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公开(公告)号：US20240084286A1
公开(公告)日：2024-03-14
申请号：US18273922
申请日：2022-01-25
申请人： The Broad Institute, Inc. , Massachusetts Institute of Technology , The General Hospital Corporation
发明人： Viktor A. Adalsteinsson , Shervin Tabrizi , Sangeeta N. Bhatia , J. Christopher Love , Maria Carmen Martin Alonso , Kan Xiong
CPC分类号： C12N15/1006 , A61K9/5123 , A61K38/005
摘要： This disclosure provides a method for substantially increasing the concentration of cfDNA in a patient. By injecting a patient with lipid and/or polymer nanoparticles, agents that bind cfDNA, or inhibit deoxyribonucleases prior to collection of a sample of cfDNA, e.g., by way of a liquid biopsy, major pathways for the degradation of cfDNA are temporarily blocked, permitting transient accumulation of cfDNA. This strategy has the potential to dramatically enhance the quality of detection achieved by downstream cfDNA e analytical applications, such as sequencing applications.
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公开(公告)号：US20240084287A1
公开(公告)日：2024-03-14
申请号：US18327345
申请日：2023-06-01
发明人： Paul Blainey , Navpreet Ranu , Todd Gierahn , J. Christopher Love
IPC分类号： C12N15/10 , C12N1/20 , C12Q1/6806 , C12Q1/6869 , C40B30/04 , C40B40/06 , C40B40/10 , C40B50/06
CPC分类号： C12N15/1006 , C12N1/205 , C12Q1/6806 , C12Q1/6869 , C40B30/04 , C40B40/06 , C40B40/10 , C40B50/06 , C12N2310/20 , C12R2001/465 , C12Y301/11 , C12Y302/02027
摘要： The present invention relates to the analysis of complex single cell sequencing libraries. Disclosed are methods for enrichment of library members based on the presence of cell-of origin barcodes to identify and concentrate DNA that is relevant to interesting cells or components that would be expensive or difficult to study otherwise. Also, disclosed are methods of capturing cDNA library molecules by use of CRISPR systems, hybridization or PCR. The present invention allows for identifying the properties of rare cells in single cell RNA-seq data and accurately profile them through clustering approaches. Further information on transcript abundances from subpopulations of single cells can be analyzed at a lower sequencing effort. The methods also allow for linking TCR alpha and beta chains at the single cell level.
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公开(公告)号：US11702649B2
公开(公告)日：2023-07-18
申请号：US16758640
申请日：2018-10-23
发明人： Paul Blainey , Navpreet Ranu , Todd Gierahn , J. Christopher Love
IPC分类号： C12N15/10 , C12Q1/6806 , C12Q1/6869 , C40B30/04 , C40B50/06 , C12N1/20 , C40B40/06 , C40B40/10 , C12R1/465
CPC分类号： C12N15/1006 , C12N1/205 , C12Q1/6806 , C12Q1/6869 , C40B30/04 , C40B40/06 , C40B40/10 , C40B50/06 , C12N2310/20 , C12R2001/465 , C12Y301/11 , C12Y302/02027
摘要： The present invention relates to the analysis of complex single cell sequencing libraries. Disclosed are methods for enrichment of library members based on the presence of cell-of origin barcodes to identify and concentrate DNA that is relevant to interesting cells or components that would be expensive or difficult to study otherwise. Also, disclosed are methods of capturing cDNA library molecules by use of CRISPR systems, hybridization or PCR. The present invention allows for identifying the properties of rare cells in single cell RNA-seq data and accurately profile them through clustering approaches. Further information on transcript abundances from subpopulations of single cells can be analyzed at a lower sequencing effort. The methods also allow for linking TCR alpha and beta chains at the single cell level.
