YAC-STS content mapping

The goals of physical mapping are to provide (1) an ordered set of all the DNA of the chromosome (or genome), (2) accurate distances between a dense set of DNA markers, and (3) a set of DNA clones from which direct DNA sequencing can be done. High-resolution physical mapping of a certain chromosomal interval or even the whole genome implies that large-insert genomic clones with overlapping inserts are assembled and ordered according to their position in the genome. Physical mapping usually involves the construction of YAC, BAC, and/or BAC contigs. Ideally, a contig covers the defined chromosomal region or even an entire chromosome without gaps. Because of their large size, YACs have enabled the rapid construction of physical maps by ordered clone mapping and contig building. Conventional contig assembly is performed primarily by PCR assays (STS content mapping), by hybridization-based techniques, or by restriction fingerprinting. The chromosomal location of a contig can be determined by anchoring it to genetic and radiation hybrid maps. STS content mapping is a commonly used, robust, and effective technique, which is applicable to all kinds of cloning systems and has been employed for the physical mapping of the human and mouse genome (Hudson et al., 1995; Nusbaum et al., 1999). The disadvantages are that the isolation of endclones is laborious and often does not result in any suitable clone, a large number of preexisting evenly distributed STS markers is required, and the large number of primers required results in significant costs. The alternative strategy is based on the screening of large-insert libraries spotted on high-density gridded filters by hybridization. Subcloned genomic fragments, end sequences of genomic clones, oligonucleotides, or interrepeat sequences are mostly used as hybridization probes. This method allows the efficient screening of high genome coverage by a single hybridization. Hybridization-based physical maps have been constructed, for example, of the human chromosome (Hattori et al., 2000) and the mouse genome (Schalkwyk et al., 2001). Keywords: YAC; STS; physical mapping; interrepeat PCR