Patents by Inventor Yir-Shyuan Wu
Yir-Shyuan Wu has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Patent number: 11535890Abstract: An example of a sequencing kit includes a flow cell, an encapsulation matrix precursor composition, and a radical initiator. The flow cell includes a plurality of chambers and primers attached within each of the plurality of chambers. The encapsulation matrix precursor composition consists of a fluid, a monomer or polymer including a radical generating and chain elongating functional group, a radical source, and a crosslinker. The radical initiator is part of the encapsulation matrix precursor composition or is a separate component.Type: GrantFiled: January 23, 2020Date of Patent: December 27, 2022Assignee: Illumina, Inc.Inventors: Xi-Jun Chen, Yir-Shyuan Wu, Tarun Kumar Khurana, Liangliang Qiang, Andrew J. Price, Elisabet Rosas
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Patent number: 11499192Abstract: An example of a sequencing kit includes a flow cell, an encapsulation matrix precursor composition, and a radical initiator. The flow cell includes a plurality of chambers and primers attached within each of the plurality of chambers. The encapsulation matrix precursor composition consists of a fluid, a monomer or polymer including a radical generating and chain elongating functional group, a radical source, and a crosslinker. The radical initiator is part of the encapsulation matrix precursor composition or is a separate component.Type: GrantFiled: January 23, 2020Date of Patent: November 15, 2022Assignee: Illumina, Inc.Inventors: Xi-Jun Chen, Yir-Shyuan Wu, Tarun Kumar Khurana, Liangliang Qiang, Andrew J. Price, Elisabet Rosas
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Publication number: 20220331792Abstract: An example of a flow cell includes a substrate, which includes nano-depressions defined in a surface of the substrate, and interstitial regions separating the nano-depressions. A hydrophobic material layer has a surface that is at least substantially co-planar with the interstitial regions and is positioned to define a hydrophobic barrier around respective sub-sets of the nano-depressions.Type: ApplicationFiled: April 26, 2022Publication date: October 20, 2022Inventors: Tarun Kumar Khurana, Arnaud Rival, Lewis J. Kraft, Steven Barnard, M. Shane Bowen, Xi-Jun Chen, Yir-Shyuan Wu, Jeffrey S. Fisher, Dajun Yuan
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Publication number: 20220275443Abstract: Embodiments provided herewith are directed to self-assembled methods of preparing a patterned surface for sequencing applications including, for example, a patterned flow cell or a patterned surface for digital fluidic devices. The methods utilize photolithography to create a patterned surface with a plurality of microscale or nanoscale contours, separated by hydrophobic interstitial regions, without the need of oxygen plasma treatment during the photolithography process. In addition, the methods avoid the use of any chemical or mechanical polishing steps after the deposition of a gel material to the contours.Type: ApplicationFiled: May 5, 2022Publication date: September 1, 2022Inventors: Yir-Shyuan Wu, Yan-You Lin, M. Shane Bowen, Cyril Delattre, Fabien Abeille, Tarun Khurana, Arnaud Rival, Poorya Sabounchi, Dajun Yuan, Maria Candelaria Rogert Bacigalupo
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Publication number: 20220243269Abstract: Implementations of a method for seeding sequence libraries on a surface of a sequencing flow cell that allow for spatial segregation of the libraries on the surface are provided. The spatial segregation can be used to index sequence reads from individual sequencing libraries to increase efficiency of subsequent data analysis. In some examples, hydrogel beads containing encapsulated sequencing libraries are captured on a sequencing flow cell and degraded in the presence of a liquid diffusion barrier to allow for the spatial segregation and seeding of the sequencing libraries on the surface of the flow cell. Additionally, examples of systems, methods and compositions are provided relating to flow cell devices configured for nucleic acid library preparation and single cell sequencing. Some examples include flow cell devices having a hydrogel with genetic material disposed therein, and which is retained within the hydrogel during nucleic acid processing.Type: ApplicationFiled: April 13, 2022Publication date: August 4, 2022Inventors: Tarun Kumar Khurana, Yir-Shyuan Wu, Xi-Jun Chen, Filiz Gorpe-Yasar, Yan-You Lin, Victoria Popic, Erich B. Jaeger, Mostafa Ronaghi
