Chemical sensor array having multiple sensors per well

Abstract

In one embodiment, a device is described. The device includes a material defining a reaction region. The device also includes a plurality of chemically-sensitive field effect transistors have a common floating gate in communication with the reaction region. The device also includes a circuit to obtain respective output signals from the chemically-sensitive field effect transistors indicating an analyte within the reaction region.

Description

BACKGROUND

The present disclosure relates to sensors for chemical analysis, and to methods for manufacturing such sensors.

A variety of types of chemical sensors have been used in the detection of chemical processes. One type is a chemically-sensitive field effect transistor (chemFET). A chemFET includes a source and a drain separated by a channel region, and a chemically sensitive area coupled to the channel region. The operation of the chemFET is based on the modulation of channel conductance, caused by changes in charge at the sensitive area due to a chemical reaction occurring nearby. The modulation of the channel conductance changes the threshold voltage of the chemFET, which can be measured to detect and/or determine characteristics of the chemical reaction. The threshold voltage may for example be measured by applying appropriate bias voltages to the source and drain, and measuring a resulting current flowing through the chemFET. As another example, the threshold voltage may be measured by driving a known current through the chemFET, and measuring a resulting voltage at the source or drain.

An ion-sensitive field effect transistor (ISFET) is a type of chemFET that includes an ion-sensitive layer at the sensitive area. The presence of ions in an analyte solution alters the surface potential at the interface between the ion-sensitive layer and the analyte solution, due to the protonation or deprotonation of surface charge groups caused by the ions present in the analyte solution. The change in surface potential at the sensitive area of the ISFET affects the threshold voltage of the device, which can be measured to indicate the presence and/or concentration of ions within the solution.

Arrays of ISFETs may be used for monitoring chemical reactions, such as DNA sequencing reactions, based on the detection of ions present, generated, or used during the reactions. See, for example, U.S. Pat. No. 7,948,015 to Rothberg et al., which is incorporated by reference herein. More generally, large arrays of chemFETs or other types of chemical sensors may be employed to detect and measure static and/or dynamic amounts or concentrations of a variety of analytes (e.g. hydrogen ions, other ions, compounds, etc.) in a variety of processes. The processes may for example be biological or chemical reactions, cell or tissue cultures or monitoring neural activity, nucleic acid sequencing, etc.

An issue that arises in the operation of large scale chemical sensor arrays is the susceptibility of the sensor output signals to noise. Specifically, the noise affects the accuracy of the downstream signal processing used to determine the characteristics of the chemical and/or biological process being detected by the sensors.

It is therefore desirable to provide devices including low noise chemical sensors, and methods for manufacturing such devices.

SUMMARY

In one embodiment, a device is described. The device includes a material defining a reaction region. The device also includes a plurality of chemically-sensitive field effect transistors have a common floating gate in communication with the reaction region. The device also includes a circuit to obtain individual output signals from the chemically-sensitive field effect transistors indicating an analyte within the reaction region.

In another embodiment, a method for manufacturing a device is described. The method includes forming a material defining a reaction region. The method further includes forming a plurality of chemically-sensitive field effect transistors having a common floating gate in communication with the reaction region. The method further includes forming a circuit to obtain individual output signals from the chemically-sensitive field effect transistors indicating an analyte within the reaction region.

Particular aspects of one more implementations of the subject matter described in this specification are set forth in the drawings and the description below. Other features, aspects, and advantages of the subject matter will become apparent from the description, the drawings, and the claims.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 illustrates a block diagram of components of a system for nucleic acid sequencing.

FIG. 2 illustrates cross-sectional and expanded views of a portion of an integrated circuit device and flow cell.

FIG. 3 illustrates a schematic diagram of a portion of the integrated circuit device 100 including a sensor array having multiple chemical sensors coupled to the same reaction region.

FIG. 4 is a flow chart of an example process for calculating a resultant output signal for a group of chemical sensors coupled to a single reaction region.

FIG. 5 illustrates a cross-sectional view of portions of two groups of chemical sensors and their corresponding reaction regions according to a first embodiment.

FIGS. 6 to 10 illustrate stages in a manufacturing process for forming a device including multiple chemical sensors coupled to the same reaction region according to a first embodiment.

FIG. 11 illustrates a cross-sectional view of portions of two groups of chemical sensors and their corresponding reaction regions according to a second embodiment.

FIGS. 12 to 14 illustrate stages in a manufacturing process for forming a device including multiple chemical sensors coupled to the same reaction region according to a second embodiment.

FIGS. 15 to 18 illustrate stages in a manufacturing process for forming a device including multiple chemical sensors coupled to the same reaction region according to a third embodiment.

FIGS. 19 to 21 illustrate stages in a manufacturing process for forming a device including multiple chemical sensors coupled to the same reaction region according to a fourth embodiment.

DETAILED DESCRIPTION

A chemical detection device is described that includes multiple chemical sensors for concurrently detecting a chemical reaction within the same, operationally associated reaction region. The multiple sensors can provide redundancy, as well as improved accuracy in detecting characteristics of the chemical reaction.

By utilizing multiple chemical sensors to separately detect the same chemical reaction, the individual output signals can be combined or otherwise processed to produce a resultant, low noise output signal. For example, the individual output signals can be averaged, such that the signal-to-noise ratio (SNR) of the resultant output signal is increased by as much as the square root of the number of individual output signals. In addition, the resultant output signal can compensate for differences among the values of the individual output signals, caused by variations in chemical sensor performance which could otherwise complicate the downstream signal processing. As a result of the techniques described herein, low-noise chemical sensor output signals can be provided, such that the characteristics of reactions can be accurately detected.

FIG. 1 illustrates a block diagram of components of a system for nucleic acid sequencing according to an exemplary embodiment. The components include a flow cell 101 on an integrated circuit device 100, a reference electrode 108, a plurality of reagents 114 for sequencing, a valve block 116, a wash solution 110, a valve 112, a fluidics controller 118, lines 120/122/126, passages 104/109/111, a waste container 106, an array controller 124, and a user interface 128. The integrated circuit device 100 includes a microwell array 107 of reaction regions overlying groups of chemical sensors of a sensor array as described herein. The flow cell 101 includes an inlet 102, an outlet 103, and a flow chamber 105 defining a flow path of reagents over the microwell array 107.

