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. 1988 Sep 12;16(17):8233–8243. doi: 10.1093/nar/16.17.8233

Diagnosis of alpha 1-antitrypsin deficiency by enzymatic amplification of human genomic DNA and direct sequencing of polymerase chain reaction products.

C R Newton 1, N Kalsheker 1, A Graham 1, S Powell 1, A Gammack 1, J Riley 1, A F Markham 1
PMCID: PMC338555  PMID: 3262215

Abstract

We have compared sequencing of cloned "polymerase chain reaction" (PCR) products and the direct sequencing of PCR products in the examination of individuals from six families affected with alpha 1-antitrypsin (AAT) deficiency. In families where paternity was in question we confirmed consanguinity by DNA fingerprinting using a panel of locus-specific minisatellite probes. We demonstrate that direct sequencing of PCR amplification products is the method of choice for the absolutely specific diagnosis of AAT deficiency and can distinguish normals, heterozygotes and homozygotes in a single, rapid and facile assay. Furthermore, we demonstrate the reproducibility of the PCR and a rapid DNA isolation procedure. We have also shown that two loci can be simultaneously amplified and that the PCR product from each locus can be independently examined by direct DNA sequencing.

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Selected References

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

  1. Abbott C. M., McMahon C. J., Kelsey G. D., Parkar M., Whitehouse D. B., Corney G., Povey S., Hopkinson D. A., Mieli-Vergani G., Mowat A. Alpha 1-antitrypsin-related gene (ATR) for prenatal diagnosis. Lancet. 1987 Jun 20;1(8547):1425–1426. doi: 10.1016/s0140-6736(87)90607-6. [DOI] [PubMed] [Google Scholar]
  2. Alter B. P. Advances in the prenatal diagnosis of hematologic diseases. Blood. 1984 Aug;64(2):329–340. [PubMed] [Google Scholar]
  3. Carrell R. W., Jeppsson J. O., Laurell C. B., Brennan S. O., Owen M. C., Vaughan L., Boswell D. R. Structure and variation of human alpha 1-antitrypsin. Nature. 1982 Jul 22;298(5872):329–334. doi: 10.1038/298329a0. [DOI] [PubMed] [Google Scholar]
  4. Cox D. W., Billingsley G. D., Mansfield T. DNA restriction-site polymorphisms associated with the alpha 1-antitrypsin gene. Am J Hum Genet. 1987 Nov;41(5):891–906. [PMC free article] [PubMed] [Google Scholar]
  5. Cox D. W., Billingsley G. D. Restriction enzyme MaeIII for prenatal diagnosis of alpha 1-antitrypsin deficiency. Lancet. 1986 Sep 27;2(8509):741–742. doi: 10.1016/s0140-6736(86)90250-3. [DOI] [PubMed] [Google Scholar]
  6. Cox D. W., Mansfield T. Prenatal diagnosis for alpha 1-antitrypsin deficiency. Lancet. 1985 Jan 26;1(8422):230–230. doi: 10.1016/s0140-6736(85)92078-1. [DOI] [PubMed] [Google Scholar]
  7. Cox D. W., Mansfield T. Prenatal diagnosis of alpha 1 antitrypsin deficiency and estimates of fetal risk for disease. J Med Genet. 1987 Jan;24(1):52–59. doi: 10.1136/jmg.24.1.52. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. 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]
  9. Eriksson S., Carlson J., Velez R. Risk of cirrhosis and primary liver cancer in alpha 1-antitrypsin deficiency. N Engl J Med. 1986 Mar 20;314(12):736–739. doi: 10.1056/NEJM198603203141202. [DOI] [PubMed] [Google Scholar]
  10. Feinberg A. P., Vogelstein B. "A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity". Addendum. Anal Biochem. 1984 Feb;137(1):266–267. doi: 10.1016/0003-2697(84)90381-6. [DOI] [PubMed] [Google Scholar]
  11. Feinberg A. P., Vogelstein B. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal Biochem. 1983 Jul 1;132(1):6–13. doi: 10.1016/0003-2697(83)90418-9. [DOI] [PubMed] [Google Scholar]
  12. Hanahan D. Studies on transformation of Escherichia coli with plasmids. J Mol Biol. 1983 Jun 5;166(4):557–580. doi: 10.1016/s0022-2836(83)80284-8. [DOI] [PubMed] [Google Scholar]
  13. Hejtmancik J. F., Sifers R. N., Ward P. A., Harris S., Mansfield T., Cox D. W. Prenatal diagnosis of alpha 1-antitrypsin deficiency by restriction fragment length polymorphisms, and comparison with oligonucleotide probe analysis. Lancet. 1986 Oct 4;2(8510):767–770. doi: 10.1016/s0140-6736(86)90297-7. [DOI] [PubMed] [Google Scholar]
  14. Jeppsson J. O., Franzén B. Typing of genetic variants of alpha 1-antitrypsin by electrofocusing. Clin Chem. 1982 Jan;28(1):219–225. [PubMed] [Google Scholar]
  15. Kidd V. J., Wallace R. B., Itakura K., Woo S. L. alpha 1-antitrypsin deficiency detection by direct analysis of the mutation in the gene. Nature. 1983 Jul 21;304(5923):230–234. doi: 10.1038/304230a0. [DOI] [PubMed] [Google Scholar]
  16. 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]
  17. 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]
  18. Messing J. New M13 vectors for cloning. Methods Enzymol. 1983;101:20–78. doi: 10.1016/0076-6879(83)01005-8. [DOI] [PubMed] [Google Scholar]
  19. 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]
  20. Nukiwa T., Satoh K., Brantly M. L., Ogushi F., Fells G. A., Courtney M., Crystal R. G. Identification of a second mutation in the protein-coding sequence of the Z type alpha 1-antitrypsin gene. J Biol Chem. 1986 Dec 5;261(34):15989–15994. [PubMed] [Google Scholar]
  21. Nukiwa T., Takahashi H., Brantly M., Courtney M., Crystal R. G. alpha 1-Antitrypsin nullGranite Falls, a nonexpressing alpha 1-antitrypsin gene associated with a frameshift to stop mutation in a coding exon. J Biol Chem. 1987 Sep 5;262(25):11999–12004. [PubMed] [Google Scholar]
  22. 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]
  23. 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]
  24. Satoh K., Nukiwa T., Brantly M., Garver R. I., Jr, Hofker M., Courtney M., Crystal R. G. Emphysema associated with complete absence of alpha 1- antitrypsin in serum and the homozygous inheritance [corrected] of a stop codon in an alpha 1-antitrypsin-coding exon. Am J Hum Genet. 1988 Jan;42(1):77–83. [PMC free article] [PubMed] [Google Scholar]
  25. Schreier P. H., Cortese R. A fast and simple method for sequencing DNA cloned in the single-stranded bacteriophage M13. J Mol Biol. 1979 Mar 25;129(1):169–172. doi: 10.1016/0022-2836(79)90068-8. [DOI] [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]

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