Skip to main content

Amplification Refractory Mutation System and Molecular Diagnostics

  • Protocol
Medical Biomethods Handbook

Part of the book series: Springer Protocols Handbooks ((SPH))

  • 2081 Accesses

Abstract

Allele-specific polymerase chain reaction (PCR) was first described in 1989, with variations arising over the next few years such as allele-specific oligonucleotide PCR, mutant-allele-specific amplification (MASA), PCR amplification of specific alleles (PASA), and the amplification refractory mutation system (ARMS) (15). For convenience, the term ARMS will be used here when referring to them collectively.

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

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight 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

Institutional subscriptions

References

  1. Okayama, H., Curiel, D. T., Brantly, M. L., Holmes, M. D., and Crystal, R. G. (1989) Rapid, nonradioactive detection of mutations in the human genome by allele-specific amplification. J. Lab. Clin. Med. 114, 105–113.

    PubMed  CAS  Google Scholar 

  2. Newton, C. R., Graham, A., Heptinstall, L. E., et al. (1989) Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Res. 17, 2503–2516.

    Article  PubMed  CAS  Google Scholar 

  3. Hayashi, N., Ito, I., Yanagisawa, A., et al. (1995) Genetic diagnosis of lymph-node metastasis in colorectal cancer. Lancet 345, 1257–1259.

    Article  PubMed  CAS  Google Scholar 

  4. Sommer, S. S., Groszbach, A. R., and Bottema, C. D. (1992) PCR amplification of specific alleles (PASA) is a general method for rapidly detecting known single-base changes. Biotechniques 12, 82–87.

    PubMed  CAS  Google Scholar 

  5. Richter, S. and Seth, A. (1998) One step direct detection of recurrent mutations in the breast cancer susceptibility gene, BRCA1. Int. J. Oncol. 12, 1263–1267.

    PubMed  CAS  Google Scholar 

  6. Maher, C., Crowley, D., Cullen, C., Wall, C., Royston, D., and Fanning, S. (1999) Double fluorescent-amplification refractory mutation detection (dF-ARMS) of the factor V Leiden and prothrombin mutations. Thromb. Haemost. 81, 76–80.

    Google Scholar 

  7. Humeny, A., Rodel, F., Rodel, C., et al. (2003) MDR1 single nucleotide polymorphism C3435T in normal colorectal tissue and colorectal carcinomas detected by MALDI-TOF mass spectrometry. Anticancer Res. 23, 2735–2740.

    PubMed  CAS  Google Scholar 

  8. Bengra, C., Mifflin, T. E., Khripin, Y., et al. (2002) Genotyping of essential hypertension singlenucleotide polymorphisms by a homogeneous PCR method with universal energy transfer primers. Clin. Chem. 48, 2131–2140.

    PubMed  CAS  Google Scholar 

  9. Myakishev, M. V., Khripin, Y., Hu, S., and Hamer, D. H. (2001) High-throughput SNP genotyping by allele-specific PCR with universal energy-transfer-labeled primers. Genome Res. 11, 163–169.

    Article  PubMed  CAS  Google Scholar 

  10. Gelsthorpe, A. R., Wells, R. S., Lowe, A. P., Tonks, S., Bodmer, J. G., and Bodmer, W. F. (1999) High-throughput class I HLA genotyping using fluorescence resonance energy transfer (FRET) probes and sequence-specific primer-polymerase chain reaction (SSP-PCR). Tissue Antigens 54, 603–614.

    Article  PubMed  CAS  Google Scholar 

  11. Graur, D. and Li, W.-H. (2000) Fundamentals of Molecular Evolution, 2nd ed., Sinauer Associates, Sunderland, MA, p XIV.

    Google Scholar 

  12. Cotton, R. G. and Horaitis, O. (2002) The HUGO Mutation Database Initiative. Human Genome Organization. Pharmacogenom. J., 2, 16–19.

    Article  CAS  Google Scholar 

  13. Finn, G. K., Kurz, B. W., Cheng, R. Z., and Shmookler Reis, R. J. (1989) Homologous plasmid recombination is elevated in immortally transformed cells. Mol. Cell Biol. 9, 4009–4017.

    PubMed  CAS  Google Scholar 

  14. Ayyadevara, S., Thaden, J. J., and Shmookler Reis, R. J. (2000) Discrimination of primer 3′-nucleotide mismatch by taq DNA polymerase during polymerase chain reaction. Anal. Biochem. 284, 11–18.

    Article  PubMed  CAS  Google Scholar 

  15. Ye, S., Dhillon, S., Ke, X., Collins, A. R., and Day, I. N. (2001) An efficient procedure for genotyping single nucleotide polymorphisms. Nucleic Acids Res. 29, E88.

    Article  PubMed  CAS  Google Scholar 

  16. Roberts, R., Joyce, P., and Kennedy, M. A. (2000) Rapid and comprehensive determination of cytochrome P450 CYP2D6 poor metabolizer genotypes by multiplex polymerase chain reaction. Hum. Mutat. 16, 77–85.

