SSCP: a tool for contig building of duplicated genomic regions

Abstract

Center for Human Genetics, Flanders Interuniversity Institute for Biotechnology, University of Leuven, Leuven, Belgium▼High-resolution physical maps are constructed by thegeneration of a contiguous set of overlapping YAC, BAC,PAC or cosmid clones representing a genomic region ofinterest. This is usually achieved by STS-content mappingand fingerprinting of the clones. If there are many STSsthen screening a genomic library can isolate a contiguousset of clones directly.Although chromosome walking has been highly success-ful for most genomic regions, it is not successful when theregion of interest is not unique in the genome. When STSsderived from such a region are used as a probe to screena genomic library, they will identify clones containing in-serts derived from different genomic regions. This results in‘branching’ of the contig during contig construction. Notsurprisingly, the gaps in the present-day human genomicmapsareinpreciselytheregionsofthehumangenomethatcontain duplications or regions with low-copy-number re-peats.Thepericentromericregionsaretheparadigmforthis(Ref. 1–4).Different observations can point to ‘branching’ of acontig:1. the number of clones isolated with an STS exceeds thegenomic representation in the library;2. neither of the two insert ends of a newly isolated clonemap back to the parent clone;3. more than one hybridization signal is detected whenthe STS is used as a probe for Southern blot or fluores-cent