METHODS AND APPARATUS FOR MEASURING ANALYTES USING LARGE SCALE FET ARRAYS

• US 20100197507A1
• Filed: 03/10/2010
• Published: 08/05/2010
• Est. Priority Date: 12/14/2006
• Status: Active Grant

• Current Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Original Assignee: ION Torrent Systems Incorporated (Thermo Fisher Scientific Incorporated)
• Inventors: Rothberg, Jonathan M., Hinz, Wolfgang, Johnson, Kim L., Bustillo, James
• Granted Patent: US 8,306,757 B2
• Time in Patent Office: Days
• US Class Current: 506/2
• 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

1-106. -106. (canceled)

107. A method for sequencing a plurality of template nucleic acids, the method comprising the steps of:

(a) disposing a plurality of template nucleic acids into a plurality of reaction chambers disposed on a sensor array formed in a semiconductor substrate and comprised of a plurality of sensors, each reaction chamber being disposed on at least one sensor and each sensor of the array comprising a field-effect transistor configured to provide at least one output signal representative of a sequencing reaction byproduct proximate thereto, such output signal being substantially the same for each sensor of the array in response to the same amount of sequencing reaction byproduct proximate thereto, wherein each of the template nucleic acids is hybridized to a sequencing primer and is bound to a polymerase;

(b) introducing a known nucleotide triphosphate into the reaction chambers;

(c) detecting incorporation at a 3′

end of the sequencing primer of one or more nucleotide triphosphates by a sequencing reaction byproduct if such one or more nucleotide triphosphates are complementary to corresponding nucleotides in the template nucleic acid;

(d) washing unincorporated nucleotide triphosphates from the reaction chambers; and

(e) repeating steps (b) through (d) until the plurality of template nucleic acids are sequenced.

108. The method of claim 107 wherein said sequencing reaction byproduct is hydrogen ion concentration and wherein each of said reaction chambers provides weak buffer conditions.

109. The method of claim 108 wherein said sensors of said array each occupy an area of 100 μ

m or less and have a pitch of 10 μ

m or less and wherein each of said reaction chambers has a volume in the range of from 1 μ

m³ to 1500 μ

m³.

110. The method of claim 109 wherein said step of detecting includes measuring a change in said hydrogen ion concentration within each of said reaction chambers and wherein each of said reaction chambers contains at least 10⁵ copies of one of said template nucleic acids.

111. The method of claim 110 wherein said nucleic acid templates are attached to a solid support.

112. The method of claim 109 wherein said plurality of said reaction chambers and said plurality of said sensors are each greater than 256,000.