公开(公告)号：US20240263227A1

公开(公告)日：2024-08-08

申请号：US17904394

申请日：2021-02-17

申请人： Universal Sequencing Technology Corporation

发明人： Zhoutao Chen ,  Devin Porter ,  Haibiao Gong

IPC分类号： C12Q1/6869 ,  C12Q1/6806 ,  C12Q1/6841 ,  C12Q1/6844

CPC分类号： C12Q1/6869 ,  C12Q1/6806 ,  C12Q1/6841 ,  C12Q1/6844

摘要： The present invention provides methods to barcode nucleic acid for detection and sequencing. It applies a barcode template in a compartment with various targets, including nucleic acid fragments, nuclei and/or cells. After clonal amplification within the compartment, barcode sequence will integrate into its targets before the compartment is broken so that it will effectively barcode nucleic acid fragments originated from a nucleic acid fragment, a nucleus or a cell clonally. The barcode information can be used for tracking the origin of the fragment, nucleus or cell and be used for haplotype phasing and a variety of single cell-based applications including whole genome sequencing, targeted sequencing, RNA sequencing and immune repertoire sequencing.

公开(公告)号：US12054783B2

公开(公告)日：2024-08-06

申请号：US17210191

申请日：2021-03-23

申请人： GUARDANT HEALTH, INC.

发明人： AmirAli Talasaz

IPC分类号： C12P19/34 ,  C12N15/10 ,  C12Q1/6806 ,  C12Q1/6869 ,  C12Q1/6874 ,  C12Q1/6886 ,  G16B30/00 ,  G16B30/10

CPC分类号： C12Q1/6886 ,  C12N15/1065 ,  C12Q1/6806 ,  C12Q1/6869 ,  C12Q1/6874 ,  G16B30/00 ,  G16B30/10 ,  C12Q2600/118 ,  C12Q2600/156 ,  C12Q2600/158 ,  C12Q2600/16 ,  C12Q1/6869 ,  C12Q2537/165 ,  C12Q2545/114

摘要： The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease.

公开(公告)号：US12054775B2

公开(公告)日：2024-08-06

申请号：US16897052

申请日：2020-06-09

申请人： The Regents of the University of California

发明人： Mark A. Akeson ,  David W. Deamer ,  William B. Dunbar ,  Kate Lieberman ,  Noah A. Wilson

IPC分类号： C12Q1/6869 ,  C12Q1/54 ,  C12Q1/6874 ,  C25B3/29 ,  G01N27/327 ,  G01N27/416 ,  G01N33/487

CPC分类号： C12Q1/6874 ,  C12Q1/54 ,  C12Q1/6869 ,  C25B3/29 ,  G01N27/3278 ,  G01N27/4166 ,  G01N33/48721 ,  C12Q1/6869 ,  C12Q2522/101 ,  C12Q2565/631 ,  C12Q1/6869 ,  C12Q2565/631 ,  C12Q2525/301 ,  C12Q2523/307 ,  C12Q1/6869 ,  C12Q2565/631 ,  C12Q2521/101 ,  C12Q2527/127

摘要： Devices and methods that can detect and control an individual polymer in a mixture is acted upon by another compound, for example, an enzyme, in a nanopore are provided. The devices and methods also determine (˜>50 Hz) the nucleotide base sequence of a polynucleotide under feedback control or using signals generated by the interactions between the polynucleotide and the nanopore. The invention is of particular use in the fields of molecular biology, structural biology, cell biology, molecular switches, molecular circuits, and molecular computational devices, and the manufacture thereof.

公开(公告)号：US12054774B2

公开(公告)日：2024-08-06

申请号：US18316870

申请日：2023-05-12

申请人： GUARDANT HEALTH, INC.

发明人： AmirAli Talasaz ,  Helmy Eltoukhy ,  Stefanie Ann Ward Mortimer

IPC分类号： C12P19/34 ,  C12Q1/6869 ,  C12Q1/6886 ,  G16B15/00

CPC分类号： C12Q1/6869 ,  C12Q1/6886 ,  C12Q2535/122 ,  C12Q2600/158 ,  G16B15/00

摘要： Disclosed herein in are methods and systems for determining genetic variants (e.g., copy number variation) in a polynucleotide sample. A method for determining copy number variations includes tagging double-stranded polynucleotides with duplex tags, sequencing polynucleotides from the sample and estimating total number of polynucleotides mapping to selected genetic loci. The estimate of total number of polynucleotides can involve estimating the number of double-stranded polynucleotides in the original sample for which no sequence reads are generated. This number can be generated using the number of polynucleotides for which reads for both complementary strands are detected and reads for which only one of the two complementary strands is detected.

公开(公告)号：US12054772B2

公开(公告)日：2024-08-06

申请号：US16979804

申请日：2019-03-13

申请人： SARMAL, INC.

发明人： Inanc Ortac

IPC分类号： C12Q1/6869 ,  C12Q1/48 ,  C12Q1/66

CPC分类号： C12Q1/6869 ,  C12Q1/485 ,  C12Q1/66

摘要： Provided herein are methods and systems for sequencing a single nucleic acid molecule utilizing a polymerase enzyme, a template nucleic acid, and a polymerase reagent solution, including components for a luminescence reaction.

公开(公告)号：US12054712B2

公开(公告)日：2024-08-06

申请号：US17022597

申请日：2020-09-16

申请人： ILLUMINA, INC.

