Dual filter optical detection device and method related thereto

Abstract

The present application relates to, but is not limited to, a dual filter optical detection device and methods related thereto. An optical detection device and a corresponding method are provided. The device includes a reaction structure to contain a reaction solution and at least one reaction site, which generates light emission in response to incident excitation light after being treated with the reaction solution. The device also includes a plurality of light sensors and device circuits. The device also includes a plurality of light guides extending from an input area that receives excitation light and light emission from at least one corresponding reaction groove toward at least one corresponding light sensor. The light guide includes a first filtering area and a second filtering area, wherein the first filtering area filters the excitation light and allows the light emission of a first wavelength to be transmitted to at least one corresponding light sensor, and the second filtering area filters the excitation light and allows the light emission of a second wavelength to be transmitted to at least one corresponding light sensor.

Description

[0001] This application is a divisional application of an application with a filing date of December 20, 2018, application number 201811565071.0, and invention name “Dual filter optical detection device and related methods”.

[0002] CROSS-REFERENCE TO RELATED APPLICATIONS

[0003] This patent application claims priority to U.S. Provisional Patent Application No. 62 / 609,903, filed on December 22, 2017, and entitled “Two-Filter Light Detection Devices and Methods of Manufacturing Same” and Netherlands Application No. 2020625, filed on March 20, 2018, and entitled “Two-Filter Light Detection Devices and Methods of Manufacturing Same”. The entire contents of each of the above applications are hereby incorporated herein by reference. Technical Field

[0004] The present application relates to but is not limited to the field of detection. Background Art

[0005] Various schemes in biological research or chemical research involve carrying out a large number of controlled reactions on a local support surface or in a predetermined reaction chamber. The specified reaction can then be observed or detected, and subsequent analysis can help identify or reveal the properties of the chemicals involved in the reaction. For example, in some multiple determinations, an unknown analyte with an identifiable marker (such as a fluorescent marker) can be exposed to thousands of known probes under controlled conditions. Each known probe can be deposited in the corresponding well of a microplate. Any chemical reaction observed between the known probe and the unknown analyte in the well can help identify or reveal the properties of the analyte. Other examples of such schemes include known DNA sequencing processes, such as synthetic sequencing (SBS) or cycle array sequencing.

[0006] In some conventional fluorescence detection schemes, an optical system is used to direct excitation light to a fluorescently labeled analyte and also to detect a fluorescent signal that may be emitted from the analyte. However, such an optical system may be relatively expensive and involve a relatively large benchtop footprint. For example, such an optical system may include an arrangement of lenses, filters, and a light source.

[0007] In other proposed detection systems, a controlled reaction occurs on a local support surface or within a predetermined reaction chamber disposed on an electronic solid-state photodetector or imager (e.g., a complementary metal oxide semiconductor (CMOS) detector or a charge coupled device (CCD) detector) that does not involve large optical components for detecting fluorescent emissions. However, such proposed solid-state imaging systems may have some limitations. For example, there may be challenges in fluidly delivering reagents (e.g., fluorescently labeled molecules) to analytes located on electronic devices of such systems. For example, in some cases, reagent solutions may damage electronic devices and corrode their components. Summary of the invention

[0008] In one aspect of the present disclosure, a device is provided. The device includes a reaction structure to contain a reaction solution and a plurality of reaction sites, and the reaction sites generate light emission in response to incident excitation light after being treated with the reaction solution. The reaction solution can trigger a reaction and / or form a reaction product at the reaction site, and the reaction site generates light emission in response to the excitation light. The reaction structure is positioned above the device base of the device. The device also includes a plurality of light sensors in the device base and a device circuit in the device base, the device circuit being electrically coupled to the plurality of light sensors and configured to transmit data signals based on photons detected by the light sensors. The device also includes a plurality of light guides having an input area to receive excitation light and light emission from at least one corresponding reaction site, and the light guide extends from the input area toward at least one corresponding light sensor into the device base. Each of the plurality of light guides includes a first filter region and a second filter region, wherein the first filter region is formed by a first filter material to filter at least a first wavelength of excitation light and allow light emission of a second wavelength to pass through it to reach at least one corresponding light sensor, and the second filter region is formed by a second filter material to filter at least a first wavelength of excitation light and allow light emission of a third wavelength to pass through it to reach at least one corresponding light sensor.

[0009] In some examples, at least one first reaction site among the plurality of reaction sites emits light of at least a second wavelength and a third wavelength in response to excitation light of a first wavelength after being treated with a reaction solution (e.g., after the reaction solution has initiated a reaction at the reaction site and / or formed at least one reaction product). In some examples, at least one first reaction site among the plurality of reaction sites emits light of at least a second wavelength and a third wavelength in response to excitation light of a first wavelength and a fourth wavelength, respectively, after being treated with the reaction solution. In some examples, at least one first reaction site among the plurality of reaction sites emits light emission of a second wavelength in response to excitation light of a first wavelength after being treated with the reaction solution, and at least one second reaction site among the plurality of reaction sites emits light emission of a third wavelength in response to excitation light of a fourth wavelength after being treated with the reaction solution.

[0010] In some examples, the device also includes a support layer within the bottom portion of the light guide, the support layer extending below the bottom portion of the first filter region and around the bottom portion of the first filter region. In some such examples, the support layer is composed of an oxide, a nitride, or a combination thereof. In other such examples, the second filter region of the light guide extends above the support layer and around the first filter region. In some such examples, the first filter region and the second filter region of the light guide form an input region of the light guide.

[0011] In some examples, the device further comprises a second spacer layer positioned between the support layer at the bottom portion of the light guide and the device circuitry and positioned between the second filtering region within the top portion of the light guide and the device circuitry. In some such examples, the second spacer layer comprises a silicon nitride shielding layer. In some examples, the device circuitry of the device base forms a complementary metal oxide semiconductor (CMOS) circuitry.

[0012] In some examples, the first filter material further filters light emissions at a third wavelength, and the second filter material further filters light emissions at a second wavelength. In some examples, the first filter material is a polymer material having a first dye, and the second filter material is a polymer material having a second dye different from the first dye. In some examples, each of the plurality of reaction sites is secured to the reaction structure within at least one reaction recess of the reaction structure.

[0013] In some examples, the reaction solution initiates a reaction and / or forms a reaction product at a reaction site that generates light emission of a second wavelength and a third wavelength in response to incident excitation light. In some such examples, at least one reaction site includes at least one analyte, and the reaction solution includes an aqueous solution containing at least one fluorescently labeled molecule. In some such examples, the at least one analyte includes an oligonucleotide, and the at least one fluorescently labeled molecule includes a fluorescently labeled nucleotide.

[0014] In another aspect of the present disclosure, a biosensor is provided. The biosensor includes any of the devices described above. The biosensor also includes a flow cell mounted to the device and a reaction site contained on a reaction structure. The flow cell includes a reaction solution and at least one flow channel, the flow channel being in fluid communication with the reaction site of the reaction structure to guide the reaction solution to the reaction site.

[0015] In another aspect of the present disclosure, a method is provided. The method includes forming a plurality of trenches in a device base, the device base including a plurality of light sensors and a device circuit electrically coupled to the light sensors, the device circuit being configured to transmit a data signal based on photons detected by the light sensors. The plurality of trenches each extend from a top surface of the device base and toward at least one corresponding light sensor. The method also includes depositing a support layer over an inner surface of the plurality of trenches. The method also includes filling the plurality of trenches over the deposited support layer with a first filter material, the first filter material filtering at least a first wavelength of light and allowing a second wavelength of light to pass through it to reach at least one corresponding light sensor. The method also includes removing an upper portion of the deposited support layer within the plurality of trenches positioned between the device base and the first filter material to form a plurality of voids. The method also includes filling the plurality of voids with a second filter material, the second filter material filtering at least a first wavelength of light and allowing a third wavelength of light to pass through it to reach at least one corresponding light sensor to form a plurality of light guides. The method also includes forming a reaction structure above the device base and the plurality of light guides for accommodating a reaction solution and at least one reaction site that generates light of at least a second wavelength and a third wavelength in response to incident excitation light of at least a first wavelength after being treated with the reaction solution.

[0016] In some examples, at least one first reaction site emits at least a second wavelength and a third wavelength of light in response to excitation light of the first wavelength after being treated with the reaction solution (e.g., after the reaction solution has initiated a reaction at the reaction site and / or formed at least one reaction product). In some examples, at least one first reaction site emits at least a second wavelength and a third wavelength of light in response to excitation light of the first wavelength and a fourth wavelength, respectively, after being treated with the reaction solution. In some examples, at least one first reaction site emits light emission of the second wavelength in response to excitation light of the first wavelength after being treated with the reaction solution, and at least one second reaction site emits light emission of the third wavelength in response to excitation light of the fourth wavelength after being treated with the reaction solution.

[0017] In some examples, removing an upper portion of the deposited support layer within the plurality of grooves forms a portion of the support layer that extends below and around a bottom portion of the first filter material. In some examples, the method further includes depositing a second backing layer over the inner surfaces of the plurality of grooves and over the top surface of the device base prior to depositing the support layer, such that the support layer extends over the second backing layer. In some examples, the first filter material also filters light of a second wavelength, and the second filter material also filters light of the first wavelength. In some examples, the first filter material includes a polymer material having a first dye, and the second filter material includes a polymer material having a second dye different from the first dye.

[0018] It should be appreciated that all combinations of the foregoing aspects and additional concepts discussed in greater detail below (provided such concepts are not mutually inconsistent) are contemplated as being part of the inventive subject matter disclosed herein.

[0019] These and other objects, features and advantages of the present disclosure will become apparent from the following detailed description of the various aspects of the present disclosure taken in conjunction with the accompanying drawings. BRIEF DESCRIPTION OF THE DRAWINGS

[0020] These and other features, aspects, and advantages of the present invention will become better understood when the following detailed description is read with reference to the accompanying drawings, which are not necessarily drawn to scale and in which like reference numerals represent like aspects throughout the drawings, and in which:

[0021] Figure 1 A cross-section of a biosensor according to the present disclosure is shown in one example.

[0022] Figure 2 The figure shows an example Figure 1 Top view of the device base of the biosensor.

[0023] Figure 3 The figure shows an example Figure 1 A side cross-sectional view of a portion of a biosensor showing a portion of the reaction structure and its light guide.

[0024] Figure 4 The figure shows an example Figure 1 A top cross-sectional view of a portion of a biosensor showing an array of light guides.

[0025] Figure 5 Figure 2 shows a diagram of a reaction solution including a reaction structure in one example. Figure 3 An enlarged portion of the cross section.

[0026] Figure 6 FIG. 1 shows an example of a light detection event including Figure 3An enlarged portion of the cross section.

[0027] Figure 7 is a flow chart illustrating a method of manufacturing a biosensor according to the present disclosure in one example.

[0028] Figure 8 The figure shows the formation of a groove in a light detecting device base in one example.

[0029] Fig. 9 The figure shows an example in which Figure 8 A first pad is formed within the groove in the device base.

[0030] Fig.10 The figure shows an example in which Fig. 9 A second pad is formed within the groove of the device base.

[0031] Fig.11 The figure shows that in one example, a first filter material is filled Fig.10 A gasketed groove is provided to form a first filter area.

[0032] Fig.12 Figure 1 shows an example where an upper portion of the second liner is removed to Fig.11 A cavity is formed in the groove of the device base.

[0033] Fig.13 The figure shows that in one example, a second filter material is filled Fig.12 The cavity of the groove of the device base is formed to form a light guide having a first filtering region and a second filtering region. DETAILED DESCRIPTION

[0034] Aspects of the present disclosure and some examples, features, advantages, and details thereof are explained more fully below with reference to the non-limiting examples shown 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, although indicating various aspects of the present disclosure, are only given as examples rather than as a limiting manner. From this disclosure, various replacements, modifications, additions, and / or arrangements within the spirit and / or scope of the basic inventive concept will be apparent to those skilled in the art.

