BAC LIBRARY PRODUCTION FOR COMPARATIVE GENETICS

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The goal is to prepare BAC libraries for many species, of high quality, tailored to the scientific community's interest in comparative genomics and functional applications. The work will be done by two collaborating teams, one lead by Dr. Cheng at the Lawrence Berkeley National Laboratory (LBNL) and the other one at the Children's Hospital Oakland Research Institute, co-directed by Drs. Osoegawa & deJong. The application has four components relevant to preparing Bacterial Artificial Chromosomes (BACs): 1) BAC Library preparation, 2) Clone Arraying & Library Duplication, 3) Library Characterization, and 4) Research & Development to improve the overall process efficiency and the BAC library quality. During the first year, the consortium will generate and characterize twelve animal BAC libraries with ten-fold genome redundancy. Presuming an increasing need for additional GBACs and improved production efficiency, 17 and 22 additional libraries will be prepared and characterized in years 2 and 3 respectively. The libraries, based on current BAC cloning technology, will complement and extend the small repertoire of BAC clone collections now available for comparative genome analysis. The new clone collections will be analyzed by a standardized set of tests, including screening with a set of economic markers, limited BAC-end sequencing, BAC fingerprinting, BAC stability analysis and insert size determination. Of particular importance are quality tests to ensure low BAC stability analysis and insert size determination. Of particular importance are quality tests to ensure low levels of clonal cross contamination. Once the libraries pass the quality controls, the new resources will be made available in a format consistent with major applications. To improve the overall process efficiency, a set of Standard Operating Procedures (SOP's) will be developed to move BAC cloning away from an art form towards a routine high-throughput procedures. It is expected that the new BAC resources will contributed towards a routine-high throughput procedure. It is expected that the new BAC resources will contribute to better understanding of gene function and evolution through comparison of genes in a spectrum of animal species. The BAC clones will also become tools to create animal models for human diseases. Widespread dissemination of the clones is an unfunded but essential component of this proposal. Library information will be disseminated by publication and through our home page (http://www.chori.org/bacpac).