Advertisement

Analysis of DNA Sequence Variation in the Microarray Format

  • Ulrika Liljedahl
  • Mona Fredriksson
  • Ann-Christine Syvänen
Part of the Biological and Medical Physics, Biomedical Engineering book series (BIOMEDICAL)

Keywords

Prime Extension Multiplex Polymerase Chain Reaction Peptide Nucleic Acid Lock Nucleic Acid Primer Extension Reaction 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J et al. (2001) Initial sequencing and analysis of the human genome Nature 409: 860–921PubMedCrossRefGoogle Scholar
  2. 2.
    Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG et al. (2001) The sequence of the human genome Science 291: 1304–1351PubMedCrossRefGoogle Scholar
  3. 3.
    Evans WE and Relling MV (1999) Pharmacogenomics: translating functional genomics into rational therapeutics Science 286: 487–491PubMedCrossRefGoogle Scholar
  4. 4.
    Liljedahl U, Karlsson J, Melhus H, Kurland L, Lindersson M, Kahan T et al. (2003) A microarray minisequencing system for pharmacogenetic profiling of antihypertensive drug response Pharmacogenetics 13: 7–17PubMedCrossRefGoogle Scholar
  5. 5.
    Saiki RK, Bugawan TL, Horn GT, Mullis KB and Erlich HA (1986) Analysis of enzymatically amplified beta-globin and HLA-DQ alpha DNA with allele-specific oligonucleotide probes Nature 324: 163–166PubMedCrossRefGoogle Scholar
  6. 6.
    Mullis KB and Faloona FA (1987) Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction Methods Enzymol 155: 335–350CrossRefGoogle Scholar
  7. 7.
    Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT et al. (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase Science 239: 487–491PubMedGoogle Scholar
  8. 8.
    Shuber AP, Grondin VJ and Klinger KW (1995) A simplified procedure for developing multiplex PCRs Genome Res 5: 488–493PubMedGoogle Scholar
  9. 9.
    Schena M, Shalon D, Davis RW and Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray Science 270: 467–470PubMedGoogle Scholar
  10. 10.
    Pastinen T, Raitio M, Lindroos K, Tainola P, Peltonen L and Syvanen AC (2000) A system for specific, high-throughput genotyping by allele-specific primer extension on microarrays Genome Res 10: 1031–1042PubMedCrossRefGoogle Scholar
  11. 11.
    Lindroos K, Sigurdsson S, Johansson K, Ronnblom L and Syvanen AC (2002) Multiplex SNP genotyping in pooled DNA samples by a four-colour microarray system Nucleic Acids Res 30: e70PubMedCrossRefGoogle Scholar
  12. 12.
    Bell PA, Chaturvedi S, Gelfand CA, Huang CY, Kochersperger M, Kopla R et al. (2002) SNP stream UHT: ultra-high throughput SNP genotyping for pharma-cogenomics and drug discovery Biotechniques 30: S70–77Google Scholar
  13. 13.
    Hacia JG, Sun B, Hunt N, Edgemon K, Mosbrook D, Robbins C et al. (1998) Strategies for mutational analysis of the large multiexon ATM gene using high-density oligonucleotide arrays Genome Res 8: 1245–1258PubMedGoogle Scholar
  14. 14.
    Cho RJ, Mindrinos M, Richards DR, Sapolsky RJ, Anderson M, Drenkard E et al. (1999) Genome-wide mapping with biallelic markers in Arabidopsis thaliana Nat Genet 23: 203–207PubMedCrossRefGoogle Scholar
  15. 15.
    Fotin AV, Drobyshev AL, Proudnikov DY, Perov AN and Mirzabekov AD (1998) Parallel thermodynamic analysis of duplexes on oligodeoxyribonucleotide microchips Nucleic Acids Res 26: 1515–1521PubMedCrossRefGoogle Scholar
  16. 16.