发明人： Tingting Jiang

IPC分类号： C12N15/11 ,  A61K35/13 ,  C07K16/28 ,  C12N15/10 ,  C12Q1/6869 ,  C12Q1/6886

CPC分类号： C12N15/11 ,  A61K35/13 ,  C07K16/2818 ,  C07K16/2827 ,  C12N15/1003 ,  C12Q1/6869 ,  C12Q1/6886

摘要： Methods and systems are provided for differentiating between cancer variants and somatic variants originating from hematopoietic cells in a cell free DNA sample. In some embodiments, the cancer variants can be distinguished from somatic variants originating from hematopoietic cells based on fragment size distribution.

公开(公告)号：US20240254549A1

公开(公告)日：2024-08-01

申请号：US18290550

申请日：2022-05-26

申请人： CHAN ZUCKERBERG BIOHUB, INC. ,  The Regents of the University of California

发明人： Adam Abate ,  Xiangpeng Li ,  Benjamin Demaree

IPC分类号： C12Q1/6869 ,  C12N15/10

CPC分类号： C12Q1/6869 ,  C12N15/1065

摘要： The present disclosure provides materials and methods for partitioning cells and high throughput, single-cell multi-omic sequencing. Methods for pathogen detection and identification, microbiome analysis, personalized medicine, environmental analysis where single-cell information is critical are each provided herein.

公开(公告)号：US20240254547A1

公开(公告)日：2024-08-01

申请号：US17050686

申请日：2019-04-26

申请人： KAO CORPORATION

发明人： Shoji MATSUMURA ,  Hirayuki SATO ,  Yuki OTSUBO

IPC分类号： C12Q1/6869

CPC分类号： C12Q1/6869

摘要： Provided is a highly accurate sequencing method, specifically, a method for sequencing DNA, the method comprising: (1) preparing fragments of sample DNA; (2) subjecting the fragments of the sample DNA to PCR to produce two or more amplified fragments for each of the fragments of the sample DNA, and obtaining PCR products containing a plurality of amplified fragments; (3) sequencing the PCR products to generate one or more read sequences from the plurality of amplified fragments, and acquiring a plurality of read sequences for the plurality of amplified fragments; (4) collecting, from the plurality of read sequences acquired, read sequences containing sequence information on the same region in the sample DNA into a group to generate one or more groups of read sequences; and (5) building consensus of sequence information among read sequences included in each of the groups of read sequences.

公开(公告)号：US20240254541A1

公开(公告)日：2024-08-01

申请号：US18588930

申请日：2024-02-27

申请人： The Children's Medical Center Corporation ,  The United States of America, As Represented by the Secretary, Department of Health & Human Services

发明人： Anjana Rao ,  Mamta Tahiliani ,  Kian Peng Koh ,  Suneet Agarwal ,  Aravind Iyer

IPC分类号： C12Q1/6827 ,  C12N9/10 ,  C12Q1/26 ,  C12Q1/6806 ,  C12Q1/6869 ,  G01N33/53

CPC分类号： C12Q1/6827 ,  C12N9/1007 ,  C12Q1/26 ,  C12Q1/6806 ,  C12Q1/6869 ,  G01N33/5308 ,  C12N2501/70 ,  C12N2501/71 ,  C12N2501/724 ,  C12Q2521/531 ,  C12Q2522/10 ,  C12Q2537/164 ,  C12Q2600/154

摘要： The present invention provides for novel methods for regulating and detecting the cytosine methylation status of DNA. The invention is based upon identification of a novel and surprising catalytic activity for the family of TET proteins, namely TET1, TET2, TET3, and CXXC4. The novel activity is related to the enzymes being capable of converting the cytosine nucleotide 5-methylcytosine into 5-hydroxymethylcytosine by hydroxylation.

公开(公告)号：US20240253004A1

公开(公告)日：2024-08-01

申请号：US18595164

申请日：2024-03-04

申请人： Oxford Nanopore Technologies PLC

发明人： Jason Robert Hyde ,  Pedro Miguel Ortiz Bahamon ,  Clive Gavin Brown ,  Andrew John Heron ,  Paul Raymond Mackett

IPC分类号： B01J19/00 ,  B01L3/00 ,  C12Q1/6869 ,  G01N33/487 ,  G01N33/573

CPC分类号： B01J19/0046 ,  B01L3/5088 ,  C12Q1/6869 ,  G01N33/48721 ,  G01N33/573 ,  B01J2219/00313 ,  B01J2219/00317 ,  B01J2219/00351 ,  B01J2219/00585 ,  B01J2219/00659 ,  B01J2219/00734 ,  B01J2219/00736 ,  B01L2200/0642 ,  B01L2400/086 ,  G01N2333/974

摘要： An array of membranes comprising amphipathic molecules is formed using an apparatus comprising a support defining an array of compartments. Volumes comprising polar medium are provided within respective compartments and a layer comprising apolar medium is provided extending across the openings with the volumes. Polar medium is flowed across the support to displace apolar medium and form a layer in contact with the volumes, forming membranes comprising amphipathic molecules at the interfaces. In one construction of the apparatus, the support that comprises partitions which comprise inner portions and outer portions. The inner portions define inner recesses without gaps therebetween that are capable of constraining the volumes comprising polar medium contained in neighbouring inner recesses from contacting each other. The outer portions extend outwardly from the inner portions and have gaps allowing the flow of an apolar medium across the substrate.