Molecular Analysis using a Magnetic Sifter and Nanowell System

A method for identification of circulating tumor cells (CTCs), the method comprising:

• magnetically labeling the CTCs in a blood sample with cancer cell markers conjugated to magnetic nanoparticles;
• separating the magnetically labeled CTCs by passing the blood sample through a magnetic sifter during application of an external magnetic field;
• collecting the separated magnetically labeled CTCs to produce enriched CTCs;
• loading the enriched CTCs into a microfluidic single-cell molecular assay comprising an array of 25,600 or more nanowells, where each of the nanowells is adapted to contain at most a single one of the CTCs;
• performing multiple simultaneous multiple-color multiplexed gene expression of the CTCs using the microfluidic single-cell molecular assay and multiple fluorescent gene markers;
• imaging the array of nanowells using fluorescence signal acquisition from individual nanowells, producing images of the array of nanowells;
• analyzing the images using a signal processor to identify CTCs based on the concurrent expression of two or more genes.