Institute of Bio-Sensing Technology

Overview of Hackensack University Medical Center

Dr Stephen Suh, Laboratory Director of the Tumor Bank & Genomics Program

Translational Bioinformatics-Guided Workflow for Procurement of Patient Samples

Modern cancer research for biomarker discovery program requires solving several tasks that are directly involved with patient sample procurement. One requirement is to construct a highly efficient workflow on the clinical side for the procurement to generate a consistent supply of high quality samples for research. This undertaking needs a network of interdepartmental collaborations and participations at various levels, including physical human interactions, information technology implementations and a bioinformatics tool that is highly effective and user-friendly to busy clinicians and researchers associated with the sample procurement. Collegial participation that is sequential but continual from one department to another demands dedicated bioinformatics software coordinating between the institutional clinic and the tissue repository facility. Participants in the process include admissions, consenting process, phlebotomy, surgery center and pathology. During this multiple step procedures, clinical data are collected for detailed analytical endpoints to supplement logistics of defining and validating the discovery of biomarkers.

Bioinformatics Guided Biomarker Discovery Program

Experimental data related to differential expressions of biomarkers in genomics, proteomics, metabolomics and tissueomics have accumulated during the past two decades of research in public and private sectors. A large amount of the accrued data is publicly available but is beyond our ability to process altogether to compare and extract a clinically relevant data. From an individual laboratory setting, a small number of these studies are published on peer reviewed scientific journals due to requirements for providing mechanistic data to support and validate various omics findings. These requirements are necessary for publication, scientific logistics and funding, but also bring forth an enormous negative impact on progression of translational science by tremendously decelerating the discovery process of biomarkers.

We have started to utilize bioinformatics tools provided by Sophic Systems Alliance, a Knowledge Management Environment developed by Biomax. Three modules, BioXM, BioRS and BioLT are used to dissect the vast amount of publicly available data from multiple institutes and academic centers worldwide. The software already comes with over 70 known databases for basic science, and we are currently in the process of identifying and adding more databases that are relevant to biomarker discovery program. These databases to be added include SNP, CGH, SKY, FISH, genomic methylations, DNA mutations, protein modifications, transgenic animals (e.g. knockout mice), protein interactions and signaling pathways. Addition of publicly available databases with experimental data (e.g. microarray) from genome and proteome will be a crucial addition to complete and launch a bioinformatics guided search of biomarkers. The objective is to build a complete web-based and user friendly knowledge source for scientists and clinicians associated with cancer research. Our laboratory is currently undertaking a proof-of concept project to identify a set of biomarkers for Mantle Cell Lymphoma (MCL). The selected markers will be tested on clinical samples in vitro by biochemistry and in vivo by xenograft models for further validation. The validated markers will institute to design and construct platforms that contain a series of robust biomarkers for MCL. These diagnostic platforms will represent an array of molecular signatures from multiple segments of basic, translational and clinical science.

Biography: Dr Stephen Suh

Dr. K. Stephen Suh is currently a scientific director for the Tumor Bank and Genomics Program at the Cancer Center of Hackensack University Medical Center in New Jersey. His interest is biomarker discovery program and development of molecular diagnostic and prognostic assays for multiple human cancer types. He finished his postdoctoral training and research/staff fellowship at the National Cancer Institute (NCI) from 1998 to 2007. At NCI, he led a team of scientists to discover Chloride Intracellular Channel 4 (CLIC4) as a biomarker for tumor progression and became a world expert in molecular circuitry of CLIC pathways. He was trained in basic science by majoring in molecular and cell biology and studying tyrosine kinases at the University of Texas. He then focused on translational science by working with carcinogenesis and xenograft mouse models at the NCI and currently developing expertise in bench-to-bed side clinical science at the medical center.