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High-Density GeneChip Oligonucleotide Probe Arrays

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Part of the book series: Advances in Biochemical Engineering/Biotechnology ((ABE,volume 77))

Abstract

High-density DNA probe arrays provide a highly parallel approach to nucleic acid sequence analysis that is transforming gene-based biomedical research. Photolithographic DNA synthesis has enabled the large-scale production of GeneChip probe arrays containing hundreds of thousands of oligonucleotide sequences on a glass “chip” about 1.5 cm2 in size. The manufacturing process integrates solid-phase photochemical oligonucleotide synthesis with lithographic techniques similar to those used in the microelectronics industry. Due to their very high information content, GeneChip probe arrays are finding widespread use in the hybridization-based detection and analysis of mutations and polymorphisms (“genotyping”), and in a wide range of gene expression studies.

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References

  1. Phimister B (ed) (1999) Nat Genet Suppl 21:1

    Google Scholar 

  2. Schena R, Davis RW (2000) In: Schena M (ed) Microarray biochip technology. BioTechniques Books, Natick, MA, p 1

    Google Scholar 

  3. Fodor SPA, Read JL, Pirrung MC, Stryer LT, Lu A, Solas D (1991) Science 251:767

    Article  CAS  Google Scholar 

  4. Pease AC, Solas D, Sullivan EJ, Cronin MT, Holmes CP, Fodor SPA (1994) Proc Natl Acad Sci USA 91:5022

    Article  CAS  Google Scholar 

  5. McGall GH, Barone AD, Diggelmann M, Fodor SPA, Gentalen E, Ngo N (1997) J Am Chem Soc 119:5081

    Article  CAS  Google Scholar 

  6. Lipshutz R, Fodor SPA, Gingeras TR, Lockhart DJ (1999) Nat Genet Suppl 21:20

    Article  CAS  Google Scholar 

  7. McGall GH, Fidanza JA (2001) In: Rampal JB (ed) Methods in molecular biology. DNA arrays methods and protocols. Humana Press, Inc., Totowa, NJ, p 71

    Chapter  Google Scholar 

  8. McGall GH, Barone AD, Diggelmann M (1999) Eur Pat Appl EP 967,217

    Google Scholar 

  9. Barone AD, Beecher JE, Bury P, Chen C, Doede T, Fidanza JA, McGall GH (2001) Nucleosides Nucleotides 20:525

    Article  CAS  Google Scholar 

  10. McGall GH (1997) In: Hori W (ed) Biochip arrays. IBC Library Series, Southboro, MA, p2.1

    Google Scholar 

  11. McGall GH, Nam NQ, Rava R (2000) US Patent 6,147,205

    Google Scholar 

  12. Hasan A, Stengele K-P, Giegrich H, Cornwell P, Isham KR, Sachleben R, Pfleiderer W, Foote RS (1997) Tetrahedron 53:4247

    Article  CAS  Google Scholar 

  13. Pirrung MC, Fallon L, McGall G (1998) J Org Chem 63:241

    Article  CAS  Google Scholar 

  14. Beier M, Hoheisel JD (2000) Nucleic Acids Res 28:e11

    Article  CAS  Google Scholar 

  15. Tonisson N, Kurg A, Lohmussaar E, Metspalu A (2000) In: Schena M (ed) Microarray biochip technology. BioTechniques Books, Natick, MA, p 247

    Google Scholar 

  16. McGall G, Labadie J, Brock P, Wallraff G, Nguyen T, Hinsberg W (1996) Proc Natl Acad Sci USA 93:13555

    Article  CAS  Google Scholar 

  17. Wallraff G, Labadie J, Brock P, Nguyen T, Huynh T, Hinsberg W, McGall G (1997) Chemtech, February:22

    Google Scholar 

  18. Beecher JE, McGall GH, Goldberg MJ (1997) Preprints Am Chem Soc Div Polym Mater Sci Eng 76:597

    CAS  Google Scholar 

  19. Beecher JE, McGall GH, Goldberg MJ (1997) Preprints Am Chem Soc Div Polym Mater Sci Eng 77:394

    CAS  Google Scholar 

  20. Singh-Gasson S, Green RD, Yue Y, Nelson C, Blattner F, Sussman MR, Cerrina F (1999) Nat Biotechnol 17:974

    Article  CAS  Google Scholar 

  21. Cho RJ, Campbell MJ, Winzeler EA, Steinmetz L, Conway A, Wodicka L, Wolfsberg TG, Gabrielian AE, Landsman D, Lockhart DJ, Davis RW (1998) Mol Cell 2:65

