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: 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: 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
  • 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
  • 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
  • Patent number: 11319534
    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: Grant
    Filed: January 6, 2020
    Date of Patent: May 3, 2022
    Assignee: ILLUMINA, INC.
    Inventors: Frank J. Steemers, Sasan Amini, Kevin L. Gunderson, Natasha Pignatelli, Igor Goryshin
  • Publication number: 20220042093
    Abstract: A method of sequencing a target nucleic acid polymer by (a) modifying a target nucleic acid polymer to produce a modified nucleic acid polymer; (b) producing fragments of the modified nucleic acid polymer, wherein the fragments are attached to locations on a solid support surface (c) determining nucleotide sequences from the fragments at the locations; and (d) producing a representation of the nucleotide sequence for the target nucleic acid polymer based on the nucleotide sequences from the fragments and the relative distances between the locations on the solid support surface.
    Type: Application
    Filed: September 8, 2021
    Publication date: February 10, 2022
    Applicant: Illumina, Inc.
    Inventors: Jeffrey S. Fisher, Frank J. Steemers, Sasan Amini, Kevin L. Gunderson
  • Publication number: 20220033805
    Abstract: Provided herein are methods for preparing a sequencing library that includes nucleic acids from a plurality of single cells. In one embodiment, the method includes nuclear or cellular hashing which permits increased sample throughput and increased doublet detection at high collision rates. In one embodiment, the method includes normalization hashing which aids in estimating and removing technical noise in cell to cell variation and increases sensitivity and specificity.
    Type: Application
    Filed: March 2, 2020
    Publication date: February 3, 2022
    Inventors: Sanjay Srivatsan, Jose McFaline-Figueroa, Vijay Ramani, Junyue Cao, Gregory Booth, Jay Shendure, Cole Trapnell, Frank J. Steemers
  • Patent number: 11149310
    Abstract: A method of sequencing a target nucleic acid polymer by (a) modifying a target nucleic acid polymer to produce a modified nucleic acid polymer; (b) producing fragments of the modified nucleic acid polymer, wherein the fragments are attached to locations on a solid support surface (c) determining nucleotide sequences from the fragments at the locations; and (d) producing a representation of the nucleotide sequence for the target nucleic acid polymer based on the nucleotide sequences from the fragments and the relative distances between the locations on the solid support surface.
    Type: Grant
    Filed: March 18, 2019
    Date of Patent: October 19, 2021
    Assignee: Illumina, Inc.
    Inventors: Jeffrey S. Fisher, Frank J. Steemers, Sasan Amini, Kevin L. Gunderson
  • Publication number: 20210277388
    Abstract: Embodiments provided herein relate to methods and compositions for next generation sequencing. Some embodiments include the preparation of a template library from a target nucleic acid using one-sided transposition, sequencing the template library, and capturing the contiguity information.
    Type: Application
    Filed: March 2, 2021
    Publication date: September 9, 2021
    Inventors: Frank J. Steemers, Jeffrey S. Fisher, Kevin L. Gunderson, Sasan Amini, Christian Gloeckner
  • Publication number: 20210277043
    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: May 26, 2021
    Publication date: September 9, 2021
    Applicant: Illumina, Inc.
    Inventors: Frank J. Steemers, Kevin L. Gunderson, Kerri York, Ryan Christopher Smith
  • Patent number: 11085036
    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: October 24, 2019
    Date of Patent: August 10, 2021
    Assignee: Illumina, Inc.
    Inventors: Steven Norberg, Dmitry Pokholok, Ramesh Ramji, Frank J. Steemers, Fan Zhang
  • Patent number: 11021504
    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 16, 2019
    Date of Patent: June 1, 2021
    Assignee: Illumina, Inc.
    Inventors: Frank J Steemers, Kevin L Gunderson, Kerri York, Ryan Christopher Smith
  • 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
  • Publication number: 20210108262
    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: Application
    Filed: October 21, 2020
    Publication date: April 15, 2021
    Inventors: Sante Gnerre, Byoungsok Jung, Emrah Kostem, Alex Aravanis, Alex So, Xuyu Cai, Zhihong Zhang, Frank J. Steemers
  • Publication number: 20210102194
    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 nucleic acids that represent the whole transcriptomes from the plurality of single cells. In one embodiment, the nucleic acids include three index sequences. Also provided herein are compositions, such as compositions that include the nucleic acids having three index sequences.
    Type: Application
    Filed: June 4, 2019
    Publication date: April 8, 2021
    Applicants: Illumina, Inc., University of Washington
    Inventors: Frank J. Steemers, Jay Shendure, Junyue Cao