Methods and apparatus for measuring analytes using large scale FET arrays

• US 7,948,015 B2
• Filed: 12/14/2007
• Issued: 05/24/2011
• Est. Priority Date: 12/14/2006
• Status: Active Grant

• Current Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Original Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Inventors: Hinz, Wolfgang, Johnson, Kim L., Bustillo, James, Rothberg, Jonathan M.
• Primary Examiner(s): Le; Thao X
• Assistant Examiner(s): GORDON, MATTHEW E
• Application Number:
  US12/002,291
• Publication Number:
  US 20090127589A1
• Time in Patent Office: 1,257 Days
• Field of Search: 257/253, 257/E23.08, 438/10
• US Class Current: 257/253
• CPC Class Codes: C12Q 1/6818 involving interaction of two or more labels, e.g. resonant energy transfer
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2533/101 Primer extension
• CPC Class Codes: C12Q 2565/301 Pyrophosphate (PPi)
• CPC Class Codes: C12Q 2565/607 being a sensor, e.g. electrode
• CPC Class Codes: G01N 27/4145 specially adapted for biomolecules, e.g. gate electrode with immobilised receptors
• CPC Class Codes: G01N 27/4148 Integrated circuits therefor, e.g. fabricated by CMOS processing CMOS processing per se H01L21/82
• CPC Class Codes: G01N 33/54373 involving physiochemical end-point determination, e.g. wave-guides, FETS, gratings
• CPC Class Codes: G01N 33/5438 Electrodes
• CPC Class Codes: H01L 27/088 the components being field-effect transistors with insulated gate
• CPC Class Codes: H01L 29/42324 Gate electrodes for transistors with a floating gate
• CPC Class Codes: H01L 29/78 with field effect produced by an insulated gate H01L29/7725, H01L29/775, H01L29/778 take precedence
• CPC Class Codes: H01L 2924/01006 Carbon [C]
• CPC Class Codes: H01L 2924/01013 Aluminum [Al]
• CPC Class Codes: H01L 2924/01015 Phosphorus [P]
• CPC Class Codes: H01L 2924/01073 Tantalum [Ta]
• CPC Class Codes: H01L 2924/14 Integrated circuits
• CPC Class Codes: H01L 2924/1433 Application-specific integrated circuit [ASIC]
• CPC Class Codes: Y10T 436/22 Hydrogen, per se

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.

Claims

1. An integrated circuit chip for determining byproducts of a plurality of extension reactions, the integrated circuit chip comprising:

a sensor array of at least 10⁵ sensors formed in a semiconductor substrate, each sensor of the array comprising a field-effect transistor having a threshold voltage and a floating gate with an analyte-sensitive passivation layer, the threshold voltage depending substantially on the analyte-sensitive passivation layer and trapped charge at the floating gate wherein the field-effect transistor is configured to provide at least one output signal dependent on the threshold voltage, and wherein the trapped charge of each floating gate is such that the threshold voltage is substantially the same for each sensor in response to the same amount of extension reaction byproduct proximate thereto;

a plurality of microwells disposed on the semiconductor substrate, each microwell capable of containing a separate extension reaction and being disposed on at least one sensor; and

control circuitry in the semiconductor substrate coupled to the sensor array to receive samples of the output signals from said field effect transistors at a rate of at least twenty frames per second so that the amounts of extension reaction byproducts are determined in each microwell by the output signal produced therefrom.

2. The integrated circuit chip of claim 1 wherein each of said sensors occupies an area on said semiconductor substrate of approximately ten micrometers by ten micrometers or less.

3. The integrated circuit chip of claim 2 wherein said sensors of said sensor array have a pitch of 10 μ

m or less.

4. The integrated circuit chip of claim 3 wherein said byproduct is hydrogen ion concentration.

5. The integrated circuit chip of claim 4 wherein said output signal of each of said sensors represents changes in said hydrogen ion concentration within a range of from pH 7 to pH 9.

6. The integrated circuit chip of claim 3 wherein said sensors of said sensor array are arranged in rows and columns and wherein said control circuitry successively receives samples of output signals from sensors from multiple columns of a previously selected row during a bus settling time of a successively selected row.

7. The integrated circuit chip of claim 3 wherein each of said microwells has a volume in the range of from 1 μ

m³ to 1500 μ

m³.

8. The integrated circuit chip of claim 3 wherein said control circuitry further comprises analog-to-digital circuitry for converting samples of said output signal to digital outputs.

9. The integrated circuit chip of claim 3 wherein said output signal is a voltage signal measured in reference to a voltage of a reference electrode.

10. An integrated circuit chip for determining byproducts of a plurality of extension reactions, the integrated circuit chip comprising:

a sensor array formed in a semiconductor substrate, each sensor of the array comprising a field-effect transistor having a floating gate and a threshold voltage, the threshold voltage depending on trapped charge of the floating gate, wherein the field-effect transistor is configured to provide at least one output signal dependent on the threshold voltage, and wherein the trapped charge of each floating gate is reduced so that the threshold voltage is substantially the same for each sensor in response to the same amount of extension reaction byproduct proximate thereto;

a plurality of microwells disposed on the semiconductor substrate, each microwell capable of containing a separate extension reaction and being disposed on at least one sensor; and

control circuitry in the semiconductor substrate coupled to the sensor array to receive samples of the output signals from said field effect transistors at a rate of at least one frame per second so that the amounts of extension reaction byproducts are determined in each microwell by the output signal produced therefrom, wherein said sensors of said sensor array are arranged in rows and columns and wherein said control circuitry successively receives samples of Output signals from sensors from multiple columns of a previously selected row during a bus settling time of a successively selected row, wherein said sensor array has at least 10³ of said sensors.

11. The integrated circuit chip of claim 10 wherein each of said sensors occupies an area on said semiconductor substrate of approximately ten micrometers by ten micrometers or less.

12. The integrated circuit chip of claim 11 wherein said sensors of said sensor array have a pitch of 10 μ

m or less.

13. The integrated circuit chip of claim 12 wherein said byproduct is hydrogen ion concentration.

14. The integrated circuit chip of claim 13 wherein said output signal of each of said sensors represents changes in said hydrogen ion concentration within a range of from at least pH 7 to pH 9.

15. The integrated circuit chip of claim 12 wherein each of said microwells has a volume in the range of from 1 μ

m³ to 1500 μ

³.

16. The integrated circuit chip of claim 12 wherein said control circuitry further comprises analog-to-digital circuitry for converting samples of said output signal to digital outputs.

17. The integrated circuit chip of claim 12 wherein said output signal is a voltage signal measured in reference to a voltage of a reference electrode.