[0035] As used throughout the disclosure herein, approximate language may be applied to modify any quantitative representation that may be permitted to vary without resulting in a change in the basic function to which it is associated. Therefore, values ​​modified by one or more terms, such as "about" or "substantially", are not limited to the precise values ​​specified. For example, these terms may refer to less than or equal to ±5%, such as less than or equal to ±2%, such as less than or equal to ±1%, such as less than or equal to ±0.5%, such as less than or equal to ±0.2%, such as less than or equal to ±0.1%, such as less than or equal to ±0.05%. In some cases, approximate language may correspond to the precision of an instrument used to measure a value.

[0036] The terms used herein are only used for the purpose of describing specific examples and are not intended to be limiting. As used herein, the singular forms "a", "an" and "the" are intended to also include plural forms unless the context clearly indicates otherwise. In addition, reference to "an example" is not intended to be interpreted as excluding the existence of additional examples that also include the stated features. In addition, unless explicitly 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 linking verbs. As a result, any example of "comprises," "has," "includes," or "contains" one or more steps or elements possesses such one or more steps or elements, but is not limited to possessing only such one or more steps or elements. As used herein, the terms "may" and "may be" indicate the possibility of occurring under a set of circumstances; possessing a particular property, characteristic, or function; and / or qualifying another verb by expressing one or more of the ability, capability, or possibility associated with the qualifier. Thus, the use of "may" and "may be" indicates that the modified term is clearly suitable, capable, or suitable for the indicated capability, function, or usage, while taking into account that in some cases, the modified term may sometimes be inappropriate, unable, or unsuitable. For example, in some cases, an event or capability is expected, while in other cases, the event or capability may not occur, and this distinction is encompassed by the terms "may" and "may be."

[0037] Examples described herein can be used for various biological or chemical processes and systems about academic or commercial analysis. More specifically, examples described herein can be used for various processes and systems, where it is desirable to detect events, attributes, qualities, or characteristics indicating a specified reaction. For example, examples described herein include light detection equipment, biosensors, and parts thereof, and bioassay systems operated with biosensors. In some examples, equipment, biosensors, and systems can include a flow cell and one or more light sensors coupled together (removably or fixedly) with a substantially integral structure.

[0038] Equipment, biosensor and bioassay system can be configured to perform multiple specified reactions that can be detected individually or collectively. Equipment, biosensor and bioassay system can be configured to perform multiple cycles in which multiple specified reactions occur in parallel. For example, equipment, biosensor and bioassay system can be used for sequencing dense DNA feature arrays by iterative cycles of enzymatic manipulation (enzymatic manipulation) and light or image detection / collection. In this way, equipment, biosensor and bioassay system (for example, by one or more barrels) can include one or more microfluidic channels, and the one or more microfluidic channels deliver reagents or other reaction components in the reaction solution to the reaction site of equipment, biosensor and bioassay system. In some examples, the reaction solution can be substantially acidic, for example, comprising a pH less than or equal to about 5, or a pH less than or equal to about 4, or a pH less than or equal to about 3. In some other examples, the reaction solution can be substantially alkaline (basic) / alkaline (alkaline), for example, comprising a pH greater than or equal to about 8, or a pH greater than or equal to about 9, or a pH greater than or equal to about 10. As used herein, the term "acidity" and its grammatical variants refer to a pH value of less than about 7, while the terms "basicity," "alkalinity," and their grammatical variants refer to a pH value greater than about 7. In some examples, the reaction sites are provided or spaced apart in a predetermined manner, such as in a uniform or repeating pattern. In other examples, the reaction sites are randomly distributed. Each reaction site can be associated with one or more light guides and a light sensor that detects light from the associated reaction site. In some examples, the reaction sites are located in a reaction groove or reaction chamber that can at least partially separate a specified reaction therein.

[0039] As used herein, a "specified reaction" includes a change in at least one of the chemical, electrical, physical, or optical properties (or mass) of a chemical or biological substance of interest, such as an analyte of interest. In a specific example, the specified reaction is a positive binding event, such as the binding of a fluorescently labeled biomolecule to an analyte of interest. More generally, the specified reaction can be a chemical transformation, a chemical change, or a chemical interaction. The specified reaction can also be a change in electrical properties. In a specific example, the specified reaction includes the binding of a fluorescently labeled molecule to at least one analyte. The analyte can be an oligonucleotide, and the fluorescently labeled molecule can be a nucleotide. The specified reaction can be detected when excitation light is directed toward an oligonucleotide with labeled nucleotides and the fluorophore emits a detectable fluorescent signal. In an optional example, the detected light emission or signal is the result of chemiluminescence or bioluminescence. The specified reaction can also be, for example, by increasing fluorescence (or ) resonance energy transfer (FRET), reducing FRET by separating the donor and acceptor fluorophores, increasing fluorescence by separating the quencher from the fluorophore, or decreasing fluorescence by co-localizing the quencher and fluorophore.

[0040] As used herein, "reaction solution," "reaction component," or "reactant" includes any substance that can be used to obtain at least one specified reaction. For example, reaction components include reagents, enzymes, samples, other biomolecules, and buffer solutions. The reaction components can be transported to the reaction site in solution and / or fixed at the reaction site. The reaction components can interact directly or indirectly with another substance, such as an analyte of interest fixed at the reaction site. In some examples, the reaction solution can be relatively highly acidic (e.g., pH less than or equal to about 5) or relatively highly alkaline / basic (e.g., pH greater than or equal to about 8).

[0041] As used herein, the term "reaction site" is a local area where at least one specified reaction can occur. The reaction site can include a support surface of a reaction structure or a substrate, where a substance can be fixed thereon. For example, a specific reaction site can include a substantially flat surface of a reaction structure (which can be positioned in the channel of a flow cell), which has a community of nucleic acids thereon. In some examples, the nucleic acids in the community have the same sequence, and the sequence is a cloned copy of a single-stranded or double-stranded template, for example. However, in some examples, the reaction site can only include a single nucleic acid molecule, for example, in the form of a single strand or double strand. In addition, a plurality of reaction sites can be randomly distributed along the reaction structure or arranged in a predetermined manner (for example, in a matrix, for example, side by side in a microarray). The reaction site can also include a reaction chamber or groove that at least partially defines a spatial region or volume, which is configured to separate a specified reaction. As used herein, the term "reaction chamber" includes a defined spatial region of a support structure (which is usually in fluid communication with a flow channel). The reaction groove can be at least partially separated from the surrounding environment or other spatial regions. For example, a plurality of reaction grooves can be separated from each other by a shared wall. As a more specific example, the reaction recess may be a nanowell that includes an indentation, pit, well, groove, open cavity or depression defined by an interior surface and defines an opening or aperture such that the nanowell is in fluid communication with a flow channel.

[0042] In some examples, the size and shape of the reaction groove of the reaction structure are designed relative to the solid (including semi-solid) so that the solid can be inserted therein in whole or in part. For example, the size and shape of the reaction groove can be designed to accommodate capture beads. The capture beads can have cloned amplified DNA or other substances thereon. Alternatively, the size and shape of the reaction groove can be designed to receive an approximate number of beads or solid substrates. As another example, the reaction groove can be filled with a porous gel or substance that is configured to control diffusion or filter fluids that may flow into the reaction groove.

[0043] In some examples, a light sensor (e.g., a photodiode) is associated with a corresponding reaction site. The light sensor associated with the reaction site is configured to detect light emission from the associated reaction site via at least one light guide when a specified reaction occurs at the associated reaction site. In some cases, multiple light sensors (e.g., several pixels of a light detection or camera device) can be associated with a single reaction site. In other cases, a single light sensor (e.g., a single pixel) can be associated with a single reaction site or a group of reaction sites. Light sensors, reaction sites, and other features of the biosensor can be configured so that at least some light is detected directly by the light sensor without being reflected.

[0044] As used herein, "biological or chemical substances" include biomolecules, samples of interest, analytes of interest, and other compounds. Biological or chemical substances can be used to detect, identify, or analyze other compounds, or as vehicles for studying or analyzing other compounds. In a specific example, biological or chemical substances include biomolecules. As used herein, "biomolecules" include 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 any other biologically active compounds, such as analogs or mimetics of the above substances. In another example, biological or chemical substances or biomolecules include enzymes or reagents for detecting another reaction product such as enzymes or reagents in a coupled reaction, such as enzymes or reagents for detecting pyrophosphate in a pyrophosphate sequencing reaction. Enzymes and reagents for pyrophosphate detection are described, for example, in U.S. Patent Publication No. 2005 / 0244870A1, which is incorporated by reference in its entirety.

[0045] Biomolecules, samples, and biological or chemical substances can be naturally occurring or synthetic and can be suspended in a solution or mixture in a reaction groove or region. Biomolecules, samples, and biological or chemical substances can also be combined with a solid phase or gel material. Biomolecules, samples, and biological or chemical substances can also include pharmaceutical compositions. In some cases, the biomolecules, samples, and biological or chemical substances of interest can be referred to as targets, probes, or analytes.

[0046] As used herein, "biosensor" includes a device including a reaction structure with multiple reaction sites, which is configured to detect a specified reaction occurring at or near the reaction site. The biosensor may include a solid-state light detection or "imaging" device (e.g., CCD or CMOS light detection device) and a flow cell optionally mounted thereon. The flow cell may include at least one flow channel in fluid communication with the reaction site. As a specific example, the biosensor is configured to be fluidically and electrically coupled to a bioassay system. The bioassay system may deliver a reaction solution to the reaction site according to a predetermined scheme (e.g., synthetic sequencing) and perform multiple imaging events. For example, the bioassay system may guide the reaction solution to flow along the reaction site. At least one of the reaction solutions may include nucleotides of the same or different fluorescently labeled types. Nucleotides may be combined with the reaction site, such as combined with the corresponding oligonucleotides at the reaction site. The bioassay system may then use an excitation light source (e.g., a solid-state light source, such as a light emitting diode (LED)) to irradiate the reaction site. The excitation light may have one or more predetermined wavelengths, including a range of wavelengths. Fluorescent markers excited by incident excitation light can provide an emission signal (eg, light of one or more wavelengths different from the excitation light and potentially different from each other) that can be detected by a light sensor.

[0047] As used herein, when used with respect to biomolecules or biological or chemical substances, the term "immobilization" includes attaching the biomolecules or biological or chemical substances substantially to a surface at a molecular level, such as to a detection surface of a light detection device or a reaction structure. For example, adsorption techniques (including non-covalent interactions (e.g., electrostatic forces, van der Waals forces, and hydrophobic interface dehydration)) and covalent binding techniques (wherein functional groups or linkers facilitate attachment of the biomolecules to the surface) can be used to immobilize the biomolecules or biological or chemical substances to the surface. Immobilizing the biomolecules or biological or chemical substances to the surface can be based on the properties of the surface, the liquid medium carrying the biomolecules or biological or chemical substances, and the properties of the biomolecules or biological or chemical substances themselves. In some cases, the surface can be functionalized (e.g., chemically modified or physically modified) to facilitate the immobilization of the biomolecules (or biological or chemical substances) to the surface.

[0048] In some examples, nucleic acid can be fixed on the reaction structure, for example, fixed on the surface of its reaction groove.In a specific example, equipment described herein, biosensor, bioassay system and method can include using natural nucleotides and also using enzymes configured to interact with natural nucleotides.Natural nucleotides include, for example, ribonucleotides or deoxyribonucleotides.Natural nucleotides can be monophosphate form, diphosphate form or triphosphate form, and can have a base selected from adenine (A), thymine (T), uracil (U), guanine (G) or cytosine (C).However, it is to be understood that non-natural nucleotides, modified nucleotides or the analogs of the above-mentioned nucleotides can be used.

