined for drug safety surveillance.

The promise of augmenting pharmacovigilance with patient-generated data drawn from the Internet was called out by a scientific committee charged with conducting a review of the current and planned pharmacovigilance practices of the US Food and Drug Administration (FDA). To this end, we present a study on harnessing behavioral data drawn from Internet search logs to detect adverse drug reactions (ADRs). By analyzing search queries collected from 80 million consenting users and by using a widely recognized benchmark of ADRs, we found that the performance of ADR detection via search logs is comparable and complementary to detection based on the FDA's adverse event reporting system (AERS). We show that by jointly leveraging data from the AERS and search logs, the accuracy of ADR detection can be improved by 19% relative to the use of each data source independently. The results suggest that leveraging nontraditional sources such as online search logs could supplement existing pharmacovigilance approaches.

Signal-detection algorithms (SDAs) are recognized as vital tools in pharmacovigilance. However, their performance characteristics are generally unknown. By leveraging a unique gold standard recently made public by the Observational Medical Outcomes Partnership (OMOP) and by conducting a unique systematic evaluation, we provide new insights into the diagnostic potential and characteristics of SDAs that are routinely applied to the US Food and Drug Administration (FDA) Adverse Event Reporting System (AERS). We find that SDAs can attain reasonable predictive accuracy in signaling adverse events. Two performance classes emerge, indicating that the class of approaches that address confounding and masking effects benefits safety surveillance. Our study shows that not all events are equally detectable, suggesting that specific events might be monitored more effectively using other data sources. We provide performance guidelines for several operating scenarios to inform the trade-off between sensitivity and specificity for specific use cases. We also propose an approach and demonstrate its application in identifying optimal signaling thresholds, given specific misclassification tolerances.

With increasing adoption of electronic health records (EHRs), there is an opportunity to use the free-text portion of EHRs for pharmacovigilance. We present novel methods that annotate the unstructured clinical notes and transform them into a deidentified patient-feature matrix encoded using medical terminologies. We demonstrate the use of the resulting high-throughput data for detecting drug-adverse event associations and adverse events associated with drug-drug interactions. We show that these methods flag adverse events early (in most cases before an official alert), allow filtering of spurious signals by adjusting for potential confounding, and compile prevalence information. We argue that analyzing large volumes of free-text clinical notes enables drug safety surveillance using a yet untapped data source. Such data mining can be used for hypothesis generation and for rapid analysis of suspected adverse event risk.

Objective: Data-mining algorithms that can produce accurate signals of potentially novel adverse drug reactions (ADRs) are a central component of pharmacovigilance. We propose a signal-detection strategy that combines the adverse event reporting system (AERS) of the Food and Drug Administration and electronic health records (EHRs) by requiring signaling in both sources. We claim that this approach leads to improved accuracy of signal detection when the goal is to produce a highly selective ranked set of candidate ADRs., Materials and Methods: Our investigation was based on over 4 million AERS reports and information extracted from 1.2 million EHR narratives. Well-established methodologies were used to generate signals from each source. The study focused on ADRs related to three high-profile serious adverse reactions. A reference standard of over 600 established and plausible ADRs was created and used to evaluate the proposed approach against a comparator., Results: The combined signaling system achieved a statistically significant large improvement over AERS (baseline) in the precision of top ranked signals. The average improvement ranged from 31% to almost threefold for different evaluation categories. Using this system, we identified a new association between the agent, rasburicase, and the adverse event, acute pancreatitis, which was supported by clinical review., Conclusions: The results provide promising initial evidence that combining AERS with EHRs via the framework of replicated signaling can improve the accuracy of signal detection for certain operating scenarios. The use of additional EHR data is required to further evaluate the capacity and limits of this system and to extend the generalizability of these results.