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Publication number: 20220226820Abstract: Described herein are systems and methods for analyzing biological samples. Including a method for processing an analyte, comprising providing a fluidic device comprising the analyte and one or more polymer precursors; selecting a discrete area within said fluidic device; providing an energy source in optical communication with fluidic device; and selectively supplying a unit of energy generated from the energy source to the fluidic device to generate a polymer matrix within the fluidic device, wherein the polymer matrix is within the discrete area or adjacent to the discrete area.Type: ApplicationFiled: April 7, 2022Publication date: July 21, 2022Inventors: Tarun Kumar KHURANA, Ali AGAH, Yir-Shyuan WU, Filiz Gorpe YASAR
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Patent number: 11390864Abstract: In the examples set forth herein, nucleic acid extraction materials are capable of selectively extracting cell free nucleic acids, including cell free DNA, directly from whole blood samples or plasma. Also included are methods of making and using the nucleic acid extraction materials. One example of a nucleic acid extraction material includes a substrate. This example of the nucleic acid extraction material also includes a polycation bonded to at least a portion of a surface of the substrate. In this example, the polycation consists of a polymer of a quaternized monomer selected from the group consisting of a quaternized 1-vinylimidazole monomer and a quaternized dimethylaminoethyl methacrylate monomer, or a copolymer of a neutral monomer and the quaternized monomer.Type: GrantFiled: June 28, 2018Date of Patent: July 19, 2022Assignees: Illumina, Inc., Illumina Cambridge LimitedInventors: Brian D. Mather, Cyril Delattre, Tarun Kumar Khurana, Yir-Shyuan Wu, Pallavi Daggumati, Behnam Javanmardi, Filiz Gorpe-Yasar, Sebastien Georg Gabriel Ricoult, Xavier von Hatten, Daniel Leonard Fuller
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Publication number: 20220219170Abstract: Described herein are systems and methods for analyzing biological samples. Including a method for processing an analyte, comprising providing a fluidic device comprising the analyte and one or more polymer precursors; selecting a discrete area within said fluidic device; providing an energy source in optical communication with fluidic device; and selectively supplying a unit of energy generated from the energy source to the fluidic device to generate a polymer matrix within the fluidic device, wherein the polymer matrix is within the discrete area or adjacent to the discrete area.Type: ApplicationFiled: February 10, 2022Publication date: July 14, 2022Inventors: Tarun Kumar KHURANA, Ali AGAH, Yir-Shyuan WU, Filiz Gorpe YASAR
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Publication number: 20220195519Abstract: In an example, a target material is immobilized on two opposed sequencing surfaces of a flow cell using first and second fluids. The first fluid has a density less than a target material density and the second fluid has a density greater than the target material density; or the second fluid has a density less than the target material density and the first fluid has a density greater than the target material density. The first fluid (including the target material) is introduced into the flow cell, whereby at least some of the target material becomes immobilized by capture sites on one of the sequencing surfaces. The first fluid and non-immobilized target material are removed. The second fluid (including target material) is introduced into the flow cell, whereby at least some of the target material becomes immobilized by capture sites on another of the sequencing surfaces.Type: ApplicationFiled: December 11, 2020Publication date: June 23, 2022Inventors: Jeffrey S. Fisher, Tarun Kumar Khurana, Mathieu Lessard-Viger, Clifford Lee Wang, Yir-Shyuan Wu
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Publication number: 20220184622Abstract: In accordance with embodiments herein a method for capturing cells of interest in a digital microfluidic system is provided, comprising utilizing a droplet actuator to transport a sample droplet to a microwell device. The microwell device includes a substrate having a plurality of microwells that open onto a droplet operations surface of the microwell device. The sample droplet includes cells of interest that enter the microwells. The method introduces capture beads to the microwells, and the capture elements are immobilized on the capture beads. The method utilizes the droplet actuator to transport a cell lysis reagent droplet to the microwell device. Portions of the cell lysis reagent droplet enter the microwells and, during an incubation period, cause the cells of interest to release analyte that is captured by the capture elements on the capture beads.Type: ApplicationFiled: December 17, 2021Publication date: June 16, 2022Inventors: Arash Jamshidi, Yan-you Lin, Farnaz Absalan, Sarah Stuart, Gordon Cann, Yir-Shyuan Wu, Tarun Khurana, Jeffrey S. Fisher
