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The Electronic Medical Records and Genomics (eMERGE) Network: past, present, and future.

ABSTRACT: The Electronic Medical Records and Genomics Network is a National Human Genome Research Institute-funded consortium engaged in the development of methods and best practices for using the electronic medical record as a tool for genomic research. Now in its sixth year and second funding cycle, and comprising nine research groups and a coordinating center, the network has played a major role in validating the concept that clinical data derived from electronic medical records can be used successfully for genomic research. Current work is advancing knowledge in multiple disciplines at the intersection of genomics and health-care informatics, particularly for electronic phenotyping, genome-wide association studies, genomic medicine implementation, and the ethical and regulatory issues associated with genomics research and returning results to study participants. Here, we describe the evolution, accomplishments, opportunities, and challenges of the network from its inception as a five-group consortium focused on genotype-phenotype associations for genomic discovery to its current form as a nine-group consortium pivoting toward the implementation of genomic medicine.

SUBMITTER: Gottesman O

PROVIDER: S-EPMC3795928 | biostudies-literature |

REPOSITORIES: biostudies-literature

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electronic Medical Records & Genomics (eMERGE)

Project description:electronic Medical Records & Genomics (eMERGE)

| PRJNA158491 | ENA

Electronic medical records and genomics (eMERGE) network exploration in cataract: several new potential susceptibility loci.

Project description:PurposeCataract is the leading cause of blindness in the world, and in the United States accounts for approximately 60% of Medicare costs related to vision. The purpose of this study was to identify genetic markers for age-related cataract through a genome-wide association study (GWAS).MethodsIn the electronic medical records and genomics (eMERGE) network, we ran an electronic phenotyping algorithm on individuals in each of five sites with electronic medical records linked to DNA biobanks. We performed a GWAS using 530,101 SNPs from the Illumina 660W-Quad in a total of 7,397 individuals (5,503 cases and 1,894 controls). We also performed an age-at-diagnosis case-only analysis.ResultsWe identified several statistically significant associations with age-related cataract (45 SNPs) as well as age at diagnosis (44 SNPs). The 45 SNPs associated with cataract at p<1×10(-5) are in several interesting genes, including ALDOB, MAP3K1, and MEF2C. All have potential biologic relationships with cataracts.ConclusionsThis is the first genome-wide association study of age-related cataract, and several regions of interest have been identified. The eMERGE network has pioneered the exploration of genomic associations in biobanks linked to electronic health records, and this study is another example of the utility of such resources. Explorations of age-related cataract including validation and replication of the association results identified herein are needed in future studies.

| S-EPMC4168835 | biostudies-literature

Alphaherpesvirus Genomics: Past, Present and Future.

Project description:Alphaherpesviruses, as large double-stranded DNA viruses, were long considered to be genetically stable and to exist in a homogeneous state. Recently, the proliferation of high-throughput sequencing (HTS) and bioinformatics analysis has expanded our understanding of herpesvirus genomes and the variations found therein. Recent data indicate that herpesviruses exist as diverse populations, both in culture and in vivo, in a manner reminiscent of RNA viruses. In this review, we discuss the past, present, and potential future of alphaherpesvirus genomics, including the technical challenges that face the field. We also review how recent data has enabled genome-wide comparisons of sequence diversity, recombination, allele frequency, and selective pressures, including those introduced by cell culture. While we focus on the human alphaherpesviruses, we draw key insights from related veterinary species and from the beta- and gamma-subfamilies of herpesviruses. Promising technologies and potential future directions for herpesvirus genomics are highlighted as well, including the potential to link viral genetic differences to phenotypic and disease outcomes.

| S-EPMC7946737 | biostudies-literature

Return of individual research results from genome-wide association studies: experience of the Electronic Medical Records and Genomics (eMERGE) Network.

Project description:Return of individual genetic results to research participants, including participants in archives and biorepositories, is receiving increased attention. However, few groups have deliberated on specific results or weighed deliberations against relevant local contextual factors.The Electronic Medical Records and Genomics (eMERGE) Network, which includes five biorepositories conducting genome-wide association studies, convened a return of results oversight committee to identify potentially returnable results. Network-wide deliberations were then brought to local constituencies for final decision making.Defining results that should be considered for return required input from clinicians with relevant expertise and much deliberation. The return of results oversight committee identified two sex chromosomal anomalies, Klinefelter syndrome and Turner syndrome, as well as homozygosity for factor V Leiden, as findings that could warrant reporting. Views about returning findings of HFE gene mutations associated with hemochromatosis were mixed due to low penetrance. Review of electronic medical records suggested that most participants with detected abnormalities were unaware of these findings. Local considerations relevant to return varied and, to date, four sites have elected not to return findings (return was not possible at one site).The eMERGE experience reveals the complexity of return of results decision making and provides a potential deliberative model for adoption in other collaborative contexts.

| S-EPMC3723451 | biostudies-literature

ePhenotyping for Abdominal Aortic Aneurysm in the Electronic Medical Records and Genomics (eMERGE) Network: Algorithm Development and Konstanz Information Miner Workflow.

