Patents Assigned to Illumina Cambridge Limited
  • Deep Learning-Based Variant Classifier
    Publication number: 20190220704
    Abstract: The technology disclosed directly operates on sequencing data and derives its own feature filters. It processes a plurality of aligned reads that span a target base position. It combines elegant encoding of the reads with a lightweight analysis to produce good recall and precision using lightweight hardware. For instance, one million training examples of target base variant sites with 50 to 100 reads each can be trained on a single GPU card in less than 10 hours with good recall and precision. A single GPU card is desirable because it a computer with a single GPU is inexpensive, almost universally within reach for users looking at genetic data. It is readily available on could-based platforms.
    Type: Application
    Filed: January 14, 2019
    Publication date: July 18, 2019
    Applicants: Illumina, Inc., Illumina Cambridge Limited
    Inventors: Ole Benjamin SCHULZ-TRIEGLAFF, Anthony James COX, Kai-How FARH
  • Flexible tape-based chemistry apparatus
    Patent number: 10351846
    Abstract: An apparatus and method for applying a chemistry to samples of interest are provided. The apparatus and method include a flexible tape mounted on an arrangement of guide rollers. Samples of interest (e.g., clusters of DNA templates) are bound to at least one surface of the flexible tape. The method and apparatus further comprise one or more read heads in relation to the flexible tape and a plurality of reservoirs along a path of the flexible tape. The reservoirs comprise liquids comprising chemical reagents for performing the chemistry on the samples of interest bound to the at least one surface of the flexible tape. The method and apparatus further comprise a drive system for driving at least one of the guide rollers to advance the flexible tape into and out of the reservoirs.
    Type: Grant
    Filed: September 11, 2015
    Date of Patent: July 16, 2019
    Assignee: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Jonathan Mark Boutell, Gary Mark Skinner, Gareth Jenkins
  • Recombinase mutants
    Patent number: 10344269
    Abstract: Presented herein are recombinases for improved recombinase-mediated amplification of nucleic acids, such as a PCR-library having single-stranded adapter regions, on a patterned flow cell surface for improved cluster amplification, as well as methods and kits using the same.
    Type: Grant
    Filed: May 11, 2018
    Date of Patent: July 9, 2019
    Assignee: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Erin Bomati, Matthew William Kellinger, Jonathan Mark Boutell
  • Methods for sequencing polynucleotides
    Patent number: 10329613
    Abstract: Provided herein is a method for sequencing a polynucleotide molecules. The method includes the steps of providing a plurality of polynucleotide molecules attached to a surface, wherein a first portion of each polynucleotide molecule is attached to a first location of the surface and a second portion of each polynucleotide molecule is attached to a second location of the surface, the relative proximity of the first and second locations being correlated with the probability that the first and second portions are paired, separating the first and second portions of the polynucleotide molecules on the surface, determining the sequences of the first and second portions of the polynucleotide molecules and comparing the relative proximities and the sequences to determine which first and second portions are paired and to determine the sequence of the target polynucleotide molecules.
    Type: Grant
    Filed: April 10, 2015
    Date of Patent: June 25, 2019
    Assignee: Illumina Cambridge Limited
    Inventors: Roberto Rigatti, Niall Anthony Gormley, Jonathan Mark Boutell
  • Methods of nucleic acid sequencing
    Patent number: 10267804
    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: February 1, 2017
    Date of Patent: April 23, 2019
    Assignee: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Niall Anthony Gormley, Louise Fraser, Paula Kokko-Gonzales
  • Method of preparing libraries of template polynucleotides
    Patent number: 10253359
    Abstract: The present invention relates to a method for preparing a library of template polynucleotides and use thereof in methods of solid-phase nucleic acid amplification. More specifically, the invention relates to a method for preparing a library of template polynucleotides that have common sequences at their 5? ends and at their 3? ends.
    Type: Grant
    Filed: June 3, 2016
    Date of Patent: April 9, 2019
    Assignee: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Niall Anthony Gormley, Geoffrey Paul Smith, David Bentley, Roberto Rigatti, Shujun Luo
  • Polymethine compounds with long stokes shifts and their use as fluorescent labels
    Patent number: 10239909
    Abstract: The present disclosure relates to new compounds and their use as fluorescent labels. The compounds may be used as fluorescent labels for nucleotides in nucleic acid sequencing applications. The labels are advantageous due to their long Stokes shifts.
