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Proteomic and genomic technologies for biomarker discovery

Where are the biomarkers?


  1. 1

    Etzioni, R., Urban, N., Ramsey, S., et al. (2003) The case for early detection. Nat. Rev. Cancer 3, 243–252.

    PubMed  Article  CAS  Google Scholar 

  2. 2

    Bast, R. C., Jr., Klug, T. L., St. John, E., et al. (1983) A radioimmunoassay using a monoclonal antibody to monitor the course of epithelial ovarian cancer. N. Engl. J. Med. 309, 883–887.

    PubMed  Article  Google Scholar 

  3. 3

    Celis, A., Rasmussen, H. H., Celis, P., et al. (1999) Short-term culturing of low-grade superficial bladder transitional cell carcinomas leads to changes in the expression levels of several proteins involved in key cellular activities. Electrophoresis 20, 355–361.

    PubMed  Article  CAS  Google Scholar 

  4. 4

    Kageyama, S., Isono, T., Iwaki, H., et al. (2004) Identification by proteomic analysis of calreticulin as a marker for bladder cancer and evaluation of the diagnostic accuracy of its detection in urine. Clin. Chem. 50, 857–866.

    PubMed  Article  CAS  Google Scholar 

  5. 5

    Wang, X., Yu, J., Sreekumar, A., et al. (2005) Autoantibody signatures in prostate cancer. N. Engl. J. Med. 353, 1224–1235.

    PubMed  Article  CAS  Google Scholar 

  6. 6

    Petricoin, E. F., Ardekani, A. M., Hitt, B. A., et al. (2002) Use of proteomic patterns in serum to identify ovarian cancer. Lancet 359, 572–577.

    PubMed  Article  CAS  Google Scholar 

  7. 7

    Caprioli, R. M. (2005) Deciphering protein molecular signatures in cancer tissues to aid in diagnosis, prognosis, and therapy. Cancer Res. 65, 10,642–10,645.

    Article  CAS  Google Scholar 

  8. 8

    Yanagisawa, K., Shyr, Y., Xu, B. J., et al. (2003) Proteomic patterns of tumor subsets in non-small-cell lung cancer. Lancet 362, 433–439.

    PubMed  Article  CAS  Google Scholar 

  9. 9

    Martin, D. B., Gifford, D. R., Wright, M. E., et al. (2004) Quantitative proteomic analysis of proteins released by neoplastic prostate epithelium. Cancer Res. 64, 347–355.

    PubMed  Article  CAS  Google Scholar 

  10. 10

    Perou, C. M., Sorlie, T., Eisen, M. B., et al. (2000) Molecular portraits of human breast tumors. Nature 406, 747–752.

    PubMed  Article  CAS  Google Scholar 

  11. 11

    Alizadeh, A. A., Ross, D. T., Perous, C. M., and van de Rijn, M. (2001) Towards a novel classification of human malignancies based on gene expression patterns. J. Pathol. 195, 41–52.

    PubMed  Article  CAS  Google Scholar 

  12. 12

    Weigelt, B., Hu, Z., He, X., et al. (2005) Molecular portraits and 70-gene prognosis signature are preserved throughout the metastatic process of breast cancer. Cancer Res. 65, 9144–9158.

    Article  Google Scholar 

  13. 13

    Alizadeh, A. A., Eisen, M. B., Davis, R. E., et al. (2000) Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403, 503–511.

    PubMed  Article  CAS  Google Scholar 

  14. 14

    Rosenwald, A., Wright, G., Chan, W. C., et al. (2002) Lymphoma/leukemia molecular profiling project: The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma. N. Engl. J. Med. 346, 1937–1947.

    PubMed  Article  Google Scholar 

  15. 15

    Bhattacharjee, A., Richards, W. G., Staunton, J., et al. (2001) Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc. Natl. Acad. Sci. USA 98, 13,790–13,795.

    Article  CAS  Google Scholar 

  16. 16

    Ramaswamy, S., Ross, K. N., Lander, E. S., and Golub, T. R. (2003) A molecular signature of metastasis in primary solid tumors. Nat. Genet. 33, 49–54.

    PubMed  Article  CAS  Google Scholar 

  17. 17

    Pemeroy, S. L., Tamayo, P., Gaasenbeek, M., et al. (2002) Prediction of central nervous system embryonal tumor outcome based on gene expression. Nature 415, 436–442.

    Article  CAS  Google Scholar 

  18. 18

    Iizuka, N., Hammoto, Y., and Oka, M. (2004) Predicting individual outcomes in hepatocellular carcinoma. Lancet 364, 1837–1839.

