Concept of Genome Scanning

Abstract

Genome scanning is defined as the high-speed survey of the presence or absence of landmarks throughout a genome and the measurement of their copy number in each locus. Originally, the concept of genome scanning arose from the idea of overall detection of the physical condition of whole genomic DNA. From this standpoint, it would be simplest to detect all fragments of genomic DNA generated by restriction-enzyme cleavage after electrophoresis and staining with ethidium bromide. Initially, efforts were made to visualize whole genomic DNA fragments according to this approach using the E. coli genome [1]. However, this approach has been limited to small-sized genomes (Fig. 1.1). As the complexity of the genome increases, the copy number of DNA molecules of the haploid genome equivalent decreases in proportion to the amount of genomic DNA. In the case of the human genome, which is 3 × 10⁹bp (approximately 10³-fold of E. coli genome), a single copy locus per haploid genome of 1 μg human genomic DNA produces only 0.5 attomol (5 × l0^-19mol) fragments. Also, as the genome complexity increases, it becomes more difficult to separate and detect the large number of DNA fragments produced from the large-sized genome of higher organisms. Generally, to achieve the high resolution needed for DNA separation of such large genomes, the total amount of genomic DNA is technically limited, with separation steps of DNA fragments such as electrophoretic techniques.