Patents Assigned to Illumina Cambridge Limited
  • Patent number: 11884976
    Abstract: An example of a resin composition includes a free radical curable resin matrix including an acrylate and a siloxane, and a free radical photoinitiator. When cured, the resin composition has low or no autofluorescence when exposed to blue excitation wavelengths ranging from about 380 nm to about 480 nm or green excitation wavelengths ranging from about 510 nm to about 560 nm.
    Type: Grant
    Filed: July 18, 2019
    Date of Patent: January 30, 2024
    Assignees: Illumina, Inc., Illumina Cambridge Limited
    Inventors: Timothy J. Merkel, Wayne N. George, Andrew A. Brown, Audrey Zak, Gianluca Andrea Artioli, Julia Morrison, Nikolai Romanov, Lorenzo Berti, Graham Boud
  • Patent number: 11884825
    Abstract: The present application relates to exocyclic amine-substituted coumarin derivatives and their uses as fluorescent labels. These compounds may be used as fluorescent labels for nucleotides in nucleic acid sequencing applications.
    Type: Grant
    Filed: July 1, 2022
    Date of Patent: January 30, 2024
    Assignee: Illumina Cambridge Limited
    Inventors: Nikolai Nikolaevich Romanov, Carole Anastasi, Patrick McCauley
  • Publication number: 20240026348
    Abstract: Materials and methods for preparing nucleic acid libraries for next-generation sequencing are described herein. A variety of approaches are described relating to the use of unique molecular identifiers with transposon-based technology in the preparation of sequencing libraries. Also described herein are sequencing materials and methods for identifying and correcting amplification and sequencing errors.
    Type: Application
    Filed: September 28, 2023
    Publication date: January 25, 2024
    Applicants: Illumina, Inc., Illumina Cambridge Limited
    Inventors: Susan C. Verity, Robert Scott Kuersten, Niall Anthony Gormley, Andrew B. Kennedy, Sarah E. Shultzaberger, Andrew Slatter, Emma Bell, Sebastien Georg Gabriel Ricoult, Grace DeSantis, Fiona Kaper, Han-Yu Chuang, Oliver Jon Miller, Jason Richard Betley, Stephen M. Gross, Mats Ekstrand
  • Patent number: 11873480
    Abstract: Embodiments provided herein relate to methods and compositions for preparing an immobilized library of barcoded DNA fragments of a target nucleic acid, identifying genomic variants, determining the contiguity information, phasing information, and methylation status of the target nucleic acid.
    Type: Grant
    Filed: October 16, 2015
    Date of Patent: January 16, 2024
    Assignee: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Frank J. Steemers, Kevin L. Gunderson, Fan Zhang, Jason Richard Betley, Niall Anthony Gormley, Wouter Meuleman, Jacqueline Weir, Avgousta Ioannou, Gareth Jenkins, Rosamond Jackson, Natalie Morrell, Dmitry K. Pokholok, Steven J. Norberg, Molly He, Amirali Kia, Igor Goryshin, Rigo Pantoja
  • Publication number: 20240011014
    Abstract: A method may be implemented for in-tip flow-through magnetic bead processing. A biological solution may include a plurality of magnetic beads suspended therein. The biological solution may be introduced to a tube via an opening in a tip portion of the tube. The tip portion of the tube may include a magnetizable material arranged in a flow path of the biological solution. The magnetizable material may include a ferromagnetic matrix or a wire within the tip portion. A magnetic field may be applied proximate to the tip portion of the tube using an electromagnetic coil. The electromagnetic coil may be wound around the tip portion. The biological solution may be removed from the tube, for example, via the opening in the tip portion. The plurality of magnetic beads may be captured within the magnetizable material in the tip portion using the magnetic field.
    Type: Application
    Filed: June 30, 2023
    Publication date: January 11, 2024
    Applicants: Illumina, Inc., Illumina Cambridge Limited
    Inventors: Gianluca Artioli, Brian Mather, Dave Jones
  • Patent number: 11866780
    Abstract: The present invention relates to the field of molecular biology, and more specifically to methods for reducing the complexity of a nucleic acid sample.
    Type: Grant
    Filed: June 29, 2017
    Date of Patent: January 9, 2024
    Assignee: Illumina Cambridge Limited
    Inventor: Jonathan Mark Boutell
  • Patent number: 11858923
    Abstract: The present application relates to secondary amine-substituted coumarin compounds and their uses as fluorescent labels. The compounds may be used as fluorescent labels for nucleotides in nucleic acid sequencing applications.
