Flow cell and related method

Abstract

A flow cell and corresponding methods are provided. The flow cell may include a support frame having a top surface and a back surface, and at least one cavity extending from the top surface. The flow cell may include at least one optical detection device having an active area disposed in the at least one cavity. The flow cell may include a support member disposed in the at least one cavity between the support frame and an outer periphery of the at least one optical detection device, the support member connecting the support frame to the outer periphery of the at least one optical detection device. The flow cell may include a lid connected to the support frame, extending over the at least one optical detection device and about the outer periphery of the at least one optical detection device. The lid and at least the top surface of the at least one optical detection device form a flow path therebetween.

Description

Technical Field

[0001] Related Applications and Cross - References This patent application claims priority to U.S. Provisional Patent Application No. 62 / 731,785, entitled Flow Cells and Methods Related to Same, filed on September 14, 2018, the entire contents of which are incorporated herein by reference.

[0002] Various protocols in biological or chemical research involve performing a number of controlled reactions on a local support body surface or within a predefined reaction chamber. The specified reactions are then observed or detected, and subsequent analysis may help identify or elucidate the properties of the substances involved in the reaction. For example, in some multiplex assays, an unknown analyte having a distinguishable label (e.g., a fluorescent label) may be exposed to thousands of known probes under controlled conditions. Each known probe may be deposited in a corresponding well of a microplate. Observing any chemical reaction that occurs between the known probe and the unknown analyte in the well may help identify or elucidate the properties of the analyte. Other examples of such protocols include known DNA sequencing processes, such as sequencing by synthesis (SBS) or cyclic array sequencing. In some conventional fluorescence detection protocols, an optical system is used to irradiate a fluorescence - labeled analyte with excitation light and detect the fluorescence signal that may be emitted from the analyte. However, such optical systems are relatively expensive and may involve a relatively large benchtop footprint. For example, such an optical system may include the arrangement of lenses, filters, and light sources.

[0003] In other proposed detection systems, the controlled reaction occurs on a local support surface of a flow cell or within a predefined reaction chamber that does not involve a large-scale optical assembly for detecting fluorescence emission. The flow cell includes an electronic solid-state light detector device or an imaging device (e.g., a complementary metal-oxide semiconductor (CMOS) light detector device or a charge-coupled device (CCD) light detector device) disposed adjacent to (e.g., below) the support body surface / chamber for detecting the emission from the reaction. However, such proposed solid imaging systems may have several limitations. For example, the flow cell of such a system may be designed as a single-use consumable. Thus, it may be beneficial if the flow cell is a small and inexpensive device. In a relatively small flow cell, it may be beneficial to utilize as much as possible the biosensor active area of the light detection device and / or to provide as large a biosensor active area as possible.

[0004] Many current flow cell designs prevent full utilization of the biosensor active area by making the lid portion of the flow cell coupled to the active area, thereby preventing access to such area by a reagent solution (e.g., a solution having fluorescently labeled molecules) and / or preventing the area from containing reaction sites (e.g., containing an analyte). Further, the biosensor active area is often provided by a single sensor, and relatively large sensors having a relatively large biosensor active area are costly. Many current flow cell designs also provide only a limited number of wiring configurations to the light detection device. SUMMARY OF THE INVENTION

[0005] In one aspect of the present disclosure, a flow cell is provided. The flow cell includes a support frame including an upper surface, a back surface, and at least one cavity extending from the upper surface toward the lower surface. ​ The flow cell further includes a support member disposed within at least one cavity between the support frame and the outer periphery of at least one light detection device, the support member coupling the support frame and the at least one light detection device. The flow cell also includes a lid extending over at least one light detection device and coupled to the upper surface of the support frame about the outer periphery of the at least one light detection device and includes. The lid and at least the upper surface of the at least one light detection device form a flow path therebetween.

[0006] In some examples, the support frame further includes at least one conductive via extending from the upper surface to the lower surface. In some such examples, the at least one light detection device includes at least one solid-state light detection device including a base wafer portion, a plurality of light sensors, a device circuit for transmitting a data signal based on photons detected by the light sensors and electrically coupled to the light sensors, and a plurality of light guides associated with the plurality of light sensors. In some such examples, the device circuit of the at least one solid-state light detection device is electrically coupled to at least one conductive via on the upper surface of the support frame.

[0007] In some examples, the lid is indirectly coupled to the upper surface of the support frame. In some examples, the at least one cavity includes a cavity having a plurality of light detection devices disposed therein. In some such examples, the plurality of light detection devices include separate light detection devices spaced apart from each other, and the support member further extends between adjacent light detection devices. In some other such examples, the plurality of light detection devices include at least two integrated light detection devices, and the support member extends between the support frame and the outer peripheries of the at least two integrated light detection devices.

[0008] In some such examples, at least one light detection device includes a plurality of light detection devices. In some such examples, at least one light detection device includes a plurality of cavities, and each light detection device of the plurality of light detection devices is disposed within a different cavity of a support frame. In some such examples, at least one light detection device includes at least one solid state light detection device including a base wafer portion, a plurality of light sensors, a device circuit electrically coupled to the light sensors to transmit a data signal based on photons detected by the light sensors, and a plurality of light guides associated with the plurality of light sensors. In some such examples, at least one cavity extends through the support frame from an upper side to a lower side, the device circuit includes vias extending through the base wafer portion, and the flow cell further includes electrical contacts disposed at least partially along a back side of the support frame and electrically coupled to the vias. In some other such examples, at least one light detection device further includes a reaction structure disposed on top of the plurality of light guides forming its upper surface, the reaction structure including a plurality of nanowells disposed within an active region.

[0009] In some examples, at least one cavity extends only partially through the support frame from an upper side towards a lower side. In some examples, at least one light detection device includes at least one complementary metal oxide semiconductor (CMOS) light sensor.

[0010] In some examples, the flow path extends across the entire active region of at least one light detection device.

[0011] In another aspect of the present disclosure, a method is provided. The method includes attaching an upper surface of a support frame to a planar support surface of a substrate, where the support frame includes at least one cavity extending from an upper surface to a lower surface of the substrate. The method further includes disposing at least one light detection device within at least one cavity such that an upper surface thereof is disposed on a planar support surface of the substrate and an end of the cavity extends between an outer periphery of the support frame and an outer periphery of at least one light detection device, where the at least one light detection device includes an active region and an upper surface). The method also includes filling an end of the cavity with a support material for coupling the support frame and the at least one light detection device). The method further includes separating the support frame from the substrate). The method also includes attaching a lid to an upper surface of the support frame about an outer periphery of the at least one light detection device to form a flow cell, where the lid extends over the at least one light detection device and forms a flow path between the lid and at least an upper surface of the at least one light detection device including).

[0012] In some examples, the at least one light detection device includes at least one solid-state light detection device including a base wafer portion forming a back surface, a plurality of light sensors, a device circuit electrically coupled to the light sensors to transmit a data signal based on photons detected by the light sensors, and a plurality of light guides associated with the plurality of light sensors, the support frame further includes at least one electrically conductive via extending from an upper surface to a lower surface, and the method further includes electrically coupling the device circuit of the at least one solid-state light detection device to the at least one electrically conductive via on the upper surface of the support frame).

[0013] In some examples, at least one photodetector device includes at least one base wafer portion forming a back surface, a plurality of optical sensors, a device circuit electrically coupled to the optical sensors and configured to transmit a data signal based on photons detected by the optical sensors, and a plurality of light guides associated with the plurality of optical sensors. The device circuit includes vias extending through the base wafer portion to the back surface of the base wafer portion. The method further includes coupling electrical contacts disposed at least partially along the back surface of the support frame to vias on the back surface of the base wafer portion.

[0014] In some examples, the method further includes forming a reaction structure on at least one photodetector device before attaching the lid. The reaction structure forms an upper surface of the at least one photodetector device and includes a plurality of nanowells disposed within the active region. In some such examples, separating the support frame from the substrate exposes a recessed upper surface of the support material extending downward between the upper surface of the support frame and the upper surface of the at least one photodetector device. The reaction structure extends between the recessed upper surface of the support material and the upper surface of the support frame. The reaction structure forms a planar upper surface along which the plurality of nanowells extend.

[0015] In some examples, the method further includes obtaining at least one photodetector device, which includes dicing at least one complementary metal oxide semiconductor (CMOS) optical sensor from a plurality of integrated CMOS optical sensors.

[0016] In some examples, the flow path extends across the entire active region of the at least one photodetector device.

[0017] In another aspect of the present disclosure, another method is provided. The method includes depositing a first support material at the bottom of at least one cavity of a support frame, where at least one cavity extends only partially through the support frame from top to bottom. The method further includes placing at least one light detection device within at least one cavity and on top of the deposited first support material such that an end of at least one cavity extends between the support frame and an outer periphery of at least one light detection device, where at least one light detection device includes an active region and a top surface. The method also includes filling an end of the cavity with a second support material. The method further includes attaching a lid to the top surface of the support frame about an outer periphery of at least one light detection device to form a flow cell, where the lid extends over at least one light detection device and forms a flow path between the lid and at least the top surface of at least one light detection device.

[0018] In some examples, the flow path extends across the entire active region of at least one light detection device.

[0019] It is to be understood that all combinations of the foregoing aspects and additional concepts discussed in more detail below are part of the subject matter of the present invention, provided such concepts are not mutually inconsistent, and are contemplated to achieve the advantages disclosed herein.

[0020] These and other objects, features, and advantages of the present disclosure will become apparent from the following detailed description of various aspects of the present disclosure taken in conjunction with the accompanying drawings.

[0021] These and other features, aspects, and advantages of the present disclosure will be better understood when the following detailed description is read in conjunction with the accompanying drawings. The accompanying drawings are not necessarily drawn to scale, and like reference numerals throughout the drawings represent like aspects.

[0022] FIG. 1 shows a cross-section of a photodetector device, as an example, in accordance with one or more aspects of the present disclosure.

[0023] FIG. 2 shows a cross-section of another photodetector device, as an example, in accordance with one or more aspects of the present disclosure.

[0024] FIG. 3 shows a support structure including a support frame and a substrate for forming a flow cell, in one embodiment, in accordance with one or more aspects of the present disclosure.

[0025] FIG. 4 shows placing a photodetector device within a cavity of the support structure of FIG. 3, in one example, in accordance with one or more aspects of the present disclosure.

[0026] FIG. 5 shows a cross-section of a photodetector device disposed within a cavity of the support structure of FIG. 3, as an example, in accordance with one or more aspects of the present disclosure.

[0027] FIG. 6 shows a cross-section of a photodetector device disposed within a cavity of another support structure, in one example, in accordance with one or more aspects of the present disclosure.

[0028] FIG. 7 shows a cross-section of a photodetector device disposed within a cavity of another support structure, in one example, in accordance with one or more aspects of the present disclosure.

[0029] FIG. 8 shows a cross-section of a photodetector device disposed within a cavity of another support structure, in one example, in accordance with one or more aspects of the present disclosure.

[0030] FIG. 9 shows filling a cavity extending around a periphery of a photodetector device disposed within a cavity of the support structure of FIG. 4 with a filling material, in one embodiment, in accordance with one or more aspects of the present disclosure.

[0031] FIG. 10 shows the removal of the substrate from the support frame of the support structure of FIG. 4 in accordance with one or more aspects of the present disclosure in one embodiment.

[0032] FIG. 11A shows a cross-section of a plurality of photodetector devices coupled within a plurality of cavities of the support frame of FIG. 4 with the substrate removed, in accordance with one or more aspects of the present disclosure in one embodiment.

[0033] FIG. 11B shows a top view of a plurality of photodetector devices coupled within the cavity support frame of FIG. 11A, in accordance with one or more aspects of the present disclosure in one embodiment.

[0034] FIG. 12A shows a cross-section of a plurality of photodetector devices coupled within a cavity of the support frame with the substrate removed, in accordance with one or more aspects of the present disclosure in one embodiment.

[0035] FIG. 12B shows a top view of a plurality of photodetector devices coupled within the cavity of the support frame of FIG. 12A, in accordance with one or more aspects of the present disclosure in one embodiment.

[0036] FIG. 13A shows a cross-section of a plurality of photodetector devices coupled within another cavity of the support frame with the substrate removed, in accordance with one or more aspects of the present disclosure in one embodiment.

[0037] FIG. 13B shows a top view of a plurality of photodetector devices coupled within the cavity of the support frame of FIG. 13A, in accordance with one or more aspects of the present disclosure in one embodiment.

[0038] FIG. 14 shows a cross-section of a plurality of photodetector devices coupled within a cavity of another support frame, in accordance with one or more aspects of the present disclosure in one embodiment.

[0039] FIG. 15A shows, as an example, a cross-section of a light detection device and a filling material within a cavity of a support frame in accordance with one or more aspects of the present disclosure.

[0040] FIG. 15B shows, in one embodiment, a cross-section of a light detection device and a filling material within a cavity of the support frame of FIG. 15A having a reaction structure disposed thereon in accordance with one or more aspects of the present disclosure.

[0041] FIG. 16A shows, in one embodiment, a cross-section of an intermediate flow cell device including a plurality of light detection devices coupled within a plurality of cavities of a support frame in accordance with one or more aspects of the present disclosure.

[0042] FIGS. 16B - 16D illustrate, in one embodiment, the formation of backside contacts on the intermediate flow cell device of FIG. 16A.

[0043] FIG. 17A shows, in one embodiment, a cross-section of another intermediate flow cell device including a plurality of light detection devices coupled within a plurality of cavities of a support frame in accordance with one or more aspects of the present disclosure.

[0044] FIGS. 17B and 17C illustrate, in one embodiment, the formation of backside contacts on the intermediate flow cell device of FIG. 17A.

[0045] FIG. 18A shows, in one embodiment, a cross-section of another intermediate flow cell device including a plurality of light detection devices coupled within a plurality of cavities of a support frame in accordance with one or more aspects of the present disclosure.

[0046] FIGS. 18B and 18C illustrate, in one embodiment, the formation of backside contacts on the intermediate flow cell device of FIG. 18A.

[0047] FIG. 19A shows, in one embodiment, a cross-section of another intermediate flow cell device including a plurality of light detection devices coupled within a plurality of cavities of a support frame in accordance with one or more aspects of the present disclosure.

[0048] Figures 19B and 19C illustrate the formation of back contacts on the intermediate flow cell device of Figure 19A in one embodiment.

[0049] Figure 20 shows a plurality of flow cells formed through the intermediate flow cell device of Figure 19C in accordance with one or more aspects of the present disclosure in one embodiment.

[0050] Figure 21 shows, as an example, the flow path and active region of the photodetection device of the flow cell of Figure 20 in accordance with one or more aspects of the present disclosure.

[0051] Figure 22 shows a plurality of different flow cells that may be formed from the plurality of flow cells of the flow cell of Figure 20 in accordance with one or more aspects of the present disclosure in one embodiment. **DETAILED DESCRIPTION OF THE INVENTION**

[0052] Aspects, specific examples, features, advantages, and details of the present disclosure are further described in more detail below with reference to the non-limiting examples illustrated in the accompanying drawings. Descriptions of well-known materials, manufacturing tools, processing techniques, etc. are omitted so as not to unnecessarily obscure the relevant details. However, it should be understood that the detailed description and specific examples are provided only by way of illustration and not by way of limitation while showing aspects of the present disclosure. Various substitutions, modifications, additions, and / or arrangements within the spirit and / or scope of the underlying inventive concept will be apparent to those skilled in the art from this disclosure.