[0049] As mentioned above, biomolecules or biological or chemical substances can be fixed at the reaction site in the reaction groove of the reaction structure. Such biomolecules or biological substances can be physically maintained or fixed in the reaction groove by interference fit, adhesion, covalent bond or encapsulation (entrapment). The example of the article or solid that can be arranged in the reaction groove includes polymer beads, granules, agarose gel, powder, quantum dots or other solids that can be compressed and / or maintained in the reaction chamber. In some embodiments, the reaction groove can be coated or filled with a hydrogel layer that can covalently bind DNA oligonucleotides. In a specific example, a nucleic acid superstructure, such as a DNA ball, can be arranged in the reaction groove or at the reaction groove by, for example, being attached to the inner surface of the reaction groove or by being left in the liquid in the reaction groove. DNA balls or other nucleic acid superstructures can be carried out, and then they are arranged in the reaction groove or at the reaction groove. Selectively, DNA balls can be synthesized in situ at the reaction groove. The material fixed in the reaction groove can be solid, liquid or gaseous.

[0050] Figure 1-8 A cross-section of a portion of a biosensor 100 formed according to one example is shown. As shown, the biosensor 100 may include a flow cell 102 directly or indirectly coupled to a light detection device 104. The flow cell 102 may be mounted to the light detection device 104. In the illustrated example, the flow cell 102 is directly fixed to the light detection device 104 by one or more fixing mechanisms (e.g., adhesives, bonds, fasteners, and the like). In some examples, the flow cell 102 may be removably coupled to the light detection device 104.

[0051] Biosensor 100 and / or detection device 104 can be configured for biological or chemical analysis to obtain any information or data related thereto. In a specific example, biosensor 100 and / or detection device 104 may include a nucleic acid sequencing system (or sequencer) configured for various applications, including but not limited to de novo sequencing (de novosequencing), resequencing of the whole genome or target genome region, and metagenomics. The sequencing system can be configured to perform DNA or RNA analysis. In some examples, biosensor 100 and / or detection device 104 are configured to perform a large number of parallel reactions in biosensor 100 and / or detection device 104 to obtain information related thereto.

[0052] Flow cell 102 can comprise one or more flow channels, and these one or more flow channels guide solution to reaction site 114 on detection device 104 or guide towards reaction site 114 on detection device 104, as further explained below.Therefore flow cell 102 and / or biosensor 100 can comprise fluid storage system (not shown), perhaps be in communication with this fluid storage system fluid, and fluid storage system can store various reaction components or reactant for example for carrying out the reaction of specifying therein.Fluid storage system can also store the fluid for cleaning or cleaning fluid network and biosensor 100 and / or detection device 104 and for diluting reactant potentially.For example, fluid storage system can comprise various reservoirs, to store sample, reagent, enzyme, other biomolecule, buffer solution, aqueous solution, oil and other non-polar solution and the like.As mentioned above, the fluid or solution provided on reaction structure 126 can be relatively acidic (for example, pH is less than or equal to about 5) or alkaline / alkaline (for example, pH is greater than or equal to about 8). Additionally, the fluid storage system may also include a waste reservoir for receiving waste products from the biosensor 100 and / or the detection device 104 .

[0053] In the illustrated example, the light detection device 104 includes a device base 125 and a reaction structure 126 covering the device base 125. Figure 1 and Figure 3-8 In a specific example, the device base 125 includes a plurality of stacked layers (e.g., silicon layers or wafers, dielectric layers, metal-dielectric layers, etc.). The device base 125 may include a sensor array 124 of light sensors 140 and a guide array of light guides 118, such as Figure 3 As shown in Figure 1 and Figure 3-8As shown in , the reaction structure 126 may include an array of reaction grooves 108 in which at least one corresponding reaction site 114 is disposed (e.g., fixed on its surface). In some examples, the light detection device 104 is configured so that each light sensor 140 corresponds to a single light guide 118 and / or a single reaction groove 108 (and is potentially aligned therewith) so that it receives photons only therefrom. However, in other examples, a single light sensor 140 may receive photons through more than one light guide 118 and / or more than one reaction groove 108. Thus, a single light sensor 140 may form one pixel or more than one pixel. Similarly, a single light sensor 140 may receive photons from a reaction site 114 or from multiple reaction sites 114. Thus, a single light sensor 140 may form one pixel or more than one pixel.

[0054] like Figure 2 As shown in , the array of reaction grooves 108 and / or light guides 118 (and potential light sensors 140) can be arranged in a defined repeating pattern, so that at least some of the grooves 108 and / or light guides 118 (and potential light sensors 140) are equally spaced from each other in a defined position pattern. In other examples, the reaction grooves 108 and / or light guides 118 (and potential light sensors 140) can be arranged in a random pattern, and / or at least some of the reaction grooves 108 and / or light guides 118 (and potential light sensors 140) can be variably spaced from each other.

[0055] like Figure 1 and Figure 2 , the reaction structure 126 of the detection device 104 can define a detector surface 112 on which the reaction solution can flow and stay, as explained further below. The detector surface 112 of the reaction structure 126 can be the top exposed surface of the detection device 104. The detector surface 112 can include the surface of the grooves 108 and the gap areas 113 extending between and around the grooves 108.

[0056] The detector surface 112 of the light detection device 104 can be functionalized (e.g., chemically modified or physically modified in a suitable manner for performing a specified reaction). For example, the detector surface 112 can be functionalized and can include a plurality of reaction sites 114 having one or more biomolecules immobilized thereon, such as Figure 1 , Figure 3 and Figure 4As described above, the detector surface 112 can include an array of reaction recesses 108 (e.g., open reaction chambers). Each of the reaction recesses 108 can include one or more of the reaction sites 114. The reaction recesses 108 can be defined by, for example, a variation in depth (or thickness) along the detector surface 112. In other examples, the detector surface 112 can be substantially planar.

[0057] like Figure 3 and Figure 4 As shown in , the reaction sites 114 can be distributed in a pattern along the detector surface 112, for example, in the reaction groove 108. For example, the reaction sites 114 can be positioned in rows and columns along the reaction groove 108 in a manner similar to a microarray. However, it should be understood that various patterns of reaction sites 114 can be used. The reaction sites 114 may include biological or chemical substances that emit light signals, as further explained below. For example, the biological or chemical substances of the reaction sites 114 can generate light emission in response to the excitation light 101. In a specific example, the reaction sites 114 include clusters or communities of biomolecules (e.g., oligonucleotides) fixed on the detector surface 112 in the reaction groove 108.

[0058] like Figure 1 As shown in , in one example, the flow cell 102 includes at least one side wall and a flow cover 110. The at least one side wall can be coupled to the detector surface 112 and extend between the flow cover 110 and the detector surface 112. The flow cell 102 can be configured such that a flow channel 119 is formed between the flow cover 110 and the detector surface 112 of the light detection device 104. In some examples, the flow channel 119 can include a height (extending between the flow cover 110 and the detector surface 112) in the range of about 50 μm to about 400 μm (micrometers), or, for example, in the range of about 80 μm to about 200 μm. In one example, the height of the flow channel 119 is about 100 μm. As shown in FIG. Figure 1 As shown in , the flow cover 110 may include a material (e.g., plastic, glass, or polymer material) that is transparent to the excitation light 101 that propagates from the exterior of the biosensor 100 and toward / enters the flow channel 119. Note that the excitation light 101 may approach the flow cover 110 from any angle and along the same or different angles.

[0059] The excitation light 101 may be emitted or generated from any illumination system or source (not shown) that may or may not be part of a bioassay system, biosensor 100, or light detection device 104. In some examples, the illumination system may include a light source (e.g., one or more LEDs) and potentially multiple optical components to illuminate at least the reaction structure 126 of the detection device 104. Examples of light sources may include lasers, arc lamps, LEDs, or laser diodes. The optical components may be, for example, reflectors, dichroic mirrors, beam splitters, collimators, lenses, filters, wedges, prisms, mirrors, detectors, and the like. In a particular example, the illumination system is configured to direct the excitation light 101 to the reaction site 114 within the groove 108 of the reaction structure 126 of the detection device 104. In some examples, the illumination system may emit an excitation light 101 of a wavelength or within a range of wavelengths, such as within a range of about 300 nm to about 700 nm or within a range of about 400 nm to about 600 nm. In some examples, the illumination system can emit excitation light 101 at a certain wavelength or more wavelengths, which excites the biological or chemical substances of the reaction sites 114 to emit light of different one or more wavelengths. For example, in one example, where the device includes reaction sites 114 within a single reaction recess 108 or different reaction recesses 108, the different reaction recesses 108 including a first fluorophore and a second fluorophore excited by blue wavelength light, the excitation light can be about 400 nm, the light emission from the reaction site 114 having the first fluorophore can be about 500 nm (or in the range of about 450 nm to about 550 nm), and the light emission from the reaction site 114 having the second fluorophore can be about 650 nm (or in the range of about 600 nm to about 550 nm).

[0060] In some other examples, the illumination system can emit excitation light 101 at wavelengths in different wavelength ranges (which do not overlap), which independently or selectively excites different biological substances or chemicals at different reaction sites 114 to emit light emissions of different wavelengths or wavelength ranges. For example, in one example, where the device includes reaction sites 114 within a single reaction recess 108 or different reaction recesses 108, wherein the different reaction recesses 108 include a first fluorophore and a second fluorophore that are excited by light of different wavelengths or wavelength ranges, the illumination system can emit first excitation light 101 at a first wavelength or wavelength range (e.g., blue excitation light (e.g., about 400 nm) or green excitation light (e.g., about 530 nm)), which causes the reaction sites 114 having the first fluorophore to emit light of the first wavelength or wavelength range (e.g., in the range of about 450 nm to about 550 nm or in the range of about 550 nm to about 550 nm). The first laser 101 emits light of a first wavelength or wavelength range (e.g., blue excitation light of (e.g., about 400 nm) or green excitation light of (e.g., about 530 nm)) during the same time period or during a different time period from the first laser 101 (i.e., during a single light detection event or during different light detection events), which causes the reaction site 114 with a second fluorophore to emit light of a second wavelength or wavelength range (e.g., in the range of about 450 nm to about 550 nm or in the range of about 600 nm to about 550 nm).

[0061] Also like Figure 1 As shown in , the flow cover 110 may include at least one port 120 configured to fluidically engage the flow channel 119 and potentially engage other ports (not shown). For example, the other ports may come from a cartridge or workstation containing a reaction solution or other biological or chemical substances. The flow channel 119 may be configured (e.g., sized and shaped) to guide a fluid or solution, such as a reaction solution, along the detector surface 112.

[0062] Figure 3 and Figure 4 Compare Figure 1 An example of the detection device 104 is shown in more detail. More specifically, Figure 3 and Figure 4 A single light sensor 140, a single light guide 118 for directing and transmitting light emissions from at least one reaction site 114 associated therewith toward the light sensor 140, and associated circuitry 146 for transmitting signals based on the light emissions (e.g., photons) detected by the light sensor 140 are shown. It should be understood that the sensor array 124 ( Figure 1 and 2) can be configured in the same or similar manner. However, it should also be understood that the light detection device 104 does not need to be manufactured uniformly throughout the process. Instead, one or more light sensors 140 and / or related components can be manufactured differently or have different relationships to each other.

[0063] The circuit 146 may include interconnected conductive elements (e.g., conductors, traces, vias, interconnects, etc.) capable of conducting an electrical current (e.g., transmission of a data signal based on detected photons). For example, in some examples, the circuit 146 may include a microcircuit arrangement. The light detection device 104 and / or the device base 125 may include at least one integrated circuit having an array of light sensors 140. The circuit 146 positioned within the detection device 104 may be configured for at least one of signal amplification, digitization, storage, and processing. The circuit 146 may collect (and possibly analyze) the detected light emissions and generate a data signal for transmitting the detection data to a biometric system. The circuit 146 may also perform additional analog and / or digital signal processing in the light detection device 104.