    Type: Grant
    Filed: May 23, 2016
    Date of Patent: March 26, 2019
    Assignee: Illumina Cambridge Limited
    Inventors: Nikolai Romanov, Xiaolin Wu
  • Method for pairwise sequencing of target polynucleotides
    Patent number: 10221452
    Abstract: The invention relates to methods for pairwise sequencing of a double-stranded polynucleotide template, which methods result in the sequential determination of nucleotide sequences in two distinct and separate regions of the polynucleotide template. Using the methods of the invention it is possible to obtain two linked or paired reads of sequence information from each double-stranded template on a clustered array, rather than just a single sequencing read from one strand of the template.
    Type: Grant
    Filed: October 12, 2015
    Date of Patent: March 5, 2019
    Assignee: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Roberto Rigatti, Tobias William Barr Ost
  • Coumarin compounds and their uses as fluorescent labels
    Patent number: 10214768
    Abstract: The present application relates to new 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: December 21, 2017
    Date of Patent: February 26, 2019
    Assignee: Illumina Cambridge Limited
    Inventor: Nikolai Romanov
  • 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
  • Modified nucleotide linkers
    Patent number: 10190157
    Abstract: Some embodiments of the present application relate to novel modified nucleotide linkers for increasing the efficiency of nucleotide incorporation in Sequencing by Synthesis applications. Methods of preparing these modified nucleotide linkers are also provided herewith.
    Type: Grant
    Filed: August 7, 2015
    Date of Patent: January 29, 2019
    Assignee: Illumina Cambridge Limited
    Inventors: Xiaolin Wu, Xiaohai Liu
  • METHOD FOR SEQUENCING A POLYNUCLEOTIDE TEMPLATE
    Publication number: 20180363047
    Abstract: The invention provides methods for pairwise sequencing of a double-stranded polynucleotide template, which methods result in the sequential determination of nucleotide sequences in two distinct and separate regions of the polynucleotide template.
    Type: Application
    Filed: June 11, 2018
    Publication date: December 20, 2018
    Applicant: Illumina Cambridge Limited
    Inventors: Geoffrey Paul Smith, Jonathan Mark Boutell, Colin Lloyd Barnes, Roberto Rigatti, Niall Anthony Gormley, David Bentley, Tobias William Barr Ost, Vincent Peter Smith, Graham John Worsley, Eric Hans Vermaas
  • Preparation of Templates for Nucleic Acid Sequencing
    Publication number: 20180353926
    Abstract: The invention relates to methods of generating templates for a nucleic acid sequencing reaction which comprise: providing at least one double-stranded nucleic acid molecule, wherein both strands of the double-stranded nucleic acid molecule are attached to a solid support at the 5? end, cleaving one or both strands of the double-stranded nucleic acid molecule, and subjecting the cleaved strand(s) to denaturing conditions to remove the portion of the cleaved strand(s) not attached to the solid support, thereby generating a partially or substantially single-stranded template for a nucleic acid sequencing reaction.
    Type: Application
    Filed: June 18, 2018
    Publication date: December 13, 2018
    Applicant: Illumina Cambridge Limited
    Inventors: Xiaohai Liu, John Milton, Geoffrey Paul Smith, Colin Lloyd Barnes, Isabelle Rasolonjatovo, Roberto Rigatti, Xiaolin Wu, Tobias William Barr Ost, Graham John Worsley, David James Earnshaw, Gerardo Turcatti, Anthony Romieu
  • Polymethine compounds and their use as fluorescent labels
    Patent number: 10144967
    Abstract: The present disclosure relates to new compounds and their use as fluorescent labels. The compounds may be used as fluorescent labels for nucleotides in nucleic acid sequencing applications.
