Patent Publication Number: US-11028438-B2

Title: Windowed sequencing

Description:
CROSS-REFERENCE TO RELATED APPLICATIONS 
     This application is a continuation of U.S. patent application Ser. No. 16/153,898 filed Oct. 8, 2018, which is a division of U.S. patent application Ser. No. 15/043,296 filed Feb. 12, 2016, now U.S. Pat. No. 10,100,357, which is a continuation of U.S. patent application Ser. No. 13/891,023 filed May 9, 2013, now abandoned, which disclosures are herein incorporated by reference in their entirety. 
    
    
     FIELD OF THE INVENTION 
     This disclosure, in general, relates to methods for nucleic acid sequencing. 
     BACKGROUND 
     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 in its entirety. 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 methods for reducing noise in output signals of chemical sensors and improving signal to noise ratio and readout of chemical sensors. 
     SUMMARY 
     In one implementation, a method is described. The method includes determining an operational characteristic of sensors of a sensor array. The method further includes selecting a group of sensors in the array based on the operational characteristic of sensors in the group. The method further includes enabling readout of the sensors in the selected group. The method further includes receiving output signals from the enabled sensors, the output signals indicating chemical reactions occurring proximate to the sensors of the sensor array. 
     In one embodiment, the operational characteristic of sensors of a sensor array is selected from the group of a bead loading quality of the sensors of the sensor array, a noise spectrum of the sensors of the sensor array, and a threshold voltage value of the sensors of the sensor array. In another embodiment, readout of remaining sensors of the sensor array is bypassed. According to another embodiment, the selecting a group of sensors in the array is based on more than one operational characteristic of sensors in the group. In a further embodiment, the sensors in the sensor array include chemically-sensitive field effect transistors. According to once embodiment, the chemically-sensitive field effect transistors are arranged in rows and columns and the selecting includes selecting contiguous rows of chemically-sensitive field effect transistors in the sensor array. In another embodiment, the output signals further indicate an ion concentration due to sequencing reactions occurring proximate to the chemically-sensitive field effect transistors. According to one embodiment, the output signals are analog signals and the method further includes converting the output signals into digital signals and the receiving output signals further includes receiving the converted digital signals. 
     In another implementation, a method for nucleic acid sequencing is described. The method includes providing template nucleic acids to at least some of a plurality of locations coupled to sensors of an array. The method further includes analyzing output signals of the sensors of the array to identify which locations in the plurality of locations contain the disposed template nucleic acids. The method further includes selecting a group of sensors coupled to identified locations containing the disposed template nucleic acids. The method further includes introducing known nucleotides within at least some of the plurality of locations. The method further includes measuring the output signals of the selected sensors to detect sequencing reaction byproducts resulting from incorporation of the introduced known nucleotides into one of more primers hybridized to at least one of the disposed template nucleic acids. 
     In one embodiment, the method further comprises enabling readout of the sensors in the selected group, and bypassing readout of remaining sensors of the sensor array. In another embodiment, the sequencing reaction byproducts comprise hydrogen ions. In yet another embodiment, the sequencing reaction byproducts resulting from incorporation are of chemically similar composition for each of the known nucleotides. In one embodiment, the method further comprises determining at least a portion of sequences of at least a portion of the template nucleic acids based on the introduced known nucleotides and further based on the measured output signals. According to one embodiment, the sensors comprise field-effect transistors having a chemically sensitive portion responsive to the sequencing reaction byproducts and disposed in proximity to the locations such that the at least one of the sequencing reaction byproducts diffuse or contact the sensors to thereby be detected. According to another embodiment, the chemically sensitive portion of the field-effect transistors of the array is responsive to a plurality of different sequencing reaction byproducts. In yet another embodiment, the locations are within respective reaction chambers. In one embodiment, the measured output signals are analog signals and the method further includes converting the output signals into digital signals and the receiving output signals further includes receiving the converted digital signals. 
