Methods and apparatus for detecting molecular interactions using FET arrays

An apparatus for predicting responsiveness of a subject to a therapeutic regimen, the apparatus comprising:

• an assembly for assaying a biological sample obtained from the subject for a nucleotide sequence of interest that is associated with responsiveness to the therapeutic regimen, comprising:
• a chemical-sensitive field effect transistor (chemFET) array comprising a plurality of chemFET sensors and further comprising at least one target nucleic acid sample or at least one interrogating nucleic acid disposed thereon or associated therewith, the chemFET sensors having a gate-oxide, a floating gate comprising conductors formed in a plurality of conductor layers and electrically coupled to one another, and a passivation layer overlying the floating gate, the sample analyzer further comprising signal lines for the sensors within at least one of the conductor layers;
• a fluidics assembly comprising:
• a reaction assembly for contacting the chemFET array with the at least one target nucleotide sample when the at least one interrogating nucleic acid is disposed on or associated with the chemFET array or an assembly for contacting the chemFET array with the at least one interrogating nucleic acid when the at least one target nucleotide sample is disposed on or associated therewith the chemFET array;
• a washing assembly for removing at least a portion of unbound interrogating nucleic acid or target nucleic acid sample from the chemFET array;
• and
• a detection system for detecting an electrical output from the chemFET array, wherein the electrical output is indicative of a binding interaction between the at least one target nucleic acid and the at least one interrogating nucleic acid;
• and
• an analysis system for generating an evaluation of responsiveness of the subject to the therapeutic agent on the basis of the hybridization interactions for the at least one biological sample.