Patents by Inventor M. SHANE BOWEN
M. SHANE BOWEN 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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Publication number: 20230145389Abstract: Systems and methods for conducting designated reactions utilizing a base instrument and a removable cartridge. The removable cartridge includes a fluidic network that receives and fluidically directs a biological sample to conduct the designated reactions. The removable cartridge also includes a flow-control valve that is operably coupled to the fluidic network and is movable relative to the fluidic network to control flow of the biological sample therethrough. The removable cartridge is configured to separably engage a base instrument. The base instrument includes a valve actuator that engages the flow-control valve of the removable cartridge. A detection assembly held by at least one of the removable cartridge or the base instrument may be used to detect the designated reactions.Type: ApplicationFiled: December 22, 2022Publication date: May 11, 2023Inventors: Alex Aravanis, Boyan Boyanov, M. Shane Bowen, Dale Buermann, Alexander Hsiao, Behnam Javanmardi, Tarun Khurana, Poorya Sabounchi, Hai Quang Tran
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Publication number: 20230109614Abstract: An example of an array includes a support, a cross-linked epoxy polyhedral oligomeric silsesquioxane (POSS) resin film on a surface of the support, and a patterned hydrophobic polymer layer on the cross-linked epoxy POSS resin film. The patterned hydrophobic polymer layer defines exposed discrete areas of the cross-linked epoxy POSS resin film, and a polymer coating is attached to the exposed discrete areas. Another example of an array includes a support, a modified epoxy POSS resin film on a surface of the support, and a patterned hydrophobic polymer layer on the modified epoxy POSS resin film. The modified epoxy POSS resin film includes a polymer growth initiation site, and the patterned hydrophobic polymer layer defines exposed discrete areas of the modified epoxy POSS resin film. A polymer brush is attached to the polymer growth initiation site in the exposed discrete areas.Type: ApplicationFiled: October 25, 2022Publication date: April 6, 2023Inventors: Wayne N. George, Alexandre Richez, M. Shane Bowen, Andrew A. Brown, Dajun Yuan, Audrey Rose Zak, Sean M. Ramirez, Raymond Campos
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Patent number: 11590494Abstract: Systems and methods for conducting designated reactions utilizing a base instrument and a removable cartridge. The removable cartridge includes a fluidic network that receives and fluidically directs a biological sample to conduct the designated reactions. The removable cartridge also includes a flow-control valve that is operably coupled to the fluidic network and is movable relative to the fluidic network to control flow of the biological sample therethrough. The removable cartridge is configured to separably engage a base instrument. The base instrument includes a valve actuator that engages the flow-control valve of the removable cartridge. A detection assembly held by at least one of the removable cartridge or the base instrument may be used to detect the designated reactions.Type: GrantFiled: June 6, 2019Date of Patent: February 28, 2023Assignee: ILLUMINA, INC.Inventors: Alex Aravanis, Boyan Boyanov, M. Shane Bowen, Dale Buermann, Alexander Hsiao, Behnam Javanmardi, Tarun Khurana, Poorya Sabounchi, Hai Quang Tran
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Publication number: 20230002759Abstract: A structured substrate includes a substrate body having an active side. The substrate body includes reaction cavities that open along the active side and interstitial regions that separate the reaction cavities. The structured substrate includes an ensemble amplifier positioned within each of the reaction cavities. The ensemble amplifier includes a plurality of nanostructures configured to at least one of amplify electromagnetic energy that propagates into the corresponding reaction cavity or amplify electromagnetic energy that is generated within the corresponding reaction cavity.Type: ApplicationFiled: September 9, 2022Publication date: January 5, 2023Inventors: M. Shane Bowen, Dajun Yuan
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Publication number: 20230002822Abstract: An example of a flow cell includes a substrate; a first primer set attached to a first region on the substrate, the first primer set including an un-cleavable first primer and a cleavable second primer; and a second primer set attached to a second region on the substrate, the second primer set including a cleavable first primer and an un-cleavable second primer.Type: ApplicationFiled: June 14, 2022Publication date: January 5, 2023Inventors: Jeffrey S. Fisher, Brian D. Mather, Maria Candelaria Rogert Bacigalupo, Justin Fullerton, Ludovic Vincent, Lewis J. Kraft, Sahngki Hong, Boyan Boyanov, M. Shane Bowen, Sang Park, Wayne N. George, Andrew A. Brown
