公开(公告)号：US11827934B2

公开(公告)日：2023-11-28

申请号：US17187560

申请日：2021-02-26

申请人： Pacific Biosciences of California, Inc.

发明人： Thang Pham ,  Arunashree Bhamidipati ,  Kevin Travers ,  Eric Olivares ,  Tyson A. Clark ,  Jonas Korlach

IPC分类号： C12Q1/6874 ,  C12Q1/6869 ,  G01N33/543 ,  B01L9/00 ,  C40B60/14

CPC分类号： C12Q1/6874 ,  B01L9/523 ,  C12Q1/6869 ,  G01N33/54313 ,  G01N33/54353 ,  C40B60/14 ,  G01N2333/922 ,  C12Q1/6869 ,  C12Q2521/543 ,  C12Q2523/303 ,  C12Q2525/301

摘要： Compositions, methods and systems are provided for isolating nucleic acids. A polymerase-nucleic acid complex can be formed by mixing a polymerase enzyme comprising strand displacement activity and a mixture of double stranded nucleic acids. Nucleic acid synthesis can then be initiated by the polymerase enzyme to produce a nascent strand complementary to the first strand, thereby displacing a portion of the second strand. After halting or reducing the rate of nucleic acid synthesis, a hybridizing a hook oligonucleotide can be used hybridize to the nucleic acid through a capture region on the hook oligonucleotide that is complementary to the displaced portion of the second strand. The nucleic acid can then be isolated from the mixture of nucleic acids using the hook oligonucleotide.

公开(公告)号：US11827932B2

公开(公告)日：2023-11-28

申请号：US17153309

申请日：2021-01-20

申请人： Illumina, Inc.

发明人： Robert C. Kain ,  Xiaohai Liu ,  Wenyi Feng ,  Bernard Hirschbein ,  Helmy A. Eltoukhy ,  Xiaolin Wu ,  Geoffrey Paul Smith ,  Jonathan Mark Boutell ,  Thomas Joseph ,  Randall Smith ,  Min-Jui Richard Shen ,  Carolyn Tregidgo ,  Kay Klausing

IPC分类号： C12Q1/68 ,  C12Q1/6874 ,  C12Q1/6869

CPC分类号： C12Q1/6874 ,  C12Q1/6869 ,  C12Q1/6874 ,  C12Q2525/113 ,  C12Q2535/122 ,  C12Q2563/107

摘要： The present disclosure provides methods and systems for detecting multiple different nucleotides in a sample. In particular, the disclosure provides for detection of multiple different nucleotides in a sample utilizing fewer detection moieties than the number of nucleotides being detected and/or fewer imaging events than the number of nucleotides being detected.

公开(公告)号：US20230374567A1

公开(公告)日：2023-11-23

申请号：US18194062

申请日：2023-03-31

申请人： OXFORD NANPORE TECHNOLOGIES PLC

发明人： David Jackson Stoddart ,  James White

IPC分类号： C12Q1/6806 ,  C12Q1/6869

CPC分类号： C12Q1/6806 ,  C12Q1/6869 ,  C12Q2521/10 ,  C12Q2525/155 ,  C12Q2525/191 ,  C12Q2521/513 ,  C12Q2535/122 ,  C12Q2565/631 ,  C12Q2522/101

摘要： The invention relates to a method for modifying a template double stranded polynucleotide, especially for characterisation using nanopore sequencing. The method produces from the template a plurality of modified double stranded polynucleotides. These modified polynucleotides can then be characterised.

公开(公告)号：US11821033B2

公开(公告)日：2023-11-21

申请号：US17111167

申请日：2020-12-03

申请人： University of Washington through its Center for Commercialization

发明人： Jens H. Gundlach ,  Andrew Laszlo

IPC分类号： C12Q1/6869

CPC分类号： C12Q1/6869 ,  C12Q1/6869 ,  C12Q2523/31 ,  C12Q2565/631

摘要： The present disclosure provides methods and reagents for improving nanopore-based analyses of polymers. Specifically, the disclosure provides a method of analyzing a polymer that includes a polymer analyte that contains an end domain that has at least one charged moiety. The disclosure also provides a method of increasing the interaction rate between a polymer analyte and a nanopore, wherein the polymer analyte contains an end domain that has at least one charged moiety. The disclosure also provide compositions for use with the described methods, including adapter compositions that contain charged moieties, such as phosphate or sulfate groups, and that are configured to being linked to an polymer analyte domain.

