The invention provides a system for high-throughput multiplex analysis of target samples. A sample and reagent delivery unit is operatively connected to a thermal cycler for amplification of target nucleic acids. Microspheres are hybridized to the resulting amplicons in the thermal cycler. A flow cytometer is operatively connected to the thermal cycler or optionally a bead trap for washing the microspheres.
STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
 This invention was made with government support under Contract No. W-7405-ENG-48 between the U.S. Department of Energy and the University of California, for the operation of Lawrence Livermore National Laboratory. The government has certain rights in the invention.