The BayGenomics project is organized into nine components involving three institutions: The J. David Gladstone Institute for Cardiovascular Disease, the University of California, San Francisco (UCSF), and the University of California at Berkeley (UCB). Each component of this Program for Genomic Applications (PGA) is making major contributions to the National Heart, Lung, and Blood Institute's (NHLBI) genomics program and help to decipher new genes that are important for cardiopulmonary disease and development.
BayGenomics Components
1. Gene Trapping in Embryonic Stem Cells: William Skarnes (UCB), Marc Tessier-Lavigne (Stanford, HHMI), Stephen G. Young (Gladstone, UCSF).
2. Computational Methods for Predicting Gene Function: Patricia C. Babbitt, Thomas E. Ferrin (UCSF).
3. In Situ Hybridization: Pao-Tien Chuang, Didier Stainier (UCSF).
4. Gene-expression Profiling and Analysis: Bruce Conklin (Gladstone, UCSF).
5. Mouse Resource for Lipid Metabolism and Atherogenesis: Stephen G. Young (Gladstone, UCSF), Karen Reue (UCLA).
6. Mouse Resource for Pulmonary Disease: Dean Sheppard (UCSF).
7. Mouse Resource for Cardiopulmonary Development: Pao-Tien Chuang (UCSF).
8. Cardiopulmonary Genomics Education: Patricia C. Babbitt, Thomas E. Ferrin (UCSF).
9. Administration: Stephen G. Young (Gladstone, UCSF).
A role of Component 1 is to use gene-trap vectors to inactivate ~2,500 genes per year in ES cells. All of our "trapped" ES cells are posted on our website and are distributed for a nominal charge by the NIH/NCRR-sponsored Mutant Mouse Regional Resource Center (MMRRC) to the scientific community for the purpose of producing knockout mice.
Components 2, 3, and 4 are organized to assess which of the ES cell clones are involved in cardiopulmonary development and common cardiopulmonary diseases, thereby increasing the value of our resource to investigators. We use computational approaches to gain insight into expression patterns and to assess functions of novel genes. In addition, we obtain probes for our "trapped" genes for use in in situ hybridization experiments to define expression patterns in development and in specific cardiopulmonary diseases. We also use microarray studies to define which of the trapped genes might be important for cardiopulmonary diseases.
The roles of components 5, 6, and 7 are to select a subset of ES cell clones determined to be most important to understanding cardiopulmonary development and disease, and to produce knockout mice for the purpose of further analysis. Selection of genes for the production of knockout mice is based on our group's long-standing biological interests and on the anticipated level of interest in those mice by the broader research community.
Component 8 focuses on education aimed at the scientific research community, especially cardiopulmony investigators. We conduct periodic "hands-on" workshops and provide extensive educational material on-line at the BayGenomics website.
See Specific Aims for additional information on the goals of each component.