Rules of evidence for cancer molecular-marker discovery and validation (original) (raw)
Ramaswamy, S. & Perou, C. M. DNA microarrays in breast cancer: the promise of personalised medicine. Lancet361, 1576–1577 (2003). PubMed Google Scholar
Kolata, G. Breast cancer: genes are tied to death rates. New York TimesA1 (December 19, 2002).
Zhu, W. et al. Detection of cancer-specific markers amid massive mass spectral data. Proc. Natl Acad. Sci. USA100, 14666–14671 (2003). ArticleCASPubMedPubMed Central Google Scholar
US Preventive Services Task Force. Guide to clinical preventive services 2nd edn Ch. 2 (US Government Prinitng Office, 1996).
Woolf, S. H. Practice guidelines, a new reality in medicine. II. Methods of developing guidelines. Arch. Intern. Med.152, 946–952 (1992). ArticleCASPubMed Google Scholar
Tannock, I. F. & Warr, D. G. Unconventional therapies for cancer: a refuge from the rules of evidence? CMAJ159, 801–802 (1998). CASPubMedPubMed Central Google Scholar
Vogelstein, B. et al. Genetic alterations during colorectal-tumor development. N. Engl J. Med.319, 525–532 (1988). ArticleCASPubMed Google Scholar
Ahlquist, D. A. et al. Colorectal cancer screening by detection of altered human DNA in stool: feasibility of a multitarget assay panel. Gastroenterology119, 1219–1227 (2000). ArticleCASPubMed Google Scholar
Stears, R. L., Martinsky, T. & Schena, M. Trends in microarray analysis. Nature Med.9, 140–145 (2003). ArticleCASPubMed Google Scholar
Thomson, D. M., Krupey, J., Freedman, S. O. & Gold, P. The radioimmunoassay of circulating carcinoembryonic antigen of the human digestive system. Proc. Natl Acad. Sci. USA64, 161–167 (1969). ArticleCASPubMedPubMed Central Google Scholar
Reid, M. C., Lachs, M. S. & Feinstein, A. R. Use of methodological standards in diagnostic test research. Getting better but still not good. JAMA274, 645–651 (1995). ArticleCASPubMed Google Scholar
Ransohoff, D. F. & Feinstein, A. R. Problems of spectrum and bias in evaluating the efficacy of diagnostic tests. N. Engl. J. Med.299, 926–930 (1978). ArticleCASPubMed Google Scholar
Sackett, D. L. Zlinkoff honor lecture: basic research, clinical research, clinical epidemiology, and general internal medicine. J. Gen. Intern. Med.2, 40–47 (1987). ArticleCASPubMed Google Scholar
Feinstein, A. R. Clinical biostatistics XXXI. On the sensitivity, specificity, and discrimination of diagnostic tests. Clin. Pharmacol. Ther.17, 104–116 (1975). ArticleCASPubMed Google Scholar
Ransohoff, D. F. Challenges and opportunities in evaluating diagnostic tests. J. Clin. Epid.55, 1178–1182 (2002). Article Google Scholar
Sullivan Pepe, M. et al. Phases of biomarker development for early detection of cancer. J. Natl Cancer Inst.93, 1054–1061 (2001). Article Google Scholar
Sackett, D. L., Haynes, R. B., Tugwell, P. & Guyatt, G. H. Clinical Epidemiology: a Basic Science for Clinical Medicine (Little, Brown and Company, Boston, 1991). Google Scholar
Bogardus, S. T., Concato, J. & Feinstein, A. R. Clinical epidemiological quality in molecular genetic research: the need for methodological standards. JAMA281, 1919–1926 (1999). ArticlePubMed Google Scholar
Deyo, R. A. & Jarvik, J. J. New diagnostic tests: breakthrough approaches or expensive add-ons? Ann. Intern. Med.139, 950–951 (2003). ArticlePubMed Google Scholar
Wasson, J. H., Sox, H. C., Neff, R. K. & Goldman, L. Clinical prediction rules. Applications and methodological standards. N. Engl. J. Med.313, 793–799 (1985). ArticleCASPubMed Google Scholar
Lachs, M. S. et al. Spectrum bias in the evaluation of diagnostic tests: lessons from the rapid dipstick test for urinary tract infection. Ann. Intern. Med.117, 135–140 (1992). ArticleCASPubMed Google Scholar
Jaeschke, R., Guyatt, G. & Sackett, D. L. Users' guides to the medical literature. III. How to use an article about a diagnostic test. A. Are the results of the study valid? Evidence-Based Medicine Working Group. JAMA271, 389–391 (1994). ArticleCASPubMed Google Scholar
Bossuyt, P. M. et al. Towards complete and accurate reporting of studies of diagnostic accuracy: The STARD Initiative. Ann. Intern. Med.138, 40–44 (2003). ArticlePubMed Google Scholar
Bossuyt, P. M. et al. The STARD statement for reporting studies of diagnostic accuracy: explanation and elaboration. Ann. Intern. Med.138, W1–W12 (2003). ArticlePubMed Google Scholar
Potter, J. D. At the interfaces of epidemiology, genetics and genomics. Nature Rev. Genet.2, 142–147 (2001). ArticleCASPubMed Google Scholar
Ambroise, C. & McLachlan, G. J. Selection bias in gene extraction on the basis of microarray gene-expression data. Proc. Natl Acad. Sci. USA99, 6562–6566 (2002). ArticleCASPubMedPubMed Central Google Scholar
