Patent Application
20230160806
This invention generally relates to processes, methods and devices for protein and particle detection, testing or to analyze markers in patient specimens and samples such as saliva, sputum, urine, blood or blood components (for example, serum, plasma) for investigating biology and for clinical diagnosis and public health applications. In alternative embodiments, provided are processes, methods, kits, devices and software for testing and detecting proteins such as antigens, cytokines or antibodies, particles or cells in specimens of or samples from human or animals; and in alternative embodiments the protein are induced by or derived from viruses, bacteria, an immune system, a cancer cell or any cell which can cause a disease, infection or condition such as a COVID-19 infection. In alternative embodiments, provided are portable imaging systems comprising flat static surfaces or slides, wherein the flat static surfaces or slides can comprise or be fabricated as printed microarrays, biochips, protein precipitates, beads or high throughput imaging systems of 2D planes in liquids. In alternative embodiments, portable imaging systems as provided herein can enable point-of-care diagnosis, immunity analysis, epidemiological surveillance, and/or therapeutics and vaccine development.
In recent years, mobile electronic devices such as smart phones, single board computers, and wearables have become more sophisticated and advanced. These devices feature a variety of sensors such as high-resolution cameras, are equipped with the latest communication technology including wireless data transfer, and possess computational power exceeding previously available desktop computers. Due to these properties, portable devices have great potential in biomedical applications allowing fast, inexpensive on-site biodetection and bioanalysis, especially using imaging-based methods.
Various adapters for microscopy using portable devices such as cell phones have been developed. In mobile devices, different illuminations strategies have been reported including on-axis epi-illumination [1], off-axis inclined illumination [2], butt-coupling [3], and total internal reflection [4]. In order to avoid out-of-focus background with these illumination schemes, either the sample is compressed to a thickness of approximately 10 μm by mounting it between two glass slides [5] or physical properties of the sample such as plasmonic enhancement due to the presence of a metal surface [2] or total internal reflection due to the presence of a refractive index change are exploited [4].
Protein and biological particles (for example, cells, bacteria, viruses) detection is of great importance in research and clinical diagnostics. Numerous assay platforms are available including, for example, immunohistochemistry (IHC), enzyme linked-immunosorbent assay (ELISA), flow cytometry, mass spectrometry, lateral flow test, chemiluminescent immunoassay, and other types of immunoassays. Protein and particle detection assay formats often involve capturing the target analytes on a solid surface such as an array or bead, followed by subsequent staining steps with, for example, luminophores to “light up” the target, prior to analysis. For particles such as a cell or proteins associated with a cell, they can be directly marked, without a solid surface support, using luminescent probes. An exemplary format of protein detection assay comprises a microarray that are coated with cognate biological molecules to detect target proteins such as antibodies in serology or a serological assay or detect multiple isotypes against tens, hundreds or thousands of antigens in a high throughput manner. Because multiple targets are incorporated in the microarray, it can achieve very high specificity and readily distinguish one disease marker from another. One such example that is of clinical interest is to discriminate different respiratory infections, for example diagnosing SARS-CoV-2 infection from Severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), Flu, and other common coronaviruses. One such example of antigen microarrays for SARS-CoV-2 detection is reported by Khan and Assis [6,7]. They demonstrated a coronavirus antigen microarray that included antigens from SARS-CoV-2 and tested it on human sera collected prior to the pandemic to demonstrate low cross-reactivity with antibodies from human coronaviruses that cause the common cold, particularly for the S1 domain. Microarrays can also be used for low cost, high throughput testing on the scale of greater than 100,000 samples, which is critical to (repeatedly) test large populations. While biomarker labeling and assay chemistries are generally established, a major remaining roadblock in protein and biological particle detection is the lack of portable, easy-to-use, cost-effective yet high quality imaging and analysis modules. For instance, while microarrays and microbeads can be assayed with a minimal number of reagents and a simple infrastructure within minutes to hours, reading the stained specimen (for example, microarray slides after staining) by fluorescence imaging currently requires expensive ($10,000 or more) and sophisticated instruments that are not currently equipped in many clinics, hospitals and testing labs and are difficult to move to mobile testing sites such as drive through and field clinics. For instance, current microarray imaging systems comprise large laser scanners that depend on high precision 2D movement of the slide (or optical apparatus), a high-power laser and PMT detectors. Due to their outdated complexity, laser scanners often cost $50,000-$100,000. There are camera-based imagers available, however, despite their simpler designs, these devices are still pricy at $10,000-$30,000, power inefficient, too complex, large and heavy. These devices are also restricted to using a specific format such as a slide of fixed dimensions and are not compatible with randomly oriented samples and detection within liquids. In order to widely test a large population for a disease, and generally for bioanalysis purposes, portable, easy-of-use, and inexpensive imagers or analyzers need to be developed and integrated with protein and particle detection methods including for example microarray and microbead assays.
In alternative embodiments, provided are products of manufacture fabricated or manufactured as portable devices equipped with sensors, which can be inexpensive but powerful, such as for example a camera, paired with on-device and an online data processing. These exemplary products of manufacture have great potential in providing point-of-care high accuracy diagnosis and greatly improve human health related aspects, especially in the presence of epidemics/pandemics. Products of manufacture as provided herein can enable large scale, high throughput imaging of two-dimensional (2D) planes on substrates such as microarrays or microwells, and also within liquids such as contained in a cuvette, a capillary or a flow cell, relevant to antibody testing with (fluorescence) detection based on use of cameras, for example, mobile device cameras. In alternative embodiments, the easy-to-manufacture, low-cost portable devices as provided herein enable and use epi-illumination or light sheet illumination and imaging of surfaces and liquids in one or multiple spectral windows. Geared towards large scale protein detection such as antibody testing including viruses such as SARS-CoV-2, products of manufacture as provided herein can be very powerful for protecting the public's health.
In alternative embodiments, a product of manufacture, a device, an apparatus or a system for testing for the presence of a target analyte in a sample, as provided herein: is cheaper than most comparable devices; is portable; combines large, uniform field of view (optionally a field of view greater than (>) about 10 mm to about 20 mm) with high spatial resolution (and optionally the high spatial resolution is better than about 10 μm); provides fast imaging speed (optionally the acquisition time is less than (<) about 1 second (s) per image; and/or provides multichannel acquisition (and optionally the multichannel acquisition is greater than (>) about 2 or 3 channels.
In alternative embodiments, provided are products of manufacture, devices, apparatus or systems for testing for the presence of a target analyte in a sample,
In alternative embodiments, a product of manufacture, device, apparatus or system as provided herein further comprises: (d) a software and/or a computer program to visualize, analyze, share and/or store data representing the images, and optionally the software and/or the program visualizes, analyzes, shares and/or stores the data on the product of manufacture, device, apparatus or system itself or by connecting the product of manufacture, device, apparatus or system to a server or cloud computing-based storage and/or sharing system.
In alternative embodiments, a product of manufacture, device, apparatus or system as provided herein comprises an about 0.2 to 200 megapixels charge-coupled device (CCD) or a Complementary Metal Oxide Semiconductor (CMOS) color or monochrome camera coupled to a lens or lens system of between about 1 mm to about 1400 mm focal length to yield a field of view of between about 1 mm to about 75 mm with a pixel size at the sample of between about 0.1 μm to 100 μm for 2D imaging of: surfaces with epi-illumination, or solutions with light sheet illumination, and optionally a fluorescent, luminescent or phosphorescent light is filtered with a long pass, band pass or short pass emission filter to prevent excitation light from reaching the camera sensor.