[0053] Throughout the disclosure, approximation language, as used herein, may be applied to modify any quantitative representation that could permissibly vary without resulting in a change in the basic function to which it is related. Accordingly, values modified by terms such as "about" or "substantially" are not to be limited to the exact values specified. In some embodiments, the approximation language can correspond to the precision of an instrument for measuring a value. These terms can refer to, for example, within ±5% or less, for example within ±2% or less, for example within ±1% or less, for example within ±0.5% or less, for example within ±0.2% or less, for example within ±0.1% or less, for example within ±0.05% or less, and the like. In some cases, the approximation language may correspond to the precision of the instrument for measuring the value.

[0054] The terms used in this specification are for the purpose of describing particular examples only and are not intended to be limiting. As used in this specification, the singular forms "a", "an", and "the" are intended to include the plural forms as well, unless the context clearly indicates otherwise. Further, reference to "one example" is not intended to be construed as excluding the existence of additional examples that also incorporate the recited features. Further, unless expressly stated to the contrary, the terms "comprising" (and any form of "comprise", such as "comprises" and "comprising"), "have" (and any form of "have", such as "has" and "having"), "include" (and any form of "include", such as "includes" and "including"), and "contain" (and any form of "contain", such as "contains" and "containing") are used as open-ended conjunctive verbs. As a result, an example of "comprises", "has", "includes", or "contains" has one or more steps or elements, but is not limited to having only such one or more steps or elements. As used in this specification, the terms "may" and "may be" indicate the modification of other verbs by expressing one or more of the possibility of occurrence within a series of circumstances, the possession of a particular property, characteristic, or function, and / or the ability, capacity, or possibility associated with the modified verb. Thus, the usage of "may" and "may be" indicates that the modified term is clearly appropriate, possible, or suitable for the indicated ability, function, or usage, but takes into account that in some circumstances the modified term may or may not be appropriate, possible, or suitable. For example, in one circumstance, an event or ability may be expected, and in another circumstance, that event or ability may not occur - this distinction is captured by the terms "may" and "may be".

[0055] As used herein, unless otherwise indicated, the term "whole" (and any other form of "whole") means at least a substantial portion, such as at least 95% or at least 99%. As used herein, the term "whole" (and any other form of "whole") is thereby not limited to 100% unless otherwise indicated. As used herein, the term "layer" is not limited to a single continuous body of material unless otherwise indicated. A "layer" may include a plurality of sub-layers that may be the same material or different materials and / or may include coatings, adhesives, etc. Further, to provide the features disclosed herein, one or more layers (or sub-layers) of the flow cells disclosed herein may be modified (e.g., may be etched, may be deposited with material, etc.).

[0056] The flow cells described herein may be used in a variety of biological or chemical processes and systems for academic or commercial analysis. More specifically, the flow cells described herein may be used in a variety of processes and systems where it is desired to detect events, properties, qualities, or characteristics indicative of a specified reaction. For example, the flow cells described herein may include or be integrated with photodetector devices, biosensors, and their components, as well as bioassay systems that operate using biosensors.

[0057] The flow cell may be configured to facilitate a plurality of specified reactions that can be detected individually or collectively. The flow cell may be configured to perform a number of cycles in which a plurality of specified reactions occur in parallel. For example, the flow cell may be used to sequence a dense array of DNA features through iterative cycles of enzymatic manipulation and light or image detection / acquisition. Thus, the flow cell may be communicatively coupled to one or more microfluidic channels that deliver reagents or other reaction components in a reaction solution to a reaction site of the flow cell. The reaction sites may be provided in a predetermined manner such as a uniform or repeating pattern, or may be spaced apart. Alternatively, the reaction sites may be randomly distributed. Each of the reaction sites may be associated with one or more light guides and one or more light sensors that detect light from associated reaction sites. In some flow cells, the reaction sites may be disposed within reaction recesses or chambers, which may at least partially compartmentalize the specified reactions therein.

[0058] As used herein, a "specified reaction" involves at least one change in a chemical, electrical, physical, or optical property (or quality), and includes chemical or biological substances such as an analyte of interest. In a particular flow cell, the specified reaction may be, for example, a positive binding event such as binding a fluorescently labeled biomolecule to a substance of interest. More generally, the specified reaction may be a chemical conversion, chemical change, or chemical interaction. The specified reaction may also be a change in an electrical property. In a particular flow cell, the specified reaction includes incorporating a fluorescently labeled molecule into an analyte. The analyte may be an oligonucleotide, and the fluorescently labeled molecule may be a nucleotide. The specified reaction may be detected when excitation light is directed at an oligonucleotide having a labeled nucleotide and the fluorophore emits a detectable fluorescent signal. In an alternative flow cell, the detected fluorescence is the result of chemiluminescence or bioluminescence. The predetermined reaction may also, for example, increase fluorescence (or Förster) resonance energy transfer (FRET) by bringing a donor fluorophore in proximity to an acceptor fluorophore, decrease FRET by separating the donor fluorophore and the acceptor fluorophore, increase fluorescence by separating a quencher from a fluorophore, or decrease fluorescence by co-localizing a quencher and a fluorophore.

[0059] As used herein, a "reaction solution", "reaction component", or "reactant" includes any substance that can be used to obtain at least one specified reaction. For example, potential reaction components include, for example, reagents, enzymes, samples, other biomolecules, and buffers. Reaction components may be delivered in solution to a reaction site within a flow cell disclosed herein and / or may be immobilized at the reaction site. Reaction components may interact directly or indirectly with another substance such as an analyte immobilized at the reaction site of the flow cell.

[0060] As used herein, the term "reaction site" is a local region where at least one specified reaction can occur. The reaction site may include the surface of a support of a reaction structure or substrate to which a substance may be immobilized thereon. For example, the reaction site may include the surface of a reaction structure (which may be disposed within the flow channel of a flow cell) having reaction components such as colonies of nucleic acids thereon. In some flow cells, the nucleic acids within the colony have the same sequence and are, for example, clone copies of single-stranded or double-stranded templates. However, in some flow cells, the reaction site may include only a single nucleic acid molecule, for example, in single-stranded or double-stranded form.

[0061] Multiple reaction sites may be randomly arranged along the reaction structure of the flow cell or may be arranged in a predetermined manner (e.g., side by side within a matrix such as a microarray). The reaction site can also include a reaction chamber or recess that at least partially defines a spatial region or volume configured to compartmentalize the specified reaction. As used herein, the term "reaction chamber" or "reaction recess" includes a defined spatial region of a support structure (which often is in fluid communication with a flow channel). The reaction recess may be at least partially separated from the surrounding environment or other spatial regions. For example, multiple reaction recesses may be separated from each other by a shared wall. As a more specific example, the reaction recess may be a nanowell formed by a depression, pit, well, groove, cavity, or indentation defined by the inner surface of a detection surface, and the nanowell may have an opening or openings such that it can be in fluid communication with the flow channel (i.e., an open face).

[0062] In some flow cells, the reaction recesses of the reaction structure of the flow cell are sized and shaped such that a solid (including semi-solid) may be fully or partially inserted therein. For example, the reaction recess may have a size and shape for accommodating capture beads. The capture beads may have clonally amplified DNA or other substances therein. Alternatively, the reaction recess may be sized and shaped to receive an approximate number of beads or solid substrates. As another example, the reaction recess may be filled with a porous gel or substance configured to control diffusion, or may be filled with a substance configured to filter a fluid that may flow into the reaction recess.

[0063] The optical sensors (e.g., photodiodes) of one or more optical detection devices of the flow cell may be associated with corresponding reaction sites. The optical sensor associated with the reaction site detects the light emission from the associated reaction site via at least one light guide when a predetermined reaction occurs at the associated reaction site. In some flow cells, multiple optical sensors (e.g., multiple pixels of an optical detection device or a camera device) may be associated with a single reaction site. In other flow cells, a single optical sensor (e.g., a single pixel) may be associated with a single reaction site or may be associated with a group of reaction sites. The optical sensors, reaction sites, and other features of the flow cell may be configured such that at least a portion of the light is directly detected by the optical sensor without being reflected.

[0064] As used herein, "biological or chemical substances" include biomolecules, samples of interest, analytes of interest, and other chemical compounds. Biological or chemical substances may be used to detect, identify, or analyze other chemical substances, or may function as intermediates for studying or analyzing other chemical substances. In particular, in a flow cell, biological or chemical substances include biomolecules. As used herein, "biomolecule" includes at least one of biopolymers, nucleosides, nucleic acids, polynucleotides, oligonucleotides, proteins, enzymes, polypeptides, antibodies, antigens, ligands, receptors, polysaccharides, carbohydrates, polyphosphates, cells, tissues, organisms, or fragments thereof, or other biologically active chemical compounds (plural) such as analogs or mimetics of the foregoing species. In further examples, biological or chemical substances or biomolecules include enzymes or reagents used in binding reactions to detect the products of another reaction, for example, enzymes or reagents used to detect pyrophosphate in a pyrosequencing reaction.

[0065] Biomolecules, samples, and biological or chemical substances may be naturally occurring or synthetic and may be suspended in a solution or mixture within a reaction recess or region. Also, biomolecules, samples, and biological or chemical substances may be bound to a solid phase or gel material. Biomolecules, samples, and biological or chemical substances may also include pharmaceutical compositions. In some embodiments, biomolecules, samples, and biological or chemical substances of interest may be referred to as targets, probes, or analytes.

[0066] As used herein, a "flow cell" includes a device that includes a lid extending over a reaction structure that forms a flow path cooperatively therebetween and that communicates with a plurality of reaction sites among a plurality of reaction sites of the reaction structure, and includes at least one light detection device configured to detect a designated reaction occurring at or proximate to the reaction sites. The flow cell may include a solid state light detection device or an "imaging" device (e.g., a CCD or CMOS light detection device). As one specific example, the flow cell may be configured to be fluidly and / or electrically coupled to a cartridge incorporating a pump, and the cartridge may be configured to be fluidly and / or electrically coupled to a bioassay system. The cartridge and / or the bioassay system may deliver a reaction solution to the reaction sites of the flow cell and perform a plurality of imaging events according to a predetermined protocol (e.g., sequencing by synthesis). For example, the cartridge and / or the bioassay system may direct one or more reaction solutions through the flow path of the flow cell and thereby along the reaction sites. At least one of the reaction solutions may include four types of nucleotides having the same or different fluorescent labels. The nucleotides may bind to the reaction sites of the flow cell, such as corresponding oligonucleotides of the reaction sites. Next, the cartridge and / or the bioassay system may illuminate the reaction sites using an excitation light source (e.g., a solid state light source such as a light emitting diode (LED)). The excitation light may have a wavelength including a predetermined wavelength or wavelength range. The fluorescent labels excited by the incident excitation light may provide an emission signal (e.g., light of a wavelength different from the excitation light and potentially light of different wavelengths from each other) that can be detected by the light sensors of the flow cell.

[0067] As used herein, the term "immobilized", when used with respect to a biomolecule or a biological or chemical substance, includes substantially attaching the biomolecule or biological or chemical substance at the molecular level to a surface such as the detection surface of a reaction structure on a light detection device of a flow cell. For example, the biomolecule or biological or chemical substance may be immobilized on the detection surface of the reaction structure of the flow cell using adsorption techniques including non-covalent interactions (e.g., electrostatic forces, van der Waals, dehydration of hydrophobic interfaces), and covalent techniques where functional groups or linkers facilitate attachment of the biomolecule to the detection surface. The immobilization of a biomolecule or biological or chemical substance to the detection surface of the reaction structure of the flow cell may be based on the properties of the surface, the liquid medium carrying the biomolecule or biological or chemical substance, and the properties of the biomolecule or biological or chemical substance itself. In some cases, the detection surface may be functionalized (e.g., chemically or physically modified) to facilitate immobilization of the biomolecule (or biological or chemical substance).

[0068] In some examples, nucleic acids can be immobilized to the reaction structure of a flow cell, such as on the surface of a reaction recess or the surface of its nanowells. Native nucleotides and enzymes configured to interact with native nucleotides can be utilized. Native nucleotides include, for example, ribonucleotides or deoxyribonucleotides. Native nucleotides can be in mono-, di-, or triphosphate form and can have a base selected from adenine (A), thymine (T), uracil (U), guanine (G), or cytosine (C). However, it will be understood that non-native nucleotides, modified nucleotides, or analogs of the nucleotides can be utilized.

[0069] As described above, biomolecules or biological or chemical substances may be immobilized at reaction sites within the nanowells of the reaction structure of the flow cell. Such biomolecules or biological substances may be physically retained or immobilized within the reaction recess via interference fit, adhesion, covalent bonding, or entrapment. An item or solid may be disposed within the reaction recess and may include, for example, polymer beads, pellets, agarose gel, powder, quantum dots, or other solids that may be compressed and / or retained within the nanowell. In certain embodiments, the nanowell may be coated or filled with a hydrogel layer capable of covalently bonding DNA oligonucleotides. Nucleic acid superstructures such as DNA balls may be disposed within or on the nanowell, for example, by attachment to the inner surface of the nanowell or by retention in the liquid within the nanowell. A DNA ball or other nucleic acid superstructure may be implemented and then disposed within or in the nanowell. Alternatively, a DNA ball may be synthesized in situ in the nanowell. The substance immobilized within the nanowell may be in a solid state, liquid state, or gaseous state.

[0070] The disclosed flow cell may be configured for biological or chemical analysis to obtain any information or data related thereto. Certain flow cells may include a part of a nucleic acid sequencing system (or sequencer) configured for various applications including, but not limited to, de novo sequencing, re-sequencing of whole genomes or target genomic regions, and metagenomics. The sequencing system may be configured to perform DNA or RNA analysis. The flow cell may be configured to perform a number of parallel reactions on its active surface to obtain information related to the reaction.

[0071] The flow cell may include one or more flow channels that direct a solution over, or towards, reaction sites on the active region / surface of the reaction structure via one or more light detection devices, as further described below. In use, the flow cell may be in fluid communication with a fluid storage system (not shown) that may thereby store various reaction components or reactants used to perform a specified reaction within the flow cell, for example. The fluid storage system may also store fluid for flushing or washing the plurality of flow channels of the flow cell and / or for diluting reactants. For example, the fluid storage system may include various reservoirs for storing samples, reagents, enzymes, other biomolecules, buffers, aqueous solutions, non-polar solutions, and the like. Further, the fluid storage system may include a waste reservoir for receiving waste from the flow cell.

[0072] Figure 1 shows an example of a light detection device 10 that can be utilized in the flow cell of the present disclosure. The light detection device 10 may be composed of a plurality of stacked layers such as a base layer or wafer 14, and a plurality of dielectric layers and metal-dielectric layers extending thereon. As shown in Figure 1, the light detection device 10 includes a sensor array of light sensors 12 and a guide array of light guides 18. Further, the light detection device 10 may include a reaction structure 20 extending along the upper portion 22 of the light detection device 10, including over openings of the light guides 18. The light detection device 10 may be configured such that each light sensor 12 corresponds to or aligns with a single light guide and / or a single reaction recess 16 (e.g., a nanowell) of the reaction structure 20 disposed on the upper surface 22 of the light detection device 10, and in such a case, the light detection device 10 receives photons only therefrom. However, in other examples, a single light sensor 12 may receive photons via one or more light guides 18 and / or from one or more reaction recesses 16. A single light sensor 12 may thereby form one pixel or one or more pixels. As shown in Figure 1, the reaction recess 16 may be defined, for example, by a depression or a change in depth (or thickness) of the upper surface of the reaction structure 20.

