Patents Assigned to Illumina Cambridge Limited
  • Method of nucleic acid amplification
    Patent number: 9902951
    Abstract: A nucleic acid molecule can be annealed to an appropriate immobilized primer. The primer can then be extended and the molecule and the primer can be separated from one another. The extended primer can then be annealed to another immobilized primer and the other primer can be extended. Both extended primers can then be separated from one another and can be used to provide further extended primers. The process can be repeated to provide amplified, immobilized nucleic acid molecules. These can be used for many different purposes, including sequencing, screening, diagnosis, in situ nucleic acid synthesis, monitoring gene expression, nucleic acid fingerprinting, etc.
    Type: Grant
    Filed: May 2, 2013
    Date of Patent: February 27, 2018
    Assignees: Illumina, Inc., Illumina Cambridge Limited
    Inventors: Eric H. Kawashima, Laurent Farinelli, Pascal Mayer
  • Methods of localizing nucleic acids to arrays
    Patent number: 9889422
    Abstract: Methods and compositions are disclosed relating to the localization of nucleic acids to arrays such as silane-free arrays, and of sequencing the nucleic acids localized thereby.
    Type: Grant
    Filed: May 23, 2016
    Date of Patent: February 13, 2018
    Assignee: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Mark Edward Brennan Smith, Andrea Sabot, Isabelle Marie Julia Rasolonjatovo, Jean-Ernest Sohna Sohna, Adrian Martin Horgan, Harold Philip Swerdlow
  • Preparation of templates for methylation analysis
    Patent number: 9868982
    Abstract: The invention relates to a method of preparing and using a library of template polynucleotides suitable for use as templates in solid-phase nucleic acid amplification and sequencing reactions to determine the methylation status of the cytosine bases in the library. In particular, the invention relates to a method of preparing and analyzing a library of template polynucleotides suitable for methylation analysis.
    Type: Grant
    Filed: February 7, 2008
    Date of Patent: January 16, 2018
    Assignees: ILLUMINA CAMBRIDGE LIMITED, MASSACHUSETTS INSTITUTE OF TECHNOLOGY
    Inventors: Niall Gormley, Andreas Gnirke, David Jaffe, Harris Nusbaum
  • METHODS FOR SEQUENCING A POLYNUCLEOTIDE TEMPLATE
    Publication number: 20170342482
    Abstract: The invention relates to methods for pairwise sequencing of a polynucleotide template which result in the sequential determination of nucleotide sequence in two distinct and separate regions of the polynucleotide template.
    Type: Application
    Filed: August 15, 2017
    Publication date: November 30, 2017
    Applicant: Illumina Cambridge Limited
    Inventor: Harold Philip Swerdlow
  • NUCLEIC ACID ARRAYS
    Publication number: 20170342406
    Abstract: The present invention provides methods for creating an array of features on a surface based on content transferred from a plurality of beads to the surface. Nucleic acid content can be transferred using a method including the steps of (a) providing a surface having one or more primer oligonucleotides attached to the surface; (b) providing a pool of beads, wherein beads in the pool have a plurality of templates attached thereto, the plurality comprising multiple copies of a single nucleic acid template sequence; (c) arraying the beads onto the surface by hybridizing the templates to the primer oligonucleotides; and (d) extending the primers to produce copies of the templates attached to the surface.
    Type: Application
    Filed: June 12, 2017
    Publication date: November 30, 2017
    Applicant: Illumina Cambridge Limited
    Inventors: Roberto Rigatti, Geoffrey Paul Smith, Jonathan Mark Boutell
  • Reducing DNA damage during sample preparation and sequencing using siderophore chelators
    Patent number: 9828627
    Abstract: Embodiments disclosed herein provide reagents and kits for nucleic acid preparation comprising a siderophore. Embodiments disclosed herein provide methods for preparing a nucleic acid library, which comprise: providing a plurality of nucleic acid molecules from a sample; and manipulating the plurality of nucleic acid molecules in a reagent for nucleic acid preparation comprising a siderophore. Further, embodiments disclosed herein provide methods for reducing oxidative damage to a nucleic acid molecule or increasing the Q (phred) score of a sequencing reaction, which methods comprise preparing the nucleic acid molecule in the absence of EDTA.