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Patent number: 11352668Abstract: Implementations of a method for seeding sequence libraries on a surface of a sequencing flow cell that allow for spatial segregation of the libraries on the surface are provided. The spatial segregation can be used to index sequence reads from individual sequencing libraries to increase efficiency of subsequent data analysis. In some examples, hydrogel beads containing encapsulated sequencing libraries are captured on a sequencing flow cell and degraded in the presence of a liquid diffusion barrier to allow for the spatial segregation and seeding of the sequencing libraries on the surface of the flow cell. Additionally, examples of systems, methods and compositions are provided relating to flow cell devices configured for nucleic acid library preparation and single cell sequencing. Some examples include flow cell devices having a hydrogel with genetic material disposed therein, and which is retained within the hydrogel during nucleic acid processing.Type: GrantFiled: July 31, 2018Date of Patent: June 7, 2022Assignee: ILLUMINA, INC.Inventors: Tarun Kumar Khurana, Yir-Shyuan Wu, Xi-Jun Chen, Filiz Gorpe-Yasar, Yan-You Lin, Victoria Popic, Erich B. Jaeger, Mostafa Ronaghi
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Patent number: 11332788Abstract: Embodiments provided herewith are directed to self-assembled methods of preparing a patterned surface for sequencing applications including, for example, a patterned flow cell or a patterned surface for digital fluidic devices. The methods utilize photolithography to create a patterned surface with a plurality of microscale or nanoscale contours, separated by hydrophobic interstitial regions, without the need of oxygen plasma treatment during the photolithography process. In addition, the methods avoid the use of any chemical or mechanical polishing steps after the deposition of a gel material to the contours.Type: GrantFiled: January 20, 2021Date of Patent: May 17, 2022Assignee: Illumina, Inc.Inventors: Yir-Shyuan Wu, Yan-You Lin, M. Shane Bowen, Cyril Delattre, Fabien Abeille, Tarun Khurana, Arnaud Rival, Poorya Sabounchi, Dajun Yuan, Maria Candelaria Rogert Bacigalupo
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Publication number: 20220143603Abstract: A method for making on-flow cell three-dimensional polymer structures includes loading a polymer precursor solution onto a flow cell. The polymer precursor solution includes a monomer, a crosslinker, and a photoinitiator. The flow cell includes at least one channel for receiving the polymer precursor solution. The at least one channel has an upper interior surface and a lower interior surface. The method further includes illuminating the polymer precursor solution through a patterned photomask using a light at a wavelength sufficient to activate the photoinitiator. Activation of the photoinitiator polymerizes at least some of the polymer precursor solution underneath apertures in the patterned photomask and forms three-dimensional polymer structures that extend from the upper interior surface to the lower interior surface of the at least one channel.Type: ApplicationFiled: November 25, 2020Publication date: May 12, 2022Inventors: Tarun Kumar Khurana, Elisabet ROSAS-CANYELLES, Yir-shyuan WU, Hayden Black, Mathieu LESSARD-VIGER, Max Zimmerly, Sean Ramirez
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Patent number: 11318462Abstract: An example of a flow cell includes a substrate, which includes nano-depressions defined in a surface of the substrate, and interstitial regions separating the nano-depressions. A hydrophobic material layer has a surface that is at least substantially co-planar with the interstitial regions and is positioned to define a hydrophobic barrier around respective sub-sets of the nano-depressions.Type: GrantFiled: January 23, 2020Date of Patent: May 3, 2022Assignee: Illumina, Inc.Inventors: Tarun Kumar Khurana, Arnaud Rival, Lewis J. Kraft, Steven Barnard, M. Shane Bowen, Xi-Jun Chen, Yir-Shyuan Wu, Jeffrey S. Fisher, Dajun Yuan