    Type: Grant
    Filed: July 1, 2022
    Date of Patent: January 2, 2024
    Assignee: Illumina Cambridge Limited
    Inventors: Nikolai Nikolaevich Romanov, Patrick McCauley, Carole Anastasi, Xiaolin Wu, Niall Hynes
  • Publication number: 20230420074
    Abstract: Systems, methods, and apparatus are described herein for identifying callable regions and performing variant calling while operating within allocated memory. A sequencing subsystem may comprise a variant caller or variant caller subsystem. The variant caller may include a calling subsystem configured to identify callable regions and may send the callable regions to a downstream genotyping subsystem of the variant caller. The calling subsystem of the variant caller may be configured to detect a callable region of the sequencing data when a depth of the plurality of reads is above a callable region depth threshold. The calling subsystem of the variant caller may monitor memory used by the callable region and, when the memory used exceeds a memory threshold of a total amount of memory allocated, the calling subsystem may split or spill at least a portion of the callable region to operate within the total amount of allocated memory.
    Type: Application
    Filed: June 23, 2023
    Publication date: December 28, 2023
    Applicants: ILLUMINA SOFTWARE, INC., Illumina Cambridge Limited
    Inventors: Adam Michael Birnbaum, Fabian Jobst Klötzl, Arun Visvanath
  • Publication number: 20230407388
    Abstract: Described herein is a polynucleotide for use as a sequencing template comprising multiple inserts. Also described herein are method of generating and using these polynucleotides and methods of use of such templates, including analysis of contiguity information. Further, sequencing templates comprising an insert sequence and a copy of the insert sequence can be used to correct for random errors generated during sequencing or amplification or to identify nucleobase damage or other mutation that leads to non-canonical base pairing in a double-stranded nucleic acid. Methods of performing methylation analysis are also described herein.
    Type: Application
    Filed: April 20, 2023
    Publication date: December 21, 2023
    Applicants: Illumina, Inc., Illumina Cambridge Limited
    Inventors: Tarun Khurana, Yir-Shyuan Wu, Niall Anthony Gormley, Jonathan Mark Boutell
  • Patent number: 11846580
    Abstract: A flow cell package includes first and second surface-modified patterned wafers and a spacer layer. The first surface-modified patterned wafer includes first depressions separated by first interstitial regions, a first functionalized molecule bound to a first silane or silane derivative in at least some of the first depressions, and a first primer grafted to the first functionalized molecule in the at least some of the first depressions. The second surface-modified patterned wafer includes second depressions separated by second interstitial regions, a second functionalized molecule bound to a second silane or silane derivative in at least some of the second depressions, and a second primer grafted to the second functionalized molecule in the at least some of the second depressions. The spacer layer bonds at least some first interstitial regions to at least some second interstitial regions, and at least partially defines respective fluidic chambers of the flow cell package.
    Type: Grant
    Filed: March 3, 2021
    Date of Patent: December 19, 2023
    Assignees: Illumina, Inc., Illumina Cambridge Limited
    Inventors: James Tsay, Anmiv Prabhu, David Heiner, Edwin Li, Alexandre Richez, John M. Beierle, Kevan Samiee, Kristina Munoz, Leonid Malevanchik, Ludovic Vincent, Naiqian Zhan, Peyton Shieh, Robert Yang, Samantha Schmitt, Sang Park, Scott Bailey, Sean M. Ramirez, Sunmin Ahn, Valerie Uzzell, Wei Wei, Yuxiang Huang, Tyler Jamison Dill
  • Publication number: 20230391961
    Abstract: Methods of inserting a nanopore into a polymeric membrane are provided herein. The membrane may be destabilized using a chaotropic solvent. The nanopore may be inserted into the destabilized polymer membrane. The chaotropic solvent may be removed to stabilize the polymer membrane with the nanopore inserted therein.
    Type: Application
    Filed: March 30, 2023
    Publication date: December 7, 2023
    Applicant: Illumina Cambridge Limited
    Inventors: Istvan Kocsis, Charlotte Vacogne, Oliver Uttley, Antonio Conde-Gonzalez, Alexandre Richez
  • Publication number: 20230392142
    Abstract: The present disclosure relates to methods, compositions, and kits for treating target nucleic acids, including methods and compositions for fragmenting and tagging nucleic acid (e.g., DNA) using transposome complexes bound to a solid support.
    Type: Application
    Filed: June 1, 2023
    Publication date: December 7, 2023
    Applicants: Illumina, Inc., Illumina Cambridge Limited
    Inventors: Grace Desantis, Stephen M. Gross, Jian-Sen Li, Natalie Morrell, Andrew Slatter, Kevin Shen, Samantha Snow
  • Patent number: 11834699
    Abstract: Provided herein is a method of using transposition to improve methods of sequencing RNA molecules. Provided herein is a method of tagging nucleic acid duplexes, such as DNA:RNA duplexes or DNA:DNA duplexes. The method includes the steps of providing a transposase and a transposon composition, providing one or more nucleic acid duplexes immobilized on a support, and contacting the transposase and transposon composition with the one or more nucleic acid duplexes under conditions wherein the one or more nucleic acid duplexes and transposon composition undergo a transposition reaction to produce one or more tagged nucleic acid duplexes, wherein the transposon composition comprises a double stranded nucleic acid molecule comprising a transferred strand and a non-transferred strand.
    Type: Grant
    Filed: April 1, 2019
    Date of Patent: December 5, 2023
    Assignee: Illumina Cambridge Limited
    Inventors: Niall Anthony Gormley, Louise Fraser, Paula Kokko-Gonzales
  • Publication number: 20230381718
    Abstract: Barriers including molecules covalently bonded to amphiphilic molecules, and methods of making the same, are provided herein. In some examples, a barrier between first and second fluids includes one or more layers comprising a plurality of amphiphilic molecules; and a first layer comprising a plurality of molecules covalently bonded to amphiphilic molecules of the plurality of amphiphilic molecules.
    Type: Application
    Filed: March 30, 2023
    Publication date: November 30, 2023
    Applicant: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Antonio Conde-Gonzalez, Alexandre Richez, Davide Garoldini, Oliver Uttley, Charlotte Vacogne
  • Publication number: 20230383284
    Abstract: Provided is a method, including stretching a polynucleotide over a substrate including a plurality of equally spaced cleavage regions including a plurality of transposases, cleaving the polynucleotide with two or more of the plurality of transposases to form a plurality of polynucleotide fragments, and separating, within the plurality of polynucleotide fragments, a population of longer polynucleotide fragments from a population of shorter polynucleotide fragments. Also provided is a method including stretching a polynucleotide over a substrate including a plurality of equally spaced cleavage regions including a plurality of transposases, cleaving the polynucleotide with two or more of the plurality of transposases to form a plurality of polynucleotide fragments, and separating, within the plurality of polynucleotide fragments, a population of longer polynucleotide fragments from a population of shorter polynucleotide fragments.
    Type: Application
    Filed: August 10, 2023
    Publication date: November 30, 2023
    Applicants: ILLUMINA, INC., ILLUMINA CAMBRIDGE LIMITED
    Inventors: Maria Candelaria Rogert BACIGALUPO, Frank STEEMERS, Jeffrey FISHER, Andrew SLATTER, Lewis KRAFT, Niall GORMLEY, M. Shane BOWEN
  • Patent number: 11827931
    Abstract: Embodiments of the present disclosure relate to methods of preparing growing polynucleotides using nucleotide molecules with a 3? AOM blocking group. Also provided herein are kits related to such methods.
    Type: Grant
    Filed: March 30, 2022
    Date of Patent: November 28, 2023
    Assignee: Illumina Cambridge Limited
    Inventors: Antoine Francais, Elena Cressina, Adam Culley, Angelica Mariani, Xiaolin Wu, Xiaohai Liu
  • Patent number: 11827927
    Abstract: The invention relates to a method of preparing and using a library of template polynucleotides suitable for use as templates in solid-phase nucleic acid amplification and sequencing reactions to determine the methylation status of the cytosine bases in the library. In particular, the invention relates to a method of preparing and analysing a library of template polynucleotides suitable for methylation analysis.
    Type: Grant
    Filed: February 17, 2021
    Date of Patent: November 28, 2023
    Assignees: ILLUMINA CAMBRIDGE LIMITED, MASSACHUSETTS INSTITUTE OF TECHNOLOGY
    Inventors: Niall Gormley, Andreas Gnirke, David Jaffe, Harris Nusbaum
  • Publication number: 20230357731
    Abstract: Presented herein are altered polymerase enzymes for improved incorporation of nucleotides and nucleotide analogues, in particular altered polymerases that maintain high fidelity under reduced incorporation times, as well as methods and kits using the same.
    Type: Application
    Filed: March 13, 2023
    Publication date: November 9, 2023
    Applicants: ILLUMINA, INC., ILLUMINA CAMBRIDGE LIMITED, ILLUMINA SINGAPORE PTE. LTD.
    Inventors: Kay Klausing, Hamed Tabatabaei Ghomi, Misha Golynskiy, Saurabh Nirantar, Seth McDonald, Sergio Peisajovich
  • Publication number: 20230348973
    Abstract: The present disclosure is generally directed to strategies for template capture and amplification during sequencing. In some examples, a solid support is used for template capture and amplification.
    Type: Application
    Filed: March 30, 2023
    Publication date: November 2, 2023
    Applicant: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Xiaoyu Ma, Mathieu Lessard-Viger, Eric Brustad, Jeffrey Fisher, Jonathan Boutell, Weihua Chang
  • Publication number: 20230340568
    Abstract: The present disclosure relates to methods, compositions, and kits for generating a library of tagged nucleic acid fragments without using PCR amplification, including methods and compositions for fragmenting and tagging nucleic acids (e.g., DNA) using transposome complexes immobilized on solid support.
    Type: Application
    Filed: May 12, 2023
    Publication date: October 26, 2023
    Applicant: Illumina Cambridge Limited
    Inventors: Andrew Slatter, Esther Musgrave-Brown, Susan C. Verity, Niall Anthony Gormley