The reference electrode 108 may be of any suitable type or shape, including a concentric cylinder with a fluid passage or a wire inserted into a lumen of passage 111. The reagents 114 may be driven through the fluid pathways, valves, and flow cell 101 by pumps, gas pressure, or other suitable methods, and may be discarded into the waste container 106 after exiting the outlet 103 of the flow cell 101. The fluidics controller 118 may control driving forces for the reagents 114 and the operation of valve 112 and valve block 116 with suitable software.

The microwell array 107 includes reaction regions, also referred to herein as microwells, which are operationally associated with chemical sensors of the sensor array. As described in more detail below, each reaction region is operationally associated with multiple chemical sensors suitable for detecting an analyte or reaction of interest within that reaction region. These multiple chemical sensors can provide redundancy, as well as improved detection accuracy. The microwell array 107 may be integrated in the integrated circuit device 100, so that the microwell array 107 and the sensor array are part of a single device or chip.

In exemplary embodiments described below, groups of four chemical sensors are coupled to each of the reaction regions. Alternatively, the number of chemical sensors operationally associated with a single reaction region may be different than four. More generally, two or more chemical sensors may be operationally associated with a single reaction region.

The flow cell 101 may have a variety of configurations for controlling the path and flow rate of reagents 114 over the microwell array 107. The array controller 124 provides bias voltages and timing and control signals to the integrated circuit device 100 for reading the chemical sensors of the sensor array as described herein. The array controller 124 also provides a reference bias voltage to the reference electrode 108 to bias the reagents 114 flowing over the microwell array 107.

During an experiment, the array controller 124 collects and processes individual output signals from the chemical sensors of the sensor array through output ports on the integrated circuit device 100 via bus 127. As described in more detail below, this processing can include calculating a resultant output signal for a group of sensors as a function of the individual output signals from the chemical sensors in the group. The array controller 124 may be a computer or other computing means. The array controller 124 may include memory for storage of data and software applications, a processor for accessing data and executing applications, and components that facilitate communication with the various components of the system in FIG. 1.

In the illustrated embodiment, the array controller 124 is external to the integrated circuit device 100. In some alternative embodiments, some or all of the functions performed by the array controller 124 are carried out by a controller or other data processor on the integrated circuit device 100. In yet other embodiments, a combination of resources internal and external to the integrated circuit device 100 is used to obtain the individual output signals and calculate the resultant output signal for a group of sensors using the techniques described herein.

The value of a resultant output signal for a group of chemical sensors indicates physical and/or chemical characteristics of one or more reactions taking place in the corresponding reaction region. For example, in an exemplary embodiment, the values of the resultant output signals may be further processed using the techniques disclosed in Rearick et al., U.S. patent application Ser. No. 13/339,846, filed Dec. 29, 2011, based on U.S. Prov. Pat. Appl. Nos. 61/428,743, filed Dec. 30, 2010, and 61/429,328, filed Jan. 3, 2011, and in Hubbell, U.S. patent application Ser. No. 13/339,753, filed Dec. 29, 2011, based on U.S. Prov. Pat. Appl. No 61/428,097, filed Dec. 29, 2010, each of which are incorporated by reference herein.

The user interface 128 may display information about the flow cell 101 and the output signals received from chemical sensors of the sensor array on the integrated circuit device 100. The user interface 128 may also display instrument settings and controls, and allow a user to enter or set instrument settings and controls.

The fluidics controller 118 may control delivery of the individual reagents 114 to the flow cell 101 and integrated circuit device 100 in a predetermined sequence, for predetermined durations, at predetermined flow rates. The array controller 124 can then collect and analyze the output signals of the chemical sensors indicating chemical reactions occurring in response to the delivery of the reagents 114.

During the experiment, the system may also monitor and control the temperature of the integrated circuit device 100, so that reactions take place and measurements are made at a known predetermined temperature.

The system may be configured to let a single fluid or reagent contact the reference electrode 108 throughout an entire multi-step reaction during operation. The valve 112 may be shut to prevent any wash solution 110 from flowing into passage 109 as the reagents 114 are flowing. Although the flow of wash solution may be stopped, there may still be uninterrupted fluid and electrical communication between the reference electrode 108, passage 109, and the microwell array 107. The distance between the reference electrode 108 and the junction between passages 109 and 111 may be selected so that little or no amount of the reagents flowing in passage 109 and possibly diffusing into passage 111 reach the reference electrode 108. In an exemplary embodiment, the wash solution 110 may be selected as being in continuous contact with the reference electrode 108, which may be especially useful for multi-step reactions using frequent wash steps.

FIG. 2 illustrates cross-sectional and expanded views of a portion of the integrated circuit device 100 and flow cell 101. The integrated circuit device 100 includes the microwell array 107 of reaction regions operationally associated with sensor array 205. During operation, the flow chamber 105 of the flow cell 101 confines a reagent flow 208 of delivered reagents across open ends of the reaction regions in the microwell array 107. The volume, shape, aspect ratio (such as base width-to-well depth ratio), and other dimensional characteristics of the reaction regions may be selected based on the nature of the reaction taking place, as well as the reagents, byproducts, or labeling techniques (if any) that are employed.

The chemical sensors of the sensor array 205 are responsive to (and generate output signals related to) chemical reactions within associated reaction regions in the microwell array 107 to detect an analyte of interest. The chemical sensors of the sensor array 205 may for example be chemically sensitive field-effect transistors (chemFETs), such as ion-sensitive field effect transistors (ISFETs). Examples of chemical sensors and array configurations that may be used in embodiments are described in U.S. Patent Application Publication No. 2010/0300559, No. 2010/0197507, No. 2010/0301398, No. 2010/0300895, No. 2010/0137143, and No. 2009/0026082, and U.S. Pat. No. 7,575,865, each which are incorporated by reference herein.