     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 according to an exemplary embodiment. 
         FIG. 2  illustrates a cross-sectional view of a portion of the integrated circuit device and flow cell according to an exemplary embodiment. 
         FIG. 3  illustrates a cross-sectional view of representative chemical sensors and corresponding reaction regions according to an exemplary embodiment. 
         FIG. 4  illustrates a block diagram of an exemplary chemical sensor array of coupled to an array controller, according to an exemplary embodiment. 
         FIG. 5  illustrates a method, according to an exemplary embodiment. 
         FIG. 6  illustrates a method for nucleic acid sequencing, according to an exemplary embodiment. 
         FIG. 7  illustrates examples of two different groups of sensors in an array that have been selected based on an operational characteristic of sensors in the group, according to an exemplary embodiment. 
     
    
    
     DETAILED DESCRIPTION 
     Methods for reducing noise in output signals of chemical sensors and improving readout of output signal of chemical sensors based on the operational characteristic of the chemical sensors are described. For example, an integrated circuit may comprise an array of chemically sensitive sensors arranged in rows and columns. Output signals from the sensors indicating chemical reactions occurring proximate to the sensors of the sensor array may be read out. Determining an operational characteristic of sensors of a sensor array before the chemical reactions occur and reading out sensors based on the determined operational characteristic results in improved signal quality of output signals, for example. 
       FIG. 1  illustrates a block diagram of components of a system for nucleic acid sequencing according to an exemplary embodiment. The components include flow cell  101  on integrated circuit device  100 , reference electrode  108 , plurality of reagents  114  for sequencing, valve block  116 , wash solution  110 , valve  112 , fluidics controller  118 , lines  120 / 122 / 126 , passages  104 / 109 / 111 , waste container  106 , array controller  124 , and user interface  128 . Integrated circuit device  100  includes microwell array  107  overlying a sensor array that includes chemical sensors as described herein. Flow cell  101  includes inlet  102 , outlet  103 , and flow chamber  105  defining a flow path for reagents over microwell array  107 . 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 . Reagents  114  may be driven through the fluid pathways described above, valve block  116  and valve  112 , and flow cell  101  by pumps, gas pressure, or other suitable methods, and may be discarded into waste container  106  after exiting outlet  103  of flow cell  101 . Fluidics controller  118  may control driving forces for reagents  114  and the operation of valve  112  and valve block  116  with suitable software. Flow cell  101  may have a variety of configurations for controlling the path and flow rate of reagents  114  over microwell array  107 . Array controller  124  provides bias voltages and timing and control signals to integrated circuit device  100  for reading the chemical sensors of the sensor array. Array controller  124  also provides a reference bias voltage to reference electrode  108  to bias reagents  114  flowing over microwell array  107 . Microwell array  107  includes an array of reaction regions as described herein, also referred to herein as microwells, which are operationally associated with corresponding chemical sensors in the sensor array. For example, each reaction region may be coupled to a chemical sensor suitable for detecting an analyte or reaction property of interest within that reaction region. Microwell array  107  may be integrated in integrated circuit device  100 , so that microwell array  107  and the sensor array are part of a single device or chip. 
     During an experiment, array controller  124  collects and processes output signals from the chemical sensors of the sensor array through output ports on integrated circuit device  100  via bus  127 . Array controller  124  may be a computer or other computing means. 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 . The values of the output signals of the chemical sensors indicate physical and/or chemical parameters of one or more reactions taking place in the corresponding reaction regions in microwell array  107 . For example, in an exemplary embodiment, the values of the output signals may be 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 which are incorporated by reference herein in their entirety. User interface  128  may display information about flow cell  101  and the output signals received from chemical sensors in the sensor array on integrated circuit device  100 . User interface  128  may also display instrument settings and controls, and allow a user to enter or set instrument settings and controls. 
     In an exemplary embodiment, during the experiment fluidics controller  118  may control delivery of individual reagents  114  to flow cell  101  and integrated circuit device  100  in a predetermined sequence, for predetermined durations, at predetermined flow rates. 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 reagents  114 . During the experiment, the system may also monitor and control the temperature of 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 reference electrode  108  throughout an entire multi-step reaction during operation. Valve  112  may be shut to prevent any wash solution from flowing into passage  109  as reagents  114  are flowing. Although the flow of wash solution may be stopped, there may still be uninterrupted fluid and electrical communication between reference electrode  108 , passage  109 , and microwell array  107 . The distance between reference electrode  108  and 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 reference electrode  108 . In an exemplary embodiment, wash solution  110  may be selected as being in continuous contact with 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 integrated circuit device  100  and flow cell  101 . During operation, flow chamber  105  of flow cell  101  confines reagent flow  208  of delivered reagents across open ends of the reaction regions in 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 sensor array  205  are responsive to (and generate output signals to) chemical reactions within associated reaction regions in microwell array  107  to detect an analyte or reaction property of interest. The chemical sensors of 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 in their entirety. 
       FIG. 3  illustrates a cross-sectional view of two representative chemical sensors and their corresponding reaction regions according to an exemplary embodiment. In  FIG. 3 , two chemical sensors  350 ,  351  are shown, representing a small portion of a sensor array that can include millions of chemical sensors. Chemical sensor  350  is coupled to corresponding reaction region  301 , and chemical sensor  351  is coupled to corresponding reaction region  302 . Chemical sensor  350  is representative of the chemical sensors in the sensor array. In the illustrated example, chemical sensor  350  is an ion-sensitive field effect transistor. Chemical sensor  350  includes floating gate structure  318  having a floating gate conductor (referred to herein as the sensor plate) separated from reaction region  301  by sensing material  316 . As shown in  FIG. 3 , sensor plate  320  is the uppermost patterned layer of conductive material in floating gate structure  318  underlying reaction region  301 . 
     In the illustrated example, floating gate structure  318  includes multiple patterned layers of conductive material within layers of dielectric material  319 . The upper surface of sensing material  316  acts as sensing surface  317  for chemical sensor  350 . In the illustrated embodiment, sensing material  316  is an ion-sensitive material, such that the presence of ions or other charged species in a solution in the reaction region  301  alters the surface potential of sensing surface  317 . The change in the surface potential is due to the protonation or deprotonation of surface charge groups at the sensing surface caused by the ions present in the solution. The sensing material may be deposited using various techniques, or naturally formed during one or more of the manufacturing processes used to form chemical sensor  350 . In some embodiments, sensing material  316  is a metal oxide, such as an oxide of silicon, tantalum, aluminum, lanthanum, titanium, zirconium, hafnium, tungsten, palladium, iridium, etc, or any other suitable metal oxide, or combination thereof. In some embodiments, sensing material  316  is an oxide of the upper layer of conductive material of sensor plate  320 . For example, the upper layer of sensor plate  320  may be titanium nitride, and sensing material  316  may comprise titanium oxide or titanium oxynitride. More generally, sensing material  316  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 implementation. 
     The chemical sensor also includes source region  321  and drain region  322  within semiconductor substrate  354 . Source region  321  and drain region  322  comprise doped semiconductor material have a conductivity type different from the conductivity type of substrate  354 . For example, source region  321  and drain region  322  may comprise doped P-type semiconductor material, and the substrate may comprise doped N-type semiconductor material. Channel region  323  separates source region  321  from drain region  322 . Floating gate structure  318  overlies channel region  323 , and is separated from substrate  354  by gate dielectric  352 . Gate dielectric  352  may be for example silicon dioxide. Alternatively, other suitable dielectrics may be used for gate dielectric  352 . Reaction region  301  extends through fill material  310  on dielectric material  319 . The fill material may for example comprise one or more layers of dielectric material, such as silicon dioxide or silicon nitride. Sensor plate  320 , sensing material  316  and reaction region  301  may for example have circular cross-sections. Alternatively, these may be non-circular. For example, the cross-section may be square, rectangular, hexagonal, or irregularly shaped. The device in  FIG. 3  can also include additional elements such as array lines (e.g. word lines, bit lines, etc.) for accessing the chemical sensors, additional doped regions in substrate  354 , and other circuitry (e.g. access circuitry, bias circuitry etc.) used to operate the chemical sensors, depending upon the device and array configuration in which the chemical sensors described herein are implemented. In some embodiments, the device may for example be manufactured using techniques 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 in their entirety. 
