公开(公告)号：US20240084289A1

公开(公告)日：2024-03-14

申请号：US18510295

申请日：2023-11-15

申请人： GRAIL, LLC

发明人： Byoungsok Jung ,  Alex Aravanis

IPC分类号： C12N15/10 ,  C12Q1/6844 ,  C12Q1/6869 ,  C12Q1/6874 ,  C12Q1/6886 ,  C40B40/08

CPC分类号： C12N15/1058 ,  C12N15/101 ,  C12N15/1093 ,  C12N15/1096 ,  C12Q1/6844 ,  C12Q1/6869 ,  C12Q1/6874 ,  C12Q1/6886 ,  C40B40/08 ,  C12Q2600/16 ,  C40B20/00

摘要： Methods for preparing enriched sequencing libraries from test samples that contain double-stranded deoxyribonucleic acid (dsDNA) are provided.

公开(公告)号：US20240079089A1

公开(公告)日：2024-03-07

申请号：US18506554

申请日：2023-11-10

申请人： Nantomics LLC

发明人： Andrew Nguyen ,  John Zachary Sanborn ,  Shahrooz Rabizadeh

IPC分类号： G16B25/10 ,  C12Q1/6827 ,  C12Q1/6869 ,  G16B20/00 ,  G16B20/20 ,  G16B30/10 ,  G16B40/00 ,  G16H50/20 ,  G16H50/30

CPC分类号： G16B25/10 ,  C12Q1/6827 ,  C12Q1/6869 ,  G16B20/00 ,  G16B20/20 ,  G16B30/10 ,  G16B40/00 ,  G16H50/20 ,  G16H50/30 ,  G01N2570/00 ,  Y02A90/10

摘要： Systems and methods for prediction of the treatment outcome for immune therapy are presented in which omics data of a patient tumor sample are used. Most typically, the omics data are processed to identify mutational signatures (especially APOBEC/POLE signatures), immune checkpoint expression, and MSI status as leading indicators to predict the treatment outcome for immune therapy. Such prediction advantageously integrates various parameters that would otherwise, when individually considered, skew prediction outcome.

公开(公告)号：US20240076720A1

公开(公告)日：2024-03-07

申请号：US18166986

申请日：2023-02-09

申请人： Cambridge Epigenetix Limited

发明人： Shankar BALASUBRAMANIAN ,  Jens FULLGRABE ,  Walraj Singh GOSAL ,  Joanna Dawn HOLBROOK ,  Sidong LIU ,  David MORLEY ,  Oliver NENTWICH ,  Tobias OST ,  Michael STEWARD ,  Albert VILELLA ,  Nicolas James WALKER ,  Shirong YU ,  Helen Rachel BIGNELL ,  Rita Santo SAN-BENTO

IPC分类号： C12Q1/6827 ,  C12N15/10 ,  C12N15/52 ,  C12Q1/6806 ,  C12Q1/6811 ,  C12Q1/686 ,  C12Q1/6869

CPC分类号： C12Q1/6827 ,  C12N15/1058 ,  C12N15/52 ,  C12Q1/6806 ,  C12Q1/6811 ,  C12Q1/686 ,  C12Q1/6869

摘要： Provided herein are methods, systems, and compositions for determining a base in a polynucleotide. In various aspects, the methods, systems, and compositions presented herein are useful for performing 4-base, 5-base, or 6-base sequencing of polynucleotide molecules, for example, from liquid biopsy samples or wherein the base is a low frequency mutation.

公开(公告)号：US11920193B2

公开(公告)日：2024-03-05

申请号：US16972039

申请日：2019-06-06

申请人： Oxford Nanopore Technologies PLC

发明人： James Anthony Clarke ,  James White ,  Richard Muscat ,  Jessica Mary May Johnson ,  Ramiz Iqbal Nathani ,  Andrew John Heron ,  Mark John Bruce ,  Lakmal Nishantha Jayasinghe ,  Domenico Caprotti ,  David Jackson Stoddart ,  Rebecca Victoria Bowen ,  Christopher James Wright ,  Paul Richard Moody

IPC分类号： C12Q1/6869 ,  G01N33/487

CPC分类号： C12Q1/6869 ,  G01N33/48721

摘要： Methods of characterizing an analyte using a detector such as a nanopore and an enzyme are provided. One aspect features methods for characterizing a double-stranded polynucleotide using a detector, e.g., without using a hairpin connecting a template and a complement of the double-stranded polynucleotide. Another aspect features methods for characterizing an analyte using a tag-modified nanopore with increased sensitivity and/or higher throughput. Compositions and systems including, e.g., adaptors for attachment to double-stranded polynucleotides and tag-modified nanopores, which can be used in the methods are also provided.

