Skip to main content
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1989 Apr 11;17(7):2503–2516. doi: 10.1093/nar/17.7.2503

Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS).

C R Newton 1, A Graham 1, L E Heptinstall 1, S J Powell 1, C Summers 1, N Kalsheker 1, J C Smith 1, A F Markham 1
PMCID: PMC317639  PMID: 2785681

Abstract

We have improved the "polymerase chain reaction" (PCR) to permit rapid analysis of any known mutation in genomic DNA. We demonstrate a system, ARMS (Amplification Refractory Mutation System), that allows genotyping solely by inspection of reaction mixtures after agarose gel electrophoresis. The system is simple, reliable and non-isotopic. It will clearly distinguish heterozygotes at a locus from homozygotes for either allele. The system requires neither restriction enzyme digestion, allele-specific oligonucleotides as conventionally applied, nor the sequence analysis of PCR products. The basis of the invention is that unexpectedly, oligonucleotides with a mismatched 3'-residue will not function as primers in the PCR under appropriate conditions. We have analysed DNA from patients with alpha 1-antitrypsin (AAT) deficiency, from carriers of the disease and from normal individuals. Our findings are in complete agreement with allele assignments derived by direct sequencing of PCR products.

Full text

PDF
2503

Images in this article

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Chehab F. F., Doherty M., Cai S. P., Kan Y. W., Cooper S., Rubin E. M. Detection of sickle cell anaemia and thalassaemias. Nature. 1987 Sep 24;329(6137):293–294. doi: 10.1038/329293b0. [DOI] [PubMed] [Google Scholar]
  2. Chien A., Edgar D. B., Trela J. M. Deoxyribonucleic acid polymerase from the extreme thermophile Thermus aquaticus. J Bacteriol. 1976 Sep;127(3):1550–1557. doi: 10.1128/jb.127.3.1550-1557.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Conner B. J., Reyes A. A., Morin C., Itakura K., Teplitz R. L., Wallace R. B. Detection of sickle cell beta S-globin allele by hybridization with synthetic oligonucleotides. Proc Natl Acad Sci U S A. 1983 Jan;80(1):278–282. doi: 10.1073/pnas.80.1.278. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Cooper D. N., Youssoufian H. The CpG dinucleotide and human genetic disease. Hum Genet. 1988 Feb;78(2):151–155. doi: 10.1007/BF00278187. [DOI] [PubMed] [Google Scholar]
  5. Dermer S. J., Johnson E. M. Rapid DNA analysis of alpha 1-antitrypsin deficiency: application of an improved method for amplifying mutated gene sequences. Lab Invest. 1988 Sep;59(3):403–408. [PubMed] [Google Scholar]
  6. Engelke D. R., Hoener P. A., Collins F. S. Direct sequencing of enzymatically amplified human genomic DNA. Proc Natl Acad Sci U S A. 1988 Jan;85(2):544–548. doi: 10.1073/pnas.85.2.544. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Estivill X., Farrall M., Scambler P. J., Bell G. M., Hawley K. M., Lench N. J., Bates G. P., Kruyer H. C., Frederick P. A., Stanier P. A candidate for the cystic fibrosis locus isolated by selection for methylation-free islands. 1987 Apr 30-May 6Nature. 326(6116):840–845. doi: 10.1038/326840a0. [DOI] [PubMed] [Google Scholar]
  8. Farrall M., Estivill X., Williamson R. Indirect cystic fibrosis carrier detection. Lancet. 1987 Jul 18;2(8551):156–157. doi: 10.1016/s0140-6736(87)92354-3. [DOI] [PubMed] [Google Scholar]
  9. Feldman G. L., Williamson R., Beaudet A. L., O'Brien W. E. Prenatal diagnosis of cystic fibrosis by DNA amplification for detection of KM-19 polymorphism. Lancet. 1988 Jul 9;2(8602):102–102. doi: 10.1016/s0140-6736(88)90030-x. [DOI] [PubMed] [Google Scholar]
  10. Kan Y. W., Dozy A. M. Antenatal diagnosis of sickle-cell anaemia by D.N.A. analysis of amniotic-fluid cells. Lancet. 1978 Oct 28;2(8096):910–912. doi: 10.1016/s0140-6736(78)91629-x. [DOI] [PubMed] [Google Scholar]
  11. Kogan S. C., Doherty M., Gitschier J. An improved method for prenatal diagnosis of genetic diseases by analysis of amplified DNA sequences. Application to hemophilia A. N Engl J Med. 1987 Oct 15;317(16):985–990. doi: 10.1056/NEJM198710153171603. [DOI] [PubMed] [Google Scholar]
