Abstract
This CoLab will show how Fabric GEM, a novel AI method for fast Mendelian disease diagnostics, can dramatically accelerate genome interpretation while increasing diagnostics rate. Professor Mark Yandel, Co-Director of the Utah Center for Genetic Discovery of the University of Utah, will show how GEM not just prioritizes variants for review, but can also assess the strength of overlap of the patient’s phenotypes with known gene-disease associations. He will also describe how GEM discovers & scores structural variants (SVs) while dealing effectively with false positive SV calls for increased diagnostic rates. Further, Dr. Shimul Chowdhury, Director of the Clinical Laboratory of Rady Children’s Institute for Genomic Medicine, will present the results of a retrospective study to benchmark the performance of Fabric GEM for identifying causal genes in 160 previously diagnosed rapid-WGS cases from seriously ill children in the Rady Hospital NICU, including trios, singletons, and SVs.
Speakers
Mark Yandell, PhD
Co-Director of the Utah Center for Genetic Discovery of the University of Utah
Mark Yandell, PhD has led software development groups in both industry and academia. As a postdoc at the Human Genome Project at Washington University, St. Louis, he was a co-developer of the PolyBayes package, the first probabilistic algorithm for sequence variant discovery. Thereafter, he joined Celera Genomics, where he directed the 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 Howard Hughes Medical Institute (HHMI), where he led the comparative genomics group at the Berkeley Drosophila Genome Project. Since 2005, he has been a faculty member in the Eccles Institute of Human Genetics at the University of Utah. Dr. Yandell is an internationally recognized expert in software for comparative and functional genomics. He has served on the Scientific Advisory Boards of numerous genome projects. He is Director of the Eccles Institute’s Bioinformatics program, and 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 NSF program grant for annotation of plant genomes; NIGMS support for genomics-based venom studies using the cone snail Conus bullatus; and support from the NHGRI and NIGMS for VAAST, a probabilistic disease gene finder for personal genome sequences. Dr. Yandell is technical director of the Utah Genome Project (UGP), an intramural, multi-million dollar effort to improve patient care and facilitate research on undiagnosed diseases, Co-director of the Utah Center for Genetic Discovery, Adjunct Professor of Biomedical Informatics, a member of the Huntsman Cancer Institute’s Cancer Control and Population Sciences Program, and H.A. and Edna Benning Presidential Endowed Chair at the University of Utah.
Shimul Chowdhury, PhD
Clinical Laboratory Director,
Rady Children's Institute for Genomic Medicine
Shimul Chowdhury serves as a clinical laboratory director at the Rady Children’s Institute for Genomic Medicine (RCIGM). Prior to joining the RCIGM team, Dr. Chowdhury served as a Senior Scientist in the Illumina Clinical Services Laboratory in which he reviewed and analyzed patient genomes for rare and undiagnosed disease as well as healthy individuals. Dr. Chowdhury has also served as a clinical laboratory director at Quest Diagnostics. Dr. Chowdhury is licensed as a clinical laboratory director for molecular genetics by the state of California. He conducted his American Board of Medical Genetics and Genomics (ABMGG) clinical molecular genetics fellowship at Sacred Heart Medical Center in Spokane, Washington. He obtained his PhD in Clinical and Translational Sciences at the University of Arkansas for Medical Sciences, and his Bachelors of Science at the University of Minnesota-Twin Cities. He is an active member of the Association for Molecular Pathology, the American Society of Human Genetics and is a fellow of the American College of Medical Genetics and Genomics.
