Predicting drug side-effects by chemical systems biology

Chemical systems biology approaches can explain unexpected observations of drug inefficacy or side-effects

Evaluating risk detection methods to uncover ontogenic-mediated adverse drug effect mechanisms in children

Background Identifying adverse drugs effects (ADEs) in children, overall and within pediatric age groups, is essential for preventing disability and death from marketed drugs. At the same time, however, detection is challenging due to dynamic biological processes during growth and maturation, called ontogeny, that alter pharmacokinetics and pharmacodynamics. As a result, methodologies in pediatric drug safety have been limited to event surveillance and have not focused on investigating adverse event mechanisms. There is an opportunity to identify drug event patterns within observational databases for evaluating ontogenic-mediated adverse event mechanisms. The first step of which is to establish statistical models that can identify temporal trends of adverse effects across childhood. Results Using simulation, we evaluated a population stratification method (the proportional reporting ratio or PRR) and a population modeling method (the generalized additive model or GAM) to identify and quantify ADE risk at varying reporting rates and dynamics. We found that GAMs showed improved performance over the PRR in detecting dynamic drug event reporting across child development stages. Moreover, GAMs exhibited normally distributed and robust ADE risk estimation at all development stages by sharing information across child development stages. Conclusions Our study underscores the opportunity for using population modeling techniques, which leverage drug event reporting across development stages, as biologically-inspired detection methods for evaluating ontogenic mechanisms

3D Pharmacophoric Similarity improves Multi Adverse Drug Event Identification in Pharmacovigilance

Adverse drugs events (ADEs) detection constitutes a considerable concern in patient safety and public health care. For this reason, it is important to develop methods that improve ADE signal detection in pharmacovigilance databases. Our objective is to apply 3D pharmacophoric similarity models to enhance ADE recognition in Offsides, a pharmacovigilance resource with drug-ADE associations extracted from the FDA Adverse Event Reporting System (FAERS). We developed a multi-ADE predictor implementing 3D drug similarity based on a pharmacophoric approach, with an ADE reference standard extracted from the SIDER database. The results showed that the application of our 3D multi-type ADE predictor to the pharmacovigilance data in Offsides improved ADE identification and generated enriched sets of drug-ADE signals. The global ROC curve for the Offsides ADE candidates ranked with the 3D similarity score showed an area of 0.7. The 3D predictor also allows the identification of the most similar drug that causes the ADE under study, which could provide hypotheses about mechanisms of action and ADE etiology. Our method is useful in drug development, screening potential adverse effects in experimental drugs, and in drug safety, applicable to the evaluation of ADE signals selected through pharmacovigilance data mining

Ten Simple Rules to Enable Multi-site Collaborations through Data Sharing

Open access, open data, and software are critical for advancing science and enabling collaboration across multiple institutions and throughout the world. Despite near universal recognition of its importance, major barriers still exist to sharing raw data, software, and research products throughout the scientific community. Many of these barriers vary by specialty [1], increasing the difficulties for interdisciplinary and/or translational researchers to engage in collaborative research. Multi-site collaborations are vital for increasing both the impact and the generalizability of research results. However, they often present unique data sharing challenges. We discuss enabling multi-site collaborations through enhanced data sharing in this set of Ten Simple Rules

3D Pharmacophoric Similarity improves Multi Adverse Drug Event Identification in Pharmacovigilance

Adverse drugs events (ADEs) detection constitutes a considerable concern in patient safety and public health care. For this reason, it is important to develop methods that improve ADE signal detection in pharmacovigilance databases. Our objective is to apply 3D pharmacophoric similarity models to enhance ADE recognition in Offsides, a pharmacovigilance resource with drug-ADE associations extracted from the FDA Adverse Event Reporting System (FAERS). We developed a multi-ADE predictor implementing 3D drug similarity based on a pharmacophoric approach, with an ADE reference standard extracted from the SIDER database. The results showed that the application of our 3D multi-type ADE predictor to the pharmacovigilance data in Offsides improved ADE identification and generated enriched sets of drug-ADE signals. The global ROC curve for the Offsides ADE candidates ranked with the 3D similarity score showed an area of 0.7. The 3D predictor also allows the identification of the most similar drug that causes the ADE under study, which could provide hypotheses about mechanisms of action and ADE etiology. Our method is useful in drug development, screening potential adverse effects in experimental drugs, and in drug safety, applicable to the evaluation of ADE signals selected through pharmacovigilance data mining

ROMOP: a light-weight R package for interfacing with OMOP-formatted electronic health record data.

Objectives:Electronic health record (EHR) data are increasingly used for biomedical discoveries. The nature of the data, however, requires expertise in both data science and EHR structure. The Observational Medical Out-comes Partnership (OMOP) common data model (CDM) standardizes the language and structure of EHR data to promote interoperability of EHR data for research. While the OMOP CDM is valuable and more attuned to research purposes, it still requires extensive domain knowledge to utilize effectively, potentially limiting more widespread adoption of EHR data for research and quality improvement. Materials and methods:We have created ROMOP: an R package for direct interfacing with EHR data in the OMOP CDM format. Results:ROMOP streamlines typical EHR-related data processes. Its functions include exploration of data types, extraction and summarization of patient clinical and demographic data, and patient searches using any CDM vocabulary concept. Conclusion:ROMOP is freely available under the Massachusetts Institute of Technology (MIT) license and can be obtained from GitHub (http://github.com/BenGlicksberg/ROMOP). We detail instructions for setup and use in the Supplementary Materials. Additionally, we provide a public sandbox server containing synthesized clinical data for users to explore OMOP data and ROMOP (http://romop.ucsf.edu)

Coherent Functional Modules Improve Transcription Factor Target Identification, Cooperativity Prediction, and Disease Association

Transcription factors (TFs) are fundamental controllers of cellular regulation that function in a complex and combinatorial manner. Accurate identification of a transcription factor's targets is essential to understanding the role that factors play in disease biology. However, due to a high false positive rate, identifying coherent functional target sets is difficult. We have created an improved mapping of targets by integrating ChIP-Seq data with 423 functional modules derived from 9,395 human expression experiments. We identified 5,002 TF-module relationships, significantly improved TF target prediction, and found 30 high-confidence TF-TF associations, of which 14 are known. Importantly, we also connected TFs to diseases through these functional modules and identified 3,859 significant TF-disease relationships. As an example, we found a link between MEF2A and Crohn's disease, which we validated in an independent expression dataset. These results show the power of combining expression data and ChIP-Seq data to remove noise and better extract the associations between TFs, functional modules, and disease

An integrative method for scoring candidate genes from association studies: application to warfarin dosing

BackgroundA key challenge in pharmacogenomics is the identification of genes whose variants contribute to drug response phenotypes, which can include severe adverse effects. Pharmacogenomics GWAS attempt to elucidate genotypes predictive of drug response. However, the size of these studies has severely limited their power and potential application. We propose a novel knowledge integration and SNP aggregation approach for identifying genes impacting drug response. Our SNP aggregation method characterizes the degree to which uncommon alleles of a gene are associated with drug response. We first use pre-existing knowledge sources to rank pharmacogenes by their likelihood to affect drug response. We then define a summary score for each gene based on allele frequencies and train linear and logistic regression classifiers to predict drug response phenotypes.ResultsWe applied our method to a published warfarin GWAS data set comprising 181 individuals. We find that our method can increase the power of the GWAS to identify both VKORC1 and CYP2C9 as warfarin pharmacogenes, where the original analysis had only identified VKORC1. Additionally, we find that our method can be used to discriminate between low-dose (AUROC=0.886) and high-dose (AUROC=0.764) responders.ConclusionsOur method offers a new route for candidate pharmacogene discovery from pharmacogenomics GWAS, and serves as a foundation for future work in methods for predictive pharmacogenomics

Detection of drug-drug interactions by modeling interaction profile fingerprints

Drug-drug interactions (DDIs) constitute an important problem in postmarketing pharmacovigilance and in the development of new drugs. The effectiveness or toxicity of a medication could be affected by the co-administration of other drugs that share pharmacokinetic or pharmacodynamic pathways. For this reason, a great effort is being made to develop new methodologies to detect and assess DDIs. In this article, we present a novel method based on drug interaction profile fingerprints (IPFs) with successful application to DDI detection. IPFs were generated based on the DrugBank database, which provided 9,454 well-established DDIs as a primary source of interaction data. The model uses IPFs to measure the similarity of pairs of drugs and generates new putative DDIs from the non-intersecting interactions of a pair. We described as part of our analysis the pharmacological and biological effects associated with the putative interactions; for example, the interaction between haloperidol and dicyclomine can cause increased risk of psychosis and tardive dyskinesia. First, we evaluated the method through hold-out validation and then by using four independent test sets that did not overlap with DrugBank. Precision for the test sets ranged from 0.4–0.5 with more than two fold enrichment factor enhancement. In conclusion, we demonstrated the usefulness of the method in pharmacovigilance as a DDI predictor, and created a dataset of potential DDIs, highlighting the etiology or pharmacological effect of the DDI, and providing an exploratory tool to facilitate decision support in DDI detection and patient safety.This work was supported by grants R01 LM010016 (CF), R01 LM010016-0S1 (CF), R01 LM010016-0S2 (CF), R01 LM008635 (CF), “Plan Galego de Investigación, Innovación e Crece-mento 2011–2015 (I2C)”, European Social Fund (ESF) and Angeles Alvariño program from Xunta de Galicia (Spain)S