Patents by Inventor Mostafa Ronaghi

Mostafa Ronaghi 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: 20220243261
    Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.
    Type: Application
    Filed: January 13, 2022
    Publication date: August 4, 2022
    Applicant: Illumina, Inc.
    Inventors: Min-Jui Richard Shen, Jonathan Mark Boutell, Kathryn M. Stephens, Mostafa Ronaghi, Kevin L. Gunderson, Bala Murali Venkatesan, M. Shane Bowen, Kandaswamy Vijayan
  • Publication number: 20220243269
    Abstract: Implementations of a method for seeding sequence libraries on a surface of a sequencing flow cell that allow for spatial segregation of the libraries on the surface are provided. The spatial segregation can be used to index sequence reads from individual sequencing libraries to increase efficiency of subsequent data analysis. In some examples, hydrogel beads containing encapsulated sequencing libraries are captured on a sequencing flow cell and degraded in the presence of a liquid diffusion barrier to allow for the spatial segregation and seeding of the sequencing libraries on the surface of the flow cell. Additionally, examples of systems, methods and compositions are provided relating to flow cell devices configured for nucleic acid library preparation and single cell sequencing. Some examples include flow cell devices having a hydrogel with genetic material disposed therein, and which is retained within the hydrogel during nucleic acid processing.
    Type: Application
    Filed: April 13, 2022
    Publication date: August 4, 2022
    Inventors: Tarun Kumar Khurana, Yir-Shyuan Wu, Xi-Jun Chen, Filiz Gorpe-Yasar, Yan-You Lin, Victoria Popic, Erich B. Jaeger, Mostafa Ronaghi
  • Patent number: 11352668
    Abstract: Implementations of a method for seeding sequence libraries on a surface of a sequencing flow cell that allow for spatial segregation of the libraries on the surface are provided. The spatial segregation can be used to index sequence reads from individual sequencing libraries to increase efficiency of subsequent data analysis. In some examples, hydrogel beads containing encapsulated sequencing libraries are captured on a sequencing flow cell and degraded in the presence of a liquid diffusion barrier to allow for the spatial segregation and seeding of the sequencing libraries on the surface of the flow cell. Additionally, examples of systems, methods and compositions are provided relating to flow cell devices configured for nucleic acid library preparation and single cell sequencing. Some examples include flow cell devices having a hydrogel with genetic material disposed therein, and which is retained within the hydrogel during nucleic acid processing.
    Type: Grant
    Filed: July 31, 2018
    Date of Patent: June 7, 2022
    Assignee: ILLUMINA, INC.
    Inventors: Tarun Kumar Khurana, Yir-Shyuan Wu, Xi-Jun Chen, Filiz Gorpe-Yasar, Yan-You Lin, Victoria Popic, Erich B. Jaeger, Mostafa Ronaghi
  • Publication number: 20220106588
    Abstract: Systems, methods, and compositions provided herein relate to preparation of beads encapsulating long DNA fragments for high-throughput spatial indexing. Some embodiments include preparation of nucleic acid libraries within the bead, wherein the bead includes pores that allow diffusion of reagents while retaining genetic material.
    Type: Application
    Filed: October 21, 2021
    Publication date: April 7, 2022
    Inventors: Yir-Shyuan Wu, Filiz Gorpe-Yasar, Tarun Kumar Khurana, Victoria Popic, Erich B. Jaeger, Mostafa Ronaghi
  • Patent number: 11254976
    Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.
    Type: Grant
    Filed: August 19, 2019
    Date of Patent: February 22, 2022
    Assignee: Illumina, Inc.
    Inventors: Min-Jui Richard Shen, Jonathan Mark Boutell, Kathryn M. Stephens, Mostafa Ronaghi, Kevin L. Gunderson, Bala Murali Venkatesan, M. Shane Bowen, Kandaswamy Vijayan
  • Patent number: 11180752
    Abstract: Systems, methods, and compositions provided herein relate to preparation of beads encapsulating long DNA fragments for high-throughput spatial indexing. Some embodiments include preparation of nucleic acid libraries within the bead, wherein the bead includes pores that allow diffusion of reagents while retaining genetic material.
    Type: Grant
    Filed: February 11, 2019
    Date of Patent: November 23, 2021
    Assignee: ILLUMINA, INC.
    Inventors: Yir-Shyuan Wu, Filiz Gorpe-Yasar, Tarun Kumar Khurana, Victoria Popic, Erich B. Jaeger, Mostafa Ronaghi
  • Publication number: 20210164040
    Abstract: This disclosure provides a method of determining a sequence of nucleotides for a nucleic acid template. The method can include the steps of contacting the nucleic acid template with a conformationally labeled polymerase and at least four different nucleotide species under conditions wherein the conformationally labeled polymerase catalyzes sequential addition of the nucleotide species to form a nucleic acid complement of the nucleic acid template, wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase and wherein the rate or time duration for the conformational signal change is distinguishable for each different nucleotide species; detecting a series of changes in the signal from the conformationally labeled polymerase under the conditions; and determining the rates or time durations for the changes in the signal, thereby determining the sequence of nucleotides for the nucleic acid template.
