公开(公告)号：US11987836B2

公开(公告)日：2024-05-21

申请号：US15510331

申请日：2015-09-17

申请人： Global Life Sciences Solutions USA LLC

发明人： Ryan Charles Heller ,  Nichole Lea Wood ,  Robert Scott Duthie ,  John Richard Nelson ,  Wei Gao ,  Michael James Rishel ,  Klaus Gustav Hentrich

IPC分类号： C12Q1/6806 ,  C12Q1/6844 ,  C12Q1/6858 ,  C12Q1/6869

CPC分类号： C12Q1/6806 ,  C12Q1/6844 ,  C12Q1/6858 ,  C12Q1/6869 ,  C12Q1/6844 ,  C12Q2521/501 ,  C12Q2531/125

摘要： A method is provided for generating single-stranded DNA circles from a biological sample. The method comprises the steps of: treating the biological sample with an extractant to release nucleic acids, thereby forming a sample mixture; neutralizing the extractant; denaturing the released nucleic acids to generate single-stranded nucleic acids; and contacting the single-stranded nucleic acids with a ligase that is capable of template-independent, intramolecular ligation of single-stranded DNA to generate the single-stranded DNA circles. All the steps of the method are performed without any intermediate nucleic acid isolation or nucleic acid purification. The single-stranded DNA circles may be amplified and further analyzed. Also provided is a kit which comprises compositions for carrying out the novel methods.

公开(公告)号：US20240158843A1

公开(公告)日：2024-05-16

申请号：US16639220

申请日：2018-08-23

申请人： EAWAG, SWISS FEDERAL INSTITUTE OF AQUATIC SCIENCE AND TECHNOLOGY

发明人： Manu Tamminen ,  Timothy Julian ,  Jenny Spaak ,  Lea Caduff ,  Hanna Schiff

IPC分类号： C12Q1/6855 ,  C12Q1/6869

CPC分类号： C12Q1/6855 ,  C12Q1/6869

摘要： A next generation DNA sequencing method and use for accurate and massively parallel quantification of one or more nucleic acid targets. More particularly, the present disclosure is related to the method and a kit comprising probes for detecting and quantifying genetic targets in complex DNA pools primarily used for genetic target and variant detection in human and animal populations and environmental samples. Furthermore, the present disclosure finds particular application in the field of detection of disease-causing genetic alterations in samples obtained from human body, including without limiting biopsies, saliva and other secretions, exhaled moisture extracts, tissue, blood plasma (liquid biopsies) or the like. The present disclosure includes one or more target-specific nucleic acid probes per genetic target (left probe and right probe) and a bridge oligo.

公开(公告)号：US11983790B2

公开(公告)日：2024-05-14

申请号：US15147835

申请日：2016-05-05

申请人： Pacific Biosciences of California, Inc.

发明人： Scott E. Helgesen ,  Marco Milletti ,  Mark T. Lakata ,  James N. LaBrenz

IPC分类号： G06T1/20 ,  C12Q1/6869 ,  G16B30/00 ,  G16B50/30

CPC分类号： G06T1/20 ,  C12Q1/6869 ,  G16B30/00 ,  G16B50/30 ,  G06T2200/28

摘要： Exemplary embodiments for a multiprocessor pipeline architecture that converts signals from sequencing sample acquisition into sequence data, comprising: a custom coprocessor card configured to directly receive a stream of serialized sensor data generated by an image sensor, wherein the sensor data represents frame-by-frame intensity values for pixels comprising the image sensor, wherein the image sensor captures images of light emitted from a plurality of reaction cells of a removable integrated sequencing chip; a first coprocessor that continually receives the stream of serialized sensor data and transposes the frame-by-frame intensity values into reaction cell chunks, each of the reaction cell chunks representing movie data of the pixel intensity values of a corresponding reaction cell across the frames over a predetermined time window; a buffer that repeatedly receives the reaction cell chunks and stores in contiguous memory locations the reaction cell chunks for each respective reaction cell over a larger predetermined time window to create larger reaction cell chunks; and a plurality of second coprocessors that retrieve the larger reaction cell chunks from the buffer and convert, in parallel, the pixel intensity values into base-by-base sequence data even as additional reaction cell chunks are received by the buffer, such that the second coprocessors begin raw base calling before all the sensor data for the sequencing sample acquisition is obtained. Aspects of the invention include methods for base calling using single instruction multiple data vector processing units.

公开(公告)号：US20240150827A1

公开(公告)日：2024-05-09

申请号：US18488801

申请日：2023-10-17

申请人： Illumina Cambridge Limited

发明人： Antoine FRANCAIS ,  Elena CRESSINA ,  Adam CULLEY ,  Angelica MARIANI ,  Xiaolin WU ,  Xiaohai LIU

IPC分类号： C12Q1/6869 ,  C07H19/06 ,  C07H19/16 ,  C07H21/00

CPC分类号： C12Q1/6869 ,  C07H19/06 ,  C07H19/16 ,  C07H21/00

摘要： Embodiments of the present disclosure relate to nucleotide molecules with a 3′ AOM blocking group. Also provided herein are methods to prepare such nucleotide molecules, and the uses of fully functionalized nucleotides containing the 3′-OH blocking group for sequencing applications.

公开(公告)号：US20240150751A1

公开(公告)日：2024-05-09

申请号：US18279555

申请日：2022-04-22

申请人： Gordian Biotechnology, Inc.