    Article  CAS  Google Scholar 

  22. Cho RJ, Huang M, Dong H, Steinmetz L, Sapinoso L, Hampton G, Elledge SJ, Davis RW, Lockhart DJ, Campbell MJ (2001) Nat Genet 27:48

    CAS  Google Scholar 

  23. Debouck C, Goodfellow PN (1999) Nat Genet Suppl 21:48

    Article  CAS  Google Scholar 

  24. Liotta L, Petricoin E (2000) Nat Rev Genet 1:48

    Article  CAS  Google Scholar 

  25. Chen YW, Zhao P, Borup R, Hoffman EP (2000) J Cell Biol 151:1321

    Article  CAS  Google Scholar 

  26. Wilson SB, Kent SC, Horton HF, Hill AA, Bollyky PL, Hafler DA, Strominger JL, Byrne MC (2000) Proc Natl Acad Sci USA 97:7411

    Article  CAS  Google Scholar 

  27. Lee CK, Klopp RG, Weindruch R, Prolla TA (1999) Science 285:1390

    Article  CAS  Google Scholar 

  28. Ly DH, Lockhart DJ, Lerner RA, Schultz PG (2000) Science 287:2486

    Article  CAS  Google Scholar 

  29. Alon U, Barkai N, Notterman DA, Gish K, Ybarra S, Mack D, Levine AJ (1999) Proc Natl Acad Sci USA 96:6745

    Article  CAS  Google Scholar 

  30. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, Bloomfield CD, Lander ES (1999) Science 286:531

    Article  CAS  Google Scholar 

  31. Chee M, Yang R, Hubbell E, Berno A, Huang XC, Stern D, Winkler J, Lockhart DJ, Morris MS, Fodor SP (1996) Science 274:610

    Article  CAS  Google Scholar 

  32. Hacia JG, Sun B, Hunt N, Edgemon K, Mosbrook D, Robbins C, Fodor SP, Tagle DA, Collins FS (1998) Genome Res 8:1245

    CAS  Google Scholar 

  33. Hacia JG, Brody LC, Chee MS, Fodor SP, Collins FS (1996) Nat Genet 14:441

    Article  CAS  Google Scholar 

  34. Hacia JG (1999) Nat Genet 21:42

    Article  CAS  Google Scholar 

  35. Ahrendt SA, Halachmi S, Chow JT, Wu L, Halachmi N, Yang SC, Wehage S, Jen J, Sidransky D (1999) Proc Natl Acad Sci USA 96:7382

    Article  CAS  Google Scholar 

  36. Wikman FP, Lu ML, Thykjaer T, Olesen SH, Andersen LD, Cordon-Cardo C, Orntoft TF (2000) Clin Chem 46:1555

    CAS  Google Scholar 

  37. Liu WW, Webster T, Aggarwal A, Pho M, Cronin M, Ryder T (1997) Am J Hum Genet 61:1494

    Google Scholar 

  38. Kozal MJ, Shah N, Shen N, Yang R, Fucini R, Merigan TC, Richman DD, Morris D, Hubbell E, Chee M, Gingeras TR (1996) Nat Med 2:753

    Article  CAS  Google Scholar 

  39. Gunthard HF, Wong JK, Ignacio CC, Havlir DV, Richman DD (1998) AIDS Res Hum Retroviruses 14:869

    Article  CAS  Google Scholar 

  40. Wang DG, Fan JB, Siao CJ, Berno A, Young P, Sapolsky R, Ghandour G, Perkins N, Winchester E, Spencer J, Kruglyak L, Stein L, Hsie L, Topaloglou T, Hubbell E, Robinson E, Mittmann M, Morris MS, Shen N, Kilburn D, Rioux J, Nusbaum C, Rozen S, Hudson TJ, Lander ES, et al (1998) Science 280:1077

    Article  CAS  Google Scholar 

  41. Cargill M, Altshuler D, Ireland J, Sklar P, Ardlie K, Patil N, Shaw N, Lane CR, Lim EP, Kalyanaraman N, Nemesh J, Ziaugra L, Friedland L, Rolfe A, Warrington J, Lipshutz R, Daley GQ, Lander ES (1999) Nat Genet 22:231

