Skip to main content

Use of DNA Fingerprinting to Detect Genetic Rearrangements in Human Cancer

  • Protocol
  • 361 Accesses

Part of the book series: Methods in Molecular Medicine ((MIMM,volume 68))

Abstract

The polymerase chain reaction (PCR) has revolutionized the isolation and analysis of nucleic acid fragments from a wide variety of sources. PCR-based methods for nucleic acid detection and fingerprinting have become vital to modern molecular genetics, whether for the analysis of populations of organisms to determine population structure of an ecosystem, sampling a set of DNA sequences to infer evolutionary history, sampling genetic loci to build a map, or sampling differentially expressed genes to identify phenotypic markers. PCR can be used to generate high resolution genetic maps of human and comparative genomes. Compared with Southern blot analysis, which detects restriction fragment length polymorphisms (RFLPs) and hypervariable minisatellite loci, PCR is faster, less labor-intensive, less expensive, and requires relatively small amounts of DNA. Additionally, PCR may be a more practical approach for large-scale mapping projects.

This is a preview of subscription content, log in via an institution.

Buying options

Protocol
USD   49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. Williams, J. G., Kubelik, A. R., Livak, K. J., Rafalski, J. A., and Tingey, S. V. (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 18, 6531–6535.

    Article  PubMed  CAS  Google Scholar 

  2. Caetano-Anolles, G., Bassam, B. J., and Gresshoff, P. M. (1991) DNA amplification fingerprinting using very short arbitrary oligonucleotide primers. Biotechnology (NY) 9, 553–557.

    Article  CAS  Google Scholar 

  3. Caetano-Anolles, G., Bassam, B. J., and Gresshoff, P. M. (1992) DNA fingerprinting: MAAPing out a RAPD redefinition? Bio/Technology 19, 937.

    Article  Google Scholar 

  4. Welsh, J. and McClelland, M. (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res. 18, 7213–7218.

    Article  PubMed  CAS  Google Scholar 

  5. Welsh, J. and McClelland, M. (1991) Genomic fingerprinting using arbitrarily primed PCR and a matrix of pairwise combinations of primers. Nucleic Acids Res. 19, 5275–5279.

    Article  PubMed  CAS  Google Scholar 

  6. Welsh, J., Pretzman, C., Postic, D., Saint Girons, I., Baranton, G., and McClelland, M. (1992) Genomic fingerprinting by arbitrarily primed polymerase chain reaction resolves Borrelia burgdorferi into three distinct phyletic groups. Intl. J. Syst. Bacteriol. 42, 370–373.

    Article  CAS  Google Scholar 

  7. Preus, H. R., Haraszthy, V. I., Zambon, J. J., and Genco, R. J. (1993) Differentiation of strains of Actinobacillus actinomycetemcomitans by arbitrarily primed polymerase chain reaction. J. Clin. Microbiol. 31, 2773–2776.

    PubMed  CAS  Google Scholar 

  8. Peinado, M. A., Malkhosyan, S., Velazquez, A., and Perucho, M. (1992) Isolation and characterisation of allelic losses and gains in colorectal tumors by arbitrarily primed polymerase chain reaction. Proc. Natl. Acad. Sci. USA 89, 10,065–10,069.

    Article  PubMed  CAS  Google Scholar 

  9. Ionov, Y., Peinado, M. A., Malkhosyan, S., Shibata, D., and Perucho, M. (1993) Ubiquitous somatic mutations in simple repeated sequences reveal a new mechanism for colonic carcinogenesis. Nature 10, 558–563.

    Article  Google Scholar 

  10. Roninson, I. B., Chin, J. E., Choi, K. G., Gros, P., Housman, D. E., Fojo, A., et al. (1986) Isolation of human mdr DNA sequences amplified in multidrug-resistant KB carcinoma cells. Proc. Natl. Acad. Sci. USA 83, 4538–4542.

    Article  PubMed  CAS  Google Scholar 

  11. Wesley, C. S., Ben, M., Kreitman, M., Hagag, N., and Eanes, W. F. (1990) Cloning regions of the Drosophila genome by microdissection of polytene chromosome DNA and PCR with nonspecific primer. Nucleic Acids Res. 18, 599–603.

    Article  PubMed  CAS  Google Scholar 

  12. Welsh, J., Chada, K., Dalal, S. S., Cheng, R., Ralph, D., and McClelland, M. (1992) Arbitrarily primed PCR fingerprinting of RNA. Nucleic Acids Res. 20, 4965–4970.

    Article  PubMed  CAS  Google Scholar 

  13. Nelson, D. L., Ledbetter, S. A., Corbo, L., Victoria, M. F., Ramirez-Solis, R., Webster, T. D., et al. (1989) Alu polymerase chain reaction: a method for rapid isolation of human-specific sequences from complex DNA sources. Proc. Natl. Acad. Sci. USA 86, 6686–6690.

    Article  PubMed  CAS  Google Scholar 

  14. McKie, A. B., Iwamura, T., Leung, H. Y., Hollingsworth, M. A., and Lemoine, N. R. (1997) Alu-polymerase chain reaction genomic fingerprinting technique identifies multiple genetic loci associated with pancreatic tumourigenesis. Genes Chrom. Cancer 18, 30–41.

    Article  PubMed  CAS  Google Scholar 

  15. Nystrom-Lahti, M., Kristo, P., Nicolaides, N. C., Chang, S. Y., Aaltonen, L.A., Moisio, A. L., et al. (1995) Founding mutations and Alu-mediated recombination in hereditary colon cancer. Nat. Med. 1, 1203–1206.

    Article  PubMed  CAS  Google Scholar 

  16. Tycko, B., Smith, S. D., and Sklar, J. (1991) Chromosomal translocations joining LCK and TCRB loci in human T cell leukemia. J. Exp. Med. 174, 867–873.

    Article  PubMed  CAS  Google Scholar 

  17. Chissoe, S. L., Bodenteich, A., Wang, Y. F., Wang, Y. P., Burian, D., Clifton, S. W., et al. (1995) Sequence and analysis of the human ABL gene, the BCR gene, and regions involved in the Philadelphia. Genomics 27, 67–82.

    Article  PubMed  CAS  Google Scholar 

  18. Skowronski, J., Fanning, T. G., and Singer, M. F. (1988) Unit-length line-1 transcripts in human teratocarcinoma cells. Mol. Cell. Biol. 8, 1385–1397.

    PubMed  CAS  Google Scholar 

  19. Jurka, J. (1990) Novel families of interspersed repetitive elements from the human genome. Nucleic Acids Res. 18, 137–141.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2002 Humana Press Inc.

About this protocol

Cite this protocol

Sirivatanauksorn, V., Sirivatanauksorn, Y., McKie, A.B., Lemoine, N.R. (2002). Use of DNA Fingerprinting to Detect Genetic Rearrangements in Human Cancer. In: Boultwood, J., Fidler, C. (eds) Molecular Analysis of Cancer. Methods in Molecular Medicine, vol 68. Humana Press. https://doi.org/10.1385/1-59259-135-3:107

Download citation

  • DOI: https://doi.org/10.1385/1-59259-135-3:107

  • Publisher Name: Humana Press

  • Print ISBN: 978-0-89603-622-2

  • Online ISBN: 978-1-59259-135-0

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics