Patents Assigned to ELEMENT BIOSCIENCES, INC.
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Patent number: 11915444Abstract: Methods and systems for image analysis are provided, and in particular for identifying a set of base-calling locations in a flow cell for DNA sequencing. These include capturing flow cell images after each sequencing step performed on the flow cell, and identifying candidate cluster centers in at least one of the flow cell images. Intensities are determined for each candidate cluster center in a set of flow cell images. Purities are determined for each candidate cluster center based on the intensities. Each candidate cluster center with a purity greater than the purity of the surrounding candidate cluster centers within a distance threshold is added to a template set of base-calling locations.Type: GrantFiled: June 30, 2022Date of Patent: February 27, 2024Assignee: Element Biosciences, Inc.Inventors: Chunhong Zhou, Semyon Kruglyak, Francisco Garcia, Minghao Guo, Haosen Wang, Ryan Kelly
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Patent number: 11891651Abstract: The present disclosure provides compositions and methods that employ the compositions for conducting pairwise sequencing and for generating concatemer template molecules for pairwise sequencing. The concatemers can be generated using a rolling circle amplification reaction which is conducted either on-support, or conducted in-solution and then distributed onto a support. The rolling circle amplification reaction generates concatemers containing tandem copies of a sequence of interest and at least one universal adaptor sequence. An increase in the number of tandem copies in a given concatemer increases the number of sites along the concatemer for hybridizing to multiple sequencing primers which serve as multiple initiation sites for polymerase-catalyzed sequencing reactions. When the sequencing reaction employs detectably labeled nucleotides and/or detectably labeled multivalent molecules (e.g.Type: GrantFiled: November 8, 2021Date of Patent: February 6, 2024Assignee: Element Biosciences, Inc.Inventors: Sinan Arslan, Junhua Zhao, Molly He, Samantha Snow, William Light, Matthew Kellinger, Michael Previte, Michael Kim, Hua Yu, Yu-Hsien Hwang-Fu, Marco Tjioe, Andrew Boddicker
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Patent number: 11859241Abstract: The present disclosure provides compositions and methods that employ the compositions for conducting pairwise sequencing and for generating concatemer template molecules for pairwise sequencing. The concatemers can be generated using a rolling circle amplification reaction which is conducted either on-support, or conducted in-solution and then distributed onto a support. The rolling circle amplification reaction generates concatemers containing tandem copies of a sequence of interest and at least one universal adaptor sequence. An increase in the number of tandem copies in a given concatemer increases the number of sites along the concatemer for hybridizing to multiple sequencing primers which serve as multiple initiation sites for polymerase-catalyzed sequencing reactions. When the sequencing reaction employs detectably labeled nucleotides and/or detectably labeled multivalent molecules (e.g.Type: GrantFiled: February 8, 2023Date of Patent: January 2, 2024Assignee: Element Biosciences, Inc.Inventors: Sinan Arslan, Junhua Zhao, Molly He, Samantha Snow, William Light, Matthew Kellinger, Michael Previte, Michael Kim, Hua Yu, Yu-Hsien Hwang-Fu, Marco Tjioe, Andrew Boddicker, Mark Ambroso, Tyler Lopez, Michael Klein, Virginia Saade
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Patent number: 11795504Abstract: Fluorescence imaging system designs are described that provide larger fields-of-view, increased spatial resolution, improved modulation transfer and image quality, higher spatial sampling frequency, faster transitions between image capture when repositioning the sample plane to capture a series of images (e.g., of different fields-of-view), and improved imaging system duty cycle, and thus enable higher throughput image acquisition and analysis for genomics and other imaging applications.Type: GrantFiled: January 12, 2022Date of Patent: October 24, 2023Assignee: ELEMENT BIOSCIENCES, INC.Inventors: Steve Xiangling Chen, Minghao Guo, Michael Previte, Chunhong Zhou, Derek Fuller
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Patent number: 11788075Abstract: Provided herein are engineered variants of archaeal polymerases that exhibit exonuclease-minus activity, enhanced thermostability, enhanced incorporation of 3? modified nucleotides, improved uracil-tolerance and/or reduce sequence-specific errors in polymerase-catalyzed nucleotide binding and extension reactions relative to wild type polymerase enzymes. Also provided are uses of the engineered polymerases for forming complexed polymerases and forming binding complexes, and uses for conducting nucleic acid sequencing reactions.Type: GrantFiled: January 27, 2023Date of Patent: October 17, 2023Assignee: ELEMENT BIOSCIENCES, INC.Inventors: Jendrik Hentschel, Tyler Lopez, Michael Klein, Virginia Saade, Matthew Kellinger, Mark Ambroso
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Publication number: 20230326064Abstract: Image data analysis, particularly identifying cluster locations for performing base-calling in a digital flow cell image during DNA sequencing, is described. Each nucleic acid template molecule immobilized on a support may include an insert sequence and a sample index sequence. The sample index sequence may include a k-mer sequence. A sequencing system may conduct k cycles of sequencing reactions of the k-mer sequence before conducting one or more cycles of the insert sequence sequencing reactions and generate a first plurality of flow cell images. Pixel intensities may be determined for pixels of the first plurality of flow cell images. A base calling template may be determined and include base calling locations based on the pixel intensities and respective color purities of the pixel intensities. The base calling template may register a second plurality of flow cell images of the support in one or more cycles subsequent to the k cycles.Type: ApplicationFiled: December 9, 2022Publication date: October 12, 2023Applicant: Element Biosciences, Inc.Inventors: Chunhong ZHOU, Semyon KRUGLYAK, Francisco GARCIA, Minghao GUO, Haosen WANG, Ryan KELLY
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Patent number: 11781185Abstract: Provided herein are fluorescently-labeled nucleotide conjugates for nucleic acid analysis. Also provided are reagents used for forming binding complexes between a fluorescently-labeled nucleotide conjugate and a target nucleic acid sequence in the presence of one or more reagents disclosed herein. Binding complexes can be detected in the presence of the one or more reagents. For example, the one or more reagents may contain a photobleaching reducing agent configured to reduce photobleaching resulting from use of the fluorescently-labeled nucleotide conjugate to form the binding complex in a nucleic acid analysis. Such nucleic acid analysis may be used to identify sites of nucleobase binding or incorporation between the target nucleic acid sequence and one or more nucleotide moieties of the fluorescently-labeled nucleotide conjugate in a nucleic acid sequence reaction.Type: GrantFiled: September 19, 2022Date of Patent: October 10, 2023Assignee: ELEMENT BIOSCIENCES, INC.Inventors: Sinan Arslan, Molly He, Michael Previte, Ramreddy Tippana, Hua Yu, William Light, Junhua Zhao
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Patent number: 11535892Abstract: The present disclosure provides compositions and methods that employ the compositions for conducting pairwise sequencing and for generating concatemer template molecules for pairwise sequencing. The concatemers can be generated using a rolling circle amplification reaction which is conducted either on-support, or conducted in-solution and then distributed onto a support. The rolling circle amplification reaction generates concatemers containing tandem copies of a sequence of interest and at least one universal adaptor sequence. An increase in the number of tandem copies in a given concatemer increases the number of sites along the concatemer for hybridizing to multiple sequencing primers which serve as multiple initiation sites for polymerase-catalyzed sequencing reactions. When the sequencing reaction employs detectably labeled nucleotides and/or detectably labeled multivalent molecules (e.g.Type: GrantFiled: July 15, 2021Date of Patent: December 27, 2022Assignee: Element Biosciences, Inc.Inventors: Sinan Arslan, Junhua Zhao, Molly He, Samantha Snow, William Light, Matthew Kellinger, Michael Previte, Michael Kim, Hua Yu, Yu-Hsien Hwang-Fu, Marco Tjioe, Andrew Boddicker
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Patent number: 11459608Abstract: Fluorescence imaging system designs are described that provide larger fields-of-view, increased spatial resolution, improved modulation transfer and image quality, higher spatial sampling frequency, faster transitions between image capture when repositioning the sample plane to capture a series of images (e.g., of different fields-of-view), and improved imaging system duty cycle, and thus enable higher throughput image acquisition and analysis for genomics and other imaging applications.Type: GrantFiled: July 9, 2021Date of Patent: October 4, 2022Assignee: ELEMENT BIOSCIENCES, INC.Inventors: Steve Xiangling Chen, Minghao Guo, Michael Previte, Chunhong Zhou, Derek Fuller
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Patent number: 11426732Abstract: Flow cell devices, cartridges, and systems are described that provide reduced manufacturing complexity, lowered consumable costs, and flexible system throughput for nucleic acid sequencing and other chemical or biological analysis applications. The flow cell device can include a capillary flow cell device or a microfluidic flow cell device.Type: GrantFiled: October 28, 2020Date of Patent: August 30, 2022Assignee: ELEMENT BIOSCIENCES, INC.Inventors: Minghao Guo, Leon Zilun Zhang, Chunhong Zhou, Matthew Kellinger, Michael Previte
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Patent number: 11427855Abstract: The present disclosure provides compositions and methods that employ the compositions for conducting pairwise sequencing and for generating concatemer template molecules for pairwise sequencing. The concatemers can be generated using a rolling circle amplification reaction which is conducted either on-support, or conducted in-solution and then distributed onto a support. The rolling circle amplification reaction generates concatemers containing tandem copies of a sequence of interest and at least one universal adaptor sequence. An increase in the number of tandem copies in a given concatemer increases the number of sites along the concatemer for hybridizing to multiple sequencing primers which serve as multiple initiation sites for polymerase-catalyzed sequencing reactions. When the sequencing reaction employs detectably labeled nucleotides and/or detectably labeled multivalent molecules (e.g.Type: GrantFiled: July 15, 2021Date of Patent: August 30, 2022Assignee: Element Biosciences, Inc.Inventors: Sinan Arslan, Junhua Zhao, Molly He, Samantha Snow, William Light, Matthew Kellinger, Michael Previte, Michael Kim, Hua Yu, Yu-Hsien Hwang-Fu, Marco Tjioe, Andrew Boddicker
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Patent number: 11408032Abstract: Imaging systems and methods comprising imaging a first interior surface and a second interior surface of a flow cell are described. In some embodiments, the imaging systems may comprise: a) an objective lens; b) at least one image sensor; and c) at least one tube lens disposed in an optical path between the objective lens and the at least one image sensor; wherein the at least one tube lens is configured to correct imaging performance such that images of the first interior surface of the flow cell and the second interior surface of the flow cell have substantially the same optical resolution.Type: GrantFiled: September 9, 2020Date of Patent: August 9, 2022Assignee: ELEMENT BIOSCIENCES, INC.Inventors: Steve Xiangling Chen, Minghao Guo, Michael Previte, Chunhong Zhou, Derek Fuller
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Patent number: 11397870Abstract: Methods and systems for image analysis are provided, and in particular for identifying a set of base-calling locations in a flow cell for DNA sequencing. These include capturing flow cell images after each sequencing step performed on the flow cell, and identifying candidate cluster centers in at least one of the flow cell images. Intensities are determined for each candidate cluster center in a set of flow cell images. Purities are determined for each candidate cluster center based on the intensities. Each candidate cluster center with a purity greater than the purity of the surrounding candidate cluster centers within a distance threshold is added to a template set of base-calling locations.Type: GrantFiled: December 10, 2021Date of Patent: July 26, 2022Assignee: Element Biosciences, Inc.Inventors: Chunhong Zhou, Semyon Kruglyak, Francisco Garcia, Minghao Guo, Haosen Wang, Ryan Kelly
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Patent number: 11365444Abstract: Fluorescence imaging system designs are described that provide larger fields-of-view, increased spatial resolution, improved modulation transfer and image quality, higher spatial sampling frequency, faster transitions between image capture when repositioning the sample plane to capture a series of images (e.g., of different fields-of-view), and improved imaging system duty cycle, and thus enable higher throughput image acquisition and analysis for genomics and other imaging applications.Type: GrantFiled: July 9, 2021Date of Patent: June 21, 2022Assignee: ELEMENT BIOSCIENCES, INC.Inventors: Steve Xiangling Chen, Minghao Guo, Michael Previte, Chunhong Zhou, Derek Fuller
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Patent number: 11339433Abstract: Methods and systems for sequencing a nucleic acid molecule are described that comprise imaging a first surface and an axially-displaced second surface using a compensation-free optical system, the system comprising an objective lens and at least one image sensor, wherein said optical system has a numerical aperture (NA) of less than 0.6 and a field-of-view (FOV) of greater than 1.0 mm2; and) processing the images of the first surface and the axially-displaced second surface to correct for optical aberration such that the images of the first surface and the axially-displaced second surface have substantially the same optical resolution.Type: GrantFiled: October 7, 2021Date of Patent: May 24, 2022Assignee: ELEMENT BIOSCIENCES, INC.Inventors: Steve Xiangling Chen, Minghao Guo, Michael Previte, Chunhong Zhou, Derek Fuller
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Patent number: 11287422Abstract: Multivalent binding compositions including a particle-nucleotide conjugate having a plurality of copies of a nucleotide attached to the particle are described. The multivalent binding compositions allow one to localize detectable signals to active regions of biochemical interaction, e.g., sites of protein-protein interaction, protein-nucleic acid interaction, nucleic acid hybridization, or enzymatic reaction, and can be used to identify sites of base incorporation in elongating nucleic acid chains during polymerase reactions and to provide improved base discrimination for sequencing and array based applications.Type: GrantFiled: June 24, 2021Date of Patent: March 29, 2022Assignee: ELEMENT BIOSCIENCES, INC.Inventors: Michael Previte, Molly Min He, Junhua Zhao, Hui Zhen Mah, Chunhong Zhou, Sinan Arslan, Matthew Kellinger, Lorenzo Berti, Steve Xiangling Chen
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Patent number: 11261489Abstract: Fluorescence imaging system designs are described that provide larger fields-of-view, increased spatial resolution, improved modulation transfer and image quality, higher spatial sampling frequency, faster transitions between image capture when repositioning the sample plane to capture a series of images (e.g., of different fields-of-view), and improved imaging system duty cycle, and thus enable higher throughput image acquisition and analysis for genomics and other imaging applications.Type: GrantFiled: July 9, 2021Date of Patent: March 1, 2022Assignee: ELEMENT BIOSCIENCES, INC.Inventors: Steve Xiangling Chen, Minghao Guo, Michael Previte, Chunhong Zhou, Derek Fuller
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Patent number: 11236388Abstract: The present disclosure provides compositions and methods that employ the compositions for conducting pairwise sequencing and for generating concatemer template molecules for pairwise sequencing. The concatemers can be generated using a rolling circle amplification reaction which is conducted either on-support, or conducted in-solution and then distributed onto a support. The rolling circle amplification reaction generates concatemers containing tandem copies of a sequence of interest and at least one universal adaptor sequence. An increase in the number of tandem copies in a given concatemer increases the number of sites along the concatemer for hybridizing to multiple sequencing primers which serve as multiple initiation sites for polymerase-catalyzed sequencing reactions. When the sequencing reaction employs detectably labeled nucleotides and/or detectably labeled multivalent molecules (e.g.Type: GrantFiled: July 15, 2021Date of Patent: February 1, 2022Assignee: Element Biosciences, Inc.Inventors: Sinan Arslan, Junhua Zhao, Molly He, Samantha Snow, William Light, Matthew Kellinger, Michael Previte
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Patent number: 11220707Abstract: The present disclosure provides compositions and methods that employ the compositions for conducting pairwise sequencing and for generating concatemer template molecules for pairwise sequencing. The concatemers can be generated using a rolling circle amplification reaction which is conducted either on-support, or conducted in-solution and then distributed onto a support. The rolling circle amplification reaction generates concatemers containing tandem copies of a sequence of interest and at least one universal adaptor sequence. An increase in the number of tandem copies in a given concatemer increases the number of sites along the concatemer for hybridizing to multiple sequencing primers which serve as multiple initiation sites for polymerase-catalyzed sequencing reactions. When the sequencing reaction employs detectably labeled nucleotides and/or detectably labeled multivalent molecules (e.g.Type: GrantFiled: July 15, 2021Date of Patent: January 11, 2022Assignee: Element Biosciences, Inc.Inventors: Sinan Arslan, Junhua Zhao, Molly He, Samantha Snow, William Light, Matthew Kellinger, Michael Previte
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Patent number: 11198121Abstract: Flow cell devices, cartridges, and systems are described that provide reduced manufacturing complexity, lowered consumable costs, and flexible system throughput for nucleic acid sequencing and other chemical or biological analysis applications. The flow cell device can include a capillary flow cell device or a microfluidic flow cell device.Type: GrantFiled: March 30, 2021Date of Patent: December 14, 2021Assignee: ELEMENT BIOSCIENCES, INC.Inventors: Minghao Guo, Leon Zilun Zhang, Chunhong Zhou, Matthew Kellinger, Michael Previte, Sinan Arslan, Molly He, Hui Zhen Mah, Lei Sun