In alternative embodiments of a product of manufacture, device, apparatus or system as provided herein, the sample slide is illuminated by one or more light sources from the top, bottom and/or side at an angle of between about 0° to 90° to the optical axis or with a light sheet at an angle of between about 60° to 120° to the signal detection axis with the one or multiple light sources,
In alternative embodiments of a product of manufacture, device, apparatus or system as provided herein, illumination comprises or the light source emits epi-illumination, or the illumination comprises or the light source emits light in the form of a sheet or single plane of light at the sample plane,
In alternative embodiments of a product of manufacture, device, apparatus or system as provided herein, the components of the imaging system are designed or fabricated to image surfaces, slides, biochips, microarrays or other target analytes in a sample or solution stained with a detectable dye or particle,
In alternative embodiments of a product of manufacture, device, apparatus or system as provided herein, the firmware and/or software or computer program used to acquire, store and process images from the imaging system in a manner suitable for storing, identifying, quantifying and optionally classifying target analytes comprises a firmware and/or computer software to interface with the camera or 2D imaging equivalent,
In alternative embodiments of a product of manufacture, device, apparatus or system as provided herein, a barcode attached or printed on the sample slide or cuvette or equivalent,
In alternative embodiments of a product of manufacture, device, apparatus or system as provided herein:
In alternative embodiments of a product of manufacture, device, apparatus or system as provided herein, the device further comprises or is fabricated to have:
a hollow tubing for flowing or moving a liquid sample, wherein the hollow tubing is operatively linked to a transparent sample flow cell, a pump and optionally an automated axial sample holder, wherein a liquid sample flows through the hollow tubing, the transparent sample flow cell and the pump;
a pump operatively linked to the hollow tubing, wherein flow of a liquid in and through the hollow tubing and the transparent sample flow cell is controlled and driven by the pump,
an automated axial sample holder and a mechano-electric component, wherein movement of the automated axial sample holder is controlled by the mechano-electric component, and the automated axial sample holder positions the transparent sample flow cell before a source of light or illumination or an excitation light or excitation beam,
wherein optionally the automated axial sample holder comprises or is fabricated as a piezo actuator or voice coil actuator;
and optionally the transparent sample flow cell is or is fabricated as a cuvette or equivalent,
and optionally the source of light or illumination is or is fabricated as a sample illumination or sample luminescence, fluorescence or phosphorescent excitation device capable of or fabricated to produce an excitation light or excitation beam,
and optionally in combination with flowing the liquid solution through the transparent sample flow cell (optionally a cuvette or equivalent) a volume of liquid (optionally between about 0.1 ml to about 10 ml liquid) is imaged (optionally in a few minutes) with the ability to detect the presence of a particle (optionally able to detect only a single particle).
In alternative embodiments, provided is a product of manufacture, device, apparatus or system for use in detecting one or a plurality of biomarkers, optionally one or a plurality of proteins, optionally one or a plurality of viral or a microbial antigens, optionally one or a plurality of antibodies, optionally one or a plurality of cytokines, optionally one or a plurality of biological particles, optionally one or a plurality of cells, or diagnosing, or optionally measuring immune response to, a viral or a microbial infection, cancer, autoimmune disorder, or inflammation comprising use of a product of manufacture, device, apparatus or system as provided herein.
In alternative embodiments, provided are uses of a product of manufacture, device, apparatus or system for detecting one or a plurality of biomarkers, optionally one or a plurality of proteins, optionally one or a plurality of viral or a microbial antigens, optionally one or a plurality of antibodies, optionally one or a plurality of cytokines, optionally one or a plurality of biological particles, optionally one or a plurality of cells, or diagnosing, or optionally measuring immune response to, a viral or a microbial infection, cancer, autoimmune disorder, or inflammation, wherein the product of manufacture, device, apparatus or system is a product of manufacture, device, apparatus or system as provided herein.
In alternative embodiments, provided are methods for detecting one or a plurality of biomarkers, optionally one or a plurality of proteins, optionally one or a plurality of viral or a microbial antigens, optionally one or a plurality of antibodies, optionally one or a plurality of cytokines, optionally one or a plurality of biological particles, optionally one or a plurality of cells, or diagnosing, or optionally measuring immune response to, a viral or a microbial infection, cancer, autoimmune disorder, or inflammation, comprising:
(a) providing of having provided a product of manufacture, device, apparatus or system as provided herein;
(b) contacting the product of manufacture, device, apparatus or system with a biological sample or a sample derived from a biological source comprising a target analyte,
wherein optionally the biological sample or the sample derived from the biological source comprising a target analyte comprises or is derived from a solid tissue sample, a biopsy or a biological liquid, wherein optionally the biological liquid comprises or is derived from a serum, blood, urine, cerebral spinal fluid, mucous or sputum sample;
(c) determining if the biological sample or the sample derived from the biological source comprises a composition (optionally a protein) that specifically binds to a target analyte affixed on the product of manufacture, device, apparatus or system.
In alternative embodiments of methods as provided herein, the target analyte comprises or is a substantially stained or detectably labeled target analyte,
In alternative embodiments of methods as provided herein: the determining if the biological sample or the sample derived from the biological source comprises using a composition (optionally a protein) that specifically binds to a specific target analyte affixed on the product of manufacture, device, apparatus or system, and the composition comprises a substantially stained or a detectable agent or moiety that can specifically bind to a target analyte that is specifically bound to an assay surface of the product of manufacture, device, apparatus or system, wherein optionally the composition is detectably (optionally fluorescently) stained, and optionally the composition is in solution or in a liquid form.
In alternative embodiments, provided are methods for treating or ameliorating a disease, a condition, or a viral or a microbial infection, comprising:
(a) testing or screening an individual in need thereof with a product of manufacture, device, apparatus or system as provided herein, to determine if the individual in need thereof is infected with a pathogen, a virus or a microbe, or has a disease or condition,
(b) and if the individual in need thereof is found to be infected with the pathogen, the virus or microbe, or is determined to have or is diagnosed with the disease or condition, administering a drug or a treatment or agent for ameliorating or decreasing the symptoms of the disease, condition, pathogen virus or microbe, or administering a drug or a treatment to treat or ameliorate or decrease the symptoms of a condition, disease, infection or symptom caused by the pathogen, virus or microbe,
wherein optionally the disease or condition is cancer or a condition comprising inflammation.
In alternative embodiments, provided are kits or packages comprising:
(a) a product of manufacture, device, apparatus or system as provided herein;
(b) at least one set of buffer or media suitable for binding and washing;
(c) at least one set of detectable dyes or particles;
and optionally the kit further comprises detecting or secondary antibodies conjugated to detectable dyes,
and optionally further comprising a sample collection device or a target analyte processing device,
and optionally the target analyte processing device comprises a component or reagent for enrichment, extraction, purification, labeling, conjugation of the target analyte.
The details of one or more exemplary embodiments of the invention are set forth in the accompanying drawings and the description below. Other features, objects, and advantages of the invention will be apparent from the description and drawings, and from the claims.