[0073] As shown in FIG. 1, the arrangement of the light guide 18 and the reaction recesses 16 of the reaction structure 20 (and potentially the light sensor 12) may be provided in a defined repeating pattern such that at least a portion of the recesses 16 and / or the light guide 18 (and potentially the light sensor 12) are equidistant from each other in a defined position pattern. In other examples, the reaction recesses 16 and / or the light guide 18 (and potentially the light sensor 12) may be provided in a random pattern, and / or at least a portion of the reaction recesses 16 and / or the light guide 18 (and potentially the light sensor 12) may be variably spaced from each other. The interstitial region between the arrangements of the reaction recesses 16 may be a substantially flat surface. As further described below, the arrangement of the reaction recesses 16 of the reaction structure 20 may have at least one corresponding reaction site provided therein (e.g., immobilized on its surface).

[0074] Of the light detection device 10, the region sensitive to light is referred to as the active region of the device 10. The active region of the light detection device 10 thereby includes the region including the light guide 18 that directs light to the light sensor 12. As described above, the upper surface 22 of the light detection device 10 may include an arrangement of reaction recesses 16 disposed thereon to include at least one corresponding reaction site available / accessible for reagent delivery and reaction (e.g., in response to an analyte in the reaction fluid) and illumination during operation of the flow cell. As shown in FIG. 1, the reaction structure 20 may extend across the entire active region of the light detection device 10 (e.g., at least 95%, or at least 99%, or 100%). In such a configuration, the top or detector surface of the reaction structure 20 may thereby define the active surface of the light detection device 10 where the reaction fluid flows and may interact with the reaction sites formed within the reaction recesses 16. The active surface of the light detection device 10 may be composed of the surface of the recesses 16 and the interstitial region extending between and around the recesses 16.

[0075] The exposed upper surface of the reaction structure 20 (i.e., the exposed upper surface of the reaction recess 16 and / or the exposed upper surface of the interstitial region extending therebetween) may include a smooth plane / surface. In certain examples, the exposed upper surface of the interstitial region of the reaction structure 20 and / or the reaction recess 16 may be a smooth plane / surface for preventing a reaction solution or other biological or chemical substance from being captured or remaining thereon and / or for preventing pad hopping errors. For example, the upper surface exposed surface of the reaction structure 20 may include a surface roughness in the range of micrometers of surface roughness, such as a surface roughness of 20 μm or less, or a surface roughness of 1 μm or less. In some examples, the reaction structure 20 may include a surface roughness of 100 nm or less, or a surface roughness of 10 nm or less.

[0076] The reaction structure 20 may be composed of one or more layers. In one example, the reaction structure 20 includes a plurality of overlapping layers. The reaction structure 20 is configured such that an excitation light signal and / or an emission light signal from a reaction site within the reaction recess 16 (after treatment with a reaction solution) can pass therethrough and reach one or more corresponding openings of the light guides 18 and potentially one or more corresponding light sensors 12 (e.g., depending on the configuration of the light guide 18). As another example, the reaction structure 20 may include one or more layers that prevent crosstalk or "sharing" of emission light from a specific reaction site within the reaction recess 16 from propagating or passing to non-corresponding sensors 12. The reaction structure 20 may provide a solid surface that allows a chemical substance, a biomolecule, or other analyte to be immobilized thereon. For example, each of the reaction sites on the reaction recess 16 may include a cluster of biomolecules immobilized on its exposed outer surface. Thus, the reaction structure 20 may be composed of a material that allows immobilization of the reaction sites to the reaction recess 16. The reaction structure 20 may be physically or chemically modified to facilitate immobilization of biomolecules for forming reaction sites and / or to facilitate detection of luminescence therefrom. Examples of layers that may form the reaction structure 20 include at least one SiN layer and at least one TaO layer. However, the reaction structure 20 may be composed of different layers (e.g., different layers, fewer layers, and / or additional layers) and / or different materials.

[0077] The light guide 18 may be composed of a filter material configured to filter an excitation light or a wavelength range including the same, and to propagate light emitted from at least one reaction site (or a wavelength range including the same) of at least one corresponding reaction recess 16 through the light guide 18 and toward at least one corresponding photosensor 12. The light guide 18 may be, for example, an absorption filter (e.g., an organic absorption filter) such that the filter material absorbs a predetermined wavelength (or a wavelength range) and passes at least one predetermined wavelength (or a wavelength range). Each light guide 18 of the array may include substantially the same filter material, or different light guides 18 may include different filter materials. Each light guide 18 may be configured relative to the material (e.g., a dielectric material) surrounding the device 10 to form a light guiding structure. For example, the light guide 18 may have a refractive index of at least about 2.0. In a particular configuration, the light guide 18 may be configured such that the optical density (OD) or absorbance of the excitation light is at least about 4 OD.

[0078] As shown in FIG. 1, the light detection device 10 may include a circuit 24 that transmits or conducts a signal when light emission (e.g., photons) is detected by the photosensor 12. As described above, the light emission is emitted from and / or by at least one reaction site associated with the reaction recess 16 of the reaction structure 20 and may be directed or passed to the photosensor 12 associated by at least one light guide 18. The circuit device 24 may include interconnected conductive elements (e.g., conductors, traces, vias, interconnects, etc.) capable of passing an electric current, such as transmitting a data signal based on the detected photons. For example, the circuit 24 may be similar to or include an arrangement of microcircuits. The light detection device 10 may include at least one integrated circuit having an array of photosensors 12 electrically coupled to the circuit 24. The circuit 24 within the light detection device 10 may be configured for at least one of signal amplification, digitization, storage, and processing. The circuit 24 may collect (and potentially analyze) the light emission detected by the sensor 12 and generate a data signal for communicating the detection data to the bioassay system. Also, the circuit 24 may perform additional analog and / or digital signal processing in the light detection device 10.

[0079] As shown in FIG. 1, the device circuitry 24 of the photodetection device 10 may extend adjacent to or potentially only partially through the base portion 14. The base portion 14 may thereby be a cavity for an electrically conductive via or other portion of the device circuitry 24 that extends therethrough. The back surface 26 of the base portion 14, which may form the exposed back surface 26 of the photodetection device 10, may be a cavity for the device circuitry 24. In other words, the device circuitry 24 may be disposed entirely on top of the back surface 26 of the base portion 14 within the photodetection device 10 such that the device circuitry 24 has no access to the back surface 26 of the base portion 14 and / or the device 10 itself. However, as shown in FIG. 1, the device circuitry 24 may extend to the top surface of the photodetection device 10. For example, the device circuitry 24 may extend through the photodetection device 10 to the reaction structure 20 and potentially through the reaction structure 20. The top surface of the photodetection device 10 may be formed by the exposed top surface of the reaction structure 20 (if present), and thereby may include the device circuitry 24 as shown in FIG. 1. In other words, the device circuitry 24 may be exposed and accessible at the top surface of the photodetection device 10 and thereby may be the top surface (if present) of the reaction structure 20 as shown in FIG. 1.

[0080] The light detection device may be manufactured using an integrated circuit manufacturing process, such as a process used to manufacture a charge-coupled device circuit (CCD) or a complementary metal-oxide semiconductor (CMOS) device or circuit. The light detection device may thereby include, for example, one or more semiconductor materials and may take the form of, for example, a CMOS light detection device (e.g., a CMOS image sensor) or a CCD image sensor, which is another type of image sensor. Also, in the present embodiment, the light detection device 10 is a CMOS type imaging device as shown in FIG. 1, but other types of imaging devices may be used. For example, the light detection device 10 may be semiconductor-based as shown in FIG. 1 and may be composed of a plurality of stacked bodies including a device base portion 14, which may be, for example, a silicon layer or a wafer.

[0081] When configured as the CMOS type light detection device 10, "complementary" means including both n-type and p-type metal-oxide semiconductor field-effect transistors (MOSFETs) in an integrated circuit (IC) fabricated using CMOS technology. Each MOSFET has a metal gate having a gate insulator such as an oxide (thus, the "metal oxide" part of the name) and a semiconductor material (corresponding to the "semiconductor" in the name) under the gate. When the light detection device 10 is configured as shown in FIG. 1, the light sensor 12 may be electrically coupled to the circuit 24, for example, via a gate.

[0082] As a semiconductor-based photodetector device 10, at least a portion of the device circuitry 24 may be provided within a device layer or substrate layer in which the light guides 118 may each extend. Each of the substrate layers may include interconnected conductive elements that form at least a portion of the device circuitry 24, with a dielectric material surrounding or adjacent to the conductive elements of the circuitry. The conductive elements of the device circuitry 24 may thereby be embedded within the dielectric material. The light guides 18 may also extend through the dielectric material and may be spaced apart from the circuit device. A variety of metal elements and / or dielectric materials may be used, for example, those suitable for integrated circuit manufacturing (e.g., CMOS manufacturing). For example, the conductive element / circuit 24 may be a metal element such as a W (tungsten) element, a Cu (copper) element, an Al (aluminum) element, or a combination thereof, although it is understood that other materials and configurations may be used. The dielectric material may be a low dielectric material such as SiO2 and / or a silicon-containing material, although it is understood that other dielectric materials and configurations may be used.

[0083] The photodetector device 10 may be an integrated circuit die. For example, the photodetector device 10 may be manufactured as part of a large batch of multiple photodetector devices 10 provided on a single base portion (e.g., a wafer) of electron grade silicon (EGS) or other semiconductor (e.g., GaAs). The multiple fabricated devices are thereby integrally formed, adjacently disposed, and disposed very close to each other. The wafer is cut (i.e., diced) into a number of pieces, each including at least one different photodetector device 10. As shown in FIG. 1, a single separate photodetector device 10 may be formed (i.e., diced) from multiple integrally fabricated devices of the wafer. Alternatively, multiple integrally adjacent photodetector devices 10 may be formed (i.e., die formed) from multiple of the integrally fabricated devices of the wafer.

[0084] FIG. 1 shows another example of a light detection device 110 that can be utilized in the flow cell of the present disclosure. The light detection device 110 of FIG. 2 is similar to the light detection device 10 of FIG. 1, and thus, like reference numerals preceded by “1” are used to indicate similar components, aspects, functions, processes, or operations, and the above description directed thereto applies equally and will not be repeated for purposes of brevity and clarity. As shown in FIG. 2, the light detection device 110 differs from the light detection device 10 in that the light detection device 110 does not include a reaction structure (forming reaction recesses and interstitial regions extending therebetween) disposed on its upper surface 122. Rather, the as-manufactured or diced light detection device 110 may not include the reaction structure. The reaction structure may be disposed on the upper surface 122 of the diced light detection device 110, such as after processing of the light detection device 110 as further described below.

[0085] The light detection device 110 also differs from the light detection device 10 in that the circuit 124 includes vias 128 that extend completely through the base wafer portion 114, as shown in FIG. 2. The vias 128 are thereby exposed and accessible at the back surface 126 of the base wafer portion 114 and the device 110 itself. Also, as shown in FIG. 2, the back surface 126 of the base wafer portion 114 (and the device 110 itself) includes one or more spacer portions 130 that extend from the back surface 126 of the base wafer portion 114. At least one spacer portion 130 may be spaced apart from the vias 128 on the back surface 126 of the base wafer portion 114, may be adjacent to the vias 128, or may be arranged such that they only partially overlap. In this way, at least one spacer portion 130 may be arranged on the back surface 126 of the base wafer portion 114 such that at least a portion of each via 128 is exposed and available at the back surface 126 of the base wafer portion 114 and the back surface 126 of the device 110 itself. As shown in FIG. 2, the light detection device 110 may include at least two spacer portions 130 that extend along opposite lateral sides of the back surface 126 of the base wafer portion 114. At least one spacer portion 130 may provide structural support or rigidity to the base wafer portion 114, thereby providing the device 10 itself (which may be damaged or weakened by the vias 128). In some light detection devices 110, at least one spacer portion 130 may be electrically insulating or non-conductive (or semiconductor), for example, so as not to interfere with the operation of the sensor 112 and / or the circuit 124. Examples of materials for forming at least one spacer portion 130 include, but are not limited to, glass, fused silica, quartz, silicon, fiber glass, plastic, epoxy, ceramic, dielectric composite materials, paper, or combinations thereof.

[0086] As shown in FIGS. 3-5, a support structure 32 including a support frame 34 and a support substrate 44 may be utilized to form the flow cell of the present disclosure. The support frame 34 may define an upper surface 36, a lower surface 38, and at least one cavity 40 (e.g., a cavity or opening) extending through the frame 34 between the upper and lower surfaces 36, 38. The support structure 32 may include any number of cavities 44. As shown in FIGS. 3 and 4, the support frame 34 may include an array of cavities 40 spaced at a plurality of different intervals. The array of cavities 40 may be spaced from each other such that a portion of the support frame 34 extends completely across each cavity 40 and thereby extends between adjacent cavities 40. The array of cavities 40 may be defined in a repeating (potentially uniform) pattern such that the cavities 40 are evenly or consistently spaced. Alternatively, the array of cavities 40 may be randomly distributed such that at least some of the cavities 40 are unevenly spaced. As shown in FIG. 5, each cavity 40 may be formed by an inner sidewall 50 of the support frame 34 extending between the upper and lower surfaces 36, 38. In some embodiments, the inner sidewall 50 of the support frame 34 defining the cavity 40 may extend vertically between the upper and lower surfaces 36, 38 such that the size of the cavity 40 defines the same size or shape at the upper surface 36 and the lower surface 38.

[0087] As shown in FIGS. 4 and 5, each cavity 40 may be sized and shaped to include one or more photodetection devices, such as the photodetection device 110 of FIG. 2 described above. However, as further described below, one or more photodetection devices of different configurations may be utilized in the cavities 40 of the support frame 34, for example, but not limited to, like the photodetection device 10 of FIG. 1 described above. Further, at least one photodetection device of a first configuration may be utilized in one or more first cavities 40 of the support frame 34, and at least one photodetection device of a second configuration may be utilized in one or more second cavities 40 of the support frame 34.

[0088] The support frame 34 may be substantially planar. For example, the upper surface 36 and / or the lower surface 38 of the support frame 34 may be planar and parallel. In some configurations, the upper surface 36 and / or the lower surface 38 may be substantially smooth, such as including a surface roughness on the submicron scale. In some configurations, the upper surface 36 and / or the lower surface 38 may include a surface roughness of 50 nm or less or 10 nm or less. In some examples, the upper surface 36 and / or the lower surface 38 may include a surface roughness in the range of 1 - 2 nm. As further described below, the upper surface 36 of the support frame 34 may cooperate with the detection surface (e.g., the active surface of the device) of the reaction structure of the photodetection device to form a flow path of a flow cell for delivering a reagent solution, or the reaction structure, one or more other layers, and / or a lid may be disposed on the upper surface 36 of the support frame 34 and the upper portion 122 of the photodetection device. Thus, the flatness / smoothness of the upper surface 36 (and the upper surface of the reaction structure) of the support frame 34 may be configured to allow a fluid (s) flow of the reagent with or without entrainment of the fluid (s).

[0089] The support frame 34, and potentially the substrate 44, may be relatively rigid so as to securely hold and couple the photodetection device 110 within the cavity 40 and prevent damaged strain / deformation of the photodetection device 110 during the manufacture, handling, and / or use of the flow cell of the present disclosure. In some configurations, the support frame 34 (and potentially the substrate 44) includes a Young's modulus of at least 50 GPa, or at least 70 GPa. In some configurations, the support frame 34 (and potentially the substrate 44) includes a coefficient of thermal expansion (CTE) of at least about 20 per degree Celsius, or at least about 30 per degree Celsius. For example, the support frame 34 may be composed of borosilicate glass (e.g., Corning® Eagle XG® glass) including a Young's modulus in the range of 70 - 80 GPa and a CTE in the range of 30 - 35 per degree Celsius, or may be composed of silicon including a Young's modulus in the range of 160 - 170 GPa and a CTE in the range of 35 - 40 per degree Celsius.