    Radtkey R, Feng L, Muralhidar M, Duhon M, Canter D, DiPierro D et al. (2000) Rapid, high fidelity analysis of simple sequence repeats on an electronically active DNA microchip Nucleic Acids Res 28: E17PubMedCrossRefGoogle Scholar
  17. 17.
    Ross PL, Lee K and Belgrader P (1997) Discrimination of single-nucleotide polymorphisms in human DNA using peptide nucleic acid probes detected by MALDI-TOF mass spectrometry Anal Chem 69: 4197–4202PubMedCrossRefGoogle Scholar
  18. 18.
    Orum H, Jakobsen MH, Koch T, Vuust J and Borre MB (1999) Detection of the factor V Leiden mutation by direct allele-specific hybridization of PCR amplicons to photoimmobilized locked nucleic acids Clin Chem 45: 1898–1905PubMedGoogle Scholar
  19. 19.
    Landegren U, Kaiser R, Sanders J and Hood L (1988) A ligase-mediated gene detection technique Science 241: 1077–1080PubMedGoogle Scholar
  20. 20.
    Lizardi PM, Huang X, Zhu Z, Bray-Ward P, Thomas DC and Ward DC (1998) Mutation detection and single-molecule counting using isothermal rolling-circle amplification Nat Genet 19: 225–232PubMedCrossRefGoogle Scholar
  21. 21.
    Broude NE, Woodward K, Cavallo R, Cantor CR and Englert D (2001) DNA microarrays with stem-loop DNA probes: preparation and applications Nucleic Acids Res 29: E92PubMedGoogle Scholar
  22. 22.
    Gerry NP, Witowski NE, Day J, Hammer RP, Barany G and Barany F (1999) Universal DNA microarray method for multiplex detection of low abundance point mutations J Mol Biol 292: 251–262PubMedCrossRefGoogle Scholar
  23. 23.
    Iannone MA, Taylor JD, Chen J, Li MS, Rivers P, Slentz-Kesler KA et al. (2000) Multiplexed single nucleotide polymorphism genotyping by oligonucleotide ligation and flow cytometry Cytometry 39: 131–140PubMedCrossRefGoogle Scholar
  24. 24.
    Nilsson M, Malmgren H, Samiotaki M, Kwiatkowski M, Chowdhary BP and Landegren U (1994) Padlock probes: circularizing oligonucleotides for localized DNA detection Science 265: 2085–2088PubMedGoogle Scholar
  25. 25.
    Hardenbol P, Baner J, Jain M, Nilsson M, Namsaraev EA, Karlin-Neumann GA et al. (2003) Multiplexed genotyping with sequence-tagged molecular inversion probes Nat Biotechnol 21: 673–678PubMedCrossRefGoogle Scholar
  26. 26.
    Oliphant A, Barker DL, Stuelpnagel JR and Chee MS (2002) Bead Array technology: enabling an accurate, cost-effective approach to high-throughput genotyping Biotechniques Suppl: 56–58, 60–51Google Scholar
  27. 27.
    Syvanen AC, Aalto-Setala K, Harju L, Kontula K and Soderlund H (1990) A primer-guided nucleotide incorporation assay in the genotyping of apolipoprotein E Genomics 8: 684–692PubMedCrossRefGoogle Scholar
  28. 28.
    Syvanen AC (1999) From gels to chips:”minisequencing”; primer extension for analysis of point mutations and single nucleotide polymorphisms Hum Mutat 13: 1–10PubMedCrossRefGoogle Scholar
  29. 29.
    Pastinen T, Kurg A, Metspalu A, Peltonen L and Syvanen AC (1997) Minisequencing: a specific tool for DNA analysis and diagnostics on oligonucleotide arrays Genome Res 7: 606–614PubMedGoogle Scholar
  30. 30.
