Detection of DNA sequence polymorphisms by enzymatic amplification and direct genomic sequencing (original) (raw)

. 1989 Oct;45(4):547–555.

Abstract

The discovery of RFLPs and their utilization as genetic markers has revolutionized research in human molecular genetics. However, only a fraction of the DNA sequence polymorphisms in the human genome affect the length of a restriction fragment and hence result in an RFLP. Polymorphisms that are not detected as RFLPs are typically passed over in the screening process though they represent a potentially important source of informative genetic markers. We have used a rapid method for the detection of naturally occurring DNA sequence variations that is based on enzymatic amplification and direct sequencing of genomic DNA. This approach can detect essentially all useful sequence variations within the region screened. We demonstrate the feasibility of the technique by applying it to the human retinoblastoma susceptibility locus. We screened 3,712 bp of genomic DNA from each of nine individuals and found four DNA sequence polymorphisms. At least one of these DNA sequence polymorphisms was informative in each of three families with hereditary retinoblastoma that were not informative with any of the known RFLPs at this locus. We believe that direct sequencing is a reasonable alternative to other methods of screening for DNA sequence polymorphisms and that it represents a step forward for obtaining informative markers at well-characterized loci that have been minimally informative in the past.

547

Images in this article

Selected References

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

  1. Aldridge J., Kunkel L., Bruns G., Tantravahi U., Lalande M., Brewster T., Moreau E., Wilson M., Bromley W., Roderick T. A strategy to reveal high-frequency RFLPs along the human X chromosome. Am J Hum Genet. 1984 May;36(3):546–564. [PMC free article] [PubMed] [Google Scholar]
  2. Amselem S., Nunes V., Vidaud M., Estivill X., Wong C., d'Auriol L., Vidaud D., Galibert F., Baiget M., Goossens M. Determination of the spectrum of beta-thalassemia genes in Spain by use of dot-blot analysis of amplified beta-globin DNA. Am J Hum Genet. 1988 Jul;43(1):95–100. [PMC free article] [PubMed] [Google Scholar]
  3. Asmussen M. A., Clegg M. T. Multiallelic restriction fragment polymorphisms in genetic counseling: population genetic considerations. Hum Hered. 1985;35(3):129–142. doi: 10.1159/000153533. [DOI] [PubMed] [Google Scholar]
  4. Bishop D. T., Williamson J. A., Skolnick M. H. A model for restriction fragment length distributions. Am J Hum Genet. 1983 Sep;35(5):795–815. [PMC free article] [PubMed] [Google Scholar]
  5. Boehm T. L., Werle A., Drahovsky D. A rapid and efficient screening method for DNA restriction fragment length polymorphisms. Clin Genet. 1987 Nov;32(5):349–354. doi: 10.1111/j.1399-0004.1987.tb03300.x. [DOI] [PubMed] [Google Scholar]
  6. Bookstein R., Lee E. Y., To H., Young L. J., Sery T. W., Hayes R. C., Friedmann T., Lee W. H. Human retinoblastoma susceptibility gene: genomic organization and analysis of heterozygous intragenic deletion mutants. Proc Natl Acad Sci U S A. 1988 Apr;85(7):2210–2214. doi: 10.1073/pnas.85.7.2210. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Botstein D., White R. L., Skolnick M., Davis R. W. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet. 1980 May;32(3):314–331. [PMC free article] [PubMed] [Google Scholar]
  8. Cooper D. N., Clayton J. F. DNA polymorphism and the study of disease associations. Hum Genet. 1988 Apr;78(4):299–312. doi: 10.1007/BF00291724. [DOI] [PubMed] [Google Scholar]
  9. Cooper D. N., Schmidtke J. DNA restriction fragment length polymorphisms and heterozygosity in the human genome. Hum Genet. 1984;66(1):1–16. doi: 10.1007/BF00275182. [DOI] [PubMed] [Google Scholar]
