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    REFERENCE FREE SPOT DECONVOLUTION IN SPATIAL TRANSCRIPTOMICS
    2.
    发明公开
    REFERENCE FREE SPOT DECONVOLUTION IN SPATIAL TRANSCRIPTOMICS 审中-公开

    公开(公告)号：US20240287599A1

    公开(公告)日：2024-08-29

    申请号：US18587627

    申请日：2024-02-26

    Applicant: 10x Genomics, Inc.

    Inventor： Stephen R. Williams ,  Govinda M. Kamath ,  Joseph Glenn Arthur

    IPC: C12Q1/6874 ,  C12Q1/6841 ,  C12Q1/6881 ,  G16B20/00 ,  G16B40/20

    CPC classification number: C12Q1/6874 ,  C12Q1/6881 ,  G16B20/00 ,  G16B40/20 ,  C12Q1/6841

    Abstract: Systems and methods for determining cell type are provided. Information is obtained including, for each spot in a set of capture spots, a position in a tissue image and analyte abundances in the tissue. A current iteration of cell types, set to a maximum number, is determined using the analyte abundances, where each cell type has an abundance value for each analyte. When the current iteration exceeds a minimum number of cell types, a distance metric between each cell type in the current iteration is determined based on cell type analyte abundance values and the current iteration is reformed by merging a first and second cell type having a smallest distance metric. The procedure is repeated until the current iteration matches the minimum number. For each current iteration, output is determined including, for each cell type, for each spot, a proportion of cells in the spot having the cell type.

    SYSTEMS AND METHODS FOR IDENTIFYING REGIONS OF ANEUPLOIDY IN A TISSUE
    5.
    发明公开
    SYSTEMS AND METHODS FOR IDENTIFYING REGIONS OF ANEUPLOIDY IN A TISSUE 审中-公开

    公开(公告)号：US20230167495A1

    公开(公告)日：2023-06-01

    申请号：US18054474

    申请日：2022-11-10

    Applicant: 10X Genomics, Inc.

    Inventor： Stephen R. Williams ,  Juan Pablo Romero Riojas

    IPC: C12Q1/6869 ,  G16B20/20

    CPC classification number: C12Q1/6869 ,  G16B20/20

    Abstract: Systems and methods for identifying regions of aneuploidy in a tissue include obtaining nucleic acid sequence reads, each including a spatial barcode, associating the read with a feature in a two-dimensional array of features on a substrate contacting the tissue, and a unique molecular identifier (UMI). The reads serve to determine a count data structure comprising, for each of a plurality of genomic regions, a respective UMI count for each feature in the two-dimensional array of features on the substrate. For each feature in the array of features, a respective bin count is made for each respective bin in a plurality of bins corresponding to the respective feature, where the plurality of bins span a genome. Copy number state respective features in the array are determined using feature bin counts. The copy number state of each feature in the array of features serves to identify regions of tissue aneuploidy.

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