    PubMed  Article  Google Scholar 

  19. 19

    van de Vijver, M. J., He, Y. D., van't Veer, I. J., et al. (2002) A gene-expression signature as a predictor of survival in breast cancer. N. Engl. J. Med. 347, 1999–2009.

    PubMed  Article  Google Scholar 

  20. 20

    van't Veer, I. J. and Weigelt, B. (2003) Road map to metastasis. Nat. Med. 9, 999–1000.

    Article  CAS  Google Scholar 

  21. 21

    Lossos, I. S., Czerwinski, D. K., Alizadeh, A. A., et al. (2004) Prediction of survival in diffuse large-B-cell lymphoma based on the expression of six genes. N. Engl. J. Med. 350, 1828–1837.

    PubMed  Article  CAS  Google Scholar 

  22. 22

    Cronin, M., Pho, M., Dutta, D., et al. (2004) Measurement of gene expression in archival paraffin-embedded tissues: development and performance of a 92-gene reverse transcriptase-polymerase chain reaction assay. Am. J. Pathol. 164, 35–42.

    PubMed  CAS  Google Scholar 

  23. 23

    Bast, R. C., Jr., Ravdin, P., Hayes, D. F., et al. (2000) Update of recommendations for the use of tumor markers in breast and colorectal cancer: clinical practice guidelines of the American Society of Clinical Oncology. J. Clin. Oncol. 19, 1865–1878.

    Google Scholar 

  24. 24

    Finne, P., Finne, R., Auvinen, A., et al. (2000) Predicting the outcome of prostate biopsy in screen-positive men by a multilayer perceptron network. Urology 56, 418–422.

    PubMed  Article  CAS  Google Scholar 

  25. 25

    Stephan, C., Cammann, H., Semjonow, A., et al. (2002) Multicenter evaluation of an artificial neural network to increase the prostate cancer detection rate and reduce unnecessary biopsies. Clin. Chem. 48, 1279–1287.

    PubMed  CAS  Google Scholar 

  26. 26

    Diamandis, E. P. (2003) Point: proteomic patterns in biological fluids: do they represent the future of cancer diagnostics? Clin. Chem. 49, 1272–1275.

    PubMed  Article  CAS  Google Scholar 

  27. 27

    Diamandis, E. P. (2003) Analysis of serum proteomic patterns for early cancer diagnosis: drawing attention to potential problems. J. Natl. Cancer Inst. 96, 353–356.

    Google Scholar 

  28. 28

    Karsan, A., Eigl, B. J., Fibotte, S., et al. (2005) Analytical and preanalytical biases in serum proteomic pattern analysis for breast cancer diagnosis. Clin. Chem. 51, 1525–1528.

    PubMed  Article  CAS  Google Scholar 

  29. 29

    Banks, R. E., Stanley, A. J., Cairns, D. A., et al. (2005) Influences of blood sample processing on low-molecular-weight-proteome identified by surface-enhanced laser desorption/ionization mass spectrometry. Clin. Chem. 51, 1637–1649.

    PubMed  Article  CAS  Google Scholar 

  30. 30

    Baggerly, K. A., Morris, J. S., Edmonson, S. R., and Coombes, K. R. (2005) Signal in noise: evaluating reported reproducibility of serum proteomic tests for ovarian cancer. J. Natl. Cancer Inst. 97, 307–309.

    PubMed  CAS  Article  Google Scholar 

  31. 31

    Ransohoff, D. F. (2005) Lessons from controversy: ovarian cancer screening and serum proteomics. J. Natl. Cancer Inst. 97, 315–319.

    PubMed  CAS  Article  Google Scholar 

  32. 32

    Elias, J. E., Haas, W., Faherty, B. K., and Gygi, S. P. (2005) Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nat. Methods 2, 667–675.

    PubMed  Article  CAS  Google Scholar 

  33. 33

    Michiels, S., Koscielny, S., and Hill, C. (2005) Prediction of cancer outcome with microarrays: a multiple random validation strategy. Lancet 365, 488–492.

    PubMed  Article  CAS  Google Scholar 

  34. 34

    Ioannidis, J. P. (2005) Microarrays and molecular research: noise discovery? Lancet 365, 454–455.

    PubMed  Google Scholar 

  35. 35

    Branca, M. A. (2005) Omic diagnostics trip up on way to clinic. Nat Biotechnol. 23, 769.

    PubMed  Article  CAS  Google Scholar 

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Correspondence to Eleftherios P. Diamandis.

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Kulasingam, V., Diamandis, E.P. Proteomic and genomic technologies for biomarker discovery. Clin Proteom 2, 5–11 (2006).

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