Methods and Apparatus for Measuring Analytes Using Large Scale FET Arrays

Abstract

Methods and apparatus relating to very large scale FET arrays for analyte measurements. 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. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis.

1 - 106 . (canceled) 
     
     
         107 . A method for nucleic acid sequence detection comprising:
 (a) disposing a plurality of sample nucleic acids at discrete locations on a substrate associated with a semiconductor based sensor array, each discrete location associated with at least one sensor comprising a field-effect transistor configured to provide output signals representative of reaction byproducts proximate thereto;   (b) introducing known nucleotides or probes and enzyme into the discrete locations;   (c) providing conditions sufficient to permit the enzyme to act in connection with the sample nucleic acids and the known nucleotides or probes to produce reaction byproducts;   (d) detecting the reaction byproducts formed or brought in proximity to the at least one sensor;   (e) outputting at least one signal indicative of the at least one sensor detecting the at least one reaction byproducts.   
     
     
         108 . The method of  claim 107  wherein the sensors of the sensor array have a chemically sensitive portion responsive to one or more of the sample reaction byproducts and disposed in proximity to the substrate such that the at least one reaction byproducts diffuse or contact the sensors to thereby be detected. 
     
     
         109 . The method of  claim 108  wherein the chemically sensitive portion of the sensors of the sensor array is responsive to a plurality of different reaction byproducts. 
     
     
         110 . The method of  claim 109  wherein the chemically sensitive portion is responsive to byproducts generated by enzymatic reaction of sample nucleic acids with the nucleotides or probes. 
     
     
         111 . The method of  claim 109  wherein the chemically sensitive portion is responsive to changes in ion concentration resulting from the presence or generation of the reaction byproducts. 
     
     
         112 . The method of  claim 109  wherein the chemically sensitive portion is responsive to changes in hydrogen ion concentration formed by the presence or generation of the reaction byproducts. 
     
     
         113 . The method of  claim 107  wherein the reaction byproducts comprise hydrogen ions that are detected by the at least one sensor. 
     
     
         114 . The method of  claim 107  wherein the output signals for the sensors of the sensor array are configured to be similar in response to similar amounts of detected reaction byproducts. 
     
     
         115 . The method of  claim 107  wherein the discrete locations are disposed within individual reaction chambers. 
     
     
         116 . The method of  claim 115  wherein the reactions are conducted in a fluidic environment. 
     
     
         117 . A method for nucleic acid sequence detection comprising:
 (a) disposing a plurality of sample nucleic acids at discrete locations on a substrate associated with a semiconductor based sensor array, each discrete location associated with at least one sensor comprising a field-effect transistor configured to provide output signals representative of reaction byproducts proximate thereto;   (b) introducing known nucleotides and enzyme into the discrete locations;   (c) providing conditions sufficient to permit the enzyme to act in connection with the sample nucleic acids and the known nucleotides to produce reaction byproducts;   (d) detecting the reaction byproducts formed or brought in proximity to the at least one sensor;   (e) outputting at least one signal indicative of the at least one sensor detecting the at least one reaction byproducts; and   (f) associating output signals and known nucleotide identities with corresponding nucleotides in the sample nucleic acids.   
     
     
         118 . The method  claim 117  further comprising repeating steps (b) through (f) to discern a plurality of nucleotides associated with the sequence of at least a portion of the plurality of sample nucleic acids. 
     
     
         119 . The method of  claim 117  wherein the sensors of the sensor array have a chemically sensitive portion responsive to one or more of the sample reaction byproducts and disposed in proximity to the substrate such that the at least one reaction byproducts diffuse or contact the sensors to thereby be detected. 
     
     
         120 . The method of  claim 119  wherein the chemically sensitive portion of the sensors of the sensor array is responsive to a plurality of different reaction byproducts. 
     
     
         121 . The method of  claim 119  wherein the chemically sensitive portion is responsive to byproducts generated by enzymatic reaction of sample nucleic acids with the nucleotides. 
     
     
         122 . The method of  claim 119  wherein the chemically sensitive portion is responsive to changes in ion concentration resulting from the presence or generation of the reaction byproducts. 
     
     
         123 . The method of  claim 119  wherein the chemically sensitive portion is responsive to changes in hydrogen ion concentration formed by the presence or generation of the reaction byproducts. 
     
     
         124 . The method of  claim 117  wherein the reaction byproducts comprise hydrogen ions that are detected by the at least one sensor. 
     
     
         125 . The method of  claim 117  wherein the output signals for the sensors of the sensor array are configured to be similar in response to similar amounts of detected reaction byproducts. 
     
     
         126 . The method of  claim 117  wherein the discrete locations are disposed within individual reaction chambers. 
     
     
         127 . The method of  claim 117  wherein the reactions are conducted in a fluidic environment.