公开(公告)号：US20240354607A1

公开(公告)日：2024-10-24

申请号：US18629826

申请日：2024-04-08

Applicant: 10X Genomics, Inc.

Inventor： Alexander Y. Wong ,  Jeffrey Mellen ,  Kevin J. Wu ,  Paul Ryvkin ,  Preyas Shah ,  Patrick Marks ,  Niranjan Srinivas

IPC: G06N7/01 ,  G06F16/28 ,  G06F16/904 ,  G16B25/10 ,  G16B40/00 ,  G16B45/00 ,  G16B50/30

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.

公开(公告)号：US20240339178A1

公开(公告)日：2024-10-10

申请号：US18742999

申请日：2024-06-13

Applicant: 10x Genomics, Inc.

Inventor： Sofia Kyriazopoulou-Panagiotopoulou ,  Patrick Marks

IPC: G16B40/00 ,  C12Q1/6809 ,  C12Q1/6869 ,  C40B40/06 ,  G06F18/24 ,  G06N5/01 ,  G06N5/025 ,  G06N7/01 ,  G16B5/00 ,  G16B20/00 ,  G16B25/00 ,  G16B30/20

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.

公开(公告)号：US20190332963A1

公开(公告)日：2019-10-31

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

IPC: G06N7/00 ,  G06F16/28 ,  G06F16/904

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.

公开(公告)号：US10366777B2

公开(公告)日：2019-07-30

申请号：US15842647

申请日：2017-12-14

Applicant: 10X Genomics, Inc.

Inventor： Sofia Kyriazopoulou-Panagiotopoulou ,  Patrick Marks

IPC: G01N33/48 ,  G01N33/50 ,  G16B40/00 ,  G16B5/00 ,  G16B20/00 ,  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 events by calculating a plurality of 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.

公开(公告)号：US20190065664A1

公开(公告)日：2019-02-28

申请号：US15842647

申请日：2017-12-14

Applicant: 10X Genomics, Inc.

Inventor： Sofia Kyriazopoulou-Panagiotopoulou ,  Patrick Marks

IPC: G06F19/12 ,  G06K9/62 ,  C40B40/06

CPC classification number: G16B40/00 ,  B01J2219/00317 ,  C12Q1/6809 ,  C12Q1/6869 ,  C40B40/06 ,  G06K9/6267 ,  G06N5/003 ,  G06N5/025 ,  G16B5/00 ,  G16B20/00 ,  G16B25/00 ,  G16B30/20

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 events by calculating a plurality of 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.

公开(公告)号：US20170235876A1

公开(公告)日：2017-08-17

申请号：US15242256

申请日：2016-08-19

Applicant: 10X GENOMICS, INC.

Inventor： David Jaffe ,  Patrick Marks ,  Michael Schnall-Levin ,  Neil Weisenfeld

IPC: G06F19/22

CPC classification number: G16B30/00

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.

公开(公告)号：US20250059606A1

公开(公告)日：2025-02-20

申请号：US18934042

申请日：2024-10-31

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.

公开(公告)号：US20240384348A1

公开(公告)日：2024-11-21

申请号：US18786391

申请日：2024-07-26

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.

公开(公告)号：US20210295947A1

公开(公告)日：2021-09-23

申请号：US17098139

申请日：2020-11-13

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

IPC: G16B20/20 ,  G16B30/00 ,  G16B20/00 ,  G16B30/10

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.

公开(公告)号：US20210134393A1

公开(公告)日：2021-05-06

申请号：US16934994

申请日：2020-07-21

Applicant: 10X Genomics, Inc.

Inventor： Sofia Kyriazopoulou-Panagiotopoulou ,  Patrick Marks

IPC: G16B40/00 ,  G16B5/00 ,  G16B20/00 ,  G16B30/20 ,  G06N7/00 ,  C40B40/06 ,  G06K9/62

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.