Seminar Presentation
Mark Yandell, PhD
Associate Professor, Dept of Human Genetics
Adjunct Associate Professor, Biomedical Informatics
Location: HSEB 4100B
Date: Sep. 15, 2011
Time: 4:15 - 5:15 pm
Abstract
VAAST is a probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences. VAAST builds upon existing amino acid substitution (AAS) and aggregative approaches to variant prioritization, combining elements of both into a single unified likelihood-framework that allows users to identify damaged genes and deleterious variants with greater accuracy, and in an easy-to-use, BLAST-like fashion. VAAST can score both coding and non-coding variants, evaluating the cumulative impact of both types of variants simultaneously. VAAST can identify rare variants causing rare genetic diseases, and it can also use both rare and common variants to identify genes responsible for common diseases. VAAST thus has a much greater scope of use than any existing methodology. Here we demonstrate its ability to identify damaged genes using small cohorts (n=3) of unrelated individuals, wherein no two share the same deleterious variants, and for common, multigenic diseases using as few as 150 cases.
Bio
Mark Yandell, PhD. is an internationally recognized expert in comparative and functional genomics. As a Post-doc at the Human Genome Project at Washington University, St. Louis, he was a co-developer of the widely commercially licensed PolyBayes package, a probabilistic algorithm for sequence variant discovery. Thereafter he joined Celera Genomics, where he led the software group that wrote much of the software used to annotate and analyze the Drosophila, Human, Mouse, and mosquito genomes. From 2001-2005 he was a senior scientist for HHMI where he led a comparative genomics group at the Berkeley Drosophila Genome Project. Since 2005, he has been an Associate Professor in the Eccles Institute of Human Genetics, University of Utah. He has served on the Scientific Advisory Boards of the Saccharomyces Genome Database, the Rice Genome Annotation Project and VectorBase. He is currently Director of the Eccles Institute’s Bioinformatics program, and (co)-teaches Bioinformatics Programming for Molecular Biology and Evolutionary Genetics & Genomics. He is a frequent guest lecturer in several CSHL courses on genomics, programming and sequence analysis. He is also co-author of the O’Reilly Book on BLAST. Current projects in his laboratory include an NHGRI funded project for the development of software for the creation and quality control of genome annotations, an NHGRI funded project to develop software tools for Personal Genomes analyses, and an NIGMS funded project to develop software for high-throughput Image analysis.