Informatics operations
Overview
The informatics team developed and implemented a Laboratory Information Management System (LIMS) and an issue tracking system, to ensure accuracy and timeliness of CGR laboratory services. These information management systems provide querying and reporting capabilities to staff members within the CGR. These systems directly benefit in vestigators by providing a mechanism for staff to generate the most up-to-date status reports.
Laboratory Information Management System (LIMS)
In order to meet the rigorous demands of high-throughput genotyping operations , the CGR has developed and implemented a Laboratory Information Manag ement System (LIMS). The LIMS electronically tracks all DNA samples arriving at the CGR, assists in Standard Operating Procedures (SOP) compliance by laboratory technic ians, and interfaces with robotics, instrumentation and analysis software developed by a third party or in-house.
The CGR uses Sapphire from LabVantage Solutions to implement LIMS. Sapphire has three-tier architecture consis ting of a relational database, a J2EE compliant application server, and a web browser. All CGR employees can access the LIMS through their existing web browser without needing additional software installation on their workstation. Additionally, Sapphire provides an application programming interface (API) in the Java programming langua ge and Evergreen, a proprietary web page design tool. Evergreen allows CGR's Bioinformatics team to rapidly customize the LIMS to adapt to new technology or SOP modific ations.
Currently, informatics staff have integrated several high-throughput laboratory SOPs and software into LIMS. The informatics group has incorporated the CGR Sample Handling Protocol which describes procedures for initial sample receipt, sample barcoding, racking, storing and qualifying o f the sample for specific projects (see Sample Handling). The LIMS interfaces with the REMP Small Size Store (SSS) at NCI-Frederick's DNA Extraction and Staging Lab (DESL). Through this interface, laboratory staff have access to real-time information on the quality and quantity of DNA samples that are extracted and staged at DESL prior to the delivery of these s amples to the CGR. Real-time access to this data ensures optimal sample selection for our laboratory.s genotyping and sequencing projects. Staff have also integrated in to LIMS the SOPs for several genotyping platforms including ABI's Taqman, Fluidigm's BioMark Assay,Illumina's Whole Genome Infinium, and Illumina's Custom Infinium (iSelect), as well as software such as Geospiza's GeneSifter for sequencing platforms.
Project Management/Issue Tracking System
Staff at the CGR use FogBugz by FogCreek Software to record and monitor the progress on internal issues as w ell as track the status of projects.
The CGR also employs an in-house developed Analytical Information System (AIMS). The AIMS integrates information on sample handling with genotypic and phenotypic data. The objective of AIMS is to streamline internal processes that include assay validation, quality control, and consolidation of data into final analytic datasets.