    Article  PubMed  CAS  Google Scholar 

  17. Albis-Camps, M. and Blasczyk, R. (1999) Fluorotyping of HLA-DRB by sequence-specific priming and fluorogenic probing. Tissue Antigens 53, 301–307.

    Article  PubMed  CAS  Google Scholar 

  18. Bartlett, S., Straub, J., Tonks, S., Wells, R. S., Bodmer, J. G., and Bodmer, W. F. (2001) Alkalinemediated differential interaction (AMDI): a simple automatable single-nucleotide polymorphism assay. Proc. Natl. Acad. Sci. USA 98, 2694–2697.

    Article  PubMed  CAS  Google Scholar 

  19. Montanaro, L. and Arciola, C. R. (2002) Detection of the G_T polymorphism at the Sp1 binding site of the collagen type I alpha 1 gene by a novel ARMS-PCR method. Genet. Test. 6, 53–57.

    Article  PubMed  CAS  Google Scholar 

  20. Thong, M. K., Law, H. Y., and Ng, I. S. (1996) Molecular heterogeneity of beta-thalassaemia in Malaysia: a practical approach to diagnosis. Ann. Acad. Med. Singapore 25, 79–83.

    PubMed  CAS  Google Scholar 

  21. Yandava, C. N., Zappulla, D. C., Korf, B. R., and Neufeld, E. J. (1996) ARMS test for diagnosis of factor VLeiden mutation, a common cause of inherited thrombotic tendency. J. Clin. Lab. Anal. 10, 414–417.

    Article  PubMed  CAS  Google Scholar 

  22. Hezard, N., Cornillet, P., Droulle, C., Gillot, L., Potron, G., and Nguyen, P. (1997) Factor V Leiden: detection in whole blood by ASA PCR using an additional mismatch in antepenultimate position. Thromb. Res. 88, 59–66.

    Article  PubMed  CAS  Google Scholar 

  23. Bathelier, C., Champenois, T., and Lucotte, G. (1998) ARMS test for diagnosis of factor V Leiden mutation and allele frequencies in France. Mol. Cell. Probes 12, 121–123.

    Article  PubMed  CAS  Google Scholar 

  24. Samuel, D., Beard, S., Yang, H., Saunders, N., and Jin, L. (2003) Genotyping of measles and mumps virus strains using amplification refractory mutation system analysis combined with enzyme immunoassay: a simple method for outbreak investigations. J. Med. Virol. 69, 279–285.

    Article  PubMed  CAS  Google Scholar 

  25. Fan, X. Y., Hu, Z. Y., Xu, F. H., Yan, Z. Q., Guo, S. Q., and Li, Z. M. (2003) Rapid detection of rpoB gene mutations in rifampin-resistant Mycobacterium tuberculosis isolates in shanghai by using the amplification refractory mutation system. J. Clin. Microbiol. 41, 993–997.

    Article  PubMed  CAS  Google Scholar 

  26. Lio, D., Pes, G. M., Carru, C., et al. (2003) Association between the HLA-DR alleles and longevity: a study in Sardinian population. Exp. Gerontol. 38, 313–317.

    Article  PubMed  CAS  Google Scholar 

  27. Ito, H., Sudo-Yamaji, A., Abe, M., Murase, T., and Tsubota, T. (2003) Sex identification by alternative polymerase chain reaction methods in falconiformes. Zool. Sci. 20, 339–344.

    Article  PubMed  CAS  Google Scholar 

  28. Sasaki, Y., Fushimi, H., Cao, H., Cai, S. Q., and Komatsu, K. (2002) Sequence analysis of Chinese and Japanese curcuma drugs on the 18S rRNA gene and trnK gene and the application of amplification-refractory mutation system analysis for their authentication. Biol. Pharm. Bull. 25, 1593–1599.

    Article  PubMed  CAS  Google Scholar 

  29. Wetton, J. H., Tsang, C. S., Roney, C. A., and Spriggs, A. C. (2002) An extremely sensitive speciesspecific ARMS PCR test for the presence of tiger bone DNA. Forensic Sci. Int. 126, 137–144.

    Article  PubMed  CAS  Google Scholar 

  30. Pusch, C. M., Kayademir, T., Prangenberg, K., Conard, N. J., Czarnetzki, A., and Blin, N. (2002) Documenting ancient DNA quality via alpha satellite amplification and assessment of clone sequence diversity. J. Appl. Genet. 43, 351–364.

    PubMed  Google Scholar 

  31. Steinborn, R., Schinogl, P., Wells, D. N., Bergthaler, A., Muller, M., and Brem, G. (2002) Coexistence of Bos taurus and B. indicus mitochondrial DNAs in nuclear transfer-derived somatic cattle clones. Genetics 162, 823–829.

    PubMed  CAS  Google Scholar 

  32. Bahar, A. Y., Taylor, P. J., Andrews, L., et al. (2001) The frequency of founder mutations in the BRCA1, BRCA2, and APC genes in Australian Ashkenazi Jews: implications for the generality of U.S. population data. Cancer 92, 440–445.

