Methods and apparatus for measuring analytes using large scale FET arrays

• US 8,262,900 B2
• Filed: 12/17/2007
• Issued: 09/11/2012
• 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: Rothberg, Jonathan M., Hinz, Wolfgang
• Primary Examiner(s): Ball, J. Christopher
• Application Number:
  US12/002,781
• Publication Number:
  US 20090026082A1
• Time in Patent Office: 1,730 Days
• Field of Search: 257/253, 205/789, 205/792, 205/793.5, 422 8201- 8203, 435/6, 435/285.1, 435/287.1, 435/287.2, 436103-105, 436/150, 436/182, 506/1, 506/9
• US Class Current: 205/793.5
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• 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 27/414 Ion-sensitive or chemical field-effect transistors, i.e. ISFETS or CHEMFETS
• 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: H01L 21/306 Chemical or electrical treatment, e.g. electrolytic etching to form insulating layers H01L21/31
• CPC Class Codes: H01L 2224/04105 Bonding areas formed on an encapsulation of the semiconductor or solid-state body, e.g. bonding areas on chip-scale packages
• CPC Class Codes: H01L 2224/16 of an individual bump connector
• CPC Class Codes: H01L 2224/76155 Jetting means, e.g. ink jet
• CPC Class Codes: H01L 2224/82102 using jetting, e.g. ink jet
• CPC Class Codes: H01L 24/18 High density interconnect [HDI] connectors; Manufacturing methods related thereto interconnection structure between a plurality of semiconductor chips H01L23/5389
• CPC Class Codes: H01L 24/20 Structure, shape, material or disposition of high density interconnect preforms
• CPC Class Codes: H01L 24/82 by forming build-up interconnects at chip-level, e.g. for high density interconnects [HDI] interconnection structure between a plurality of semiconductor chips H01L23/5389
• CPC Class Codes: H01L 27/088 the components being field-effect transistors with insulated 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 2924/00 Indexing scheme for arrangements or methods for connecting or disconnecting semiconductor or solid-state bodies as covered by H01L24/00
• CPC Class Codes: H01L 2924/01005 Boron [B]
• CPC Class Codes: H01L 2924/01006 : Carbon [C]
• CPC Class Codes: H01L 2924/01011 : Sodium [Na]
• CPC Class Codes: H01L 2924/01012 : Magnesium [Mg]
• CPC Class Codes: H01L 2924/01013 : Aluminum [Al]
• CPC Class Codes: H01L 2924/01015 : Phosphorus [P]
• CPC Class Codes: H01L 2924/01019 : Potassium [K]
• CPC Class Codes: H01L 2924/0102 : Calcium [Ca]
• CPC Class Codes: H01L 2924/01023 : Vanadium [V]
• CPC Class Codes: H01L 2924/01024 : Chromium [Cr]
• CPC Class Codes: H01L 2924/01027 : Cobalt [Co]
• CPC Class Codes: H01L 2924/01029 : Copper [Cu]
• CPC Class Codes: H01L 2924/0103 : Zinc [Zn]
• CPC Class Codes: H01L 2924/01033 : Arsenic [As]
• CPC Class Codes: H01L 2924/01046 : Palladium [Pd]
• CPC Class Codes: H01L 2924/01047 : Silver [Ag]
• CPC Class Codes: H01L 2924/01052 : Tellurium [Te]
• CPC Class Codes: H01L 2924/01056 : Barium [Ba]
• CPC Class Codes: H01L 2924/01059 : Praseodymium [Pr]
• CPC Class Codes: H01L 2924/01073 : Tantalum [Ta]
• CPC Class Codes: H01L 2924/01074 : Tungsten [W]
• CPC Class Codes: H01L 2924/01075 : Rhenium [Re]
• CPC Class Codes: H01L 2924/01082 : Lead [Pb]
• CPC Class Codes: H01L 2924/1306 : Field-effect transistor [FET]
• CPC Class Codes: H01L 2924/13091 : Metal-Oxide-Semiconductor Field-Effect Transistor [MOSFET]
• CPC Class Codes: H01L 2924/14 : Integrated circuits
• CPC Class Codes: H01L 2924/1433 : Application-specific integrated circuit [ASIC]
• CPC Class Codes: H01L 2924/19041 : being a capacitor
• CPC Class Codes: H01L 2924/19042 : being an inductor
• CPC Class Codes: H01L 2924/19043 : being a resistor
• CPC Class Codes: H01L 2924/30105 : Capacitance
• CPC Class Codes: H01L 2924/3011 : Impedance
• CPC Class Codes: H01L 2924/3025 : Electromagnetic shielding