     In operation, reactants, wash solutions, and other reagents may move in and out of reaction region  301  by diffusion mechanism  340 . Chemical sensor  350  is responsive to (and generates an output signal related to) the amount of charge  324  present on sensing material  316  opposite sensor plate  320 . Changes in charge  324  cause changes in the voltage on floating gate structure  318 , which in turn changes in the threshold voltage of the transistor. This change in threshold voltage can be measured by measuring the current in channel region  323  between source region  321  and drain region  322 . As a result, chemical sensor  350  can be used directly to provide a current-based output signal on an array line connected to source region  321  or drain region  322 , or indirectly with additional circuitry to provide a voltage-based output signal. In an embodiment, reactions carried out in reaction region  301  can be analytical reactions to identify or determine characteristics or properties of an analyte of interest. Such reactions can generate directly or indirectly byproducts that affect the amount of charge adjacent to sensor plate  320 . 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 reaction region  301  at the same time in order to increase the output signal generated. In an embodiment, multiple copies of an analyte may be attached to solid phase support  312 , either before or after deposition into reaction region  301 . The solid phase support may be microparticles, nanoparticles, beads, solid or porous gels, or the like. For simplicity and ease of explanation, solid phase support may also be 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. 
       FIG. 4  illustrates a block diagram of an exemplary chemical sensor array coupled to an array controller, according to an exemplary embodiment. In various exemplary implementations, array controller  124  may be fabricated as a “stand alone” controller, or as a computer compatible “card” forming part of a computer  460 , (See FIG. 8 in U.S. Pat. No. 7,948,015 for further details, which is incorporated by reference in its entirety herein). In one aspect, the functions of the array controller  124  may be controlled by computer  460  through an interface block  452  (e.g., serial interface, via USB port or PCI bus, Ethernet connection, etc.), as shown in  FIG. 4 . In one embodiment, array controller  124  is fabricated as a printed circuit board into which integrated circuit device  100  plugs; similar to a conventional IC chip (e.g., integrated circuit device  100  is configured as an ASIC that plugs into the array controller). In one aspect of such an embodiment, all or portions of array controller  124  may be implemented as a field programmable gate array (FPGA) configured to perform various array controller functions. For example, having determined an operational characteristic of sensors of the sensor array, the FPGA may be configured to select a group of sensors in the array based on the operational characteristic of sensors in the group and enable readout of the sensors in the selected group. Suitable readout circuitry may receive output signals from the enabled sensors, the output signals indicating chemical reactions occurring proximate to the sensors of the sensor array. 
     Generally, array controller  124  provides various supply voltages and bias voltages to integrated circuit device  100 , as well as various signals relating to row and column selection, sampling of pixel outputs and data acquisition. In particular, array controller  124  reads the two analog output signals Vout 1  (for example, odd columns) and Vout 2  (for example, even columns) including multiplexed respective pixel voltage signals from integrated circuit device  100  and then digitizes these respective pixel signals to provide measurement data to computer  460 , which in turn may store and/or process the data. In some implementations, array controller  124  also may be configured to perform or facilitate various array calibration and diagnostic functions, and an optional array UV irradiation treatment (See FIG. 11A in U.S. Pat. No. 7,948,015, which is incorporated by reference in its entirety herein, for further details). In general, the array controller provides the integrated circuit device with the analog supply voltage and ground (VDDA, VSSA), the digital supply voltage and ground (VDDD, VSSD), and the buffer output supply voltage and ground (VDDO, VSSO). In one exemplary implementation, each of the supply voltages VDDA, VDDD and VDDO is approximately 3.3 Volts. 
     As discussed above, in one aspect each of these power supply voltages is provided to integrated circuit device  100  via separate conducting paths to facilitate noise isolation. In another aspect, these supply voltages may originate from respective power supplies/regulators, or one or more of these supply voltages may originate from a common source in power supply  458  of array controller  124 . Power supply  458  also may provide the various bias voltages required for array operation (e.g., VB 1 , VB 2 , VB 3 , VB 4 , VBO 0 , V BODY ) and the reference voltage VREF used for array diagnostics and calibration. In another aspect, power supply  458  includes one or more digital-to-analog converters (DACs) that may be controlled by computer  460  to allow any or all of the bias voltages, reference voltage, and supply voltages to be changed under software control (i.e., programmable bias settings). For example, power supply  458  responsive to computer control may facilitate adjustment of the bias voltages VB 1  and VB 2  for pixel drain current, VB 3  for column bus drive, VB 4  for column amplifier bandwidth, and VBO 0  for column output buffer current drive. In some aspects, one or more bias voltages may be adjusted to optimize settling times of signals from enabled pixels. Additionally, the common body voltage V BODY  for all ISFETs of the array may be grounded during an optional post-fabrication UV irradiation treatment to reduce trapped charge, and then coupled to a higher voltage (e.g., VDDA) during diagnostic analysis, calibration, and normal operation of the array for measurement/data acquisition. Likewise, the reference voltage VREF may be varied to facilitate a variety of diagnostic and calibration functions. Reference electrode  108  which is typically employed in connection with an analyte solution to be measured by integrated circuit device  100  (See FIG. 1 in U.S. Pat. No. 7,948,015, which is incorporated by reference in its entirety herein, for further details), may be coupled to power supply  458  to provide a reference potential for the pixel output voltages. For example, in one implementation reference electrode  108  may be coupled to a supply ground (e.g., the analog ground VSSA) to provide a reference for the pixel output voltages based on Eq. (3) in U.S. Pat. No. 7,948,015. In one exemplary implementation, the reference electrode voltage may be set by placing a solution/sample of interest having a known pH level in proximity to integrated circuit device  100  and adjusting the reference electrode voltage until the array output signals Vout 1  and Vout 2  provide pixel voltages at a desired reference level, from which subsequent changes in pixel voltages reflect local changes in pH with respect to the known reference pH level. In general, it should be appreciated that a voltage associated with reference electrode  108  need not necessarily be identical to the reference voltage VREF discussed in U.S. Pat. No. 7,948,015 (which may be employed for a variety of array diagnostic and calibration functions), although in some implementations the reference voltage VREF provided by power supply  458  may be used to set the voltage of reference electrode  108 . 
