Genomic analysis is a powerful new tool permitting unprecedented insights into how brain tumors form and has been enabled primarily through microarray technology. ProbeSetAnalyzer.com, a new web based tool, is aiming to help clinicians and researchers take the massive amount of data created by microarrays and better visualize gene expression levels and how they relate to the overall survival of brain cancer patients.
The free tool allows anyone to enter a gene description term or probe set id and instantly see if the gene they are looking for is a predictor of survival. With over 22,000 probe sets available on 164 patients, there is a tremendous amount of data available to all willing to ask questions. This service is primarily intended to allow brain cancer researchers to identify genes of interest for further study.
The tool was a collaborative effort between Dr. Timothy Cloughesy, UCLA Neuro-Oncology, Dr. Stanley F. Nelson, UCLA Department of Human Genetics and Michael Quinn, product developer of SiliconMED.
Unique to the Probeset Analyzer is the ability to quickly compare multiple probes normally sharing the same gene description term, the integration of a statistical engine to calculate p-values based on Kaplan-Meier curves, and the ability to quickly screen results based on "Newly Diagnosed" or "Recurrent" tumor and/or by pathological diagnosis.
"In reality there are over 1600 variables the probe set analyzer could screen against. In this initial release, we tried to keep the interface as simple as possible," said Michael Quinn.
The current set of array and survival data comes from consented patients treated by UCLA’s Neuro-Oncology program. Array creation and normalization of gene expression data were performed by the Stanley F. Nelson Laboratory at UCLA. The current array contained tissue samples identified as "Newly" diagnosed or "Recurrent" primary Brain Tumor and samples were further categorized by Pathologic Diagnosis. 79.9% of the current samples had a diagnosis of Glioblastoma Multiforme (GBM), followed by Anaplastic Astrocytoma (AA) 6.7% , Anaplastic Mixed Glioma (AMG) 6.7% and Anaplastic Oligodendroglioma (AO) 6.7%. "We are delighted to organize and provide these data back to the research community for the benefit of all cancer patients", said Dr. Stanley F. Nelson, a human genetic researcher leading the genomic analysis of brain cancers. " Genomic experiments are expensive to perform. Even though the results are published, there is still substantial additional information that can only be unearthed through expert mining which this system greatly facilitates. We hope that this facilitates specific exploration of individual genes."
"As a part of the UCLA Neuro-Oncology’s commitment to accelerate the process of new discovery through translational research projects, we decided we wanted to begin to share what we know about these samples in hope to stimulate feedback from the community," said Dr, Timothy Cloughesy, director of the UCLA Neuro-Oncology Program. "We feel our translation research information system is leading the way. We currently have over 3000 consented patients in our system with detailed clinical information. 2100 of those patients have uncompressed DICOM imaging instantly available and 1600 of those patients have tissue resources available in our tissue bank ready for researchers who have legitimate research questions. It is truly a rich resource available to those willing to focus on curing this disease. "