Patents by Inventor Andrew Slatter

Andrew Slatter 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: 20250146049
    Abstract: Presented are methods and compositions for preparing samples for amplification and sequencing. Particular embodiments relate to methods of preparing nucleic acid-containing cellular samples for library amplification, wherein the methods include lysing cells of the sample to form a lysate, amplifying the nucleic acids from the lysed samples, exposing the amplified nucleic acids to a solid surface, and clonallyr amplifying the amplified nucleic acids to generate clusters.
    Type: Application
    Filed: January 6, 2025
    Publication date: May 8, 2025
    Inventors: Louise Fraser, Paula Kokko-Gonzales, Andrew Slatter
  • Patent number: 12234451
    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: Grant
    Filed: June 1, 2023
    Date of Patent: February 25, 2025
    Assignee: Illumina, Inc.
    Inventors: Grace Desantis, Stephen M. Gross, Jian-Sen Li, Natalie Morrell, Andrew Slatter, Kevin Shen, Samantha Snow
  • Patent number: 12188078
    Abstract: Presented are methods and compositions for preparing samples for amplification and sequencing. Particular embodiments relate to methods of preparing nucleic acid containing cellular samples for library amplification, wherein the methods include lysing cells of the sample to form a lysate, amplifying the nucleic acids from the lysed samples, wherein there is no purification of the nucleic acids from the lysate prior to the amplification, wherein amplifying comprises tagmentation, and sequencing the nucleic acids, wherein the sample is a blood sample or a formalin-fixed paraffin-embedded (FFPE) sample.
    Type: Grant
    Filed: September 15, 2021
    Date of Patent: January 7, 2025
    Assignee: Illumina Cambridge Limited
    Inventors: Louise Fraser, Paula Kokko-Gonzales, Andrew Slatter
  • Publication number: 20240287583
    Abstract: Aptamer detection techniques with dynamic range compression are described that permit removal of a portion of more abundant aptamers in an aptamer-based assay. In an embodiment, a mixture of tagged probes and dummy probes can be used such that the dummy probes bind abundant aptamers and in turn are not captured or amplified for detection in downstream steps. Other techniques are also contemplated, including targeted removal of or cleavage of probes that bind to excess aptamers.
    Type: Application
    Filed: April 6, 2023
    Publication date: August 29, 2024
    Inventors: Andrew Slatter, Carlo Randise-Hinchliff, Andrew Price, Niall Anthony Gormley, Andrea Manzo, Nithya Subramanian, Fiona Kaper, David Jones, Steven Norberg
  • Publication number: 20240287504
    Abstract: Genomic library preparation using Cas-gRNA RNPs, and targeted epigenetic assays, are provided herein. Some compositions include, from a first species, substantially only single-stranded polynucleotides; from a second species, substantially only double-stranded polynucleotides; and amplification primers ligated to ends of the second double-stranded polynucleotides and substantially not ligated to any ends of the first double-stranded polynucleotides. Some compositions include first and second molecules of a target polynucleotide having a sequence, the first molecule having a first end at a first subsequence, the second molecule having a first end at a second subsequence, wherein the first subsequence only partially overlaps with the second subsequence. Some examples provide a composition that includes a target polynucleotide and a first fusion protein including a Cas-gRNA RNP coupled to a transposase having an amplification adapter coupled thereto.
    Type: Application
    Filed: March 8, 2022
    Publication date: August 29, 2024
    Applicants: Illumina, Inc., Illumina Cambridge Limited
    Inventors: Andrew Kennedy, Sarah Shultzaberger, Emma Bell, Oliver Miller, Kim Schneider, Esther Musgrave-Brown, Niall Gormley, Andrew Slatter, Feng Chen
  • Publication number: 20240271126
    Abstract: Nucleic acid techniques are disclosed. Embodiments include modified nucleotides with oligonucleotide adapters that are coupled via cleavable linkers. Incorporation of the modified nucleotide at a 3? end of a nucleic acid permits end-adapterization via ligation of a free 5? end of the oligonucleotide adapter to a 3? reactive group of the modified nucleotide and cleavage at the cleavable linker to liberate a free 3? end.
    Type: Application
    Filed: May 26, 2022
    Publication date: August 15, 2024
    Inventors: Niall Anthony Gormley, Carlo Randise-Hinchliff, Jeffrey Brodin, Esther Musgrave-Brown, Sarah E. Shultzaberger, Andrew Slatter, Jeffrey S. Fisher
  • Publication number: 20240084384
    Abstract: Aspects of the present invention include analyzing nucleic acids from single cells using methods that include using tagged polynucleotides containing multiplex identifier sequences.
