We propose to establish a high throughput sequencing team capable of efficiently producing 50-100 megabases of high quality genomic sequence per year at a competitive cost. The essential elements of any high throughput sequencing center are an infrastructure of experienced sequencing personnel, software, and equipment that can efficiently produce DNA sequence data. We will establish such a center with an emphasis on quality at all levels of the sequencing process from clone verification to the correct determination of each specific base. We propose in a three year period to expand to a level that would allow us in the subsequent 1-2 years to reach 50-100 megabases of sequence if this were needed programmatically. We further propose to sequence 3 megabases in year 1,9 megabases in year 2, and 24 megabases in year 3. This will put us in a position to fish the sequence of chromosome 18 prior to the target date for schedule completion of the first reference sequence. We also propose to use Optical Mapping to facilitate the assembly of sequence, especially in difficult regions of the genome. Having the detailed structure of a region often provides clues to the order of contigs during assembly. This will facilitate linking of contigs as well as suggest strategies for the closure of gaps based on the estimated gap size. We will also use these maps to verify the completed assemblies as part of our quality control program.
