Patents by Inventor Dmitry K. Pokholok

Dmitry K. Pokholok 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).

  • Analysis of multiple analytes using a single assay
    Patent number: 12104281
    Abstract: Embodiments of systems, methods, and compositions provided herein relate to methods of simultaneously analyzing multiple analytes in a single sample using a single assay. Some embodiments relate to simultaneous analysis of DNA and RNA in a single sample, for example, to the simultaneous generation of DNA and RNA libraries.
    Type: Grant
    Filed: November 25, 2019
    Date of Patent: October 1, 2024
    Assignee: ILLUMINA, INC.
    Inventors: Frank J. Steemers, Fan Zhang, Dmitry K. Pokholok, Steven Norberg
  • Modulating polymer beads for DNA processing
    Patent number: 11999945
    Abstract: Systems, methods, and compositions provided herein relate to preparation of beads encapsulating biomolecules for performing sequential reactions on the biomolecules. Some embodiments include preparation of nucleic acid reactions within the bead, wherein the bead includes pores that allow diffusion of molecules into or out of the beads while retaining other molecules of interest.
    Type: Grant
    Filed: July 1, 2021
    Date of Patent: June 4, 2024
    Assignee: Illumina, Inc.
    Inventors: Steven Norberg, Dmitry K. Pokholok, Ramesh Ramji, Frank J. Steemers, Fan Zhang
  • LONG INDEXED-LINKED READ GENERATION ON TRANSPOSOME BOUND BEADS
    Publication number: 20240018584
    Abstract: Embodiments of systems, methods, and compositions provided herein relate to on bead tagmentation and droplet indexing. Some embodiments include performing co-assays on partitioned beads, including nucleic acid sequencing, indexed PCR, preparing nucleic acid libraries, determining methylation status, identifying genomic variants, or protein analysis.
    Type: Application
    Filed: July 26, 2023
    Publication date: January 18, 2024
    Inventors: Lena Christiansen, Frank J. Steemers, Gary Schroth, Jerushah Thomas, Dmitry K. Pokholok
  • Contiguity preserving transposition
    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
  • CONTIGUITY PARTICLE FORMATION AND METHODS OF USE
    Publication number: 20220333157
    Abstract: Embodiments of systems, methods, and compositions provided herein relate to hollow beads encapsulating single cells. Some embodiments include performing multiple co-assays on a single cell encapsulated within a hollow bead, including nucleic acid sequencing, preparing nucleic acid libraries, determining methylation status, identifying genomic variants, or protein analysis.
    Type: Application
    Filed: May 16, 2022
    Publication date: October 20, 2022
    Inventors: Frank J. Steemers, Ramesh Ramji, Steven Norberg, Lena Christiansen, Dmitry K. Pokholok, Fan Zhang
  • Contiguity Preserving Transposition
    Publication number: 20220282242
    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: Application
    Filed: April 12, 2022
    Publication date: September 8, 2022
    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
  • METHODS AND MEANS FOR PREPARING A LIBRARY FOR SEQUENCING
    Publication number: 20220195507
    Abstract: Embodiments of systems, methods, and compositions provided herein relate to assays for selectively controlling enzymatic reactions. Some embodiments relate to methods of inhibiting, reducing, or eliminating secondary DNA (such as mitochondrial DNA) sequencing reads from open chromatic sequencing, whole genome sequencing, or targeted sequencing.
    Type: Application
    Filed: December 13, 2019
    Publication date: June 23, 2022
    Inventors: Frank J. Steemers, Dmitry K. Pokholok, Lena Christiansen
  • ANALYSIS OF MULTIPLE ANALYTES USING A SINGLE ASSAY
    Publication number: 20220195504
    Abstract: Embodiments of systems, methods, and compositions provided herein relate to methods of simultaneously analyzing multiple analytes in a single sample using a single assay. Some embodiments relate to simultaneous analysis of DNA and RNA in a single sample, for example, to the simultaneous generation of DNA and RNA libraries.
