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    COPY NUMBER VARIATION (CNV) BREAKPOINT DETECTION
    32.
    发明公开
    COPY NUMBER VARIATION (CNV) BREAKPOINT DETECTION 审中-公开

    公开(公告)号：US20240112751A1

    公开(公告)日：2024-04-04

    申请号：US18477346

    申请日：2023-09-28

    申请人： Illumina, Inc.

    发明人： Anindita Dutta ,  Elahe Aghapour

    IPC分类号： G16B20/10 ,  G16B40/00

    CPC分类号： G16B20/10 ,  G16B40/00

    摘要： A method of processing sequence data comprising a known location of the start of a copy number variant breakpoint to generate a prediction for the location of the end of the copy number variant breakpoint. The method comprises an encoder and a copy number variation (CNV) caller guide. The encoder processes an anchor sequence and corresponding subject candidate sequence to generate a learned representation of the anchor sequence and a learned representation of the corresponding subject candidate sequence. The CNV caller guide determines a similarity between the learned representation of the anchor sequence and a learned representation of the corresponding subject candidate sequence. Similarity between anchor sequence and subject candidate sequence is used as a proxy for likelihood that the end of the CNV breakpoint is located on the subject candidate sequence.

    FAST PULSING FOR NANOPORE SENSORS
    33.
    发明公开
    FAST PULSING FOR NANOPORE SENSORS 审中-公开

    公开(公告)号：US20240110889A1

    公开(公告)日：2024-04-04

    申请号：US18471484

    申请日：2023-09-21

    申请人： ILLUMINA, INC.

    发明人： Boyan Boyanov

    IPC分类号： G01N27/447 ,  C12Q1/6869

    CPC分类号： G01N27/44713 ,  C12Q1/6869 ,  G01N27/44791

    摘要： Sequencing systems and methods are provided that include a nanopore well that includes a cis well associated with a cis electrode and a trans well associated with a trans electrode, a membrane separating the cis well and the trans well, and a nanopore well embedded in the membrane providing a channel through the membrane; a command node connected directly to the nanopore well. The command node is configured to apply a potential across the nanopore well and a command pulse. The system further includes an amplifier with a feedback loop coupled to the nanopore well and a switch disposed between the amplifier and the nanopore well. The switch is driven by a clock pulse and configured to ground an inverting input of the amplifier.

    QUALITY SCORE COMPRESSION
    37.
    发明公开
    QUALITY SCORE COMPRESSION 审中-公开

    公开(公告)号：US20240062853A1

    公开(公告)日：2024-02-22

    申请号：US18237187

    申请日：2023-08-23

    申请人： Illumina, Inc.

    发明人： Guillaume Alexandre Pascal Rizk

    IPC分类号： G16B50/50 ,  H03M7/30

    CPC分类号： G16B50/50 ,  H03M7/3071 ,  H03M7/6011

    摘要： Methods, systems, and computer programs for compressing nucleic acid sequence data. A method can include obtaining nucleic acid sequence data representing: (i) a read sequence, and (ii) a plurality of quality scores, determining whether the read sequence includes at least one “N” base, based on a determination that the read sequence includes at least one “N” base, generating, by one or more computers, a first encoding data set by using a first encoding process to encode each set of four quality scores of the read sequence into a single byte of memory, and using a second encoding process to encode the first encoded data set, thereby compressing the data to be compressed.

    Flexible Seed Extension for Hash Table Genomic Mapping
    38.
    发明公开
    Flexible Seed Extension for Hash Table Genomic Mapping 审中-公开

    公开(公告)号：US20240061843A1

    公开(公告)日：2024-02-22

    申请号：US18497830

    申请日：2023-10-30

    申请人： Illumina, Inc.

    发明人： Michael Ruehle

    IPC分类号： G06F16/2455 ,  G06F16/22 ,  G16B30/10

    CPC分类号： G06F16/24566 ,  G06F16/2282 ,  G16B30/10

    摘要： Methods, systems, and apparatuses, including computer programs for generating and using a hash table configured to improve mapping of reads are disclosed that include obtaining a first seed of K nucleotides from a reference sequence, generating a seed extension tree having a nodes, wherein each node of the nodes corresponds to (i) an extended seed that is an extension of the first seed and has a nucleotide length of K* and (ii) one or more locations, in a seed extension table, that include data describing reference sequence locations that match the extended seed, and for each node: storing interval information at a location of the hash table that corresponds to an index key for the extended seed, wherein the interval information references one or more locations in the seed extension table that include reference sequence locations that match the extended seed associated with the node.

    OBTAINING INFORMATION FROM A BIOLOGICAL SAMPLE IN A FLOW CELL
    39.
    发明公开
    OBTAINING INFORMATION FROM A BIOLOGICAL SAMPLE IN A FLOW CELL 审中-公开

    公开(公告)号：US20240060954A1

    公开(公告)日：2024-02-22

    申请号：US18385442

    申请日：2023-10-31

    申请人： ILLUMINA, INC.

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

    IPC分类号： G01N33/483 ,  G01N33/50 ,  G01N33/53

    CPC分类号： G01N33/4836 ,  G01N33/5047 ,  G01N33/5308 ,  A61K39/12

    摘要： 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.