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 the concentration of inorganic pyrophosphate (PPi), hydrogen ions, and nucleotide triphosphates.

What is claimed is: 
     
         1 .- 23 . (canceled) 
     
     
         24 . An apparatus comprising:
 a substrate including an array of sensors;   an array of wells disposed over the substrate, a well of the array of wells corresponding to a sensor of the array of sensors; and   a cover disposed over the array of wells and defining a flow volume between the array of wells and the cover, the cover defining a fluid inlet and a fluid outlet in fluid communication with the flow volume, the flow volume at a diffuser including a non-flat wall defining a curved boundary of the flow volume, the non-flat wall being the top or the bottom wall, the fluid flow at the diffuser being more restricted in the center of the flow volume than at the edges of the flow volume when viewed in cross-section perpendicular to the fluid flow.   
     
     
         25 . The apparatus of  claim 24 , wherein the non-flat wall defines a bottom boundary of the flow volume. 
     
     
         26 . The apparatus of  claim 24 , wherein the non-flat wall defines a top boundary of the flow volume. 
     
     
         27 . The apparatus of  claim 24 , wherein the sensor is a field effect transistor. 
     
     
         28 . The apparatus of  claim 27 , wherein the field effect transistor is an ion sensitive field effect transistor. 
     
     
         29 . The apparatus of  claim 24 , wherein the fluid inlet corresponds with a first corner of the array of wells and the fluid outlet corresponds with a second corner of the array of wells. 
     
     
         30 . The apparatus of  claim 24 , wherein the cover further comprises flow disruptors extending into the flow volume. 
     
     
         31 . The apparatus of  claim 24 , wherein a width of the flow volume is smaller at a first position in proximity to the fluid inlet than at a second position further from the fluid inlet than the first position. 
     
     
         32 . The apparatus of  claim 31 , wherein a width of the flow volume is smaller at a third position in proximity to the fluid outlet than at the second position. 
     
     
         33 . A system comprising:
 a fluidic system including a fluid source;   a computational system; and   an apparatus comprising:
 a substrate including an array of sensors; 
 an array of wells disposed over the substrate, a well of the array of wells corresponding to a sensor of the array of sensors; and 
 a cover disposed over the array of wells and defining a flow volume between the array of wells and the cover, the cover defining a fluid inlet and a fluid outlet in fluid communication with the flow volume, the flow volume at a diffuser including a non-flat wall defining a curved boundary of the flow volume, the non-flat wall being the top or the bottom wall, the fluid flow at the diffuser being more restricted in the center of the flow volume than at the edges of the flow volume when viewed in cross-section perpendicular to the fluid flow. 
   
     
     
         34 . The system of  claim 33 , wherein the non-flat wall defines a top boundary of the flow volume. 
     
     
         35 . The system of  claim 33 , wherein the sensor is a field effect transistor. 
     
     
         36 . The system of  claim 35 , wherein the field effect transistor is an ion sensitive field effect transistor. 
     
     
         37 . The system of  claim 33 , wherein the fluid inlet corresponds with a first corner of the array of wells and the fluid outlet corresponds with a second corner of the array of wells. 
     
     
         38 . The system of  claim 33 , wherein the cover further comprises flow disruptors extending into the flow volume. 
     
     
         39 . The system of  claim 33 , wherein a width of the flow volume is smaller at a first position in proximity to the fluid inlet than at a second position further from the fluid inlet than the first position. 
     
     
         40 . The system of  claim 39 , wherein a width of the flow volume is smaller at a third position in proximity to the fluid outlet than at the second position. 
     
     
         41 . A method of sequencing a nucleic acid, the method comprising:
 flowing a reagent solution into a fluid inlet of an apparatus, the apparatus comprising:
 a substrate including an array of sensors; 
 an array of wells disposed over the substrate, a well of the array of wells corresponding to a sensor of the array of sensors; and 
 a cover disposed over the array of wells and defining a flow volume between the array of wells and the cover, the cover defining a fluid inlet and a fluid outlet in fluid communication with the flow volume, the flow volume at a diffuser including a non-flat wall defining a curved boundary of the flow volume, the non-flat wall being the top or the bottom wall, the fluid flow at the diffuser being more restricted in the center of the flow volume than at the edges of the flow volume when viewed in cross-section perpendicular to the fluid flow; and 
   measuring a signal from the sensor of the array of sensors.   
     
     
         42 . The method of  claim 41 , wherein a nucleic acid is disposed within the well and the reagent solution includes a nucleotide, wherein measuring the signal includes measuring with the sensor a byproduct released in response to incorporation of the nucleotide. 
     
     
         43 . The method of  claim 41 , wherein a width of the flow volume is smaller at a first position in proximity to the fluid inlet than at a second position further from the fluid inlet than the first position.