    Type: Application
    Filed: November 25, 2019
    Publication date: June 23, 2022
    Inventors: Frank J. Steemers, Fan Zhang, Dmitry K. Pokholok, Steve Norberg
  • Contiguity particle formation and methods of use
    Patent number: 11359226
    Abstract: Embodiments of systems, methods, and compositions provided herein relate to hollow beads encapsulating single cells. Some embodiments include performing multiple co-assays on a single cell encapsulated within a hollow bead, including nucleic acid sequencing, preparing nucleic acid libraries, determining methylation status, identifying genomic variants, or protein analysis.
    Type: Grant
    Filed: April 15, 2019
    Date of Patent: June 14, 2022
    Assignee: ILLUMINA, INC.
    Inventors: Frank J. Steemers, Ramesh Ramji, Steven Norberg, Lena Christiansen, Dmitry K. Pokholok, Fan Zhang
  • METHODS FOR INCREASING YIELD OF SEQUENCING LIBRARIES
    Publication number: 20210380972
    Abstract: The present disclosure is concerned with compositions, methods, and kits for preparing a sequencing library. In one embodiment, methods include producing a library of target nucleic acids having the same adapter at each end and then switching the identity of one adapter to result in target nucleic acids flanked by distinct adapters.
    Type: Application
    Filed: June 10, 2021
    Publication date: December 9, 2021
    Applicants: Illumina, Inc., Illumina Cambridge Limited, Oregon Health & Science University
    Inventors: Andrew C. Adey, Ryan Mulqueen, Frank Steemers, Dmitry K Pokholok, Fan Zhang, Esther Musgrave-Brown
  • COMPOSITIONS AND METHODS FOR THE AMPLIFICATION OF NUCLEIC ACIDS
    Publication number: 20210129107
    Abstract: The present disclosure relates to systems and methods for the amplification of nucleic acids, including, but not limited to, the amplification of nucleic acid libraries and whole genome amplification.
    Type: Application
    Filed: November 16, 2020
    Publication date: May 6, 2021
    Inventors: Jian-Bing Fan, Kevin L. Gunderson, Frank J. Steemers, Dmitry K. Pokholok, Fiona Kaper
  • Compositions and methods for the amplification of nucleic acids
    Patent number: 10870099
    Abstract: The present disclosure relates to systems and methods for the amplification of nucleic acids, including, but not limited to, the amplification of nucleic acid libraries and whole genome amplification.
    Type: Grant
    Filed: February 21, 2013
    Date of Patent: December 22, 2020
    Assignee: Illumina, Inc.
    Inventors: Jian-Bing Fan, Kevin L. Gunderson, Frank J. Steemers, Dmitry K. Pokholok, Fiona Kaper
  • POLYNUCLEOTIDE ENRICHMENT USING CRISPR-CAS SYSTEM
    Publication number: 20200165650
    Abstract: A method for enriching a target nucleic acid comprising providing an endonuclease system having a crRNA or a derivative thereof, and a Cas protein or a variant thereof. The crRNA or the derivative thereof contains a target-specific nucleotide region substantially complementary to a region of the target nucleic acid; contacting the target nucleic acid with the endonuclease system to form a complex; and separating the complex and thereby enriching for the target nucleic acid.
    Type: Application
    Filed: October 21, 2019
    Publication date: May 28, 2020
    Inventors: Gordon M. Cann, Jeffrey G. Mandell, Alex Aravanis, Steven Norberg, Dmitry K. Pokholok, Frank J. Steemers, Farnaz Absalan, Leila Bazargan
  • CONTIGUITY PARTICLE FORMATION AND METHODS OF USE
    Publication number: 20190352591
    Abstract: Embodiments of systems, methods, and compositions provided herein relate to hollow beads encapsulating single cells. Some embodiments include performing multiple co-assays on a single cell encapsulated within a hollow bead, including nucleic acid sequencing, preparing nucleic acid libraries, determining methylation status, identifying genomic variants, or protein analysis.
