The Human Genome Project is now focused on obtaining the complete sequence of our genome. It is only with this information in hand can we identify all the genes and regulatory elements that make up the human blueprint. The start of any sequencing project requires a suitable template. For large-scale sequencing efforts, the obvious point is a non-trivial matter. In particular, the physical maps of the human genome are not comprised of clones which are readily sequenced. These YAC-based STS content maps and radiation hybrid maps do not have the resolution and marker density to enable ready assembly of BAC and/or PAC contigs. In the absence of a sequence-ready map, one must be constructed at a rate that will sustain the sequencing effort with an uninterrupted flow of well characterized clones. Sufficient contig depth is needed to ensure the integrity of the clones selected to represented the minimal tiling path. Sequencing accuracy is a moot point if deleted or rearranged clones are selected as the representation of the genome.
The specific aim of this project is to assemble a sequence-ready map of human chromosome 18 in support of a large-scale sequencing effort directed at sequencing this 85 megabase segment of the human genome. This will be accomplished in two phases. The initial phase will focus on a marker-dense region of the chromosome in order to generate quickly a selection of BAC clones to jump-start the sequencing effort. One accomplished, the second phase will then be directed at constructing a sequence-ready map of the entire chromosome. Gap closure and continuity will be a prime objective such that an efficient tiling path can be selected in order to reduce the amount of redundant sequencing. BAC clones will be initially isolated by hybridization of publicly available mapped markers to high-density filters of arrayed clones. For closure, additional clones will be isolated using probes developed from end-walk sequences and random reads derived from selected YAC clones. All clones will be finger-printed using complete restriction enzyme digests and agarose gel electrophoresis. Contigs will be assembled using the FPC software package that identifies clone overlap by comparing restriction patter similarities.