    Article  CAS  Google Scholar 

  42. Lindblad-Toh K, Winchester E, Daly MJ, Wang DG, Hirschhorn JN, Laviolette JP, Ardlie K, Reich DE, Robinson E, Sklar P, Shah N, Thomas D, Fan JB, Gingeras T, Warrington J, Patil N, Hudson TJ, Lander ES (2000) Nat Genet 24:381

    Article  CAS  Google Scholar 

  43. Lindblad-Toh K, Tanenbaum DM, Daly MJ, Winchester E, Lui WO, Villapakkam A, Stanton SE, Larsson C, Hudson TJ, Johnson BE, Lander ES, Meyerson M (2000) Nat Biotechnol 18:1001

    Article  CAS  Google Scholar 

  44. Mei R, Galipeau PC, Prass C, Berno A, Ghandour G, Patil N, Wolff RK, Chee MS, Reid BJ, Lockhart DJ (2000) Genome Res 10:1126

    Article  CAS  Google Scholar 

  45. Fan JB, Chen X, Halushka MK, Berno A, Huang X, Ryder T, Lipshutz RJ, Lockhart DJ, Chakravarti A (2000) Genome Res 10:853

    Article  CAS  Google Scholar 

  46. Shoemaker DD, Lashkari DA, Morris D, Mittmann M, Davis RW (1996) Nat Genet 14:450

    Article  CAS  Google Scholar 

  47. Giaever G, Shoemaker DD, Jones TW, Liang H, Winzeler EA, Astromoff A, Davis RW (1999) Nat Genet 21:278

    Article  CAS  Google Scholar 

  48. Winzeler EA, Shoemaker DD, Astromoff A, Liang H, Anderson K, Andre B, Bangham R, Benito R, Boeke JD, Bussey H, Chu AM, Connelly C, Davis K, Dietrich F, Dow SW, El Bakkoury M, Foury F, Friend SH, Gentalen E, Giaever G, Hegemann JH, Jones T, Laub M, Liao H, Davis RW, et al (1999) Science 285:901

    Article  CAS  Google Scholar 

  49. Hanes J, Jermutus L, Pluckthun A (2000) Methods Enzymol 328:404

    Article  CAS  Google Scholar 

  50. Cho RJ, Fromont-Racine M, Wodicka L, Feierbach B, Stearns T, Legrain P, Lockhart DJ, Davis RW (1998) Proc Natl Acad Sci USA 95:3752

    Article  CAS  Google Scholar 

  51. Winzeler EA, Richards DR, Conway AR, Goldstein AL, Kalman S, McCullough MJ, McCusker JH, Stevens DA, Wodicka L, Lockhart DJ, Davis RW (1998) Science 281:1194

    Article  CAS  Google Scholar 

  52. Winzeler EA, Lee B, McCusker JH, Davis RW (1999) Parasitology 118:S73

    Article  CAS  Google Scholar 

  53. Salamon H, Kato-Maeda M, Small PM, Drenkow J, Gingeras TR (2000) Genome Res 10:2044

    Article  CAS  Google Scholar 

  54. Milner N, Mir KU, Southern EM (1997) Nat Biotechnol 15:537

    Article  CAS  Google Scholar 

  55. Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S (2001) Genes Dev 15:1637

    Article  CAS  Google Scholar 

  56. Takizawa PA, DeRisi JL, Wilhelm JE, Vale RD (2000) Science 290:341

    Article  CAS  Google Scholar 

  57. Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, Simon I, Zeitlinger J, Schreiber J, Hannett N, Kanin E, Volkert TL, Wilson CJ, Bell SP, Young RA (2000) Science 290:2306

    Article  CAS  Google Scholar 

  58. Gunderson KL, Huang XC, Morris MS, Lipshutz RJ, Lockhart DJ, Chee MS (1998) Genome Res 8:1142

    CAS  Google Scholar 

  59. Bulyk ML, Gentalen E, Lockhart DJ, Church GM (1999) Nat Biotechnol 17:573

    Article  CAS  Google Scholar 

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© 2002 Springer-Verlag Berlin Heidelberg

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McGall, G.H., Christians, F.C. (2002). High-Density GeneChip Oligonucleotide Probe Arrays. In: Hoheisel, J., et al. Chip Technology. Advances in Biochemical Engineering/Biotechnology, vol 77. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45713-5_2

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  • DOI: https://doi.org/10.1007/3-540-45713-5_2

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  • Print ISBN: 978-3-540-43215-9

  • Online ISBN: 978-3-540-45713-8

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