[0064] Device base 125 and circuitry 146 may be fabricated using integrated circuit fabrication processes, such as those used to fabricate charge coupled devices or circuits (CCDs) or complementary metal oxide semiconductor (CMOS) devices or circuits. Figure 3 As shown in FIG. 1 , the device base 125 may be a CMOS device including a plurality of stacked layers including a sensor base 141. In some examples, the sensor base 141 may be a silicon layer (e.g., a wafer). The sensor base 141 may include a light sensor 140 and gates 143 formed thereon. The gates 143 may be electrically coupled to the light sensor 140. When the light detection device 104 is as shown in FIG. Figure 3 When configured as shown, photosensor 140 may be electrically coupled to circuitry 146 via gate 143, for example.

[0065] At least some of the circuits 146 may be disposed within a device substrate layer of the device base 125 of the detection device 104, through which each of the light guides 118 may extend / into the substrate layer. In some examples, each of the substrate layers may include interconnected conductive elements that form at least a portion of the device circuits 146 and dielectric material 142 adjacent to (and potentially surrounding) the conductive elements of the circuits 146, such as Figure 3 As shown. The conductive elements of the circuit 146 can be embedded in the dielectric material 142. Figure 3As shown in , the light guide 118 can extend through the dielectric material 142 and can be spaced apart from the circuit 146. Various metal elements and / or dielectric materials can be used, such as those suitable for integrated circuit manufacturing (CMOS manufacturing). For example, in some examples, the conductive element / circuit 146 can be a metal element, such as a W (tungsten) element, a Cu (copper) element, an Al (aluminum) element, or a combination thereof (but it should be understood that other materials and configurations can be used). In some examples, the dielectric material can be SiO2 (but it should be understood that other materials and configurations can be used).

[0066] As used herein, unless otherwise noted, the term "layer" is not limited to a single continuous body of material. For example, the sensor layer 141 and / or the device layer of the device base 125 may include multiple sub-layers of different materials and / or may include coatings, adhesives, and the like. In addition, one or more of the layers (or sub-layers) may be modified (e.g., etched, deposited with materials, etc.) to provide the features described herein.

[0067] like Figure 3 and Figure 4 As shown in , the reaction structure 126 may include one or more layers formed with the reaction groove 104 extending therein. The reaction structure 126 may extend along the top outer surface of the device base 125. In the illustrated example, the reaction structure 126 is deposited directly along the top surface or outer surface of the first backing layer 154 and the top surface or outer surface of the first filter material 116 and the second filter material 115 of the device base 125, as further described below. However, in other examples, an intermediate layer may be arranged between the reaction structure 126 and the device base 125. The reaction structure 126 may include one or more materials that are configured to allow the excitation light signal 101 and the light signal emitted from the reaction site 114 (after treatment with the reaction solution) within the groove 108 to pass therethrough and enter the opening 158 of one or more light guides 118 corresponding to a specific reaction groove 108. In some examples, reaction structure 126 may include one or more layers or other features that prevent crosstalk or “sharing” of emitted light from a particular reaction site 114 / reaction recess 108 to a non-corresponding sensor 140 .

[0068] The reaction structure 126 may include a plurality of different layers, such as Figure 3 and Figure 4In the illustrated example, the reactive structure 126 may include a first reactive layer 160 that extends (directly or indirectly) over the device base 125 (e.g., over the first backing layer 154) and over the opening 158 of the light guide 118 (e.g., the first filter material 116 and the second filter material 115) of the device base 125, as shown in FIG. Figure 3 and Figure 4 As shown in Figure 3 and Figure 4 As shown in the illustrated example, the reaction structure 126 also includes a second layer 162 extending (directly or indirectly) over the first layer 160. The illustrated example reaction structure 126 also includes a third layer 164 extending (directly or indirectly) over the second layer 162 and a fourth layer 166 extending (directly or indirectly) over the third layer 164. The reaction recess 108 may extend at least into the third layer 164.

[0069] like Figure 3 and Figure 4 As shown in , the fourth layer 166 can form the inner surface (e.g., sidewalls and bottom wall) of the reaction groove 108 by extending over an indentation (e.g., a cavity or void) in the third layer 164. Figure 3 and Figure 4 As shown in , the fourth layer 166 and potentially the second layer 162 can form the detector surface 112. In some cases, the fourth layer 166 and potentially the second layer 162 can be configured to provide a solid surface that allows chemicals, biomolecules or other analytes of interest to be fixed thereon. For example, each of the reaction sites 114 can include a biomolecule cluster fixed to the detector surface 112, and the detector surface 112 can include the fourth layer 166 and possibly the second layer 162. Therefore, the fourth layer 166 and potentially the second layer 162 can include a material that allows the reaction site 114 to be fixed thereto. The first layer 160 and the fourth layer 166 (and potentially the second layer 162 and the third layer 164) can include a material that is at least substantially transparent to the excitation light 101 and the emission light of the reaction site 114. In addition, the fourth layer 166 and potentially the second layer 162 can be physically modified or chemically modified to facilitate the fixation of biomolecules and / or to facilitate the detection of light emission.

[0070] For example, if Figure 3 and Figure 4As shown in the illustrated example, the first layer 160 and the third layer 164 may include a first material, and the second layer 162 and the fourth layer 166 may include a second material different from the first material. In some such examples, the first material is SiN and the second material is TaO. However, the reaction structure 126 may include different layers (e.g., different layers, fewer layers, and / or additional layers) and / or different materials.

[0071] like Figure 3 and Figure 4 As shown in , the device base 125 of the detection device 104 may include a first shielding layer 150 that extends (directly or indirectly) over the stacked layers (e.g., metal-dielectric layers) of the device base 125, such as over the dielectric material 142 and the conductive circuit components 146. The first shielding layer 150 may include a material configured to block, reflect, and / or significantly attenuate the excitation light 101 and / or light emissions from the reaction sites 114 (e.g., light signals propagating from the flow channel 118). By way of example only, the first shielding layer 150 may include tungsten (W).

[0072] The first shielding layer 150 may include at least one hole therethrough, the at least one hole being at least partially aligned with at least one corresponding light guide 118. The first shielding layer 150 may include an array of such holes. In some examples, the first shielding layer 150 may extend completely around the hole therein. In this way, the light signal from the excitation light 101 and / or the light emission from the reaction site 114 may be blocked, reflected, and / or significantly attenuated to prevent the light signal from passing through the device base 125 outside the light guide 118 and being detected by the light sensor 140. In some examples, the first shielding layer 150 extends continuously between adjacent holes or light guides 118 and / or openings extending thereto. In some other examples, the first shielding layer 150 does not extend continuously between adjacent holes or light guides 118, so that one or more other holes are present in the first shielding layer 150, which may allow the excitation light 101 and / or the light emission from the reaction site 114 to pass therethrough.

[0073] In some examples, the device base 125 of the detection device 104 may include a second shielding layer 152 extending (directly or indirectly) above the first shielding layer 150, such as Figure 3 and Figure 4. Second shielding layer 152 may include an anti-reflective material and / or a material that prevents contamination of portions below device base 125. By way of example only, second shielding layer 152 may include SiON. In some examples, second shielding layer 152 may be configured to prevent contaminants such as sodium from interacting with conductive (e.g., metal) components of first shielding layer 150, dielectric material 142, and / or device circuitry 146. In some examples, second shielding layer 152 may mimic the configuration of first shielding layer 150. For example, second shielding layer 152 may include at least one hole therethrough that is at least partially aligned with at least one light guide 118, such as Figure 3 and Figure 4 . The second shielding layer 152 may include an array of such holes. In some examples, the second shielding layer 152 may extend around the holes therein. In some examples, the second shielding layer 152 extends continuously between adjacent light guides 118 and / or openings extending thereto. In some other examples, the second shielding layer 152 does not extend continuously between adjacent light guides 118 and / or openings extending thereto, such that one or more other holes are present in the second shielding layer 152, such as Figure 3 and Figure 4 as shown in .

[0074] In some examples, the light detection device 104 may include a first backing layer 154 that extends on the device base 125 and around the light guide 118, such as Figure 3 and Figure 4 As shown. The first pad layer 154 can be a continuous conformal layer formed on the device base 125. The first pad layer 154 may not have a defined hole. However, the first pad layer 154 may include internal discontinuous parts, pores, ruptures, etc., which allow liquids or solutions such as reaction solutions to flow through it, as further explained below. The first pad layer 154 can be chemically reactive relative to the reaction solution. For example, due to the composition of the reaction solution (e.g., water and / or oil) and / or relatively high acidity (e.g., equal to or less than a pH of about 5) or relatively high alkalinity (e.g., equal to or greater than a pH of about 8), the reaction solution can react chemically with the material of the first pad layer 154 when exposed thereto, and cause the material to dissolve or otherwise separate (i.e., etch the pad layer 154). During the exposure time, the reaction solution can thus etch through the first pad layer 154, and eventually interact with the device circuit 146 and corrode the device circuit 146 or otherwise interfere with the function of the device circuit 146. For example, the first liner layer 154 may be a silicon nitride layer (or otherwise include SiN), and a relatively highly acidic or alkaline reactive solution may etch the SiN when exposed to the SiN.

[0075] In the example shown, the first spacer layer 154 extends in the gap region 113 between the reaction structure 126 on the top upper portion of the device base 125 (and / or any layer on the top or upper portion of the device base 125) and the second shielding layer 152, and extends along the light guide 118, as shown in FIG. Figure 3 and Figure 4 In the example shown, the first backing layer 154 extends around the light guide 118 and adjacent to the dielectric material 142 of the device base 125, as shown in FIG. Figure 3 and Figure 4 As shown. Figure 3 and Figure 4 As shown, the first liner layer 154 can extend around the light guide 118 so that it is positioned between the dielectric material 142 of the device base 125 and the support liner 130 and the second filter region 115 of the light guide 118 (e.g., directly positioned therebetween). The first liner layer 154 can be configured as an anti-reflection layer or a reflective layer (e.g., to ensure that light emitted from the reaction site 114 passes through the light guide 118), a contamination prevention layer (e.g., to prevent sodium contaminants from entering the device base 125), and / or an adhesion layer (e.g., to adhere the support liner 130 and the second filter region 115 of the light guide 118 to the dielectric material 142). In some examples, the liner layer 154 can be configured as a contamination prevention layer that prevents any ionic species from penetrating into the device layer (e.g., the metal-dielectric layer). In some examples, the liner layer 154 includes SiN. In some examples, the liner layer 154 includes a SiN layer.

[0076] like Figure 3 and Figure 4 As shown, the first pad layer 154 can have a substantially uniform thickness. In other examples, the thickness of the first pad layer 154 can vary. For example, the portion of the first pad layer 154 that extends over the top portion of the device base 125 can be a first thickness, and the portion of the first pad layer 154 that extends around the light guide 118 can be a second thickness that is thicker or thinner than the first thickness. As another example, the thickness of the portion of the first pad layer 154 that extends around the light guide 118 can vary along the depth within the device base 125 (e.g., can taper as the depth into the device base 125). In some examples, the thickness of the first pad layer 154 can be in the range of about 10nm to about 100nm. In the example shown, the first pad layer 154 is about 50nm thick.

[0077] like Figure 3As shown, the device base 125 can also include a second padding layer 155 positioned within the device layer and below the light guide 118. The second padding layer 155 can be substantially similar or identical to the first padding layer 154, except for its position within the device base 125. In some examples, the second padding layer 155 can extend along the bottom of the light guide 118 directly below the support pad 130, such as Figure 3 In this manner, the first backing layer 154 and the second backing layer 155 can extend completely around the light guide 118 , except for the opening 158 of the light guide 118 below the reaction recess 108 .

