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).
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Patent number: 9079148Abstract: 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: GrantFiled: March 11, 2014Date of Patent: July 14, 2015Assignee: Illumina Cambridge LimitedInventors: Roberto Rigatti, Geoffrey Paul Smith, Jonathan Mark Boutell
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Publication number: 20150148263Abstract: The invention provides methods for controlling the density of different molecular species on the surface of a solid support. A first mixture of different molecular species is attached to a solid support under conditions to attach each species at a desired density, thereby producing a derivatized support having attached capture molecules. The derivatized support is treated with a second mixture of different molecular species, wherein different molecular species in the second mixture bind specifically to the different capture molecules attached to the solid support. One or more of the capture molecules can be reversibly modified such that the capture molecules have a different activity before and after the second mixture of molecular species are attached. In particular embodiments, the different molecular species are nucleic acids that are reversibly modified to have different activity in an amplification reaction.Type: ApplicationFiled: February 2, 2015Publication date: May 28, 2015Applicant: ILLUMINA, INC.Inventors: Andrea Sabot, Roberto Rigatti, Min-Jui Richard Shen
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Patent number: 9029103Abstract: 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: GrantFiled: August 26, 2011Date of Patent: May 12, 2015Assignee: Illumina Cambridge LimitedInventors: Roberto Rigatti, Niall Anthony Gormley, Jonathan Mark Boutell
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Patent number: 9012184Abstract: 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: GrantFiled: February 7, 2007Date of Patent: April 21, 2015Assignee: Illumina Cambridge LimitedInventors: Roberto Rigatti, Niall Anthony Gormley, Helen Rachel Bignell
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Patent number: 8999642Abstract: The invention provides methods for controlling the density of different molecular species on the surface of a solid support. A first mixture of different molecular species is attached to a solid support under conditions to attach each species at a desired density, thereby producing a derivatized support having attached capture molecules. The derivatized support is treated with a second mixture of different molecular species, wherein different molecular species in the second mixture bind specifically to the different capture molecules attached to the solid support. One or more of the capture molecules can be reversibly modified such that the capture molecules have a different activity before and after the second mixture of molecular species are attached. In particular embodiments, the different molecular species are nucleic acids that are reversibly modified to have different activity in an amplification reaction.Type: GrantFiled: August 25, 2009Date of Patent: April 7, 2015Assignee: Illumina, Inc.Inventors: Andrea Sabot, Roberto Rigatti, Min-Jui Richard Shen
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Publication number: 20150050657Abstract: Provided herein is a method of selecting target nucleic acids on a support. The method includes providing a plurality of beads each bead comprising one or more oligonucleotides, providing a support with a plurality of primers with a sequence complementary to at least a portion of the oligonucleotides on the beads, contacting the beads with the support wherein the oligonucleotides on the beads bind to the primers on the support, performing an extension reaction by extending the primers on the support to produce capture oligonucleotides, contacting the support comprising the capture oligonucleotides with the target nucleic acids, and extending the capture oligonucleotides bound to target nucleic acids to produce target extension products comprising a sequence complementary to at least a portion of the target nucleic acids. Optionally, the method further includes amplifying the target extension products.Type: ApplicationFiled: May 28, 2013Publication date: February 19, 2015Applicant: Illumina Cambridge LimitedInventors: Roberto Rigatti, Jonathan Boutell
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Patent number: 8945835Abstract: 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: GrantFiled: April 11, 2012Date of Patent: February 3, 2015Assignee: Illumina Cambridge LimitedInventors: Eric Hans Vermaas, Graham John Worsley, Jonathan Mark Boutell, Colin Lloyd Barnes, Roberto Rigatti, Niall Anthony Gormley, Geoffrey Paul Smith, Vincent Peter Smith, Tobias William Barr Ost, David Bentley
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Publication number: 20140349891Abstract: 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: ApplicationFiled: January 28, 2014Publication date: November 27, 2014Applicant: ILLUMINA CAMBRIDGE LIMITEDInventors: Xiaohai Liu, John Milton, Geoffrey Paul Smith, Colin Lloyd Barnes, Isabelle Marie Julia Rasolonjatovo, Roberto Rigatti, Xiaolin Wu, Tobias William Barr Ost, Graham John Worsley, David James Earnshaw, Gerardo Turcatti, Anthony Romieu
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Publication number: 20140336057Abstract: 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: ApplicationFiled: May 19, 2014Publication date: November 13, 2014Applicant: ILLUMINA CAMBRIDGE LIMITEDInventors: Roberto Rigatti, Tobias William Barr Ost
