Platform Expansion (PER)
This project ended on March 31, 2008 

PER projects served include:

Diagnostic Applications of Microarrays in Organ Transplantation
Principal Investigator: Dr. Philip F. Halloran, University of Alberta

This project hypothesizes that transcriptosome-based measurements can provide new tests for screening (on blood) and definitive diagnosis (on biopsy) that will become the new routine diagnostic system in organ transplantation and the endpoint for clinical trials.

Bioinformatics Services Provided

Large databases are being generated and integrated, consisting of transcriptosome (human and mouse), pathology (human and mouse), and clinical information. The clinical database includes demographic variables, clinical observations, population analyses, drug data, organ function, preservation data, transplant infectious diseases and cancer data, and outcomes.

Bioinformatics plays two key roles in this project. It is vital to: (1) coordinate, communicate, and archive large quantities of data from a number of sources, (2) integration and interpretation of the microarray, clinical, and pathology databases and ultimately the development of FDA-approved diagnostic microarray assays.

Infrastructure

Development of a customized Laboratory Information Management System (LIMS) to manage and coordinate data, allowing sample tracking, monitoring results, storing data, communicating information between multiple labs and investigators, and most importantly - ensuring quality control.

Building the Metabolomics Toolbox - Enabling Rapid Disease Diagnosis Through Metabolic Profiling
Principal Investigator: Dr. David Wishart, University of Alberta.

"Building the Metabolomics Toolbox" is a large-scale project aimed at characterizing or completing the human metabolome. The metabolome (like the genome or proteome) can be described as the complete complement of small molecule chemicals (metabolites) found in or produced by an organism. Metabolomics, or metabolic profiling, is an emerging branch of genetic research that uses metabolites as very sensitive reporters to detect tiny changes or mutations that happen to genes. Metabolic profiling is also used to monitor and/or measure the larger-scale physiological changes that occur in response to subtle changes in the environment. Physicians and scientists around the world are now beginning to realize that metabolic profiling could have a significant impact on the diagnosis, prediction, prevention, and monitoring of many genetic, infectious, and environmental diseases.

This project has two main objectives: (1) creating a set of comprehensive metabolite databases, (2) developing new medical tools (a toolbox of instruments and software) to facilitate the rapid and inexpensive profiling of metabolites for disease diagnosis and management.

Bioinformatics Services Provided

Bioinformatics will play two key roles in this project. It is vital to (1) develop algorithms to accelerate spectral pattern analysis in MS/NMR data, and assist in the design of clinical cohort studies, pathway mapping, and literature or text search software to maintain the compound library, (2) assist with customizing the LIMS for this project.