FIG. 3 illustrates a schematic diagram of a portion of the integrated circuit device 100 including sensor array 205 having multiple chemical sensors coupled to the same reaction region. In the illustrated embodiment, sixteen chemical sensors and four reaction regions are illustrated, representing a small section of the sensor array 205 and microwell array 107 that can include millions of chemical sensors and reaction regions.

The integrated circuit device 100 includes an access circuit for accessing the chemical sensors of the sensor array 205. In the illustrated example, the access circuit includes a row select circuit 310 coupled to the sensor array 205 via row lines 311-314. The access circuit also includes column output circuit 320 coupled to the sensor array 205 via column lines 321-328.

The row select circuit 310 and the column output circuit 320 are responsive to timing and control signals provided by the array controller 124 in FIG. 1 to select the various chemical sensors and operate the sensor array 205 as described below. The array controller 124 also provides a reference bias voltage to the reference electrode (See, FIG. 1, reference numeral 108) to bias the reagents flowing across open ends of the reaction regions 380, 382, 384, 386 of the microwell array 107 during operation.

In the illustrated embodiment, groups of four chemical sensors are operationally associated with each of the reaction regions 380, 382, 384, 386. Alternatively, the number of chemical sensors operationally associated with a single reaction region may be different than four. More generally, two or more chemical sensors may be operationally associated with a single reaction region. In some embodiments, the number of chemical sensors operationally associated with a single reaction region may be greater than four, such as sixteen or more.

The group containing chemical sensors 331.1-331.4 is representative of the groups of sensors of the sensor array 205. In the illustrated embodiment, each chemical sensor 331.1-331.4 includes a chemically-sensitive field effect transistor 341.1-341.5 and a row select switch 351.1-351.4.

The chemically-sensitive field effect transistors 341.1-341.4 have a common floating gate 370 in communication with the reaction region 380. That is, the common floating gate 370 is coupled to channels of each of the chemically-sensitive field effect transistors 341.1-341.5. The chemically-sensitive field effect transistors 341.1-341.5 may each include multiple patterned layers of conductive elements within layers of dielectric material.

The common floating gate 370 may for example include an uppermost conductive element (referred to herein as a sensor plate) that defines a surface (e.g. a bottom surface) of the reaction region 380. That is, there is no intervening deposited material layer between the uppermost electrical conductor and the surface of the reaction region 380. In some alternative embodiments, the uppermost conductive element of the common floating gate 370 is separated from the reaction region 380 by a deposited sensing material (discussed in more detail below).

In operation, reactants, wash solutions, and other reagents may move in and out of the reaction region 380 by a diffusion mechanism. The chemical sensors 331.1-331.4 are each responsive to (and generate individual output signals related to) chemical reactions within the reaction region 380 to detect an analyte or reaction property of interest. Changes in the charge within the reaction region 380 cause changes in the voltage on the common floating gate 370, which in turn changes the individual threshold voltages of each of the chemically-sensitive field effect transistors 341.1-341.4 of the sensors 331.1-331.4.

In a read operation of a selected chemical sensor 331.1, the row select circuit 310 facilitates providing a bias voltage to row line 311 sufficient to turn on row select transistor 351.1. Turning on the row select transistor 351.1 couples the drain terminal of the chemically-sensitive transistor 341.1 to the column line 321. The column output circuit 320 facilitates providing a bias voltage to the column line 321, and providing a bias current on the column line 321 that flows through the chemically-sensitive transistor 341.1. This in turn establishes a voltage at the source terminal of the chemically-sensitive transistor 341.1, which is coupled to the column line 322. In doing so, the voltage on the column line 322 is based on the threshold voltage of the chemically-sensitive transistor 341.1, and thus based on the amount of charge within the reaction region 380. Alternatively, other techniques may be used to read the selected chemical sensor 331.1.

The column output circuit 320 produces an individual output signal for the chemically-sensitive transistor 341.1 based on the voltage on the column line 322. The column output circuit 320 may include switches, sample and hold capacitors, current sources, buffers, and other circuitry used to operate and read the chemical sensors, depending upon the array configuration and read out technique. In some embodiments, the column output circuit 320 may include circuits such as those described in U.S. Patent Application Publication No. 2010/0300559, No. 2010/0197507, No. 2010/0301398, No. 2010/0300895, No. 2010/0137143, and No. 2009/0026082, and U.S. Pat. No. 7,575,865, which were incorporated by reference above.

The individual output signals of the other chemical sensors 331.2-331.4 coupled to the reaction region 380 can be read out in a similar fashion. In doing so, the column output circuit 320 produces individual output signals for each of the chemical sensors 331.1-331.4.

The individual output signals for each of the chemical sensors 331.1-331.4 can then be combined or otherwise processed by the array controller 124 (or other data processor) to calculate a resultant, low noise output signal for the group of chemical sensors 331.1-331.4. For example, the resultant output signal may be an average of the individual output signals. In such a case, the SNR of the resultant output signal can be increased by as much as the square root of the number of individual output signals. In addition, the resultant output signal can compensate for differences among the values of the individual output signals, caused by variations in performance of the chemical sensors 331.1-331.4 which could otherwise complicate the downstream signal processing.

FIG. 4 is a flow chart of an example process for calculating a resultant output signal for a group of chemical sensors coupled to a single reaction region. Other embodiments may perform different or additional steps than the ones illustrated in FIG. 4. For convenience, FIG. 4 will be described with reference to a system that performs a process. The system can be for example, the system of FIG. 1.

At step 400, a chemical reaction is initiated within a reaction region coupled to a group of two or more chemical sensors. The group of chemical sensors may for example include respective chemically-sensitive field effect transistors having a common floating gate in communication with the reaction region, as described above with respect to FIG. 3. The chemical reaction may be a sequencing reaction, as described above.