All publications, patents, patent applications cited herein are hereby expressly incorporated by reference in their entireties for all purposes.
The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
The drawings set forth herein are illustrative of exemplary embodiments provided herein and are not meant to limit the scope of the invention as encompassed by the claims.
the sample is illuminated either from above and/or below with a light source parallel or at an angle with respect to the detection axis, and optionally the light source comprises a light-emitting diode (LED) or a laser diode;
optionally one filter or multiple filters is/are or comprises a spectral filter that can be used to further define the detection spectral window (for example, a short pass or band pass in one or multiple windows of between about 5 nm to 50 nm), and optionally the spectral filter is used to block excitation light, for example, long pass, single band or multi band in windows of between about 5 nm to about 200 nm;
a camera or equivalent capable of taking or capturing fluorescence images of the microarray, and optionally the camera or equivalent is capable of taking images of between about 0.2 to 200, or between about 1 to 100, megapixels, and optionally the camera or equivalent is fabricated as a charge-coupled device (CCD) or a Complementary Metal Oxide Semiconductor (CMOS) device, and optionally the camera or equivalent can take color or monochrome images), and the camera is operably coupled or connected to a lens or lens system (and optionally the lens is or comprises a plastic, glass or composite lens, and optionally the lens has a focal length of between about 1 to about 100 mm;
and optionally the exemplary sample slide comprises a barcode attached or printed on the slide to allow for unambiguous identification of each slide, for example, for when the slide is scanned with a device camera or an external reader;
Like reference symbols in the various drawings indicate like elements.
In alternative embodiments, provided are portable imaging systems and related kits, and methods for using them, for example, for the detection and analysis of analytes or biomarkers either: captured or immobilized on two-dimensional (2D) solid surfaces or slides, including microarrays or biochips; or, in solution or liquid phase by imaging 2D plane(s).
In alternative embodiments, provided are compositions, including products of manufacture and kits, and methods, for imaging, reading and/or analyzing proteins, antigens, or antibodies or biological particles based on 2D imaging detection devices such as microarrays, biochips and/or microbead assays. In alternative embodiments, provided are stationary or portable imaging systems to image, read, or analyze protein or antigen microarrays and particles (for example, cells, microbeads, nanoparticles) on surfaces and in fluids.
In alternative embodiments, imaging systems as provided herein are robust, inexpensive (for example, can cost between about $50.00 to $50,000.00), and can be deployed immediately at a point-of-care setting including those with minimal infrastructure including clinics, hospitals, pharmacies, drive through testing sites, customs and border checkpoints (for example, airports), and people's homes. In alternative embodiments, by uploading the resulting image data for cloud-based analysis with a smartphone or other mobile internet device, actionable results can be made available within minutes. In alternative embodiments, platforms as provided herein can make great impact to manage diseases and infections, contaminations, and control epidemics and pandemics such as COVID-19.
In alternative embodiments, products of manufacture as provide herein can be used to reliably read microarrays or other assay formats that have analytes captured, immobilized, or precipitated on solid surfaces (collectively called “slides” or otherwise 2D surfaces), and can: a) provide a large (for example, about 1 to 75 mm), uniform, undistorted field of view with high spatial resolution (for example, about 1 to 10 μm), b) enable sensor calibration to ensure a linear response in a quantitative or semi-quantitative fashion, c) provide the possibility to combine several spectral windows for illumination and detection to enable sample multiplexing, d) provide the possibility of light source and detector modulation to enable time-resolved detection of one or multiple targets, e) ensure consistent, homogeneous illumination and detection across all replicates of the device, f) interface to a data bank or computational facility to safely store and analyze patient data.
In alternative embodiments, products of manufacture as provide herein can be used to test a broad population for disease or infection screening, or screening during an epidemic/pandemic, in an inexpensive, high throughput manner. Alternative embodiments provide a portable imager or a reader that is: a) portable and of low cost, b) easy to use by non-experts with minimal training, c) feature low power consumption to allow battery powered operation, d) possible to manufacture on a large scale in a simple fashion.
In alternative embodiments, products of manufacture as provide herein can be used to detect analytes or particles in fluids in high throughput.
In alternative embodiments, provided are multiplexed, image analysis methods, apparatus and systems comprising, but not limited to, three major components: the hardware, the software or firmware, and the sample container (for example, a slide or a cuvette or a capillary or a flow cell); a block diagram of an exemplary device is shown in
1) an optics module to generate homogeneous illumination of the sample, a lens or lens system to magnify the field of view of the camera, and one or multiple optical filters specific to the sample emission light (see for example,
2) optionally, the optics module can contain a cylindrical lens to generate a light sheet at the sample plane (see for example,
3) a camera for 2D image sensing that is either part of a mobile device or a stand-alone unit (see for example,
4) a laser or light-emitting diode (LED) light source to illuminate the sample in epi configuration or as a light sheet (see for example,
5) a laser or LED driver to generate the laser or LED current (see for example,
6) optionally, a microprocessor to control the light source, detection unit, and optionally the sample position (see for example,
7) optionally, a Bluetooth, WiFi, Ethernet, or USB module for communication of the microprocessor with a mobile device or stationary computer (see for example,
8) optionally, a rechargeable battery or power adapter to supply power to all components (see for example,
The software or firmware can comprise:
1) a mobile device application that uses the Bluetooth or WiFi connection of the camera device to interface with the microprocessor of the imaging device (see for example,
2) optionally, a wired or wireless connection to a stationary computer can be used to interface and control the sensing device (see for example,
3) functions of the application or software include, but are not limited to, after sample insertion the app will automatically choose the optimum illumination power, focus, exposure time and camera gain (self-calibration), for data acquisition the sample is moved in a manual or automated fashion (see for example,
4) the sample can be imaged with the mobile device camera optionally followed by automatic data analysis. Mobile device apps can be developed for multiple platforms (for example Apple iOS, Android).