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. A method for sequencing a nucleic acid, comprising:

disposing a plurality of template nucleic acids into each of a plurality of reaction chambers, at least one reaction chamber of the plurality of reaction chambers coupled to at least one chemical-sensitive field effect transistor (chemFET) having a floating gate;

synthesizing a new nucleic acid strand from at least one template nucleic acid disposed in the at least one reaction chamber by incorporating one or more known nucleotide triphosphates sequentially from an end of a sequencing primer hybridized to the at least one template nucleic acid, synthesizing the new nucleic acid strand performed at least in part in the presence of a polymerase; and

detecting incorporation of the one or more known nucleotide triphosphates by a change in current in the at least one chemFET having the floating gate.

2. The method of claim 1, wherein the change in current is indicative of incorporation of at least one nucleotide triphosphate.

3. The method of claim 1, wherein the change in current is indicative of incorporation of a plurality of identical nucleotide triphosphates.

4. The method of claim 1, wherein the plurality of template nucleic acids are bound to a bead, and at least one bead is disposed into each of the plurality of reaction chambers.

5. The method of claim 1, wherein the synthesizing step is performed from a 3′

end of the sequencing primer.

6. The method of claim 1, wherein the plurality of reaction chambers includes at least 10⁵ reaction chambers.

7. The method of claim 1, further comprising synthesizing a plurality of new nucleic acid strands from a corresponding plurality of template nucleic acids disposed in the at least one reaction chamber.

8. The method of claim 1, wherein the floating gate of the at least one chemFET is coupled to the at least one reaction chamber via a passivation layer sensitive to hydrogen ions.

9. The method of claim 1, wherein the change in the current is due to a change in threshold voltage of the at least one chemFET resulting from the incorporation of the one or more known nucleotide triphosphates.

10. A method for sequencing a nucleic acid, comprising:

disposing a plurality of template nucleic acids into each of a plurality of reaction chambers, at least one reaction chamber of the plurality of reaction chambers coupled to at least one chemical-sensitive field effect transistor (chemFET) having a floating gate;

synthesizing a new nucleic acid strand from at least one template nucleic acid disposed in the at least one reaction chamber by incorporating one or more known nucleotide triphosphates sequentially from an end of a sequencing primer hybridized to the at least one template nucleic acid, synthesizing the new nucleic acid strand performed at least in part in the presence of a polymerase; and

detecting incorporation of the one or more known nucleotide triphosphates by a change in current in the at least one chemFET having the floating gate, wherein a center-to-center distance between adjacent reaction chambers is selected from a range of about 1 μ

m to about 10 μ

m.

11. The method of claim 10, wherein the plurality of reaction chambers includes at least 10⁵ reaction chambers.

12. The method of claim 10, wherein the floating gate of the at least one chemFET is coupled to the at least one reaction chamber via a passivation layer sensitive to hydrogen ions.

13. The method of claim 10, wherein the change in the current is due to a change in threshold voltage of the at least one chemFET resulting from the incorporation of the one or more known nucleotide triphosphates.

14. A method for sequencing a nucleic acid, comprising:

disposing a plurality of template nucleic acids into each of a plurality of reaction chambers, at least one reaction chamber of the plurality of reaction chambers coupled to at least one chemical-sensitive field effect transistor (chemFET) having a floating gate;

synthesizing a new nucleic acid strand from at least one template nucleic acid disposed in the at least one reaction chamber by incorporating one or more known nucleotide triphosphates sequentially from an end of a sequencing primer hybridized to the at least one template nucleic acid, synthesizing the new nucleic acid strand performed at least in part in the presence of a polymerase; and

detecting a change in the level of a sequencing byproduct as an indicator of an incorporation of the one or more known nucleotide triphosphates.

15. The method of claim 14, wherein the sequencing byproduct is an inorganic pyrophosphate (PPi).

16. The method of claim 15, wherein the PPi is bound to a PPi receptor in the at least one reaction chamber.

17. The method of claim 14, wherein the plurality of reaction chambers includes at least 10⁵ reaction chambers.

18. The method of claim 14, wherein the floating gate of the at least one chemFET is coupled to the at least one reaction chamber via a passivation layer sensitive to hydrogen ions.

19. The method of claim 14, wherein detecting the change in the level of the sequencing byproduct comprises detecting a threshold voltage of the at least one chemFET.