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Publication number: 20140329246Abstract: 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: ApplicationFiled: June 9, 2014Publication date: November 6, 2014Applicant: ILLUMINA CAMBRIDGE LIMITEDInventors: Roberto Rigatti, Jonathan Mark Boutell, Min-Jui Richard Shen
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Publication number: 20140296109Abstract: 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: ApplicationFiled: March 11, 2014Publication date: October 2, 2014Applicant: Illumina Cambridge LimitedInventors: Roberto Rigatti, Geoffrey Paul Smith, Jonathan Mark Boutell
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Publication number: 20140287415Abstract: 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: ApplicationFiled: December 20, 2013Publication date: September 25, 2014Applicant: ILLUMINA, INC.Inventors: Geoffrey Paul Smith, Roberto Rigatti, Tobias William Barr Ost, Shankar Balasubramanian, Raquel Maria Sanches-Kuiper
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Publication number: 20140287935Abstract: Disclosed herein are compositions and methods for sequencing nucleic acids.Type: ApplicationFiled: June 9, 2014Publication date: September 25, 2014Applicant: Illumina Cambridge LimitedInventors: Roberto Rigatti, Jonathan Mark Boutell, Jason Richard Betley, Niall Anthony Gormley
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Patent number: 8765381Abstract: 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: GrantFiled: April 4, 2013Date of Patent: July 1, 2014Assignee: Illumina Cambridge LimitedInventors: Roberto Rigatti, Tobias William Barr Ost
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Patent number: 8759038Abstract: Disclosed herein are compositions and methods for sequencing nucleic acids.Type: GrantFiled: September 28, 2011Date of Patent: June 24, 2014Assignee: Illumina Cambridge LimitedInventors: Roberto Rigatti, Jonathan Mark Boutell, Jason Richard Betley, Niall Anthony Gormley
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Patent number: 8759037Abstract: Methods for amplifying nucleic acids are provided. The methods can be used to minimize 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 minimizing GC bias during amplification reactions with multiple templates of different sequence. The methods are suited to solid phase amplification, for example, utilizing flow cells.Type: GrantFiled: February 23, 2011Date of Patent: June 24, 2014Assignee: Illumina Cambridge LimitedInventors: Roberto Rigatti, Jonathan Mark Boutell, Min-Jui Richard Shen
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Patent number: 8753816Abstract: The present technology relates to molecular sciences, such as genomics. More particularly, the present technology relates to nucleic acid sequencing.Type: GrantFiled: October 26, 2011Date of Patent: June 17, 2014Assignee: Illumina, Inc.Inventors: Roberto Rigatti, Jonathan Mark Boutell, Jason Richard Betley, Niall Anthony Gormley, Mostafa Ronaghi, Dirk Evers
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Patent number: 8741571Abstract: The present invention provides a method of creating an array of features. The method can include steps of (a) providing a plurality of beads, wherein each bead in the plurality of beads includes probe content; (b) contacting the plurality of beads with a surface to produce a layer of beads on the surface; and (c) transferring the probe content from the beads to the surface to create an array of spatially discrete features on the surface, wherein each spatially discrete feature includes probe content from a bead in the plurality of beads.Type: GrantFiled: March 13, 2013Date of Patent: June 3, 2014Assignee: Illumina Cambridge LimitedInventors: Roberto Rigatti, Geoffrey Paul Smith, Jonathan Mark Boutell
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Patent number: 8715966Abstract: 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: GrantFiled: April 19, 2012Date of Patent: May 6, 2014Assignee: Illumina Cambridge LimitedInventors: Liu Xiaohai, John Milton, Geoffrey Paul Smith, Colin Lloyd Barnes, Isabelle Marie Julia Rasolonjatovo, Roberto Rigatti, Xiaolin Wu, Tobias William Barr Ost, Graham John Worsley, David James Earnshaw, Gerardo Turcatti, Anthony Romieu
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Publication number: 20140080721Abstract: Provided herein is a method of inhibiting degradation of nucleic acids during a nucleic acid processing step selected from fragmentation and detection comprising contacting the nucleic acids with a solution comprising gallic acid, analogues, derivatives thereof or mixtures thereof, during the processing step, wherein the contacting inhibits degradation of the nucleic acids. Also provided herein is a method of inhibiting light-induced degradation of nucleic acids. Additionally, provided herein is a method of reducing or inhibiting nucleic acid damage during preparation of a nucleic acid sample comprising fragmenting the nucleic acid sequences in the sample in a solution comprising one of more compounds, the compounds inhibiting degradation of the nucleic acid sequences in the sample.Type: ApplicationFiled: January 12, 2012Publication date: March 20, 2014Applicant: ILLUMINA, INC.Inventors: Kay Klausing, Min-Jui Richard Shen, John Moore, Vincent Peter Smith, Kevin Hall, Niall Anthony Gormley, Avgousta Ioannou, Epameinondas Fritzilas, Roberto Rigatti