At step 410, individual output signals are obtained from the chemical sensors in the group. The individual output signals may for example be obtained by selecting and reading out the individual chemical sensors using the techniques described above. In some embodiments, flowing of reagent(s) causes chemical reactions within the reaction region that release hydrogen ions, and the amplitude of the individual output signals from the chemical sensors is related to the amount of hydrogen ions detected.

At step 420, a resultant output signal for the group is calculated based on one or more of the individual output signals. The resultant output signal may for example be an average of the individual output signals. Alternatively, other techniques may be used to calculate the resultant output signal.

At step 430, a characteristic of the chemical reaction is determined based on the resultant output signal. For example, the characteristic of the chemical reaction may be determined based on the value of the resultant output signal using the techniques disclosed in Rearick et al., U.S. patent application Ser. No. 13/339,846, filed Dec. 29, 2011, based on U.S. Prov. Pat. Appl. Nos. 61/428,743, filed Dec. 30, 2010, and 61/429,328, filed Jan. 3, 2011, and in Hubbell, U.S. patent application Ser. No. 13/339,753, filed Dec. 29, 2011, based on U.S. Prov. Pat. Appl. No 61/428,097, filed Dec. 29, 2010, each of which were incorporated by reference above.

FIG. 5 illustrates a cross-sectional view of portions of two groups of chemical sensors and their corresponding reaction regions according to a first embodiment. In FIG. 5, the chemically-sensitive field effect transistors 341.1, 341.2 of the chemical sensors 331.1, 331.2 in the group of sensors 331.1-331.4 coupled to the reaction region 380 are visible. The chemically-sensitive field effect transistors 341.3, 341.4 of the other chemical sensors 331.3, 331.4 in the group lie behind this cross-section. Similarly, the cross-section of FIG. 5 shows the chemically-sensitive field effect transistors of two chemical sensors in the group of chemical sensors that is coupled to the adjacent reaction region 382. In this illustration, the select switches of the chemical sensors, access lines and other connections are omitted for simplicity.

The chemical sensor 331.1 is representative of the group of chemical sensors 331.1-331.4. In the illustrated example, the chemically-sensitive field effect transistor 341.1 of the chemical sensor 331.1 is a chemically-sensitive field effect transistor (chemFET), more specifically an ion-sensitive field effect transistor (ISFET) in this example.

The chemically-sensitive field effect transistor 341.1 includes common floating gate 370 having a conductive element 520 coupled to the reaction region 380. The conductive element 520 is the uppermost floating gate conductor (also referred to herein as a sensor plate) in the common floating gate 370. In the embodiment illustrated in FIG. 5, the common floating gate 370 includes multiple patterned layers of conductive material within layers of dielectric material 519.

In FIG. 5, the conductive element 520 electrically connects individual multi-layer floating gate structures that extend over the channel regions of each of the chemically-sensitive field effect transistors 341.1-341.4 of the group of chemical sensors 331.1-331.4. In doing so, the common floating gate 370 is shared among the chemical sensors 331.1-331.4.

The chemically-sensitive field effect transistor 341.1 includes a source region 521 and a drain region 522 within a semiconductor substrate 354. The source region 521 and the drain region 522 comprise doped semiconductor material having a conductivity type different from the conductivity type of the substrate 554. For example, the source region 521 and the drain region 522 may comprise doped P-type semiconductor material, and the substrate may comprise doped N-type semiconductor material.

Channel region 523 separates the source region 521 and the drain region 522. The common floating gate 370 includes a conductive element 551 separated from the channel region 523 by a gate dielectric 552. The gate dielectric 552 may be for example silicon dioxide. Alternatively, other dielectrics may be used for the gate dielectric 552.

As shown in FIG. 5, the reaction region 380 is within an opening extending through dielectric material 510 to the upper surface of the conductive element 520. The dielectric material 510 may comprise one or more layers of material, such as silicon dioxide or silicon nitride. The opening in the dielectric material 510 may for example have a circular cross-section. Alternatively, the opening may be non-circular. For example, the cross-section may be square, rectangular, hexagonal, or irregularly shaped. The dimensions of the openings within the dielectric material 510, and their pitch, can vary from embodiment to embodiment.

In the illustrated embodiment, the upper surface 530 of the conductive element 520 is the bottom surface of the reaction region 380. That is, there is no intervening deposited material layer between the upper surface 530 of the conductive element 520 and the reaction region 380. As a result of this structure, the upper surface 530 of the conductive element 520 acts as the sensing surface for the group of chemical sensors 331.1-331.4. The conductive element 520 may comprise one or more of a variety of different materials to facilitate sensitivity to particular ions (e.g. hydrogen ions).

During manufacturing and/or operation of the device, a thin oxide of the electrically conductive material of the conductive element 520 may be grown on the upper surface 530 which acts as a sensing material (e.g. an ion-sensitive sensing material) for the group of chemical sensors 331.1-331.4. For example, in one embodiment the conductive element 520 may be titanium nitride, and titanium oxide or titanium oxynitride may be grown on the upper surface 530 during manufacturing and/or during exposure to solutions during use. Whether an oxide is formed depends on the conductive material, the manufacturing processes performed, and the conditions under which the device is operated.

In the illustrated example, the conductive element 520 is shown as a single layer of material. More generally, the conductive element 520 may comprise one or more layers of a variety of electrically conductive materials, such as metals or ceramics, depending upon the embodiment. The conductive material can be for example a metallic material or alloy thereof, or can be a ceramic material, or a combination thereof. An exemplary metallic material includes one of aluminum, copper, nickel, titanium, silver, gold, platinum, hafnium, lanthanum, tantalum, tungsten, iridium, zirconium, palladium, or a combination thereof. An exemplary ceramic material includes one of titanium nitride, titanium aluminum nitride, titanium oxynitride, tantalum nitride, or a combination thereof.