    Type: Application
    Filed: April 15, 2019
    Publication date: November 21, 2019
    Inventors: Frank J. Steemers, Ramesh Ramji, Steven Norberg, Lena Christiansen, Dmitry K. Pokholok, Fan Zhang
  • Polynucleotide enrichment using CRISPR-Cas systems
    Patent number: 10457969
    Abstract: A method for enriching a target nucleic acid comprising providing an endonuclease system having a crRNA or a derivative thereof, and a Cas protein or a variant thereof. The crRNA or the derivative thereof contains a target-specific nucleotide region substantially complementary to a region of the target nucleic acid; contacting the target nucleic acid with the endonuclease system to form a complex; and separating the complex and thereby enriching for the target nucleic acid.
    Type: Grant
    Filed: July 20, 2015
    Date of Patent: October 29, 2019
    Assignee: Illumina, Inc.
    Inventors: Gordon M. Cann, Jeffrey G. Mandell, Alex Aravanis, Steven Norberg, Dmitry K. Pokholok, Frank J. Steemers, Farnaz Absalan, Leila Bazargan
  • ANALYSIS SYSTEM FOR ORTHOGONAL ACCESS TO AND TAGGING OF BIOMOLECULES IN CELLULAR COMPARTMENTS
    Publication number: 20190323003
    Abstract: The invention relates to a system and methods for enhancing access to nuclear informational molecules, such as DNA, RNA, and proteins, by analytical biomolecules, such as transposome complexes, by treating nuclei with a nuclear permeability enhancer, and to methods of using nuclear membrane, cell membrane, and external compartmentalization approaches as contiguity preserving elements.
    Type: Application
    Filed: June 28, 2019
    Publication date: October 24, 2019
    Applicant: ILLUMINA, INC.
    Inventors: Ramesh Ramji, Frank J. Steemers, Lena Christiansen, Dmitry K. Pokholok, Fan Zhang
  • Contiguity Preserving Transposition
    Publication number: 20190048332
    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: Application
    Filed: October 29, 2018
    Publication date: February 14, 2019
    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
  • CONTIGUITY PRESERVING TRANSPOSITION
    Publication number: 20190040382
    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: Application
    Filed: October 16, 2015
    Publication date: February 7, 2019
    Applicant: 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
  • SINGLE CELL WHOLE GENOME LIBRARIES FOR METHYLATION SEQUENCING
    Publication number: 20180355348
    Abstract: Provided herein are methods for preparing sequencing libraries for determining the methylation status of nucleic acids from a plurality of single cells. The present methods combine split-and-pool combinatorial indexing and bisulfite treatment techniques to characterize the methylation profiles of large numbers of single cells quickly, accurately and inexpensively.
    Type: Application
    Filed: June 5, 2018
    Publication date: December 13, 2018
    Applicants: OREGON HEALTH & SCIENCE UNIVERSITY, ILLUMINA, INC.
    Inventors: Andrew C. Adey, Ryan Mulqueen, Frank J. Steemers, Dmitry K. Pokholok, Steven Norberg
  • POLYNUCLEOTIDE ENRICHMENT USING CRISPR-CAS SYSTEMS
    Publication number: 20160017396
    Abstract: A method for enriching a target nucleic acid comprising providing an endonuclease system having a crRNA or a derivative thereof, and a Cas protein or a variant thereof. The crRNA or the derivative thereof contains a target-specific nucleotide region substantially complementary to a region of the target nucleic acid; contacting the target nucleic acid with the endonuclease system to form a complex; and separating the complex and thereby enriching for the target nucleic acid.
    Type: Application
    Filed: July 20, 2015
    Publication date: January 21, 2016
    Applicant: ILLUMINA, INC.
    Inventors: Gordon M. Cann, Jeffrey G. Mandell, Alex Aravanis, Steven Norberg, Dmitry K. Pokholok, Frank J. Steemers, Farnaz Absalan, Leila Bazargan