    Type: Application
    Filed: November 16, 2023
    Publication date: March 14, 2024
    Inventors: Sydney Brenner, Gi Mikawa, Robert Osborne, Andrew Slatter
  • 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
  • Publication number: 20230416803
    Abstract: Disclosed herein is a method for enriching a sequencing library comprising double-stranded nucleic acid fragments comprising preparing a library of double-stranded fragments having one or more adaptors at ends of the double-stranded fragment; denaturing the double-stranded fragments to form single-stranded fragments; and hybridizing an extension primer that binds to a target sequence of at least one insert in the library of double-stranded fragments and that does not bind to non-target sequences. In an embodiment, the adaptor is a hairpin adaptor, and extension from the extension primer using a polymerase with 5? to 3? exonuclease activity removes all or part of a sequence of the hairpin adaptor that is at least partially complementary to the amplification primer sequence. Each fragment may comprise an insert comprising double-stranded nucleic acid and a hairpin adaptor at the 5? end of one or both strands of the double-stranded fragments.
    Type: Application
    Filed: September 10, 2022
    Publication date: December 28, 2023
    Inventor: Andrew Slatter
  • Publication number: 20230409629
    Abstract: In an example method, a series of time-based clustering images is generated for a plurality of library fragments from a genome sample. Each time-based clustering image in the series is sequentially generated. To generate each time-based clustering image in the series: i) a respective sample is introduced to a flow cell, the respective sample including contiguity preserved library fragments of the plurality of library fragments, wherein the contiguity preserved library fragments are attached to a solid support or are attached to each other; ii) the contiguity preserved library fragments are released from the solid support or from each other; iii) the contiguity preserved library fragments are amplified to generate a plurality of respective template strands; iv) the respective template strands are stained; and v) the respective template strands are imaged.
    Type: Application
    Filed: May 31, 2023
    Publication date: December 21, 2023
    Inventors: Natalie Morrell, Andrew Slatter, Vicki Thomson
  • 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
  • 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
  • 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
  • Patent number: 11760994
    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: Grant
    Filed: June 25, 2021
    Date of Patent: September 19, 2023
    Assignees: 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: 11714848
    Abstract: In an example method, a series of time-based clustering images is generated for a plurality of library fragments from a genome sample. Each time-based clustering image in the series is sequentially generated. To generate each time-based clustering image in the series: i) a respective sample is introduced to a flow cell, the respective sample including contiguity preserved library fragments of the plurality of library fragments, wherein the contiguity preserved library fragments are attached to a solid support or are attached to each other; ii) the contiguity preserved library fragments are released from the solid support or from each other; iii) the contiguity preserved library fragments are amplified to generate a plurality of respective template strands; iv) the respective template strands are stained; and v) the respective template strands are imaged.
    Type: Grant
    Filed: December 1, 2020
    Date of Patent: August 1, 2023
    Assignee: Illumina Cambridge Limited
    Inventors: Natalie Morrell, Andrew Slatter, Vicki Thomson
  • Patent number: 11708573
    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: Grant
    Filed: January 4, 2021
    Date of Patent: July 25, 2023
    Assignees: Illumina, Inc.
    Inventors: Grace DeSantis, Stephen M. Gross, Jian-Sen Li, Natalie Morrell, Andrew Slatter, Kevin Shen, Samantha Snow
  • Patent number: 11685946
    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: Grant
    Filed: January 10, 2020
    Date of Patent: June 27, 2023
    Inventors: Andrew Slatter, Esther Musgrave-Brown, Susan C. Verity, Niall Anthony Gormley
  • Publication number: 20220171802
    Abstract: In an example method, a series of time-based clustering images is generated for a plurality of library fragments from a genome sample. Each time-based clustering image in the series is sequentially generated. To generate each time-based clustering image in the series: i) a respective sample is introduced to a flow cell, the respective sample including contiguity preserved library fragments of the plurality of library fragments, wherein the contiguity preserved library fragments are attached to a solid support or are attached to each other; ii) the contiguity preserved library fragments are released from the solid support or from each other; iii) the contiguity preserved library fragments are amplified to generate a plurality of respective template strands; iv) the respective template strands are stained; and v) the respective template strands are imaged.
    Type: Application
    Filed: December 1, 2020
    Publication date: June 2, 2022
    Inventors: Natalie Morrell, Andrew Slatter, Vicki Thomson
  • Patent number: 11306348
    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: Grant
    Filed: May 3, 2021
    Date of Patent: April 19, 2022
    Assignee: Illumina Cambridge Limited
    Inventors: Andrew Slatter, Esther Musgrave-Brown, Susan C. Verity, Niall Anthony Gormley
  • Publication number: 20220002711
    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: June 25, 2021
    Publication date: January 6, 2022
    Applicants: ILLUMINA, INC., ILLUMINA CAMBRIDGE LIMITED
    Inventors: Maria Candelaria Rogert BACIGALUPO, Frank STEEMERS, Jeffrey FISHER, Andrew SLATTER, Lewis KRAFT, Niall GORMLEY, M. Shane BOWEN