[0090] The support frame 34 may be in contact with reagent solutions and / or other materials / solutions during the formation of reaction sites on the reaction structure disposed on the upper portion 122 of the photodetection device 110, during illumination / detection and / or the preparation and / or cleaning of the flow cell of the present disclosure. The support frame 34 may be composed of one or more materials that are non-reactive with respect to sequencing reagents such as sequencing reagents utilized for DNA grafting, clustering, cleavage, incorporation, and / or reading. For example, the sequencing solution may be an aqueous solution and / or may be composed of oil.

[0091] Support frame 34 may undergo a chemical mechanical polishing (CMP) process during the formation of one or more flow cells of its own, as will be further described below. Support frame 34 may be composed of one or more materials that are non-reactive to the CMP slurry or mixture that contacts support frame 34 during the formation of one or more flow cells of its own. For example, the CMP slurry or mixture may be composed of abrasive particles and a base liquid. In some examples, the base liquid may be composed of water (e.g., deionized water) and / or oil. In some examples, the abrasive particles may be composed of oxides such as, for example, silicon dioxide, cerium oxide, and / or aluminum oxide.

[0092] Support frame 34 may electrically insulate at least one light detection device 110 disposed within each cavity 40 so as not to interfere with its light detection operation. At least a part of the thickness / cross-section of the portion of support frame 34 surrounding / forming cavity 40 (extending between upper surface 36 and lower surface 38) may be composed of an electrically insulating (i.e., non-conductive) material (or semiconductor material). For example, at least a part of the thickness / cross-section of the portion of support frame 34 surrounding / forming cavity 40 extending from upper surface 36, or an inner portion spaced between upper surface 36 and lower surface 38, may be composed of an electrically insulating (i.e., electrically non-conductive) material (or semiconductor material). In some embodiments, support frame 34 may be composed of only electrically insulating materials. Exemplary electrically insulating materials that may form at least a part of the support frame include silicon, glass (e.g., quartz, fused silica, fiber glass, borosilicate glass (e.g., alkaline earth borosilicate glass such as Corning® Eagle XG® glass), float borosilicate glass (e.g., Borofloat® 33 glass, etc.), or other low autofluorescence glass), ceramic, polymer (e.g., plastic, epoxy, silicon charge epoxy or UV curable epoxy or adhesive), dielectric composite material, paper, or a combination thereof, etc.

[0093] However, as further described below, a portion of the support frame 34 may be composed of a conductive material such as a metallic material. For example, as further described below, the support frame 34 may include conductive vias that extend (exposed at the upper and lower surfaces 36, 38) proximate to (e.g., adjacent to) a cavity 40 that extends between the upper and lower surfaces 36, 38 through a portion of the thickness / cross-section of the support frame 34. In some embodiments, a portion of the thickness / cross-section of the support frame 34 that surrounds / forms the cavity 40 extending from the upper surface 36 and / or the lower surface 34 may include a conductive material (which may include a portion of the vias).

[0094] The support frame 34 may include a plurality of visual displays / markings 45, as shown in FIG. 4. The visual display 45 can be utilized to reference the position and / or orientation of the support frame 34 as a whole, and / or one or more components (e.g., the cavity 40 and one or more light detection devices 110 disposed within the cavity 40, as further described below) that are part of or coupled thereto. In this way, the visual display 45 can be utilized as an alignment mark while processing the support frame 34 (and components coupled thereto, as further described below) in one or more intermediate flow cell devices and / or flow cell devices (as further described below). For example, the visual display 45 can be utilized for alignment during a reading and / or dicing operation to form one or more intermediate flow cell devices and / or flow cell devices.

[0095] The visual representation 45 may be composed of any material that is visually different from the support frame 34 with respect to the human eye and / or an imaging device (e.g., a digital camera). In some examples, the visual representation 45 may be composed of pigments, paints, dyes, luminescent materials, metals, oxides, or combinations thereof. The visual representation 45 may be composed of one or more materials that are non-reactive with respect to the sequencing reagent and / or the CMP slurry.

[0096] The visual representation 45 may be provided on the lower surface 38 of the support frame 34 (as shown in FIG. 4), on the upper surface 36 of the support frame 34, at least partially embedded within the thickness of the support frame 34 between the upper surface 36 and the lower surface 38 of the support frame 34, or combinations thereof. The visual representation 45 may be formed on the support frame 34 via any process. In some examples, the visual representation 45 may be formed on the support frame 34 via a printing process such as a spray process or a lithography process.

[0097] As shown in FIGS. 4 and 5, the support structure 32 may include the upper surface 36 of the support frame 34 coupled to the upper surface 46 of the substrate or carrier 44. The support frame 34 and the substrate 44 may be removably coupled or fixedly coupled. In some support structures 32, the substrate 44 may be composed of the same or a similar material as the support frame 34. In some other support structures 32, the substrate 44 may be composed of a material different from the support frame 34. The upper surface 46 of the substrate 44 may be substantially smooth and planar such that the upper surface 36 of the support frame 34 and the upper surface 46 of the substrate 44 are parallel and potentially substantially coplanar. In some embodiments, the upper surface 46 of the substrate 44 may define the same or a similar surface smoothness as the upper surface 36 of the support frame 34.

[0098] As also shown in FIGS. 4 and 5, with the upper surface 36 of the support frame 34 coupled to the upper surface 46 of the substrate 44, at least one diced light detection device 110 may be disposed "face down" within the cavity 40 such that the upper surface 122 of the at least one light detection device 110 is disposed on or adjacent to the upper surface 46 of the substrate 44. In this way, the upper surface 122 of the at least one light detection device may be substantially aligned (e.g., coplanar) with the upper surface 36 of the support frame 34. Similarly, when at least one diced light detection device 110 includes a reaction structure provided on the upper surface 122 (e.g., similar to the light detection device 10 of FIG. 1), the upper surface of the detector / reaction surface of the reaction structure may be disposed on or adjacent to the upper surface 46 of the substrate 44, and the interstitial portion may be substantially aligned (e.g., coplanar) with the upper surface 36 of the support frame 34.

[0099] As shown in FIG. 5, the support frame 34 may be thinner than at least one light detection device 110 such that its back surface 126 extends beyond the support frame 34 of the lower surface 38. In some other configurations of the support frame 34, the support frame 34 of the lower surface 38 may be at the same height as the back surface 126 of at least one light detection device 110 or may be below the back surface 126 of at least one light detection device 110. At least one light detection device 110 may define a corresponding size that is smaller than the cavity 40. The at least one diced light detection device 110 may thereby be disposed within the cavity 40 of the support structure 32 such that the outer perimeter of the at least one light detection device 110 is spaced from the inner sidewall 50 of the support frame 34, as shown in FIG. 5. For example, a portion of the cavity 40 may extend to form a groove or end cavity portion 52 that extends between the inner sidewall 50 of the cavity 40 of the support frame 34 and the outer perimeter of the at least one light detection device 110 for the outer perimeter of the at least one light detection device 110.

[0100] At least one light detection device 110 may lie freely directly on the upper surface 46 of the substrate 44 within the cavity 40. In some such arrangements, at least one light detection device 110 may be mechanically held within the cavity 40 via a tool or support member.

[0101] Another example of a support structure 232 according to the present disclosure is shown in FIG. 6. The support structure 232 of FIG. 6 is similar to the support structure 32 of FIGS. 3 - 5, and thus, similar reference numerals preceded by "2" are used to indicate similar components, aspects, functions, processes, or features, and the above description directed thereto applies equally and will not be repeated for purposes of brevity and clarity. As shown in FIG. 6, the support structure 232 differs from the support structure 32 in that it includes an interposer member or layer 248 that chemically bonds / binds the top 122 of at least one light detection device 210 to the top surface 246 of the substrate 244 within the cavity 244. The interposer layer 248 may be any temporary or removable bonding material (e.g., via one or more chemical, mechanical, and / or irradiation processes). In one example, the interposer layer 248 may be composed of a polymeric material (e.g., one or more cyclic olefin copolymers), and this polymeric material may be provided within a solvent cast bonding material composition. For example, the interposer layer 248 may be composed of a BrewerBond® temporary bonding material sold by Brewer Science, Inc., such as BrewerBond® 220 or BrewerBond® 305. In another example, the interposer layer 248 may be composed of a high UV absorbing release layer and / or adhesive layer, such as a JSR ELPAC TA series temporary bonding material sold by JSR Corporation. The interposer layer 248 may be formed, for example, by spin coating, spray coating, dye slot coating, or laminating onto the upper surface 246 of the substrate 244.

[0102] The interposer layer 248 may be composed of one or more layers of material extending over the upper surface 246 of the substrate 244 within the cavity 240. The upper portion 122 of at least one light detection device 110 may thereby be positioned over the upper surface 247 of the interposer layer 248 within the cavity 244. The interposer layer 248 may also extend between the upper surface 246 of the substrate 244 and the upper surface 236 of the support frame 234, as shown in FIG. 6. The upper surface 236 of the support frame may thereby extend beyond the upper surface 247 of the interposer layer 248, and the interposer layer 248 may extend beyond the upper surface 246 of the substrate 244.

[0103] Another example of the support structure 332 according to the present disclosure is shown in FIG. 7. The support structure 332 of FIG. 7 is similar to the support structure 32 of FIGS. 3-5 and the support structure 232 of FIG. 6, and thus, similar reference numerals preceded by "3" are used to indicate similar components, aspects, functions, processes or functions, and the above description directed thereto is equally applicable and will not be repeated for the purpose of brevity and clarity. As shown in FIG. 7, the support structure 332 differs from the support structure 32 and the support structure 232 in that it includes a spacer member / layer 349 that spatially separates the upper surface 346 of the substrate 344 from the upper portion 122 of at least one light detection device 110. The spacer member / layer 349 may extend only between the upper surface 346 of the substrate 344 and the upper surface 336 of the support frame 334, and thus may not extend through the cavity 340. In this way, the spacer layer 349 raises the upper surface 336 of the support frame 334 from the upper surface 346 of the substrate 344 that the upper surface portion 122 of at least one light detection device 110 overlaps. In this way, the spacer layer 349 spaces out the upper surface 122 of at least one light detection device 110 beyond (i.e., above) the upper surface 336 of the support frame 334 in the direction extending from the back surface 126 to the upper surface 122 of at least one light detection device 110. The spacer layer 349 may be composed of the same or a similar material as the interposer layer 248. The spacer layer 349 may be formed, for example, by spin coating, spray coating, dye slot coating or lamination on the upper surface 346 of the substrate 344. The support structure 332 of FIG. 7 is shown as not including an interposer layer (for example, the interposer layer 248 of the support structure 232 of FIG. 6), but the support structure 332 may include an interposer that extends beyond the upper surface 336 of the substrate 344 and beyond the cavity 340 between the substrate 344 and the support frame 334.

[0104] Another example of the support structure 432 according to the present disclosure is shown in FIG. 8. The support structure 432 in FIG. 8 is similar to the support structure 32 in FIGS. 3-5, the support structure 232 in FIG. 6, and the support structure 332 in FIG. 7. Thus, similar reference numerals preceded by "4" are used to indicate similar components, aspects, functions, processes, or functions, and the above descriptions directed thereto apply equally and will not be repeated for the purposes of brevity and clarity. As shown in FIG. 8, the support structure 432 is different from the support structures 32, 232, and 332 in the configuration of the side wall 450 of the cavity 440.

[0105] As shown in FIG. 8, each cavity 440 may be formed by an inner side wall 450 of a support frame 434 that extends between an upper surface 436 and a lower surface 438. The inner side wall 450 of the support frame 434 that defines the cavity 440 extends inwardly toward the interior of the cavity 440 such that the size of the cavity 440 is smaller or narrower at the upper surface 436 compared to the lower surface 438 (i.e., the opening of each cavity 440 at the lower surface 438 is larger than the corresponding opening at the upper surface 436) and extends from the lower surface 438 to the upper surface 436. Note that the side wall 450 may extend very close to the outer periphery of at least one light detection device 110 at the upper surface 436, but may still be spaced apart. Correspondingly, the end cavity portion 452 of the cavity 440 that extends between the inner side wall 450 and the outer periphery of at least one light detection device 110 may become narrower as it extends from the lower surface 438 to the upper surface 436.

[0106] The shape or configuration of the inner wall 450 may be formed by any configuration of the support frame 434 and / or the manufacturing or processing technology. For example, the support frame 434 may include a plurality of support frame layers having different-sized openings that, when stacked together, form an opening that forms the cavity 40. As another example, the shape or configuration of the inner side wall 450 may be formed by etching or otherwise shaping or forming the support frame 434.

[0107] In one example, the inner side wall 450 may extend linearly at an angle from the upper surface 436 to the lower surface 434 (i.e., be planar), as shown in FIG. 8, and may extend inwardly toward the interior of the cavity 440. In other examples, the inner side wall 450 may not extend linearly (i.e., may not be planar). For example, the inner side wall 450 may extend linearly, curvilinearly, or a combination thereof from the lower surface 438 toward the upper surface 436 such that the size of the cavity 440 is smaller or narrower at the upper surface 436 compared to the lower surface 438. In such an example, a portion of the inner side wall 450 of the support frame 434 that defines the cavity 440 may extend vertically from the lower surface 438 toward the upper surface 436 along a portion of the thickness of the support frame 534, and another portion may extend at an angle (i.e., an angled plane) linearly from there toward the upper surface 436 and into the interior of the cavity 540.

[0108] Figures 9 through 11B illustrate coupling a single discrete photodetection device 110 via a support / fill material 60 within each cavity 40 of the support frame 34 of the support structure 32 of FIGS. 3 through 5. As shown in FIG. 9, the support material 60 may be introduced from its exposed side adjacent the lower surface 38 of the support frame 34 into an end cavity portion 52 between the sidewall 50 of the support frame 34 and the outer perimeter of the photodetection device 110. The support member 60 may securely couple the support frame 34 and the photodetection device 110. Specifically, as shown in FIGS. 11A and 11B, the support material 60 may extend about the outer perimeter of the sideward side of the photodetection device 110 disposed within the cavity 40. The support material 60 may thereby extend between and / or be joined with the outer perimeter of the sideward side of the photodetection device 110 disposed within the cavity 40 and the sidewall 50 of the cavity 40. In some examples, after the support material 60 is deposited within each cavity 40, the lower surface 38 of the support frame 34, the support material 60, and / or the photodetection device(s) 110 within each cavity 40 may be subject to one or more CMP operations. For example, the support material 60 and / or the photodetection device(s) 110 within at least one cavity 40 may extend higher (i.e., upward) than at least the adjacent portion of the lower surface 38 of the support frame 34, and one or more CMP operations may remove a portion of the support material 60 and / or the photodetection device(s) 110 to planarize the lower surface 38 of the support frame 34, the support material 60, and the photodetection device(s) 110.

