Illumina Corporation

Cyvera Corporation

Other

Electronics and Telecommunications Research Institute

Tuo Li

Martin A Putnam

John A Moon

Alan D Kersey

Joseph Traynor

David Fournier

Paul S Szczepanek

Anthony Rauseo

James R Dunphy

F Kevin Didden

An optical reader system including a source light assembly that has a code-reading beam and a fluorescence-excitation beam that are configured to illuminate encoded substrates. The substrates have optically readable codes that provide output signals when the code-reading beam is incident thereon. The output signals are indicative of the codes. The reader system also includes a fluorescence detector that is configured to detect fluorescent signals from the substrates and code pickup optics that are configured to project the output signals from the optically readable codes onto a Fourier plane. The reader system also includes a code detector that is positioned to detect the output signals in the Fourier plane.

Optical reader system for substrates having an optically readable code

A method of identifying analytes that react with probes on encoded particles. The method includes providing a support substrate that has a plurality of the particles randomly distributed on the support substrate. The particles have elongated bodies with codes that extend along the corresponding bodies. The codes identify probes that are attached to the corresponding bodies, wherein at least some of the probes include fluorescent labels from reactions with the analytes. The method also includes detecting fluorescent signals that are emitted from the fluorescent labels. The fluorescent signals emit from random spatial locations along the support substrate. The method also includes detecting the codes of the particles at the random spatial locations along the support substrate and analyzing the codes and the fluorescent signals to identify the analytes that react with the probes on the particles.

Methods of identifying analytes and using encoded particles

An assay stickincludes a transparent reaction vessel or tubehaving one or more microbeadsdisposed therein. The microbeadshave a plurality of unique identification digital codes based on a diffraction gratingdisposed therein that are detected when illuminated by incident light. The incident lightmay be directed transversely onto the side or onto an end of the tubewith a narrow band (single wavelength) or multiple wavelength source, in which case the code is represented by a spatial distribution of light or a wavelength spectrum, respectively. The assay stickmay be reused or disposed upon completion of the assay. Alternatively, the beads may be attached to a strip or planar surface. The encoded beads can also provide traceability, quality-control, and authenticity of each beadto its source and/or to the chemistry on each bead. Also, the low sample volume of the assay stick allows for faster reactions and better sensitivity.

Diffraction grating-based encoded microparticle assay stick

An optical reader system that includes a plurality of substrates. The substrates have an optically readable code disposed therein and a source light assembly that is configured to illuminate the substrates with a code-reading beam and another beam for detecting another optically readable property of the substrate. The code-reading beam and the other beam form beam spots on the substrates that have different shapes. The system also includes a reader that is configured to receive output signals from the code-reading beam and the other beam when the substrates are illuminated. The output signals from the code-reading beam are indicative of the code.

A system for writing an optical code within or on a fiber substrate. The system includes a holding device that has a plurality of supports spaced apart from each other. The fiber substrate is wound about the supports such that the fiber substrate forms at least one flat section extending between adjacent supports. The system also includes at least one light source that is configured to write an optical code within or on the flat section of the fiber substrate.

Methods and systems for writing an optical code within or on a fiber substrate

A method of identifying an analyte. The method includes providing a plurality of microparticles. The microparticles have optically detectable codes extending along bodies of the corresponding microparticle. The microparticles have the chemical probes attached thereto. Each of the chemical probes is associated with a corresponding one of the codes. The method also includes selectively binding target analytes to the chemical probes on the microparticles to produce labeled microparticles and distributing the labeled microparticles to random locations of a substrate. The method also includes determining the codes for the labeled microparticles in the random array and code positions of the codes in the random array. The method further includes detecting the label on the labeled microparticles in the random array and label positions of the labels in the random array. The method also includes using the code positions and the label positions to analyze the target analyte.

Methods of identifying an analyte and nucleic acid analysis

A method and apparatus for performing an assay process, featuring providing microbeads in a solution, each microbead having a particle substrate with a grating with a superposition of different predetermined regular periodic variations of the index of refraction disposed in the particle along a grating axis and indicative of a code; placing the microbeads on an alignment substrate; reading codes of the microbeads and the position thereof on the alignment substrate; reading the fluorescence on each microbead and the position order thereof on the alignment substrate; and determining an assay result based on bead position order and bead code of the earlier reading steps.

