Physical mapping of complex genomes by sampled sequencing: a theoretical analysis

A method for high-throughput, high-resolution physical mapping of complex genomes and human chromosomes called Genomic Sequence Sampling (GSS) has recently been proposed (Smith et al., 1994, Nature Genet. 7: 40-47). This mapping strategy employs high-density cosmid contig assembly over 200-kb to 1-Mb regions of the target genome coupled with DNA sequencing of the cosmid ends. The relative order and spacing of the sequence fragments is determined from the template contig, resulting in a physical map of 1- to 5-kb resolution that contains a substantial portion of the entire sequence at one-pass accuracy. The purpose of this paper is to determine the theoretical parameters for GSS mapping, to evaluate the effectiveness of the contig-building strategy, and to calculate the expected fraction of the target genome that can be recovered as mapped sequence. A novel aspect of the cosmid fingerprinting and contig-building strategy involves determining the orientation of the genomic inserts relative to the cloning vectors, so that the sampled sequence fragments can be mapped with high resolution. The algorithm is based upon complete restriction enzyme digestion, contig assembly by matching fragments, and end-orientation of individual cosmids by determining the best consistent fit of the labeled cosmid end fragments in the consensus restriction map.