公开(公告)号：US11821032B2

公开(公告)日：2023-11-21

申请号：US16999329

申请日：2020-08-21

申请人： IsoPlexis Corporation

发明人： Luisa Andruzzi ,  Jimmy Adediran ,  Timothy Pelletier ,  Austin Ricker ,  Angela DeLucia ,  Ben McNally ,  Dona Hevroni ,  Mong Sano Marma ,  John Andrew Sheridan

IPC分类号： C12P19/34 ,  C12Q1/6869 ,  C12Q1/6876 ,  C12Q1/6806 ,  C07D275/03

CPC分类号： C12Q1/6869 ,  C12Q1/6806 ,  C12Q1/6876 ,  C07D275/03 ,  C12Q2525/113 ,  C12Q2525/186 ,  C12Q2600/16 ,  C12Q1/6869 ,  C12Q2525/113 ,  C12Q2525/117 ,  C12Q2525/186

摘要： The present invention provides methods, compositions, mixtures and kits utilizing 5-Chloro-2-methyl-4-isothiazolin-3-one in sequencing reactions, and in particular, sequencing reactions where deoxynucleoside triphosphates comprising a 3′-O position capped by a disulfide-based 3′-terminator group are used. In one embodiment, the deoxynucleoside triphosphates comprise a 3′-O position capped by a group comprising methylenedisulfide as a cleavable protecting group and a detectable label reversibly connected to the nucleobase of said deoxynucleoside. In addition, thiol-containing compounds and scavengers of thio-containing compounds are described. Such compounds provide new possibilities for future sequencing technologies, including but not limited to Sequencing by Synthesis.

公开(公告)号：US11821027B2

公开(公告)日：2023-11-21

申请号：US16476856

申请日：2018-01-10

申请人： Juno Therapeutics, Inc.

发明人： Mark L. Bonyhadi ,  David G. Kugler ,  Timothy G. Johnstone ,  Ronald James Hause, Jr. ,  Lucas J. Thompson ,  Ryan P. Larson

IPC分类号： C12Q1/6827 ,  G16B30/10 ,  C12Q1/6806 ,  C12Q1/6869 ,  C12Q1/6886 ,  G16B20/20 ,  G16B40/10 ,  G16B20/10

CPC分类号： C12Q1/6827 ,  C12Q1/6806 ,  C12Q1/6869 ,  C12Q1/6886 ,  G16B20/10 ,  G16B20/20 ,  G16B30/10 ,  G16B40/10 ,  C12Q2600/142 ,  C12Q2600/154 ,  C12Q2600/156

摘要： Provided herein are methods of identifying genomic region(s) predictive of an outcome of treatment with a cell therapy and/or of a phenotype of function of the cells. In some embodiments, the methods include epigenetic and/or epigenomic analyses of the cells in connection with methods for preparing engineered cells for cell therapy and/or predicting response to a cell therapy, e.g., engineered cells for cell therapy. In some embodiments, the methods include steps to assess, characterize and analyze changes or modifications in an epigenetic property of gene region or regions, such as chromatin accessibility, nucleosome occupancy, histone modification, spatial chromosomal conformation, transcription factor occupancy and/or DNA methylation. In some embodiments, the epigenetic and/or epigenomic analysis includes determining the epigenetic properties of a cell, e.g., an engineered cell for cell therapy.

公开(公告)号：US20230366020A1

公开(公告)日：2023-11-16

申请号：US18316454

申请日：2023-05-12

申请人： INTEGRATED DNA TECHNOLOGIES, INC.

