Dataset Information

EPGA: A Web-Based Information System for Translational Pharmacogenomics.

ABSTRACT: One of the challenges that arise from the advent of personal genomics services is to efficiently couple individual data with state of the art Pharmacogenomics (PGx) knowledge. Existing services are limited to either providing static views of PGx variants or applying a simplistic match between individual genotypes and existing PGx variants. Moreover, there is a considerable amount of haplotype variation associated with drug metabolism that is currently insufficiently addressed. Here, we present a web-based electronic Pharmacogenomics Assistant (ePGA; http://www.epga.gr/) that provides personalized genotype-to-phenotype translation, linked to state of the art clinical guidelines. ePGA's translation service matches individual genotype-profiles with PGx gene haplotypes and infers the corresponding diplotype and phenotype profiles, accompanied with summary statistics. Additional features include i) the ability to customize translation based on subsets of variants of clinical interest, and ii) to update the knowledge base with novel PGx findings. We demonstrate ePGA's functionality on genetic variation data from the 1000 Genomes Project.

SUBMITTER: Lakiotaki K

PROVIDER: S-EPMC5025168 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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ePGA: A Web-Based Information System for Translational Pharmacogenomics.

Lakiotaki Kleanthi K Kartsaki Evgenia E Kanterakis Alexandros A Katsila Theodora T Patrinos George P GP Potamias George G

PloS one 20160915 9

One of the challenges that arise from the advent of personal genomics services is to efficiently couple individual data with state of the art Pharmacogenomics (PGx) knowledge. Existing services are limited to either providing static views of PGx variants or applying a simplistic match between individual genotypes and existing PGx variants. Moreover, there is a considerable amount of haplotype variation associated with drug metabolism that is currently insufficiently addressed. Here, we present a ...[more]

PMID: 27631363

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Project description:BackgroundAn increasing number of research laboratories and core analytical facilities around the world are developing high throughput metabolomic analytical and data processing pipelines that are capable of handling hundreds to thousands of individual samples per year, often over multiple projects, collaborations and sample types. At present, there are no Laboratory Information Management Systems (LIMS) that are specifically tailored for metabolomics laboratories that are capable of tracking samples and associated metadata from the beginning to the end of an experiment, including data processing and archiving, and which are also suitable for use in large institutional core facilities or multi-laboratory consortia as well as single laboratory environments.ResultsHere we present MASTR-MS, a downloadable and installable LIMS solution that can be deployed either within a single laboratory or used to link workflows across a multisite network. It comprises a Node Management System that can be used to link and manage projects across one or multiple collaborating laboratories; a User Management System which defines different user groups and privileges of users; a Quote Management System where client quotes are managed; a Project Management System in which metadata is stored and all aspects of project management, including experimental setup, sample tracking and instrument analysis, are defined, and a Data Management System that allows the automatic capture and storage of raw and processed data from the analytical instruments to the LIMS.ConclusionMASTR-MS is a comprehensive LIMS solution specifically designed for metabolomics. It captures the entire lifecycle of a sample starting from project and experiment design to sample analysis, data capture and storage. It acts as an electronic notebook, facilitating project management within a single laboratory or a multi-node collaborative environment. This software is being developed in close consultation with members of the metabolomics research community. It is freely available under the GNU GPL v3 licence and can be accessed from, https://muccg.github.io/mastr-ms/.

Project description:BackgroundNowadays there is a worldwide consensus on the importance of conducting wildlife disease surveillance. Indeed, 60% of emerging infectious diseases are zoonotic in nature, and the majority of these (71.8%) originate in wildlife. Surveillance of wildlife diseases is crucial to prevent negative effects on human and animal health. Data digitization and sharing are among the main goals for the present and coming years. Geographic Information Systems (GIS) are increasingly used to analyze the geographical distribution of diseases and the relationships between pathogenic factors and their geographic environments.MethodsWild animal's samples collected in the Abruzzo and Molise regions and delivered to our laboratory are entered in our Laboratory Information System and processed to be displayed through the Web-GIS mash-up presented in this paper. We built it using both open source and proprietary solutions, to produce data driven interactive maps, charts and tables to help to understand the epidemiology of wild animal diseases, their spread and trend.ResultsSince 2013, 9.606 samples collected from wild animals have been analyzed in the laboratories of the IZS-Teramo and have been recorded in the system, facilitating the reporting to the judicial authorities and the identification of highly risky areas to set up control and repression measures. Moreover, thanks to the monitoring health protocol, a canine distemper epidemic in wolves has been detected and monitored in its temporal and spatial evolution, as well as cases of bovine tuberculosis in wild boars.ConclusionsWhile it is more evident that the starting point is to choose the right sampling method, it is for sure less obvious that the information system in which data is stored is equally important. In fact, it should give the possibility to consult it in an easy and instructive way. GIS allows immediately grasping the spatial relationships between the data itself and those between the data and the territory; it is an important tool to support veterinary services in managing epidemic and non-epidemic emergencies and performing epidemiological investigations, but also to examine control plans and identify new gaps and challenges.

Project description:BACKGROUND: There is great concern within health surveillance, on how to grapple with environmental degradation, rapid urbanization, population mobility and growth. The Internet has emerged as an efficient way to share health information, enabling users to access and understand data at their fingertips. Increasingly complex problems in the health field require increasingly sophisticated computer software, distributed computing power, and standardized data sharing. To address this need, Web-based mapping is now emerging as an important tool to enable health practitioners, policy makers, and the public to understand spatial health risks, population health trends and vulnerabilities. Today several web-based health applications generate dynamic maps; however, for people to fully interpret the maps they need data source description and the method used in the data analysis or statistical modeling. For the representation of health information through Web-mapping applications, there still lacks a standard format to accommodate all fixed (such as location) and variable (such as age, gender, health outcome, etc) indicators in the representation of health information. Furthermore, net-centric computing has not been adequately applied to support flexible health data processing and mapping online. RESULTS: The authors of this study designed a HEalth Representation XML (HERXML) schema that consists of the semantic (e.g., health activity description, the data sources description, the statistical methodology used for analysis), geometric, and cartographical representations of health data. A case study has been carried on the development of web application and services within the Canadian Geospatial Data Infrastructure (CGDI) framework for community health programs of the New Brunswick Lung Association. This study facilitated the online processing, mapping and sharing of health information, with the use of HERXML and Open Geospatial Consortium (OGC) services. It brought a new solution in better health data representation and initial exploration of the Web-based processing of health information. CONCLUSION: The designed HERXML has been proven to be an appropriate solution in supporting the Web representation of health information. It can be used by health practitioners, policy makers, and the public in disease etiology, health planning, health resource management, health promotion and health education. The utilization of Web-based processing services in this study provides a flexible way for users to select and use certain processing functions for health data processing and mapping via the Web. This research provides easy access to geospatial and health data in understanding the trends of diseases, and promotes the growth and enrichment of the CGDI in the public health sector.

Dataset Information

EPGA: A Web-Based Information System for Translational Pharmacogenomics.

Publications

ePGA: A Web-Based Information System for Translational Pharmacogenomics.

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