5) analysis of data recorded with the image sensing device can be done by an application using the hardware resources of the mobile device (offline data analysis). The results can be communicated to a server/cloud service to be shared with others (online databank), see for example,
In alternative embodiments, the sample is contained on or in a movable and adaptable sample container:
1) On a slide (2D functionalized surface, for example, printed microarray), or in a cuvette-like container (for example, to contain fluids). Slides can be standard coverglass slides (for example, 75 mm×25 mm×1 mm) that can have several pads or compartments (for example, nitrocellulose pads for protein printing), see for example,
2) in a cuvette-like container including spectroscopy cuvettes, capillaries, flow cells, or microfluidic cells (see for example,
3) the sample container can be inserted into a sample holder that can be movable, optionally automated, in order to image a larger portion or the entire sample (see for example,
In alternative embodiments, provided are camera sensing devices and multiplexed, microarray analysis methods, apparatus and systems comprising:
1) optical components for surface, slide and/or fluid imaging in a point-of-care device enclosure. In alternative embodiments, all components including illumination, detection optics, and the sample holder are integrated in a CAD/CAM model that can be manufactured on a large scale at low cost, for example, by 3D printing or injection molding. In alternative embodiments, a portable electronic device equipped with a camera-like sensor is used. In alternative embodiments, the components integrated into a device having external dimensions of between about 25 mm to 500 mm, and can include: a) light-emitting diode (LED) array or laser and LED or laser driver circuit, b) excitation filter, c) slide or cuvette holder, d) emission filter, e) a between about 0.2 to 200 megapixels camera (CMOS or CCD, color or monochrome) with external or integrated lens or lens system (see for example
In alternative embodiments, sample slides or cuvettes are inserted directly into the device in a dedicated slot that maintains the correct distance/position to the illumination (for example, between about 0 to 30 cm) and detectors (for example, between about 0 to 30 cm). Optionally, the sample is contained in a cassette or sled to adapt samples of different sizes (for example, between about 1 to 100 mm) to the same imaging device. A cassette or sled can also allow to quickly (for example, between 1 min to 15 min) image a larger number of samples (for example, between about 1 to 10 slides) at a time on a single device. For example, a sled as depicted in
In alternative embodiments, the slide holding mechanism ensures proper positioning to make sure that the individual pads of a slide can be indexed correctly (for example, see
An exemplary 3D CAD/CAM model of a single channel imager as provided herein is illustrated in
An exemplary schematic of a multichannel imager as provided herein is illustrated in
2) Flexible Sample Illumination. In alternative embodiments, the sample slide is illuminated from the top, bottom, or side at an angle of between about 0 to 90° to the optical axis with one or multiple light sources in the visible (for example, between about 400 to 700 nm), near UV (for example, between about 250 to 400 nm), and/or near IR (for example, between about 700 to 1300 nm) range such as a light-emitting diode (LED) or a laser diode. Alternatively to epi-illumination, a light sheet can be generated with a cylindrical lens at the focal plane of the detection lens for fluorescence excitation. Optionally, broad band excitation light can be used and spectrally cleaned with optical filters (absorption or interference filters, short pass, long pass, or band pass with for example, between about 1 to 100 nm bandwidth). As an example, excitation in the microarray imaging prototype is realized with 2 LEDs mounted above the sample (
3) Camera Detection. In alternative embodiments, images of slides or cuvettes can be acquired with a CMOS or CCD, color or monochrome camera with between about 0.2 to 200 megapixels coupled to a lens adjusted to a field of view of between about 1 to 75 mm. This can be a stand-alone camera interfaced by a computer or mobile device or a mobile device with integrated camera such as a smartphone. In alternative embodiments, spectral channels can be generated using a color camera and/or optical filters (optionally, long pass or band pass of between about 5 to 200 nm bandwidth). As an example (
In alternative embodiments, the camera can be part of an integrated device such as a smartphone or a stand-alone camera module that is interfaced by a wired (USB, ethernet or dedicated) or wireless (Bluetooth or WiFi) connection.
In alternative embodiments, image acquisition comprises the following:
In alternative embodiments, an exemplary device as provided herein can:
In alternative embodiments, an exemplary device as provided herein can use particle tracking or image correlation spectroscopy to quantify the movement and concentration of particles and molecules in solution. Example algorithms include:
For image or image series acquisition and/or data analysis, a smartphone or tablet app can be used using a commercial development platform such as Appy Pie (www.appypie.com/); Alpha Anywhere (https://www.alphasoftware.com/) and Appery.io (https://appery.io/); or equivalents. This app could also utilize common APIs such as Google Drive. This way, the mobile app can sync the images to a cloud storage account where they can be stored and/or analyzed using custom routines and software as mentioned above or using third party software such as Mapix-CS (https://www.innopsys.com/en/lifesciences-products/microarrays/software/trial-versions). To ensure privacy, data must be protected by encryption with a personal account and password. In alternative embodiments, the patient or a health care professional can create an account with access code to review and store that microarray data. In alternative embodiments, the data management system must comply with the Health Information Portability and Accountability Act, as amended (HIPAA) (29 U.S. Code § 1181 et seq.) to protect information held by a covered entity that concerns health status, provision of healthcare or payment for healthcare that can be linked to an individual. With patient consent, de-identified anonymized data can be made available for clinical studies, statisticians, Institutional Review Boards (IRBs), and regulators. Clinical trial individual-level participant data (IPD) can be shared either as microdata (individual-level raw data) or through an online portal. These microdata can be one or more flat files or databases. The data can be analyzed only by qualified investigators (QIs) that are registered and have signed a HIPAA agreement. In alternative embodiments, when an online portal is used, the QI can access the data only through a remote computer interface, such that the raw data and all analyses shall reside on site. Data users do not download any microdata to their own local computers through this portal. Under this model, all actions can be audited.
In alternative embodiments, for example for clinical diagnostic purposes, target identification and classification can be accomplished by means of artificial intelligence (AI), machine learning, or deep learning of the recorded images or image series based on intensity, lifetime, spectral, size or morphology of the analyte. Types of algorithms include supervised learning, unsupervised learning, semi-supervised learning, and reinforcement learning.
In alternative embodiments, exemplary devices as provided herein use a general workflow or process of a surface or a slide (for example, microarray)-based analysis comprising: sample or specimen, sample collection, optionally sample processing, incubating the sample with capture slides, optionally a washing step, staining with dyes (or fluorophores, quantum dots) tethered with an affinity tag (for example, antibodies, oligonucleotides, peptides, proteins, aptamers, streptavidin, biotin, engineered tag or any combination of these molecules), optionally a washing step, followed by imaging and analysis with our portable system.
In alternative embodiments, exemplary devices as provided herein use a general workflow or process of microbead-based analysis comprising: specimen collection, optionally sample processing, incubating the sample with capture microbeads, capture antibodies or antigens, optionally a washing step, staining with dyes (or fluorophores, quantum dots) tethered with an affinity tag (for example, antibodies, oligonucleotides, peptides, proteins, aptamers, biotin, engineered tag or any combination of these molecules), optionally a washing step (for example magnetic separation based on magnetic microparticles), followed by imaging and analysis with our portable system.
In alternative embodiments, exemplary devices as provided herein use a general workflow or process of detecting and quantifying target analytes in solution. Example targets include viruses, bacteria, proteins, and other pathogens or molecular markers. Example human health related applications include the detection of bacterial infection, for example, presence of bacteria in urine, such as occurring in urinary tract infection (UTI), or sputum, such as occurring during upper respiratory tract infections (URI) as well as the presence of bacteria in potable water sources or food.
In alternative embodiments, exemplary devices as provided herein use a sample container with at least two optically clear apertures perpendicular to each other, one for imaging and one for sheet illumination. The sample is contained within such cuvette, capillary or flow cell. Optionally, the sample container is movable to image multiple regions of the sample. Liquid specimen together with assay solution are loaded into such sample cuvette or solid specimen are brought into solution before loading into the sample cuvette. Assay solution contains reagents and markers to generate image contrast to detect and quantify targets. Example reagents include antibodies, antigens, capture beads, nanoparticles, and fluorescent markers.
In alternative embodiments, exemplary devices as provided herein use a pump or other fluidic or microfluidic device is used to move the sample through the sample container or flow cell to increase the screening volume or to allow imaging of a time-resolved process or biochemical reaction or to process multiple samples in an automated fashion.
In alternative embodiments, exemplary devices as provided herein use an optical component arrangement for light sheet microscopy in a mobile device enclosure. All components including light sheet illumination, detection optics and the sample holder are attached to a mobile device enclosure. The device can be matched to the dimensions of any mobile device equipped with a camera.