[0078] As discussed above, the device base 125 of the detection device 104 may include a support pad or layer 130 positioned at a bottom portion of the light guide 118, such as Figure 3 The support pad 130 may extend (directly or indirectly) between the first filter region 116 and the dielectric material 142 and between the first filter region 116 and the second liner layer 155. For example, the support pad 130 may surround the first filter region 116 and extend (directly or indirectly) between the first filter region 116 and the first liner layer 154, as shown in FIG. Figure 3 In this manner, the support pad 130 may extend around a bottom portion of the first filter region 116, including around its side surfaces and bottom surface. The support pad 130 may extend completely around the first filter material 116 of the light guide 118. Figure 3 As shown, the second filter region 115 can extend above the support pad 130 in the upper portion of the light guide 118. Thus, the support pad 130 can support the second filter region 115 or extend below the second filter region 115. In some examples, the support pad 130 can extend directly below the second filter region 115. The support pad 130 and the second filter region 115 can thus be combined to form a layer that extends around the first filter material 116 and is positioned between the first filter material 116 and the device base 125 and / or the dielectric material 142, as shown. Figure 3 shown.

[0079] The thickness of the support pad 130 can be any thickness. In some examples, the thickness of the support pad 130 can be in the range of about 100 nm and about 1 micron, or in the range of about 100 nm and about 500 nm. In some examples, the thickness of the support pad 130 can be the same or substantially similar thickness as the thickness of the second filter region 115, such as at least a portion of the support pad 130 adjacent to the second filter region 115 or positioned proximate to the second filter region 115. In some examples, the thickness of the support pad 130 below the first filter region 116 at the bottom of the light guide 118 (between the first filter region 116 and the second backing layer 155 and / or the dielectric material 142) can be the same or substantially similar thickness as the thickness of the support pad 130 extending around the side surface of the first filter region 116 (between the first filter region 116 and the first backing layer 154 and / or the dielectric material 142).

[0080] The support pad 130 may be free of predefined holes or other voids that would allow a liquid or solution, such as a reaction solution, to flow through. The support pad 130 may also be free of any internal discontinuities, pores, cracks, ruptures, etc. that would allow a liquid or solution, such as a reaction solution, to flow through or prevent their formation. Thus, the support pad 130 may be a liquid-impermeable barrier. A liquid-impermeable layer herein refers to a layer that can prevent any liquid or solution (e.g., a reaction solution) from passing through it, such as preventing at least about 99% of the reaction solution by volume that contacts the protective layer 130 at atmospheric pressure from passing through it. The support pad 130 may also be chemically inert relative to the reaction solution, such that when the reaction solution contacts the support pad 130, the reaction solution (which may include relatively high acidity or relatively high alkalinity, as described above) does not etch the support pad 130 or etches less than about one (1) angstrom of the thickness of the support pad 130 per hour at about 100 degrees Celsius and about atmospheric pressure. For example, the composition of the support pad 130 may not chemically react or chemically react only to a relatively small extent with the composition of the reaction solution (which may include relatively high acidity or relatively high alkalinity) such that when the reaction solution contacts the support pad 130, the reaction solution does not etch the support pad 130 or etches less than about one (1) angstrom of the thickness of the support pad 130 per hour at about 100 degrees Celsius and about atmospheric pressure. Thus, the support pad 130 may include an etch-resistant layer relative to the reaction solution (which may, for example, include a pH equal to or less than about 5 or a pH equal to or greater than about 8) to prevent the reaction solution from penetrating therethrough (over time) and ultimately interacting with, corroding, or otherwise interfering with the device circuitry 146. Thus, the support pad 130 is configured to prevent liquids or solutions (e.g., the reaction solution) that may penetrate through the filter material 116 of the reaction structure 126 and the light guide 118 to the support pad 130 from interacting with the device circuitry 146.

[0081] The support pad 130 may include any material different from the material of the first pad layer 154 and the first filter material 116, and such that it allows light emitted from the reaction site 114 to pass through it and reach at least one corresponding light sensor 140 via the corresponding light guide 118. For example, the support pad 130 may include any material that allows light emitted from the reaction site 114 of the associated reaction recess 108 that is not filtered by the first and second filter regions 116, 115 to pass through. As further explained below, the support pad 130 may include any material different from the material of the first pad layer 154 and the first filter material 116, such that an upper portion of the support pad 130 may be selectively removed (e.g., etched) to form the support pad 130 only in the lower portion or bottom portion of the light guide 118. In some examples, the support pad 130 may include an oxide, a nitride, or a combination thereof. In some such examples, the support pad 130 may include SiO2, a metal oxide, or a combination thereof.

[0082] In some examples, the support pad 130 may include a material that is chemically inert to the reaction solution. For example, the support pad 130 may include any material that does not chemically react or chemically reacts only to a relatively small extent with the reaction solution (which may include, for example, a pH equal to or less than about 5 or a pH equal to or greater than about 8), such that when the reaction solution contacts the support pad 130, the reaction solution does not etch the support pad 130 or etches less than about one (1) angstrom of the thickness of the support pad 130 per hour at about 100 degrees Celsius and about atmospheric pressure. For example, the support pad 130 may include an oxide, a nitride, or a combination thereof. In some examples, the support pad 130 may include silicon dioxide, a metal oxide, a metal nitride, or a combination thereof. In some examples, the support pad 130 may include silicon dioxide, silicon oxynitride, silicon monoxide, silicon carbide, silicon oxycarbide, nitro silicon carbide, metal oxide, metal nitride, or a combination thereof. In some examples, the pH of the reaction solution is greater than or equal to about 8, and the support pad 130 may include silicon dioxide, silicon oxynitride, silicon monoxide, silicon carbide, silicon oxycarbide, nitro silicon carbide, metal oxide, metal nitride, or a combination thereof. In some examples, the pH of the reaction solution is less than or equal to about 5, and the support pad 130 includes silicon carbide, silicon oxycarbide, nitro silicon carbide, metal oxide, metal nitride, or a combination thereof.

[0083] As discussed above, the light guide 118 can extend from the opening 158 into the device base 125, for example, through the dielectric material layer 142 and toward the at least one image sensor 140. In a specific example, the light guide 118 is elongated and extends from its hole 158 from the vicinity of at least one corresponding reaction groove 108 toward at least one corresponding light sensor 140 in the sensor layer 141. The light guide 118 can extend longitudinally along a central longitudinal axis. The light guide 118 can be configured as a three-dimensional shape that allows and / or promotes light emitted from the reaction site 112 of at least one corresponding reaction groove 108 to at least one corresponding light sensor 140, such as a substantially cylindrical or frustoconical shape with a circular opening 158. The longitudinal axis of the light guide 118 can extend through the geometric center of the cross section. However, other geometric shapes can be used in optional examples. For example, the cross section of the light guide 118 can be substantially square or octagonal. The light guide 118 can include a first filter area 116, a second filter area 115 and a support pad 130.

[0084] As discussed above and in Figure 3 and Figure 4, the light guide 118 may include a first filter region 116 and a second filter region 115. The first filter region 116 may be frustoconical, and the second filter region 115 may be an annular sleeve or pad extending around the first filter region 116 (above the annular support pad or sleeve 130). The first filter region 116 may include a first filter material configured to filter excitation light 101 of a first wavelength or wavelength range (and potentially a fourth wavelength or wavelength range), and allow light emission of a second wavelength or wavelength range from at least one reaction site 114 of at least one corresponding reaction recess 108 to pass therethrough and propagate toward at least one corresponding light sensor 140. Similarly, the second filter region 115 may include a second filter material configured to filter excitation light 101 of a first wavelength or wavelength range (and potentially a fourth wavelength or wavelength range), and allow light emission of a third wavelength or wavelength range from at least one reaction site 114 of at least one corresponding reaction recess 108 to pass therethrough and propagate toward at least one corresponding light sensor 140. In some examples, first filter region 116 may also filter light emissions of a third wavelength or wavelength range from at least one reaction site 114 (i.e., prevent such emitted light from passing therethrough), and / or second filter region 115 may also filter light emissions of a second wavelength or wavelength range from at least one reaction site 114 (i.e., prevent such emitted light from passing therethrough). In other examples, first filter region 116 may allow light emissions of a third wavelength or wavelength range from at least one reaction site 114 to pass therethrough, and / or second filter region 115 may allow light emissions of a second wavelength or wavelength range from at least one reaction site 114 to pass therethrough. Each of light guides 118 of array light guides 118 of device 104 may include substantially the same configuration (e.g., filtering properties) of first and second filter regions 116, 115, or different light guides 118 may include different configurations (e.g., filtering properties) of first and second filter regions 116, 115.

[0085] The first filter region 116 and the second filter region 115 of the light guide 118 may be, for example, absorption filters (e.g., organic absorption filters) such that they absorb respective wavelengths or wavelength ranges and allow at least one predetermined wavelength or wavelength range to pass through them. By way of example only, at least one first reaction site 114 of at least one reaction recess 108 of the device 104 may be configured to generate a first light emission of a first wavelength or wavelength range upon incident excitation light 101 of a third wavelength or wavelength range, and at least one second reaction site 114 of at least one reaction recess 108 of the device 104 may be configured to generate a second light emission of a second wavelength or wavelength range that is different from (or does not overlap with) the first light emission upon incident excitation light 101 of a third wavelength or wavelength range. The first and second reaction sites 114 may be the same reaction site 114, may be different reaction sites 114 disposed within a common reaction recess 108, or may be different reaction sites 114 disposed within different reaction recesses 108. In such an example, the first filter region 116 may absorb the excitation light 101 and the second light emission, but allow the first light emission from the first reaction site to pass through it. Similarly, the second filter region 115 can absorb the excitation light 101 and the first light emission, but allow the second light emission from the first reaction site to pass therethrough.

[0086] As another example, at least one first reaction site 114 of at least one reaction recess 108 of the device 104 can be configured to generate a first light emission of a first wavelength or wavelength range upon incident first excitation light 101 of a third wavelength or wavelength range, and at least one second reaction site 114 of at least one reaction recess 108 of the device 104 can be configured to generate a second light emission of a second wavelength or wavelength range upon incident second excitation light 101 of a fourth wavelength or wavelength range. The first wavelength, the second wavelength, the third wavelength, and the fourth wavelength or wavelength range can be different (and non-overlapping, if wavelength ranges). The third and fourth excitation lights 101 can be emitted simultaneously (e.g., during the same light detection event), or the third and fourth excitation lights 101 can be emitted independently or individually at different times (e.g., during different light detection events). The first and second reaction sites 114 can be the same reaction site 114, can be different reaction sites 114 disposed in a common reaction recess 108, or can be different reaction sites 114 disposed in different reaction recesses 108. In such an example, the first filter region 116 can absorb at least the first excitation light 101 and the second light emission, but allow the first light emission from the first reaction site to pass therethrough. The first filter region 116 can also absorb the second excitation light 101. Similarly, the second filter region 115 can absorb at least the second excitation light 101 and the first light emission, but allow the second light emission from the first reaction site to pass therethrough. The second filter region 115 can also absorb the first excitation light 101.

[0087] The material of the first filter area and the second filter area 116, 115 can be any material that prevents the excitation light from passing through it (for example, reflects, refracts and / or absorbs such light) and allows the emission light of a predefined or predetermined wavelength or wavelength range (from at least one reaction site 114) to pass through it. For example, the material of the first filter area and the second filter area 116, 115 can be a polymer material (the same polymer material or different polymer materials) with different dyes. For example, the material of the first filter area and the second filter area 116, 115 can be a polymer material (the same polymer material or different polymer materials) with different dyes. In such an example, the polymer material can include a CHO-based matrix, and different dyes can be, for example, different metal organic complex molecules. However, any other suitable material can be used. As discussed above, in some examples, the first filter area and the second filter area 116, 115 can allow the emission light of different wavelengths or wavelength ranges (from at least one reaction site 114) to pass through it. Thus, in some examples, first filter region 116 of light guide 118 may filter (i.e., block) emission light (from at least one reaction site 114) that is allowed to pass through it by second filter region 115 of light guide 118, and / or second filter region 115 of light guide 118 may filter (i.e., block) emission light (from at least one reaction site 114) that is allowed to pass through it by first filter region 116 of light guide 118.