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Publication number: 20220410146Abstract: 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: August 29, 2022Publication date: December 29, 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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Patent number: 11512339Abstract: An example of an array includes a support, a cross-linked epoxy polyhedral oligomeric silsesquioxane (POSS) resin film on a surface of the support, and a patterned hydrophobic polymer layer on the cross-linked epoxy POSS resin film. The patterned hydrophobic polymer layer defines exposed discrete areas of the cross-linked epoxy POSS resin film, and a polymer coating is attached to the exposed discrete areas. Another example of an array includes a support, a modified epoxy POSS resin film on a surface of the support, and a patterned hydrophobic polymer layer on the modified epoxy POSS resin film. The modified epoxy POSS resin film includes a polymer growth initiation site, and the patterned hydrophobic polymer layer defines exposed discrete areas of the modified epoxy POSS resin film. A polymer brush is attached to the polymer growth initiation site in the exposed discrete areas.Type: GrantFiled: December 20, 2017Date of Patent: November 29, 2022Assignees: Illumina, Inc., Illumina Cambridge LimitedInventors: Wayne N. George, Alexandre Richez, M. Shane Bowen, Andrew A. Brown, Dajun Yuan, Audrey Rose Zak, Sean M. Ramirez, Raymond Campos
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Publication number: 20220341837Abstract: Flow cells and corresponding methods are provided. The flow cells may include a support frame with top and back sides, and at least one cavity extending from the top side. The flow cells may include at least one light detection device with an active area disposed within the at least one cavity. The flow cells may include a support material disposed within the at least one cavity between the support frame and the periphery of the at least one light detection device coupling them together. The flow cells may include a lid extending over the at least one light detection device and coupled to the support frame about the periphery of the at least one light detection device. The lid and at least a top surface of the at least one light detection device form a flow channel therebetween.Type: ApplicationFiled: July 11, 2022Publication date: October 27, 2022Applicant: Illumina, Inc.Inventors: Arnaud RIVAL, Ali AGAH, Tracy H. FUNG, Dietrich DEHLINGER, Poorya SABOUNCHI, Tarun KHURANA, Craig M. CIESLA, M. Shane BOWEN
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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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Patent number: 11466268Abstract: A structured substrate includes a substrate body having an active side. The substrate body includes reaction cavities that open along the active side and interstitial regions that separate the reaction cavities. The structured substrate includes an ensemble amplifier positioned within each of the reaction cavities. The ensemble amplifier includes a plurality of nanostructures configured to at least one of amplify electromagnetic energy that propagates into the corresponding reaction cavity or amplify electromagnetic energy that is generated within the corresponding reaction cavity.Type: GrantFiled: December 21, 2020Date of Patent: October 11, 2022Assignee: ILLUMINA, INC.Inventors: M. Shane Bowen, Dajun Yuan
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Patent number: 11442017Abstract: An inspection apparatus is provided that comprises an optical target including a solid host material and a fluorescing material embedded in the solid host material. The solid host material has a predetermined phonon energy HOSTPE. The fluorescing material exhibits a select ground energy level and a target excitation (TE) energy level separated from the ground energy level by a first energy gap corresponding to a fluorescence emission wavelength of interest. The fluorescing material has a next lower lying (NLL) energy level relative to the TE energy level. The NLL energy level is spaced a second energy gap FMEG2 below the TE energy level, wherein a ratio of the FMEG2/HOSTPE is three or more.Type: GrantFiled: November 4, 2020Date of Patent: September 13, 2022Assignee: ILLUMINA, INC.Inventors: John Gerhardt Earney, Joseph Francis Pinto, M. Shane Bowen, Michael S. Graige, Arthur Pitera, Bala Murali K. Venkatesan, 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: 20220276169Abstract: A system includes: an objective lens; a first light source to feed first illuminating light through the objective lens and into a flowcell (e.g., with a relatively thin film waveguide) to be installed in the system, the first illuminating light to be fed using a first grating on the flowcell; and a first image sensor to capture imaging light using the objective lens, wherein the first grating is positioned outside a field of view of the first image sensor. Dual-surface imaging can be performed. Flowcells with multiple swaths bounded by gratings can be used. An auto-alignment process can be performed.Type: ApplicationFiled: May 16, 2022Publication date: September 1, 2022Inventors: Yinghua Sun, Stanley S. Hong, Frederick Erie, Alex Nemiroski, M. Shane Bowen, Danilo Condello, Dietrich Dehlinger, Marco A. Krumbuegel, Anthony Lam, Aaron Liu, Bojan Obradovic, Mark Pratt