    Type: Application
    Filed: November 6, 2020
    Publication date: June 3, 2021
    Applicant: Illumina, Inc.
    Inventors: Molly He, Cheng-Yao Chen, Eric Kool, Mostafa Ronaghi, Michael Previte, Rigo Pantoja
  • Patent number: 10837056
    Abstract: This disclosure provides a method of determining a sequence of nucleotides for a nucleic acid template. The method can include the steps of contacting the nucleic acid template with a conformationally labeled polymerase and at least four different nucleotide species under conditions wherein the conformationally labeled polymerase catalyzes sequential addition of the nucleotide species to form a nucleic acid complement of the nucleic acid template, wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase and wherein the rate or time duration for the conformational signal change is distinguishable for each different nucleotide species; detecting a series of changes in the signal from the conformationally labeled polymerase under the conditions; and determining the rates or time durations for the changes in the signal, thereby determining the sequence of nucleotides for the nucleic acid template.
    Type: Grant
    Filed: March 13, 2019
    Date of Patent: November 17, 2020
    Assignee: Illumina, Inc.
    Inventors: Molly He, Cheng-Yao Chen, Eric Kool, Mostafa Ronaghi, Michael Previte, Rigo Pantoja
  • Publication number: 20200216895
    Abstract: Implementations of a method for seeding sequence libraries on a surface of a sequencing flow cell that allow for spatial segregation of the libraries on the surface are provided. The spatial segregation can be used to index sequence reads from individual sequencing libraries to increase efficiency of subsequent data analysis. In some examples, hydrogel beads containing encapsulated sequencing libraries are captured on a sequencing flow cell and degraded in the presence of a liquid diffusion barrier to allow for the spatial segregation and seeding of the sequencing libraries on the surface of the flow cell. Additionally, examples of systems, methods and compositions are provided relating to flow cell devices configured for nucleic acid library preparation and single cell sequencing. Some examples include flow cell devices having a hydrogel with genetic material disposed therein, and which is retained within the hydrogel during nucleic acid processing.
    Type: Application
    Filed: July 31, 2018
    Publication date: July 9, 2020
    Inventors: Tarun Kumar Khurana, Yir-Shyuan Wu, Xi-Jun Chen, Filiz Gorpe-Yasar, Yan-You Lin, Victoria Popic, Erich B. Jaeger, Mostafa Ronaghi
  • Publication number: 20200181699
    Abstract: A method for synthesizing a nucleic acid includes synthesizing one or more nucleic acid fragments on a substrate. The synthesized one or more nucleic acid fragments may be amplified on the substrate. The method also includes sequencing the synthesized or amplified one or more nucleic acid fragments on the substrate. The sequencing may provide feedback to designs of the one or more nucleic acid fragments. The method further includes harvesting the synthesized or amplified one or more nucleic acid fragments based on sequencing. The synthesized or amplified one or more nucleic acid fragments may be assembled to generate a target nucleic acid.
    Type: Application
    Filed: December 5, 2019
    Publication date: June 11, 2020
    Inventors: Mostafa RONAGHI, Molly HE, Cheng-yao CHEN, Michael PREVITE, M. Shane BOWEN
  • Patent number: 10570447
    Abstract: A method for synthesizing a nucleic acid includes synthesizing one or more nucleic acid fragments on a substrate. The synthesized one or more nucleic acid fragments may be amplified on the substrate. The method also includes sequencing the synthesized or amplified one or more nucleic acid fragments on the substrate. The sequencing may provide feedback to designs of the one or more nucleic acid fragments. The method further includes harvesting the synthesized or amplified one or more nucleic acid fragments based on sequencing. The synthesized or amplified one or more nucleic acid fragments may be assembled to generate a target nucleic acid.
    Type: Grant
    Filed: May 14, 2015
    Date of Patent: February 25, 2020
    Assignee: Illumina, Inc.
    Inventors: Mostafa Ronaghi, Molly He, Cheng-yao Chen, Michael Previte, M. Shane Bowen
  • Publication number: 20200040386
    Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.
    Type: Application
    Filed: August 19, 2019
    Publication date: February 6, 2020
    Applicant: Illumina, Inc.
    Inventors: Min-Jui Richard Shen, Jonathan Mark Boutell, Kathryn M. Stephens, Mostafa Ronaghi, Kevin L. Gunderson, Bala Murali Venkatesan, M. Shane Bowen, Kandaswamy Vijayan
  • Publication number: 20190376136
    Abstract: This disclosure provides a method of determining a sequence of nucleotides for a nucleic acid template. The method can include the steps of contacting the nucleic acid template with a conformationally labeled polymerase and at least four different nucleotide species under conditions wherein the conformationally labeled polymerase catalyzes sequential addition of the nucleotide species to form a nucleic acid complement of the nucleic acid template, wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase and wherein the rate or time duration for the conformational signal change is distinguishable for each different nucleotide species; detecting a series of changes in the signal from the conformationally labeled polymerase under the conditions; and determining the rates or time durations for the changes in the signal, thereby determining the sequence of nucleotides for the nucleic acid template.
