Advertisement

Application of Microarray Technologies for Translational Genomics

  • Spyro Mousses
  • Natasha Caplen
  • Mark Basik
  • Anne Kallioniemi
  • Olli Kallioniemi
Part of the Biological and Medical Physics, Biomedical Engineering book series (BIOMEDICAL)

Keywords

cDNA Microarrays Microarray Technology Candidate Gene Target Recipient Block Tissue Microarray Analysis 
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.
    Birney E, Bateman A, Clamp ME, Hubbard TJ. Mining the draft human genome. Nature 2001, 409:827–828PubMedCrossRefGoogle Scholar
  2. 2.
    Collins FS, Patrinos A, Jordan E, Chakravarti A, Gesteland R, Walters L. New goals for the US Human Genome Project. 1998–2003. Science 1998, 282:682–689PubMedCrossRefGoogle Scholar
  3. 3.
    Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W et al.. Initial sequencing and analysis of the human genome. Nature 2001, 409:860–921PubMedCrossRefGoogle Scholar
  4. 4.
    Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA et al.. The sequence of the human genome. Science 2001, 291:1304–1351PubMedCrossRefGoogle Scholar
  5. 5.
    Wolfsberg TG, McEntyre J, Schuler GD. Guide to the draft human genome. Nature 2001, 409:824–826PubMedCrossRefGoogle Scholar
  6. 6.
    Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H, Brown EL. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 1996, 14:1675–1680PubMedCrossRefGoogle Scholar
  7. 7.
    Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995, 270:467–470PubMedGoogle Scholar
  8. 8.
    Schena M, Shalon D, Heller R, Chai A, Brown PO, Davis RW. Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc Natl Acad Sci USA 1996, 93:10614–10619PubMedCrossRefGoogle Scholar
  9. 9.
    Shoemaker DD, Schadt EE, Armour CD, He YD, Garrett-Engele P, McDonagh PD, Loerch PM, Leonardson A, Lum PY, Cavet G et al.. Experimental annotation of the human genome using microarray technology. Nature 2001, 409:922–927PubMedCrossRefGoogle Scholar
  10. 10.
    Bittner M, Meltzer P, Chen Y, Jiang Y, Seftor E, Hendrix M, Radmacher M, Simon R, Yakhini Z, Ben-Dor A et al.. Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature 2000, 406:536–540PubMedCrossRefGoogle Scholar
  11. 11.
    DeRisi J, Penland L, Brown PO, Bittner ML, Meltzer PS, Ray M, Chen Y, Su YA, Trent JM. Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat Genet 1996, 14:457–460PubMedCrossRefGoogle Scholar
  12. 12.
    Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA et al.. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 1999, 286:531–537PubMedCrossRefGoogle Scholar
  13. 13.
    Perou CM, Sorlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, Pollack JR, Ross DT, Johnsen H, Akslen LA et al.. Molecular portraits of human breast tumours. Nature 2000, 406:747–752PubMedCrossRefGoogle Scholar
  14. 14.
    Kallioniemi OP, Wagner U, Kononen J, Sauter G. Tissue microarray technology for high-throughput molecular profiling of cancer. Hum Mol Genet 2001, 10:657–662PubMedCrossRefGoogle Scholar
  15. 15.
    Kononen J, Bubendorf L, Kallioniemi A, Bärlund M, Schraml P, Leighton S, Torhorst J, Mihatsch MJ, Sauter G, Kallioniemi OP. Tissue microarrays for high-throughput molecular profiling of tumor specimens. Nat Med 1998, 4:844–847PubMedCrossRefGoogle Scholar
  16. 16.
    Kononen J, Hostetter G, Sauter G, Kallioniemi OP. Construction of tissue microarrays. In A Companion to Molecular Cloning, vol 4, edn 3. Edited by Bowtell D, Sambrook J. Cold Spring Harbor: Cold Spring Harbor Laboratory Press, 2001: in pressGoogle Scholar
  17. 17.
