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The molecular analysis of disseminated tumor cells from blood or lymph represents an important diagnostic tool as metastasis is the primary cause of patient mortality due to cancer. Isolating tumor cells from blood is technically challenging due to the miniscule ratio of tumor cells to normal cells. Although RT-PCR and flow-based methods have been used for molecular profiling of the captured cells, it requires cell destruction and the loss of morphological information. Here, we present a combined strategy to isolate tumor cells with magnetic nanoparticles, followed by multiple biomarker analysis using targeted quantum dots (QD) nanoparticles. The magnetic nanoparticles and QDs will allow efficient isolation and quantitative analysis of intact captured cells. Through this technology, patient monitoring and more effective and personalized therapy will be possible. Preliminary studies have demonstrated that the molecular profile of the cells is unaltered by the isolation procedure. Results from studies involving the isolation and profiling of cancer cells from human blood are presented.