    Type: Application
    Filed: March 13, 2019
    Publication date: December 12, 2019
    Inventors: Molly He, Cheng-Yao Chen, Eric Kool, Mostafa Ronaghi, Michael Previte, Rigo Pantoja
  • Patent number: 10385384
    Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.
    Type: Grant
    Filed: August 8, 2017
    Date of Patent: August 20, 2019
    Assignee: Illumina, Inc.
    Inventors: Min-Jui Richard Shen, Jonathan Mark Boutell, Kathryn M. Stephens, Mostafa Ronaghi, Kevin L. Gunderson, Bala Murali Venkatesan, M. Shane Bowen, Kandaswamy Vijayan
  • Publication number: 20190249171
    Abstract: Systems, methods, and compositions provided herein relate to preparation of beads encapsulating long DNA fragments for high-throughput spatial indexing. Some embodiments include preparation of nucleic acid libraries within the bead, wherein the bead includes pores that allow diffusion of reagents while retaining genetic material.
    Type: Application
    Filed: February 11, 2019
    Publication date: August 15, 2019
    Inventors: Yir-Shyuan Wu, Filiz Gorpe-Yasar, Tarun Kumar Khurana, Victoria Popic, Erich B. Jaeger, Mostafa Ronaghi
  • Patent number: 10337059
    Abstract: The present method involves sequencing by synthesis in which a template strand having an attached primer is immobilized in a small volume reaction mixture. In one embodiment, the reaction mixture is in contact with a sensitive heat sensor, which detects the heat of reaction from incorporation of a complementary base (dNTP) in the presence of appropriate reagents (DNA polymerase, and polymerase reaction buffer). Alternatively, or in addition, a change in pH resulting from the incorporation of nucleotides in the DNA polymerase reaction is measured. A device is provided having delivery channels for appropriate reagents, including dNTPs, which may be delivered sequentially or in a mixture. Preferably, the dNTPs are added in a predetermined sequence, and the dNTP is incorporated or not depending on the template sequence.
    Type: Grant
    Filed: September 21, 2015
    Date of Patent: July 2, 2019
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Hesaam Esfandyarpour, Mostafa Ronaghi
  • Patent number: 10233493
    Abstract: This disclosure provides a method of determining a sequence of nucleotides for a nucleic acid template. The method can include the steps of contacting the nucleic acid template with a conformationally labeled polymerase and at least four different nucleotide species under conditions wherein the conformationally labeled polymerase catalyzes sequential addition of the nucleotide species to form a nucleic acid complement of the nucleic acid template, wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase and wherein the rate or time duration for the conformational signal change is distinguishable for each different nucleotide species; detecting a series of changes in the signal from the conformationally labeled polymerase under the conditions; and determining the rates or time durations for the changes in the signal, thereby determining the sequence of nucleotides for the nucleic acid template.
    Type: Grant
    Filed: December 22, 2017
    Date of Patent: March 19, 2019
    Assignee: Illumina, Inc.
    Inventors: Molly He, Cheng-Yao Chen, Eric Kool, Mostafa Ronaghi, Michael Previte, Rigo Pantoja
  • Patent number: 10167506
    Abstract: A method of sequencing nucleic acids, which can include steps of contacting a substrate having spatially distinguishable features with a plurality of nucleic acids to seed a subset of the features, thereby generating a seeded subset; amplifying the nucleic acids in the seeded subset to form nucleic acid colonies; repeating the preceding steps to increase the number of seeded features, thereby generating an array of nucleic acid colonies; and sequencing the array of nucleic acid colonies.
    Type: Grant
    Filed: October 2, 2017
    Date of Patent: January 1, 2019
    Assignee: Illumina, Inc.
    Inventors: Mostafa Ronaghi, Helmy A. Eltoukhy
  • Publication number: 20180155783
    Abstract: This disclosure provides a method of determining a sequence of nucleotides for a nucleic acid template. The method can include the steps of contacting the nucleic acid template with a conformationally labeled polymerase and at least four different nucleotide species under conditions wherein the conformationally labeled polymerase catalyzes sequential addition of the nucleotide species to form a nucleic acid complement of the nucleic acid template, wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase and wherein the rate or time duration for the conformational signal change is distinguishable for each different nucleotide species; detecting a series of changes in the signal from the conformationally labeled polymerase under the conditions; and determining the rates or time durations for the changes in the signal, thereby determining the sequence of nucleotides for the nucleic acid template.
    Type: Application
    Filed: December 22, 2017
    Publication date: June 7, 2018
    Inventors: Molly He, Cheng-Yao Chen, Eric Kool, Mostafa Ronaghi, Michael Previte, Rigo Pantoja
  • Publication number: 20180044732
    Abstract: The present technology relates to molecular sciences, such as genomics. More particularly, the present technology relates to methods for obtaining long lengths of sequencing data.
    Type: Application
    Filed: October 2, 2017
    Publication date: February 15, 2018
    Applicant: ILLUMINA, INC.
    Inventors: Mostafa Ronaghi, Helmy A. Eltoukhy