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    PAIRED-END SEQUENCING
    11.
    发明公开
    PAIRED-END SEQUENCING 审中-公开

    公开(公告)号：US20230295719A1

    公开(公告)日：2023-09-21

    申请号：US18184556

    申请日：2023-03-15

    Applicant: ILLUMINA, INC.

    Inventor： Aathavan Karunakaran ,  Nileshi Saraf ,  Samantha Antonio Leong ,  Ramir Villa Vega ,  Gery Vessere

    IPC: C12Q1/6874 ,  C12Q1/6844

    CPC classification number: C12Q1/6874 ,  C12Q1/6844

    Abstract: Systems and methods of identifying nucleobases in a template polynucleotide are disclosed. In one embodiment, such a method may include providing a substrate comprising a plurality of double stranded template polynucleotides in a cluster. Each double stranded template polynucleotide may comprise a first strand and a second strand. The method may further include contacting the plurality of double stranded template polynucleotides with first primers which bind to the first strand and second primers which bind to the second strand. The method may further include extending the first primers and the second primers by contacting the cluster with labeled nucleobases to form first labeled primers and second labeled primers. The method may further include stimulating light emissions from the first and second labeled primers, wherein an amplitude of the signal generated by the first labeled primers is greater than an amplitude of the signal generated by the second labeled primers. The method may further include identifying the labeled nucleobases added to the first primers and the second primers based on the amplitude of the signal generated by the labeled nucleobases.

    FLOW CELL WITH SELECTIVE DEPOSITION OR ACTIVATION OF NUCLEOTIDES
    13.
    发明申请
    FLOW CELL WITH SELECTIVE DEPOSITION OR ACTIVATION OF NUCLEOTIDES 有权

    公开(公告)号：US20220410154A1

    公开(公告)日：2022-12-29

    申请号：US17898663

    申请日：2022-08-30

    Applicant: ILLUMINA, INC.

    Inventor： Ali Agah ,  Aathavan Karunakaran ,  Tarun Khurana ,  Stanley Hong ,  Merek Siu ,  Arvin Emadi ,  Craig Ciesla

    IPC: B01L3/00 ,  G11C13/02 ,  B01J19/00

    Abstract: An apparatus includes a flow cell body, a plurality of electrodes, an integrated circuit, and an imaging assembly. The flow cell body defines one or more flow channels and a plurality of wells. Each flow channel is configured to receive a flow of fluid. Each well is fluidically coupled with the corresponding flow channel. Each well is configured to contain at least one polynucleotide. Each electrode is positioned in a corresponding well of the plurality of wells. The electrodes are operable to effect writing of polynucleotides in the corresponding wells. The integrated circuit is operable to drive selective deposition or activation of selected nucleotides to attach to polynucleotides in the wells to thereby generate polynucleotides representing machine-written data in the wells. The imaging assembly is operable to capture images indicative of one or more nucleotides in a polynucleotide.

    FLOW CELL WITH ONE OR MORE BARRIER FEATURES
    14.
    发明申请
    FLOW CELL WITH ONE OR MORE BARRIER FEATURES 有权

    公开(公告)号：US20220317100A1

    公开(公告)日：2022-10-06

    申请号：US17846538

    申请日：2022-06-22

    Applicant: ILLUMINA, INC.

    Inventor： Tarun Khurana ,  Ali Agah ,  Aathavan Karunakaran ,  Stanley Hong ,  Merek Siu ,  Arvin Emadi ,  Craig Ciesla

    IPC: G01N30/74 ,  C12Q1/6874

    Abstract: An apparatus includes a flow cell body, a plurality of electrodes, an imaging assembly, and one or more barrier features. The flow cell body defines one or more flow channels and a plurality of wells defined as recesses in the floor of each flow channel. Each well is fluidically coupled with the corresponding flow channel. The flow cell body further defines interstitial surfaces between adjacent wells. Each well defines a corresponding depth. Each electrode is positioned in a corresponding well of the plurality of wells. The electrodes are to effect writing of polynucleotides in the wells. The imaging assembly is to capture images of polynucleotides written in the wells. The one or more barrier features are positioned in the wells, between the wells, or above the wells. The one or more barrier features contain reactions in each well, reduce diffusion between the wells, or reduce optical cross-talk between the wells.

    CONTEXT-DEPENDENT BASE CALLING
    16.
    发明公开
    CONTEXT-DEPENDENT BASE CALLING 审中-公开

    公开(公告)号：US20240212791A1

    公开(公告)日：2024-06-27

    申请号：US18391487

    申请日：2023-12-20

    Applicant: Illumina, Inc.

    Inventor： Gery Vessere ,  David Olmstead Bracher ,  Aathavan Karunakaran

    IPC: G16B30/00 ,  G16B40/00

    CPC classification number: G16B30/00 ,  G16B40/00

    Abstract: The technology disclosed is directed to context-dependent base calling. The technology disclosed describes a system including memory storing k-mer-specific centroids for k-mers. The k-mer-specific centroids are learned by training a base calling pipeline to represent base calls of an already base called sequence in k-mer-specific time series, transform the k-mer-specific time series into predicted k-mer-specific centroids, merge the predicted k-mer-specific centroids on a sequencing cycle-by-sequencing cycle basis to generate predicted per-sequencing cycle intensity values, determine a training loss (e.g., a transformation loss) based on comparing the predicted per-sequencing cycle intensity values against known intensity values of the base calls, update the predicted k-mer-specific centroids based on the determined training loss, and store the updated centroids as the k-mer-specific centroids. The system also includes runtime logic that uses the k-mer-specific centroids to base call bases in a yet-to-be base called sequence in dependence upon k-mer context.