  10. Cooper D. N., Smith B. A., Cooke H. J., Niemann S., Schmidtke J. An estimate of unique DNA sequence heterozygosity in the human genome. Hum Genet. 1985;69(3):201–205. doi: 10.1007/BF00293024. [DOI] [PubMed] [Google Scholar]
  11. Devor E. J. The relative efficiency of restriction enzymes: an update. Am J Hum Genet. 1988 Jan;42(1):179–182. [PMC free article] [PubMed] [Google Scholar]
  12. Donis-Keller H., Green P., Helms C., Cartinhour S., Weiffenbach B., Stephens K., Keith T. P., Bowden D. W., Smith D. R., Lander E. S. A genetic linkage map of the human genome. Cell. 1987 Oct 23;51(2):319–337. doi: 10.1016/0092-8674(87)90158-9. [DOI] [PubMed] [Google Scholar]
  13. Drmanac R., Petrović N., Glisin V., Crkvenjakov R. A calculation of fragment lengths obtainable from human DNA with 78 restriction enzymes: an aid for cloning and mapping. Nucleic Acids Res. 1986 Jun 11;14(11):4691–4692. doi: 10.1093/nar/14.11.4691. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Dryja T. P., Rapaport J. M., Joyce J. M., Petersen R. A. Molecular detection of deletions involving band q14 of chromosome 13 in retinoblastomas. Proc Natl Acad Sci U S A. 1986 Oct;83(19):7391–7394. doi: 10.1073/pnas.83.19.7391. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Feder J., Yen L., Wijsman E., Wang L., Wilkins L., Schroder J., Spurr N., Cann H., Blumenberg M., Cavalli-Sforza L. L. A systematic approach for detecting high-frequency restriction fragment length polymorphisms using large genomic probes. Am J Hum Genet. 1985 Jul;37(4):635–649. [PMC free article] [PubMed] [Google Scholar]
  16. Friend S. H., Bernards R., Rogelj S., Weinberg R. A., Rapaport J. M., Albert D. M., Dryja T. P. A human DNA segment with properties of the gene that predisposes to retinoblastoma and osteosarcoma. Nature. 1986 Oct 16;323(6089):643–646. doi: 10.1038/323643a0. [DOI] [PubMed] [Google Scholar]
  17. Friend S. H., Horowitz J. M., Gerber M. R., Wang X. F., Bogenmann E., Li F. P., Weinberg R. A. Deletions of a DNA sequence in retinoblastomas and mesenchymal tumors: organization of the sequence and its encoded protein. Proc Natl Acad Sci U S A. 1987 Dec;84(24):9059–9063. doi: 10.1073/pnas.84.24.9059. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Fung Y. K., Murphree A. L., T'Ang A., Qian J., Hinrichs S. H., Benedict W. F. Structural evidence for the authenticity of the human retinoblastoma gene. Science. 1987 Jun 26;236(4809):1657–1661. doi: 10.1126/science.2885916. [DOI] [PubMed] [Google Scholar]
  19. Harbour J. W., Lai S. L., Whang-Peng J., Gazdar A. F., Minna J. D., Kaye F. J. Abnormalities in structure and expression of the human retinoblastoma gene in SCLC. Science. 1988 Jul 15;241(4863):353–357. doi: 10.1126/science.2838909. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Horowitz J. M., Yandell D. W., Park S. H., Canning S., Whyte P., Buchkovich K., Harlow E., Weinberg R. A., Dryja T. P. Point mutational inactivation of the retinoblastoma antioncogene. Science. 1989 Feb 17;243(4893):937–940. doi: 10.1126/science.2521957. [DOI] [PubMed] [Google Scholar]
  21. Hudson R. R. Estimating genetic variability with restriction endonucleases. Genetics. 1982 Apr;100(4):711–719. doi: 10.1093/genetics/100.4.711. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Jeffreys A. J. DNA sequence variants in the G gamma-, A gamma-, delta- and beta-globin genes of man. Cell. 1979 Sep;18(1):1–10. doi: 10.1016/0092-8674(79)90348-9. [DOI] [PubMed] [Google Scholar]
  23. Lee E. Y., To H., Shew J. Y., Bookstein R., Scully P., Lee W. H. Inactivation of the retinoblastoma susceptibility gene in human breast cancers. Science. 1988 Jul 8;241(4862):218–221. doi: 10.1126/science.3388033. [DOI] [PubMed] [Google Scholar]