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公开(公告)号：US11806714B2
公开(公告)日：2023-11-07
申请号：US17075116
申请日：2020-10-20
发明人： Armon R. Sharei , Viktor A. Adalsteinsson , Nahyun Cho , Robert S. Langer , J. Christopher Love , Klavs F. Jensen
IPC分类号： B01L3/00 , C12N5/09 , C12N5/078 , G01N15/14 , C12Q1/04 , G01N33/574 , G01N1/30 , G01N15/10 , B82Y30/00 , C12M3/06 , G01N15/00
CPC分类号： B01L3/502761 , C12N5/0634 , C12N5/0693 , C12Q1/04 , G01N15/1459 , G01N15/1484 , G01N33/574 , B01L2200/0652 , B01L2300/08 , B01L2400/0487 , B82Y30/00 , C12M23/16 , G01N1/30 , G01N2015/0065 , G01N2015/1006 , G01N2015/1081
摘要： Isolating or identifying a cell based on a physical property of said cell can include providing a cell suspension; passing said suspension through a microfluidic channel that includes a constriction; passing the cell suspension through the constriction; and, contacting said cell suspension solution with a compound. The constriction can be sized to preferentially deform a relatively larger cell compared to a relatively smaller cell.
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公开(公告)号：US20230348899A1
公开(公告)日：2023-11-02
申请号：US18333730
申请日：2023-06-13
发明人： Peter van Galen , Volker Hovestadt , Travis Hughes , Marc H. Wadsworth II , Bradley Bernstein , Alexander K. Shalek , Todd M. Gierahn , J. Christopher Love , Ang A. Tu
IPC分类号： C12N15/10 , C12Q1/6886 , C12Q1/6888 , C12Q1/686
CPC分类号： C12N15/1065 , C12Q1/686 , C12Q1/6886 , C12Q1/6888 , C12Q2600/158
摘要： The present invention relates to methods of detecting region(s) of interest in a gene comprising a polyA tail. The region(s) of interest can include gene(s), region(s), mutation(s), deletion(s), insertion(s), indel(s), and/or translocation(s). The region(s) can be greater than or less than 1 kilobases from the polyA tail. Methods can include forming a library of single cell transcripts comprising the region(s) in close proximity to a cell barcode and a unique molecular identifier (UMI). Methods for distinguishing cells by genotype can include amplifying the transcripts using PCR methods and detecting the cell barcode and UMI using single cell sequencing methods. Transcripts can be enriched using tagged region-specific PCR primers. Cell barcodes can be brought into close proximity to the region(s) by circularizing the transcripts. Sequencing of the transcripts can include using primer binding sites added during PCR amplification and library indexes for multiplexed sequencing.
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公开(公告)号：US11732257B2
公开(公告)日：2023-08-22
申请号：US16758485
申请日：2018-10-23
发明人： Peter van Galen , Volker Hovestadt , Travis Hughes , Marc H. Wadsworth, II , Bradley Bernstein , Alexander K. Shalek , Todd M. Gierahn , J. Christopher Love , Ang A. Tu
IPC分类号： C12P19/34 , C12N15/10 , C12Q1/686 , C12Q1/6886 , C12Q1/6888
CPC分类号： C12N15/1065 , C12Q1/686 , C12Q1/6886 , C12Q1/6888 , C12Q2600/158
摘要： The present invention relates to methods of detecting region(s) of interest in a gene comprising a polyA tail. The region(s) of interest can include gene(s), region(s), mutation(s), deletion(s), insertion(s), indel(s), and/or translocation(s). The region(s) can be greater than or less than 1 kilobases from the polyA tail. Methods can include forming a library of single cell transcripts comprising the region(s) in close proximity to a cell barcode and a unique molecular identifier (UMI). Methods for distinguishing cells by genotype can include amplifying the transcripts using PCR methods and detecting the cell barcode and UMI using single cell sequencing methods. Transcripts can be enriched using tagged region-specific PCR primers. Cell barcodes can be brought into close proximity to the region(s) by circularizing the transcripts. Sequencing of the transcripts can include using primer binding sites added during PCR amplification and library indexes for multiplexed sequencing.
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公开(公告)号：US10776608B2
公开(公告)日：2020-09-15
申请号：US16102118
申请日：2018-08-13
IPC分类号： G06K9/00 , B01L3/00 , G01N15/14 , G01N35/00 , G02B21/16 , G02B21/26 , H04N5/225 , G01N33/483 , G06K9/03 , G06K9/46 , G01N15/00 , G01N15/10
摘要： Described herein are systems, methods, and apparatus for automatically identifying and recovering individual cells of interest from a sample of biological matter, e.g., a biological fluid. Also described are methods of enriching a cell type of interest. These systems, methods, and apparatus allow for coordinated performance of two or more of the following, e.g., all with the same device, thereby enabling high throughput: cell enrichment, cell identification, and individual cell recovery for further analysis (e.g., sequencing) of individual recovered cells.