[0088] Thus, each light guide 118 can be configured relative to the surrounding materials of the device base 125 (e.g., the dielectric material 142 and / or the first and second backing layers 154, 155) to form a light guide structure. For example, the light guide 118 can have a refractive index of at least about 2. In some examples, the light guide 118 is configured such that the optical density (OD) or absorbance of the excitation light is at least about 4 OD. More specifically, the filter material 116 of the light guide 118 can be selected and the light guide 118 can be sized to achieve at least about 4 OD. In more specific examples, the light guide 118 can be configured to achieve at least about 5 OD or at least about 6 OD.

[0089] Initially, the reaction sites 114 of one or more reaction recesses 108 of the reaction structure 126 of the device 104 or biological component 100 may not include a designated reaction. As discussed above, the reaction sites 114 may include biological substances or chemicals fixed to the detector surface 112, or more specifically on the base and / or side surfaces of the reaction recesses 108. In a specific example, the reaction sites 114 are positioned proximate to the openings 158 of at least one corresponding light guide 118, so that after the designated reaction occurs (via treatment with a reaction solution), the pre-designated light emission emitted from the reaction sites 114 propagates through the reaction structure 126, through the openings 158 and the first and / or second filter materials 116, 115, through the support pad 130 (and potentially the first and / or second pad layers 154, 155) and reaches the at least one corresponding light sensor 140.

[0090] The biological substances or chemicals of a single reaction site 114 can be similar or identical (e.g., a community of analytes (e.g., oligonucleotides) with a common sequence). However, in other examples, a single reaction site 114 and / or a reaction groove can include different biological substances or chemicals. Similarly, the reaction site 114 of a single reaction groove 108 can include different biological substances or chemicals (and thus designated reactions with different fluorescent labels). Before the designated reaction, the reaction site 114 can include at least one analyte (e.g., an analyte of interest). For example, the analyte can be an oligonucleotide or a community thereof (e.g., an oligonucleotide of interest). The oligonucleotide can have an effective common sequence and bind to a predefined or specific fluorescently labeled biomolecule, such as a fluorescently labeled nucleotide. Different reaction sites 114 can therefore include different fluorescently labeled biomolecules, such as different fluorescently labeled nucleotides.

[0091] However, before the designated reaction, the fluorophore of the fluorescently labeled biomolecule is not incorporated into or bound to the biological substance or chemical substance (e.g., oligonucleotide) at the reaction site 114. In order to achieve or obtain the designated reaction (i.e., to bind the fluorescently labeled biomolecule to the biological substance or chemical substance at / at the reaction site 114), the flow cell can provide a flow of the reaction solution 170 to the reaction structure 126 of the light detection device 104, such as Figure 5 In this manner, the reaction solution 170 can initiate a reaction and / or form a reaction product at the reaction site 114 that generates light emission when an excitation light is incident thereon.

[0092] The reaction solution may include one or more sequencing reagents for, for example, DNA grafting, clustering, cleaving, incorporating, and / or reading. However, the reaction solution may be any solution. For example, the reaction solution 170 may be an aqueous solution and / or may contain oil; however, it should be understood that the reaction solution 170 may include any other liquid. The reaction solution 170 may include one or more components that will tend to react with the circuit 146, corrode, dissolve, degrade the circuit 146, or otherwise make the circuit 146 inoperable or less effective than the circuit (i.e., transmitting signals or electronics). For example, the reaction solution 170 may be an aqueous solution that, if it interacts with the circuit 146, will tend to oxidize the metal portion of the circuit 146.

[0093] In one example, the reaction solution 170 comprises one or more nucleotide types, at least some of which are fluorescently labeled, and the reaction solution 170 also comprises one or more biomolecules, such as a polymerase, which incorporates nucleotides into the growing oligonucleotides at the reaction site 114, thereby labeling the oligonucleotides with fluorescently labeled nucleotides. In this embodiment, the flow cell provides a washing solution to remove any free nucleotides that fail to be incorporated into the oligonucleotides. The reaction site 114 is then irradiated with an excitation light 101 of a first wavelength, causing fluorescence of a second wavelength or a third wavelength in those reaction sites 114 where fluorescently labeled nucleotides are incorporated. The reaction sites 114 where fluorescently labeled nucleotides are not incorporated do not emit light.

[0094] As in Figure 5 As shown in the illustrated example, the reaction solution 170 can be arranged in the reaction groove 118 to achieve a specified reaction, such as at least one fluorescently labeled molecule is combined or merged with a biological substance or chemical substance fixed at the reaction site 114. In some examples, the biological substance or chemical substance of the reaction site 114 can be an analyte, and the fluorescently labeled molecule can include at least one fluorophore combined or merged with the analyte. In such an example, the analyte can include an oligonucleotide, and at least one fluorescently labeled molecule includes a fluorescently labeled nucleotide. The reaction solution 170 can include different fluorescently labeled molecules, which emit light of different wavelengths or wavelength ranges in response to the incident excitation light. (The same or different reaction grooves 108) different reaction sites 114 can therefore be configured to emit light of different wavelengths or wavelength ranges in response to the incident excitation light.

[0095] When the biological substances or chemicals (e.g., oligonucleotides) of the reaction sites 114 are similar or identical, for example, have a common sequence, the reaction sites 114 can be configured to produce a common light emission after a specified reaction, and the excitation light 101 is absorbed by the fluorescently labeled molecules bound or merged therewith from the reaction solution 170. When the biological substances or chemicals (e.g., oligonucleotides) of the reaction sites 114 are different, for example, have different sequences, the reaction sites 114 can be configured to produce different light emissions (different wavelengths or wavelength ranges) after a specified reaction, and the excitation light 101 is absorbed by different fluorescently labeled molecules bound or merged therewith (e.g., provided by the reaction solution 170). In this way, the first filtering region 116 of the light guide 118 can be selected or configured to allow light emissions from reaction sites 114 having a first designated reaction to propagate therethrough and reach the corresponding light sensor 140 (and prevent excitation light and potentially light emissions from reaction sites 114 having a second designated reaction from passing therethrough and reaching the corresponding light sensor 140), and the second filtering region 115 of the light guide 118 can be selected or configured to allow light emissions from reaction sites 114 having a second designated reaction different from the first designated reaction (e.g., comprising different fluorescently labeled molecules that emit light of a different wavelength or wavelength range) to propagate therethrough and reach the corresponding light sensor 140 (and prevent excitation light and potentially light emissions from reaction sites 114 having the first designated reaction from passing therethrough and reaching the corresponding light sensor 140).

[0096] like Figure 6 As shown, after the reaction solution 170 has interacted with the biological or chemical substances (e.g., oligonucleotides) of the reaction sites 114, the specified reaction has occurred, so that the reaction sites 114 include fluorescently labeled molecules (same or different fluorescently labeled molecules), such as fluorophores, which emit light of a predefined or predetermined wavelength or wavelength range when excited by the excitation light 101 (i.e., when the excitation light 101 is incident on the reaction sites 114). The excitation light 101 can thus be configured based on the fluorescently labeled molecules of the reaction solution 170, or vice versa. Figure 6 As shown, when excited by the excitation light 101 , the reaction sites 114 may emit emitted light 172 or a signal having a wavelength or wavelength range different from that of the excitation light 101 .

[0097] like Figure 6As shown, the emission light 172 from the reaction site 114 can be emitted in all directions (e.g., isotropically) so that, for example, a portion of the emission light 172 is guided into at least one corresponding light guide 118, and a portion of the light 172 is guided into the flow channel 119 or the reaction structure 126. For the portion guided into the light guide 118, the device 104 is configured to facilitate detection of the photons by at least one corresponding light sensor 140. Specifically, the emission light 172 from the reaction site 114 that passes through the opening 158 of the corresponding light guide 118 will propagate through its first filter region or the second filter region 116, 115 to the light sensor 140. However, the excitation light 101 will be absorbed by the first filter region and / or the second filter region 116, 115 or otherwise prevented from propagating through the light guide 118 to the light sensor 140, as shown in FIG. Figure 6 shown.

[0098] like Figure 6As shown, some reaction sites 114 can be configured to emit light 172 of a first wavelength or wavelength range that is not filtered by the first filter region 116 but is filtered (i.e., prevented from passing through) by the second filter region 115, and some reaction sites 114 can be configured to emit light 172 of a second wavelength or wavelength range that is not filtered by the second filter region 115 but is filtered (i.e., prevented from passing through) by the first filter region 116. As mentioned above, in some examples, some reaction sites 114 of the device 104 can be configured to emit light 172 of a first wavelength or wavelength range upon incident excitation light 101 of a third wavelength, and some other reaction sites 114 of the device 104 can be configured to emit light 172 of a second wavelength or wavelength range upon incident excitation light 101 of a third wavelength. In such examples, both the first and second filter regions 116, 115 can be configured to filter the excitation light 101 of the third wavelength. Still further, in some other examples, some reaction sites 114 of the device 104 can be configured to emit light 172 of a first wavelength or wavelength range when incident excitation light 101 of a third wavelength or wavelength range, and some other reaction sites 114 of the device 104 can be configured to emit light 172 of a second wavelength or wavelength range when incident excitation light 101 of a fourth wavelength or wavelength range. In such examples, both the first and second filter regions 116, 115 can be configured to filter excitation light 101 of the third and fourth wavelengths or wavelength ranges, or the first and second filter regions 116, 115 can be configured to filter one of the excitation light 101 of the third and fourth wavelengths or wavelength ranges (e.g., the first filter region 116 can be configured to filter excitation light 101 of the third wavelength or wavelength range, and the second filter region 115 can be configured to filter excitation light 101 of the fourth wavelength or wavelength range). The device circuit 146 electrically coupled to the light sensor 140 transmits a data signal based on the photons detected by the light sensor 140. In this way, the mere presence of a designated reaction at reaction site 114 via treatment with a reaction solution will result in emission light 172 being detected even by light sensor 140 during light detection (i.e., a reaction resulting in emission light 172 that is not filtered by at least one of first filter region 116 and second filter region 115).

[0099] like Figure 6As shown, a portion of the emitted light 172 from the reaction sites 114 that enters the at least one corresponding light guide 118 may propagate directly through its first filter material 116 or second filter material 115 and reach the at least one corresponding light sensor 140. For example, at least a majority of the emitted light 172 from the reaction sites 114 that enters the at least one corresponding light guide 118 via the openings 158 may directly (e.g., linearly or substantially linearly) pass through the first filter material 116 or second filter material 115 to reach the at least one corresponding light sensor 140. A small amount of the emitted light 172 from the reaction sites 114 that enters the at least one corresponding light guide 118 may travel at an angle such that it passes through the support pad 130, the pad layer 154, and enters the dielectric material layer 142. Such light may be reflected by the circuit 146 or other metal or reflective structures embedded in the dielectric material layer 142 and potentially return to the corresponding light guide 118 (and potentially reach the at least one corresponding light sensor 140). In some examples, support pad 130 and / or pad layer 154 may be transparent to light, such as transparent or substantially transparent to at least emitted light 172 from reaction sites 114 .

[0100] Figure 7-Figure 13 The figure shows the manufacture of a light detection device such as Figure 1-Figure 6 An example of a method 200 for detecting a light detection device 104 of the present invention is provided. Therefore, the same reference numerals preceded by "2" as opposed to "1" are used to indicate the same components, aspects, functions, processes, or functions, and the above descriptions thereof are equally applicable and are not repeated for the purpose of brevity and clarity. For example, the method 200 can adopt the structure or aspects of various examples (e.g., systems and / or methods) discussed herein. In various examples, certain steps can be omitted or added, certain steps can be combined, certain steps can be performed simultaneously, certain steps can be performed in parallel, certain steps can be divided into multiple steps, certain steps can be performed in a different order, or certain steps or certain series of steps can be re-performed in an iterative manner.