  24. Lee W. H., Bookstein R., Hong F., Young L. J., Shew J. Y., Lee E. Y. Human retinoblastoma susceptibility gene: cloning, identification, and sequence. Science. 1987 Mar 13;235(4794):1394–1399. doi: 10.1126/science.3823889. [DOI] [PubMed] [Google Scholar]
  25. McGee T. L., Yandell D. W., Dryja T. P. Structure and partial genomic sequence of the human retinoblastoma susceptibility gene. Gene. 1989 Aug 1;80(1):119–128. doi: 10.1016/0378-1119(89)90256-4. [DOI] [PubMed] [Google Scholar]
  26. Mullis K. B., Faloona F. A. Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods Enzymol. 1987;155:335–350. doi: 10.1016/0076-6879(87)55023-6. [DOI] [PubMed] [Google Scholar]
  27. Myers R. M., Maniatis T., Lerman L. S. Detection and localization of single base changes by denaturing gradient gel electrophoresis. Methods Enzymol. 1987;155:501–527. doi: 10.1016/0076-6879(87)55033-9. [DOI] [PubMed] [Google Scholar]
  28. Nakamura Y., Leppert M., O'Connell P., Wolff R., Holm T., Culver M., Martin C., Fujimoto E., Hoff M., Kumlin E. Variable number of tandem repeat (VNTR) markers for human gene mapping. Science. 1987 Mar 27;235(4796):1616–1622. doi: 10.1126/science.3029872. [DOI] [PubMed] [Google Scholar]
  29. Saiki R. K., Bugawan T. L., Horn G. T., Mullis K. B., Erlich H. A. Analysis of enzymatically amplified beta-globin and HLA-DQ alpha DNA with allele-specific oligonucleotide probes. Nature. 1986 Nov 13;324(6093):163–166. doi: 10.1038/324163a0. [DOI] [PubMed] [Google Scholar]
  30. Schumm J. W., Knowlton R. G., Braman J. C., Barker D. F., Botstein D., Akots G., Brown V. A., Gravius T. C., Helms C., Hsiao K. Identification of more than 500 RFLPs by screening random genomic clones. Am J Hum Genet. 1988 Jan;42(1):143–159. [PMC free article] [PubMed] [Google Scholar]
  31. Sheffield V. C., Cox D. R., Lerman L. S., Myers R. M. Attachment of a 40-base-pair G + C-rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes. Proc Natl Acad Sci U S A. 1989 Jan;86(1):232–236. doi: 10.1073/pnas.86.1.232. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. T'Ang A., Varley J. M., Chakraborty S., Murphree A. L., Fung Y. K. Structural rearrangement of the retinoblastoma gene in human breast carcinoma. Science. 1988 Oct 14;242(4876):263–266. doi: 10.1126/science.3175651. [DOI] [PubMed] [Google Scholar]
  33. Wainscoat J. S., Hill A. V., Boyce A. L., Flint J., Hernandez M., Thein S. L., Old J. M., Lynch J. R., Falusi A. G., Weatherall D. J. Evolutionary relationships of human populations from an analysis of nuclear DNA polymorphisms. Nature. 1986 Feb 6;319(6053):491–493. doi: 10.1038/319491a0. [DOI] [PubMed] [Google Scholar]
  34. Weichselbaum R. R., Beckett M., Diamond A. Some retinoblastomas, osteosarcomas, and soft tissue sarcomas may share a common etiology. Proc Natl Acad Sci U S A. 1988 Apr;85(7):2106–2109. doi: 10.1073/pnas.85.7.2106. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. White R., Leppert M., Bishop D. T., Barker D., Berkowitz J., Brown C., Callahan P., Holm T., Jerominski L. Construction of linkage maps with DNA markers for human chromosomes. Nature. 1985 Jan 10;313(5998):101–105. doi: 10.1038/313101a0. [DOI] [PubMed] [Google Scholar]
  36. Wiggs J., Nordenskjöld M., Yandell D., Rapaport J., Grondin V., Janson M., Werelius B., Petersen R., Craft A., Riedel K. Prediction of the risk of hereditary retinoblastoma, using DNA polymorphisms within the retinoblastoma gene. N Engl J Med. 1988 Jan 21;318(3):151–157. doi: 10.1056/NEJM198801213180305. [DOI] [PubMed] [Google Scholar]
  37. 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]
  38. Youssoufian H., Wong C., Aronis S., Platokoukis H., Kazazian H. H., Jr, Antonarakis S. E. Moderately severe hemophilia A resulting from Glu----Gly substitution in exon 7 of the factor VIII gene. Am J Hum Genet. 1988 Jun;42(6):867–871. [PMC free article] [PubMed] [Google Scholar]