SEQUENCING HUMAN CHROMOSOME 22 CENTROMERE TO NF2

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The major goal of the research in this project is to systematically sequence approximately half of human chromosome 22 within the next 5 years. The sequencing will be accomplished by officially linking our laboratory based in Oklahoma in a partnership with the GESTEC for Mapping Chromosome 22 based in Philadelphia and with Dr. John Sulston and his colleagues at the Sanger Center, Hinxton, England. Through these collaborations will be jointly coordinating efforts to sequence the entire chromosome, as well as efforts to improve the efficiency of sequence data collection, analysis, annotation, and release. To achieve this goal, we now propose to 1. expand the megabase sequencing capabilities at the University of Oklahoma Advanced Center for Genome Technology (ACGT). ACGT is built upon the graduate student/postdoctoral training-based approach to genomic sequencing that has led to successfully completing approximately 1 million bases of human DNA sequence within the past year. We will produce at least 2 Mb of finished sequence in year 1 by doubling our existing sequencing capabilities, from 4 to 8 ABI 373A fluorescent sequencing instruments. Then, with the addition of 4 new sequencing instruments in each of the next two years and with the anticipated improvements, will produce 4 Mb of finished sequence in year 2, and 5 Mb of finished sequence in each of years 3, 4, and 5. By employing and refining our already established protocols, we can complete approximately one-half the sequence of human chromosome 22 within the proposed grant 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 our DNA sequencing efficiency. 3. To rapidly release annotated DNA sequence data to the community following the C. elegans paradigm as outlined in our collaborative arrangement with the Sanger Center, Hinxton, England. With the existing technology, we can clearly document the predictions based on our own productivity, that of the Washington University (C. elegans), and the Sanger Center (yeast, C. elegans, and human). The cost per base of final sequence is slightly under $1 as calculated by taking the total NCHGR funding to the PI, including indirect cost and pro-rating equipment over the total grant period, and dividing by the total number o~ bases deposited in GenBank. With the modest improvements in technology and efficiency, we can realistically expect that approximately half of human chromosome 22 can be sequenced within the 5 year proposed grant period at a cost approaching 50 cents per base of final sequence. Throughout this period, we 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.