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公开(公告)号：US12163191B2
公开(公告)日：2024-12-10
申请号：US16898984
申请日：2020-06-11
Applicant: 10X GENOMICS, INC.
Inventor： Michael Schnall-Levin , Mirna Jarosz , Christopher Hindson , Kevin Ness , Serge Saxonov , Benjamin Hindson , Xinying Zheng , Patrick Marks , John Stuelpnagel
IPC: C12Q1/6883 , C12Q1/6827 , G16B30/00 , G16B30/10 , G16B30/20
Abstract: The present disclosure relates to methods, compositions and systems for haplotype phasing and copy number variation assays. Included within this disclosure are methods and systems for combining the barcode comprising beads with samples in multiple separate partitions, as well as methods of processing, sequencing and analyzing barcoded samples.
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公开(公告)号：US11954614B2
公开(公告)日：2024-04-09
申请号：US16442800
申请日：2019-06-17
Applicant: 10X Genomics, Inc.
Inventor： Alexander Y. Wong , Jeffrey Mellen , Kevin J. Wu , Paul Ryvkin , Preyas Shah , Patrick Marks , Niranjan Srinivas
CPC classification number: G06N7/01 , G06F16/285 , G06F16/904 , G16B25/10 , G16B40/00 , G16B45/00 , G16B50/30
Abstract: A visualization system comprising a persistent memory, storing a dataset, and a non-persistent memory implements a pattern visualizing method. The dataset contains discrete attribute values for each first entity of a first type in a plurality of first entities of the first type and discrete attribute values for each first entity of a second type in a plurality of first entities of the second type for each second entity in a plurality of second entities. The dataset is compressed by blocked compression and represents discrete attribute values in both compressed sparse row and column formats. The discrete attribute values are clustered to assign each second entity to a cluster in a plurality of clusters.
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公开(公告)号：US11081208B2
公开(公告)日：2021-08-03
申请号：US15242256
申请日：2016-08-19
Applicant: 10X GENOMICS, INC.
Inventor： David Jaffe , Patrick Marks , Michael Schnall-Levin , Neil Weisenfeld
Abstract: Described are computer-implemented methods, systems, and media for de novo phased diploid assembly of nucleic acid sequence data generated from a nucleic acid sample of an individual utilizing nucleic acid tags to preserve long-range sequence context for the individual such that a subset of short-read sequence data derived from a common starting sequence shares a common tag. The phased diploid assembly is achieved without alignment to a reference sequence derived from organisms other than the individual. The methods, systems, and media described are computer-resource efficient, allowing scale-up.
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公开(公告)号：US20210123103A1
公开(公告)日：2021-04-29
申请号：US16898984
申请日：2020-06-11
Applicant: 10X GENOMICS, INC.
Inventor： Michael Schnall-Levin , Mirna Jarosz , Christopher Hindson , Kevin Ness , Serge Saxonov , Benjamin Hindson , Xinying Zheng , Patrick Marks , John Stuelpnagel
IPC: C12Q1/6883 , G16B30/00 , C12Q1/6827
Abstract: The present disclosure relates to methods, compositions and systems for haplotype phasing and copy number variation assays. Included within this disclosure are methods and systems for combining the barcode comprising beads with samples in multiple separate partitions, as well as methods of processing, sequencing and analyzing barcoded samples.
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5.发明授权公开(公告)号：US10854315B2
公开(公告)日：2020-12-01
申请号：US15019928
申请日：2016-02-09
Applicant: 10X Genomics, Inc.
Inventor： Sofia Kyriazopoulou-Panagiotopoulou , Patrick Marks , Michael Schnall-Levin , Xinying Zheng , Mirna Jarosz , Serge Saxonov , Kristina Giorda , Patrice Mudivarti , Heather Ordonez , Jessica Terry , William Haynes Heaton
Abstract: Systems and methods for determining structural variation and phasing using variant call data obtained from nucleic acid of a biological sample are provided. Sequence reads are obtained, each comprising a portion corresponding to a subset of the test nucleic acid and a portion encoding a barcode independent of the sequencing data. Bin information is obtained. Each bin represents a different portion of the sample nucleic acid. Each bin corresponds to a set of sequence reads in a plurality of sets of sequence reads formed from the sequence reads such that each sequence read in a respective set of sequence reads corresponds to a subset of the nucleic acid represented by the bin corresponding to the respective set. Binomial tests identify bin pairs having more sequence reads with the same barcode in common than expected by chance. Probabilistic models determine structural variation likelihood from the sequence reads of these bin pairs.
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Patent Agency Ranking
公开(公告)号：US12054773B2
公开(公告)日：2024-08-06
申请号：US17003790
申请日：2020-08-26
Applicant: 10X GENOMICS, INC.
