Concept of Genome Scanning

  • Yoshihide Hayashizaki
Part of the Springer Lab Manuals book series (SLM)


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.


Sickle Cell Anemia Restriction Landmark Genomic Scanning Probe Polymerase Chain Reaction Single Copy Locus Tonemal Complex 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Fisher SG, Lerman LS (1979) Length-independent separation of DNA restriction fragments in two-dimensional gel electrophoresis. Cell 16:191–200CrossRefGoogle Scholar
  2. 2.
    Burke DT, Carle GF, Olson MV (1987) Cloning of large segments of exogenous DNA into yeast by means of artificial chromosome vectors. Science 236:806–812PubMedCrossRefGoogle Scholar
  3. 3.
    Shizuya H, Birren B, Kim UJ, Mancino V, Slepak T, Tachiiri Y, Simon M (1992) Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc Natl Acad Sci USA 89:8794–8797PubMedCrossRefGoogle Scholar
  4. 4.
    Ioannou PA, Amemiya CT, Games J, Kroisel PM, Shibya H, Chen C, Batzer MA, Jong PJ (1994) A new bacteriophage P1-derived vector for the propagation of large human DNA fragments. Nat Genet 6:84–89PubMedCrossRefGoogle Scholar
  5. 5.
    Cohen D, Chumakov I, Weissenbach J (1993) A first-generation physical map of the human genome. Nature 366:698–701PubMedCrossRefGoogle Scholar
  6. 6.
    Collins FS (1995) Positional cloning moves from perditional to traditional. Nat Genet 9:347–350PubMedCrossRefGoogle Scholar
  7. 7.
    Southern EM (1975) Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol 98:503–517PubMedCrossRefGoogle Scholar
  8. 8.
    Saiki RK, Scharf S, Faloona F, Mullis KB, Horn GT, Erlich HA, Arnheim N (1985) Enzymatic amplification of β-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 230:1350–1354PubMedCrossRefGoogle Scholar
  9. 9.
    Uitterlinden AG, Slagboom PE, Knook DL, Vijg J (1989) Two dimensional DNA fingerprinting of human individuals. Proc Natl Acad Sci USA 86:2742–2746PubMedCrossRefGoogle Scholar
  10. 10.
    Brilliant MH, Gondo Y, Eicher EM (1991) Direct molecular identification of the mouse pink-eyed unstable mutation by genome scanning. Science 252:566–569PubMedCrossRefGoogle Scholar
  11. 11.
    Nelson DL, Ledbetter SA, Corbo L, Victoria MF, Ramirez-Slis R, Webster TD, Ledbetter DH, Caskey CT (1989) Alu polymerase chain reaction: a method for rapid isolation of human-specific sequences from complex DNA sources. Proc Natl Acad Sci USA 86:6686–6690PubMedCrossRefGoogle Scholar
  12. 12.
    Dietrich W, Katz H, Lincoln SE, Shin H-S, Friedman J, Dracopoli NC, Lander ES (1992) A genetic map of the mouse suitable for typing intraspecific crosses. Genetics 131:423–447PubMedGoogle Scholar
  13. 13.
    Hayashizaki Y, Hirotsune S, Okazaki Y, Muramatsu M, Asakawa J (1994) Fundamentals and applications: restriction landmark genomic scanning (RLGS). In: Meyers RA (ed) The encyclopedia of molecular biology. VCH, Weinheim, pp 813–817Google Scholar
  14. 14.
    Hatade I, Hayashizaki Y, Hirotsune S, Komatsubara H, Mukai TA (1991) Genomic scanning method of higher organisms using restriction sites as landmarks. Proc Natl Acad Sci USA 88:9523–9527CrossRefGoogle Scholar
  15. 15.
    Hayashizaki Y, Hirotsune S, Okazaki Y, Hatada I, Shibata H, Kawai J, Hirose K, Watanabe S, Fushiki S, Wada S, Sugimoto T, Kobayakawa K, Kawara T, Sibuya T, Mukai T (1993) Restriction landmark genomic scanning method and its various applications. Electrophoresis 14:251–258PubMedCrossRefGoogle Scholar
  16. 16.
    Okazaki Y, Okuizumi S, Sasaki N, Ohsumi T, Kuromitsu J, Kataoka H, Muramatsu M, Iwadate A, Hirota N, Kitajima M, Plass C, Chapman VM, Hayashizaki Y (1994) A genetic linkage map of the mouse using an expanded production system of restriction landmark genomic scanning (RLGS Ver.1.8). Biochem Biophys Res Commun 205:1922–1929PubMedCrossRefGoogle Scholar
  17. 17.
    Suzuki H, Yaoi T, Kawai J, Hara A, Kuwajima G, Watanabe S (1996) Restriction landmark cDNA scanning (RLCS): a novel cDNA display system using two-dimensional gel electrophoresis. Nucleic Acids Res 24:289–294PubMedCrossRefGoogle Scholar

Copyright information

© Springer Japan 1997

Authors and Affiliations

  • Yoshihide Hayashizaki

There are no affiliations available

Personalised recommendations