In alternative embodiments, exemplary devices as provided herein record images or image series with an application or program using the hardware resources of the mobile device. The results can be analyzed on the device itself or communicated to a server or cloud service to be analyzed and stored and shared online.
In alternative embodiments, exemplary devices as provided herein use image processing to detect and quantify the presence of analytes, for example using pattern recognition, single particle localization and tracking, spectral and lifetime information, particle shape and size, and image fluctuation and image correlation spectroscopy-based analysis such as pair correlation and image mean square displacement analysis to measure particle number/concentration and velocity.
In alternative embodiments, specimens used to practice devices or methods as provided herein can be derived from human or animals (for example, a mouse, rat, or primate). Specimen types can include blood, serum, plasma, nasopharyngeal wash/aspirate or swab, nasal aspirate or swab, oropharyngeal (for example, throat swab), sputum, saliva, urine, tissues, and stool. These specimens can be collected using swabs for example in the cases of nasopharyngeal swabs, rectal swab and oropharyngeal swab. Sample processing steps, if needed, are well-established in the art for these specimens to extract, enrich, separate, isolate, purify, dilute or otherwise prepare target analytes prior to analysis.
In alternative embodiments, as an example, for COVID-19 or SARS-CoV-2 detection, specimens comprise blood, serum or plasma. Blood samples can be collected using apheresis collection, a syringe through venipuncture or a finger prick (or fingerstick) device. Plasma samples can be prepared from blood using centrifuge or a microfluidic device (for example, centrifugal microfluidic biochip, or CD microfluidics). For serum, blood is allowed to clot prior to separation by centrifugation. In alternative embodiments the samples are placed in appropriate tubes or container prior to analysis. Alternatively, upon collection using a finger prick, blood specimens can be collected and immediately flow through a device (for example, a microfluidic device) where be separated with a separate or automated device. (for example, automated flow through to the microarray or sample cuvette or capillary or flow cell). There are many automated or semi-automated devices or systems including cartridges that can perform blood draws, sample transport using flow-based mechanisms (for example, using capillary flow, lateral flow, pumps) and (in-line) sample processing such as plasma separation prior to analysis that we can use for this application (see, for example, Technology (Singap World Sci). 2018 6(2): 59-66). In alternative embodiments, as few as one drop of blood (or approximately 20 μl) can be sufficient for many clinical testing such as COVID-19 testing.
In alternative embodiments, the entire assay process including probing and imaging can be integrated. In alternative embodiments, for example, the process of probing the microarray or microbeads with sera including washing, incubation with the secondary antibody, incubation with substrate, and analysis of the results is automated. Robots and integration can be used in order to reduce the exposure risk of the operator and accelerate the process flow. In alternative embodiments, the microarray is printed on a rotating platform, or compact disc (CD), together with microfluidics (optionally, centrifugal microfluidic biochip or CD microfluidics) to drive, process and react the sample fluids and assay solutions within the system in a manual or automated fashion. In alternative embodiments, the assay solution (for example, containing capture beads and fluorescent markers), is pumped through a flow cell or capillary with microfluidics (optionally, centrifugal microfluidics) to drive, process and react the sample fluids and assay solutions within the system in a manual or automated fashion. The aforementioned imager can be part of such a system to include the imaging step. Instead of a sample holder/cassette, the imager can have a slot into which the CD can fit while still able to freely rotate. After the sample reaction, the sample can then be rotated into the appropriate position to take fluorescence images as described in previous embodiments.
In alternative embodiments, samples used to practice devices or methods as provided herein are derived from research and development processes such as proteins, cells, cell lines, cell lysates, tissue lysates, cell culture, biochemical reactions, drug and therapeutic manufacture process. In alternative embodiments, samples used to practice devices or methods as provided herein are drugs (or drug formulations) or therapeutics (or therapeutic formulations) including, for example, biologics, antibodies, and cell therapeutics. Sample processing steps, if needed, are well-established in the art for these samples to extract, enrich, separate, isolate, purify, dilute or otherwise prepare target analytes prior to analysis.
In alternative embodiments, samples used to practice devices or methods as provided herein are environmental samples, food, meat, water, beverage (for example, beer) for agriculture and environmental applications. Sample processing steps, if needed, are well-established in the art for these samples to extract, enrich, separate, isolate, purify, dilute or otherwise prepare target analytes prior to analysis.
target analyte can be a biomarker, protein, biologic, pharmaceutical, and a biological particle. A biomarker can be a DNA, RNA, protein, polypeptides, lipids, carbohydrates, polysaccharide, small molecules, metabolites. It is understood that multiple different analytes can be used and detected in a multiplex fashion to, for example, diagnose a disease.
Protein in this disclosure can be a peptide, epitope, polypeptide, antibody and antibody derivatives (for example, nanobodies, bispecific antibodies), antigen, cytokine, chemokine, enzyme, glycoprotein, hormone, signaling receptor, protein complex (for example, homodimer, heterodimer, or a multi-unit complex or structure), recombinant protein, synthetic protein, de novo designed protein, fusion protein, protein conjugate, modified protein (for example with polyethylene glycol (PEG), Fc domain, histidine, albumin, a dye) or a protein-based therapeutic. Particles in this disclosure comprise biological particles including, but not limited to, cells, mammalian cells, cancer cells, circulating tumor cells (CTC), mycoplasmas, platelets, immune cells, neural cells, engineered cells, fused cells, hybridoma, animal cells, plant cells, bacteria, viruses, fungi, parasites, pathogens, droplets, emulsions, therapeutic cells (for example, stem cells, T cells), a single molecule, a macromolecule such as protein and nucleic acid, a molecular product of a biochemical or enzymatic reaction, a RCA product, a RCA product labeled with dyes, or aggregates of biological molecules such as protein and nucleic acids. Particles in this disclosure also comprise microparticles, microspheres, microbeads, magnetic beads, nanoparticles (for example, quantum dots, qDot, silica nanoparticles, gold nanoparticles). The size of particles can range from 10 nm to 1,000 μm, and optionally from 100 nm to 100 μm. It is understood that particles can be in different shapes. Beads can be barcoded for downstream identification or target quantification (for example, as an internal reference) purposes based on size, shape, fluorescence spectral, lifetime and intensity properties by, for example, tuning composition of associated dyes, or using an oligonucleotide or a nucleic acid barcode.
In alternative embodiments, exemplary devices as provided herein, for example, microarrays or microbeads, can be used to analyze almost any type of molecules or particles in blood or other specimens, including immunoglobulins or antibodies (for example, IgG, IgM, IgA, IgD and IgE and their subclasses) that are produced as the immune system reacts to infections. In alternative embodiments, multiple isotype forms of antibodies including IgM, IgG and IgA will be analyzed using our technology for COVID-19 testing.
