BIOMARKER PROFILING CORE

Emory University, Atlanta GA

Investigators

Linked publications, trials & patents

Abstract

The goal of the WCI BPC is to provide state-of-the-art analytical technologies to impact cancer biomarker discovery, development, and clinical translation. The BPC technologies are concentrated in three synergistic disciplines: (1) medical genomics[unreadable] operated out of the Center for Medical Genomics (CMG) and directed by Dr. Mark Bouzyk, (2) microarray analysis[unreadable] operated out of the WCI Microarray Core (WCIMC), and directed by Dr. Carlos Moreno, and (3) proteomics and mass spectrometry (PMSC)[unreadable] operated out of the Proteomics and Mass Spectrometry Facility and directed by Dr. Junmin Peng. The CMG provides state-of-the-art service in DNA extraction (sources that range from whole blood and saliva to formalin-fixed paraffin-embedded tissues), genomic sequencing, genotyping, and SNP detection/typing. The CMG utilizes instrumentation and automation from Qiagen, Applied Biosystems and Beckman Coulter, which are supported by Thermofisher Nautilus Laboratory Information System (LIMS) comprehensive data management architecture. The WCIMC provides services and platforms for expression profiling of fresh, frozen, or formalin-fixed paraffin-embedded tissues that includes equipment from Affymetrix, Applied Biosystems, and Illumina platforms. It provides comprehensive services from RNA preparation, quality control analysis, microarray hybridization, TaqMan QPCR validation, and data analysis. Bioinformatics support is provided to users by a team of analysts using a variety of standard and custom software tools. The PMSC provides a range of technologies and mass spectrometry (MS)-based platforms. Hundreds to thousands of proteins can be identified by orthogonal methodologies including electrophoresis, multiple types of liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Large-scale protein profiling is achieved by label-free direct quantification (DQUAN) or stable isotope dilution MS (e.g. iTRAQ and SILAC) to determine differential expression in normal versus diseased states. PMSC actively pursues new developments in extensive fractionation technologies of tissue or biofluid samples, such as human plasma and CSF, and continuously upgrades its analytical MS capabilities to form a foundation for protein biomarker discovery. Most activities follow CLIA regulations, thereby allowing the facility to generate molecular data that can directly impact patient care. BPC operation under CLIA standards of high-throughput instrumentation for gene expression and genotype determination will meet increasing demands for generation of clinically useable molecular data in the context of NIH-supported translational research. During CY2007, BPC supported peer-reviewed studies from over 40 WCI members from all four programs. Over the last ten years, the core has been funded four times by NIHNCRR (total >$1.1 million;success rate of 80%) with wide PI participation (ranging between 21 and 49 Emory investigators per application) and receiving laudatory comments from the Study Panels.