发明人： Martin Borch Jensen ,  Daniel Fuentes

IPC分类号： C12N15/10 ,  C12Q1/6869 ,  G01N33/50

CPC分类号： C12N15/1079 ,  C12N15/1086 ,  C12Q1/6869 ,  G01N33/5082 ,  C12Q2600/136

摘要： Provided herein are compositions and methods of use thereof for screening a plurality of uniquely identifiable therapeutic moieties by identifying one or more reporters indicative of a cell state. The methods include the administration of a library of expression cassettes, comprising a plurality of nucleic acid sequences, each encoding a different therapeutic moiety operably linked to a therapeutic moiety barcode; a plurality of nucleic acid sequences encoding one or more reporters that collectively, when expressed in a cell or an isolated nucleus, are indicative of a cell state or a likelihood of a cell state of the cell; and one or more sequences encoding a non-coding nuclear retention RNA motif.

公开(公告)号：US20240149536A1

公开(公告)日：2024-05-09

申请号：US18545879

申请日：2023-12-19

申请人： Roche Sequencing Solutions, Inc.

发明人： Roger J.A. Chen ,  Randy Davis

IPC分类号： B29C67/20 ,  B82Y5/00 ,  C12Q1/6869 ,  G01N33/487

CPC分类号： B29C67/20 ,  B82Y5/00 ,  C12Q1/6869 ,  G01N33/48721 ,  B82Y10/00

摘要： Techniques for forming a nanopore in a lipid bilayer are described herein. In one example, an agitation stimulus level such as an electrical agitation stimulus is applied to a lipid bilayer wherein the agitation stimulus level tends to facilitate the formation of nanopores in the lipid bilayer. In some embodiments, a change in an electrical property of the lipid bilayer resulting from the formation of the nanopore in the lipid bilayer is detected, and a nanopore has formed in the lipid bilayer is determined based on the detected change in the lipid bilayer electrical property.

公开(公告)号：US11976326B2

公开(公告)日：2024-05-07

申请号：US18178764

申请日：2023-03-06

申请人： Personalis, Inc.

发明人： Gabor T. Bartha ,  Gemma Chandratillake ,  Richard Chen ,  Sarah Garcia ,  Hugo Yu Kor Lam ,  Shujun Luo ,  Mark R. Pratt ,  John West

IPC分类号： C12Q1/6874 ,  C12Q1/6806 ,  C12Q1/6869 ,  G16B20/00 ,  G16B20/10 ,  G16B20/20 ,  G16B30/00 ,  G16B35/00 ,  G16B35/10 ,  G16B99/00 ,  G16C20/60

CPC分类号： C12Q1/6874 ,  C12Q1/6806 ,  G16B20/00 ,  G16B20/10 ,  G16B20/20 ,  G16B30/00 ,  G16B35/10 ,  G16B99/00 ,  C12Q1/6869 ,  G16B35/00 ,  G16C20/60

摘要： This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions.

公开(公告)号：US20240141437A1

公开(公告)日：2024-05-02

申请号：US18327305

申请日：2023-06-01

申请人： Genentech, Inc.

发明人： Sanjeev MARIATHASAN ,  Chi Yung YUEN ,  Zoe June Fergusson ASSAF ,  Carlos Ernesto BAIS ,  Romain Francois BANCHEREAU

IPC分类号： C12Q1/6886 ,  A61K45/06 ,  A61P35/00 ,  C07K16/28 ,  C12Q1/686 ,  C12Q1/6869 ,  A61K39/00

CPC分类号： C12Q1/6886 ,  A61K45/06 ,  A61P35/00 ,  C07K16/2827 ,  C12Q1/686 ,  C12Q1/6869 ,  A61K2039/505 ,  C12Q2600/106 ,  C12Q2600/112 ,  C12Q2600/158

摘要： The invention provides methods and compositions for treating urothelial carcinoma in a patient, for example, by administering a treatment regimen that includes a PD-1 axis binding antagonist (e.g., atezolizumab) to the patient as a neoadjuvant or an adjuvant therapy based on the presence or level of ctDNA in a biological sample obtained from the patient. Also provided are compositions (e.g., a PD-1 axis binding antagonist (e.g., atezolizumab), pharmaceutical compositions thereof, kits thereof, and articles of manufacture thereof) for use in treating urothelial carcinoma in a patient.

公开(公告)号：US20240141426A1

公开(公告)日：2024-05-02

申请号：US18341436

申请日：2023-06-26

申请人： Tecan Genomics, Inc.

发明人： Douglas A. Amorese ,  Jonathan Scolnick ,  Benjamin Schroeder

IPC分类号： C12Q1/6874 ,  C12Q1/6869

CPC分类号： C12Q1/6874 ,  C12Q1/6869 ,  C12Q2525/179 ,  C12Q2525/191

摘要： The present invention provides methods, compositions and kits for detecting duplicate sequencing reads. In some embodiments, the duplicate sequencing reads are removed.

公开(公告)号：US11970738B2

公开(公告)日：2024-04-30

申请号：US17098101

申请日：2020-11-13

申请人： The Regents of the University of California

发明人： Mark A. Akeson ,  David W. Deamer ,  William B. Dunbar ,  Roger Jinteh Arrigo Chen ,  Noah A. Wilson

IPC分类号： C12Q1/6874 ,  C12Q1/54 ,  C12Q1/6869 ,  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.