    Bärlund M, Forozan F, Kononen J, Bubendorf L, Chen Y, Bittner ML, Torhorst J, Haas P, Bucher C, Sauter G et al.. Detecting activation of ribosomal protein S6 kinase by complementary DNA and tissue microarray analysis. J Natl Cancer Inst 2000, 92:1252–1259PubMedCrossRefGoogle Scholar
  18. 18.
    Moch H, Schraml P, Bubendorf L, Mirlacher M, Kononen J, Gasser T, Mihatsch MJ, Kallioniemi OP, Sauter G. High-throughput tissue microarray analysis to evaluate genes uncovered by cDNA microarray screening in renal cell carcinoma. Am J Pathol 1999, 154:981–986PubMedGoogle Scholar
  19. 19.
    Sugita M, Geraci M, Gao B, Powell RL, Hirsch FR, Johnson G, Lapadat R, Gabrielson E, Bremnes R, Bunn PA and Franklin WA. Combined use of oligonucleotide and tissue microarrays identifies cancer/testis antigens as bio-markers in lung carcinoma. Cancer Res 2002;62(14): 3971–9PubMedGoogle Scholar
  20. 20.
    Sallinen SL, Sallinen PK, Haapasalo HK, Helin HJ, Helen PT, Schraml P, Kallioniemi OP, Kononen J. Identification of differentially expressed genes in human gliomas by DNA microarray and tissue chip techniques. Cancer Res 2000, 60:6617–6622PubMedGoogle Scholar
  21. 21.
    Ginestier C, Charafe-Jauffret E, Bertucci F, Eisinger F, Geneix J, Bechlian D, Conte N, Adelaide J, Toiron Y, Nguyen C, Viens P, Mozziconacci MJ, Houlgatte R, Birnbaum D, Jacquemier J. Distinct and complementary information provided by use of tissue and DNA microarrays in the study of breast tumor markers. Am J Path 2002;161(4):1223–33PubMedGoogle Scholar
  22. 22.
    Mousses, S., Bubendorf, L., Wagner, U., Hostetter, G., Kononen, J., Cornelison, R., Goldberger, N., Elkahloun, A.G., Willi, N., Koivisto, P., Ferhle, W., Raffeld, M., Sauter, G., Kallioniemi, OP. Clinical validation of candidate genes associated with prostate cancer progression in the CWR22 model system using tissue microarrays. Cancer Research 2002; 62(5): 1256–60PubMedGoogle Scholar
  23. 23.
    Dhanasekaran SM, Barrette TR, Ghosh D, Shah R, Varambally S, Kurachi K, Pienta KJ, Rubin MA, Chinnaiyan AM. Delineation of prognostic bio-markers in prostate cancer. Nature 2001, 412:822–826PubMedCrossRefGoogle Scholar
  24. 24.
    Toby GG, Golemis EA. Using the yeast interaction trap and other two-hybridbased approaches to study protein-protein interactions. Methods 2001, 24:201–217PubMedCrossRefGoogle Scholar
  25. 25.
    Vidal M, Endoh H. Prospects for drug screening using the reverse two-hybrid system. Trends Biotechnol 1999, 17:374–381PubMedCrossRefGoogle Scholar
  26. 26.
    Ziauddin J, Sabatini DM. Microarrays of cells expressing defined cDNAs. Nature 2001, 411:107–110.1PubMedCrossRefGoogle Scholar
  27. 27.
    Caplen NJ, Parrish S, Imani F, Fire A, Morgan RA. Specific inhibition of gene expression by small double-stranded RNAs in invertebrate and vertebrate systems. Proc Natl Acad Sci USA 2001, 98:9742–9747PubMedCrossRefGoogle Scholar
  28. 28.
    Elbashir SM, Lendeckel W, Tuschl T. RNA interference is mediated by 21— and 22-nucleotide RNAs. Genes Dev 2001, 15:188–200PubMedCrossRefGoogle Scholar
  29. 29.
    Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K, Tuschl T. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 2001, 411:494–498PubMedCrossRefGoogle Scholar
  30. 30.
    Hannon GJ. RNA interference. Nature 2002;418:244–51PubMedCrossRefGoogle Scholar
  31. 31.
    Khan J, Wei JS, Ringner M, Saal LH, Ladanyi M, Westermann F, Berthold F, Schwab M, Antonescu CR, Peterson C, Meltzer PS. Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Nat Med 2001, 7:673–679PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Spyro Mousses
  • Natasha Caplen
  • Mark Basik
  • Anne Kallioniemi
  • Olli Kallioniemi

There are no affiliations available

Personalised recommendations