    Type: Grant
    Filed: March 1, 2016
    Date of Patent: December 4, 2018
    Assignee: Illumina Cambridge Limited
    Inventor: Nikolai Nikolaevich Romanov
  • Labelled nucleotides
    Patent number: 10144754
    Abstract: The invention provides a nucleotide or nucleoside having a base attached to a detectable label via a cleavable linker, characterized in that the cleavable linker contains a moiety selected from the group comprising: Formula (I) (wherein X is selected from the group comprising O, S, NH and NQ wherein Q is a C1-10 substituted or unsubstituted alkyl group, Y is selected from the group comprising O, S, NH and N(allyl), T is hydrogen or a C1-10 substituted or unsubstituted alkyl group and * indicates where the moiety is connected to the remainder of the nucleotide or nucleoside).
    Type: Grant
    Filed: July 6, 2016
    Date of Patent: December 4, 2018
    Assignee: Illumina Cambridge Limited
    Inventors: Xiaohai Liu, John Milton, Silke Ruediger
  • Modified nucleosides or nucleotides
    Patent number: 10138514
    Abstract: Some embodiments described herein relate to modified nucleotide and nucleoside molecules with novel 3?-hydroxy protecting groups. Also provided herein are methods to prepare such modified nucleotide and nucleoside molecules and sequencing by synthesis processes using such modified nucleotide and nucleoside molecules.
    Type: Grant
    Filed: February 28, 2017
    Date of Patent: November 27, 2018
    Assignee: Illumina Cambridge Limited
    Inventors: Xiaohai Liu, Xiaolin Wu, Geoffrey Paul Smith
  • Labelled nucleotides
    Patent number: 10125390
    Abstract: Nucleosides and nucleotides are disclosed that are linked to detectable labels via a cleavable linker group.
    Type: Grant
    Filed: July 5, 2016
    Date of Patent: November 13, 2018
    Assignee: Illumina Cambridge Limited
    Inventors: Shankar Balasubramanian, Colin Barnes, Xiaohai Liu, John Milton
  • COMPOSITIONS AND METHODS FOR IMPROVING SAMPLE IDENTIFICATION IN INDEXED NUCLEIC ACID LIBRARIES
    Publication number: 20180305753
    Abstract: The present invention is concerned with compositions and methods for improving the rate of correct sample identification in indexed nucleic acid library preparations for multiplex next generation sequencing by exonuclease treatment and optionally blocking the 3? ends of pooled indexed polynucleotides from multiple samples prior to amplification and sequencing.
    Type: Application
    Filed: April 23, 2018
    Publication date: October 25, 2018
    Applicant: Illumina Cambridge Limited
    Inventors: Michael Chesney, Vincent Peter Smith, Claire Bevis-Mott, Jonathan Mark Boutell, Angela Kalbande
  • COMPOSITIONS AND METHODS FOR IMPROVING SAMPLE IDENTIFICATION IN INDEXED NUCLEIC ACID LIBRARIES
    Publication number: 20180305752
    Abstract: The present invention is concerned with compositions and methods for improving the rate of correct sample identification in indexed nucleic acid library preparations for multiplex next generation sequencing by modifying or blocking 5? and 3? ends of pooled indexed polynucleotides from multiple samples, with an optional exonuclease treatment, prior to amplification and sequencing.
    Type: Application
    Filed: April 23, 2018
    Publication date: October 25, 2018
    Applicants: Illumina, Inc., Illumina Cambridge Limited
    Inventors: Eric Hans Vermaas, Mahdieh Khosroheidari, Claire Bevis-Mott
  • COMPOSITIONS AND METHODS FOR IMPROVING SAMPLE IDENTIFICATION IN INDEXED NUCLEIC ACID LIBRARIES
    Publication number: 20180305750
    Abstract: The present invention is concerned with compositions and methods for improving the rate of correct sample identification in indexed nucleic acid library preparations for multiplex next generation sequencing by blocking the 3? ends of pooled indexed polynucleotides from multiple samples prior to amplification and sequencing.
    Type: Application
    Filed: April 23, 2018
    Publication date: October 25, 2018
    Applicant: Illumina Cambridge Limited
    Inventors: Vincent Peter Smith, Claire Bevis-Mott, Jonathan Mark Boutell