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Patent number: 11427868Abstract: Fiducial markers are provided on patterned arrays of the type that may be used for molecular analysis, such as sequencing. The fiducials may have configurations that enhance their detection in image or detection data, that facilitate or improve processing, that provide encoding of useful information, and so forth. Examples of the fiducials may include a non-closed shape that may encode information, allow for bubbles to escape during manufacture, and provide additional advantages over closed shape fiducials.Type: GrantFiled: January 31, 2018Date of Patent: August 30, 2022Assignee: Illumina, Inc.Inventors: John S. Vieceli, Alex Nemiroski, Paul Belitz, Robert Langlois, M. Shane Bowen, Danny Yuan Chan, Bala Murali K. Venkatesan, Hui Han, Kevan Samiee, Stephen Tanner
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Publication number: 20220250066Abstract: An interposer for a flow cell comprises a base layer having a first surface and a second surface opposite the first surface. The base layer comprises black polyethylene terephthalate (PET). A first adhesive layer is disposed on the first surface of the base layer. The first adhesive layer comprises methyl acrylic adhesive. A second adhesive layer is disposed on the second surface of the base layer. The second adhesive layer comprises methyl acrylic adhesive. A plurality of microfluidic channels extends through each of the base layer, the first adhesive layer, and the second adhesive layer.Type: ApplicationFiled: April 22, 2022Publication date: August 11, 2022Applicant: ILLUMINA, Inc.Inventors: Maxwell Zimmerley, LiangLiang Qiang, M. Shane Bowen, Steven H. Modiano, Dajun Yuan, Randall Smith, Arthur J. Pitera, Hai Quang Tran, Gerald Kreindl
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Publication number: 20220243261Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.Type: ApplicationFiled: January 13, 2022Publication date: August 4, 2022Applicant: Illumina, Inc.Inventors: Min-Jui Richard Shen, Jonathan Mark Boutell, Kathryn M. Stephens, Mostafa Ronaghi, Kevin L. Gunderson, Bala Murali Venkatesan, M. Shane Bowen, Kandaswamy Vijayan
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Patent number: 11384392Abstract: An example of a flow cell includes a substrate; a first primer set attached to a first region on the substrate, the first primer set including an un-cleavable first primer and a cleavable second primer; and a second primer set attached to a second region on the substrate, the second primer set including a cleavable first primer and an un-cleavable second primer.Type: GrantFiled: December 31, 2020Date of Patent: July 12, 2022Assignees: Illumina, Inc., Illumina Cambridge LimitedInventors: Jeffrey S. Fisher, Brian D. Mather, Maria Candelaria Rogert Bacigalupo, Justin Fullerton, Ludovic Vincent, Lewis J. Kraft, Sahngki Hong, Boyan Boyanov, M. Shane Bowen, Sang Park, Wayne N. George, Andrew A. Brown
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Patent number: 11385162Abstract: Flow cells and corresponding methods are provided. The flow cells may include a support frame with top and back sides, and at least one cavity extending from the top side. The flow cells may include at least one light detection device with an active area disposed within the at least one cavity. The flow cells may include a support material disposed within the at least one cavity between the support frame and the periphery of the at least one light detection device coupling them together. The flow cells may include a lid extending over the at least one light detection device and coupled to the support frame about the periphery of the at least one light detection device. The lid and at least a top surface of the at least one light detection device form a flow channel therebetween.Type: GrantFiled: January 13, 2021Date of Patent: July 12, 2022Assignee: ILLUMINA, INC.Inventors: Arnaud Rival, Ali Agah, Tracy H. Fung, Dietrich Dehlinger, Poorya Sabounchi, Tarun Khurana, Craig M. Ciesla, M. Shane Bowen
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Patent number: 11360027Abstract: A system includes: an objective lens; a first light source to feed first illuminating light through the objective lens and into a flowcell (e.g., with a relatively thin film waveguide) to be installed in the system, the first illuminating light to be fed using a first grating on the flowcell; and a first image sensor to capture imaging light using the objective lens, wherein the first grating is positioned outside a field of view of the first image sensor. Dual-surface imaging can be performed. Flowcells with multiple swaths bounded by gratings can be used. An auto-alignment process can be performed.Type: GrantFiled: March 12, 2019Date of Patent: June 14, 2022Assignee: Illumina, Inc.Inventors: Yinghua Sun, Stanley S. Hong, Frederick Erie, Alex Nemiroski, M. Shane Bowen, Danilo Condello, Dietrich Dehlinger, Marco A. Krumbuegel, Anthony Lam, Aaron Liu, Bojan Obradovic, Mark Pratt
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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