In some alternative embodiments, an additional conformal sensing material (not shown) is deposited on the sidewall of the opening in the dielectric material 510 and on the upper surface 530 of the sensor plate 520. In such a case, an inner surface of the deposited sensing material defines the reaction region 380. The sensing material may comprise one or more of a variety of different materials to facilitate sensitivity to particular ions. For example, silicon nitride or silicon oxynitride, as well as metal oxides such as silicon oxide, aluminum or tantalum oxides, generally provide sensitivity to hydrogen ions, whereas sensing materials comprising polyvinyl chloride containing valinomycin provide sensitivity to potassium ions. Materials sensitive to other ions such as sodium, silver, iron, bromine, iodine, calcium, and nitrate may also be used, depending upon the embodiment.

In operation, reactants, wash solutions, and other reagents may move in and out of the reaction region 580 by a diffusion mechanism 540. Each of the chemical sensors 331.1-331.4 are responsive to (and generates an output signal related to) the amount of charge 524 proximate to the conductive element 520. The presence of charge 524 in an analyte solution alters the surface potential at the interface between the analyte solution and the conductive element 520, due to the protonation or deprotonation of surface charge groups. Changes in the charge 524 cause changes in the voltage on the floating gate structure 518, which in turn changes in the threshold voltages of the chemically-sensitive transistors 341.1-341.4 of each of the chemical sensors 331.1-331.4. The respective changes in threshold voltages can be measured by measuring the current through the respective channel regions (e.g. channel region 523 of sensor 331.1). As a result, each of the chemical sensors 331.1-331.4 can be operated to provide individual current-based or voltage-based output signals on an array line connected to its corresponding source region or drain region.

In an embodiment, reactions carried out in the reaction region 380 can be analytical reactions to identify or determine characteristics or properties of an analyte of interest. Such reactions can directly or indirectly generate byproducts that affect the amount of charge 524 adjacent to the conductive element 520. If such byproducts are produced in small amounts or rapidly decay or react with other constituents, multiple copies of the same analyte may be analyzed in the reaction region 380 at the same time in order to increase the individual output signals generated by the group of chemical sensors 331.1-331.4. In an embodiment, multiple copies of an analyte may be attached to a solid phase support 512, either before or after deposition into the reaction region 380. The solid phase support 512 may be microparticles, nanoparticles, beads, solid or porous gels, or the like. For simplicity and ease of explanation, solid phase support 512 is also referred herein as a particle. For a nucleic acid analyte, multiple, connected copies may be made by rolling circle amplification (RCA), exponential RCA, Recombinase Polymerase Amplification (RPA), Polymerase Chain Reaction amplification (PCR), emulsion PCR amplification, or like techniques, to produce an amplicon without the need of a solid support.

In various exemplary embodiments, the methods, systems, and computer readable media described herein may advantageously be used to process and/or analyze data and signals obtained from electronic or charged-based nucleic acid sequencing. In electronic or charged-based sequencing (such as, pH-based sequencing), a nucleotide incorporation event may be determined by detecting ions (e.g., hydrogen ions) that are generated as natural by-products of polymerase-catalyzed nucleotide extension reactions. This may be used to sequence a sample or template nucleic acid, which may be a fragment of a nucleic acid sequence of interest, for example, and which may be directly or indirectly attached as a clonal population to a solid support, such as a particle, microparticle, bead, etc. The sample or template nucleic acid may be operably associated to a primer and polymerase and may be subjected to repeated cycles or “flows” of deoxynucleoside triphosphate (“dNTP”) addition (which may be referred to herein as “nucleotide flows” from which nucleotide incorporations may result) and washing. The primer may be annealed to the sample or template so that the primer's 3′ end can be extended by a polymerase whenever dNTPs complementary to the next base in the template are added. Then, based on the known sequence of nucleotide flows and on measured output signals from the chemical sensors indicative of ion concentration during each nucleotide flow, the identity of the type, sequence and number of nucleotide(s) associated with a sample nucleic acid present in a reaction region coupled to a group of chemical sensors can be determined.

FIGS. 6 to 10 illustrate stages in a manufacturing process for forming a device including multiple chemical sensors coupled to the same reaction region according to a first embodiment.

FIG. 6 illustrates a structure 600 formed in a first stage. The structure 600 includes partially completed floating gate structures for the field effect transistors of the chemical sensors. For example, the structure 600 includes partially completed floating gate structure 618 for the chemically-sensitive field effect transistor 341.1 of the chemical sensor 331.1.

The structure 600 can be formed by depositing a layer of gate dielectric material on the semiconductor substrate 554, and depositing a layer of polysilicon (or other electrically conductive material) on the layer of gate dielectric material. The layer of polysilicon and the layer gate dielectric material can then be etched using an etch mask to form the gate dielectric elements (e.g. gate dielectric 552) and the lowermost conductive material element (e.g. conductive element 551) of the floating gate structures. Following formation of an ion-implantation mask, ion implantation can then be performed to form the source and drain regions (e.g. source region 52 land a drain region 522) of the chemical sensors.

A first layer of the dielectric material 519 can then be deposited over the lowermost conductive material elements. Conductive plugs can then be formed within vias etched in the first layer of dielectric material 519 to contact the lowermost conductive material elements of the floating gate structures. A layer of conductive material can then be deposited on the first layer of the dielectric material 519 and patterned to form second conductive material elements electrically connected to the conductive plugs. This process can then be repeated multiple times to form the partially completed floating gate structures shown in FIG. 6. Alternatively, other and/or additional techniques may be performed to form the structure.

Forming the structure 600 in FIG. 6 can also include forming additional elements such as array lines (e.g. row lines, column lines, etc.) for accessing the chemical sensors, additional doped regions in the substrate 554, and other circuitry (e.g. select switches, access circuitry, bias circuitry etc.) used to operate the chemical sensors, depending upon the device and array configuration in which the chemical sensors are implemented.

Next, conductive material 700 is formed on the structure illustrated in FIG. 6 to contact the partially completed floating gate structures. An etch mask including mask elements 720, 722 is then formed on the conductive material 700, resulting in the structure illustrated in FIG. 7.