[0109] The support material 60 may be any material that can flow into or otherwise be introduced into the end cavity portion 52 (in a first state, such as a liquid or powder state), and can securely bond the support frame 34 and the light detection device 110 in the cavity 40 together (in a second state, such as a cured or hardened state). The support material 60 may be electrically insulating or non-conductive (or semi-conductive) so as not to interfere with the operation of the light detection device 110 (such as the operation of the sensor 112 and / or the circuit 124). The support material 60 may be in contact with the reagent solution and / or other materials / solutions during the formation of the reaction structure, the formation of reaction sites on the reaction structure, illumination / detection, and / or the preparation and / or cleaning of the flow cell of the present disclosure. Thus, the support material 60 may be composed of one or more materials that are non-reactive with respect to sequencing reagents such as sequencing reagents utilized for DNA grafting, clustering, cleavage, incorporation, and / or reading. For example, the sequencing reagent may include water and / or oil. Exemplary materials for the support material 60 include silicon, glass (such as quartz, fused silica, fiber glass, borosilicate glass (such as an alkaline earth borosilicate glass like Corning® Eagle XG® glass), float borosilicate glass (such as Borofloat® 33 glass), etc.), or other low autofluorescent glass), ceramics, polymers (such as plastics, epoxies, silicone charge epoxies or UV curable epoxies or adhesives), dielectric composite materials, or combinations thereof, etc.

[0110] As shown in FIGS. 10 to 11B, after the support material 60 fills the end cavity portion 52 and fixedly couples the support frame 34 and at least one light detection device 110 in at least one cavity 40, the remaining portion of the support structure 32 may be removed therefrom. For example, as shown in FIG. 10, the substrate 44, and any associated interposer and / or spacer layer / member may be removed from the upper surface 36 of the support frame 34, the upper surface 122 of the light detection device 110, and the upper surface of the support member 60. The separated support frame 34, at least one light detection device 110 disposed in at least one cavity 40, and the deposited support material 60 may include an intermediate flow cell device 62, as shown in FIGS. 11A and 11B. The intermediate flow cell device 62 may be processed into one or more flow cells, as further described below. As described above, the light detection device 110 of FIG. 2 is illustrated within the arrangement of the cavities 40 of the support frame 34 of the intermediate flow cell device 62 of FIGS. 9 to 11B, but other configured light detection devices, such as the light detection device 10 of FIG. 1, may be similarly or equally utilized within at least one cavity 40 of the support frame 34.

[0111] Modes or methods for removing the intermediate flow cell device 62 from other part(s) of the support structure 32 may be related, at least in part, to the materials of the support frame 34 and the substrate 44 (and / or any interposer and / or spacer layer / member associated therewith), and / or their attachment modes. In some configurations, the intermediate flow cell device 62 may be decoupled from the remaining part of the support structure 32. In some configurations, the substrate 44, and any interposer and / or spacer layer / member associated therewith if present, may be etched chemically and / or mechanically from the intermediate flow cell device 62. In some configurations, the substrate 44, and any interposer and / or spacer layer / member associated therewith if present, may be removed from the intermediate flow cell device 62 via air blow, blade insertion, vacuum debonding, or mechanical lift, with or without pre-treatment (such as edge trimming or laser patterning).

[0112] As shown in FIGS. 9 - 11B, in some configurations, a single separate photodetection device 110 may be disposed within at least one cavity 40 of the support frame 34. As described above and as shown in FIGS. 9 - 11B, in such a configuration, the support member 60 may be disposed within the end cavity portion 52 between the sidewall 50 of the support frame 34 and the outer periphery of the single separate photodetection device 110 in each cavity 40 to couple the support frame 34 and the single separate photodetection device 110 together.

[0113] As shown in FIGS. 12A and 12B, in the configuration of some other intermediate flow cell devices 662, a plurality of spaced-apart separate light detection devices 110A, 110B, 110C may be disposed within at least one cavity 640 of the support frame 634. Although three light detection devices 110A, 110B, 110C are used herein to illustrate the use of a plurality of light detection devices, any number of light detection devices may be equally employed (e.g., two light detection devices, three light detection devices, four light detection devices, five light detection devices, etc.). It should be noted that the intermediate flow cell devices 662 of FIGS. 12A and 12B are similar to the intermediate flow cell devices 62 of FIGS. 11A and 11B. Thus, similar reference numerals preceded by "6" instead of "1" are used to indicate similar components, aspects, functions, processes, or operations, and the above description directed thereto applies equally and is not repeated for purposes of brevity and clarity.

[0114] As shown in FIGS. 12A and 12B, in such a configuration of the intermediate flow cell device 662, the support member 660 may be disposed within an end cavity portion 652 between a side wall 650 of the support frame 634 and the outer perimeters of a plurality of separate light detection devices 110A, 110B, 110C that are adjacent to and / or spaced apart from each other, for coupling the support frame 634 and the light detection devices 110A, 110B, 110C together. Further, as shown in FIGS. 12A and 12B, the separate light detection devices 110A, 110B, 110C may be spaced apart from each other such that an interstitial or inter-device portion 653 of the cavity 640 is disposed between adjacent separate light detection devices 110A, 110B, 110C. The support member 660 may be disposed within a gap portion 652 between adjacent separate light detection devices 110A, 110B, 110C for coupling the adjacent separate light detection devices 110A, 110B, 110C together and to the support frame 634. In this way, the support member 660 may extend about the outer perimeters of the separate light detection devices 110A, 110B, 110C that are spaced apart and disposed within the cavity 640.

[0115] As shown in FIGS. 13A and 13B, in some other configurations of the intermediate flow cell device 762, a plurality of integrated, coupled, or non-spaced-apart separate light detection devices 110A, 110B, 110C may be disposed within at least one cavity 740 of the support frame 734. The intermediate flow cell devices 762 of FIGS. 13A and 13B are similar to the intermediate flow cell devices 62 of FIGS. 11A and 11B and the intermediate flow cell devices 662 of FIGS. 12A and 12B, and thus, similar reference numerals prefixed with “7” instead of “1” or “6” are used to indicate similar components, aspects, functions, processes, or features, and the above description directed thereto applies similarly and is not repeated for purposes of brevity and clarity.

[0116] As shown in FIGS. 13A and 13B, in such a configuration of the intermediate flow cell device 762, the support material 760 couples the support frame 734 with the photodetection devices 110A, 110B, 110C together, and is disposed within the end cavity portion 752 between the sidewall 750 of the support frame 734 and the exposed peripheral sides of a plurality of integral, coupled or non-spaced different photodetection devices 110A, 110B, 110C adjacent to and / or facing it. Since the plurality of photodetection devices 110A, 110B, 110C are integral, coupled or non-spaced, the cavity portion 740 does not extend between the adjacent devices 110A, 110B, 110C (thus, the support member 760 does not extend between the adjacent devices 110A, 110B, 110C). As described above, the plurality of separate photodetection devices 110A, 110B, 110C may be manufactured as part of a wafer of a plurality of integrated or coupled separate photodetection devices 110A, 110B, 110C. The wafer of devices may be diced into single separate photodetection devices (as shown in FIGS. 10 - 12B) and / or a plurality of integrated or coupled separate photodetection devices (composed of any number of individual separate devices, as shown in FIGS. 13A and 13B).

[0117] FIG. 14 shows an intermediate flow cell device 862 formed through at least one light detection device 10 within a frame 834 and one or more of its cavities 840, without including a base substrate or associated interposer and / or spacer layer. The intermediate flow cell device 862 of FIG. 14 is similar to the intermediate flow cell devices 62 of FIGS. 11A and 11B, the intermediate flow cell devices 662 of FIGS. 12A and 12B, and the intermediate flow cell devices 762 of FIGS. 13A and 13B. Thus, similar reference numerals preceded by "8" are used to indicate similar components, aspects, functions, processes, or functions, and the above descriptions directed thereto apply similarly and are not repeated for purposes of brevity and clarity. In FIGS. 15A and 15B, only a single light detection device 110 is illustrated within each cavity 840, but as described above, the cavity 840 may include a plurality of spaced-apart light detection devices 110, and the support member 860 may extend between adjacent spaced-apart light detection devices 110. Further, although the light detection device 10 of FIG. 1 is shown in each cavity 840, as discussed above, other light detection devices 10 may be utilized as well, such as, for example, the light detection device 110 of FIG. 2.

[0118] The intermediate flow cell device 862 differs from the intermediate flow cell device 62, the intermediate flow cell device 662, and the intermediate flow cell device 762 in the configuration of the cavities 840 of the support frame 834 and the support member 860. As shown in FIG. 14, the cavity 840 extends only partially through the thickness of the support frame 840. The cavity 840 extends from the upper surface 836, through a portion thereof, towards the lower surface 838 of the support frame 840. The lower portion 841 of the support frame 841 thereby extends between the lower surface 843 of the cavity 840 and the lower surface 838 of the support frame 840, as shown in FIG. 14.

[0119] As also shown in FIG. 14, the bottom layer or portion 863 of the support material 860 may extend over the lower surface 843 of the cavity 840, and at least one light detection device 10 may be disposed thereon. Thus, the bottom layer or portion 863 of the support material 860 may extend between the lower surface 26 of at least one light detection device 10 and the lower surface 843 of each cavity 840.

[0120] In some examples, the support material 860 may first be provided on the lower surface 843 of the cavity 840 to form its lower portion 863, and at least one light detection device 10 disposed thereon may be positioned such that the lower portion 863 of the support material 860 couples or otherwise holds at least one light detection device 10 in a predetermined position within each cavity 840 for further processing. For example, after disposing at least one light detection device 10 on top of the lower portion 863 of the support material 860 (e.g., the lower surface 26 of at least one light detection device 10 disposed on the exposed upper surface of the lower portion 863 of the support material 860), additional support material 860 may be introduced into the end cavity portion 852 between the sidewall 850 of the support frame 834 and the outer periphery of at least one light detection device 10 and onto the exposed portion of the (previously formed) lower portion 863 of the support material 860. In some other examples, the lower portion 863 of the support material 860 may not be present, and at least one light detection device 10 may be disposed directly on the lower surface 838 of the support frame 840 (or another layer or material may be disposed therebetween).

[0121] As shown in FIGS. 15A and 15B, after forming the intermediate flow cell device 962, the upper surface 961 of the support material 960 within the cavity 940 may be exposed. The intermediate flow cell device 962 of FIGS. 15A and 15B is similar to the intermediate flow cell device 62 of FIGS. 11A and 11B, the intermediate flow cell device 662 of FIGS. 12A and 12B, the intermediate flow cell device 762 of FIGS. 13A and 13B, and the intermediate flow cell device 862 of FIG. 14, and thus, similar reference numerals preceded by "9" are used to indicate similar components, aspects, functions, processes, or features, and the foregoing descriptions directed thereto apply equally and are not repeated for purposes of brevity and clarity. For example, the intermediate flow cell device 962 may be formed via removal or separation of the support substrate and any associated interposer layer and spacer layer from the upper surface 936 of the support frame 934, the upper surface 961 of the support member 960, and the upper surface 122 of the light detection device 110. Alternatively, the intermediate flow cell device 962 may be formed without a support substrate, such as when the cavity 840 only partially extends through the support frame 834.

[0122] As shown in FIGS. 15A and 15B, at least a portion of the exposed upper surface 961 of the support member 960 may extend downward between the upper surface / side 936 of the support frame 931 and the adjacent upper surface 122 of at least one light detection device 110 disposed within each cavity 940. In FIGS. 15A and 15B, only a single light detection device 110 is illustrated, but as described above, the cavity 940 may include a plurality of spaced-apart light detection devices 110, and the support member 960 may extend between adjacent spaced-apart light detection devices 110. In such an example, the upper surface 961 of such a portion of the support material 960 may extend downward and between the upper surfaces 122 of adjacent light detection devices 110. The upper surface 961 of the support material 960 disposed throughout each cavity 940 may thereby include a concave upper surface portion disposed below the upper surface 936 of the support frame 931 and a concave upper surface portion disposed between the upper surface portions 122 of at least one light detection device 110 disposed within each cavity 940.

[0123] In some such intermediate flow cell devices 962, as shown in FIG. 15A, the upper portion 122 of at least one light detection device 110 disposed within each cavity 940 may not include a reaction structure extending thereabove. As shown in FIG. 15B, in some such intermediate flow cell devices 962, the reaction structure 120 may be disposed over the upper portion 122 of at least one light detection device 110 and the upper portion 961 of the support material 960 within each cavity 940 to fill any recesses thereof to form a planar upper surface from which a plurality of nanowells 16 extend.

[0124] Note that the reaction structure 120 can be disposed over the upper portion 122 of at least one photodetector device 110 across the entire active region of the at least one photodetector device 110. The planar upper surface of the reaction structure 120 may thereby include the upper surface of the portion of the reaction structure 120 disposed on the support material 960 within each cavity 940, and the upper surface of the interstitial region of the reaction structure 120 may be disposed over at least one photodetector device 110 within each cavity 940. The upper surface of the portion of the reaction structure 120 disposed on the support material 960 within each cavity 940 and the upper surface of the interstitial region of the reaction structure 120 disposed over at least one photodetector device 110 within each cavity 940 may thereby be coplanar.

[0125] As also shown in FIG. 15B, the reaction structure 120 may further extend over the upper surface 936 of the support frame 934. The planar upper surface of the reaction structure 120 may thereby extend over at least the upper surface 936 of the support frame 934 for each cavity 940. The upper surface of the portion of the reaction structure 120 disposed on the support material 960 within each cavity 40, the upper surface of the portion of the reaction structure 120 disposed over the upper surface 936 of the support frame 934 for each cavity 940, and the upper surface of the interstitial region of the reaction structure 120 disposed over at least one photodetector device 110 within each cavity 940 may thereby be coplanar.

[0126] Layer formation processes that can be used to form the reaction structure 120 include photolithography, etching (e.g., reactive ion etching), sputtering, deposition, casting (e.g., spin coating), chemical deposition, electroplating, epitaxy, thermal oxidation, physical deposition, and the like. In some examples, the reaction structure 120 may be formed using a shadow method. In some examples, the reaction structure 12 may be formed using nanolithography such as nanoimprint lithography (NIL). In one example, the reaction structure 120 may be formed in respective cavities 940 via one or more NIL-related processes through one or more layers of an ultraviolet (UV) curable resin disposed on the upper surface 936 of the support frame 934, the upper surface 122 of at least one photodetection device 110, and the upper surface 961 of the support material 960.

[0127] In one example, the reaction structure 120 may include at least one layer disposed on at least an upper portion 122 of the photodetection device 110 configured to have an array of reaction recesses 16 (e.g., nanowells) (as described above with respect to FIG. 1). In another example, at least one layer of the reaction structure 120 may include pre-formed reaction recesses 16. Optionally, at least one layer of the reaction structure 120 may be etched to remove a portion thereof to form at least a portion of the reaction recesses 16.

[0128] In another example, the reaction structure 120 having the reaction recess 16 may be formed by forming at least one layer of the reaction structure 120. For example, the NIL material may be deposited on at least the upper portion 122 of the light detection device 110. The NIL material may be composed of a material that can be imprinted using NIL technology. For example, the NIL material may be composed of a polymer. Next, the NIL material may be imprinted or stamped using a mold (also called a template) having a pattern of features that form the reaction recesses 16 of the NIL layer. In some configurations, the mold is transparent to allow ultraviolet or visible light to propagate therethrough. In such a configuration, the NIL material may be composed of a photocurable polymer that cures by ultraviolet or visible light while the mold is being pressed into the NIL material. Thus, the NIL material may cure (e.g., harden) to form the reaction recesses 16. This process may be the same as or similar to step and flash imprint lithography (SFIL). In other configurations, the NIL material may cure by the application of thermal energy and / or pressure.

