Established in 1999, the Cancer Genomics Core Laboratory has implemented many core technologies: cDNA microarray, SAGE, real-time PCR, SNP assay, and tissue microarray. For Microarray technology, we developed and printed a number of focused arrays with either cDNA or long oligonucleotide(70mer) arrays tailored for the different needs of specific cancer research programs. Since 2004, we have switched to the whole genome 44K arrays from Agilent, which is also based on long oligonucleotide (60mer), which we believe provides better specificity. High quality results have been obtained with Agilent microarrays in several projects. Real-time PCR assays based on ABI's assay-on-demand are routinely used for validation purpose and for genotyping projects. Our Core Lab has also provided service in high density array CGH to a number of investigators. Recently, our Core begins to provide service in microRNA array analysis. Tissue microarray facility, which is headed by Dr. Gregory Fuller, the Chief of Neuropathology and Immunohistochemistry, provides an important validation of genomics studies at the protein and cell levels.

In 2004, the Core Lab implementated the reverse phase protein lysate array technology to profile protein expression. A cell line array that contains 90 different cell lines has been made available to MDACC investigators. A new analysis method has been developed and a paper describing the method has been published in Bioinformatics. A glioma lysate array project led to a publication highlighted on the cover of Proteomics of the April issue in 2006. A breast cancer lysate array paper is highlighted on the cover of Technology in Cancer Research and Treatment. A comprehensive paper from the 90 cell line arrays has been published in the Journal of Proteome Research.

The Core Lab personnel closely interact with MDACC investigators in RNA quality control, microarray result validation, and protein microarrays. The Core Lab has organized several workshops and minisymposium on microarrays at MDACC. The Core Lab has provided support to close to 100 MDACC investigators and a number external collaborators in the areas of microarray, SAGE, SNP, real-time PCR, imaging and data analysis. The Core Lab has been assisting numerous MDACC investigators in grant applications and has already been successful in a number of cases including the GU SPORE, RO1's and R21. The Core lab is also part of NCI funded Cancer Center Support Grant. The Core Lab researchers have published several books on genomics and many papers in the area of genomics and informatics (see publication list). Our goal is to help investigators to apply genomics and proteomics in their discoviery program. Our measure of success is scientific publication.
June 2007