Fri, Feb 18, 2011 @ 11:30 AM - 01:00 PM
Alfred E. Mann Department of Biomedical Engineering
Conferences, Lectures, & Seminars
Speaker: Simon Lin, M.D., Clinical and Translational Sciences Institute, Northwestern University
Talk Title: Reducing Time-to-action in Clinical Genomics Studies by Using an
Abstract: A major bottleneck in large-scale clinical genomics studies, especially those utilizing next generation sequencing and microarrays, is the bioinformatics analysis. A delayed time-to-action of six months by bioinformatics may lose the first-mover advantage and waste the initial capital investment as much as 46%. We propose a two-step strategy to accelerate the biomarker prioritization process: 1) reducing the noise of a biological system by integrating multiple-omics data, and 2) utilizing the disease ontology annotation of potential biomarkers to prioritize the disease-relevant ones. This strategy is based on our strategic investment of annotating the human genome with Disease Ontology (BMC Genomics 2009) and the development of the GeneAnswers package in Bioconductor (BMC Research Notes 2010). In this talk, I will demonstrate our success in a recent collaborative study with the Bulun Lab on leiomyomata. Uterine leiomyomata (uterine fibroids) are benign smooth muscle tumors that occur in up to 80% of all women of reproductive age and a leading cause of hysterectomies. By overlaying epigenetic data onto gene expression data, we narrowed down more than one thousand biomarkers to the most valuable 55 with a 20:1 prioritization rate. In addition, a disease ontology analysis allowed us to further categorize the 55 biomarkers into 8 disease pathways for follow-up evaluation in the wet lab. A major advantage of this strategy is that my team can finish this study within one day using the open-source GeneAnswers package we created.
Location: Harkness Auditorium, CSC 250, IGM Building
For Additional information contact: 323-442-3849 or 323-442-2596
Biography: Simon Lin, M.D.
Clinical and Translational Sciences Institute, Northwestern University.
Host: Dr. Parag Mallick, Center for Applied Molecular Medicine
Audiences: Everyone Is Invited
Contact: Yvonne Suarez