Methods and apparatus for detecting molecular interactions using fet arrays

Abstract

Methods and apparatuses relating to large scale FET arrays for analyte detection and measurement are provided. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes.

1 - 116 . (canceled) 
     
     
         117 ) A method for detecting 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);   disposing at least one interrogating nucleic acid in proximity to at least a portion of the chemFETs wherein the at least one interrogating nucleic acid is at least partially complimentary to the at least one target nucleic acid of interest;   disposing at least one target nucleic acid of interest in proximity to at least a portion of the chemFETs 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 chemFETs; and   identifying 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 chemFETs indicating presence of the at least one target nucleic acid of interest in the sample.   
     
     
         118 ) The method of  claim 117 , wherein at least one of the interrogating nucleic acid or the target nucleic acid is immobilized, bound to, or coupled with the chemFETs. 
     
     
         119 ) The method of  claim 117 , wherein the chemFETs further comprise a passivation layer and wherein the at least one the interrogating nucleic acid or the target nucleic acid is bound to or coupled with the passivation layer. 
     
     
         120 ) The method of  claim 117 , wherein the changes in electrical properties of the chemFETs comprise changes in voltage or current. 
     
     
         121 ) The method of  claim 117 , wherein the at least one interrogating nucleic acid and the at least one target nucleic acid are unlabeled or unmodified. 
     
     
         122 ) The method of  claim 117 , wherein the chemFETs each comprise a floating gate with substantially zero trapped charge reducing variations in sensitivity between the chemFETs. 
     
     
         123 ) The method of  claim 117 , wherein the at least one interrogating nucleic acid and the at least one target nucleic acid are at least partially complimentary and interact by hybridizing to effectuate changes in at least one electrical property of at least a portion of the chemFETs. 
     
     
         124 ) The method of  claim 117 , wherein the plurality of chemFETs comprises more than 256 chemFETs, each chemFET having a microwell disposed thereon. 
     
     
         125 ) A method of detecting nucleic acid sequence variations, said method comprising:
 providing a sample analyzer comprising a plurality of chemical-sensitive field effect transistors (chemFETs);   disposing at least one interrogating nucleic acid in proximity to at least a portion of the chemFETs wherein the at least one interrogating nucleic acid is at least partially complimentary to 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 in at least one predetermined position;   disposing the at least one target nucleic acid of interest in proximity to at least a portion of the chemFETs 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 chemFETs; and   identifying the presence of a nucleic acid variation 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 chemFETs.   
     
     
         126 ) The method of  claim 125 , wherein at least one of the interrogating nucleic acid or the target nucleic acid is immobilized, bound to, or coupled with the chemFETs. 
     
     
         127 ) The method of  claim 125 , wherein the chemFETs further comprise a passivation layer and wherein the at least one the interrogating nucleic acid or the target nucleic acid is bound to or coupled with the passivation layer. 
     
     
         128 ) The method of  claim 125 , wherein the changes in electrical properties of the chemFETs comprise changes in voltage or current. 
     
     
         129 ) The method of  claim 125 , wherein the at least one interrogating nucleic acid and the at least one target nucleic acid are unlabeled or unmodified. 
     
     
         130 ) The method of  claim 125 , wherein the chemFETs each comprise a floating gate with substantially zero trapped charge reducing variations in sensitivity between the chemFETs. 
     
     
         131 ) The method of  claim 125 , wherein the plurality of chemFETs comprises more than 256 chemFETs, each chemFET having a microwell disposed thereon. 
     
     
         132 ) A method for determining a copy number for 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);   disposing at least one nucleic acid responsive agent in proximity to at least a portion of the chemFETs wherein the at least one nucleic acid responsive agent is sensitive to at least one target nucleic acid of interest;   disposing the at least one target nucleic acid of interest in proximity to at least a portion of the chemFETs wherein interactions between the at least one nucleic acid responsive 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 copy number of the at least one target nucleic acid of interest.   
     
     
         133 ) The method of  claim 132 , wherein at least one of the nucleic acid responsive agent or the target nucleic acid is immobilized, bound to, or coupled with the chemFETs. 
     
     
         134 ) The method of  claim 132 , wherein the chemFETs further comprise a passivation layer and wherein the at least one the nucleic acid responsive agent or the target nucleic acid is bound to or coupled with the passivation layer. 
     
     
         135 ) The method of  claim 132 , wherein the changes in electrical properties of the chemFETs comprise changes in voltage or current. 
     
     
         136 ) The method of  claim 132 , wherein the at least one nucleic acid responsive agent and the at least one target nucleic acid are unlabeled or unmodified. 
     
     
         137 ) The method of  claim 132 , wherein the chemFETs each comprise a floating gate with substantially zero trapped charge reducing variations in sensitivity between the chemFETs. 
     
     
         138 ) The method of  claim 132 , wherein the plurality of chemFETs comprises more than 256 chemFETs, each chemFET having a microwell disposed thereon. 
     
     
         139 ) A method for comparing nucleic acid expression levels between a first sample and a second sample, the method comprising:
 assaying the first sample and the second sample for an expression level of one or more nucleic acids of interest, comprising:
 providing a sample analyzer comprising a plurality of chemical-sensitive field effect transistors (chemFETs); 
   disposing at least one at least one nucleic acid responsive agent in proximity to or in contact with at least a portion of the chemFETs wherein the at least one at least one nucleic acid responsive agent is sensitive to at least one target nucleic acid of the first sample;   disposing the at least one target nucleic acid of the first sample in proximity to or in contact with at least a portion of the chemFETs wherein interactions between the at least one nucleic acid responsive 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 nucleic acid responsive 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 the first sample, and   repeating with the second sample; and   comparing the expression level of one or more nucleic acids of interest between the first sample and the second sample.   
     
     
         140 ) The method of  claim 139 , wherein at least one of the nucleic acid responsive agent or the target nucleic acid is immobilized, bound to, or coupled with the chemFETs. 
     
     
         141 ) The method of  claim 139 , wherein the chemFETs further comprise a passivation layer and wherein the at least one the nucleic acid responsive agent or the target nucleic acid is bound to or coupled with the passivation layer. 
     
     
         142 ) The method of  claim 139 , wherein the changes in electrical properties of the chemFETs comprise changes in voltage or current. 
     
     
         143 ) The method of  claim 139 , wherein the at least one nucleic acid responsive agent and the at least one target nucleic acid are unlabeled or unmodified. 
     
     
         144 ) The method of  claim 139 , wherein the chemFETs each comprise a floating gate with substantially zero trapped charge reducing variations in sensitivity between the chemFETs. 
     
     
         145 ) The method of  claim 139 , wherein the plurality of chemFETs comprises more than 256 chemFETs, each chemFET having a microwell disposed thereon.