发明人： Mollie Schubert ,  Thomas Osborne ,  Matthew McNeill ,  Garrett Rettig

IPC分类号： C12Q1/6869 ,  C12Q1/6851

CPC分类号： C12Q1/6869 ,  C12Q1/6851 ,  C12Q1/6806

摘要： Described herein is a system and process for long read sequencing using PCR primers with incorporated Unique Molecular Identifiers (UMIs) for generating a single molecule consensus for each starting molecule in the sample population. This method reduces the sequencing error rate by generating a consensus from the individual reads in each UMI group, averaging out sequencing errors to give better confidence in the actual sequence, to allow for increased accuracy of quantifying the precise knock-in event, and reporting perfect HDR integration.

公开(公告)号：US20230366019A1

公开(公告)日：2023-11-16

申请号：US18309752

申请日：2023-04-28

申请人： 454 Corporation

发明人： Jonathan M. Rothberg ,  Isaac Bean ,  William A. Hansen ,  Jose Camara ,  Lawrence C. West ,  Henry Kemble ,  Lindsay Schneider ,  David Honeybun ,  Jaime Scott Zahorian

IPC分类号： C12Q1/6869

CPC分类号： C12Q1/6869

摘要： The disclosure is directed to a method for nucleic acid sequencing, comprising: using evanescent wave imaging to identify a 3′-unblocked protected nucleotide incorporated into a sequencing primer.

公开(公告)号：US20230366018A1

公开(公告)日：2023-11-16

申请号：US18045436

申请日：2022-10-10

申请人： Pacific Biosciences of California, Inc.

发明人： Lubomir SEBO ,  Gene SHEN ,  Stephen YUE ,  Honey OSUNA ,  Yuri LAPIN ,  Louis BROGLEY ,  Andrei FEDOROV

IPC分类号： C12Q1/6869 ,  C09B69/10 ,  C07H19/10 ,  C07H19/207 ,  C07K19/00

CPC分类号： C12Q1/6869 ,  C07H19/10 ,  C07H19/207 ,  C07K19/00 ,  C09B69/105

摘要： Labeled nucleotide analogs comprising at least one avidin protein, at least one dye-labeled compound, and at least one nucleotide compound are provided. The analogs are useful in various fluorescence-based analytical methods, including the analysis of highly multiplexed optical reactions in large numbers at high densities, such as single molecule real time nucleic acid sequencing reactions. The analogs are detectable with high sensitivity at desirable wavelengths. They contain structural components that modulate the interactions of the analogs with DNA polymerase, thus decreasing photodamage and improving the kinetic and other properties of the analogs in sequencing reactions. Also provided are nucleotide and dye-labeled compounds of the subject analogs, as well as intermediates useful in the preparation of the compounds and analogs. Compositions comprising the compounds, methods of synthesis of the intermediates, compounds, and analogs, and mutant DNA polymerases are also provided.

公开(公告)号：US20230366007A1

公开(公告)日：2023-11-16

申请号：US18195207

申请日：2023-05-09

申请人： Centre for Novostics Limited

发明人： Yuk-Ming Dennis Lo ,  Rossa Wai Kwun Chiu ,  Kwan Chee Chan ,  Pelyong Jiang ,  Qing Zhou

IPC分类号： C12Q1/6806 ,  C12Q1/686 ,  C12Q1/6869 ,  C12Q1/6883 ,  G16B30/10

CPC分类号： C12Q1/6806 ,  C12Q1/686 ,  C12Q1/6869 ,  C12Q1/6883 ,  G16B30/10

摘要： Cell-free nucleic acid from extracellular particles (EPs) is analyzed. A sample can be purified for the extracellular particles. As examples, the purification can include centrifuging, washing, and a nuclease treatment. To increase the fetal fraction, the purification can enrich a sample for a certain type of EPs (e.g., long EPs). In this manner, a desired population of particles can be selected for the analysis of their nucleic acids. As part of an analysis of the nucleic acid molecules (fragments) from an enriched sample, nucleic acid molecules greater than a certain size can be selected, which can increase genetic and/or epigenetic informativeness, without an adverse effect (e.g., the reduction of fetal DNA fraction). The long nucleic acid fragments can be analyzed in various ways, including using short read sequencing techniques that perform fragmentation before sequencing and using long read sequencing techniques.