Simon, R., Radmacher, M. D., Dobbin, K. & McShane, L. M. Pitfalls in the use of DNA microarray data for diagnostic and prognostic classification. J. Natl Cancer Inst.95, 14–18 (2003). ArticleCASPubMed Google Scholar
Katz, M. H. Multivariable analysis: a primer for readers of medical research. Ann. Intern. Med.138, 644–650 (2003). ArticlePubMed Google Scholar
Selaru, F. M. et al. Artificial neural networks distinguish among subtypes of neoplastic colorectal lesions. Gastroenterology122, 606–613 (2002). ArticlePubMed Google Scholar
Petricoin, E. F. et al. Use of proteomic patterns in serum to identify ovarian cancer. Lancet359, 572–577 (2002). ArticleCASPubMed Google Scholar
Qu, Y. et al. Boosted decision tree analysis of surface-enhanced laser desorption/ionization mass spectral serum profiles discriminates prostate cancer from noncancer patients. Clin. Chem.48, 1835–1843 (2002). CASPubMed Google Scholar
Huang, E. et al. Gene expression predictors of breast cancer outcomes. Lancet361, 1590–1596 (2003). ArticleCASPubMed Google Scholar
Harrell, F. E. Jr. Regression Modeling Strategies: With Applications to Linear Models, Logistic Regression, And Survival Analysis (Springer–Verlag, New York, 2001). Book Google Scholar
Ntzani, E. E. & Ioannidis, J. P. Predictive ability of DNA microarrays for cancer outcomes and correlates: an empirical assessment. Lancet362, 1439–1444 (2003). ArticleCASPubMed Google Scholar
van de Vijver, M. J. et al. A gene-expression signature as a predictor of survival in breast cancer. N. Engl. J. Med.347, 1999–2009 (2002). ArticleCASPubMed Google Scholar
van 't Veer, L. J. et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature415, 530–536 (2002). ArticleCASPubMed Google Scholar
Ransohoff, D. F. Gene-expression signatures in breast cancer. N. Engl. J. Med.348, 1715–1717 (2003). ArticlePubMed Google Scholar
Baker, S. G., Kramer, B. S. & Srivastava, S. Markers for early detection of cancer: statistical guidelines for nested case–control studies. BMC Med. Res. Methodol.2, 4 (2002). ArticlePubMedPubMed Central Google Scholar
Chang, J. C. et al. Gene expression profiling for the prediction of therapeutic response to docetaxel in patients with breast cancer. Lancet362, 362–369 (2003). ArticleCASPubMed Google Scholar
Brenton, J. D. & Caldas, C. Predictive cancer genomics: what do we need? Lancet362, 340–341 (2003). ArticlePubMed Google Scholar
Rosenwald, A. et al. The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma. N. Engl. J. Med.346, 1937–1947 (2002). ArticlePubMed Google Scholar
Hunter, K. W. Allelic diversity in the host genetic background may be an important determinant in tumor metastatic dissemination. Cancer Lett.200, 97–105 (2003). ArticleCASPubMed Google Scholar
Masters, J. R. & Lakhani, S. R. How diagnosis with microarrays can help cancer patients. Nature404, 921 (2000). ArticleCASPubMed Google Scholar
Pharmalicensing. Agenda to develop microarray-based breast cancer test using Agilent Technologies' gene expression platform [online], (cited 22 Sept. 2003) (2003).
Wooster, R. & Weber, B. L. Breast and ovarian cancer. N. Engl. J. Med.348, 2339–2347 (2003). ArticleCASPubMed Google Scholar
Feinstein, A. R. Multivariable Analysis: An Introduction (Yale University Press, New Haven, 1996). Book Google Scholar
Fletcher, R. H., Fletcher, S. W. & Wagner, E. H. Clinical Epidemiology: The Essentials 3rd edn (Williams & Wilkins, Baltimore, 1996). Google Scholar
Bleeker, S. E. et al. External validation is necessary in prediction research: a clinical example. J. Clin. Epidemiol.56, 826–832 (2003). ArticleCASPubMed Google Scholar
Sorace, J. M. & Zhan, M. A data review and re-assessment of ovarian cancer serum proteomic profiling. BMC Bioinformatics4, 24 (2003). ArticlePubMedPubMed Central Google Scholar
Baggerly, K. A., Morris, J. S. & Coombes, K. R. Reproducibility of SELDI–TOF protein patterns in serum: comparing data sets from different experiments. Bioinformatics. 29 Jan 2004. (doi:10.1093/bioinformatics/btg484)
Hingorani, S. R. et al. Preinvasive and invasive ductal pancreatic cancer and its early detection in the mouse. Cancer Cell4, 437–450 (2003). ArticleCASPubMed Google Scholar
Feinstein, A. R. Clinical Epidemiology: The Architecture of Clinical Research (WB Saunders, Philadelphia, 1985). Google Scholar
Hennekens, C. H. & Buring, J. E. Epidemiology in Medicine (Little, Brown and Company, Boston, 1987). Google Scholar
Freiman, J. A., Chalmers, T. C., Smith, H. Jr & Kuebler, R. R. The importance of β, the type II error and sample size in the design and interpretation of the randomized control trial. Survey of 71 'negative' trials. N. Engl. J. Med.299, 690–694 (1978). ArticleCASPubMed Google Scholar
Ransohoff, D. F. Discovery-based research and fishing. Gastroenterology125, 290 (2003). ArticlePubMed Google Scholar