Methods and apparatus for detecting molecular interactions using FET arrays

A method of detecting nucleic acid sequence variations, said method comprising:

• providing a sample analyzer comprising an array of at least 105 sensors found in a substrate, the sensors comprising a field-effect transistor 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;
• disposing at least one interrogating nucleic acid in proximity to or in contact with at least a portion of the sensors of the array wherein the at least one interrogating nucleic acid is at least partially complimentary to the at least one target nucleic acid of interest and wherein the at least one interrogating nucleic acid comprises a sequence corresponding to a nucleic acid variation or mutation at least one predetermined position;
• disposing at least one target nucleic acid of interest in proximity to or in contact with at least a portion of the sensors of the array wherein interactions between the at least one interrogating nucleic acid and the at least one target nucleic acid effectuate changes in at least one electrical property of at least a portion of the sensors of the array;
• and
• identifying the presence of a nucleic acid variation or mutation associated with the at least one target nucleic acid on the basis of hybridization interactions between the at least one interrogating nucleic acid and the at least one target nucleic acid by detecting the changes in electrical properties of at least a portion of the sensors of the array.

A method for determining expression levels of at least one target nucleic acid of interest in a sample, the method comprising:

• providing a sample analyzer comprising a plurality of chemical-sensitive field effect transistors (chemFETs), the chemFETs 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;
• disposing at least one capture agent in proximity to or in contact with at least a portion of the chemFETs wherein the at least one capture agent is reactive or sensitive to at least one target nucleic acid of interest;
• disposing the at least one target nucleic acid of interest in proximity to or in contact with at least a portion of the chemFETs wherein interactions between the at least one capture agent and the at least one target nucleic acid effectuate changes in at least one electrical property of at least a portion of the chemFETs;
• identifying interactions between the at least one capture agent and the at least one target nucleic acid by detecting the changes in electrical properties of at least a portion of the chemFETs;
• and
• identifying chemFETs whose electrical properties change in response to the interactions to determine the expression level of the at least one target nucleic acid of interest.