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：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.

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.

公开(公告)号：US20210327544A1

公开(公告)日：2021-10-21

申请号：US17233029

申请日：2021-04-16

Applicant: 10x Genomics, Inc.

Inventor： David Jaffe ,  Sreenath Krishnan ,  Wyatt McDonnell ,  Michael Stubbington

IPC: G16B45/00 ,  G16B25/10 ,  G16B30/00

Abstract: An interactive visualization system is disclosed herein. The system includes a data source, user input device, processor, and display. The data source obtains a B cell receptor and/or T cell receptor data source. The user input device receives a user selected parameter under which to analyze the data set. The processor identifies a clonotype group in the data set using the parameter, identifies subclonotypes within the clonotype group (wherein each identified subclonotype comprises cells having identical V(D)J transcripts), and processes the data to define a visualization model that can display a compressed view of the identified clonotype group. The display renders a visualization of said data set according to said visualization model. The visualization displays the clonotype group by identified subclonotype.

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

IPC: G01N33/48 ,  G01N33/50 ,  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.