Project description:We designed an algorithm to identify abdominal aortic aneurysm cases and controls from electronic health records to be shared and executed within the "electronic Medical Records and Genomics" (eMERGE) Network. Structured Query Language, was used to script the algorithm utilizing "Current Procedural Terminology" and "International Classification of Diseases" codes, with demographic and encounter data to classify individuals as case, control, or excluded. The algorithm was validated using blinded manual chart review at three eMERGE Network sites and one non-eMERGE Network site. Validation comprised evaluation of an equal number of predicted cases and controls selected at random from the algorithm predictions. After validation at the three eMERGE Network sites, the remaining eMERGE Network sites performed verification only. Finally, the algorithm was implemented as a workflow in the Konstanz Information Miner, which represented the logic graphically while retaining intermediate data for inspection at each node. The algorithm was configured to be independent of specific access to data and was exportable (without data) to other sites. The algorithm demonstrated positive predictive values (PPV) of 92.8% (CI: 86.8-96.7) and 100% (CI: 97.0-100) for cases and controls, respectively. It performed well also outside the eMERGE Network. Implementation of the transportable executable algorithm as a Konstanz Information Miner workflow required much less effort than implementation from pseudo code, and ensured that the logic was as intended. This ePhenotyping algorithm identifies abdominal aortic aneurysm cases and controls from the electronic health record with high case and control PPV necessary for research purposes, can be disseminated easily, and applied to high-throughput genetic and other studies.

| S-EPMC4820287 | biostudies-literature

Functional genomics in osteoarthritis: Past, present, and future.

Project description:Osteoarthritis (OA) is a common complex disease of high public health burden. OA is characterized by the degeneration of affected joints leading to pain and reduced mobility. Over the last few years, several studies have focused on the genomic changes underpinning OA. Here, we provide a comprehensive overview of genome-wide, non-hypothesis-driven functional genomics (methylation, gene, and protein expression) studies of knee and hip OA in humans. Individual studies have generally been limited in sample size and hence power, and have differed in their approaches; nonetheless, some common themes have started to emerge, notably the role played by biological processes related to the extracellular matrix, immune response, the WNT pathway, angiogenesis, and skeletal development. Larger-scale studies and streamlined, robust methodologies will be needed to further elucidate the biological etiology of OA going forward. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 34:1105-1110, 2016.

| S-EPMC4980743 | biostudies-literature

A Robust e-Epidemiology Tool in Phenotyping Heart Failure with Differentiation for Preserved and Reduced Ejection Fraction: the Electronic Medical Records and Genomics (eMERGE) Network.

Project description:Identifying populations of heart failure (HF) patients is paramount to research efforts aimed at developing strategies to effectively reduce the burden of this disease. The use of electronic medical record (EMR) data for this purpose is challenging given the syndromic nature of HF and the need to distinguish HF with preserved or reduced ejection fraction. Using a gold standard cohort of manually abstracted cases, an EMR-driven phenotype algorithm based on structured and unstructured data was developed to identify all the cases. The resulting algorithm was executed in two cohorts from the Electronic Medical Records and Genomics (eMERGE) Network with a positive predictive value of >95 %. The algorithm was expanded to include three hierarchical definitions of HF (i.e., definite, probable, possible) based on the degree of confidence of the classification to capture HF cases in a whole population whereby increasing the algorithm utility for use in e-Epidemiologic research.

| S-EPMC4651838 | biostudies-literature

The Medical Management of Cerebral Edema: Past, Present, and Future Therapies.

Project description:Cerebral edema is commonly associated with cerebral pathology, and the clinical manifestation is largely related to the underlying lesioned tissue. Brain edema usually amplifies the dysfunction of the lesioned tissue and the burden of cerebral edema correlates with increased morbidity and mortality across diseases. Our modern-day approach to the medical management of cerebral edema has largely revolved around, an increasingly artificial distinction between cytotoxic and vasogenic cerebral edema. These nontargeted interventions such as hyperosmolar agents and sedation have been the mainstay in clinical practice and offer noneloquent solutions to a dire problem. Our current understanding of the underlying molecular mechanisms driving cerebral edema is becoming much more advanced, with differences being identified across diseases and populations. As our understanding of the underlying molecular mechanisms in neuronal injury continues to expand, so too is the list of targeted therapies in the pipeline. Here we present a brief review of the molecular mechanisms driving cerebral edema and a current overview of our understanding of the molecular targets being investigated.

| S-EPMC6985348 | biostudies-literature

Biocrystallography: past, present, future.

Project description:The evolution of biocrystallography from the pioneers' time to the present era of global biology is presented in relation to the development of methodological and instrumental advances for molecular sample preparation and structure elucidation over the last 6 decades. The interdisciplinarity of the field that generated cross-fertilization between physics- and biology-focused themes is emphasized. In particular, strategies to circumvent the main bottlenecks of biocrystallography are discussed. They concern (i) the way macromolecular targets are selected, designed, and characterized, (ii) crystallogenesis and how to deal with physical and biological parameters that impact crystallization for growing and optimizing crystals, and (iii) the methods for crystal analysis and 3D structure determination. Milestones that have marked the history of biocrystallography illustrate the discussion. Finally, the future of the field is envisaged. Wide gaps of the structural space need to be filed and membrane proteins as well as intrinsically unstructured proteins still constitute challenging targets. Solving supramolecular assemblies of increasing complexity, developing a "4D biology" for decrypting the kinematic changes in macromolecular structures in action, integrating these structural data in the whole cell organization, and deciphering biomedical implications will represent the new frontiers.

| S-EPMC2929629 | biostudies-literature

The Cortico-Basal Ganglia-Cerebellar Network: Past, Present and Future Perspectives.

Project description:Much of our present understanding of the function and operation of the basal ganglia rests on models of anatomical connectivity derived from tract-tracing approaches in rodents and primates. However, the last years have been characterized by promising step forwards in the in vivo investigation and comprehension of brain connectivity in humans. The aim of this review is to revise the current knowledge on basal ganglia circuits, highlighting similarities and differences across species, in order to widen the current perspective on the intricate model of the basal ganglia system. This will allow us to explore the implications of additional direct pathways running from cortex to basal ganglia and between basal ganglia and cerebellum recently described in animals and humans.

| S-EPMC6831548 | biostudies-literature

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