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Classification of AML by DNA-Oligonucleotide Microarrays

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Myeloid Leukemia

Part of the book series: Methods In Molecular Medicineā„¢ ((MIMM,volume 125))

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Summary

Accurate diagnosis and classification of leukemias are the bases for the appropriate management of patients. The diagnostic accuracy and efficiency of present methods may be improved by the use of microarrays. The followin g chapter gives an overview of the method of gene expression profiling of leukemia samples, its laboratory procedure, and how to approach the analysis of the data.

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References

  1. Dugas M., Schoch C., Schnittger S., et al. (2001) A comprehensive leukemia database: integration of cytogenetics, molecular genetics and microarray data with clinical information, cytomorphology and immunophenotyping. Leukemia 15, 1805ā€“1810.

    PubMedĀ  CASĀ  Google ScholarĀ 

  2. Gubler U. and Hoffman B. J. (1983) A simple and very efficient method for generating cDNA libraries. Gene 25, 263ā€“269.

    ArticleĀ  PubMedĀ  CASĀ  Google ScholarĀ 

  3. Hoffmann E. P. (2004) Expression profiling-best practices for data generation and interpretation in clinical trials. Nat. Rev. Genet. 5, 229ā€“237.

    ArticleĀ  Google ScholarĀ 

  4. Lipshutz R. J., Fodor S. P., Gingeras T. R., and Lockhart D. J. (1999) High density synthetic oligonucleotide arrays. Nat. Genet. 21, 20ā€“24.

    ArticleĀ  PubMedĀ  CASĀ  Google ScholarĀ 

  5. Lockhart D. J., Dong H., Byrne M. C., et al. (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol. 14, 1675ā€“1680.

    ArticleĀ  PubMedĀ  CASĀ  Google ScholarĀ 

  6. Mei R., Hubbell E., Bekiranov S., et al. (2003) Probe selection for high-density oligonucleotide arrays. Proc. Natl. Acad. Sci. USA 100, 11,237ā€“11,242.

    ArticleĀ  PubMedĀ  CASĀ  Google ScholarĀ 

  7. Sambrook J., Fritsch E. F., and Maniatis T. (1989) Molecular Cloning: A Laboratory Manual (2nd edition). Cold Spring Harbor Laboratory: Cold Spring Harbor, NY.

    Google ScholarĀ 

  8. Slonim D. K. (2002) From patterns to pathways: gene expression data analysis comes of age. Nat. Genet. 32 Suppl., 502ā€“508.

    Google ScholarĀ 

  9. Golub T. R., Slonim D. K., Tamayo P., et al. (1999) Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286, 531ā€“537.

    ArticleĀ  PubMedĀ  CASĀ  Google ScholarĀ 

  10. Yeoh E. J., Ross M. E., Shurtleff S. A., et al. (2002) Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling. Cancer Cell 1, 133ā€“143.

    ArticleĀ  PubMedĀ  CASĀ  Google ScholarĀ 

  11. Quackenbush J. (2002) Microarray data normalization and transformation. Nat. Genet. 32 Suppl, 496ā€“501.

    Google ScholarĀ 

  12. Tusher V. G., Tibshirani R., and Chu G. (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. USA 98, 5116ā€“5121.

    ArticleĀ  PubMedĀ  CASĀ  Google ScholarĀ 

  13. Storey J. D. and Tibshirani R. (2003) Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. USA 100, 9440ā€“9445.

    ArticleĀ  PubMedĀ  CASĀ  Google ScholarĀ 

  14. Eisen M. B., Spellman P. T., Brown P. O., and Botstein D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95, 14,863ā€“14,868.

    ArticleĀ  PubMedĀ  CASĀ  Google ScholarĀ 

  15. Jolliffe I. T. (2002) Principal Component Analysis. Springer: New York.

    Google ScholarĀ 

  16. Guyon I., Weston J., Barnhill S., and Vapnik V. (2002) Gene selection for cancer classification using support vector machines. Machine Learning 46, 389ā€“422.

    ArticleĀ  Google ScholarĀ 

  17. Schƶlkopf B. and Smola A. J. (2002) Learning with Kernels. MIT Press: Cambridge, MA.

    Google ScholarĀ 

  18. Vapnik V. (1998) Statistical Learning Theory. Wiley: New York.

    Google ScholarĀ 

  19. Kohlmann A., Schoch C., Schnittger S., et al. (2004) Pediatric acute lymphoblastic leukemia (ALL) gene expression signatures classify an independent cohort of adult ALL patients. Leukemia 18, 63ā€“71.

    ArticleĀ  PubMedĀ  CASĀ  Google ScholarĀ 

  20. Chang C. C. and Lin C. J. (2001) LIBSVM: a library for support vector machines. Software available at http://www.csie.ntu.edu.tw/~cjlin/libsvm/

  21. Liu G., Loraine A. E., Shigeta R., et al. (2003) NetAffx: Affymetrix probesets and annotations. Nucleic Acids Res. 31, 82ā€“86.

    ArticleĀ  PubMedĀ  CASĀ  Google ScholarĀ 

  22. Dudoit S., Gentleman R. C., and Quackenbush J. (2003) Open source software for the analysis of microarray data. Biotechniques March Suppl., 45ā€“51.

    Google ScholarĀ 

  23. Warrington J. A., Nair A., Mahadevappa M., and Tsyganskaya M. (2000) Comparison of human adult and fetal expression and identification of 535 housekeeping/ maintenance genes. Physiol. Genomics 2, 143ā€“147.

    PubMedĀ  CASĀ  Google ScholarĀ 

  24. Kohlmann A., Schoch C., Schnittger S., et al. (2003) Molecular characterization of acute leukemias by use of microarray technology. Genes Chromosomes Cancer 37, 396ā€“405.

    ArticleĀ  PubMedĀ  CASĀ  Google ScholarĀ 

  25. Ross M. E., Zhou X., Song G., Shurtleff S. A., Girtman K., Williams W. K., et al. (2003) Classification of pediatric acute lymphoblastic leukemia by gene expression profiling. Blood 102, 2951ā€“2959.

    ArticleĀ  PubMedĀ  CASĀ  Google ScholarĀ 

  26. Ross M. E., Mahfouz R., Onciu M., et al. (2004) Gene expression profiling of pediatric acute myelogenous leukemia. Blood 104, 3679ā€“3687.

    ArticleĀ  PubMedĀ  CASĀ  Google ScholarĀ 

  27. Schoch C., Kohlmann A., Schnittger S., et al. (2002) Acute myeloid leukemias with reciprocal rearrangements can be distinguished by specific gene expression profiles. Proc. Natl. Acad. Sci. USA 99, 10,008ā€“10,013.

    ArticleĀ  PubMedĀ  CASĀ  Google ScholarĀ 

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Ā© 2006 Humana Press Inc.

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Kohlmann, A., Kern, W., Hiddemann, W., Haferlach, T. (2006). Classification of AML by DNA-Oligonucleotide Microarrays. In: Iland, H., Hertzberg, M., Marlton, P. (eds) Myeloid Leukemia. Methods In Molecular Medicineā„¢, vol 125. Humana Press. https://doi.org/10.1385/1-59745-017-0:213

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  • DOI: https://doi.org/10.1385/1-59745-017-0:213

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-485-2

  • Online ISBN: 978-1-59745-017-1

  • eBook Packages: Springer Protocols

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