Patents by Inventor Roberto Rigatti

Roberto Rigatti 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).

  • Patent number: 10370709
    Abstract: Disclosed herein are compositions and methods for sequencing nucleic acids.
    Type: Grant
    Filed: September 12, 2016
    Date of Patent: August 6, 2019
    Assignee: Illumina Cambridge Limited
    Inventors: Roberto Rigatti, Jonathan Mark Boutell, Jason Betley, Niall Anthony Gormley
  • 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
  • Patent number: 10287577
    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 12, 2017
    Date of Patent: May 14, 2019
    Assignee: ILLUMINA CAMBRIDGE LTD.
    Inventors: Roberto Rigatti, Geoffrey Paul Smith, Jonathan Mark Boutell
  • 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
  • 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
  • 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
  • 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
  • Publication number: 20180322243
    Abstract: The present disclosure provides methods and systems for determining and/or characterizing one or more haplotypes and/or phasing of haplotypes in a nucleic acid sample. In particular, the disclosure provides methods for determining a haplotype and/or phasing of haplotypes in a nucleic acid sample by incorporating synthetic polymorphisms into fragments of a nucleic acid sample and utilizing the synthetic polymorphisms in determining one or more haplotypes and/or phasing of haplotypes.
    Type: Application
    Filed: May 11, 2018
    Publication date: November 8, 2018
    Inventors: Roberto Rigatti, Jonathan Mark Boutell
  • Publication number: 20180273933
    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: Application
    Filed: February 10, 2016
    Publication date: September 27, 2018
    Inventors: Kevin L Gunderson, Frank J Steemers, Jeffrey S Fisher, Roberto Rigatti
  • Patent number: 10059928
    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: Grant
    Filed: June 9, 2017
    Date of Patent: August 28, 2018
    Assignee: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Geoffrey Paul Smith, Roberto Rigatti, Tobias William Barr Ost, Shankar Balasubramanian, Raquel Maria Sanches-Kuiper
  • Publication number: 20180187251
    Abstract: The invention provides methods for amplifying nucleic acids, particularly methods for reducing density-dependent GC bias and for reducing nucleic acid damage in a bridge amplification of a nucleic acid template. The invention also provides methods for evaluating the effect of reagents and/or additives on nucleic acid damage during bridge amplification of nucleic acid template strands. The methods are suited to solid phase amplification, for example, utilizing flow cells.
    Type: Application
    Filed: June 2, 2015
    Publication date: July 5, 2018
    Inventors: Jonathan Mark BOUTELL, Susan SHANAHAN, Roberto RIGATTI
  • Patent number: 10006081
    Abstract: The invention relates to a method of preparing a 5? and 3? modified library of template polynucleotides and also the use of the 5? and 3? modified library of templates in methods of solid-phase nucleic acid amplification. In particular, the invention relates to a method of preparing a 5? and 3? modified library of template polynucleotides which have common sequences at their 5? ends and at their 3? ends, wherein over-representation of “end” sequences of the primary polynucleotide molecules from when the 5? and 3? modified library is generated is greatly reduced or prevented.
    Type: Grant
    Filed: March 24, 2015
    Date of Patent: June 26, 2018
    Assignee: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Roberto Rigatti, Niall Anthony Gormley, Helen Rachel Bignell
  • Patent number: 9999866
    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: Grant
    Filed: October 6, 2016
    Date of Patent: June 19, 2018
    Assignee: 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
  • Patent number: 9994896
    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: Grant
    Filed: December 17, 2014
    Date of Patent: June 12, 2018
    Assignee: 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
  • Patent number: 9977861
    Abstract: The present disclosure provides methods and systems for determining and/or characterizing one or more haplotypes and/or phasing of haplotypes in a nucleic acid sample. In particular, the disclosure provides methods for determining a haplotype and/or phasing of haplotypes in a nucleic acid sample by incorporating synthetic polymorphisms into fragments of a nucleic acid sample and utilizing the synthetic polymorphisms in determining one or more haplotypes and/or phasing of haplotypes.
    Type: Grant
    Filed: March 11, 2013
    Date of Patent: May 22, 2018
    Assignee: Illumina Cambridge Limited
    Inventors: Roberto Rigatti, Jonathan Mark Boutell
  • Patent number: 9944924
    Abstract: The present disclosure relates to the field of molecular biology and more specifically to methods for capturing and amplifying target polynucleotides on a solid surface.
    Type: Grant
    Filed: July 10, 2015
    Date of Patent: April 17, 2018
    Assignees: ILLUMINA, INC., ILLUMINA CAMBRIDGE LIMITED
    Inventors: Roberto Rigatti, Niall Anthony Gormley, Allen E. Eckhardt, Jonathan Mark Boutell
  • Publication number: 20180037950
    Abstract: The present disclosure relates to the field of molecular biology and more specifically to microarrays and methods.
    Type: Application
    Filed: November 11, 2015
    Publication date: February 8, 2018
    Inventors: Kevin L. Gunderson, Jingwei Bai, Matthew William Kellinger, John M. Beierle, Jonathan Mark Boutell, Roberto Rigatti, Maria Candelaria Rogert Bacigalupo, Boyan Boyanov, Klaus Maisinger
  • 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
  • Publication number: 20170283794
    Abstract: The invention provides methods for generating a nucleic acid library. Target-specific primer-probes are hybridized to a target nucleic acid fragment to create a hybridization product. Each of the target-specific primer-probes comprises a target-specific sequence and a first adaptor sequence. The target nucleic acid fragment comprises a target genomic region of interest, wherein said target genomic region of interest comprises an exon of a gene and the target-specific primer-probes are tiled across the exon of the gene. The target nucleic acid fragment further comprises a second adaptor sequence different from said first adaptor sequence. Following hybridization, the target-specific primer-probes are extended to create double-stranded extension products and further amplified, thereby generating the nucleic acid library.
    Type: Application
    Filed: April 17, 2017
    Publication date: October 5, 2017
    Inventors: Andrea Sabot, Roberto Rigatti, Min-Jui Richard Shen
  • 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