Hybrid random bead/chip based microarray

An optical reader systemfor diffraction grating-based encoded microbeads (or bead reader system), comprises a reader boxwhich accepts a bead cell (or cuvette)that holds the microbeadshaving an embedded code therein. The reader boxinterfaces along lineswith a known computer systemThe reader boxinterfaces with a stage position controllerand the controllerinterfaces along a linewith the computer systemand a manual control device (or joy stick)along a lineThe reader interrogates the microbeads to determine the embedded code and/or the fluorescence level on the beads. The reader provides information similar to a bead flow cytometer but in a planar format, i.e., a virtual cytometer.

Optical reader for diffraction grating-based encoded optical identification elements

A method and apparatus are provided for aligning optical elements or microbeads, wherein each microbead has an elongated body with a code embedded therein along a longitudinal axis thereof to be read by a code reading device. The microbeads are aligned with a positioning device so the longitudinal axis of the microbeads is positioned in a fixed orientation relative to the code reading device. The microbeads are typically cylindrically shaped glass beads between 25 and 250 microns (&#x3bc;m) in diameter and between 100 and 500 &#x3bc;m long, and have a holographic code embedded in the central region of the bead, which is used to identify it from the rest of the beads in a batch of beads with many different chemical probes. A cross reference is used to determine which probe is attached to which bead, thus allowing the researcher to correlate the chemical content on each bead with the measured fluorescence signal. Because the code consists of a diffraction grating typically disposed along an axis, there is a particular alignment required between the incident readout laser beam and the readout detector in two of the three rotational axes. The third axis, rotation about the center axis of the cylinder, is azimuthally symmetric and therefore does not require alignment.

Method and apparatus for aligning microbeads in order to interrogate the same

A method of manufacturing optical identification elements that includes forming a diffraction grating in a fiber substrate along a longitudinal axis of the substrate. The grating includes a resultant refractive index variation. The method also includes cutting the substrate transversely to form a plurality of optical identification elements that have the grating therein along substantially the entire length of the elements. Each of the elements has substantially the same resultant refractive index variation.

Method of manufacturing of a diffraction grating-based optical identification element

A method and apparatus f or performing an assay process, featuring providing microbeads in a solution; placing the microbeads on an alignment substrate; reading codes of the microbeads and the position thereof on the alignment substrate; reading the fluorescence on each microbead and the position order thereof on the alignment substrate; and determining an assay result based on bead position order and bead code of the earlier reading steps, where the microbead is an encoded particle having a particle substrate; a portion of the substrate being made of a substantially single material and having at least one diffraction grating embedded therein, the grating having a resultant refractive index variation within the single material at a grating location; and the grating providing an optical output signal indicative of a code when illuminated by an incident light signal propagating from outside said substrate, the optical output signal being a result of passive, non-resonant scattering from said grating when illuminated by said incident light signal.

A method and apparatus for labeling an item using diffraction grating-based encoded optical identification elementsincludes an optical substratehaving at least one diffraction gratingdisposed therein. The gratinghas one or more colocated pitches &#x39b; which represent a unique identification digital code that is detected when illuminated by incident light. The incident lightmay be directed transversely from the side of the substrate(or from an end) with a narrow band (single wavelength) or multiple wavelength source, and the code is represented by a spatial distribution of light or a wavelength spectrum, respectively, or a combination thereof. The elementcan provide a large number of unique codes, e.g., greater than 67 million codes, and can withstand harsh environments. The encoded elementmay be used to label any desired item, such as large or small objects, products, solids, powders, liquids, gases, plants, minerals, cells and/or animals, or any combination of or portion of one or more thereof. The label may be used for many different purposes, such as for sorting, tracking, identification, verification, authentication, anti-theft/anti-counterfeit, security/anti-terrorism, or for other purposes. In a manufacturing environment, the elementsmay be used to track inventory for production information or sales of goods/products.

Method and apparatus for labeling using diffraction grating-based encoded optical identification elements

A method for manufacturing a diffusion grating-based optical identification element is provided. The optical identification element includes a known fiber substrate, having a diffraction grating disposed therein the grating being indicative of a code when exposed to incident light. A large number of elements or microbeads all having the same identification codes can be manufactured by cutting the substrate transversely where the grating is located, thereby creating a plurality of elements, at least two of the elements having the grating therein along substantially the entire length of the elements. The elements may be manufactured in many different ways, including winding the fiber onto a basket, forming the gratings in the basket openings or bays, removing the fiber and cutting the fiber to form the elements 8. Each bay may have a set of elements with a unique set of codes therein.

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East Lyme, CT, United States of America

Tuo Li