    Type: Grant
    Filed: October 26, 2015
    Date of Patent: November 28, 2017
    Assignee: Illumina Cambridge Limited
    Inventors: Vincent Peter Smith, Sohela de Rozieres
  • METHOD FOR SEQUENCING A POLYNUCLEOTIDE TEMPLATE
    Publication number: 20170327885
    Abstract: The invention relates to methods for pairwise sequencing of a double stranded polynucleotide template, which permit the sequential determination of nucleotide sequences in two distinct and separate regions on complementary strands of the double-stranded polynucleotide template. The two regions for sequence determination may or may not be complementary to each other.
    Type: Application
    Filed: May 1, 2017
    Publication date: November 16, 2017
    Applicant: Illumina Cambridge Limited
    Inventor: GEOFFREY PAUL SMITH
  • Polymers and DNA copolymer coatings
    Patent number: 9815916
    Abstract: Some embodiments described herein relate to new polymer coatings for surface functionalization and new processes for grafting pre-grafted DNA-copolymers to surface(s) of substrates for use in DNA sequencing and other diagnostic applications.
    Type: Grant
    Filed: October 29, 2015
    Date of Patent: November 14, 2017
    Assignee: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Andrew A. Brown, Wayne N. George, Alexandre Richez, Anne-Cecile Dingwall, Xavier von Hatten
  • SEQUENCING FROM MULTIPLE PRIMERS TO INCREASE DATA RATE AND DENSITY
    Publication number: 20170298430
    Abstract: The present invention relates to a sequencing method which allows for increased rates of sequencing and an increase in the density of sequencing data. The system may be based on next generation sequencing methods such as sequencing by synthesis (SBS) but uses multiple primers bound at different positions on the same nucleic acid strand.
    Type: Application
    Filed: November 4, 2015
    Publication date: October 19, 2017
    Applicant: Illumina Cambridge Limited
    Inventor: Jonathan Mark Boutell
  • Polymerases
    Publication number: 20170275602
    Abstract: Modified DNA polymerases have an affinity for DNA such that the polymerase has an ability to incorporate one or more nucleotides into a plurality of separate DNA templates in each reaction cycle. The polymerases are capable of forming an increased number of productive polymerase-DNA complexes in each reaction cycle. The modified polymerases may be used in a number of DNA sequencing applications, especially in the context of clustered arrays.
    Type: Application
    Filed: June 9, 2017
    Publication date: September 28, 2017
    Applicant: Illumina Cambridge Limited
    Inventors: Geoffrey Paul Smith, Roberto Rigatti, Tobias William Barr Ost, Shankar Balasubramanian, Raquel Maria Sanches-Kuiper
  • Methods for sequencing a polynucleotide template
    Patent number: 9765391
    Abstract: The invention relates to methods for pairwise sequencing of a polynucleotide template which result in the sequential determination of nucleotide sequence in two distinct and separate regions of the polynucleotide template.
    Type: Grant
    Filed: July 20, 2006
    Date of Patent: September 19, 2017
    Assignee: ILLUMINA CAMBRIDGE LIMITED
    Inventor: Harold Philip Swerdlow
  • Centroid markers for image analysis of high density clusters in complex polynucleotide sequencing
    Patent number: 9758825
    Abstract: Improved compositions, methods, apparatus, and kits for high-throughput nucleic acid amplification, detection and sequencing are disclosed. A nucleic acid cluster having an identifiable center is produced by generating on a solid support an immobilized nucleic acid complement from a template, one of which comprises a detectable label; and amplifying the complement and the template to obtain a nucleic acid cluster on the support, the cluster having a substantially central location marked by the detectable label and a surrounding region comprising immobilized copies. Also disclosed are nucleotide sequence determination in nucleic acid clusters so produced, center position annotation in the clusters, assignment of sequence information to overlapping clusters, and related compositions and methods.
    Type: Grant
    Filed: June 24, 2014
    Date of Patent: September 12, 2017
    Assignee: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Alan D. Kersey, Jonathan Mark Boutell
  • Dyes for labelling molecular ligands
    Patent number: 9738786
    Abstract: Cyanine dyes with improved fluorescence intensity and photostability.
