Reading bits of genetic information: Methods for single-nucleotide polymorphism analysis

Genome Research

Volumn 8, Issue 8, 1998, Pages 769-776

  Landegren, Ulf ^a   Nilsson, Mats ^a   Kwok, Pui Yan ^b  

^a UPPSALA UNIVERSITY   (Sweden)

^b WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA POLYMERASE; POLYDEOXYRIBONUCLEOTIDE SYNTHASE;

DNA HYBRIDIZATION; DNA POLYMORPHISM; GENETIC ANALYSIS; PRIORITY JOURNAL; REVIEW;

EID: 0031697439     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.8.8.769     Document Type: Review

References (53)

1. Barany, F. 1991. Genetic disease detection and DNA amplification using cloned thermostabile ligase. Proc. Natl. Acad. Sci. 88: 189-193.
2. Burke, D.T., M.A. Burns, and C. Mastrangelo. 1997. Microfabrication technologies for integrated nucleic acid analysis. Genome Res. 7: 189-197.
3. Chee, M., R. Yang, E. Hubell, A. Berno, X.C. Huang, D. Stern, J. Winkler, D.J. Lockhart, M.S. Morris, and S.P.A. Fodor. 1996. Accessing genetic information with high-density DNA arrays. Science 274: 610-614.
4. Chen, X. and P.-Y. Kwok. 1997. Template-directed dye-terminator incorporation (TDI) assay: A homogeneous DNA diagnostic method based on fluorescence resonance energy transfer. Nucleic Acids Res. 25: 347-353.
5. Chen, X., B. Zehnbauer, A. Gnirke, and P.-Y. Kwok. 1997. Fluorescence energy transfer detection as a homogeneous DNA diagnostic method. Proc. Natl. Acad. Sci. 94: 10756-10761.
6. Chen, X., K.J. Livak, and P.-Y. Kwok. 1998. A homogenous, ligase-mediated DNA diagnostic test. Genome Res. 8: 549-556.
7. Cohen, J.B. and A.D. Levinson. 1988. A point mutation in the last intron responsible for increased expression and transforming activity of the c-Ha-ras oncogene. Nature 334: 119-124.
8. Cooper, D.N., B.A. Smith, H.J. Cooke, S. Niemann, and J. Schmidtke. 1985. An estimate of unique DNA sequence heterozygosity in the human genome. Hum. Genet. 69: 201-205.
9. Cotton, R.G., V. McKusick, and C.R. Scriver. 1998. The HUGO mutation database initiative. Science 279: 10-11.
10. Day, D.J., P.W. Speiser, P.C. White, and F. Barany. 1995. Detection of steroid 21-hydroxylase alleles using gene-specific PCR and a multiplexed ligation detection reaction. Genomics 29: 152-162.
11. Day, I.N.M. and S.E. Humphries. 1994. Electrophoresis for genotyping: Microtiter array diagonal gel electrophoresis on horizontal polyacrylamide gels, hydrolink, or agarose. Anal. Biochem. 222: 389-395.
12. Fire, A. and S.-Q. Xu. 1995. Rolling replication of short DNA circles. Proc. Natl. Acad. Sci. 92: 4641-4645.
13. Fodor, S.P.A., J.L. Read, M.C. Pirrung, L. Stryer, A. Tsai Lu, and D. Solas. 1991. Light-directed, spatially addressable parallel chemical synthesis. Science 251: 767-773.
14. Grossman, P.D., W. Bloch, E. Brinson, C.C. Chang, F.A. Eggerding, S. Fung, D.A. Iovannisci, S. Woo, and E.S. Winn-Deen. 1994. High-density multiplex detection of nucleic acid sequences: Oligonucleotide ligation assay and sequence-coded separation. Nucleic Acids Res. 22: 4527-4534.
15. Hofker, M.H., M.I. Skraastad, A.A. Bergen, M.C. Wapenaar, E. Bakker, A. Millington-Ward, G.J. van Ommen, and P.L. Pearson. 1986. The X chromosome shows less genetic variation at restriction sites than the autosomes. Am. J. Hum. Genet. 39: 438-451.
