The HPCGG's current IT infrastructure includes core applications developed by the center to support clinical and research uses of genetics, genomics and proteomics. HP has contributed generously to key aspects of this development as well. Security is taken very seriously with a focus on protecting patient privacy and safeguarding researcher confidentiality.


Our integrated environment provides researchers the ability to:

• Place orders and receive results from multiple laboratories by signing on to a single system
• View order history with associated raw data files and analysis, which are archived in a secure and backed up repository
• Access to this information from any location
• Share information with collaborators quickly and securely
• Track financials including who placed orders
• View order status
• Access study specific sample catalogs in real time for samples stored within the BioSample Services Facility

Behind the scenes, the system supports laboratory workflows and integrates with instruments and other LIMS to increase data flow integrity.

On the clinical side, GIGPAD provides our Laboratory for Molecular Medicine with:

• Tools that increase data flow integrity across the testing process, from start of work to case sign-out
• Case-centric views and tools for technicians and geneticists, as well as, batch centric views for laboratory workflow
• Knowledge management and reporting infrastructure geared toward supporting the genetic testing process

The system tracks structured genetic and genomic data in a manner that facilitates integration into the electronic medical record (EMR) environment.

HPCGG Clinical IT Infrastructure		HPCGG Research Infrastructure
Click to enlarge		Click to enlarge

Core systems comprising the HPCGG IT infrastructure

Gateway for Integration of Genomic-Proteomics Applications and Data (GIGPAD):
A platform for managing the process of creating and organizing genetic, genomic and proteomic data. Enables integrated research and clinical workflows increasing data integrity across order entry, instruments processing, bioinformatics pipelines toand results return. GIGPAD is capable of managing workflows that involve multiple laboratories and integrates with 3rd party laboratory information management systems (LIMS).

GIGPAD won the BioITWorld 2005 Best Practices Award for Systems and Infrastructure. The system also won a JBoss Innovation Award Honorable Mention.

GeneInsight: A database for maintaining clinical annotations associated with genetic and genomic variations (i.e. mutations). GeneInsight integrates tightly with the Genetic Variant Interpretation Engine (below).

Genetic Variant Interpretation Engine (GVIE): Assists clinical geneticists in the generation of patient reports on identified variants. GVIE integrates with the Partners electronic medicinal record infrastructure through the Partners pathology systems.

Our infrastructure also incorporates bioinformatic routines designed by our bioinformatics group, sequencing group and outside institutions.For example, automatied data analysis for affymetrix gene expression data is provided through our bioinformatics pipeline process. This analysis is described in this document.