公开(公告)号：US11920192B2

公开(公告)日：2024-03-05

申请号：US16613593

申请日：2018-05-15

申请人： LIGHTCAST DISCOVERY LTD

发明人： Barnaby Balmforth ,  Cameron Alexander Frayling ,  Mark Dethlefsen

IPC分类号： C12Q1/6869 ,  C12Q1/6823

CPC分类号： C12Q1/6869 ,  C12Q1/6823 ,  C12Q2521/101 ,  C12Q2521/301 ,  C12Q2521/319 ,  C12Q2525/125 ,  C12Q2525/307 ,  C12Q2537/149 ,  C12Q2563/107 ,  C12Q2563/159

摘要： A method of sequencing a nucleic acid comprising (1) generating a stream of single nucleoside triphosphates by progressive enzymatic digestion of the nucleic acid; (2) producing at least one oligonucleotide used probe by reacting, in the presence of a polymerase, at least one of the single nucleoside triphosphates with a corresponding biological probe comprising (a) a first single-stranded oligonucleotide including an exonuclease blocking-site, a restriction endonuclease recognition-site located on the 5′ side of the blocking-site and including a single nucleotide capture-site e, and at least one fluorophore region and (b) a second and optionally a third single-stranded oligonucleotide each separate from the first oligonucleotide; (3) cleaving the first oligonucleotide strand of the used probe at the recognition-site with a restriction endonuclease; (4) digesting the first oligonucleotide component with an enzyme to yield fluorophores in a detectable state and (5) detecting the fluorophores released in step (4).

公开(公告)号：US20240069019A1

公开(公告)日：2024-02-29

申请号：US18459711

申请日：2023-09-01

申请人： Becton, Dickinson and Company

发明人： Christina Fan ,  Olaf Zoellner

IPC分类号： G01N33/566 ,  G16B99/00 ,  G01N33/50 ,  G01N33/543 ,  G01N33/68 ,  C12Q1/6804 ,  G16Z99/00 ,  C12N15/10 ,  C12Q1/6806 ,  C12Q1/6823 ,  C12Q1/6869 ,  C12Q1/68

CPC分类号： G01N33/566 ,  G16B99/00 ,  G01N33/505 ,  G01N33/54313 ,  G01N33/6842 ,  G01N33/6857 ,  C12Q1/6804 ,  G16Z99/00 ,  C12N15/1006 ,  C12N15/1096 ,  C12Q1/6806 ,  C12Q1/6823 ,  C12Q1/6869 ,  G01N33/54306 ,  C12Q1/68 ,  G16B25/10

摘要： Some embodiments disclosed herein provide a plurality of compositions each comprising a protein binding reagent conjugated with an oligonucleotide. The oligonucleotide comprises a unique identifier for the protein binding reagent it is conjugated with, and the protein binding reagent is capable of specifically binding to a protein target. Further disclosed are methods and kits for quantitative analysis of a plurality of protein targets in a sample and for simultaneous quantitative analysis of protein and nucleic acid targets in a sample. Also disclosed herein are systems and methods for preparing a labeled biomolecule reagent, including a labeled biomolecule agent comprising a protein binding reagent conjugated with an oligonucleotide.

公开(公告)号：US20240068038A1

公开(公告)日：2024-02-29

申请号：US18234598

申请日：2023-08-16

申请人： Siemens Healthcare Diagnostics Products GmbH

发明人： Timo KAUPPILA ,  Florian LENZ ,  Tobias ZACHERLE

IPC分类号： C12Q1/6886 ,  C12Q1/6869 ,  G16B30/00

CPC分类号： C12Q1/6886 ,  C12Q1/6869 ,  G16B30/00 ,  C12Q2600/16

摘要： The present invention relates to a method for eliminating non-natural nucleic acid sequence portions from paired-end reads of nucleic acid fragments comprising the steps of (a) providing paired-end reads of nucleic acid fragments, wherein one of the two paired-end reads that constitute a read pair of a nucleic acid fragment is converted into its reverse complement form; (b) aligning the two paired-end reads of the read pair of step (a) with each other; (c) identifying overlapping sequence regions in the aligned paired-end reads; (d) identifying a unique molecular identifier (UMI) sequence as non-natural nucleic acid sequence in the aligned paired-end reads; (e) optionally storing said identified UMI sequence; (f) deleting said identified UMI sequence, if present, at the 5′ end of each paired-end read; and (g) deleting said identified UMI sequence, if present, at the 3′ end of each paired-end read.