[0129] Figures 16A - 16D show an exemplary process of forming a plurality of back - side electrical contacts 1072 on the back - side of an intermediate flow - cell device 1062 so that data signals from a circuit 124 of at least one light - detection device 110 can be transmitted or conducted within respective cavities 1040 to send data signals to a biosensor and / or bioassay system when a flow - cell formed via the intermediate flow - cell device 1062 is utilized thereby. The intermediate flow - cell device 1062 is shown in the configuration of the intermediate flow - cell device 62 of FIGS. 11A and 11B, but the intermediate flow - cell device 1062 may have a different configuration, such as the configuration of the intermediate flow - cell device 662 of FIGS. 12A and 12B, or the configuration of the intermediate flow - cell device 762 of FIGS. 13A and 13B. Thus, similar reference numerals preceded by "10" are used to indicate similar components, aspects, functions, processes, or features, and the above - given description directed thereto applies equally and will not be repeated for the purposes of brevity and clarity. Note that the back - side contacts 1072 of the intermediate flow - cell device 1062 are coupled to back - side vias 128 of at least one light - detection device 110 within respective cavities 1040. Thus, although the intermediate flow - cell device 1062 is shown utilizing the light - detection device 110 of FIG. 2, other light - detection device configurations including back - side vias 128 may be utilized as well.

[0130] As shown in FIGS. 16A and 16B, a non-electrically conductive substrate or material 1070 is disposed on the back surface of the intermediate flow cell device 1062. As also shown in FIGS. 16A and 16B, the back surface 1074 of the substrate 1070 includes a plurality of exposed electrically conductive back surface contacts 1072 coupled thereto. The back surface contacts 1072 may be at least partially embedded within the back surface 1074 of the substrate 1070. The back surface contacts 1072 (potentially separated and distinct back surface contacts 1072) may be provided for each back via 128 of each photodetector device 110 within each cavity 1040 (i.e., the exclusively associated via 128). As shown in FIG. 16B, adjacent backside contacts 1072 may be spaced apart from each other, and a portion of the substrate 1070 may extend therebetween.

[0131] The substrate 1070 may be composed of any electrically non-conductive material or semiconductor material such as a polymer (e.g., epoxy), silicon, glass, ceramic, or a combination thereof. The back surface contacts 1072 may be composed of any conductive material such as a metal (e.g., copper). In some examples, the substrate 1070 and the back surface contacts 1072 may include a printed circuit board.

[0132] As shown in FIG. 16B, the substrate 1070 and / or the back surface contacts 1072 may include through holes 1076 that are at least partially aligned (e.g., overlap) with the back surface 126 of at least one photodetector device 110 within each cavity 1040 of the support frame 1034. The through holes 1076 thereby at least partially align (e.g., overlap) with the opening / space between the spacer 130 (if provided) and the via 128 extending through the base wafer portion 114 at the back surface 126 of at least one photodetector device 110 within each cavity 1040.

[0133] As shown in FIG. 16C, a conductive wire or other structure 1080 may be coupled between a via 128 of at least one light detection device 110 within each cavity 1040 and an adjacent or associated backside contact 1072. The wire 1080 may be composed of any conductive material such as a metal (e.g., copper). The wire 1080 can transmit a data signal from the via 128 of the circuit 124 of at least one light detection device 110 to the backside contact 1072. Each wire 1080 thereby extends from a respective contact 1072 on the backside of the intermediate flow cell device 1062, into and through an adjacent or associated through-hole 1076, and to a respective via 128 of the light detection device 110 within the cavity 1040 of the support frame 1034, as shown in FIG. 16C. In some examples, the wire 1080 may be spaced inwardly from the inner sidewall of the through-hole 1076.

[0134] With the wire 1080 coupled between each via 128 and the backside contact 1072, the wire 1080 may be covered and encapsulated / enclosed within an insulating portion 1082, as shown in FIG. 16D. The insulating portion 1082 may be composed of an electrically insulating material so as to electrically insulate the wire 1080. As shown in FIG. 16D, the insulating portion 1082 may cover a portion (or all) of the backside 126 of at least one light detection device 110 within each cavity 1040 that is exposed to the through-hole 1076. For example, the insulating portion 1082 may extend and fill the space between spacers 130 (if provided) of each light detection device 110 having a cavity 1040.

[0135] Each insulating portion 1082 may also extend beyond only a portion of the back contact 1072 associated with each cavity 1040 so as to fill the through-hole 1076 and form an exposed portion of the back contact 1072. For example, the insulating portion 1082 may extend only over a portion of the back contact 1072 that couples to (and surrounds) each wire 1080, such as a portion of the back contact 1072 that is proximate to (e.g., adjacent to) each through-hole 1076. Of the back contact 1072, a portion where the insulating portion 1082 forms a cavity (e.g., a portion distal to each through-hole 1076) may remain exposed thereby. The exposed portion of the back contact 1072 can be coupled to another structure or device to transmit data signals from at least one photodetection device 110 thereto. Note that after the insulating portion 1082 is formed, the intermediate flow cell device 1062 may be diced to form one or more flow cells therefrom, as further described below. For example, the intermediate flow cell device 1062 may be diced prior to or subsequent to the formation of the reaction structure on the photodetection device 110 (if not already formed), the formation of the reaction sites on the reaction structure of the photodetection device 110, and / or the formation of the lid (lidding).

[0136] Figures 17A - 17C illustrate another process of forming a plurality of back - side electrical contacts 1172 on the back - side of an intermediate flow - cell device 1162, which can transmit or conduct data signals from the circuit 124 of at least one photodetector device 110 within respective cavities 1140 (based on photons detected by its optical sensor 116) so as to transmit the data signals to a biosensor and / or a bioassay system when a flow - cell formed via the intermediate flow - cell device 1162 is utilized thereby. The process of forming the plurality of back - side electrical contacts 1172 and the intermediate flow - cell device 1162 in FIGS. 17A - 17C is similar to the process and the intermediate flow - cell device 1062 in FIGS. 16A - 16D. Thus, similar reference numerals starting with "11" are used to indicate similar components, aspects, functions, processes, or features, and the above - mentioned description directed thereto is equally applicable and not repeated for the purposes of brevity and clarity.

[0137] As shown in FIG. 17A, the electrically conductive backside contact 1172 is provided on the lower surface 1138 of the support frame 1134. For example, as shown in FIG. 17A, the backside contact 1172 may be at least partially embedded in the lower surface 1138 of the support frame 1134. As shown in FIG. 17A, adjacent backside contacts 1172 may be spaced apart from each other, and a portion of the support frame 1134 may extend therebetween. In some examples, the backside contact 1172 may include the bottom portion of the cavity 1140 of the support frame 1134 (i.e., a portion of the sidewall 1150 of the support frame 1134 that forms the cavity 1140). In one embodiment, the backside contact 1172 and the support frame 1134 may include a printed circuit board. As shown in FIG. 17B, the wire 1190 may extend from each via 128 of the light detection device 110, across its back surface 122, to a proximal (e.g., adjacent) backside contact 1172. After the wire is coupled to the via 128 and the backside contact 1172, as shown in FIG. 17C, the entire light detection device 110 on the back surface 122 and a portion of the backside contact 1172 to which the wire 1180 is coupled are covered by the insulating portion 1182. The wire 1180 is also completely encapsulated by the insulating portion 1182. The insulating portion 1182 only covers a portion of the backside contact 1172 to leave an exposed portion for mating with another structure or device to transmit data signals from at least one light detection device 110 thereto. After the insulating portion 1182 is formed, it should be noted that, as further described below, the intermediate flow cell device 1162 may be diced to form one or more flow cells therefrom. For example, the intermediate flow cell device 1162 may be diced prior to or subsequent to the formation of the reaction structure on the light detection device 110 (if not already formed), the formation of the reaction sites on the reaction structure of the light detection device 110, and / or the formation of the lid (lidding).

[0138] Figures 18A - 18C illustrate another process of forming a plurality of back - side electrical contacts 1272 on the back surface of an intermediate flow - cell device 1262, which can transmit or conduct data signals from a circuit 124 of at least one light - detection device 110 (based on photons detected by its optical sensor 116) within respective cavities 1240 so as to transmit the data signals to a biosensor and / or a bioassay system when a flow - cell formed via the intermediate flow - cell device 1262 is utilized thereby. The process of forming the plurality of back - side electrical contacts 1272 and the intermediate flow - cell device 1262 in Figures 18A - 18C is similar to the processes of Figures 16A - 16D and the intermediate flow - cell device 1062 and the processes of Figures 17A - 17C and the intermediate flow - cell device 1162. Thus, similar reference numerals preceded by "12" are used to indicate similar components, aspects, functions, processes, or operations, and the above - mentioned descriptions directed thereto are equally applicable and not repeated for the purposes of brevity and clarity.

[0139] As shown in Figure 18A, the intermediate flow - cell device 1262 may include at least one light - detection device 110 within each cavity 1240 where the spacer on the back surface 126 is the cavity. However, in an alternative example, (as shown in Figure 2) at least one light - detection device 110 within one or more cavities 1240 may include a spacer on the back surface 126. As shown in Figure 18A, the via 128 of the electrical circuit 124 of the light - detection device 110 may be exposed at the back surface 126. In one embodiment, as shown in Figure 18A, the exposed end of the via 128 at the back surface 126 of the light - detection device 110 may be substantially aligned (e.g., coplanar) with the back surface 1238 of the support frame 1234 and / or the back surface.

[0140] As shown in FIG. 18B, a plurality of electrically conductive inter - contacts 1278 can be disposed on the back surface of the intermediate flow cell device 1262. The inter - contacts 1278 may be composed of any conductive material such as a metal (e.g., copper) so as to transmit data signals from the associated light - detection device 110. Each inter - contact 1278 is electrically coupled to the exposed end face of each via 128 of the back surface 126 of the light - detection device 110, extends across the back surface 1265 of the filler 1260 within the channel 1252 adjacent to the light - detection device 110, and a portion of the back surface 1238 of the support frame 1234. As shown in FIG. 18B, adjacent inter - contacts 1278 on the back surface 1238 of the support frame 1234 may be spaced apart from each other, and a portion of the support frame 1234 may extend therebetween. Similarly, adjacent inter - contacts 1278 on the back surface 126 of the light - detection device 110 may be spaced apart from each other.

[0141] A plurality of back contacts 1272 may be disposed (e.g., on top) on portions of the inter - contacts 1278 such that they are electrically coupled, as shown in FIG. 18C, by the inter - contacts 1278 disposed on the back surface 1238 of the support frame 1234, the back surface 1265 of the filler material 1260, and the back surface 126 of the light - detection device 110 so as to be electrically coupled to the vias 128 of the light - detection device 110. In some examples, the back contacts 1272 may be disposed on portions of the inter - contacts 1278 such that they are (completely or partially) disposed on top of the support frame 1234 and / or the filler 1260, as shown in FIG. 18C.

[0142] As also shown in FIG. 18C, the insulating material 1282 may also be disposed on the inter-contact 1278. The insulating material 1282 may extend over the exposed surface region of the inter-contact 1278. Also, the insulating material 1282 may extend over the back surface 126 of the photodetection device 110 and over the lower surface 1238 of the support frame 1238 between the adjacent inter-contact 1278 and the back contact 1272. In this way, the insulating material 1282 may cover or enclose the back surface of the intermediate flow cell device 1262 for the back contact 1272. The exposed portion of the back contact 1272 can thereby be mated with another structure or device to transmit data signals therefrom from at least one photodetection device 110. It should be noted that after the insulating material 1282 and the back contact 1272 are formed, the intermediate flow cell device 1262 may be diced to form one or more flow cells therefrom, as further described below. For example, the intermediate flow cell device 1262 may be diced prior to or subsequent to the formation of the reaction structure on the photodetection device 110 (if not already formed), the formation of the reaction sites on the reaction structure of the photodetection device 110, and / or the formation of, for example, ridging.

[0143] Figures 19A - 19C illustrate a process of forming a plurality of back - side electrical contacts 1372 / 1398 on the back - side of an intermediate flow - cell device 1362 so that data signals from a circuit 24 of at least one light - detection device 10 can be transmitted or conducted within respective cavities 1340 (based on photons detected by its optical sensor 16) to transmit data signals to a biosensor and / or a bioassay system when a flow - cell formed via the intermediate flow - cell device 1362 is utilized thereby. The process of forming the plurality of back - side electrical contacts 1372 and the intermediate flow - cell device 1362 in Figures 19A - 19C is similar to the processes of Figures 16A - 16D and intermediate flow - cell device 1062, Figures 17A - 17C and intermediate flow - cell device 1162, and the process and intermediate flow - cell device 1262 of Figures 18A - 18C. Thus, similar reference numerals preceded by "13" are used to indicate similar components, aspects, functions, processes, or operations, and the above - mentioned descriptions directed thereto apply equally and will not be repeated for the purpose of brevity and clarity. Further, although the light - detection device 10 of Figure 1 is shown within each cavity 1340, as described above, other light - detection devices, such as the light - detection device 110 of Figure 2, may be utilized as well. Note that a light - detection device in which vias extending through its base - wafer portion 14 are cavities can be advantageously utilized for forming the support frame 1362 and the intermediate flow - cell device 1362.

[0144] As shown in FIG. 19A, the intermediate flow cell device 1362 includes a support frame 1224 having a plurality of conductive vias 1384 that extend through from the top surface 1336 to the bottom surface 1338. The vias 1384 may be composed of any conductive material such as a metal (e.g., copper) to transmit data signals from the associated light detection device 110. As shown in FIG. 19A, the portion of the via 1384 on the bottom surface 1338 of the support frame 1334 (i.e., the back surface of the intermediate flow cell device 1362) is exposed and forms a back surface electrical contact portion 1372. Similarly, as shown in FIG. 19A, the portion of the via 1384 on the top surface 1336 of the support frame 1334 (i.e., the front side of the intermediate flow cell device 1362) is exposed and forms a front side electrical contact portion 1373. The back side electrical contact portion 1372 and / or the front side electrical contact portion 1373 may be enlarged (e.g., define a larger cross-sectional area) compared to the inner portion of the via 1384 extending therefrom, as shown in FIG. 19A.

[0145] Adjacent vias 1384 of the support frame 1334 may be spaced apart from each other, and a portion of the support frame 1334 may extend therebetween. For example, as shown in FIG. 19A, adjacent front side electrical contact portions 1373 may be spaced apart from each other, and a portion of the support frame 1334 on the top surface 1336 of the support frame 1334 may extend therebetween. Similarly, adjacent back surface electrical contact portions 1372 may be spaced apart from each other, and a portion of the support frame 1334 on the bottom surface 1338 of the support frame 1334 may extend therebetween.

[0146] As shown in FIG. 19B, a plurality of electrically conductive inter - contacts 1386 may be disposed on the front side of the intermediate flow cell device 1362 to electrically couple the device circuitry 24 of at least one light - detecting device 10 within each cavity 1340 of the support frame 1334 to the electrical contact portion 1386 on the front side of the via 1384 of the support frame 1334. Each inter - contact 138 may extend over a portion of the upper surface 22 of the light - detecting device 10 including the exposed portion of the circuitry 24, over the upper surface of the support member 1360 adjacent to the light - detecting device 10 within the end - cavity portion 1352, and over the exposed upper surface of the front - side electrical contact portion 137 of the via 1384. The inter - contacts 138 thereby electrically couple the device circuitry 24 of at least one light - detecting device 10 within the cavity 1340 to the via 1384 extending through the support frame 1334 such that a data signal from at least one light - detecting device 10 is transmitted therethrough (i.e., conducted) to the back - side electrical contact portion 1373.