[0101] like Figure 7 and Figure 8 As shown, method 200 of forming device 204 may include forming (in Figure 7270 ) a plurality of grooves or cavities 280 or an array of grooves or cavities 280. As discussed above, the device base 225 may include an array of light sensors 240 and a device circuit 246 electrically coupled to the light sensors 240 that transmits a data signal based on photons detected by the light sensors 240. The device base 225 may be provided or obtained via any process. For example, the device base 225 may be obtained in a pre-assembled or pre-manufactured state, or the device base 225 may be formed or manufactured prior to forming 270 the plurality of grooves 280. The plurality of grooves may extend from an outer surface, an outer surface, or a top surface of the device base 225 and toward at least one corresponding light sensor 240 (through the thickness of the device base 225).

[0102] As discussed above, the device base 225 may be fabricated using integrated circuit fabrication techniques, such as CMOS fabrication techniques. For example, the device base 225 may include several substrate layers (e.g., dielectric material layers 242) having different modified features (e.g., metal elements) embedded therein that form the device circuit 246. A plurality of grooves 280 may be formed in the substrate layers (e.g., in the dielectric material layers 242) to correspond to portions of the device base 225 that will include the light guide 218 following the method 200. Although in Figure 8 Only one groove 280 is depicted in FIG. 2 , but as described above, the device base 225 may include an array of light guides 218 , and thus an array of grooves 280 may be formed.

[0103] like Figure 8 As shown, the trench 280 may extend through the opening in the first shield layer 250 and / or the second shield layer 252 and through the dielectric material 242 toward at least one corresponding light sensor 240. Figure 8 As shown, the inner surface of the device base 225, such as the dielectric material 242 thereof, can define a groove 280 for forming the light guide 218 therein. The groove or cavity 280 can extend to the second liner layer 255 extending through the dielectric material 242. In this manner, the second liner layer 255 can form the bottom of the groove 280. Also as shown in FIG. Figure 8 As shown, other openings in the first shielding layer 250 and / or the second shielding layer 252 may be formed in the gap region 213 of the device base 225 .

[0104] Grooves 280 may be formed by any process or technique that removes portions of dielectric material 242 (and potentially portions of first shield layer 250 and / or second shield layer 252). For example, grooves 280 may be formed by one or more selective etching processes and / or reactive ion etching processes. In one example, grooves 280 may be formed by applying at least one mask (not shown) to device base 225 and removing material (e.g., by etching) of portions of dielectric material 242 (and potentially portions of first shield layer 250 and / or second shield layer 252).

[0105] like Figure 7 and Fig. 9 As shown, after forming the plurality of trenches 280, the method 200 may include depositing (at the Figure 7 272 of the device base 225). In some examples, the first liner layer 254 can be formed over the sidewalls of the plurality of trenches 280 rather than over the second liner layer 255 at the bottom of the trenches 280. In some other examples, the first liner layer 254 can be formed over the second liner layer 255 at the bottom of the trenches 280, but then subsequently removed. The first liner layer 254 can be deposited over the second shielding layer 252 on the top surface of the device base 225 and potentially over any openings in the first shielding layer 250 and / or the second shielding layer 252 in the gap region 213 of the device base 225, such that the second shielding layer 252 extends over the dielectric material 242 in such openings, as shown. Fig. 9 shown.

[0106] First liner layer 254 can be configured as an anti-reflection layer or a reflective layer (e.g., to ensure that light emitted from the reaction site passes through the light guide), a contamination prevention layer (e.g., to prevent sodium contamination of the circuit), and / or an adhesion layer (e.g., to adhere the filter material of the light guide to the dielectric material). In some examples, first liner layer 254 can be configured as a contamination prevention layer that prevents any ionic species from penetrating into the device layer (e.g., metal-dielectric layer). In some examples, first liner layer 254 can include SiN.

[0107] The first pad layer 254 may be a continuous conformal layer formed on the device base 225. The first pad layer 254 may not have defined holes. However, the first pad layer 254 may include at least one internal discontinuous portion, pore, crack, rupture or the like that allows a liquid or solution, such as a reaction solution, to flow through the first pad layer 254. For example, the density of the first pad layer 254 may be relatively low so that its internal discontinuous portion forms a path through the first pad layer 254. As another example, the discontinuous portion extending through the first pad layer 254 may be formed by a reaction solution or any other liquid or solution to avoid reacting with the first pad layer 254 and etching through the first pad layer 254. The discontinuous portion of the first pad layer 254 may allow a liquid or solution (e.g., a reaction solution) to pass through it and eventually reach a conductive (e.g., metal) component of the device circuit 246. As discussed above, a liquid or solution (e.g., a reaction solution) may corrode the device circuit 246 or otherwise interfere with the operation of the device circuit 246.

[0108] The first liner layer 254 can be formed by any process or technique. For example, the first liner layer 254 can be formed by at least one chemical deposition process (e.g., electroplating, chemical vapor deposition (CVD), plasma enhanced CVD (PECVD), or atomic layer deposition (ALD)), a physical deposition process, a growth mode, epitaxy, or a combination thereof. In some examples, the first liner layer 254 can be conformally formed above the surface of the device base 225 and within the trench 280 (e.g., on the sidewalls of the trench 280 and above the underlying bottom surface). The first liner layer 254 can include a substantially constant thickness, or the thickness can vary.

[0109] After forming the first pad layer 254 on the device base 225 (and within the trench 280), the first pad layer 254 can be further processed. For example, at least a portion of the first pad layer 254 that extends above the top surface of the device base 225 (i.e., the gap region 213 of the first pad layer 254) can be processed to planarize, flatten, smoothen, or otherwise improve its surface topography. In some such examples, at least a portion of the first pad layer 254 that extends above the top surface of the device base 225 (i.e., the gap region 213 of the first pad layer 254) can be etched and / or polished (e.g., chemical and / or mechanical polishing / planarization) to planarize the outer surface of the first pad layer 254.

[0110] like Figure 7 and Fig.10 As shown, method 200 may include depositing (on top of) device base 225. Figure 7The support pad 230 is formed on the top surface of the device base 225 and extends within the plurality of grooves 280. In some examples, the support pad 230 may be formed on the sidewalls of the plurality of grooves 280 and on the bottom of the grooves 280. The support pad 230 may be formed on the first and second liner layers 254 and 255.

[0111] The support pad 230 can be formed by any process or technology. For example, the support pad 230 can be formed by at least one chemical deposition process (e.g., electroplating, chemical vapor deposition (CVD), plasma enhanced CVD (PECVD) or atomic layer deposition (ALD)), physical deposition process, growth mode, epitaxy or a combination thereof. In some examples, the support pad 230 can be formed conformally above the surface of the device base 225 and in the groove 280 (e.g., above the sidewall of the groove 280 and potentially above the bottom surface). The support pad 230 can include a substantially constant thickness, or the thickness can vary. As further discussed below, the support pad 230 can include a material different from the material of the first filter area 216.

[0112] As discussed above, the support liner 230 can be configured such that it forms a solid continuous barrier (without voids, cracks, or other discontinuities) that prevents any reaction solution (which may include, for example, a pH equal to or less than about 5 or a pH equal to or greater than about 8) that penetrates the reaction structure 226 and potentially penetrates the filter material 216 of the light guide 218 from interacting with the circuit 246. For example, the support liner 230 can be configured such that it is chemically inert with respect to the reaction solution such that when the reaction solution contacts the support liner 230, the reaction solution (which may include relatively high acidity or relatively high alkalinity, as described above) does not etch the support liner 230 or etches less than about one (1) angstrom of the thickness of the support liner 230 per hour at about 100 degrees Celsius and at about atmospheric pressure. For example, the support pad 230 may include an oxide, a nitride, or a combination thereof. In some examples, the support pad 230 may include silicon dioxide, a metal oxide, a metal nitride, or a combination thereof. In some examples, the support pad 230 may include silicon dioxide, silicon oxynitride, silicon monoxide, silicon carbide, silicon oxycarbide, nitro silicon carbide, metal oxide, metal nitride, or a combination thereof. In some examples, the pH of the reaction solution is greater than or equal to about 8, and the support pad 230 includes silicon dioxide, silicon oxynitride, silicon monoxide, silicon carbide, silicon oxycarbide, nitro silicon carbide, metal oxide, metal nitride, or a combination thereof. In some examples, the pH of the reaction solution is less than or equal to about 5, and the support pad 230 includes silicon carbide, silicon oxycarbide, nitro silicon carbide, metal oxide, metal nitride, or a combination thereof. Therefore, the support pad 230 can prevent the reaction solution of any other solution or liquid from interacting with the device circuit 246 (and thereby degrading the device circuit 246). The formation method, thickness and material of the support pad 230 can be configured independently or in consideration of each other such that the support pad 230 does not have any discontinuous portions that would allow any solution or liquid (e.g., a reaction solution) to pass through it, and the support pad 230 is chemically inert with respect to the reaction solution such that the support pad 230 is etch-resistant (by the reaction solution).

[0113] like Figure 7 and Fig.11 As shown, after forming the support pad 230, the method 200 may include filling (in Figure 7 276) with a plurality of padded grooves 280 to form a first filter region 216 of a plurality of light guides 218. As discussed above, at least one filter material 216 can filter light of a first wavelength or range of wavelengths (e.g., excitation light) and allow light of a second wavelength or range of wavelengths (e.g., emission light from a first reaction site) to pass therethrough to at least one corresponding light sensor 240. In some examples, the amount of filter material 216 applied to the device base 225 can exceed the available volume within the padded grooves 280. Thus, the first filter material 216 can overflow the padded grooves 280 and extend along the top of the device base 225, such as extending above the support pad 230. In such an example, at least a portion of the first filter material 216 extending above the top surface of the support pad 230 can be removed. In an optional example, the filling operation 276 can include selectively filling each of the gasketed grooves 280 so that the first filter material 216 does not clear or overflow the grooves 280 (e.g., does not extend over the top of the support gasket 230 or the first gasket layer 254). Figure 7276 of the first filter material 216 may include mechanically pressing or forcing the first filter material 216 at least into the groove 280 with the liner.

[0114] like Figure 7 and Fig.12 As shown, after depositing the first filter material 216 in the groove 280 with the liner, the method 200 may include selectively removing (at Figure 7 278) supports an upper portion of the liner 230 to form a void, gap, cavity, or open space 290 surrounding the first filter material 216 and extending between the first filter material 216 and the dielectric material 142 of each groove 280 (and the first inner liner layer 254, if present), such as Fig.12 The void 290 can extend from the top surface of the device base 225 (thus forming an opening at the top surface of the device base 225) to the remaining or unremoved bottom portion of the support pad 230. The void 290 within the light guide 218 can therefore be annular and extend from the bottom portion of the groove 280 to the top surface of the device base 225.

[0115] like Fig.12 As shown, the bottom or lower portion of the support pad 230 may not be removed and may remain within the groove 280 below the first filter material 216 and around the bottom or lower portion of the first filter material 216. In this way, after selectively removing the top portion of the support pad 230, the first filter material 216 can be a separate member (e.g., frustoconical) supported by the support pad 230 at its base or bottom portion.

[0116] The upper portion of the support pad 230 can be selectively removed so that the first filter material 216 deposited in the groove 280 remains completely or at least substantially intact. Similarly, the upper portion of the support pad 230 can be selectively removed so that the first liner layer 254 deposited in the groove remains completely or at least substantially intact. If the device base 225 does not include the first liner layer 254 in the groove 280, the upper portion of the support pad 230 can be selectively removed so that the dielectric material 242 adjacent to the groove 208 remains completely or at least substantially intact. The upper portion of the support pad 230 can be removed via any selective removal process that only removes the upper portion of the support pad 230. As discussed above, the material of the support pad 230 can be different from the material of the first liner layer 254 (and the dielectric material 242) and the first filter region 216. In some such examples, the upper portion of the support liner 230 can be removed via at least one selective chemical or plasma etching process that is material specific to the support liner 230 (rather than the material of the first liner layer 254 and the first filter region 216). For example, a free radical based chemical etching process such as Applied of Selectra TM An etching process may be used to selectively remove an upper portion of the support liner 230 .