    Article  PubMed  CAS  Google Scholar 

  33. Mouron, S. A., Abba, M. C., Guerci, A., Gomez, M. A., Dulout, F. N., and Golijow, C. D. (2000) Association between activated K-ras and c-erbB-2 oncogenes with “high-risk” and “low-risk” human papilloma virus types in preinvasive cervical lesions. Mutat. Res. 469, 127–134.

    PubMed  CAS  Google Scholar 

  34. Friend, S., Borresen, A. L., Brody, L., et al. (1995) Breast cancer information on the web. Nature Genet. 11, 238–239.

    Article  PubMed  CAS  Google Scholar 

  35. Struewing, J. P., Abeliovich, D., Peretz, T., et al. (1995) The carrier frequency of the BRCA1 185delAG mutation is approximately 1 percent in Ashkenazi Jewish individuals. Nat. Genet. 11, 198–200.

    Article  PubMed  CAS  Google Scholar 

  36. Shattuck-Eidens, D., McClure, M., Simard, J., et al. (1995) A collaborative survey of 80 mutations in the BRCA1 breast and ovarian cancer susceptibility gene. Implications for presymptomatic testing and screening. JAMA 273, 535–541.

    Article  PubMed  CAS  Google Scholar 

  37. Scully, R., Chen, J., Plug, A., et al. (1997) Association of BRCA1 with Rad51 in mitotic and meiotic cells. Cell 88, 265–275.

    Article  PubMed  CAS  Google Scholar 

  38. Eng, C. and Mulligan, L. M. (1997) Mutations of the RET proto-oncogene in the multiple endocrine neoplasia type 2 syndromes, related sporadic tumours, and hirschsprung disease. Hum. Mutat. 9, 97–109.

    Article  PubMed  CAS  Google Scholar 

  39. Low, E. O., Jones, A. M., Gibbins, J. R., and Walker, D. M. (2000) Analysis of the amplification refractory mutation allele-specific polymerase chain reaction system for sensitive and specific detection of p53 mutations in DNA. J. Pathol. 190, 512–515.

    Article  PubMed  CAS  Google Scholar 

  40. Low, E. O., Gibbins, J. R., and Walker, D. M. (2000) In situ detection of specific p53 mutations in cultured cells using the amplification refractory mutation system polymerase chain reaction. Diagn. Mol. Pathol. 9, 210–220.

    Article  PubMed  CAS  Google Scholar 

  41. Hsu, I. C., Metcalf, R. A., Sun, T., Welsh, J. A., Wang, N. J., and Harris, C. C. (1991) Mutational hotspot in the p53 gene in human hepatocellular carcinomas. Nature 350, 427–428.

    Article  PubMed  CAS  Google Scholar 

  42. Bressac, B., Kew, M., Wands, J., and Ozturk, M. (1991) Selective G to T mutations of p53 gene in hepatocellular carcinoma from southern Africa. Nature 350, 429–431.

    Article  PubMed  CAS  Google Scholar 

  43. Aguilar, F., Harris, C. C., Sun, T., Hollstein, M., and Cerutti, P. (1994) Geographic variation of p53 mutational profile in nonmalignant human liver. Science 264, 1317–1319.

    Article  PubMed  CAS  Google Scholar 

  44. Puisieux, A., Lim, S., Groopman, J., and Ozturk, M. (1991) Selective targeting of p53 gene mutational hotspots in human cancers by etiologically defined carcinogens. Cancer Res. 51, 6185–6189.

    PubMed  CAS  Google Scholar 

  45. Aguilar, F., Hussain, S. P., and Cerutti, P. (1993) Aflatoxin B1 induces the transversion of G_T in codon 249 of the p53 tumor suppressor gene in human hepatocytes. Proc. Natl. Acad. Sci. USA 90, 8586–8590.

    Article  PubMed  CAS  Google Scholar 

  46. Cerutti, P., Hussain, P., Pourzand, C., and Aguilar, F. (1994) Mutagenesis of the H-ras protooncogene and the p53 tumor suppressor gene. Cancer Res. 54, 1934s–1938s.

    PubMed  CAS  Google Scholar 

  47. Staib, F., Hussain, S. P., Hofseth, L. J., Wang, X. W., and Harris, C. C. (2003) TP53 and liver carcinogenesis. Hum. Mutat. 21, 201–216.

    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

© 2005 Humana Press Inc., Totowa, NJ

About this protocol

Cite this protocol

Kitching, R., Seth, A. (2005). Amplification Refractory Mutation System and Molecular Diagnostics. In: Walker, J.M., Rapley, R. (eds) Medical Biomethods Handbook. Springer Protocols Handbooks. Humana Press. https://doi.org/10.1385/1-59259-870-6:155

Download citation

  • DOI: https://doi.org/10.1385/1-59259-870-6:155

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-288-9

  • Online ISBN: 978-1-59259-870-0

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics