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    SOMATIC COPY NUMBER VARIATION DETECTION
    14.
    发明公开
    SOMATIC COPY NUMBER VARIATION DETECTION 审中-公开

    公开(公告)号：US20230207048A1

    公开(公告)日：2023-06-29

    申请号：US16333933

    申请日：2017-09-21

    Applicant: ILLUMINA, INC.

    Inventor： Han-Yu Chuang ,  Chen Zhao

    IPC: G16B20/10 ,  G16B20/20 ,  G16B30/10

    CPC classification number: G16B20/10 ,  G16B20/20 ,  G16B30/10

    Abstract: Presented herein are techniques for assessing copy number variation. The techniques include generating a baseline representative of or mimicing a hypothetical matched sample for an individual biological sample from a set of baseline samples that are not matched to the biological sample. Normalized sequencing data from the set of baseline samples that includes at least one copy number baseline for a region of interest is provided to a user.

    SYSTEMS AND METHODS FOR GROUPING AND COLLAPSING SEQUENCING READS
    18.
    发明公开
    SYSTEMS AND METHODS FOR GROUPING AND COLLAPSING SEQUENCING READS 审中-公开

    公开(公告)号：US20230282309A1

    公开(公告)日：2023-09-07

    申请号：US18316939

    申请日：2023-05-12

    Applicant: Illumina, Inc.

    Inventor： Chen Zhao ,  Kevin Eric Wu ,  Sven Bilke

    IPC: G16B30/10 ,  G06F16/22 ,  G06F16/2457 ,  G16B30/20

    CPC classification number: G16B30/10 ,  G06F16/2255 ,  G06F16/24578 ,  G16B30/20

    Abstract: Disclosed herein are systems and methods for collapsing sequencing reads and identifying similar sequencing reads. In one example, a method includes generating a plurality of first identifier subsequences from a first identifier sequence of each nucleotide sequencing read and generating a first signature for the nucleotide sequencing read by applying hashing to the plurality of first identifier subsequences. The method may include assigning the nucleotide sequencing read to a first particular bin of a first data structure based on the first signature and determining a nucleotide sequence for each first particular bin of the first data structure with one or more nucleotide sequencing reads assigned.

    METHODS AND SYSTEMS FOR GENERATION AND ERROR-CORRECTION OF UNIQUE MOLECULAR INDEX SETS WITH HETEROGENEOUS MOLECULAR LENGTHS
    19.
    发明申请
    METHODS AND SYSTEMS FOR GENERATION AND ERROR-CORRECTION OF UNIQUE MOLECULAR INDEX SETS WITH HETEROGENEOUS MOLECULAR LENGTHS 有权

    公开(公告)号：US20210079462A1

    公开(公告)日：2021-03-18

    申请号：US17073074

    申请日：2020-10-16

    Applicant: Illumina, Inc.

    Inventor： Kevin Wu ,  Chen Zhao ,  Han-Yu Chuang ,  Alex So ,  Stephen Tanner ,  Stephen M. Gross

    IPC: C12Q1/6869 ,  C12Q1/6855 ,  G16B25/00 ,  G16B30/00

    Abstract: The disclosed embodiments concern methods, apparatus, systems and computer program products for determining sequences of interest using unique molecular index sequences that are uniquely associable with individual polynucleotide fragments, including sequences with low allele frequencies and long sequence length. In some implementations, the unique molecular index sequences include variable-length nonrandom sequences. In some implementations, the unique molecular index sequences are associated with the individual polynucleotide fragments based on alignment scores indicating similarity between the unique molecular index sequences and subsequences of sequence reads obtained from the individual polynucleotide fragments. System, apparatus, and computer program products are also provided for determining a sequence of interest implementing the methods disclosed.

    Systems and methods for grouping and collapsing sequencing reads
    20.
    发明授权
    Systems and methods for grouping and collapsing sequencing reads 有权

    公开(公告)号：US12230365B2

    公开(公告)日：2025-02-18

    申请号：US18316939

    申请日：2023-05-12

    Applicant: Illumina, Inc.

    Inventor： Chen Zhao ,  Kevin Eric Wu ,  Sven Bilke

    IPC: G01N33/48 ,  G06F16/22 ,  G06F16/2457 ,  G16B30/10 ,  G16B30/20

    Abstract: Disclosed herein are systems and methods for collapsing sequencing reads and identifying similar sequencing reads. In one example, a method includes generating a plurality of first identifier subsequences from a first identifier sequence of each nucleotide sequencing read and generating a first signature for the nucleotide sequencing read by applying hashing to the plurality of first identifier subsequences. The method may include assigning the nucleotide sequencing read to a first particular bin of a first data structure based on the first signature and determining a nucleotide sequence for each first particular bin of the first data structure with one or more nucleotide sequencing reads assigned.

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