In alternative embodiments, products of manufacture as provided herein use any method or process of affinity, or binding, or capture-based mechanism to immobilize or capture target analytes from the sample. Many of these assay formats or surfaces (collectively called “slides”) or capture beads (functionalized micro- or nanoparticles) are established in the art such as microarrays, chips, arrays, microtiter plates (for example, for ELISA), (micro)wells, (micro)chambers, (micro)capillaries, lateral flow devices, membranes, (micro)beads, (micro)particles, nanobeads, nanoparticles, and microfluidics. In alternative embodiments, target analytes are captured on slides by covalent or non-covalent interactions. For instance, often used in the art is slides already immobilized with cognate binding molecules that capture target analytes utilizing biomolecular recognition such as antibody/antigen binding and nucleic acid hybridization. The said cognate binding or capture molecules typically are antibodies, oligonucleotides, peptides, proteins, aptamers, biotin, engineered tag or any combination of these molecules. Target analytes can also be captured on slides by other forms or interactions such as ionic, H-bonding, hydrophobic, electrostatic or metal/chelate interactions, centrifugation force, gravity or buoyancy. In alternative embodiments, target analytes can be first captured by particles (for example, microbeads) and then deposited on slides, surfaces, (micro)wells, (micro)chambers, in capillaries, cuvettes, flow cells, or encapsulated in droplets. Samples can be directly added and incubated in cuvettes, on slides or pass through the slides using a flow-cell, microfluidic device, tube, channel, or a capillary. In alternative embodiments, samples (for example, urine) can pass through a membrane or filter to collect, capture or enrich target analytes (for example, bacteria) and subsequently targets can be stained on the said membrane or filter which can be directly imaged with disclosed imagers herein. In alternative embodiments, for our fluid imaging system, samples can be directly interrogated in a container such as a cuvette or using a flow-through system such as a flow-cell, microfluidic device, tube, channel, or a capillary. In alternative embodiments, slides are manufactured with different dimensions, morphology, topography and structures to, for example, modulate binding interactions or flow dynamics.
All these “slides”, “cuvettes” or flow-through devices mentioned above including microarrays, chips, arrays, microtiter plates (for example, for ELISA), (micro)wells, (micro)chambers, (micro)capillaries, lateral flow devices, membranes, (micro)beads, (micro)particles, nanobeads, nanoparticles, microfluidics, flow-cells, tubes, and capillaries can be imaged using imagers provided herein. Here we use microarrays and square cuvettes as an example to illustrate the assay process; in alternative embodiments, any form of slide, cuvette, capillaries or flow-through systems can be used to practice products of manufacture and methods as provided herein.
In alternative embodiments, products of manufacture as provided herein use any method or process of affinity microarray preparation. In alternative embodiments, affinity moieties including nucleic acids, proteins, antigens, pathogens, carbohydrates and other affinity tags are used, and can be printed, adsorbed, deposited or chemically conjugated on an exemplary microarray format for bioanalysis, which can all be read and analyzed using an imaging system as provided herein. In alternative embodiments, microarray comprise nitrocellulose membrane, glass, silicon, plastic or a polymer substrate.
In alternative embodiments, products of manufacture as provided herein comprise or are fabricated as coronavirus antigen microarrays that can detect antibodies against a panel of antigens (see, for example,
In alternative embodiments, products of manufacture as provided herein comprise or are fabricated to use coronavirus S proteins comprising different receptor-binding domains (RBD) including S1 and S2 domains, which can be separately printed or used in combination as whole proteins (S1+S2) on microarrays. In alternative embodiments, products of manufacture as provided herein comprise or are fabricated to use antigens for SARS-CoV-2, and/or antigens for other coronaviruses such as SARS-CoV, MERS-CoV, and/or common cold coronaviruses (for example HKU1, OC43, NL63, 229E) as well as other viruses or pathogens (for example, influenza, adenovirus, MPV, PIV, RSV and HIV).
In alternative embodiments, products of manufacture as provided herein print antigens in multiple spots on a slide or equivalent surface to serve as internal replicates to increase testing accuracy. In alternative embodiments, microarray preparation is modular, and new antigen variants of viruses can be included as they continue to evolve. These antigens can be derived and prepared from viruses or expressed in host cells (for example, HEK-293 cells) through recombinant technologies. Many of them are also available at commercial vendors (for example, Sino Biological). The antigens can be printed onto microarrays including nitrocellulose-coated slides using a microarray printer. These slides can be stored in a desiccator for a long period of time or shipped without losing biological functions.
Target analytes, captured on a surface or otherwise in liquid or solution, are typically probed or detected with luminescent probes (for example, fluorescence, phosphorescence, chemiluminescence). For captured target, for example, a sandwich assay can be used involving probing the captured target with detection antibodies tagged with a luminophore (or molecules that can generate light through a biochemical reaction such as fluorogenic enzymes including, for example, horseradish peroxidase, alkaline phosphatase, β-galactosidase or luciferases) or optionally further labeled with secondary antibodies tagged with a luminophore (for example, FITC-anti-mouse IgG). In alternative embodiments, any affinity binding partners can be used, for example, (strept)avidin and biotin linkages can be used to label target with luminophores. In alternative embodiments, secondary probes can be antibody-oligonucleotide conjugates or oligonucleotide probes for multiplexing and barcoding purposes. In alternative embodiments, proximity ligation assays can be used for protein detection. In alternative embodiments, biomolecules are modified using standard bioconjugation techniques to add functional moieties such as biotin (through “biotinylation”), dyes, or purification tags (for example, Fc, histidine) to enable different purposes. In alternative embodiments, signal amplification processes established in the art such as rolling circle amplification (RCA) and tyramide signal amplification (TSA) can be conducted to amplify signals.
In alternative embodiments, capture particles (for example, microbeads) can be used with a surface chemistry that enables binding and subsequent labeling of targets with affinity luminophores prior to analysis. In alternative embodiments, the particle of interest (for example, cells, bacteria, yeast cells, viruses, protein or nucleic acid aggregates) can be marked and detected directly with luminescent probes. Labeled particle targets can be detected after precipitation from the liquid phase to a surface or directly in the liquid or solution phase using light sheet illumination. In alternative embodiments, washing steps are involved to remove unbound molecules or probes. In other embodiments, assays can be performed in a “homogenous” fashion without washing steps (for example, Förster resonance energy transfer (FRET), bioluminescence resonance energy transfer (BRET), time-resolved FRET or BRET, and molecular beacon designs).
In alternative embodiments, luminophores can be any light (for example, fluorescence, phosphorescence, chemiluminescence) emitting moieties. As an example, detectable dyes that can be used in alternative embodiments comprise: DyLight 405, FAM, FITC, Cy2, Cy3, Cy5, Alexa488, Alexa594, Alexa647, qdots (for example, QD585, QD655, QD800), polymethine dyes, luminescent lanthanide complexes, Europium, Rubrene, upconversion nanoparticles or dyes, and ultrabright fluorescent labels comprise scaffold materials associated with a plurality of dyes (for example AIE beads from Luminicell). In alternative embodiments, any light-emitting moiety can be used herein including, but not limited to, the BODIPY series, the Alexa series, the ATTO series, PE, Coumarin, PerCP, TRITC, Texas Red, and APC. In alternative embodiments, fluorescent protein (for example, Green Fluorescent Protein (GFP), Cyan Fluorescent Protein (CFP), Yellow Fluorescent Protein (YFP), and a Red Fluorescent Protein (RFP)), or split fluorescent proteins, split luciferases and other split enzymes can be used herein to emit light. In alternative embodiments, luminophores are used in combination in a bioassay such as in FRET or BRET or Time-resolved FRET or BRET.