    Fortina P, Delgrosso K, Sakazume T, Santacroce R, Moutereau S, Su HJ et al. (2000) Simple two-color array-based approach for mutation detection Eur J Hum Genet 8: 884–894PubMedCrossRefGoogle Scholar
  31. 31.
    Kurg A, Tonisson N, Georgiou I, Shumaker J, Tollett J and Metspalu A (2000) Arrayed primer extension: solid-phase four-color DNA resequencing and mutation detection technology Genet Test 4: 1–7PubMedCrossRefGoogle Scholar
  32. 32.
    Lindroos K, Liljedahl U, Raitio M and Syvanen AC (2001) Minisequencing on oligonucleotide microarrays: comparison of immobilisation chemistries Nucleic Acids Res 29: e69PubMedCrossRefGoogle Scholar
  33. 33.
    Raitio M, Lindroos K, Laukkanen M, Pastinen T, Sistonen P, Sajantila A et al. (2001) Y-chromosomal SNPs in Finno-Ugric-speaking populations analyzed by minisequencing on microarrays Genome Res 11: 471–482PubMedCrossRefGoogle Scholar
  34. 34.
    Pastinen T, Perola M, Ignatius J, Sabatti C, Tainola P, Levander M et al. (2001) Dissecting a population genome for targeted screening of disease mutations Hum Mol Genet 10: 2961–2972PubMedCrossRefGoogle Scholar
  35. 35.
    O'Meara D, Ahmadian A, Odeberg J and Lundeberg J (2002) SNP typing by apyrasemediated allele-specific primer extension on DNA microarrays Nucleic Acids Res 30: e75PubMedCrossRefGoogle Scholar
  36. 36.
    Cai H, White PS, Torney D, Deshpande A, Wang Z, Marrone B et al. (2000) Flow cytometry-based minisequencing: a new platform for high-throughput single-nucleotide polymorphism scoring Genomics 66: 135–143PubMedCrossRefGoogle Scholar
  37. 37.
    Chen J, Iannone MA, Li MS, Taylor JD, Rivers P, Nelsen AJ et al. (2000) A microsphere-based assay for multiplexed single nucleotide polymorphism analysis using single base chain extension Genome Res 10: 549–557PubMedCrossRefGoogle Scholar
  38. 38.
    Hirschhorn JN, Sklar P, Lindblad-Toh K, Lim YM, Ruiz-Gutierrez M, Bolk S et al. (2000) SBE-TAGS: an array-based method for efficient single-nucleotide polymorphism genotyping Proc Natl Acad Sci U S A 97: 12164–12169PubMedCrossRefGoogle Scholar
  39. 39.
    Fan JB, Chen X, Halushka MK, Berno A, Huang X, Ryder T et al. (2000) Parallel genotyping of human SNPs using generic high-density oligonucleotide tag arrays Genome Res 10: 853–860PubMedCrossRefGoogle Scholar
  40. 40.
    Pease AC, Solas D, Sullivan EJ, Cronin MT, Holmes CP and Fodor SP (1994) Light-generated oligonucleotide arrays for rapid DNA sequence analysis Proc Natl Acad Sci U S A 91: 5022–5026PubMedGoogle Scholar
  41. 41.
    Kwiatkowski M, Fredriksson S, Isaksson A, Nilsson M and Landegren U (1999) Inversion of in situ synthesized oligonucleotides: improved reagents for hybridization and primer extension in DNA microarrays Nucleic Acids Res 27: 4710–4714PubMedCrossRefGoogle Scholar
  42. 42.
    Beier M and Hoheisel JD (2002) Analysis of DNA-microarrays produced by inverse in situ oligonucleotide synthesis J Biotechnol 94: 15–22PubMedCrossRefGoogle Scholar
  43. 43.
    Guo Z, Guilfoyle RA, Thiel AJ, Wang R and Smith LM (1994) Direct fluorescence analysis of genetic polymorphisms by hybridization with oligonucleotide arrays on glass supports Nucleic Acids Res 22: 5456–5465PubMedGoogle Scholar
  44. 44.