The conductive material 700 includes one or more layers of electrically conductive material. For example, the conductive material 700 may include a layer of titanium nitride formed on a layer of aluminum, or a layer of titanium nitride formed on a layer of copper. Alternatively, the number of layers may be different than two, and other and/or additional conductive materials may be used. Examples of conductive materials that can be used in some embodiments include tantalum, aluminum, lanthanum, titanium, zirconium, hafnium, tungsten, palladium, iridium, etc., and combinations thereof.

The locations of the mask elements 720, 722 define the locations of the sensor plates for the chemically-sensitive field effect transistors of the corresponding groups of chemical sensors. In the illustrated embodiment, the mask elements 720, 722 comprise photoresist material which has been patterned using a lithographic process. Alternatively, other techniques and materials may be used.

Next, the conductive material 700 is etched using the mask elements 700, 722 as a mask, resulting in the structure illustrated in FIG. 8. The etching process forms conductive elements 520, 810 in electrical contact with the partially completed floating gate structures of a corresponding group of sensors. The conductive element 520 electrically connects the partially completed floating gate structures for a group of sensors 331.1-331.4, to complete the common floating gate 370 for this group of sensors. Similarly, the conductive material element 810 completes the common floating gate for the adjacent group of sensors.

Next, the mask elements 700, 722 are removed and dielectric material 510 is formed, resulting in the structure illustrated in FIG. 9. The dielectric material 510 may comprise one or more layers of deposited dielectric material, such as silicon dioxide or silicon nitride.

Next, the dielectric material 510 is etched to form openings defining reaction regions 380, 382 extending to upper surfaces of the conductive material elements 520, 810, resulting in the structure illustrated in FIG. 10.

FIG. 11 illustrates a cross-sectional view of portions of two groups of chemical sensors and their corresponding reaction regions according to a second embodiment. In contrast to the embodiment shown in FIG. 5, the common floating gate for each group of chemical sensors includes a sensor plate that is smaller than the bottom surface of the corresponding reaction region.

In FIG. 11, the floating gate structure 1118 for the group of chemical sensors 331.1-331.4 includes conductive element 1120 coupled to the reaction region 380. The conductive element 1120 is coupled to the conductive element 520 by conductive plug 1130. The conductive element 1120 is the uppermost floating gate conductor in the floating gate structure 1118, and thus acts as the sensor plate for the group of chemical sensors 331.1-331.4.

In FIG. 11, an upper surface 1122 of the conductive element 1120 is a portion of the bottom surface of the reaction region 380. That is, there is no intervening deposited material layer between the upper surface 1122 of the conductive element 1120 and the reaction region 380. As a result of this structure, the upper surface 1122 of the conductive element 1120 acts as the sensing surface for the group of chemical sensors 331.1-331.4. In the illustrated embodiment, the conductive element 1120 is within the dielectric material 1160, such that the upper surface 1122 of the conductive element 1120 is co-planar with the upper surface of the dielectric material 1160. Alternatively, the conductive element 1120 may be formed on the upper surface of dielectric material 1160, and thus protrude slightly into the reaction region 380.

As shown in FIG. 11, the upper surface 1122 of the conductive element 1120 has a width 1125 that is the less than the width of the bottom surface of the reaction region 380. As described in more detail below, having a small conductive element 1120 as the sensor plate can enable the signal-to-noise ratio (SNR) of the individual output signals of the chemical sensors 331.1-331.4 to be maximized.

The amplitude of the desired signal detected by the chemical sensors 331.1-331.4 in response to the charge 524 in an analyte solution is a superposition of the charge concentration along the interface between the conductive element 1120 and the analyte solution. Because the charge 524 is more highly concentrated at the bottom and middle of the reaction region 380, the width 1125 of the conductive element 1120 is a tradeoff between the amplitude of the desired signal detected in response to the charge 524, and the fluidic noise due to random fluctuation between the conductive element 1120 and the analyte solution. Increasing the width 1125 of the conductive element 1120 increases the fluidic interface area for the chemical sensors 331.1-331.4, which reduces fluidic noise. However, since the localized surface density of charge 524 decreases with distance from the middle of the reaction region 380, the conductive element 1120 detects a greater proportion of the signal from areas having lower charge concentration, which can reduce the overall amplitude of the detected signal. In contrast, decreasing the width 1122 of the conductive element 1120 reduces the sensing surface area and thus increases the fluidic noise, but also increases the overall amplitude of the detected signal.

For a very small sensing surface area, Applicants have found that the fluidic noise changes as a function of the sensing surface area differently than the amplitude of the desired signal. Because the SNR of an individual output signal is the ratio of these two quantities, there is an optimal width 1125 at which the SNR of the individual output signals from the chemical sensors 331.1-331.2 is maximum.

The optimal width 1125 can vary from embodiment to embodiment depending on the material characteristics of the conductive element 1120 and the dielectric materials 510, 1160, the volume, shape, aspect ratio (such as base width-to-well depth ratio), and other dimensional characteristics of the reaction regions, the nature of the reaction taking place, as well as the reagents, byproducts, or labeling techniques (if any) that are employed. The optimal width may for example be determined empirically.

FIGS. 12 to 14 illustrate stages in a manufacturing process for forming a device including multiple chemical sensors coupled to the same reaction region according to a second embodiment.

FIG. 12 illustrates a first stage of forming conductive plugs 1210, 1220 extending through dielectric material 1200 to contact the conductive elements 520, 810 of the structure illustrated in FIG. 8. The structure in FIG. 12 can be formed by removing the mask elements 720, 722 in FIG. 8 and forming dielectric material 1200 on the resulting structure. Vias can then be etched through the dielectric material 1200, and metal deposited within the vias. A planarization process (e.g. chemical mechanical polishing) can then be performed to remove the deposited metal from the upper surface of the dielectric material 1200 and form the plugs 1210, 1220. Alternatively, other techniques may be used.

Next, conductive material 1300 is formed on the structure illustrated in FIG. 12. An etch mask including mask elements 1320, 1322 is then formed on the conductive material 1300, resulting in the structure illustrated in FIG. 13.