  12. Levinson B., Janco R., Phillips J., 3rd, Gitschier J. A novel missense mutation in the factor VIII gene identified by analysis of amplified hemophilia DNA sequences. Nucleic Acids Res. 1987 Dec 10;15(23):9797–9805. doi: 10.1093/nar/15.23.9797. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Long G. L., Chandra T., Woo S. L., Davie E. W., Kurachi K. Complete sequence of the cDNA for human alpha 1-antitrypsin and the gene for the S variant. Biochemistry. 1984 Oct 9;23(21):4828–4837. doi: 10.1021/bi00316a003. [DOI] [PubMed] [Google Scholar]
  14. Ludwig E. H., Blackhart B. D., Pierotti V. R., Caiati L., Fortier C., Knott T., Scott J., Mahley R. W., Levy-Wilson B., McCarthy B. J. DNA sequence of the human apolipoprotein B gene. DNA. 1987 Aug;6(4):363–372. doi: 10.1089/dna.1987.6.363. [DOI] [PubMed] [Google Scholar]
  15. Newton C. R., Kalsheker N., Graham A., Powell S., Gammack A., Riley J., Markham A. F. Diagnosis of alpha 1-antitrypsin deficiency by enzymatic amplification of human genomic DNA and direct sequencing of polymerase chain reaction products. Nucleic Acids Res. 1988 Sep 12;16(17):8233–8243. doi: 10.1093/nar/16.17.8233. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Nukiwa T., Brantly M., Garver R., Paul L., Courtney M., LeCocq J. P., Crystal R. G. Evaluation of "at risk" alpha 1-antitrypsin genotype SZ with synthetic oligonucleotide gene probes. J Clin Invest. 1986 Feb;77(2):528–537. doi: 10.1172/JCI112333. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Orkin S. H., Markham A. F., Kazazian H. H., Jr Direct detection of the common Mediterranean beta-thalassemia gene with synthetic DNA probes. An alternative approach for prenatal diagnosis. J Clin Invest. 1983 Mar;71(3):775–779. doi: 10.1172/JCI110826. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Petersen K. B., Kølvraa S., Bolund L., Petersen G. B., Koch J., Gregersen N. Detection of alpha 1-antitrypsin genotypes by analysis of amplified DNA sequences. Nucleic Acids Res. 1988 Jan 11;16(1):352–352. doi: 10.1093/nar/16.1.352. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Saiki R. K., Gelfand D. H., Stoffel S., Scharf S. J., Higuchi R., Horn G. T., Mullis K. B., Erlich H. A. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science. 1988 Jan 29;239(4839):487–491. doi: 10.1126/science.2448875. [DOI] [PubMed] [Google Scholar]
  20. Solomon E., Bodmer W. F. Evolution of sickle variant gene. Lancet. 1979 Apr 28;1(8122):923–923. doi: 10.1016/s0140-6736(79)91398-9. [DOI] [PubMed] [Google Scholar]
  21. Southern E. M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975 Nov 5;98(3):503–517. doi: 10.1016/s0022-2836(75)80083-0. [DOI] [PubMed] [Google Scholar]
  22. Stoflet E. S., Koeberl D. D., Sarkar G., Sommer S. S. Genomic amplification with transcript sequencing. Science. 1988 Jan 29;239(4839):491–494. doi: 10.1126/science.3340835. [DOI] [PubMed] [Google Scholar]
  23. Tindall K. R., Kunkel T. A. Fidelity of DNA synthesis by the Thermus aquaticus DNA polymerase. Biochemistry. 1988 Aug 9;27(16):6008–6013. doi: 10.1021/bi00416a027. [DOI] [PubMed] [Google Scholar]
  24. Williams C., Williamson R., Coutelle C., Loeffler F., Smith J., Ivinson A. Same-day, first-trimester antenatal diagnosis for cystic fibrosis by gene amplification. Lancet. 1988 Jul 9;2(8602):102–103. doi: 10.1016/s0140-6736(88)90031-1. [DOI] [PubMed] [Google Scholar]
  25. Wong C., Antonarakis S. E., Goff S. C., Orkin S. H., Boehm C. D., Kazazian H. H., Jr On the origin and spread of beta-thalassemia: recurrent observation of four mutations in different ethnic groups. Proc Natl Acad Sci U S A. 1986 Sep;83(17):6529–6532. doi: 10.1073/pnas.83.17.6529. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Wong C., Dowling C. E., Saiki R. K., Higuchi R. G., Erlich H. A., Kazazian H. H., Jr Characterization of beta-thalassaemia mutations using direct genomic sequencing of amplified single copy DNA. 1987 Nov 26-Dec 2Nature. 330(6146):384–386. doi: 10.1038/330384a0. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES