Using EHR-Linked Biobank Data to Study Metformin Pharmacogenomics.
Ontology highlight
ABSTRACT:
SUBMITTER: Breitenstein MK
PROVIDER: S-EPMC5051541 | biostudies-literature | 2015
REPOSITORIES: biostudies-literature
Publications
Using EHR-Linked Biobank Data to Study Metformin Pharmacogenomics.
Breitenstein Matthew K MK Simon Gyorgy G Ryu Euijung E Armasu Sebastian M SM Weinshilboum Richard M RM Wang Liewei L Pathak Jyotishman J
Studies in health technology and informatics 20150101
Metformin is a commonly prescribed diabetes medication whose mechanism of action is poorly understood. In this study we utilized EHR-linked biobank data to elucidate the impact of genomic variation on glycemic response to metformin. Our study found significant gene- and SNP-level associations within the beta-2 subunit of the heterotrimeric adenosine monophosphate-activated protein kinase complex. Using EHR phenotypes where were able to add additional clarity to ongoing metformin pharmacogenomic ...[more]
Similar Datasets
Project description:Primary care EHR data are often of clinical importance to cohort studies however they require careful handling. Challenges include determining the periods during which EHR data were collected. Participants are typically censored when they deregister from a medical practice, however, cohort studies wish to follow participants longitudinally including those that change practice. Using UK Biobank as an exemplar, we developed methodology to infer continuous periods of data collection and maximize follow-up in longitudinal studies. This resulted in longer follow-up for around 40% of participants with multiple registration records (mean increase of 3.8 years from the first study visit). The approach did not sacrifice phenotyping accuracy when comparing agreement between self-reported and EHR data. A diabetes mellitus case study illustrates how the algorithm supports longitudinal study design and provides further validation. We use UK Biobank data, however, the tools provided can be used for other conditions and studies with minimal alteration.
| S-EPMC8800530 | biostudies-literature
Project description:Metformin is a first-line antihyperglycemic agent commonly prescribed in type 2 diabetes mellitus (T2DM), but whose pharmacogenomics are not clearly understood. Further, due to accumulating evidence highlighting the potential for metformin in cancer prevention and treatment efforts it is imperative to understand molecular mechanisms of metformin. In this electronic health record(EHR)-based study we explore the potential association of the flavin-containing monooxygenase(FMO)-5 gene, a biologically plausible biotransformer of metformin, and modifying glycemic response to metformin treatment. Using a cohort of 258 T2DM patients who had new metformin exposure, existing genetic data, and longitudinal electronic health records, we compared genetic variation within FMO5 to change in glycemic response. Gene-level and SNP-level analysis identified marginally significant associations for FMO5 variation, representing an EHR-driven pharmacogenetics hypothesis for a potential novel mechanism for metformin biotransformation. However, functional validation of this EHR-based hypothesis is necessary to ascertain its clinical and biological significance.
| S-EPMC4525256 | biostudies-literature
Project description:Metformin is currently considered as a promising anticancer agent in addition to its anti-diabetic effect. To better individualize metformin therapy and explore novel molecular mechanisms in cancer treatment, we conducted a pharmacogenomic study using 266 lymphoblastoid cell lines (LCLs). Metformin cytotoxicity assay was performed using the MTS assay. Genome-wide association (GWA) analyses were performed in LCLs using 1.3 million SNPs, 485k DNA methylation probes, 54k mRNA expression probe sets, and metformin cytotoxicity (IC50s). Top candidate genes were functionally validated using siRNA screening, followed by MTS assay in breast cancer cell lines. Further study of one top candidate, STUB1, was performed to elucidate the mechanisms by which STUB1 might contribute to metformin action. GWA analyses in LCLs identified 198 mRNA expression probe sets, 12 SNP loci, and 5 DNA methylation loci associated with metformin IC50 with P-values?<10?4 or?<10?5. Integrated SNP/methylation loci-expression-IC50 analyses found 3 SNP loci or 5 DNA methylation loci associated with metformin IC50 through trans-regulation of expression of 11 or 26 genes with P-value?<10?4. Functional validation of top 61 candidate genes in 4 IPA networks indicated down regulation of 14 genes significantly altered metformin sensitivity in two breast cancer cell lines. Mechanistic studies revealed that the E3 ubiquitin ligase, STUB1, could influence metformin response by facilitating proteasome-mediated degradation of cyclin A. GWAS using a genomic data-enriched LCL model system, together with functional and mechanistic studies using cancer cell lines, help us to identify novel genetic and epigenetic biomarkers involved in metformin anticancer response.
| S-EPMC6078562 | biostudies-literature
Project description:The incidence of type 2 diabetes (T2D) and its costs to the health care system continue to rise. Despite the availability of at least 10 drug classes for the treatment of T2D, metformin remains the most widely used first-line pharmacotherapy for its treatment; however, marked interindividual variability in response and few clinical or biomarker predictors of response reduce its optimal use. As clinical care moves toward precision medicine, a variety of broad discovery-based "omics" approaches will be required. Technical innovation, decreasing sequencing cost, and routine sample storage and processing has made pharmacogenomics the most widely applied discovery-based approach to date. This opens up the opportunity to understand the genetics underlying the interindividual variation in metformin responses in order for clinicians to prescribe specific treatments to given individuals for better efficacy and safety: metformin for those predicted to respond and alternative therapies for those predicted to be nonresponders or who are at increased risk for adverse side effects. Furthermore, understanding of the genetic determinants of metformin response may lead to the identification of novel targets and development of more effective agents for diabetes treatment. The goals of this workshop sponsored by the National Institute of Diabetes and Digestive and Kidney Diseases were to review the state of research on metformin pharmacogenomics, discuss the scientific and clinical hurdles to furthering our knowledge of the variability in patient responses to metformin, and consider how to effectively use this increased understanding to improve patient outcomes.
| S-EPMC4113063 | biostudies-literature
Project description:The UK Biobank is a rich national health resource that provides enormous opportunities for international researchers to examine, model, and analyze census-like multisource healthcare data. The archive presents several challenges related to aggregation and harmonization of complex data elements, feature heterogeneity and salience, and health analytics. Using 7,614 imaging, clinical, and phenotypic features of 9,914 subjects we performed deep computed phenotyping using unsupervised clustering and derived two distinct sub-cohorts. Using parametric and nonparametric tests, we determined the top 20 most salient features contributing to the cluster separation. Our approach generated decision rules to predict the presence and progression of depression or other mental illnesses by jointly representing and modeling the significant clinical and demographic variables along with the derived salient neuroimaging features. We reported consistency and reliability measures of the derived computed phenotypes and the top salient imaging biomarkers that contributed to the unsupervised clustering. This clinical decision support system identified and utilized holistically the most critical biomarkers for predicting mental health, e.g., depression. External validation of this technique on different populations may lead to reducing healthcare expenses and improving the processes of diagnosis, forecasting, and tracking of normal and pathological aging.
| S-EPMC6461626 | biostudies-literature
Project description:OBJECTIVES:The study sought to identify collaborative electronic health record (EHR) usage patterns for pediatric trauma patients and determine how the usage patterns are related to patient outcomes. MATERIALS AND METHODS:A process mining-based network analysis was applied to EHR metadata and trauma registry data for a cohort of pediatric trauma patients with minor injuries at a Level I pediatric trauma center. The EHR metadata were processed into an event log that was segmented based on gaps in the temporal continuity of events. A usage pattern was constructed for each encounter by creating edges among functional roles that were captured within the same event log segment. These patterns were classified into groups using graph kernel and unsupervised spectral clustering methods. Demographics, clinical and network characteristics, and emergency department (ED) length of stay (LOS) of the groups were compared. RESULTS:Three distinct usage patterns that differed by network density were discovered: fully connected (clique), partially connected, and disconnected (isolated). Compared with the fully connected pattern, encounters with the partially connected pattern had an adjusted median ED LOS that was significantly longer (242.6 [95% confidence interval, 236.9-246.0] minutes vs 295.2 [95% confidence, 289.2-297.8] minutes), more frequently seen among day shift and weekday arrivals, and involved otolaryngology, ophthalmology services, and child life specialists. DISCUSSION:The clique-like usage pattern was associated with decreased ED LOS for the study cohort, suggesting greater degree of collaboration resulted in shorter stay. CONCLUSIONS:Further investigation to understand and address causal factors can lead to improvement in multidisciplinary collaboration.
| S-EPMC6515526 | biostudies-literature
Project description:ObjectivesEarly recognition of dementia would allow patients and their families to receive care earlier in the disease process, potentially improving care management and patient outcomes, yet nearly half of patients with dementia are undiagnosed. Our aim was to develop and validate an electronic health record (EHR)-based tool to help detect patients with unrecognized dementia (EHR Risk of Alzheimer's and Dementia Assessment Rule [eRADAR]).DesignRetrospective cohort study.SettingKaiser Permanente Washington (KPWA), an integrated healthcare delivery system.ParticipantsA total of 16 665 visits among 4330 participants in the Adult Changes in Thought (ACT) study, who undergo a comprehensive process to detect and diagnose dementia every 2?years and have linked KPWA EHR data, divided into development (70%) and validation (30%) samples.MeasurementsEHR predictors included demographics, medical diagnoses, vital signs, healthcare utilization, and medications within the previous 2?years. Unrecognized dementia was defined as detection in ACT before documentation in the KPWA EHR (ie, lack of dementia or memory loss diagnosis codes or dementia medication fills).ResultsOverall, 1015 ACT visits resulted in a diagnosis of incident dementia, of which 498 (49%) were unrecognized in the KPWA EHR. The final 31-predictor model included markers of dementia-related symptoms (eg, psychosis diagnoses, antidepressant fills), healthcare utilization pattern (eg, emergency department visits), and dementia risk factors (eg, cerebrovascular disease, diabetes). Discrimination was good in the development (C statistic = .78; 95% confidence interval [CI] = .76-.81) and validation (C statistic = .81; 95% CI = .78-.84) samples, and calibration was good based on plots of predicted vs observed risk. If patients with scores in the top 5% were flagged for additional evaluation, we estimate that 1 in 6 would have dementia.ConclusionThe eRADAR tool uses existing EHR data to detect patients with good accuracy who may have unrecognized dementia. J Am Geriatr Soc 68:103-111, 2019.
| S-EPMC7094818 | biostudies-literature
Project description:The increasing prevalence of Type 2 diabetes has emphasized the need to optimize treatment regimens. Metformin, the most widely used oral agent, is recommended as first-line drug therapy by multiple professional organizations. Response to metformin varies significantly at the individual level; this heterogeneity may be explained in part by genetic factors. Understanding these underlying factors may aid with tailoring treatment for individual patients as well as with designing improved Type 2 diabetes therapies. The past 10 years have seen substantial progress in the understanding of the pharmacogenetics of metformin response. The majority of this work has focused on genes involved in the pharmacokinetics of metformin. Owing to the uncertainty surrounding its mechanism of action, studies of pharmacodynamic genetics have been relatively few; genome-wide approaches have the potential to illuminate the molecular details of metformin response. In this review we summarize current knowledge about metformin pharmacogenetics and suggest directions for future investigation.
| S-EPMC4121960 | biostudies-literature
Project description:BACKGROUND:As pharmacogenomics data becomes increasingly integral to clinical treatment decisions, appropriate data storage and sharing protocols need to be adopted. One promising option for secure, high-integrity storage and sharing is Ethereum smart contracts. Ethereum is a blockchain platform, and smart contracts are immutable pieces of code running on virtual machines in this platform that can be invoked by a user or another contract (in the blockchain network). The 2019 iDASH (Integrating Data for Analysis, Anonymization, and Sharing) competition for Secure Genome Analysis challenged participants to develop time- and space-efficient Ethereum smart contracts for gene-drug relationship data. METHODS:Here we design a specific smart contract to store and query gene-drug interactions in Ethereum using an index-based, multi-mapping approach. Our contract stores each pharmacogenomics observation, a gene-variant-drug triplet with outcome, in a mapping searchable by a unique identifier, allowing for time and space efficient storage and query. This solution ranked in the top three at the 2019 IDASH competition. We further improve our "challenge solution" and develop an alternate "fastQuery" smart contract, which combines together identical gene-variant-drug combinations into a single storage entry, leading to significantly better scalability and query efficiency. RESULTS:On a private, proof-of-authority network, both our challenge and fastQuery solutions exhibit approximately linear memory and time usage for inserting into and querying small databases (<1,000 entries). For larger databases (1000 to 10,000 entries), fastQuery maintains this scaling. Furthermore, both solutions can query by a single field ("0-AND") or a combination of fields ("1- or 2-AND"). Specifically, the challenge solution can complete a 2-AND query from a small database (100 entries) in 35ms using 0.1 MB of memory. For the same query, fastQuery has a 2-fold improvement in time and a 10-fold improvement in memory. CONCLUSION:We show that pharmacogenomics data can be stored and queried efficiently using Ethereum blockchain. Our solutions could potentially be used to store a range of clinical data and extended to other fields requiring high-integrity data storage and efficient access.
| S-EPMC7268467 | biostudies-literature
Project description:ObjectivesThe UK Biobank (UKB) is making primary care electronic health records (EHRs) for 500 000 participants available for COVID-19-related research. Data are extracted from four sources, recorded using five clinical terminologies and stored in different schemas. The aims of our research were to: (a) develop a semi-supervised approach for bootstrapping EHR phenotyping algorithms in UKB EHR, and (b) to evaluate our approach by implementing and evaluating phenotypes for 31 common biomarkers.Materials and methodsWe describe an algorithmic approach to phenotyping biomarkers in primary care EHR involving (a) bootstrapping definitions using existing phenotypes, (b) excluding generic, rare, or semantically distant terms, (c) forward-mapping terminology terms, (d) expert review, and (e) data extraction. We evaluated the phenotypes by assessing the ability to reproduce known epidemiological associations with all-cause mortality using Cox proportional hazards models.ResultsWe created and evaluated phenotyping algorithms for 31 biomarkers many of which are directly related to COVID-19 complications, for example diabetes, cardiovascular disease, respiratory disease. Our algorithm identified 1651 Read v2 and Clinical Terms Version 3 terms and automatically excluded 1228 terms. Clinical review excluded 103 terms and included 44 terms, resulting in 364 terms for data extraction (sensitivity 0.89, specificity 0.92). We extracted 38 190 682 events and identified 220 978 participants with at least one biomarker measured.Discussion and conclusionBootstrapping phenotyping algorithms from similar EHR can potentially address pre-existing methodological concerns that undermine the outputs of biomarker discovery pipelines and provide research-quality phenotyping algorithms.
| S-EPMC7717266 | biostudies-literature