Inventor： Vijay Kumar Sreenivasa Gopalan , Paul Ryvkin , Zachary Bent , Jessica Michele Terry , David Jaffe , Patrick Marks , Tarjei Sigurd Mikkelsen
IPC: C12Q1/68 , C12N15/10 , C12Q1/6806 , C12Q1/6844 , C12Q1/6869
CPC classification number: C12Q1/6869 , C12N15/1096 , C12Q1/6806 , C12Q1/6844
Abstract: The present disclosure provides methods and systems for producing full-length sequencing information of transcriptomes from single cells or from the bulk. Random ligation and circularization of barcoded or non-barcoded complementary deoxyribonucleic molecules can be used to provide a circular template for amplification and subsequent sequencing.
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公开(公告)号：US12046330B2
公开(公告)日：2024-07-23
申请号：US16934994
申请日：2020-07-21
Applicant: 10X Genomics, Inc.
Inventor： Sofia Kyriazopoulou-Panagiotopoulou , Patrick Marks
IPC: G01N33/48 , C40B40/06 , G01N33/50 , G06F18/24 , G06N7/01 , G16B5/00 , G16B20/00 , G16B30/20 , G16B40/00 , C12Q1/6809 , C12Q1/6869 , G06N5/01 , G06N5/025 , G16B25/00
CPC classification number: G16B40/00 , C40B40/06 , G06F18/24 , G06N7/01 , G16B5/00 , G16B20/00 , G16B30/20 , B01J2219/00317 , C12Q1/6809 , C12Q1/6869 , G06N5/01 , G06N5/025 , G16B25/00
Abstract: Systems and methods for analyzing first and second strings against a ground truth string are provided. A construct representing a plurality of components is obtained, each component for a different portion of the truth string. The construct comprises a plurality of measurement string sampling pools each having an identifier and a corresponding plurality of measurement samplings corresponding to one or two of the components. Each sampling has the identifier and a portion of the first or second string. Samplings are assigned to first, second or third classes when coding a portion of the first string, second string, or both the first and second string. First and second positions are tested for sequence events by calculating a plurality of sequence event models using assumptions on the components having samplings encompassing the first and second positions and class assignments. These assumptions are updated using the calculated models and the models are recalculated.
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公开(公告)号：US20210047684A1
公开(公告)日：2021-02-18
申请号：US17003790
申请日：2020-08-26
Applicant: 10X GENOMICS, INC.
Inventor： Vijay Kumar Sreenivasa Gopalan , Paul Ryvkin , Zachary Bent , Jessica Michele Terry , David Jaffe , Patrick Marks , Tarjei Sigurd Mikkelsen
IPC: C12Q1/6869 , C12Q1/6806 , C12N15/10 , C12Q1/6844
Abstract: The present disclosure provides methods and systems for producing full-length sequencing information of transcriptomes from single cells or from the bulk. Random ligation and circularization of barcoded or non-barcoded complementary deoxyribonucleic molecules can be used to provide a circular template for amplification and subsequent sequencing.
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公开(公告)号：US10748643B2
公开(公告)日：2020-08-18
申请号：US15692316
申请日：2017-08-31
Applicant: 10X Genomics, Inc.
Inventor： Sofia Kyriazopoulou-Panagiotopoulou , Patrick Marks
IPC: G01N33/48 , G01N33/50 , G16B40/00 , G16B5/00 , G16B20/00 , G16B30/20 , G06N7/00 , C40B40/06 , G06K9/62 , G06N5/00 , G06N5/02 , C12Q1/6809 , G16B25/00 , C12Q1/6869
Abstract: Systems and methods for analyzing first and second strings against a ground truth string are provided. A construct representing a plurality of components is obtained, each component for a different portion of the truth string. The construct comprises a plurality of measurement string sampling pools each having an identifier and a corresponding plurality of measurement samplings corresponding to one or two of the components. Each sampling has the identifier and a portion of the first or second string. Samplings are assigned to first, second or third classes when coding a portion of the first string, second string, or both the first and second string. First and second positions are tested for sequence events by calculating a plurality of sequence event models using assumptions on the components having samplings encompassing the first and second positions and class assignments. These assumptions are updated using the calculated models and the models are recalculated.
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公开(公告)号：US20150376700A1
公开(公告)日：2015-12-31
申请号：US14752589
申请日：2015-06-26
Applicant: 10X Genomics, Inc.
Inventor： Michael Schnall-Levin , Mirna Jarosz , Christopher Hindson , Kevin Ness , Serge Saxonov , Benjamin Hindson , Grace X. Y. Zheng , Patrick Marks , John Stuelpnagel
CPC classification number: C12Q1/6883 , C12Q1/6827 , C12Q2600/156 , G16B30/00 , C12Q2535/122 , C12Q2537/16 , C12Q2563/159 , C12Q2565/629
Abstract: The present disclosure relates to methods, compositions and systems for haplotype phasing and copy number variation assays. Included within this disclosure are methods and systems for combining the barcode comprising beads with samples in multiple separate partitions, as well as methods of processing, sequencing and analyzing barcoded samples.
Abstract translation: 本公开涉及用于单倍型定相和拷贝数变异测定的方法，组合物和系统。 本公开内容包括用于将包含珠粒的条形码与多个单独分区中的样本组合的方法和系统，以及处理，排序和分析条形码样本的方法。
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