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    Spatial indexing of genetic material and library preparation using hydrogel beads and flow cells
    1.
    发明授权
    Spatial indexing of genetic material and library preparation using hydrogel beads and flow cells 有权

    公开(公告)号：US11352668B2

    公开(公告)日：2022-06-07

    申请号：US16626115

    申请日：2018-07-31

    Applicant: ILLUMINA, INC.

    Inventor： Tarun Kumar Khurana ,  Yir-Shyuan Wu ,  Xi-Jun Chen ,  Filiz Gorpe-Yasar ,  Yan-You Lin ,  Victoria Popic ,  Erich B. Jaeger ,  Mostafa Ronaghi

    IPC: C12Q1/6874 ,  C12Q1/6813

    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.

    CONFORMATIONAL PROBES AND METHODS FOR SEQUENCING NUCLEIC ACIDS
    2.
    发明申请
    CONFORMATIONAL PROBES AND METHODS FOR SEQUENCING NUCLEIC ACIDS 审中-公开

    公开(公告)号：US20180155783A1

    公开(公告)日：2018-06-07

    申请号：US15853118

    申请日：2017-12-22

    Applicant: Illumina, Inc.

    Inventor： Molly He ,  Cheng-Yao Chen ,  Eric Kool ,  Mostafa Ronaghi ,  Michael Previte ,  Rigo Pantoja

    IPC: C12Q1/6874 ,  C12Q1/6806 ,  C12Q1/6818

    CPC classification number: C12Q1/6874 ,  C12Q1/6806 ,  C12Q1/6818 ,  C12Q2565/133 ,  C12Q2563/125 ,  C12Q2525/101 ,  C12Q2565/1015

    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.

    Multibase delivery for long reads in sequencing by synthesis protocols
    4.
    发明授权
    Multibase delivery for long reads in sequencing by synthesis protocols 有权
    通过合成方案进行长序读取的多碱基递送

    公开(公告)号：US09005929B2

    公开(公告)日：2015-04-14

    申请号：US14200674

    申请日：2014-03-07

    Applicant: Illumina, Inc.

    Inventor： Mostafa Ronaghi ,  Helmy A. Eltoukhy

    IPC: C12P19/34 ,  C12Q1/68

    CPC classification number: C12Q1/6874 ,  C12Q1/6837 ,  C12Q1/6869 ,  C12Q2535/122 ,  C12Q2565/543

    Abstract: A method for obtaining nucleic acid sequence information that can include steps of (a) providing a first sequencing reagent to a target nucleic acid, wherein the first sequencing reagent comprises at least two different nucleotide monomers, (b) detecting the incorporation of a nucleotide monomer present in the first sequencing reagent into a polynucleotide strand complementary to at least a portion of the target nucleic acid, (c) providing a second sequencing reagent to said target nucleic acid, wherein the second sequencing reagent comprises one or more nucleotide monomers, at least one of the one or more nucleotide monomers being different from the nucleotide monomers present in the first sequencing reagent, and wherein the second sequencing reagent is provided subsequent to providing the first sequencing reagent, and (d) detecting the incorporation of a nucleotide monomer present in the second sequencing reagent into the polynucleotide strand.

    Abstract translation: 一种获得核酸序列信息的方法，其可以包括以下步骤：（a）向靶核酸提供第一测序试剂，其中所述第一测序试剂包含至少两种不同的核苷酸单体，（b）检测核苷酸单体的掺入 将第一测序试剂存在于与靶核酸的至少一部分互补的多核苷酸链中，（c）向所述靶核酸提供第二测序试剂，其中所述第二测序试剂至少包含一种或多种核苷酸单体，至少 一个或多个核苷酸单体之一与第一测序试剂中存在的核苷酸单体不同，并且其中第二测序试剂在提供第一测序试剂后提供，和（d）检测存在于 第二个测序试剂进入多核苷酸链。

    CONFORMATIONAL PROBES AND METHODS FOR SEQUENCING NUCLEIC ACIDS
    5.
    发明公开
    CONFORMATIONAL PROBES AND METHODS FOR SEQUENCING NUCLEIC ACIDS 审中-公开

    公开(公告)号：US20230235395A1

    公开(公告)日：2023-07-27

    申请号：US18129747

    申请日：2023-03-31

    Applicant: Illumina, Inc.

    Inventor： Molly He ,  Cheng-Yao Chen ,  Eric Kool ,  Mostafa Ronaghi ,  Michael Previte ,  Rigo Pantoja

    IPC: C12Q1/6874 ,  C12Q1/6806 ,  C12Q1/6818

    CPC classification number: C12Q1/6874 ,  C12Q1/6806 ,  C12Q1/6818

    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.

    SPATIAL INDEXING OF GENETIC MATERIAL AND LIBRARY PREPARATION USING HYDROGEL BEADS AND FLOW CELLS
    8.
    发明申请
    SPATIAL INDEXING OF GENETIC MATERIAL AND LIBRARY PREPARATION USING HYDROGEL BEADS AND FLOW CELLS 有权

    公开(公告)号：US20220243269A1

    公开(公告)日：2022-08-04

    申请号：US17720187

    申请日：2022-04-13

    Applicant: ILLUMINA, INC.

    Inventor： Tarun Kumar Khurana ,  Yir-Shyuan Wu ,  Xi-Jun Chen ,  Filiz Gorpe-Yasar ,  Yan-You Lin ,  Victoria Popic ,  Erich B. Jaeger ,  Mostafa Ronaghi

    IPC: C12Q1/6874 ,  C12Q1/6813

    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.

    CONFORMATIONAL PROBES AND METHODS FOR SEQUENCING NUCLEIC ACIDS
    9.
    发明申请
    CONFORMATIONAL PROBES AND METHODS FOR SEQUENCING NUCLEIC ACIDS 有权

    公开(公告)号：US20210164040A1

    公开(公告)日：2021-06-03

    申请号：US17091845

    申请日：2020-11-06

    Applicant: Illumina, Inc.

    Inventor： Molly He ,  Cheng-Yao Chen ,  Eric Kool ,  Mostafa Ronaghi ,  Michael Previte ,  Rigo Pantoja

    IPC: C12Q1/6874 ,  C12Q1/6806 ,  C12Q1/6818

    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.

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