Optical mapping: a novel, single-molecule approach to genomic analysis.

Abstract

Increasingly, it appears likely that the ultimate success of the human genome project, and a majority of advances in molecular diagnosis of human disease, will be driven by advances in genomic analysis that permit ultrarapid physical mapping and DNA sequencing. Molecular biological approaches currently being used were developed primarily for characterization of single genes, not entire genomes and, as such, are not ideally suited to analysis of polygenic diseases, complex trait inheritance, and population-based molecular genetics. Thus, it is imperative to develop new approaches rapidly that deal with entire genomes. Physical mapping of genomes, using restriction endonucleases, has played a major role in identifying and characterizing various loci, for example, by aiding clone contig formation and by characterizing genetic lesions. Restriction maps provide precise genomic distances, unlike ordered sequence-based landmarks such as sequence tagged sites (STSs), that are essential for optimizing the efficiency of sequencing efforts and for determining the spatial relationships of specific loci (Baxendale et al. 1993). When compared to time-consuming hybridization-based fingerprinting approaches, ordered restriction maps offer relatively unambiguous clone characterization that is useful in contig formation, establishment of minimal tiling paths for sequencing, and preliminary characterization of sequence lesions. Despite the broad applications of restriction maps, the associated techniques for their generation have changed little over the last 10 years, primarily because they still utilize electrophore-