     Regarding data acquisition from integrated circuit device  100 , in one embodiment array controller  124  of  FIG. 4  may include one or more preamplifiers  253  to further buffer the output signals Vout 1  and Vout 2  from the sensor array and provide selectable gain. In one implementation, array controller  124  may include one preamplifier for each output signal (e.g., two preamplifiers for two analog output signals). In other aspects, the preamplifiers may be configured to accept input voltages from 0.0 to 3.3 Volts or from 0.1 to 5.0 Volts, may have programmable/computer selectable gains (e.g., 1, 2, 5, 10 and 20) and low noise outputs (e.g., &lt;10 nV/sqrtHz), and may provide low pass filtering (e.g., bandwidths of 5 MHz and 25 MHz). In yet another implementation, the preamplifiers may have a programmable/computer selectable offset for input and/or output voltage signals to set a nominal level for either to a desired range. The array controller  124  may also comprise one or more analog-to-digital converters  454  (ADCs) to convert the sensor array output signals Vout 1  and Vout 2  to digital outputs (e.g., 10-bit or 12-bit) so as to provide data to computer  460 . In one aspect, one ADC may be employed for each analog output of the integrated circuit device, and each ADC may be coupled to the output of a corresponding preamplifier (if preamplifiers are employed in a given implementation). In another aspect, the ADC(s) may have a computer-selectable input value ranging from 50 mV to 1 Volt, for example (e.g., 50 mV, 200 mV, 500 mV, 1 V) to facilitate compatibility with different ranges of array output signals and/or preamplifier parameters. In yet other aspects, the bandwidth of the ADC(s) may be greater than 60 MHz, and the data acquisition/conversion rate greater than 25 MHz (e.g., as high as 100 MHz or greater). ADC acquisition timing and array row and column selection may be controlled by timing generator  456 . In particular, the timing generator provides the digital vertical data and clock signals (DV, CV) to control row selection, the digital horizontal data and clock signals (DH, CH) to control column selection, and the column sample and hold signal COL SH to sample respective pixel voltages for an enabled row. (See FIG. 9 in U.S. Pat. No. 7,948,015, which is incorporated by reference in its entirety herein, for further details). In one implementation, timing generator  456  may be implemented by a microprocessor executing code and configured as a multi-channel digital pattern generator to provide appropriately timed control signals. For example, timing generator  456  may be implemented as a field-programmable gate array (FPGA). For further details of row and column circuitry, see U.S. Pat. No. 7,948,015, which is incorporated by reference in its entirety herein. 
       FIG. 5  illustrates a method  500  according to an exemplary embodiment of how various operational characteristics of sensors of a sensor array may be taken into consideration during a read operation of the sensor array. In step  501 , at least one operational characteristic of an individual sensor, a group of sensors, or all sensors of a sensor array is determined. Examples of operational characteristics of sensors include, but are not limited to, bead loading quality, a noise spectrum, and a threshold voltage value, and any combinations thereof. In step  503 , a group of sensors in the array based on the operational characteristic of sensors in the group may be selected. The selecting a group of sensors in the array may be based on more than one operational characteristic of sensors in the group. In step  505 , readout of the sensors in the selected group may be enabled. According to exemplary embodiments, readout of remaining sensors of the sensor array may be bypassed. In step  507 , output signals from the enabled sensors may be received, the output signals indicating chemical reactions occurring proximate to the sensors of the sensor array. Sensors in the sensor array may include chemically-sensitive field effect transistors. The chemically-sensitive field effect transistors may be arranged in rows and columns and the selecting includes selecting contiguous rows of chemically-sensitive field effect transistors in the sensor array. During an experiment, a fluidics controller may deliver individual reagents to the flow cell and integrated circuit device in a predetermined sequence. The output signals may indicate an ion concentration due to sequencing reactions occurring proximate to the chemically-sensitive field effect transistors. In an exemplary implementation, the output signals may be analog signals and the method may further include converting the output signals into digital signals and the receiving output signals may further include receiving the converted digital signals. 
       FIG. 6  illustrates a method  600  for nucleic acid sequencing according to an exemplary implementation. In step  601 , template nucleic acids may be provided to at least some of a plurality of locations coupled to sensors of an array. In step  603 , output signals of the sensors of the array may be analyzed to identify which locations in the plurality of locations contain the disposed template nucleic acids. In step  605 , a group of sensors coupled to the identified locations containing the disposed template nucleic acids may be selected. In step  607 , known nucleotides within at least some of the plurality of locations may be introduced. In step  609 , the output signals of the selected sensors may be measured to detect sequencing reaction byproducts resulting from incorporation of the introduced known nucleotides into one of more primers hybridized to at least one of the disposed template nucleic acids. The sequencing reaction byproducts may comprise, for example, hydrogen ions, hydroxide ions, other ions, inorganic pyrophosphates (PPi), or any other suitable reaction byproduct or combination thereof. The sequencing reaction byproducts resulting from incorporation may be of chemically similar composition for each of the known nucleotides and sensors in the array detect a same byproduct. In step  611 , readout of the sensors in the selected group, and bypassing readout of remaining sensors of the sensor array may be enabled. In step  613 , at least a portion of sequences of at least a portion of the template nucleic acids may be determined based on the introduced known nucleotides and further based on the measured output signals. The sensors may comprise field-effect transistors having a chemically sensitive portion responsive to the sequencing reaction byproducts and may be disposed in proximity to the locations such that the at least one of the sequencing reaction byproducts diffuse or contact the sensors to thereby be detected. The chemically sensitive portion of the field-effect transistors of the array is responsive to a plurality of different sequencing reaction byproducts. The locations may be within respective reaction chambers. The measured output signals may be analog signals and the method may further include converting the output signals into digital signals and the receiving output signals may further include receiving the converted digital signals. 
