There are a number of ways to multiplex, but one of the most common relies on solution-based arrays of microscopic beads measuring several microns in diameter.
Like planar microarrays, these arrays are addressable - that is, each location within the array is known. But in this case, the "array" (1) is really a set of coded microspheres, each of which has an identifying color and associated bioreceptor (e.g., antibody, oligonucleotide, receptor, or enzyme). One color class might be reserved for IL-2, say, while another is reserved for IFN-gamma. Or they may represent different SNPs.
The array is mixed and incubated with a biological sample (2), after which a detection reagent (a dye-conjugated secondary antibody, for instance) is applied (3). The beads then pass single-file through a flow cytometer, which reads the reaction using two lasers (4).
The first laser induces...