    Type: Grant
    Filed: June 10, 2016
    Date of Patent: August 22, 2017
    Assignee: Illumina Cambridge Limited
    Inventors: Nikolai Romanov, Carole Anastasi, Xiaohai Liu
  • Sample preparation on a solid support
    Patent number: 9683230
    Abstract: Presented are methods and compositions for using immobilized transposase and a transposon end for generating an immobilized library of 5?-tagged double-stranded target DNA on a surface. The methods are useful for generating 5?- and 3?-tagged DNA fragments for use in a variety of processes, including massively parallel DNA sequencing.
    Type: Grant
    Filed: March 8, 2013
    Date of Patent: June 20, 2017
    Assignee: Illumina Cambridge Limited
    Inventors: Niall Anthony Gormley, Geoffrey Paul Smith
  • Nucleic acid arrays of spatially discrete features on a surface
    Patent number: 9677069
    Abstract: The present invention provides methods for creating an array of features on a surface based on content transferred from a plurality of beads to the surface. Nucleic acid content can be transferred using a method including the steps of (a) providing a surface having one or more primer oligonucleotides attached to the surface; (b) providing a pool of beads, wherein beads in the pool have a plurality of templates attached thereto, the plurality comprising multiple copies of a single nucleic acid template sequence; (c) arraying the beads onto the surface by hybridizing the templates to the primer oligonucleotides; and (d) extending the primers to produce copies of the templates attached to the surface.
    Type: Grant
    Filed: June 5, 2015
    Date of Patent: June 13, 2017
    Assignee: Illumina Cambridge Limited
    Inventors: Roberto Rigatti, Geoffrey Paul Smith, Jonathan Mark Boutell
  • METHODS FOR INDEXING SAMPLES AND SEQUENCING MULTIPLE POLYNUCLEOTIDE TEMPLATES
    Publication number: 20170145499
    Abstract: The invention relates to methods for indexing samples during the sequencing of polynucleotide templates, resulting in the attachment of tags specific to the source of each nucleic acid sample such that after a sequencing run, both the source and sequence of each polynucleotide can be determined. Thus, the present invention pertains to analysis of complex genomes (e.g., human genomes), as well as multiplexing less complex genomes, such as those of bacteria, viruses, mitochondria, and the like.
    Type: Application
    Filed: November 30, 2016
    Publication date: May 25, 2017
    Applicant: Illumina Cambridge Limited
    Inventors: Helen Bignell, Louise Fraser, Niall Anthony Gormley
  • Method for sequencing a polynucleotide template
    Patent number: 9637786
    Abstract: The invention relates to methods for pairwise sequencing of a double-stranded polynucleotide template, which permit the sequential determination of nucleotide sequences in two distinct and separate regions on complementary strands of the double-stranded polynucleotide template. The two regions for sequence determination may or may not be complementary to each other.
    Type: Grant
    Filed: February 17, 2016
    Date of Patent: May 2, 2017
    Assignee: Illumina Cambridge Limited
    Inventor: Geoffrey Paul Smith
  • Labelled nucleotides
    Patent number: 9605310
    Abstract: Nucleosides and nucleotides are disclosed that are linked to detectable labels via a cleavable linker group.
    Type: Grant
    Filed: August 7, 2015
    Date of Patent: March 28, 2017
    Assignee: Illumina Cambridge Limited
    Inventors: Shankar Balasubramanian, Colin Barnes, Xiaohai Liu
  • Modified nucleosides or nucleotides
    Patent number: 9593373
    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: March 15, 2013
    Date of Patent: March 14, 2017
    Assignee: Illumina Cambridge Limited
    Inventors: Xiaohai Liu, Xiaolin Wu, Geoffrey Paul Smith
  • AMPLIFICATION METHODS TO MINIMISE SEQUENCE SPECIFIC BIAS
    Publication number: 20170029857
    Abstract: Methods for amplifying nucleic acids are provided. The methods can be used to minimise sequence specific bias caused by the preferential amplification of certain nucleic acid sequences. Methods are described which can lower the efficiency of AT rich templates relative to GC rich templates, thereby minimising GC bias during amplification reactions with multiple templates of different sequence. The methods are suited to solid phase amplification, for example, utilising flow cells.
    Type: Application
    Filed: October 17, 2016
    Publication date: February 2, 2017
    Applicant: Illumina Cambridge Limited
    Inventors: Roberto Rigatti, Jonathan Mark Boutell, Min-Jui Richard Shen