# US 8,540,867 B2 · Methods and apparatus for detecting molecular interactions using FET arrays

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- Number: US 8,540,867 B2
- Document ID: US8540867B2
- Status: Granted
- Kind: B2
- Application number: 13/229,439
- Filed: 2011-09-09
- Published: 2012-03-15
- Granted: 2013-09-24
- Earliest claimed: 2006-12-14
- Assignees: Life Technologies Corporation
- Applicants: Jonathan Rothberg; Wolfgang Hinz
- Inventors: Jonathan Rothberg; Wolfgang Hinz
- Web page: https://patentgrep.com/patent/US8540867B2

## CPC

- C12Q 1/6825: Nucleic acid detection involving sensors
- C12Q 1/6874: involving nucleic acid arrays, e.g. sequencing by hybridisation
- G01N 27/26: by investigating electrochemical variables; by using electrolysis or electrophoresis
- G01N 27/4145: {specially adapted for biomolecules, e.g. gate electrode with immobilised receptors}
- G01N 27/4148: {Integrated circuits therefor, e.g. fabricated by CMOS processing}
- G01N 33/54373: {involving physiochemical end-point determination, e.g. wave-guides, FETS, gratings}
- G01N 33/6818: {Sequencing of polypeptides}
- H10D 30/60: Insulated-gate field-effect transistors [IGFET] (H10D30/40 takes precedence)
- H10D 30/68: Floating-gate IGFETs
- C12Q 1/6869: Methods for sequencing
- C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q)
- H10D: INORGANIC ELECTRIC SEMICONDUCTOR DEVICES

## 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

### Claim 1

A method for detecting at least one target nucleic acid of interest in a sample, the method comprising:
providing a sample analyzer comprising an array of 105 sensors formed in a substrate, the sensors comprising a field-effect transistor including 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 sensors of the array 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 in proximity to or in contact with at least a portion of the sensors of the array 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 sensors of the array; 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 sensors of the array.

### Claim 2 (depends on 1)

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 at least a portion of the sensors of the array.

### Claim 3 (depends on 1)

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.

### Claim 4 (depends on 1)

The method of claim 1, wherein the changes in electrical properties of the at least a portion of the sensors of the array comprise changes in voltage or current.

### Claim 5 (depends on 1)

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.

### Claim 6 (depends on 1)

The method of claim 1, wherein the floating gate of each sensor of the array has substantially zero trapped charge, thereby reducing variations in sensitivity between the sensors of the array.

### Claim 7

A method of detecting nucleic acid sequence variations, said method comprising:
providing a sample analyzer comprising an array of at least 105 sensors found in a substrate, the sensors comprising a field-effect transistor 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 sensors of the array wherein the at least one interrogating nucleic acid is at least partially complimentary to the at least one target nucleic acid of interest and wherein the at least one interrogating nucleic acid comprises a sequence corresponding to a nucleic acid variation or mutation at least one predetermined position;
disposing at least one target nucleic acid of interest in proximity to or in contact with at least a portion of the sensors of the array 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 sensors of the array; and
identifying the presence of a nucleic acid variation or mutation associated with the at least one target nucleic acid on the basis of 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 sensors of the array.

### Claim 8 (depends on 7)

The method of claim 7, wherein at least one of the interrogating nucleic acid or the target nucleic acid is immobilized, bound to, or coupled with at least a portion of the sensors of the array.

### Claim 9 (depends on 7)

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

### Claim 10 (depends on 7)

The method of claim 7, wherein the changes in electrical properties of the sensors of the array comprise changes in voltage or current.

### Claim 11 (depends on 7)

The method of claim 7, wherein the at least one interrogating nucleic acid and the at least one target nucleic acid are unlabeled or unmodified.

### Claim 12 (depends on 7)

The method of claim 7, wherein the floating gate of each sensor of the array has substantially zero trapped charge, thereby reducing variations in sensitivity between the chemFETs.

### Claim 13

A method for determining expression levels of at least one target nucleic acid of interest in a sample, the method 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 capture agent in proximity to or in contact with at least a portion of the chemFETs wherein the at least one capture agent is reactive or sensitive to at least one target nucleic acid of interest;
disposing the at least one target nucleic acid of interest in proximity to or in contact with at least a portion of the chemFETs wherein interactions between the at least one capture agent and the at least one target nucleic acid effectuate changes in at least one electrical property of at least a portion of the chemFETs;
identifying interactions between the at least one capture agent and the at least one target nucleic acid by detecting the changes in electrical properties of at least a portion of the chemFETs; and
identifying chemFETs whose electrical properties change in response to the interactions to determine the expression level of the at least one target nucleic acid of interest.

### Claim 14 (depends on 13)

The method of claim 13, wherein at least one of the capture agent or the target nucleic acid is immobilized, bound to, or coupled with the chemFETs.

### Claim 15 (depends on 13)

The method of claim 13, wherein the at least one the capture agent or the target nucleic acid is bound to or coupled with the passivation layer.

### Claim 16 (depends on 13)

The method of claim 13, wherein the changes in electrical properties of the chemFETs comprise changes in voltage or current.

### Claim 17 (depends on 13)

The method of claim 13, wherein the at least one capture agent and the at least one target nucleic acid are unlabeled or unmodified.

### Claim 18 (depends on 13)

The method of claim 13, wherein the floating gate of each chemFET has substantially zero trapped charge, thereby reducing variations in sensitivity between the chemFETs.