SEQUENCING MOUSE GENOMIC CLONES

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DESCRIPTION (Adapted from the Investigator's Abstract): The major goal of the research in this project is to systematically sequence regions of the mouse genome that are syntenic with sequenced regions of the human genome. The sequencing will be accomplished by continuing the link between Dr. Roe's laboratory, based at the University of Oklahoma Department of Chemistry and Biochemistry on the Norman campus, in a partnership with the laboratory of Dr. Reeves at John Hopkins University. During the past year, this informal collaboration has resulted in the sequence of over 200 kbp of mouse chromosomal DNA that is syntenic with human 22q11. Dr. Roe now wishes to formalize this collaboration and begin transferring the technology from his group to John Hopkins by jointly coordinating efforts to begin mouse genomic sequencing on a larger scale and provide this sequence data to the community. Full length genomic clone sequencing will be performed at the University of Oklahoma and the genomic clone libraries and end sequencing will be performed at the John Hopkins University. To achieve this goal, the investigators now propose to: 1. Expand the megabase sequencing capabilities at the University of Oklahoma Advanced Center for Genome Technology to include a group dedicated to mouse genomic sequencing. ACGT is built upon the graduate student/postdoctoral training-based approach to genomic sequencing that has led to successfully completing approximately 2 million bases of human DNA sequence and approximately one-fold coverage of the Streptococcus pyogenes and Neisseria gonorrhoeae genomes within the last year. By employing and refining their already established protocols, the investigators can complete the sequence of at least 6 mouse genomic containing BACs in years 01 and 02 with an already available NSF EPSCoR funded ABI377 and double their sequencing rate in years 03 and 04 with an additional automated DNA sequencer. Thus, they will sequence approximately 4.5 M of the mouse genome that is syntenic with concurrently sequenced human genomic regions within the proposed 4 year funding period. 2. To continue to develop, improve and implement the automated procedures for DNA isolation, DNA sequence analysis, data acquisition, and data analysis, thereby increasing their DNA sequencing efficiency. 3. To rapidly release annotated DNA sequence data to the community following the C. elegans paradigm. With the existing technology, the investigators can clearly document the feasibility of this project, based on their own productivity, that of the Washington University (C. elegans), and the Sanger Center (yeast, C. elegans, and human). The present cost per base of final sequence is slightly under $1 as calculated by taking the total NCHGR funding to the investigator, including indirect cost and pro-rating equipment over the total grant period, and dividing by the total number of bases deposited in GenBank. With the modest improvement in technology and efficiency, the investigators can realistically expect that a significant region of mouse genomic DNA can be sequenced within the 4 year proposed grant period at a cost of under 50 cents per base of final sequence. Throughout this period, they also will continue to train the next generation of scientists in the basic theories and methods needed to evolve new approaches to sequencing and to data analysis.