In alternative embodiments, biological particles or cells can be directly labeled using a dye or luminophore conjugated to an affinity tag described above (for example antibody) or particles (for example beads, nanoparticles emulsions, or vesicles). For example, an antibody-dye can bind to a particular molecule on the cell membrane or inside the cell. In alternative embodiments, biological particles or cells can be labeled by other means including, for example, metabolic dyes (for example, resazurin), live or dead cell stains or viability dyes (for example, 7AAD, DAPI, PI), apoptotic marker (for example, annexin V), DNA intercalating dyes (DAPI, 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI), thiazole orange, Propidium Iodide, SYTO 9, and SYTOX or their derivatives and variants). In alternative embodiments, biological particles or cells can be marked with engineered reporters (for example, fluorescent proteins expressed in mammalian cells, or phage mediated bacterial expressing fluorescent proteins).
In alternative embodiments, antigen microarray slides provided herein as an example are probed with specimens as described above (for example, human sera, plasma, or whole blood) in appropriate media and preparations (for example, dilution) for a period of time ranging from between about 5 min to about overnight at between about room temperature (RT) to 4° C., or at RT or 4° C. In alternative embodiments, a washing step is performed prior to labeling with (for example, secondary) antibodies, for example, to human IgA and IgG, for example, conjugated to dyes, fluorophores or quantum dots or equivalents for another period of time, for example, ranging from between about 5 min to 6 hours, or about 2 to 3 hours, for example, at room temperature (RT). In alternative embodiments, a final washing step is performed with appropriate buffer to remove any unbound moieties. In alternative embodiments this entire process, or one or more steps of the process, are automated. The final sides can be analyzed immediately or dried and stored until analysis using our disclosed imaging systems as described above.
Methods, apparatus and systems as provided herein can broadly enable in vitro diagnostics (IVD) or companion diagnostics (CDx) using microarrays including for example DNA or RNA arrays (or gene chip) and protein arrays. As summarized by Wu et al. (BioTechniques 39:577-582), gene chips can be used for a variety of nucleic acid analysis including, for example gene expression, chip-based sequencing, single nucleotide polymorphism (SNP) analysis, genotyping different polymorphisms, sequence variation. An example of protein microarray is antibody microarray which can be used to profile for example disease markers, cytokines, and signaling molecules in a broad range of research (for example tissue culture, cells, cell or tissue lysates and biological manufacture processes) and clinical disease settings (for example cancer or infectious diseases).
In alternative embodiment, microarrays as provided herein and as used in devices as provided herein can be read by imagers disclosed herein and assayed using methods, apparatus and systems as provided herein, instead of using more complicated and expensive microarray scanners in the art. The methods, apparatus and systems as provided herein can therefore find a broad range of applications in therapeutic and vaccine development and in clinical diagnostics.
In alternative embodiments, microarrays as provided herein are broadly applicable to any 2D surface-based assay platforms including for example chips, glass slides, cover slides, microscope slides, microtiter plates (for example, for ELISA), (micro)wells, (micro)chambers, (micro)capillaries, lateral flow devices, membranes, (micro)beads, (micro)particles, nanobeads, nanoparticles, and microfluidics.
In alternative embodiments, provided are products of manufacture, methods and kits for detecting and analyzing proteins including, for example, cytokines, antibodies, and antigens in biological or clinical samples. In alternative embodiments, any established protein detection chemistries and assays or immunoassays can be used to practice products of manufacture, methods and kits as provided herein (for example imaging systems and methods as provided herein), for example, as described in sections “Capture target analytes on surfaces” and “Target probing and luminophores”. In alternative embodiments, any protein assay or immunoassay can be used to practice products of manufacture, methods and kits as provided herein. For illustrative purposes, we describe herein general practices using a bead-based sandwich format for protein detection. In alternative embodiments, target proteins in the sample are captured on cognate antibody-immobilized microbeads. The captured proteins are then probed in a sandwich assay using detection antibodies (or together with secondary antibodies) tagged with a fluorophore, Qdot, or ultrabright nanoparticles (for example AIE beads, or biocompatible organic fluorescent nanoparticles (AIEDots), from LUMINICELL™). In alternative embodiments, the captured protein can initiate an enzymatic reaction such as rolling circle amplification (RCA) to amplify signal. Optionally, bead washing steps are performed in between these steps. Subsequently, the microbeads are then deposited on slides, surfaces, (micro)wells, or (micro)chambers or suspended (or flowed through) in capillaries, cuvettes, or flow cells, which can be imaged and analyzed with our disclosed imaging systems herein (for example
In alternative embodiments, provided are products of manufacture, methods and kits for detecting and analyzing single or individual proteins (for example, for “digital” protein detection). In alternative embodiments, digital protein detection is enabled by imaging individual protein molecules tagged with superbright nanoparticles (for example AIE beads, or biocompatible organic fluorescent nanoparticles (AIEDots), from LUMINICELL™) or long rolling circle amplification (RCA) products.
In alternative embodiments, provided are products of manufacture and kits for practicing methods as provided herein; and optionally, products of manufacture and kits can further comprise instructions for practicing methods as provided herein. In alternative embodiments, provided to practice our disclosed slide imaging and analysis systems are a blood drawing device, a blood processing device, printed microarrays, staining reagents including antibodies, antibodies tethered with dyes, fluorophores or quantum dots, control samples, and incubation, blocking and washing buffers. In alternative embodiments, provided to practice our disclosed slide imaging and analysis systems are a blood drawing device, a blood processing device, capture (micro)beads, staining reagents including antibodies, antibodies tethered with dyes, fluorophores or quantum dots, control samples, and incubation, blocking and washing buffers.
In alternative embodiments, methods, apparatus and systems as provided herein enable point-of-care diagnosis, clinical diagnosis, immunity analysis, research, epidemiological surveillance, and/or therapeutic and/or vaccine development, patient stratification, or measuring therapeutic outcomes in a broad disease settings including for example cancer, inflammation, pain, autoimmune diseases, infections (for example, bloodstream infections, urinary tract infections, antibiotic susceptibility testing), cardiovascular diseases, central nervous system (CNS) disease. For instance, methods, apparatus and systems as provided herein can have broad utility and implications in addressing, for example, COVID-19 pandemic and other pathogenic outbreaks. In alternative embodiments methods, apparatus and systems as provided herein provide a rapid, high throughput, inexpensive serological test which can:
In alternative embodiments, methods, apparatus and systems as provided herein enable analysis of environmental samples, food, meats, beverages, and water. In alternative embodiments, methods, apparatus and systems as provided herein enable analysis and counting of yeast cells for brewing and wine industries. In alternative embodiments, methods, apparatus and systems as provided herein enable analysis and counting of somatic cell count (SCC) in milk.
Any of the above aspects and embodiments can be combined with any other aspect or embodiment as disclosed here in the Summary, Figures and/or Detailed Description sections.
As used in this specification and the claims, the singular forms “a,” “an” and “the” include plural referents unless the context clearly dictates otherwise.
Unless specifically stated or obvious from context, as used herein, the term “or” is understood to be inclusive and covers both “or” and “and”.
