Methods and apparatus for detecting molecular interactions using FET arrays

• US 8,540,868 B2
• Filed: 09/09/2011
• Issued: 09/24/2013
• 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, Hinz, Wolfgang
• Primary Examiner(s): Ball, J. Chrisopher
• Application Number:
  US13/229,456
• Publication Number:
  US 20120065093A1
• Time in Patent Office: 746 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, 204/403.01, 204/416, 204/433
• US Class Current: 205/793.5
• CPC Class Codes: C12Q 1/6825 Nucleic acid detection involving sensors
• 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: G01N 27/26 by investigating electrochemical variables; by using electrolysis or electrophoresis
• 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 33/6818 Sequencing of polypeptides
• 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 29/788 with floating gate H01L29/78391 takes precedence
• CPC Class Codes: H01L 2924/01006 Carbon [C]

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.

Claims

1. A method of evaluating responsiveness of a subject to a therapeutic regimen, the method comprising:

assaying at least one biological sample obtained from the subject for a nucleotide sequence of interest that is associated with responsiveness to the therapeutic regimen, comprising;

providing a sample analyzer comprising a plurality of chemical-sensitive field effect transistors (chemFETs), the chemFETs having a gate oxide, a floating gate comprising conductors formed in a plurality of conductor layers and electrically coupled to one another, and a passivation layer overlying the floating gate, the sample analyzer further comprising signal lines for the sensors within at least one of the conductor layers;

disposing at least one interrogating nucleic acid in proximity to or in contact with 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 associated with the biological sample in proximity to or in contact with 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 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; and

generating an evaluation of responsiveness of the subject to the therapeutic agent on the basis of the hybridization interactions for the at least one biological sample.

2. The method of claim 1, wherein the presence of the nucleotide sequence of interest in the at least one biological sample obtained from the subject provides a prediction that the subject will not respond to the therapeutic regimen.

3. The method of claim 1, wherein the presence of the nucleotide sequence of interest in the at least one biological sample obtained from the subject provides a prediction that the subject will respond to the therapeutic regimen.

4. The method of claim 1, wherein the absence of the nucleotide sequence of interest in the at least one biological sample obtained from the subject provides a prediction that the subject will not respond to the therapeutic regimen.

5. The method of claim 1, wherein the absence of the nucleotide sequence of interest in the at least one biological sample obtained from the subject provides a prediction that the subject will respond to the therapeutic regimen.

6. The method of claim 1, wherein at least one of the interrogating nucleic acid or the target nucleic acid is immobilized, bound to, or coupled with the chemFETs.

7. The method of claim 1, wherein the at least one the interrogating nucleic acid or the target nucleic acid is bound to or coupled with the passivation layer.

8. The method of claim 1, wherein the changes in electrical properties of the chemFETs comprise changes in voltage or current.

9. The method of claim 1, wherein the at least one interrogating nucleic acid and the at least one target nucleic acid are unlabeled or unmodified.

10. The method of claim 1, wherein the floating gate of each chemFET has substantially zero trapped charge, thereby reducing variations in sensitivity between the chemFETs.

11. An apparatus for predicting responsiveness of a subject to a therapeutic regimen, the apparatus comprising:

an assembly for assaying a biological sample obtained from the subject for a nucleotide sequence of interest that is associated with responsiveness to the therapeutic regimen, comprising;

a chemical-sensitive field effect transistor (chemFET) array comprising a plurality of chemFET sensors and further comprising at least one target nucleic acid sample or at least one interrogating nucleic acid disposed thereon or associated therewith, the chemFET sensors having a gate-oxide, a floating gate comprising conductors formed in a plurality of conductor layers and electrically coupled to one another, and a passivation layer overlying the floating gate, the sample analyzer further comprising signal lines for the sensors within at least one of the conductor layers;

a fluidics assembly comprising;

a reaction assembly for contacting the chemFET array with the at least one target nucleotide sample when the at least one interrogating nucleic acid is disposed on or associated with the chemFET array or an assembly for contacting the chemFET array with the at least one interrogating nucleic acid when the at least one target nucleotide sample is disposed on or associated therewith the chemFET array;

a washing assembly for removing at least a portion of unbound interrogating nucleic acid or target nucleic acid sample from the chemFET array; and

a detection system for detecting an electrical output from the chemFET array, wherein the electrical output is indicative of a binding interaction between the at least one target nucleic acid and the at least one interrogating nucleic acid; and

an analysis system for generating an evaluation of responsiveness of the subject to the therapeutic agent on the basis of the hybridization interactions for the at least one biological sample.

12. The apparatus of claim 11, wherein the presence of the nucleotide sequence of interest in the at least one biological sample obtained from the subject provides a prediction that the subject will not respond to the therapeutic regimen.

13. The apparatus of claim 11, wherein the presence of the nucleotide sequence of interest in the at least one biological sample obtained from the subject provides a prediction that the subject will respond to the therapeutic regimen.

14. The apparatus of claim 11, wherein the absence of the nucleotide sequence of interest in the at least one biological sample obtained from the subject provides a prediction that the subject will not respond to the therapeutic regimen.

15. The apparatus of claim 11, wherein the absence of the nucleotide sequence of interest in the at least one biological sample obtained from the subject provides a prediction that the subject will respond to the therapeutic regimen.

16. The apparatus of claim 11, wherein at least one of the interrogating nucleic acid or the target nucleic acid is immobilized, bound to, or coupled with the chemFETs of the chemFET array.

17. The apparatus of claim 11, wherein the at least one the interrogating nucleic acid or the target nucleic acid is bound to or coupled with the passivation layer.

18. The apparatus of claim 11, wherein the changes in electrical properties of the chemFETs comprise changes in voltage or current.

19. The apparatus of claim 11, wherein the at least one interrogating nucleic acid and the at least one target nucleic acid are unlabeled or unmodified.

20. The apparatus of claim 11, wherein the floating gate of each chemFET has substantially zero trapped charge, thereby reducing variations in sensitivity between the chemFETs.