16. Holland, P.M., R.D. Abramson, R. Watson, and D.H. Gelfland. 1991. Detection of specific polymerase chain reaction product by utilizing the 5′-3′ exonuclease activity of Thermus aquaticus DNA polymerase. Proc. Natl. Acad. Sci. 88: 7276-7280.
17. Kruglyak, L. 1997. The use of a genetic map of biallelic markers in linkage studies. Nature Genet. 17: 21-24.
18. Kwok, P.-Y., Q. Deng, H. Zakeri, S.L. Taylor, and D.A. Nickerson. 1996. Increasing the information content of STS-based genome maps: Identifying polymorphisms in mapped STSs. Genomics 31: 123-126.
19. Landegren, U. and M. Nilsson. 1997. Locked on target: Strategies for future gene diagnostics. Ann. Med. 29: 585-590.
20. Landegren, U., R. Kaiser, J. Sanders, and L. Hood. 1988. A ligase-mediated gene detection technique. Science 241: 1077-1080.
21. Lee, L.G., C.R. Connell, and W. Bloch. 1993. Allelic discrimination by nick-translation PCR with fluorogenic probes. Nucleic Acids Res. 21: 3761-3766.
22. Li, H.H., U.B. Gyllensten, C.F. Cui, R.K. Saiki, H.A. Erlich, and N. Arnheim. 1988. Amplification and analysis of DNA sequences in single human sperm and diploid cells. Nature 335: 414-417.
23. Li, W.-H. and D. Grauer. 1991. Fundamentals of molecular evolution. Sinauer Associates, Sunderland, MA.
24. Lin, D., S.L. Daubendiek, M.A. Zillman, K. Ryan, and E.T. Kool. 1996. Rolling circle DNA synthesis: Small circular oligonucleotides as efficient templates for DNA polymerases. J. Am. Chem. Soc. 118: 1587-1594.
25. Liu, Q., E.C. Thorland, J.A. Heit, and S.S. Sommer. 1997. Overlapping PGR for bidirectional PCR amplification of specific alleles: A rapid one-tube method for simultaneously differentiating homozygotes and heterozygotes. Genome Res. 7: 389-398.
26. Livak, K., J. Marmaro, and J.A. Todd. 1995. Towards fully automated genome-wide polymorphism screening. Nature Genet. 9: 341-342.
27. Lou, J., D.E. Bergstrom, and F. Barany. 1996. Improving the fidelity of Thermus thermophilus DNA ligase. Nucleic Acids Res. 24: 3071-3078.
28. Lövgren, T., P. Heinonen, P. Lehtinen, H. Hakala, J. Heinola, R. Harju, H. Takalo, V.-M. Mukkala, R. Schmid, H. Lönnberg, K. Pettersson, and A. Iitiä. 1997. Sensitive bioaffinity assays with individual microparticles and time-resolved fluorometry. Clin. Chem. 43: 1937-1943.
29. Mullis, K.B. 1991. The polymerase chain reaction in an anemic mode: How to avoid cold oligodeoxyribonuclear fusion. PCR Methods Applic. 1: 1-4.
30. Newton, C.R., A. Graham, L.E. Heptinstall, S.J. Powell, C. Summers, N. Kalsheker, J.C. Smith, and A.F. Markham. 1989. Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Res. 17: 2503-2516.
31. Nilsson, M., H. Malmgren, M. Samiotaki, M. Kwiatkowski, B.P. Chowdhary, and U. Landegren. 1994. Padlock probes: Circularizing oligonucleotides for localized DNA detection. Science 265: 2085-2088.
32. Nilsson, M., K. Krejci, J. Koch, M. Kwiatkowski, P. Gustavsson, and U. Landegren. 1997. Padlock probes reveal single-nucleotide differences, parent of origin and in situ distribution of centromeric sequences in human chromosomes 13 and 21. Nature Genet. 16: 252-255.
33. Nyrén, P., B. Pettersson, and M. Uhlén. 1993. Solid phase DNA minisequencing by an enzymatic luminometric inorganic pyrophosphate detection assay. Anal. Biochem. 208: 171-175.
34. Parik, J., M. Kwiatkowski, A. Lagerkvist, M. Lagerström-Fermér, M. Samiotaki, J. Stewart, G. Glad, M. Mendel-Hartvig, and U. Landegren. 1993. A manifold support for molecular genetic reactions. Anal. Biochem. 211: 144-150.
