Patents by Inventor Frank J. Steemers

Frank J. Steemers 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).

  • 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
  • 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
  • Patent number: 11866777
    Abstract: The disclosed embodiments concern methods, apparatus, systems and computer program products for determining sequences of interest using unique molecular index (UMI) sequences that are uniquely associable with individual polynucleotide fragments, including sequences with low allele frequencies and long sequence length. In some implementations, the UMIs include both physical UMIs and virtual UMIs. In some implementations, the unique molecular index sequences include non-random sequences. System, apparatus, and computer program products are also provided for determining a sequence of interest implementing the methods disclosed.
    Type: Grant
    Filed: October 21, 2020
    Date of Patent: January 9, 2024
    Assignee: Illumina, Inc.
    Inventors: Sante Gnerre, Byoungsok Jung, Emrah Kostem, Alex Aravanis, Alex So, Xuyu Cai, Zhihong Zhang, Frank J. Steemers
  • Publication number: 20230406874
    Abstract: Embodiments of the present disclosure include methods and compositions for functionalizing molecules, such as oligonucleotides, with functional groups, including polyhistidine tags useful in affinity methods. Some embodiments include methods for modifying and purifying complex mixtures of molecules by exchange of functional tags.
    Type: Application
    Filed: August 1, 2023
    Publication date: December 21, 2023
    Inventors: Frank J. Steemers, Kevin L. Gunderson, Kerri York, Ryan Christopher Smith
  • Publication number: 20230374493
    Abstract: Embodiments of the present invention relate to analyzing components of a cell. In some embodiments, the present invention relate to analyzing components of a single cell. In some embodiments, the methods and compositions relate to sequencing nucleic acids. In some embodiments, the methods and compositions relate to identifying and/or quantitiating nucleic acid, proteins, organelles, and/or cellular metabolites.
    Type: Application
    Filed: February 27, 2023
    Publication date: November 23, 2023
    Applicant: ILLUMINA, INC.
    Inventors: Kevin L. Gunderson, Frank J. Steemers, Jeffrey S. Fisher, Roberto Rigatti
  • Publication number: 20230323426
    Abstract: Provided herein are methods for preparing a sequencing library that includes nucleic acids from a plurality of single cells. In one embodiment, the sequencing library includes whole genome nucleic acids from the plurality of single cells. In one embodiment, the method includes generating nucleosome-depleted nuclei by chemical treatment while maintaining integrity of the nuclei. Also provided herein are compositions, such as compositions that include chemically treated nucleosome-depleted isolated nuclei.
    Type: Application
    Filed: December 5, 2022
    Publication date: October 12, 2023
    Applicants: Illumina Inc., Oregon Health & Science University
    Inventors: Andrew C. Adey, Sarah A. Vitak, Frank J. Steemers
  • Patent number: 11760772
    Abstract: Embodiments of the present disclosure include methods and compositions for functionalizing molecules, such as oligonucleotides, with functional groups, including polyhistidine tags useful in affinity methods. Some embodiments include methods for modifying and purifying complex mixtures of molecules by exchange of functional tags.
    Type: Grant
    Filed: May 26, 2021
    Date of Patent: September 19, 2023
    Assignee: Illumina, Inc.
    Inventors: Frank J. Steemers, Kevin L. Gunderson, Kerri York, Ryan Christopher Smith
  • Publication number: 20230279385
    Abstract: A variety of different types of targeted transposome complexes are described herein that may be used to mediate sequence-specific targeted transposition of nucleic acids.
    Type: Application
    Filed: February 16, 2023
    Publication date: September 7, 2023
    Applicants: Illumina, Inc., Illumina Cambridge Limited
    Inventors: Frank J. STEEMERS, Jonathan Mark BOUTELL, Pietro GATTI LAFRANCONI, Oliver Jon MILLER, Emma BELL, Sebastien Georg Gabriel RICOULT, Niall Anthony GORMLEY, Kim SCHNEIDER
  • Publication number: 20230183680
    Abstract: Embodiments of the present invention relate to sequencing nucleic acids. In particular, embodiments of the methods and compositions provided herein relate to preparing nucleic acid templates and obtaining sequence data therefrom.
    Type: Application
    Filed: January 12, 2023
    Publication date: June 15, 2023
    Inventors: Frank J. Steemers, Sasan Amini, Kevin L. Gunderson, Natasha Pignatelli, Igor Goryshin
  • Patent number: 11634707
    Abstract: Embodiments of the present invention relate to analyzing components of a cell. In some embodiments, the present invention relate to analyzing components of a single cell. In some embodiments, the methods and compositions relate to sequencing nucleic acids. In some embodiments, the methods and compositions relate to identifying and/or quantitating nucleic acid, proteins, organelles, and/or cellular metabolites.