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公开(公告)号：US09953209B2
公开(公告)日：2018-04-24
申请号：US15085175
申请日：2016-03-30
IPC分类号： G06K9/00 , B01L3/00 , G01N15/14 , G01N35/00 , G02B21/16 , G02B21/26 , H04N5/225 , G01N33/483 , G06K9/03 , G06K9/46 , G01N15/00 , G01N15/10
CPC分类号： G06K9/00147 , B01L3/5085 , B01L2300/0654 , B01L2300/0829 , B01L2300/0851 , B01L2300/0896 , B01L2300/12 , G01N15/1425 , G01N15/1463 , G01N33/4833 , G01N35/00029 , G01N35/00871 , G01N2015/0065 , G01N2015/1006 , G01N2035/00148 , G02B21/16 , G02B21/26 , G06K9/0014 , G06K9/036 , G06K9/4647 , G06K9/4652 , G06K9/4661 , H04N5/2256
摘要： Described herein are systems, methods, and apparatus for automatically identifying and recovering individual cells of interest from a sample of biological matter, e.g., a biological fluid. Also described are methods of enriching a cell type of interest. These systems, methods, and apparatus allow for coordinated performance of two or more of the following, e.g., all with the same device, thereby enabling high throughput: cell enrichment, cell identification, and individual cell recovery for further analysis (e.g., sequencing) of individual recovered cells.
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公开(公告)号：US20160217315A1
公开(公告)日：2016-07-28
申请号：US15085175
申请日：2016-03-30
IPC分类号： G06K9/00 , G06K9/46 , G06K9/03 , G01N33/483
CPC分类号： G06K9/00147 , B01L3/5085 , B01L2300/0654 , B01L2300/0829 , B01L2300/0851 , B01L2300/0896 , B01L2300/12 , G01N15/1425 , G01N15/1463 , G01N33/4833 , G01N35/00029 , G01N35/00871 , G01N2015/0065 , G01N2015/1006 , G01N2035/00148 , G02B21/16 , G02B21/26 , G06K9/0014 , G06K9/036 , G06K9/4647 , G06K9/4652 , G06K9/4661 , H04N5/2256
摘要： Described herein are systems, methods, and apparatus for automatically identifying and recovering individual cells of interest from a sample of biological matter, e.g., a biological fluid. Also described are methods of enriching a cell type of interest. These systems, methods, and apparatus allow for coordinated performance of two or more of the following, e.g., all with the same device, thereby enabling high throughput: cell enrichment, cell identification, and individual cell recovery for further analysis (e.g., sequencing) of individual recovered cells.
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10.发明申请SYSTEMS, METHODS, AND APPARATUS FOR IN VITRO SINGLE-CELL IDENTIFICATION AND RECOVERY 审中-公开体外单细胞识别和恢复的系统，方法和装置公开(公告)号：US20160209319A1
公开(公告)日：2016-07-21
申请号：US14997439
申请日：2016-01-15
CPC分类号： G06K9/00147 , B01L3/5085 , B01L2300/0654 , B01L2300/0829 , B01L2300/0851 , B01L2300/0896 , B01L2300/12 , G01N15/1425 , G01N15/1463 , G01N33/4833 , G01N35/00029 , G01N35/00871 , G01N2015/0065 , G01N2015/1006 , G01N2035/00148 , G02B21/16 , G02B21/26 , G06K9/0014 , G06K9/036 , G06K9/4647 , G06K9/4652 , G06K9/4661 , H04N5/2256
摘要： Described herein are systems, methods, and apparatus for automatically identifying and recovering individual cells of interest from a sample of biological matter, e.g., a biological fluid. Also described are methods of enriching a cell type of interest. These systems, methods, and apparatus allow for coordinated performance of two or more of the following, e.g., all with the same device, thereby enabling high throughput: cell enrichment, cell identification, and individual cell recovery for further analysis (e.g., sequencing) of individual recovered cells.
摘要翻译： 本文描述了用于从生物物质样品（例如生物流体）自动识别和回收感兴趣的个体细胞的系统，方法和装置。 还描述了丰富感兴趣的细胞类型的方法。 这些系统，方法和装置允许以下两个或多个以下协调的性能，例如全部具有相同的装置，从而实现高吞吐量：细胞富集，细胞鉴定和单个细胞恢复用于进一步分析（例如，测序） 的个体回收细胞。
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