35. Pastinen, T., J. Partanen, and A.-C. Syvänen. 1996. Multiplex, fluorescent, solid-phase minisequencing for efficient screening of DNA sequence variation. Clin. Chem. 42: 1391-1397.
36. Pastinen, T., A. Kurg, A. Metspalu, L. Peltonen, and A.-C. Syvänen. 1997. Minisequencing: A specific tool for DNA analysis and diagnostics on oligonucleotide arrays. Genome Res. 7: 606-614.
37. Risch, N. and K. Merikangas. 1996. The future of genetic studies of complex human diseases. Science 273: 1516-1517.
38. Samiotaki, M., M. Kwiatkowski, J. Parik, and U. Landegren. 1994. Dual-color detection of DNA sequence variants by ligase-mediated analysis. Genomics 20: 238-242.
39. Sarkar, G. and S.S. Sommer. 1991. Haplotyping by double PCR amplification of specific alleles. BioTechniques 10: 436-440.
40. Shuber, A.P., L.A. Michalowsky, G.S. Nass, J. Skoletsky, L.M. Hire, S.K. Kotsopoulos, M.F. Phipps, D.M. Barberio, and K.W. Klinger. 1997. High throughput parallel analysis of hundreds of patient samples for more than 100 mutations in multiple disease genes. Hum. Mol. Genet. 6: 337-347.
41. Shumaker, J.M., A. Metspalu, and C.T. Caskey. 1996. Mutation detection by solid phase primer extension. Hum. Mutat. 7: 346-354.
42. Sommers, S.S., J.D. Cassady, J.L. Sobell, and C.D.K. Bottema. 1989. A novel method for detecting point mutations or polymorphisms and its application to population screening for carriers of phenylketonuria. Mayo Clin. Proc. 64: 1361-1372.
43. Southern, E.M., U. Maskos, and J.K. Elder. 1992. Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: Evaluation using experimental models. Genomics 13: 1008-1017.
44. Syvänen, A.C., K. Aalto-Setälä, L. Harju, K. Kontula, and H. Söderlund. 1990. A primer-guided nucleotide incorporation assay in the genotyping of apolipoprotein E. Genomics 8: 684-692.
45. Syvänen, A.-C., A. Sajantila, and M. Lukka. 1993. Identification of individuals by analysis of biallelic DNA markers, using PCR and solid-phase minisequencing. Am. J. Hum. Genet. 52: 46-59.
46. Taillon-Miller, P., I. Bauer-Sardina, H. Zakeri, L. Hillier, D.G. Mutch, and P.-Y. Kwok. 1997. The homozygous complete hydatidiform mole: A unique resource for genome studies. Genomics 46: 307-310.
47. Tobe, V.O., S.L. Taylor, and D.A. Nickerson. 1996. Single-well genotyping of diallelic sequence variations by a two-color ELISA-based oligonucleotide ligation assay. Nucleic Acids Res. 24: 3728-3732.
48. Tyagi, S. and F.R. Kramer. 1996. Molecular beacons: Probes that fluoresce upon hybridization. Nature Biotechnol. 14: 303-308.
49. Tyagi, S., D.P. Bratu, and F.R. Kramer. 1998. Multicolor molecular beacons for allele discrimination. Nature Biotechnol. 16: 49-53.
50. Wallace, R.B., J. Shaffer, R.F. Murphy, J. Bonner, T. Hirose, and K. Itakura. 1979. Hybridization of synthetic oligodeoxyribonucleotides to phiX174 DNA: The effect of single base pair mismatch. Nucl. Acids Res. 6: 3543-3557.
51. Weber, J.L. and C. Wong. 1993. Mutation of short tandem repeats. Hum. Mol. Genet. 2: 1123-1128.
52. Wu, D.Y. and R.B. Wallace. 1989. Specificity of the nick-closing activity of bacteriophage T4 DNA ligase. Gene 76: 245-254.
53. Yershov, G., V. Barsky, A. Belgovskiy, E. Kirillov, E. Kreindlin, I. Ivanov, S. Parinov, D. Guschin, A. Drobishev, S. Dubiley, and A. Mirzabekov. 1996. DNA analysis and diagnostics on oligonucleotide chips. Proc. Natl. Acad. Sci. 93: 4913-4918.