       FIG. 7  illustrates examples of two different groups of sensors in an array on integrated circuit device  100  that have been selected based on an operational characteristic of sensors in the group. The sensors in the array illustrated in  FIG. 7  are arranged in rows and columns. For example, a first group of sensors (defined by sensors within area  701 ) may be selected based on one (or more) operational characteristics of sensors in the group. Another group of sensors (defined by sensors within area  702 ) may be selected based on (a) different operational characteristic(s) of sensors in the group. The sensors within the wells may comprise fluid-addressable wells  705 , and may also comprise reference wells  707 . Thus, the group of sensors that is selected may be coupled to only fluid-addressable wells  705 , only reference wells  707 , or both fluid-addressable wells  705  and reference wells  707 . In some embodiments, two or more, non-overlapping groups or partially-overlapping groups may be selected based on the same or different operational characteristics of sensors in the respective groups. Sensors in the two or more areas may be read out separately. First, sensors within area  701  may be read out, followed by sensors within area  702 , or vice versa. Sensors within area  701  and  702  may be read out at the same time, while maintaining correspondence between the output signals and their respective sensors within a defined area ( 701 / 702 , for example). The output signals from two or more corresponding areas may be compared with one another to determine which area provides an improved signal based on location of sensors on the array and/or based on the same or different operational characteristics of the sensors. The comparison may be used to predict high performance/preferred areas (sensors/sensor locations) for future experiments on unused integrated circuits/sensor arrays. The group(s) of sensors, operational characteristic(s), and the addressable area on the array may be dynamically selectable during an experiment or they may be predetermined before an experiment. The number of sensors in the group selected may vary, and the shape of the area defined by selected sensors may vary. 
     Embodiments of the above-described system provide particular technical advantages including an improvement in signal to noise ratio, and taking advantage of various operational characteristics of sensors of a sensor array, further enabling oversampling and improved speed in readout of output signals. Note that not all of the activities described above in the general description or the examples are required, that a portion of a specific activity may not be required, and that one or more further activities may be performed in addition to those described. Still further, the order in which activities are listed are not necessarily the order in which they are performed. In the foregoing specification, the concepts have been described with reference to specific embodiments. However, one of ordinary skill in the art appreciates that various modifications and changes can be made without departing from the scope of the invention as set forth in the claims below. Accordingly, the specification and figures are to be regarded in an illustrative rather than a restrictive sense, and all such modifications are intended to be included within the scope of invention. 
     Benefits, other advantages, and solutions to problems have been described above with regard to specific embodiments. However, the benefits, advantages, solutions to problems, and any feature(s) that may cause any benefit, advantage, or solution to occur or become more pronounced are not to be construed as a critical, required, or essential feature of any or all the claims. After reading the specification, skilled artisans will appreciate that certain features are, for clarity, described herein in the context of separate embodiments, may also be provided in combination in a single embodiment. Conversely, various features that are, for brevity, described in the context of a single embodiment, may also be provided separately or in any subcombination. Further, references to values stated in ranges include each and every value within that range. 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.