Skip to main content

Analysis of DNA Sequence Variation in the Microarray Format

  • Chapter
Microarray Technology and Its Applications

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  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: 860–921

    Article  PubMed  CAS  Google Scholar 

  2. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG et al. (2001) The sequence of the human genome Science 291: 1304–1351

    Article  PubMed  CAS  Google Scholar 

  3. Evans WE and Relling MV (1999) Pharmacogenomics: translating functional genomics into rational therapeutics Science 286: 487–491

    Article  PubMed  CAS  Google Scholar 

  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: 7–17

    Article  PubMed  CAS  Google Scholar 

  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: 163–166

    Article  PubMed  CAS  Google Scholar 

  6. Mullis KB and Faloona FA (1987) Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction Methods Enzymol 155: 335–350

    Article  CAS  Google Scholar 

  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: 487–491

    PubMed  CAS  Google Scholar 

  8. Shuber AP, Grondin VJ and Klinger KW (1995) A simplified procedure for developing multiplex PCRs Genome Res 5: 488–493

    PubMed  CAS  Google Scholar 

  9. Schena M, Shalon D, Davis RW and Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray Science 270: 467–470

    PubMed  CAS  Google Scholar 

  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: 1031–1042

    Article  PubMed  CAS  Google Scholar 

  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: e70

    Article  PubMed  Google Scholar 

  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: S70–77

    Google Scholar 

  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: 1245–1258

    PubMed  CAS  Google Scholar 

  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: 203–207

    Article  PubMed  CAS  Google Scholar 

  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: 1515–1521

    Article  PubMed  CAS  Google Scholar 

  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: E17

    Article  PubMed  CAS  Google Scholar 

  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: 4197–4202

    Article  PubMed  CAS  Google Scholar 

  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: 1898–1905

    PubMed  CAS  Google Scholar 

  19. Landegren U, Kaiser R, Sanders J and Hood L (1988) A ligase-mediated gene detection technique Science 241: 1077–1080

    PubMed  CAS  Google Scholar 

  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: 225–232

    Article  PubMed  CAS  Google Scholar 

  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: E92

    PubMed  CAS  Google Scholar 

  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: 251–262

    Article  PubMed  CAS  Google Scholar 

  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: 131–140

    Article  PubMed  CAS  Google Scholar 

  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: 2085–2088

    PubMed  CAS  Google Scholar 

  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: 673–678

    Article  PubMed  CAS  Google Scholar 

  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, 60–51

    Google Scholar 

  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: 684–692

    Article  PubMed  CAS  Google Scholar 

  28. Syvanen AC (1999) From gels to chips:”minisequencing”; primer extension for analysis of point mutations and single nucleotide polymorphisms Hum Mutat 13: 1–10

    Article  PubMed  CAS  Google Scholar 

  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: 606–614

    PubMed  CAS  Google Scholar 

  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: 884–894

    Article  PubMed  CAS  Google Scholar 

  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: 1–7

    Article  PubMed  CAS  Google Scholar 

  32. Lindroos K, Liljedahl U, Raitio M and Syvanen AC (2001) Minisequencing on oligonucleotide microarrays: comparison of immobilisation chemistries Nucleic Acids Res 29: e69

    Article  PubMed  CAS  Google Scholar 

  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: 471–482

    Article  PubMed  CAS  Google Scholar 

  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: 2961–2972

    Article  PubMed  CAS  Google Scholar 

  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: e75

    Article  PubMed  Google Scholar 

  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: 135–143

    Article  PubMed  CAS  Google Scholar 

  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: 549–557

    Article  PubMed  CAS  Google Scholar 

  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: 12164–12169

    Article  PubMed  CAS  Google Scholar 

  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: 853–860

    Article  PubMed  CAS  Google Scholar 

  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: 5022–5026

    PubMed  CAS  Google Scholar 

  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: 4710–4714

    Article  PubMed  CAS  Google Scholar 

  42. Beier M and Hoheisel JD (2002) Analysis of DNA-microarrays produced by inverse in situ oligonucleotide synthesis J Biotechnol 94: 15–22

    Article  PubMed  CAS  Google Scholar 

  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: 5456–5465

    PubMed  CAS  Google Scholar 

  44. Beier M and Hoheisel JD (1999) Versatile derivatisation of solid support media for covalent bonding on DNA-microchips Nucleic Acids Res 27: 1970–1977

    Article  PubMed  CAS  Google Scholar 

  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: E107–107

    Article  PubMed  CAS  Google Scholar 

  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: 23–30

    Article  PubMed  CAS  Google Scholar 

  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: 610–614

    Article  PubMed  CAS  Google Scholar 

  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: 5503–5508

    Article  PubMed  CAS  Google Scholar 

  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: 1008–1017

    Article  PubMed  CAS  Google Scholar 

  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: 244–255

    Article  PubMed  CAS  Google Scholar 

  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: 1453–1462

    Article  PubMed  CAS  Google Scholar 

  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: 1077–1082

    Article  PubMed  CAS  Google Scholar 

  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: 164–167

    Article  PubMed  CAS  Google Scholar 

  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: 604–615

    Article  PubMed  CAS  Google Scholar 

  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: 544–548

    Article  PubMed  CAS  Google Scholar 

  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: 216–223

    PubMed  Google Scholar 

Download references

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2005 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Liljedahl, U., Fredriksson, M., Syvänen, AC. (2005). Analysis of DNA Sequence Variation in the Microarray Format. In: Müller, U.R., Nicolau, D.V. (eds) Microarray Technology and Its Applications. Biological and Medical Physics, Biomedical Engineering. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-26578-3_10

Download citation

Publish with us

Policies and ethics