The conductive material 1300 may comprise one or more layers of conductive material, such as those described above with respect the conductive material 700 of FIG. 7. The locations of the mask elements 1320, 1322 define the locations of the sensor plates of the field effect transistors of the corresponding groups of chemical sensors. In the illustrated embodiment, the mask elements 1320, 1322 comprise photoresist material which has been patterned using a lithographic process. Alternatively, other techniques and materials may be used.

Next, the conductive material 1300 is etched using the mask elements 1320, 1322 as a mask to form the conductive elements 1120, 1400. Dielectric material 1160 is then formed between the conductive elements 1120, 1400, resulting in the structure illustrated in FIG. 14.

Next, dielectric material 510 is formed on the structure illustrated in FIG. 14. The dielectric material 510 is then be etched to form openings defining reaction regions 380, 382 extending to upper surfaces of the conductive elements 1120, 1400, resulting in the structure illustrated in FIG. 11. The dielectric material 1160 may comprise material different than that of dielectric material 510. For example, the dielectric material 510 may comprise material (e.g. silicon oxide) which can be selectively etched relative to the material (e.g. silicon nitride) of the dielectric material 1160 when subjected to a chosen etch process. In such a case, the dielectric material 1160 can act as an etch stop during the etching process used to form the reaction regions 380, 382. In doing so, the dielectric material 1160 can prevent etching past the conductive elements 1120, 1400, and thus can define and maintain the desired shape of the reaction regions 380, 382.

FIGS. 15 to 18 illustrate stages in a manufacturing process for forming a device including multiple chemical sensors coupled to the same reaction region according to a third embodiment.

FIG. 15 illustrates a first stage of forming dielectric material 1160 on the structure illustrated in FIG. 12. An etch mask including mask elements 1510, 1520, 1530 is then formed on the dielectric material 1160, resulting in the structure illustrated in FIG. 15. As described in more detail below, openings between the mask elements 1510, 1520, 1530 define the locations of the sensor plates of the field effect transistors of the corresponding groups of chemical sensors.

Next, the dielectric material 1160 is etched using the mask elements 1510, 1520, 1530 as an etch mask to form openings 1610, 1620 within the dielectric material 1160, resulting in the structure illustrated in FIG. 16. As shown in FIG. 16, the openings extend to the upper surfaces of the conductive plugs 1210, 1220.

Next, the mask elements 1510, 1520, 1530 are removed and conductive material 1800 is deposited on the structure illustrated in FIG. 16, resulting in the structure illustrated in FIG. 17. The conductive material 1800 may comprise one or more layers of conductive material, such as those described above with respect the conductive material 700 of FIG. 7.

Next, a planarization process (e.g. CMP) is performed to remove the conductive material 1800 from the upper surface of the dielectric material 1160, resulting in the structure illustrated in FIG. 18. The planarization process leaves remaining conductive material within the openings 1610, 1620 to form the conductive elements 1120, 1400.

Next, dielectric material 510 is formed on the structure illustrated in FIG. 18. The dielectric material 510 can then be etched to form openings defining reaction regions 380, 382 extending to upper surfaces of the conductive elements 1120, 1400, resulting in the structure illustrated in FIG. 11.

FIGS. 19 to 21 illustrate stages in a manufacturing process for forming a device including multiple chemical sensors coupled to the same reaction region according to a fourth embodiment.

FIG. 19 illustrates a first stage of forming conductive plugs 1210, 1220 extending through dielectric material 1900 to contact the conductive elements 520, 810 of the structure illustrated in FIG. 8. As described in more detail below, the dielectric material 1900, comprising one or more layers of dielectric material, acts an etch stop during the subsequent formation of the reaction regions 380, 382. The structure in FIG. 19 can be formed by removing the mask elements 720, 722 illustrated in FIG. 8 and forming the dielectric material 1900 on the resulting structure. The plugs 1210, 1220 can then be formed using the techniques described above with reference to FIG. 12. Alternatively, other techniques may be used.

Next, conductive elements 1120, 1400 are formed on the upper surface of the dielectric material 1900, resulting in the structure illustrated in FIG. 20. The conductive elements 1120, 1400 may be formed by depositing conductive material, forming an etch mask including mask elements defining the locations of the conductive elements 1120, 1400, and etching the conductive material using the mask elements as an etch mask.

Next, dielectric material 510 is formed on the structure illustrated in FIG. 20. The dielectric material 510 is then be etched to form openings defining reaction regions 380, 382 extending to upper surfaces of the conductive elements 1120, 1400, resulting in the structure illustrated in FIG. 21. As shown in FIG. 21, in this embodiment the reaction regions 380, 382 extend below the upper surfaces of the conductive elements 1120, 1400 to expose their side surfaces.

The dielectric material 1900 may comprise material different than that of dielectric material 510. For example, the dielectric material 510 may comprise material (e.g. silicon oxide) which can be selectively etched relative to the material (e.g. silicon nitride) of the dielectric material 1900 when subjected to a chosen etch process. In such a case, the dielectric material 1900 can act as an etch stop during the etching process used to form the reaction regions 380, 382. In doing so, the dielectric material 1900 can prevent etching below the conductive elements 1120, 1400, and thus can define and maintain the shape of the reaction regions 380, 382.

Various embodiments may be implemented using hardware elements, software elements, or a combination of both. Examples of hardware elements may include processors, microprocessors, circuits, circuit elements (e.g., transistors, resistors, capacitors, inductors, and so forth), integrated circuits, application specific integrated circuits (ASIC), programmable logic devices (PLD), digital signal processors (DSP), field programmable gate array (FPGA), logic gates, registers, semiconductor device, chips, microchips, chip sets, and so forth. Examples of software may include software components, programs, applications, computer programs, application programs, system programs, machine programs, operating system software, middleware, firmware, software modules, routines, subroutines, functions, methods, procedures, software interfaces, application program interfaces (API), instruction sets, computing code, computer code, code segments, computer code segments, words, values, symbols, or any combination thereof. Determining whether an embodiment is implemented using hardware elements and/or software elements may vary in accordance with any number of factors, such as desired computational rate, power levels, heat tolerances, processing cycle budget, input data rates, output data rates, memory resources, data bus speeds and other design or performance constraints.