    Flow cell with one or more barrier features
    17.
    发明授权
    Flow cell with one or more barrier features 有权

    公开(公告)号：US11867672B2

    公开(公告)日：2024-01-09

    申请号：US18107752

    申请日：2023-02-09

    Applicant: ILLUMINA, INC.

    Inventor： Tarun Khurana ,  Ali Agah ,  Aathavan Karunakaran ,  Stanley Hong ,  Merek Siu ,  Arvin Emadi ,  Craig Ciesla

    IPC: G01N30/74 ,  C12Q1/6874

    CPC classification number: G01N30/74 ,  C12Q1/6874 ,  G01N2030/746

    Abstract: An apparatus includes a flow cell body, a plurality of electrodes, an imaging assembly, and one or more barrier features. The flow cell body defines one or more flow channels and a plurality of wells defined as recesses in the floor of each flow channel. Each well is fluidically coupled with the corresponding flow channel. The flow cell body further defines interstitial surfaces between adjacent wells. Each well defines a corresponding depth. Each electrode is positioned in a corresponding well of the plurality of wells. The electrodes are to effect writing of polynucleotides in the wells. The imaging assembly is to capture images of polynucleotides written in the wells. The one or more barrier features are positioned in the wells, between the wells, or above the wells. The one or more barrier features contain reactions in each well, reduce diffusion between the wells, or reduce optical cross-talk between the wells.

    Obtaining information from a biological sample in a flow cell
    18.
    发明授权
    Obtaining information from a biological sample in a flow cell 有权

    公开(公告)号：US11835510B2

    公开(公告)日：2023-12-05

    申请号：US17470228

    申请日：2021-09-09

    Applicant: ILLUMINA, INC.

    Inventor： Tarun Khurana ,  Ali Agah ,  Aathavan Karunakaran ,  Xi-Jun Chen

    IPC: C12Q1/00 ,  G01N33/483 ,  G01N33/50 ,  G01N33/53 ,  A61K39/12

    CPC classification number: G01N33/4836 ,  G01N33/5047 ,  G01N33/5308 ,  A61K39/12 ,  G01N2500/10

    Abstract: Methods are used for obtaining, cataloguing, and/or storing data derived from a biological source using a flow cell body, electrodes, and an imaging assembly. The data may include DNA and/or RNA obtained from a biological source, such as from the cells of an organism. The methods may be used to obtain, catalog, and/or store data such as DNA or RNA sequence from a pathogen such as a virus and/or a bacteria, human health data over time, and immune system information from an individual. The data obtained using the disclosed methods may be used for a variety of different purposes, including the manufacture of vaccine compositions, and for restoring the immune system of an individual who has undergone an immune system depleting event. The methods may be used for storage of biological cells, which may be used for the screening of compounds, such as small molecules with potential for therapeutic indications.

    FLOW CELL WITH ONE OR MORE BARRIER FEATURES
    19.
    发明公开
    FLOW CELL WITH ONE OR MORE BARRIER FEATURES 审中-公开

    公开(公告)号：US20230184725A1

    公开(公告)日：2023-06-15

    申请号：US18107752

    申请日：2023-02-09

    Applicant: ILLUMINA, INC.

    Inventor： Tarun Khurana ,  Ali Agah ,  Aathavan Karunakaran ,  Stanley Hong ,  Merek Siu ,  Arvin Emadi ,  Craig Ciesla

    IPC: G01N30/74 ,  C12Q1/6874

    CPC classification number: G01N30/74 ,  C12Q1/6874 ,  G01N2030/746

    Abstract: An apparatus includes a flow cell body, a plurality of electrodes, an imaging assembly, and one or more barrier features. The flow cell body defines one or more flow channels and a plurality of wells defined as recesses in the floor of each flow channel. Each well is fluidically coupled with the corresponding flow channel. The flow cell body further defines interstitial surfaces between adjacent wells. Each well defines a corresponding depth. Each electrode is positioned in a corresponding well of the plurality of wells. The electrodes are to effect writing of polynucleotides in the wells. The imaging assembly is to capture images of polynucleotides written in the wells. The one or more barrier features are positioned in the wells, between the wells, or above the wells. The one or more barrier features contain reactions in each well, reduce diffusion between the wells, or reduce optical cross-talk between the wells.

    Flow cell with one or more barrier features
    20.
    发明授权
    Flow cell with one or more barrier features 有权

    公开(公告)号：US11604175B2

    公开(公告)日：2023-03-14

    申请号：US17846538

    申请日：2022-06-22

    Applicant: ILLUMINA, INC.

    Inventor： Tarun Khurana ,  Ali Agah ,  Aathavan Karunakaran ,  Stanley Hong ,  Merek Siu ,  Arvin Emadi ,  Craig Ciesla

    IPC: G01N30/74 ,  C12Q1/6874

    Abstract: An apparatus includes a flow cell body, a plurality of electrodes, an imaging assembly, and one or more barrier features. The flow cell body defines one or more flow channels and a plurality of wells defined as recesses in the floor of each flow channel. Each well is fluidically coupled with the corresponding flow channel. The flow cell body further defines interstitial surfaces between adjacent wells. Each well defines a corresponding depth. Each electrode is positioned in a corresponding well of the plurality of wells. The electrodes are to effect writing of polynucleotides in the wells. The imaging assembly is to capture images of polynucleotides written in the wells. The one or more barrier features are positioned in the wells, between the wells, or above the wells. The one or more barrier features contain reactions in each well, reduce diffusion between the wells, or reduce optical cross-talk between the wells.

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