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Systems and methods for identifying morphological patterns in tissue samples

A technology of morphology and patterns, applied in the preparation of test samples, biochemical equipment and methods, character and pattern recognition, etc., can solve problems such as huge and complex sequencing data sets

Active Publication Date: 2022-07-15
10X GENOMICS
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

[0007] However, such sequencing datasets are complex and often bulky, and the techniques used to map gene expression to specific regions of biological samples are labor-intensive

Method used

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  • Systems and methods for identifying morphological patterns in tissue samples
  • Systems and methods for identifying morphological patterns in tissue samples
  • Systems and methods for identifying morphological patterns in tissue samples

Examples

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example 1

[0321] refer to Image 6 , an example visualization system 100 including multiple processing cores, persistent memory, and non-persistent memory is used to perform a method for visualizing patterns in a dataset. In this example, the example visualization system 100 is a DELL Inspiron 177000 with Microsoft WINDOWS 10PRO, 16.0 gigabytes of RAM memory, and a computer with 4 cores and 8 logical processors with visualization modules 119 installed. Intel i7-8565U CPM running at 4.50 GHz. A discrete attribute value dataset 120 is stored in persistent storage, the discrete attribute value dataset including a single spatial image 125 of the tissue sample and concomitant dispersion of hundreds of loci at each of hundreds of probe spots 126 Property value 124. Using principal components derived from discrete attribute values ​​across each of the plurality of probe spots 126 across each of the plurality of loci, prior to loading into the example computer system 100 The dataset is clust...

example 2

[0328] Triple negative breast cancer (TNBC) accounts for 10-20% of all breast cancer cases diagnosed in the United States. TNBC is aggressive and exhibits poor prognosis due to resistance to conventional therapies. TNBC is complex, so understanding the underlying biology to improve outcomes is important.

[0329] Combined with the benefits of histological techniques and the massive throughput of RNA-seq, spatial transcriptomics techniques have helped address the limitations of traditional pathology examinations. Serial sections of TNBC were studied using the 10x Genomics Visium Spatial Gene Expression Solution disclosed in this disclosure, and were also disclosed to address their tumorigenic expression profiles in: Filed August 13, 2020 entitled " Systems and Methods for Determining Biological State Using Spatial Distribution of Haplotypes," US Patent Application Serial No. 16 / 992,569, Attorney Docket No. 104371-5026-US, which is hereby incorporated by reference. In the case...

example 3

[0333] The gut microbiota, populated by trillions of microorganisms, interacts closely with the host's cellular systems. The study revealed information about the average microbiota diversity and bacterial activity in the gut. However, this study of expression-based host-microbiome interactions in a spatial and high-throughput manner is a novel approach. Understanding gene expression mapping of host-microbiome interactions can provide insights into the molecular basis and broad understanding of bacterial communication mechanisms. US Patent Application No. 16 / 992,569, entitled "Systems and Methods for Determining Biological State Using the Spatial Distribution of Haplotypes," filed August 13, 2020, using the techniques disclosed herein, and also as filed at Attorney General's Reference Described in Case No. 104371-5026-US, which US patent application is hereby incorporated by reference, develops a spatial transcriptomic method that enables direct Visualize and quantify gene ex...

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Abstract

A discrete attribute value dataset associated with a plurality of probe spots each assigned a different probe spot barcode is obtained. The data set includes spatial projections, each including an image of a biological sample. Each image contains a corresponding plurality of discrete attribute values for the probe spot. Each such value is associated with a probe spot of the plurality of probe spots based on the probe spot barcode. The data set is clustered across the image of the projection using the discrete attribute values of a plurality of loci at each respective probe spot, or a dimensionally reduced component thereof, thereby assigning each probe spot to a cluster of a plurality of clusters. Morphological patterns are identified from the spatial arrangement of the probe spots in each cluster.

Description

[0001] CROSS-REFERENCE TO RELATED APPLICATIONS [0002] This application claims US Provisional Patent Application No. 63 / 041,823, entitled "Systems and Methods for Identifying Morphological Patterns in Tissue Samples," filed June 20, 2020 , the US Provisional Patent Application is hereby incorporated by reference in its entirety. This application also claims US Provisional Patent Application No. 62 / 980,077, filed February 21, 2020, entitled "Systems and Methods for Visualizing a Pattern in a Dataset" , said US Provisional Patent Application is hereby incorporated by reference in its entirety. This application also claims US Provisional Patent Application No. 62 / 909,071, entitled "Systems and Methods for Visualizing a Pattern in a Dataset," filed October 1, 2019 , the US Provisional Patent Application is hereby incorporated by reference in its entirety. technical field [0003] This specification describes techniques involved in visualizing patterns in large, complex dataset...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06T7/00C12Q1/68G06K9/62G06V10/762
CPCG06T7/0012G16B15/00G01N1/30G06T2207/30024G01N2001/302G06V10/762G06F18/2137G06F18/23
Inventor J·C·梅林J·斯塔布K·J·吴N·I·韦森菲尔德F·鲍姆加特纳B·克莱普尔
Owner 10X GENOMICS
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