Unless specifically stated or obvious from context, as used herein, the term “about” is understood as within a range of normal tolerance in the art, for example within 2 standard deviations of the mean. About can be understood as within 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12% 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.5%, 0.1%, 0.05%, or 0.01% of the stated value. Unless otherwise clear from the context, all numerical values provided herein are modified by the term “about.”
Unless specifically stated or obvious from context, as used herein, the terms “substantially all”, “substantially most of”, “substantially all of” or “majority of” encompass at least about 90%, 95%, 97%, 98%, 99% or 99.5%, or more of a referenced amount of a composition.
The entirety of each patent, patent application, publication and document referenced herein hereby is incorporated by reference. Citation of the above patents, patent applications, publications and documents is not an admission that any of the foregoing is pertinent prior art, nor does it constitute any admission as to the contents or date of these publications or documents. Incorporation by reference of these documents, standing alone, should not be construed as an assertion or admission that any portion of the contents of any document is considered to be essential material for satisfying any national or regional statutory disclosure requirement for patent applications. Notwithstanding, the right is reserved for relying upon any of such documents, where appropriate, for providing material deemed essential to the claimed subject matter by an examining authority or court.
Modifications may be made to the foregoing without departing from the basic aspects of the invention. Although the invention has been described in substantial detail with reference to one or more specific embodiments, those of ordinary skill in the art will recognize that changes may be made to the embodiments specifically disclosed in this application, and yet these modifications and improvements are within the scope and spirit of the invention. The invention illustratively described herein suitably may be practiced in the absence of any element(s) not specifically disclosed herein. Thus, for example, in each instance herein any of the terms “comprising”, “consisting essentially of”, and “consisting of” may be replaced with either of the other two terms. Thus, the terms and expressions which have been employed are used as terms of description and not of limitation, equivalents of the features shown and described, or portions thereof, are not excluded, and it is recognized that various modifications are possible within the scope of the invention. Embodiments of the invention are set forth in the following claims.
The invention will be further described with reference to the examples described herein; however, it is to be understood that the invention is not limited to such examples.
Unless stated otherwise in the Examples, all recombinant DNA techniques are carried out according to standard protocols, for example, as described in Sambrook et al. (2012) Molecular Cloning: A Laboratory Manual, 4th Edition, Cold Spring Harbor Laboratory Press, NY and in Volumes 1 and 2 of Ausubel et al. (1994) Current Protocols in Molecular Biology, Current Protocols, USA. Other references for standard molecular biology techniques include Sambrook and Russell (2001) Molecular Cloning: A Laboratory Manual, Third Edition, Cold Spring Harbor Laboratory Press, NY, Volumes I and II of Brown (1998) Molecular Biology LabFax, Second Edition, Academic Press (UK). Standard materials and methods for polymerase chain reactions can be found in Dieffenbach and Dveksler (1995) PCR Primer: A Laboratory Manual, Cold Spring Harbor Laboratory Press, and in McPherson at al. (2000) PCR—Basics: From Background to Bench, First Edition, Springer Verlag, Germany.
For point-of-care COVID-19 serology testing, the said antigen microarray slides are probed with human sera, plasma, or whole blood in appropriate media. Blood samples can be collected using apheresis collection, a syringe through venipuncture or a finger prick (or fingerstick) device. Plasma samples can be prepared from blood using a centrifuge or a microfluidic device (for example centrifugal microfluidic biochip, or CD microfluidics). For serum, blood is allowed to clot prior to separation by centrifugation. As few as one drop of blood (or approximately 20 μl) will be sufficient for COVID-19 testing. These samples are reacted with the said microarray for a period of time ranging from 5 min to overnight at room temperature or 4° C. A washing step can be performed prior to labeling with (secondary) antibodies to human IgA and IgG conjugated to dyes, fluorophores (for example, Cy3, Alexa647) or quantum dots (for example, QD585) for another period of time ranging from 5 min to 6 hours at room temperature. A final washing step can be performed with appropriate buffer to remove any unbound moieties. This entire process can be performed manually by a technician or be automated. The final sides can be analyzed immediately or dried and stored until analysis using our disclosed systems as described above. The microarray consisted of 2×8 pads of 6.5 mm×6.5 mm each. 2×4 pads were imaged simultaneously with 10 μm spatial resolution to resolve the individual dots (100-300 μm) of the microarray. A 2×8 microarray can read by taking two images. The slide holder will maintain to position of the microarrays at the appropriate distance to the camera lens during image acquisition/reading of the slides. A suitable image sensor (for example, 5-megapixel color camera with an OMNIVISION OV5647™ sensor) in combination with excitation and emission filter combinations suitable for the fluorophores of the microarray (see Table 1) will be used. Microarray images will be acquired and processed as shown in
A 3D CAD/CAM exemplary model was designed as depicted in
We designed, 3D printed, and assembled a version of the imager optimized to read the exemplary coronavirus antigen microarray slides as provided herein. A set of 8 LEDs of 365-nm were used with a battery-powered driver circuit (3 W). Test slides with ALEXAFLUOR 647™, Quantum Dots QD585 and QD655, and Cy3 and Cy5 dyes, were probed. Images (
A respiratory virus antigen microarray for serological testing was printed (https://doi.org/10.1101/2020.04.15.043364) and probed with serum samples and anti-IgG-QD800. Exemplary microarray images of 8 antigen arrays are shown in
A working prototype was constructed and several measurements were performed to demonstrate the capabilities exemplary products of manufacture as provided herein.
Specifically, a calibration slide with spots of Cy5 of decreasing concentrations was used to determine the lower limit of detection of the microarray imaging prototype. Fluorescence images of the calibration pattern can be seen in
To the detection of particles in solution with light sheet illumination, we filled sample cuvettes with yellow-green fluorescent latex particles of various sizes (100 nm, 200 nm, 500 nm) suspended in water, placed them in into the sample holder and subjected them to imaging with the cuvette-based mobile imager with light sheet illumination. For fluorescence excitation, 445-nm laser light was used and the fluorescence light was collected through a KODAK WRATTEN NO 55™ filter via the mobile device camera (here: iPhone 6S). Videos of 1920×1080 pixels were recorded at 29.9 frames per second. Regions of 512×512 pixels were extracted and subjected to iMSD analysis, example images are shown in
As an example biomedical assay for the detection of pathogens we prepared a solution of bacteria (B. subtilis) in minimal medium and stained the membrane fluorescently with FM4-64™ dye. Videos of 1920×1080 pixels were recorded at 29.9 frames per second. Regions of 256×256 pixels were extracted and subjected to iMSD analysis, an example image is shown in
A number of embodiments of the invention have been described. Nevertheless, it can be understood that various modifications may be made without departing from the spirit and scope of the invention. Accordingly, other embodiments are within the scope of the following claims.
This Patent Convention Treaty (PCT) International Application claims the benefit of priority to U.S. Provisional Application Serial No. (USSN) 63/014,845, Apr. 24, 2020. The aforementioned application is expressly incorporated herein by reference in its entirety and for all purposes.
This invention was made with government support under National Institutes of Health (NIH), DHHS, grant nos. 1 R01 AI117061 and P41-GM103540. The government has certain rights in the invention.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US2021/028778 | 4/23/2021 | WO |
| Number | Date | Country | |
|---|---|---|---|
| 63014845 | Apr 2020 | US |