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Publication number: 20220106588Abstract: Systems, methods, and compositions provided herein relate to preparation of beads encapsulating long DNA fragments for high-throughput spatial indexing. Some embodiments include preparation of nucleic acid libraries within the bead, wherein the bead includes pores that allow diffusion of reagents while retaining genetic material.Type: ApplicationFiled: October 21, 2021Publication date: April 7, 2022Inventors: Yir-Shyuan Wu, Filiz Gorpe-Yasar, Tarun Kumar Khurana, Victoria Popic, Erich B. Jaeger, Mostafa Ronaghi
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Publication number: 20220080415Abstract: An example of a flow cell includes a substrate and a cationic polymeric hydrogel on the substrate. The cationic polymeric hydrogel includes a cationic moiety that is i) integrated into a monomeric unit of an initial polymeric hydrogel or ii) attached to the monomeric unit of the initial polymeric hydrogel through a linker. The flow cell further includes an amplification primer attached to the cationic polymeric hydrogel.Type: ApplicationFiled: July 22, 2020Publication date: March 17, 2022Inventors: Yir-Shyuan Wu, Tarun Kumar Khurana, Yasaman Farshchi, Xi-Jun Chen, Bernard Hirschbein
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Publication number: 20220048004Abstract: An example of a flow cell includes a substrate, a plurality of chambers defined on or in the substrate, and a plurality of depressions defined in the substrate and within a perimeter of each of the plurality of chambers. The depressions are separated by interstitial regions. Primers are attached within each of the plurality of depressions, and a capture site is located within each of the plurality of chambers.Type: ApplicationFiled: October 31, 2021Publication date: February 17, 2022Inventors: Lewis J. Kraft, Tarun Kumar Khurana, Yir-Shyuan Wu, Xi-Jun Chen, Arnaud Rival, Justin Fullerton, M. Shane Bowen, Hui Han, Jeffrey S. Fisher, Yasaman Farshchi, Mathieu Lessard-Viger
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Patent number: 11203016Abstract: In accordance with embodiments herein a method for capturing cells of interest in a digital microfluidic system is provided, comprising utilizing a droplet actuator to transport a sample droplet to a microwell device. The microwell device includes a substrate having a plurality of microwells that open onto a droplet operations surface of the microwell device. The sample droplet includes cells of interest that enter the microwells. The method introduces capture beads to the microwells, and the capture elements are immobilized on the capture beads. The method utilizes the droplet actuator to transport a cell lysis reagent droplet to the microwell device. Portions of the cell lysis reagent droplet enter the microwells and, during an incubation period, cause the cells of interest to release analyte that is captured by the capture elements on the capture beads.Type: GrantFiled: November 30, 2016Date of Patent: December 21, 2021Assignee: Illumina, Inc.Inventors: Arash Jamshidi, Yan-you Lin, Farnaz Absalan, Sarah Stuart, Gordon Cann, Yir-Shyuan Wu, Tarun Khurana, Jeffrey S Fisher
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Patent number: 11192083Abstract: An example of a flow cell includes a substrate, a plurality of chambers defined on or in the substrate, and a plurality of depressions defined in the substrate and within a perimeter of each of the plurality of chambers. The depressions are separated by interstitial regions. Primers are attached within each of the plurality of depressions, and a capture site is located within each of the plurality of chambers.Type: GrantFiled: January 23, 2020Date of Patent: December 7, 2021Assignee: Illumina, Inc.Inventors: Lewis J. Kraft, Tarun Kumar Khurana, Yir-Shyuan Wu, Xi-Jun Chen, Arnaud Rival, Justin Fullerton, M. Shane Bowen, Hui Han, Jeffrey S. Fisher, Yasaman Farshchi, Mathieu Lessard-Viger
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Patent number: 11180752Abstract: Systems, methods, and compositions provided herein relate to preparation of beads encapsulating long DNA fragments for high-throughput spatial indexing. Some embodiments include preparation of nucleic acid libraries within the bead, wherein the bead includes pores that allow diffusion of reagents while retaining genetic material.Type: GrantFiled: February 11, 2019Date of Patent: November 23, 2021Assignee: ILLUMINA, INC.Inventors: Yir-Shyuan Wu, Filiz Gorpe-Yasar, Tarun Kumar Khurana, Victoria Popic, Erich B. Jaeger, Mostafa Ronaghi