    Type: Grant
    Filed: February 10, 2016
    Date of Patent: April 25, 2023
    Assignee: ILLUMINA, INC.
    Inventors: Kevin L Gunderson, Frank J Steemers, Jeffrey S Fisher, Roberto Rigatti
  • Publication number: 20230105642
    Abstract: Embodiments relate to the preparation of nucleic acid libraries. Some embodiments relate to the preparation of normalized nucleic acid libraries, such as libraries in which the amounts of amplified nucleic acids are substantially the same for different amounts of input nucleic acids. Some embodiments relate to preparation of indexed nucleic acid libraries with certain adaptors.
    Type: Application
    Filed: March 29, 2021
    Publication date: April 6, 2023
    Inventors: Lena Christiansen, Dmitry Pokholok, Frank J. Steemers, Rigo Pantoja, Megan Chu, Patrizia lavicoli, Weihua Chang, Jeffrey Dennis Brodin, Eric Vermaas, Jerishah Thomas, Fan Zhang
  • Patent number: 11591641
    Abstract: This invention provides methods of amplifying genomic DNA to obtain an amplified representative population of genome fragments. Methods are further provided for obtaining amplified genomic DNA representations of a desired complexity. The invention further provides methods for simultaneously detecting large numbers of typable loci for an amplified representative population of genome fragments. Accordingly the methods can be used to genotype individuals on a genome-wide scale.
    Type: Grant
    Filed: August 5, 2020
    Date of Patent: February 28, 2023
    Assignee: Illumina, Inc.
    Inventors: Kevin L. Gunderson, Frank J. Steemers
  • Publication number: 20220411859
    Abstract: Systems, methods, and compositions provided herein relate to preparation of beads encapsulating genetic material. 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: Application
    Filed: August 1, 2018
    Publication date: December 29, 2022
    Inventors: Yir-Shyuan Wu, Xi-Jun Chen, Filiz Gorpe-Yasar, Falko NoƩ, Charles Lin, Tarun Kumar Khurana, Foad Mashayekhi, Pallavi Daggumati, Frank J Steemers, Kevin Gunderson, Jeffrey S Fisher
  • Patent number: 11535883
    Abstract: Provided herein are methods for preparing a sequencing library that includes nucleic acids from a plurality of single cells. In one embodiment, the sequencing library includes whole genome nucleic acids from the plurality of single cells. In one embodiment, the method includes generating nucleosome-depleted nuclei by chemical treatment while maintaining integrity of the nuclei. Also provided herein are compositions, such as compositions that include chemically treated nucleosome-depleted isolated nuclei.
    Type: Grant
    Filed: July 21, 2017
    Date of Patent: December 27, 2022
    Assignees: Illumina, Inc., Oregon Health & Science University
    Inventors: Andrew C. Adey, Sarah A. Vitak, Frank J. Steemers
  • Patent number: 11530446
    Abstract: Embodiments disclosed herein provide methods for constructing a DNA profile comprising: providing a nucleic acid sample, amplifying the nucleic acid sample with a plurality of primers that specifically hybridize to at least one target sequence comprising a SNP and at least one target sequence comprising a tandem repeat, and determining the genotypes of the at least one SNP and at least one tandem repeat in the amplification products, thereby constructing the DNA profile of the nucleic acid sample. Embodiments disclosed herein further provide a plurality of primers that specifically hybridize to at least one short target sequence and at least one long target sequence in a nucleic acid sample, wherein amplifying the nucleic acid sample using the plurality of primers in a single reaction results in a short amplification product and a long amplification product, wherein each of the plurality of primers comprises one or more tag sequences.
    Type: Grant
    Filed: September 19, 2019
    Date of Patent: December 20, 2022
    Assignee: Illumina, Inc.
    Inventors: Kathryn M. Stephens, Cydne Holt, Carey Davis, Anne Jager, Paulina Walichiewicz, Yonmee Han, David Silva, Min-Jui Richard Shen, Sasan Amini, Frank J. Steemers
  • 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
  • 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
  • Publication number: 20220213470
    Abstract: Embodiments of the present invention relate to sequencing nucleic acids. In particular, embodiments of the methods and compositions provided herein relate to preparing nucleic acid templates and obtaining sequence data therefrom.
    Type: Application
    Filed: March 21, 2022
    Publication date: July 7, 2022
    Inventors: Frank J. Steemers, Sasan Amini, Kevin L. Gunderson, Natasha Pignatelli, Igor Goryshin
  • 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
  • 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