[0147] As shown in FIG. 19C, an insulating material portion 1382 may be disposed over the inter - contacts 1386. The insulating material portion 1382 may extend over at least the exposed surface region of the inter - contacts 1386. Also, the insulating material portion 1382 may extend over the upper surface 1336 of the support frame 1334 between adjacent inter - contacts 1386. In this way, the insulating material 1382 may cover or enclose, on the upper surface, at least a portion of the electrically conductive components or a portion of the intermediate flow cell device 1262. The insulating material 1382 may include an exposed upper surface 1383 that is substantially planar and / or smooth as shown in FIG. 19C. For example, the upper surface 1383 of the insulating material 1382 may include / define a surface roughness on the sub - micron scale. In some such examples, the upper surface 1383 of the insulating material 1382 may include / define a surface roughness of 50 nm or less, or 10 nm or less. In one example, the upper surface 1383 of the insulating material 1382 may include / define a surface roughness within the range of 1 - 2 nm.

[0148] The exposed portions of the backside contacts 1372 can mate with another structure or device to transmit data signals from their respective light detection devices 10. For example, as shown in FIG. 19C, a conductive lead wire or ball 1398 (e.g., a partial sphere), or on the exposed surface of the backside electrical contact portion 1373 of the via 1384 (e.g., on top), is disposed to transmit or conduct the signal of at least one light detection device 10 within the cavity 1340 to, for example, a biosensor and / or a bioassay system. The ball 1398 may be composed of any conductive material such as a metal solder. Each ball 1398 may extend over the exposed surface of its respective backside electrical contact portion 1373, the exposed lower surface of the support member 1360 adjacent to its respective backside electrical contact portion 1373, and a portion of the back surface 26 of the light detection device 10 associated with its respective backside electrical contact portion 1373. The ball 1398 may include a ball grid array (BGA)-type surface mounting packaging configuration of the intermediate flow cell device 1362 (and ultimately, one or more flow cells formed thereby).

[0149] At least one flow cell may be formed from the intermediate flow cell device disclosed herein, for example, by forming a reaction structure on the light detection device, forming a reaction site on the reaction structure of the light detection device, covering the light detection device, and / or dicing the intermediate flow cell device. Further, the intermediate flow cell may be diced into one or more discrete cells including at least one light detection device, a lid extending thereover, and a flow path formed between the light detection device and the lid to form at least one flow cell via the intermediate flow cell. As described above, the support frame 1334 may include a visual indication for assisting alignment, for example, during the lid and / or dicing operations.

[0150] In some examples, one or more flow cells may be formed through an intermediate flow cell prior to the formation of backside contacts that are electrically coupled to at least one of its light detection devices. For example, at least one flow cell 1302 may be formed from the intermediate flow cell device 1362 of FIG. 19A, the intermediate flow cell device 1062 of FIG. 16A, the intermediate flow cell device 1162 of FIG. 17A, the intermediate flow cell device 1262 of FIG. 18A, or the intermediate flow cell device 1362 of FIG. 19B or 19C. In some other examples, one or more flow cells may be formed through an intermediate flow cell following the formation of backside contacts that are electrically coupled to at least one of its light detection devices. For example, at least one flow cell 1302 may be formed from the intermediate flow cell device 1062 of FIG. 16D, the intermediate flow cell device 1162 of FIG. 17C, the intermediate flow cell device 1262 of FIG. 18C, or the intermediate flow cell device 1362 of FIG. 19C.

[0151] FIG. 20 illustrates one or more flow cells 1302 formed from the intermediate flow cell device 1362 of FIG. 19C. The intermediate flow cell device 1362 of FIG. 19B is shown as forming one or more flow cells 1302 of FIG. 20, but the intermediate flow cell device 1062 of FIG. 16A or 16D, the intermediate flow cell device 1162 of FIG. 17A or 17C, the intermediate flow cell device 1262 of FIG. 18A, 18B or 18C, or the intermediate flow cell device 1362 of FIG. 19A or 19B may be employed similarly, for example.

[0152] As shown in FIG. 20, the lid / cover 1396 may extend across the front / upper surface of the intermediate flow cell device 1362. For example, as shown in FIG. 20, the lower surface 1397 of the lid 1396 may adhere to the exposed upper surface of the intermediate flow cell device 1362, such as the upper surface 1383 of the insulating material 1382. In this way, the lid 1396 may extend over the upper surface portion 20 of at least one photodetector 10 disposed within each cavity 1340, which may include a reaction structure having a detector surface as described above.

[0153] As shown in FIG. 20, the lower surface 1397 of the lid 1396 may be spaced above the upper portion 22 of at least one light detection device 10 disposed within each cavity 1340 such that a flow path 1390 is formed therebetween. Each flow path 1390 is configured to direct a fluid such as a reaction solution along the detector surface of the reaction structure 20 of the associated at least one light detection device 10 (e.g., size and shape). As shown in FIG. 20, the lateral surfaces of the flow path 1390 may be defined by an insulating material 1382 and / or a front electrical contact portion 1386. The region of the flow path 1390 may be substantially aligned / overlapped with at least one light detection device 10 of each cavity 1340. For example, the region of the flow path 1390 may be substantially aligned with and coincide / overlap the active region of at least one light detection device 10 of each cavity 1340, as shown in FIG. 20. In some other examples, the region of the flow path 1390 may be substantially aligned with the active region of at least one light detection device 10 of each cavity 1340 and extend beyond the active region of at least one light detection device 10 of each cavity 1340, as shown in FIG. 21. As described above, the support frame 1334 may include a visual display for assisting in the alignment of the lid 1396.

[0154] In some examples, the flow path 1390 may include a height within a range of, for example, about 50 to 400 μm (the height extending between the lower surface 1397 of the lid 1396 and the upper portion 22 (e.g., its detection surface) of at least one light detector 10), and a height greater than that may include a height within a range of, for example, about 80 to 200 μm. In one example, the height of the flow path 1390 is about 100 μm. The overall thickness of the lid 1362 can be within a range of, for example, about 300 μm to about 1000 μm.

[0155] In some other examples, the lid 1396 may be indirectly coupled to the upper surface of at least one photodetector 10, support material 1360, and / or support frame 1334, which may or may not at least partially define the lateral surface of the flow channel 1390, and may be coupled via an intervening layer / portion other than the insulating material 1382 and / or the front electrical contact portion 1386. In other examples, the lid 1362 may be directly coupled to the upper surface of at least one photodetector 10, support material 1360, and / or support frame 1334 (e.g., its insulating material or its via 1384 such that it is directly coupled via a low autofluorescence adhesive). In such examples, the lid 1362 may include a sidewall portion that spaces the lower surface 1397 of the lid 1396 extending over at least one photodetector 10 above the upper portion 22 of at least one photodetector 10. The sidewall portion of such a lid 1362 may define the lateral surface of the flow channel 1390.

[0156] As also shown in FIG. 20, lid 1362 may include at least one port 1362 configured to fluidly engage with flow path 1390 and potentially other ports (not shown). For example, the other ports may be from a cartridge or workstation containing a reaction solution or another biological or chemical substance. In some examples, lid 1362 may include at least two ports 1392 associated within each flow path 1390 as an inlet port and an outlet port to flow path 1390. In some examples, the diameter of at least two ports 1392 may be about 750 μm. At least one port 1362 enables a reagent fluid or solution to flow through a potentially associated flow path 1390. As described above, a chemical reaction may occur between a reaction site on a detector surface on top portion 22 of reaction structure 20 within flow path 1390 and a reagent solution. When illuminated through lid 1362, light detection device 10 of flow cell 1302 can sense a chemical reaction occurring within flow path 1390 and generate a signal in response thereto. As described above, the signal may be conducted through circuit 24 of light detection device 10 to backside contact 1372 (and ball contact 1398 if provided). Lid 1362 may thereby be constructed of a material that is transparent to excitation light propagating from outside flow cell 1302 towards and / or into flow channel 1390. Note that excitation light may approach lid 1362 from any angle, along the same or different angles. In some examples, lid 1362 may include, but is not limited to, a material that is optically transparent at least to excitation light and has low or no autofluorescence, such as cyclic olefin copolymer (COC).

[0157] As shown in FIG. 20, the reaction structure 20 may be disposed on the upper portion 22 of each light detection device 10, either before or after attachment of the lid 1362 to the intermediate flow cell device 1362. As described above and further described below, the detector surface of the reaction structure 20 on the upper portion 22 of each light detection device 10 may extend across the entire active region of each light detection device 10. As described above, the detector surface of the reaction structure 20 may include nanowells 16 that extend into the reaction structure 20 and a planar interstitial surface region that extends between and around the nanowells 16.

[0158] The detector surface of each light detection device 10 may be functionalized (e.g., chemically or physically modified in a manner suitable for performing a given reaction). For example, the detector surface may be functionalized and include at least one reaction site on / within a nanowell 16 having one or more biomolecules immobilized thereon. The reaction site may comprise a biological or chemical substance configured to initiate a reaction in response to the excitation light and / or to form a reaction product that generates or emits an optical signal in response to the excitation light. In certain examples, the reaction site may include a cluster or colony of biomolecules (e.g., oligonucleotides) immobilized on the detector surface within the nanowell 16. For example, the reaction site may emit light in response to incident excitation light after being treated with a reaction solution. The excitation light may be part of the flow cell 1302 or may be emitted or generated from any illumination system or light source (not shown) that may or may not be part thereof. In some examples, the illumination system may emit the excitation light at a particular wavelength or wavelengths that excite the biological or chemical substance(s) of the reaction site (e.g., a reaction initiated by the reaction solution and / or a reaction product formed by the reaction solution at the reaction site 114).

[0159] Initially, the reaction site of the nanowell 16 of the reaction structure 20 of the photodetector device 10 may not contain a predetermined reaction. As described above, the reaction site may include a biological or chemical substance immobilized on the base and / or the detector surface of the face of the nanowell 16. In a specific example, after a designated reaction occurs through treatment in a reaction solution, a designated or predetermined luminescence released from the reaction site passes through the reaction structure 20, through at least one corresponding light guide 18, and propagates to at least one corresponding light sensor 12. For this purpose, it is arranged close to the opening of at least one corresponding light guide 18.

[0160] The biological or chemical substances of a single reaction site may be similar or identical (for example, a colony of analytes (for example, oligonucleotides) having a common sequence). However, in other examples, a single reaction site and / or the nanowell 16 may contain different biological or chemical substances. Prior to a predetermined reaction, the reaction site may include at least one analyte (for example, an analyte). For example, the analyte may be an oligonucleotide or a colony thereof (for example, an oligonucleotide-of-interest). The oligonucleotide may have a substantially common sequence and may be bound to a predefined or specific fluorescently labeled biomolecule such as a fluorescently labeled nucleotide.

[0161] However, prior to a given reaction, the fluorophore of the fluorescently labeled biomolecule is not incorporated into or bound to a biological or chemical substance (e.g., oligonucleotide) at the reaction site 114. To achieve the given reaction (i.e., incorporating the fluorescently labeled biomolecule into the biological or chemical substance at the reaction site 114), the flow cell 1303 may provide a flow of the reaction solution into the flow path 1390, thereby providing a flow into the reaction structure 20. The reaction solution may be any solution. In some examples, the reaction solution may contain a liquid. For example, the reaction solution may be an aqueous solution. In one embodiment, the reaction solution contains one or more nucleotides that are at least partially fluorescently labeled, and the reaction solution also contains one or more biomolecules such as a polymerase enzyme that incorporates the nucleotides into the oligonucleotide growing at the reaction site, thereby labeling the oligonucleotide with the fluorescently labeled nucleotides. In this embodiment, the flow cell 1302 may provide a washing solution for removing any free nucleotides that were not incorporated into the oligonucleotide. The reaction site is then illuminated with excitation light, and fluorescence can be caused at the reaction site where the fluorescently labeled nucleotides are incorporated. Reaction sites where the fluorescently labeled nucleotides are not incorporated do not emit light even when excitation light is incident thereon.

[0162] As shown in FIGS. 20 and 21, since the lid 1390 is (directly or indirectly) coupled to the region of the support frame 1334 and / or the support material 1360 associated with each cavity 1340, the region of each flow path 1390 is such that each flow path 1390 extends completely covering the detector surface of the reaction structure 20 so as to span the entire (e.g., at least 95%, or at least 99%, or 100%) active region 1306 of at least one light detection device 10 of each cavity 1340. The flow cell 1302 is configured such that the flow path 1390 aligns with or extends beyond the active region 1306 of at least one light detection device 10 of each cavity 1340 or a plurality of cavities 1340, whereby it can include approximately 100% of the active region 1306 of at least one light detection device 10 within each cavity 1340 that is available or accessible for reagent delivery and illumination. In one example, the die size of the light detection device 10 of each cavity 1340 may be about 8 mm × 9 mm, and its active region 1306 may be about 7 mm × 8 mm. However, the die size of the light detection device 10 and / or the active region 1306 can range, for example, up to about 25 mm × about 25 mm. As described above, each flow path 1390 can align with the active region 1306 of at least one light detection device 10 of each cavity 1340 or extend beyond the active region 1306 of at least one light detection device 10 (and at least one light detection device 10 itself) of each cavity 1340 or a plurality of cavities 1340. Thus, the area of the flow path 1390 may be larger than the area of the active region 1306 of at least one light detection device 10 of each cavity 1340 or a plurality of cavities 1340.

[0163] The plurality of flow cells 1302 may be formed from the intermediate flow cell devices disclosed herein. For example, FIGS. 20 and 22 illustrate the formation of one or more discrete flow cells 1302 that may be formed from an intermediate flow cell device 1362. As shown in FIG. 20, the intermediate flow cell device 1362 may be diced along dicing lines 1304 to form the desired portions of the intermediate flow cell device 1362 into one or more separate and distinct flow cells. It should be noted that the intermediate flow cell device 1362 may be diced subsequent to or prior to coupling a lid 1396 to the intermediate flow cell device 1362. Similarly, the intermediate flow cell device 1362 may be diced subsequent to or prior to the formation of reaction structures 20 and / or reaction sites on / within the nanowells 16 on the top surface of the photodetection device 10. As another example, the intermediate flow cell device 1362 may be diced subsequent to or prior to the formation of flow cell backside electrical contacts such as ball contacts 1398. As described above, the support frame 1334 may include visual indicia to assist in alignment during dicing of the intermediate flow cell device 1362.

[0164] As shown in FIG. 22, the intermediate flow cell device 1362 may be diced to form a plurality of separate and distinct flow cells 1302A, 1302B, 1302C. In this specification, three flow cells 1302A, 1302B, 1302C are used to illustrate the formation of flow cells from the intermediate flow cell device, but note that any number of flow cells may be equally formed (e.g., one flow cell, two flow cells, three flow cells, four flow cells, five flow cells, etc.). It should be noted that the diced flow cells 1302A, 1302B, 1302C may have the same number and / or configuration of the photodetection device 10 / cavity 1340, or may include those with different numbers and / or configurations of the photodetection device 10 / cavity 1340. For example, as shown in FIG. 22, the first diced flow cell 1302A formed from the intermediate flow cell device 1362 includes a single cavity 1340 (e.g., having a flow path 1390 disposed across the entire active region thereof (e.g., at least 95%, or at least 99%, or 100%)) that includes a first number of photodetection devices (e.g., one or more photodetection devices) of a first configuration (e.g., photodetection device 10 or photodetection device 110). The second diced flow cell 1302B may also be formed from the intermediate flow cell device 1362 and may include a pair of cavities 1340 that includes a second number of photodetection devices (e.g., one or more photodetection devices) of a second configuration (e.g., photodetection device 10 and / or photodetection device 110) (having a flow path 1390 disposed across the entire active region thereof (e.g., at least 95%, or at least 99%, or 100%)). The second number and / or second configuration of the photodetection devices of the second diced flow cell 1302B may be the same as or different from the number of photodetection devices of the first diced flow cell 1302A.As also shown in FIG. 22, the third die-shaped flow cell 1302C may also be formed from an intermediate flow cell device 1362 that includes three or more cavities 1340 (having flow paths 1390 disposed across the entirety (e.g., at least 95%, or at least 99%, or 100%) of their active regions) that include a third number of photodetection devices (e.g., one or more photodetection devices) of a third configuration (e.g., photodetection device 10 and / or photodetection device 110). The third number and / or third configuration of the photodetection devices of the third die-shaped flow cell 1302C may be the same as or different from the number of photodetection devices of the first die-shaped flow cell 1302A and the second die-shaped flow cell 1302B. In this way, the sensing throughput of the separate flow cells 1302A, 1302B, 1302C formed from the intermediate flow cell device 1362 may be determined or configured by the number and / or configuration of the cavities 1340 (and thus the number and / or configuration of at least one photodetection device 10) diced from the intermediate flow cell device 1362 to form the separate flow cells 1302A, 1302B, 1302C.