[0117] However, it should be noted that in some examples, the upper portion of the support liner 230 may not be removed to form the void 290. Instead, the support liner 230 may remain on the device base 225 such that it extends over the top surface of the device base 225 and within a plurality of grooves 280 extending around the first filter material 216 between the first filter material 216 and the dielectric material and device circuitry 246, as shown. Fig.11 In such an example, the method 200 may include providing a plurality of light guides 218 (where only Fig.11 The first filter material 216 and support pad 230 shown in the figure and the gap area 213 of the device base 225 (e.g., above the top surface of the device base 225, such as above the support pad 230) are formed (on the Figure 7 Thus, the support pad 230 can prevent any solution or liquid, such as a reaction solution, that may penetrate the reaction structure or the reaction structure and the light guide 218 from ultimately interacting with the device circuit 246.

[0118] If the upper portion of the support pad 230 is selectively removed to form the gap 290, as shown in FIG. Figure 7 and Fig.13As shown, the method 200 may include filling (in Figure 7 281) a plurality of gaps 290 to form a second filter region 215 of a plurality of light guides 218. Thus, the first filter region 216 and the second filter region 215 can form a light guide 218. As discussed above, the filter material of the second filter region 215 can filter light of a first wavelength or wavelength range (e.g., excitation light) and allow light of a third wavelength or wavelength range (e.g., emission light from the first reaction site) to pass through it to at least one corresponding light sensor 240. Also as mentioned above, the filter material of the second filter region 215 can filter light of a second wavelength or wavelength range that the first filter region 116 allows to pass through it. In this way, each of the first filter material 216 and the second filter region 215 can filter the wavelength or wavelength range that the other region allows to pass through it.

[0119] In some examples, the amount of second filter material 215 applied to the device base 225 can exceed the available volume within the voids 290. As a result, the second filter material 215 can overflow the voids 290 and extend along the top of the device base 225, such as extending above the support pad 230. In such examples, at least a portion of the second filter material 215 extending above the top surface of the device base 225 (e.g., above the first backing layer 254) can be removed. In optional examples, the filling operation 281 of the voids 290 can include selectively filling each void 290 so that the second filter material 215 does not clear or overflow the voids 290 (e.g., does not extend above the top of the device base 225, such as does not extend above the first backing layer 254). In some examples, filling (in Figure 7 The void 290 at 281 may include pressing the second filter material 215 (eg, using a rubber brush-like component) at least into the void 290. As shown in FIG.

[0120] Optionally, after forming the light guide 218 via the first filter region 216 and the second filter region 215, the method 200 may include removing a portion of the first filter material 216 and / or the second filter material 215 from a top portion of the device base 225 (if present) and / or from within the light guide 218, such as Fig.13 The first filter material 216 and the second filter material 215 are removed from the light guide 218 so that the opening 258 of the light guide 218 is located at a depth or position below the top surface of the first backing layer 254, as shown. Fig.13Different processes or the same process may be implemented to remove one or more portions of the first filter material 216 and / or the second filter material 215. For example, the removal operation may include at least one of etching or chemically polishing portions of the first filter material 216 and / or the second filter material 215.

[0121] After forming the light guide 218 via the first filter region 216 and the second filter region 215, the method 200 may include forming (on top of) the plurality of light guides 218 and the gap region 213 of the device base 225 (e.g., above the top surface of the device base 225, e.g., above the first backing layer 254). Figure 7 282) reaction structures (see Figure 3 As discussed above, the reaction structure disposed above the gap region 213 of the top surface of the plurality of light guides 218 and the device base 225 may include a plurality of reaction grooves, each reaction groove corresponding to at least one light guide 218, for accommodating at least one reaction site and a reaction solution, the reaction solution initiating a reaction and / or forming a reaction product at the at least one reaction site, the reaction site generating or emitting light in response to incident excitation light. As discussed above, the reaction structure may include a plurality of layers. Thus, the formation (in Figure 7 282) The reaction structure may include forming a plurality of layers (see Figure 3 ). The reactive structure may be formed by any process or technique.

[0122] Optionally, the method 200 may include providing at least one reaction site in at least one reaction recess of the formed reaction structure and / or mounting a flow cell to the device 204 (see Figure 1 ). Providing reaction sites can occur before or after the flow cell is coupled to the device 204. The reaction sites can be positioned in a predetermined pattern along the reaction groove. The reaction sites can correspond in a predetermined manner (e.g., one site corresponds to one light sensor, one site corresponds to multiple light sensors, or multiple sites correspond to one light sensor). In other examples, the reaction sites can be formed randomly along the reaction groove. As described herein, the reaction sites can include biological substances or chemicals fixed to the detector surface in the reaction groove. The biological substances or chemicals can be configured to emit light signals in response to excitation light. In a specific example, the reaction sites include clusters or communities of biomolecules (e.g., oligonucleotides) fixed on the detector surface in the reaction groove.

[0123] It is to be understood that the above description is intended to be illustrative and not restrictive. For example, the above examples (and / or aspects thereof) may be used in combination with each other. In addition, without departing from its scope, many modifications may be made to adapt specific situations or materials to the teachings of various examples. Although the size and type of material may be described herein, they are intended to define the parameters of some examples in the various examples, and they are by no means intended to be limited to all examples, but are merely exemplary. Many other examples will be apparent to those skilled in the art after consulting the above description. Therefore, the scope of the various examples should be determined with reference to the entire scope of the attached claims together with the equivalents to which these claims are entitled.

[0124] It should be appreciated that all combinations of the aforementioned concepts and the additional concepts discussed in more detail below (provided such concepts are not mutually inconsistent) are contemplated as part of the inventive subject matter disclosed herein. In particular, all combinations of the claimed subject matter appearing at the end of this disclosure are contemplated as part of the inventive subject matter disclosed herein.

[0125] In the appended claims, the terms "including" and "in which" are used as the English original meaning equivalent to the corresponding terms "comprising" and "wherein". In addition, in the appended claims, the terms "first", "second", and "third", etc. are used merely as reference labels and are not intended to impose numerical, structural, or other requirements on their objects. The form of the term "based on" herein includes relationships in which elements are partially based on as well as relationships in which elements are completely based on. The form of the term "defined" includes relationships in which elements are partially defined as well as relationships in which elements are completely defined. In addition, the limitations of the appended claims are not written in device-plus-function form and are not intended to be interpreted under 35 U.S.C. § 112, paragraph 6, unless and until the limitations of these claims expressly use the phrase "means for..." followed by a statement of function and no further structure. It should be understood that not all of the above-mentioned objects or advantages may be achieved according to any particular example. Thus, for example, those skilled in the art will recognize that the devices, systems and methods described herein may be implemented or performed in a manner that achieves or optimizes one advantage or group of advantages taught herein without necessarily achieving other objectives or advantages that may be taught or suggested herein.

[0126] Although the present disclosure is described in detail only in conjunction with a limited number of examples, it should be readily understood that the present disclosure is not limited to these disclosed examples. On the contrary, the present disclosure may be modified to incorporate any number of changes, alterations, substitutions, or equivalent arrangements that have not been described heretofore but are commensurate with the spirit and scope of the present disclosure. In addition, although various examples have been described, it should be understood that aspects of the present disclosure may include only one example or some of the described examples. In addition, although some examples are described as having a certain number of elements, it should be understood that these examples may be practiced with less than or greater than a certain number of elements.

Claims

1. A device comprising: a reaction structure, wherein the reaction structure comprises a plurality of reaction sites; Multiple light sensors; and a plurality of light guides having an input region to receive incident excitation light and light emission from at least one corresponding reaction site, the light guides extending from the input region toward at least one corresponding light sensor, wherein each of the plurality of light guides comprises a first filter region and a second filter region, the first filter region being formed of a first filter material to filter the incident excitation light of at least a first wavelength and allow the light emission of a second wavelength to pass therethrough to reach the at least one corresponding light sensor, and the second filter region being formed of a second filter material to filter the incident excitation light of at least the first wavelength and allow the light emission of a third wavelength to pass therethrough to reach the at least one corresponding light sensor, The second filter material surrounds the first filter material. 2 . The device of claim 1 , wherein each of the light guides further comprises a support layer within a bottom portion of the respective light guide, the support layer extending below and around a bottom portion of the first filter region. 3 . The device of claim 2 , wherein the support layer comprises an oxide, a nitride, or a combination thereof. 4 . The device of claim 2 , wherein the second filtering region of each light guide extends above the corresponding support layer and around the first filtering region. 5 . The device of claim 4 , wherein the first and second filtering regions form the input region of the light guide. 6 . The device of claim 2 , further comprising device circuitry electrically coupled to the light sensor to transmit a data signal based on photons detected by the light sensor.

7. The device of claim 6, further comprising a second backing layer positioned between the support layer and the device circuit at the bottom portion of the light guide and between the second filtering region and the device circuit within the top portion of the light guide. The apparatus of claim 7 , wherein the second liner layer comprises a silicon nitride shielding layer.

9. The apparatus of claim 1, wherein the first filter material also filters the light emissions at the third wavelength.

10. The apparatus of claim 1, wherein the second filter material further filters the light emissions at the second wavelength.

11. The apparatus of claim 1, wherein the first filter material is a polymer material having a first dye and the second filter material is a polymer material having a second dye different from the first dye.

12. The apparatus of claim 1, wherein each of the plurality of reaction sites is secured to the reaction structure within a reaction recess of the reaction structure.

13. The device of claim 6, wherein the device circuitry of the device base forms a complementary metal oxide semiconductor (CMOS) circuit.

14. A biosensor comprising: The device according to claim 1; as well as A flow cell is mounted to the apparatus, the flow cell comprising at least one flow channel in fluid communication with the reaction site to guide a reaction solution to the reaction site.

15. A method comprising: forming a plurality of grooves in a device base, the device base including a plurality of light sensors; depositing a support layer over inner surfaces of the plurality of trenches; filling a plurality of trenches above the deposited support layer with a first filter material that filters at least a first wavelength of light and allows a second wavelength of light to pass therethrough to at least one corresponding light sensor; removing an upper portion of the deposited support layer within the plurality of grooves positioned between the device base and the first filter material to form a plurality of voids; filling the plurality of voids with a second filter material that filters at least the first wavelength of light and allows a third wavelength of light to pass therethrough to the at least one corresponding light sensor to form a plurality of light guides, the second filter material surrounding the first filter material; as well as A reaction structure is formed above the device base and the plurality of light guides for accommodating a reaction solution and at least one reaction site, which generates light of at least one of the second wavelength and the third wavelength in response to incident excitation light of at least the first wavelength after being treated with the reaction solution.

16. The method of claim 15, wherein removing the upper portion of the deposited support layer within the plurality of grooves forms a support layer portion that extends below and around a bottom portion of the first filter material.

17. The method of claim 15, further comprising depositing a second liner layer over inner surfaces of the plurality of trenches and over a top surface of the device base prior to depositing the support layer such that the support layer extends over the second liner layer.

18. The method of claim 15, wherein the first filter material also filters light at the third wavelength, and wherein the second filter material also filters light at the second wavelength.

19. The method of claim 15, wherein the first filter material is a polymer material having a first dye and the second filter material is a polymer material having a second dye different from the first dye.

20. An apparatus comprising: a reaction structure, wherein the reaction structure comprises a plurality of reaction sites; Multiple light sensors; and a plurality of light guides having an input region to receive incident excitation light and light emission from at least one corresponding reaction site, the light guides extending from the input region toward at least one corresponding light sensor, wherein each of the plurality of light guides comprises a first filter region and a second filter region, the first filter region being formed of a first filter material to filter at least the incident excitation light of a first wavelength and allow the light emission of a second wavelength to pass therethrough, and the second filter region being formed of a second filter material to filter at least the incident excitation light of the first wavelength and allow the light emission of a third wavelength to pass therethrough, wherein at least one respective light sensor receives said light emissions at said second wavelength through said first filter material and receives said light emissions at said third wavelength through said second filter material, The second filter material surrounds the first filter material.

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