    Beier M and Hoheisel JD (1999) Versatile derivatisation of solid support media for covalent bonding on DNA-microchips Nucleic Acids Res 27: 1970–1977PubMedCrossRefGoogle Scholar
  45. 45.
    Dolan PL, Wu Y, Ista LK, Metzenberg RL, Nelson MA and Lopez GP (2001) Robust and efficient synthetic method for forming DNA microarrays Nucleic Acids Res 29: E107–107PubMedCrossRefGoogle Scholar
  46. 46.
    Rogers YH, Jiang-Baucom P, Huang ZJ, Bogdanov V, Anderson S and Boyce-Jacino MT (1999) Immobilization of oligonucleotides onto a glass support via disulfide bonds: A method for preparation of DNA microarrays Anal Biochem 266: 23–30PubMedCrossRefGoogle Scholar
  47. 47.
    Chee M, Yang R, Hubbell E, Berno A, Huang XC, Stern D et al. (1996) Accessing genetic information with high-density DNA arrays Science 274: 610–614PubMedCrossRefGoogle Scholar
  48. 48.
    Tonisson N, Zernant J, Kurg A, Pavel H, Slavin G, Roomere H et al. (2002) Evaluating the arrayed primer extension resequencing assay of TP53 tumor suppressor gene Proc Natl Acad Sci U S A 99: 5503–5508PubMedCrossRefGoogle Scholar
  49. 49.
    Southern EM, Maskos U and Elder JK (1992) Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: evaluation using experimental models Genomics 13: 1008–1017PubMedCrossRefGoogle Scholar
  50. 50.
    Cronin MT, Fucini RV, Kim SM, Masino RS, Wespi RM and Miyada CG (1996) Cystic fibrosis mutation detection by hybridization to light-generated DNA probe arrays Hum Mutat 7: 244–255PubMedCrossRefGoogle Scholar
  51. 51.
    Pastinen T, Perola M, Niini P, Terwilliger J, Salomaa V, Vartiainen E et al. (1998) Array-based multiplex analysis of candidate genes reveals two independent and additive genetic risk factors for myocardial infarction in the Finnish population Hum Mol Genet 7: 1453–1462PubMedCrossRefGoogle Scholar
  52. 52.
    Wang DG, Fan JB, Siao CJ, Berno A, Young P, Sapolsky R et al. (1998) Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome Science 280: 1077–1082PubMedCrossRefGoogle Scholar
  53. 53.
    Hacia JG, Fan JB, Ryder O, Jin L, Edgemon K, Ghandour G et al. (1999) Determination of ancestral alleles for human single-nucleotide polymorphisms using high-density oligonucleotide arrays Nat Genet 22: 164–167PubMedCrossRefGoogle Scholar
  54. 54.
    LaForge KS, Shick V, Spangler R, Proudnikov D, Yuferov V, Lysov Y et al. (2000) Detection of single nucleotide polymorphisms of the human mu opioid receptor gene by hybridization or single nucleotide extension on custom oligonu-cleotide gelpad microchips: potential in studies of addiction Am J Med Genet 96: 604–615PubMedCrossRefGoogle Scholar
  55. 55.
    Dawson E, Abecasis GR, Bumpstead S, Chen Y, Hunt S, Beare DM et al. (2002) A first-generation linkage disequilibrium map of human chromosome 22 Nature 418: 544–548PubMedCrossRefGoogle Scholar
  56. 56.
    Primdahl H, Wikman FP, von der Maase H, Zhou XG, Wolf H and Orntoft TF (2002) Allelic imbalances in human bladder cancer: genome-wide detection with high-density single-nucleotide polymorphism arrays J Natl Cancer Inst 94: 216–223PubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Ulrika Liljedahl
  • Mona Fredriksson
  • Ann-Christine Syvänen

There are no affiliations available

Personalised recommendations