[0165] It should be understood that the above description is intended to be illustrative and not restrictive. For example, the above-described embodiments (and / or aspects thereof) may be used in combination with each other. Further, many modifications may be made to adapt a particular situation or material to the teachings of various embodiments without departing from its scope. Dimensions and types of materials may be described herein, but they are intended to define some parameters of various embodiments and are not meant to limit all embodiments, but are merely illustrative. Many other examples will be apparent to those of ordinary skill in the art in view of the above description. Accordingly, the scope of various embodiments should be determined with reference to the appended claims, along with the full scope of equivalents to which such claims are entitled.

[0166] In the appended claims, the terms “including” and “in which” are used as the plain English equivalents of the respective terms “comprising” and “wherein.” Further, in the following claims, the terms “first,” “second,” “third,” etc. are used merely as reference labels and are not intended to impose numerical, structural, or other requirements on their objects. As used herein, the phrase “based on” includes both a relationship in which an element is partially based and a relationship in which an element is wholly based. The phrase “defined” includes both a relationship in which an element is partially defined and a relationship in which an element is wholly defined. Further, the limitations in the following claims are not written in means-plus-function form and are not intended to be construed under 35 U.S.C. 112, paragraph 6, until such claim limitations expressly use the phrase “means for” and are followed by a further recitation of the structural and functional limitations of the claimed apparatus. It should be understood that not all of the such objects or advantages described above may be achieved in accordance with every particular example. Thus, for example, those skilled in the art will recognize that the devices, systems, and methods described herein may be embodied or implemented in a manner that achieves or optimizes one advantage or group of advantages taught herein without necessarily achieving other objects or advantages taught herein.

[0167] Although the present disclosure has been described in detail in connection with a limited number of examples, it should be readily understood that the present disclosure is not limited to such disclosed examples. Rather, the present disclosure can be modified to incorporate any number of variations, alterations, substitutions, or equivalent arrangements that heretofore have not been described, but that are commensurate with the spirit and scope of the present disclosure. Further, while various examples have been described, it will be understood that aspects of the present disclosure can include only one of the examples or several of the described examples. Also, although some disclosures are described as having a particular number of elements, it will be understood that embodiments can be practiced with fewer elements than the particular number or with more elements than the particular number.

[0168] It should be understood that all combinations of the foregoing concepts and additional concepts discussed in greater detail below are contemplated as part of the inventive subject matter disclosed herein, provided such concepts are not mutually inconsistent. In particular, all combinations of the claimed subject matter recited at the end of this disclosure are contemplated as part of the subject matter of the invention disclosed herein. Preferred embodiments of the present invention are as follows. [1] A flow cell comprising: A support frame including an upper surface, a back surface, and at least one cavity extending from the upper surface towards the lower surface; At least one light detection device disposed within at least one cavity, the light detection device including an active region and an upper surface; A support member disposed within at least one cavity between the support frame and the outer periphery of at least one light detection device, the support member coupling the support frame and at least one light detection device; and A lid extending over at least one light detection device and coupled to the upper surface of the support frame about the outer periphery of at least one light detection device wherein a flow path is formed between the lid and at least the upper surface of at least one light detection device, the flow cell. [2] The flow cell according to [1], wherein the support frame further includes at least one conductive via extending from the upper surface to the lower surface. [3] The flow cell according to [2], wherein at least one light detection device includes at least one solid-state light detection device including a base wafer portion, a plurality of light sensors, a device circuit electrically coupled to the light sensors for transmitting a data signal based on photons detected by the light sensors, and a plurality of light guides associated with the plurality of light sensors. [4] The flow cell according to [3], wherein the device circuit of at least one solid-state light detection device is electrically coupled to at least one conductive via at the upper surface of the support frame. [5] The flow cell according to [1], wherein the lid is indirectly coupled to the upper surface of the support frame. [6] The flow cell according to [1], wherein at least one cavity includes a cavity in which a plurality of light detection devices are disposed. [7] The flow cell according to [6], wherein the plurality of light detection devices include separate light detection devices spaced apart from each other, and the support member further extends between adjacent light detection devices. [8] The flow cell according to [6], wherein the plurality of light detection devices include at least two integrated light detection devices, and the support member extends between the support frame and the outer periphery of at least two integrated light detection devices. [9] The flow cell according to [1], wherein at least one light detection device includes a plurality of light detection devices.

[10] The flow cell according to [9], wherein at least one cavity includes a plurality of cavities, and each light detection device among the plurality of light detection devices is disposed in a different cavity of the support frame.

[11] The flow cell according to [1], comprising at least one solid-state light detection device, wherein at least one light detection device includes a base wafer portion, a plurality of optical sensors, a device circuit electrically coupled to the optical sensors for transmitting a data signal based on photons detected by the optical sensors, and a plurality of light guides associated with the plurality of optical sensors.

[12] The flow cell according to

[11] , wherein at least one cavity extends through the support frame from an upper side to a lower side, the device circuit includes vias extending through the base wafer portion, and the flow cell further includes electrical contacts electrically coupled to the vias and is disposed at least partially along a back surface of the support frame.

[13] The flow cell according to

[11] , wherein at least one light detection device further includes a reaction structure disposed on a plurality of light guides forming an upper surface thereof, the reaction structure including a plurality of nanowells disposed in an active region.

[14] The flow cell according to [1], wherein at least one cavity extends only partially through the support frame from an upper side to a lower side.

[15] The flow cell according to [1], wherein at least one light detection device includes at least one complementary metal oxide semiconductor (CMOS) optical sensor.

[16] The flow cell according to [1], wherein the flow path extends across an entire active region of at least one light detection device.

[17] Attaching an upper surface of the support frame to a planar support surface of the substrate, wherein the support frame includes at least one cavity extending from an upper surface to a lower surface of the substrate; Disposing at least one light detection device in at least one cavity such that an upper surface is disposed on the planar support surface of the substrate and an end of the cavity extends between the support frame and an outer periphery of the at least one light detection device, wherein the at least one light detection device includes an active region and an upper surface; Filling an end of the cavity with a support material for coupling the support frame and the at least one light detection device; and Separating the support frame from the substrate; and Forming a flow cell by attaching a lid to the upper surface of a support frame about the outer periphery of at least one light detection device (wherein the lid extends over at least one light detection device and forms a flow path between the lid and at least the upper surface of at least one light detection device). A method comprising.

[18] The method according to

[17] , wherein at least one light detection device includes at least one solid-state light detection device including a base wafer portion forming a back surface, a plurality of light sensors, a device circuit electrically coupled to the light sensors coupled to transmit a data signal based on photons detected by the light sensors, and a plurality of light guides associated with the plurality of light sensors, the support frame further includes at least one electrically conductive via extending from the upper surface to the lower surface, and further includes electrically coupling the device circuit of the at least one solid-state light detection device to at least one electrically conductive via on the upper surface of the support frame.

[19] The method according to

[17] , wherein at least one light detection device includes at least one solid-state light detection device including a base wafer portion forming a back surface, a plurality of light sensors, a device circuit electrically coupled to the light sensors coupled to transmit a data signal based on photons detected by the light sensors, and a plurality of light guides associated with the plurality of light sensors, the device circuit includes vias extending through the base wafer portion to the back surface of the base wafer portion, and further includes electrically coupling contacts at least partially disposed along the back surface of the support frame to the vias on the back surface of the base wafer portion.

[20] The method according to

[17] , further comprising forming a reaction structure on at least one light detection device before attaching the lid, the reaction structure forming the upper surface of at least one light detection device and including a plurality of nanowells disposed within the active region.

[21] Separating the support frame from the substrate exposes a recessed upper surface of the support material extending downwardly between the upper surface of the support frame and the upper portion of at least one light detection device, the reaction structure extends between the recessed upper surface of the support material and the upper surface of the support frame, and the reaction structure forms a planar upper surface over which the plurality of nanowells extend, according to the method of

[20] .

[22] Further comprising obtaining at least one light detection device, wherein obtaining at least one light detection device includes dicing at least one complementary metal oxide semiconductor (CMOS) light sensor from a plurality of integrated CMOS light sensors, the method described in

[17] .

[23] The method described in

[17] , wherein the flow path extends across the entire active region of at least one light detection device.

[24] Depositing a first support material at the bottom of at least one cavity of the support frame, wherein at least one cavity extends only partially through the support frame from top to bottom; Placing at least one light detection device within at least one cavity and on the deposited first support material such that the ends of at least one cavity extend between the support frame and the outer periphery of at least one light detection device, wherein at least one light detection device includes an active region and an upper surface Filling the ends of the cavity with a second support material; and Attaching a lid to the upper surface of the support frame about the outer periphery of at least one light detection device to form a flow cell, wherein the lid extends over at least one light detection device and forms a flow path between the lid and at least the upper surface of at least one light detection device A method comprising.

[25] The method described in

[24] , wherein the flow path extends across the entire active region of at least one light detection device.

Claims

1. A flow cell, comprising: a) A support frame including an upper surface, a lower surface, and at least one cavity extending from the upper surface to the lower surface, the support frame further including at least one conductive via extending from the upper surface to the lower surface; b) At least one light detection device disposed within at least one cavity, the at least one light detection device comprising: i. An active region and an upper surface, and ii. A base wafer portion forming a back surface, a plurality of light sensors, a plurality of light guides associated with the plurality of light sensors, and a device circuit electrically coupled to the plurality of light sensors for transmitting a data signal based on photons detected by the plurality of light sensors, at least one solid state light detection device; Including, The device circuit further includes a via extending through the base wafer portion, The device circuit of at least one solid state light detection device is electrically coupled to at least one conductive via on the upper surface of the support frame, At least one light detection device; c) A support material disposed between the support frame and the outer periphery of at least one light detection device within at least one cavity, the support material coupling the support frame and at least one light detection device; d) For the outer periphery of at least one light detection device, a lid extending over at least one light detection device and coupled to the upper surface of the support frame, The lid and at least the upper surface of at least one light detection device form a flow path therebetween; and e) An electrical contact disposed at least partially along the lower surface of the support frame and electrically coupled to at least one conductive via in the support frame; A flow cell comprising.

2. The flow cell according to claim 1, wherein the lid is indirectly coupled to the upper surface of the support frame.

3. The flow cell according to claim 1, wherein at least one cavity includes a cavity in which a plurality of light detection devices are disposed.

4. The flow cell according to claim 3, wherein the plurality of light detection devices include separate light detection devices spaced apart from each other, and the support material further extends between adjacent light detection devices.

5. The flow cell according to claim 3, wherein the plurality of light detection devices includes at least two integrated light detection devices, and the support material extends between the support frame and the outer periphery of the at least two integrated light detection devices.

6. The flow cell according to claim 1, wherein at least one light detection device includes a plurality of light detection devices.

7. The flow cell according to claim 6, wherein at least one cavity includes a plurality of cavities, and each light detection device among the plurality of light detection devices is disposed in a different cavity of the support frame.

8. The flow cell according to claim 1, wherein at least one cavity extends through the support frame from the upper side to the lower side.

9. The flow cell according to claim 1, wherein at least one light detection device further includes a reaction structure disposed on a plurality of light guides forming its upper surface, and the reaction structure includes a plurality of nanowells disposed in an active region.

10. The flow cell according to claim 1, wherein at least one cavity extends only partially through the support frame from the upper side to the lower side.

11. The flow cell according to claim 1, wherein at least one light detection device includes at least one complementary metal oxide semiconductor (CMOS) optical sensor.

12. The flow cell according to claim 1, wherein the flow path extends across the entire active region of at least one light detection device.

13. a) attaching the upper surface of the support frame to the planar support surface of the substrate, wherein the support frame includes i. at least one cavity extending from its upper surface to its lower surface, and ii. at least one conductive via extending from the upper surface to the lower surface, ; b) disposing at least one light detection device in at least one cavity such that the upper surface is disposed on the planar support surface of the substrate and the end of the cavity extends between the support frame and the outer periphery of the at least one light detection device, wherein the at least one light detection device includes an active region and an upper surface. At least one solid-state light detection device includes a base wafer portion forming a back surface, a plurality of light sensors, a plurality of light guides associated with the plurality of light sensors, and a device circuit electrically coupled to the light sensors configured to transmit a data signal based on photons detected by the light sensors. The device circuit includes vias extending through the base wafer portion to the back surface. The device circuit of the at least one solid-state light detection device is electrically coupled to at least one conductive via on the upper surface of the support frame. c) Filling an end of the cavity with a support material to couple the support frame and the at least one light detection device. d) Separating the support frame from the substrate. e) Attaching a lid to the upper surface of the support frame about the outer periphery of the at least one light detection device to form a flow cell, where the lid extends over the at least one light detection device and forms a flow path between the lid and at least the upper surface of the at least one light detection device. f) Electrically coupling the device circuit of the at least one solid-state light detection device to at least one conductive via on the upper surface of the support frame; and g) Electrically coupling contacts disposed at least partially along the lower surface of the support frame to the vias at the back surface of the base wafer portion. A method comprising.

14. The method of claim 13, further comprising forming a reaction structure on the at least one light detection device prior to attaching the lid, the reaction structure forming an upper surface of the at least one light detection device and including a plurality of nanowells disposed within an active region.

15. Separating the support frame from the substrate exposes a recessed upper surface of the support material extending downwardly between the upper surface of the support frame and an upper portion of the at least one light detection device, the reaction structure extending between the recessed upper surface of the support material and the upper surface of the support frame, and the reaction structure forming a planar upper surface over which the plurality of nanowells extend. The method of claim 14.

16. Further comprising obtaining at least one light detection device, wherein obtaining at least one light detection device includes dicing at least one complementary metal oxide semiconductor (CMOS) light sensor from a plurality of integrated CMOS light sensors, the method according to claim 13.

17. The method according to claim 13, wherein the flow path extends across the entire active region of at least one light detection device.

18. A method of manufacturing the flow cell according to claim 1, the method comprising: Depositing a first support material at the bottom of at least one cavity of the support frame, wherein at least one cavity extends only partially through the support frame from top to bottom, and the lower portion of the support frame extends between the lower surface of the lower portion of the cavity and the lower surface of the support frame. Placing at least one light detection device within at least one cavity and on the deposited first support material such that the ends of the at least one cavity extend between the support frame and the outer periphery of the at least one light detection device, wherein the at least one light detection device includes an active region and an upper surface. Filling the ends of the cavity with a second support material; and Attaching a lid to the upper surface of the support frame about the outer periphery of the at least one light detection device to form a flow cell, wherein the lid extends over the at least one light detection device and forms a flow path between the lid and at least the upper surface of the at least one light detection device. A method comprising.

19. The method according to claim 18, wherein the flow path extends across the entire active region of at least one light detection device.

20. The method according to claim 18, wherein the first support material and the second support material are the same support material.

21. The method according to claim 18, comprising dicing the support frame.

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