Whole genome expression analysis system

A system for simultaneously determining a genetic expression profile in a liquid sample obtained from an individual member of a species relative to an entire standard genome for the species, said system comprising:

• a substrate;
• at least about 1000 reaction chambers formed in an array on said substrate, said array having a primer set and a probe for each of a plurality of polynucleotide targets within the entire standard genome, each of said reaction chambers having said primer set and said probe for at least one of said plurality of polynucleotide targets and a polymerase;
• a cover;
• amplification reagents for performing an amplification reaction;
• a filling system in fluid communication with each of said reaction chambers for filling the liquid sample and said amplification reagents into each of said reaction chambers;
• a thermal cycling system in thermal communication with each of said reaction chambers for controlling a temperature during said amplification reaction;
• an excitation system disposed proximate said reaction chambers to excite at least one of said probes to emit a signal;
• and
• a detection system detecting said signal.