Some embodiments may be implemented, for example, using a computer-readable medium or article which may store an instruction or a set of instructions that, if executed by a machine, may cause the machine to perform a method and/or operations in accordance with the embodiments. Such a machine may include, for example, any suitable processing platform, computing platform, computing device, processing device, computing system, processing system, computer, processor, or the like, and may be implemented using any suitable combination of hardware and/or software. The computer-readable medium or article may include, for example, any suitable type of memory unit, memory device, memory article, memory medium, storage device, storage article, storage medium and/or storage unit, for example, memory, removable or non-removable media, erasable or non-erasable media, writeable or re-writeable media, digital or analog media, hard disk, floppy disk, read-only memory compact disc (CD-ROM), recordable compact disc (CD-R), rewriteable compact disc (CD-RW), optical disk, magnetic media, magneto-optical media, removable memory cards or disks, various types of Digital Versatile Disc (DVD), a tape, a cassette, or the like. The instructions may include any suitable type of code, such as source code, compiled code, interpreted code, executable code, static code, dynamic code, encrypted code, and the like, implemented using any suitable high-level, low-level, object-oriented, visual, compiled and/or interpreted programming language.

While the present invention is disclosed by reference to the preferred embodiments and examples detailed above, it is to be understood that these examples are intended in an illustrative rather than in a limiting sense. It is contemplated that modifications and combinations will readily occur to those skilled in the art, which modifications and combinations will be within the spirit of the invention and the scope of the following claims.

Claims

1. An apparatus, comprising: a chemically-sensitive field effect transistor (chemFET) sensor device comprising: an array of reaction regions;at least two chemFET sensors coupled to each reaction region of the array of reaction regions, wherein each chemFET sensor of the at least two chemFET sensors comprises a chemFET and a row select transistor; anda floating gate common to the at least two chemFET sensors and in communication with each respective reaction region;a row select circuit for biasing each row select transistor of each chemFET sensor of the at least two chemFET sensors for each reaction region in the array of reaction regions;a column output circuit for coupling each chemFET of the at the least two chemFET sensors for each reaction region in the array of reaction regions to a respective column line in response to biasing each respective row select transistor; andan array controller comprising memory for storage of data and software applications, and a processor for accessing data and executing applications.

2. The apparatus of claim 1, wherein the array controller is configured to: acquire an individual output signal from each chemFET sensor of the at least two chemFET sensors for each reaction region in the array of reaction regions; andcalculate a resultant output signal for each at least two chemFET sensors for each reaction region in the array of reaction regions based on one or more of the individual output signals.

3. The apparatus of claim 1, further comprising a fluidics system including: a valve block for controllable fluid communication between a plurality of reagents and a flow cell housing the chemFET sensor device; anda reference electrode placed in fluid communication with the chemFET sensor device.

4. The apparatus of claim 3, wherein the array controller provides a reference bias voltage to the reference electrode.

5. The apparatus of claim 1, wherein the chemFET sensor device is an ion-sensitive field effect transistor (ISFET) sensor device.

6. The apparatus of claim 5, wherein the ISFET sensor device is sensitive to hydrogen.

7. The apparatus of claim 1, wherein an upper surface of a conductive element of each floating gate common to the at least two chemFET sensors for each reaction region of the array of reaction regions comprises a sensing surface including one or more conductive elements.

8. The apparatus of claim 7, wherein the conductive element of each floating gate comprises a metal or a ceramic.

9. The apparatus of claim 8, wherein the metal comprises at least one of aluminum, copper, nickel, titanium, silver, gold, platinum, hafnium, lanthanum, tantalum, tungsten, iridium, zirconium, or palladium.

10. The apparatus of claim 8, wherein the ceramic comprises at least one of titanium nitride, titanium aluminum nitride, titanium oxide, or tantalum nitride.

11. The apparatus of claim 7, wherein the conductive element of the sensing surface comprises titanium nitride, titanium oxide, or titanium oxynitride.

12. The apparatus of claim 7, wherein the sensing surface is sensitive to ions.

13. The apparatus of claim 12, wherein the sensing surface is sensitive to hydrogen.

14. A method for sequencing comprising: sequentially flowing a series of deoxynucleoside triphosphate (dNTP) solutions over an array of reaction regions, each reaction region coupled to at least two chemFET sensors having a common floating gate in communication with a respective reaction region;coupling column output circuitry to each chemFET of each respective at least two chemFET sensors of each reaction region of the array of reaction regions in response to biasing each respective row select transistor coupled to each chemFET of each respective at least two chemFET sensors;acquiring an individual output signal for each chemFET of the at least two chemFET sensors for each reaction region in the array of reaction regions in response to release of an analyte resulting from incorporation of a nucleotide to a template nucleic acid in a reaction region of the array of reaction regions; andcalculating a resultant output signal for each at least two chemFET sensors for each reaction region in the array of reaction regions based on one or more of the individual output signals.

15. The method of claim 14, wherein the method further comprises: determining a sequence corresponding for each reaction region in the array of reaction regions loaded with a template nucleic acid-containing bead based on the resultant output signal for each at least two chemFET sensors for each reaction region in the array of reaction regions.

16. The method of claim 14, wherein an upper surface of each floating gate common to the at least two chemFET sensors for each reaction region of the array of reaction regions comprises a sensing surface including one or more conductive elements.

17. The method of claim 16, wherein the sensing surface is sensitive to ions.

18. The method of claim 17, wherein the sensing surface is sensitive to hydrogen.

19. The method of claim 14, wherein the at least two chemFET sensors for each reaction region in the array of reaction regions are ion-sensitive field effect (ISFET) sensors.

20. The apparatus of claim 7, wherein the sensing surface is additionally formed on a sidewall of each corresponding reaction region of the array of reaction regions.