Informatics operations
Overview
In order to ensure the accuracy and timely completion of all CGF provided operations, the following Information Systems were developed. While the investigator does not have direct access to these systems, their availability to CGF staff members greatly aids in their querying and reporting capabilities. In turn this provides benefit to the investigator by providing the most up to date reporting possible.
Laboratory Information Management System (LIMS)
In order to help meet the rigorous demands of a high throughput genotyping laboratory, the CGF has implemented a Laboratory Information Management System (LIMS). CGF's LIMS is responsible for the electronic tracking of all DNA samples that arrive at CGF, ensuring that all of the Standard Operating Procedures (SOP) are properly followed by the laboratory technicians, and, where necessary, interface with robotics, instrumentation and analysis software developed by a third party or in-house. In 2002 , the CGF purchased the Sapphire product from LabVantage Solutions to help meet this goal. Sapphire is three-tier architecture, consisting of a relational database, a J2EE compliant application server, and a web browser. All CGF employees can access the LIMS through their existing web browser , without any additional software required to be installed on the client's workstation. Additionally, Sapphire provides an application programming interface (API) in the Java programming language, and Evergreen, a proprietary web page design tool, that allows for CGF's Bioinformatics staff to rapidly customize the system to handle any new technology or modification to an existing SOP, whenever the need arises. Currently, CGF's LIMS has implemented the current CGF Sample Handling Protocol, including the initial receipt of the samples, their subsequent barcoding, racking, storing and qualifying of the sample for a project, based both on quantity (amount of DNA) and quality by using ABI's Identifiler Assay. SOPs have also been successfully implemented for the following genotyping platforms: ABI's Taqman, Illumina's Golden Gate, Illumina's Whole Genome Infinium, and Illumina's Custom Infinium (iSelect).
Diagram from LabVantage detailing the LIMS architecture.
Analysis Information Management System
The CGF's Analysis Information Management System (AIMS) is a web-based data management and analysis system. It is developed with an open architecture using the Java-based STRUTS framework, and allows incorporation of analytical tools from other platforms.
The AIMS integrates genotypic, phenotypic data, and laboratory sample processing information together with genomic annotation, and streamlines internal processes including assay validation, pre- and post-genotyping QC, and assembly of the final data delivery package for investigators. The AIMS is being enhanced to include additional analytical modules.