公开(公告)号：US20240068036A1

公开(公告)日：2024-02-29

申请号：US18502378

申请日：2023-11-06

申请人： AGRICULTURAL GENOMICS INSTITUTE AT SHENZHEN, CHINESE ACADEMY OF AGRICULTURAL SCIENCES

发明人： Zhonglin TANG ,  Yalan YANG ,  Xinhao FAN ,  Muya CHEN

IPC分类号： C12Q1/6883

CPC分类号： C12Q1/6883 ,  C12Q1/6869

摘要： Disclosed are biomarkers and a prediction method for predicting age in days in pigs. The biomarkers for predicting age in days of pigs include one or more CpG sites with different methylation levels, and the different methylation levels of the CpG sites correspond to different ages in days of pigs. An Elastic Net linear regression model is constructed by using the methylation levels of the CpG sites and the weights corresponding to each CpG site, thereby predicting age in days of pigs to be tested. The above prediction method has high accuracy, and is accurate and reliable in detecting age in days of pigs, which fills the gap in the age prediction model of pigs based on DNA methylation, and provides an ideal model for investigating important scientific issues such as development and aging of human and animals.

公开(公告)号：US20240067951A1

公开(公告)日：2024-02-29

申请号：US18195702

申请日：2023-05-10

申请人： AbClonal Science, Inc.

发明人： Alicia DiCicco ,  Zhenyu Zhu ,  Aine Quimby

IPC分类号： C12N9/00 ,  C12Q1/6869

CPC分类号： C12N9/93 ,  C12Q1/6869 ,  C12Y605/01001

摘要： A number of T4 DNA ligase mutants exhibiting enhanced ligation activity in the presence of high salt concentrations compared to the wild-type ligase were engineered, characterized, and selected via gel electrophoresis of ligation products from a standard ligation assay. Ligase catalyzes the formation of phosphodiester bonds between the 5′ and 3′ ends of complementary cohesive ends or blunt ends of duplex DNA, a process that is vital to numerous molecular biology processes including cloning and sequencing.

公开(公告)号：US11913905B2

公开(公告)日：2024-02-27

申请号：US17534869

申请日：2021-11-24

申请人： University of Washington

发明人： Jens H. Gundlach ,  Ian M. Derrington ,  Marcus D. Collins

IPC分类号： C12Q1/68 ,  C12P19/34 ,  G01N27/447 ,  B82Y15/00 ,  C07K14/35 ,  G06F1/20 ,  G06F3/06 ,  G06F12/02 ,  B01D69/06 ,  C12Q1/6869 ,  G01N33/487 ,  G11C7/04 ,  B82Y5/00

CPC分类号： G01N27/44791 ,  B01D69/06 ,  B82Y15/00 ,  C07K14/35 ,  C12Q1/6869 ,  G01N27/447 ,  G01N27/44704 ,  G01N27/44726 ,  G01N27/44747 ,  G01N27/44786 ,  G06F1/206 ,  G06F3/061 ,  G06F3/0604 ,  G06F3/0614 ,  G06F3/0616 ,  G06F3/0625 ,  G06F3/0629 ,  G06F3/0647 ,  G06F3/0653 ,  G06F3/0659 ,  G06F3/0673 ,  G06F3/0679 ,  G06F12/0238 ,  G06F12/0246 ,  B01D2325/02 ,  B01D2325/24 ,  B82Y5/00 ,  G01N33/48721 ,  G06F2212/1016 ,  G06F2212/7206 ,  G11C7/04 ,  Y02D10/00 ,  Y10S977/712 ,  Y10S977/714 ,  Y10S977/781 ,  Y10S977/924

摘要： Provided herein are methods and systems pertaining to sequencing units of analytes using nanopores. In general, arresting constructs are used to modify an analyte such that the modified analyte pauses in the opening of a nanopore. During such a pause, an ion current level is obtained that corresponds to a unit of the analyte. After altering the modified analyte such that the modified analyte advances through the opening, another arresting construct again pauses the analyte, allowing for a second ion current level to be obtained that represents a second unit of the analyte. This process may be repeated until each unit of the analyte is sequenced. Systems for performing such methods are also disclosed.