公开(公告)号：US20240360505A1

公开(公告)日：2024-10-31

申请号：US18650407

申请日：2024-04-30

申请人： Ultima Genomics, Inc.

发明人： Nathan BECKETT ,  Gilad ALMOGY ,  Nathan CASWELL ,  Jacob A. WOLF ,  Kristopher BARBEE ,  Denis PRISTINSKI ,  Mark PRATT ,  Gene POLOVY ,  Osip SCHWARTZ ,  Stephanie KUBECKA ,  Steven MENCHEN ,  Joseph ANTHONY ,  Jose Martin SOSA ,  Phillip You Fai LEE

IPC分类号： C12Q1/6874 ,  G01N35/10

CPC分类号： C12Q1/6874 ,  G01N35/1002

摘要： Provided are systems and methods for analyte detection and analysis. A system can comprise an open substrate. The open substrate may be configured to rotate or otherwise move. The open substrate can comprise an array of individually addressable locations, with analytes immobilized thereto. The substrate may be spatially indexed to identify nucleic acid molecules from one or more sources, and/or sequences thereof, with the respective one or more sources. A solution comprising a plurality of probes may be directed across the array to couple at least one of the plurality of probes with at least one of the analytes to form a bound probe. A detector can be configured to detect a signal from the bound probe via scanning of the substrate while minimizing temperature fluctuations of the substrate or optical aberrations caused by bubbles.

公开(公告)号：US20240352518A1

公开(公告)日：2024-10-24

申请号：US18682716

申请日：2022-08-12

申请人： The Johns Hopkins University

发明人： Bert Vogelstein ,  Kenneth W. Kinzler ,  Nickolas Papadopoulos ,  Austin Mattox ,  Joshua David Cohen ,  Yuxuan Wang

IPC分类号： C12Q1/6874 ,  C12Q1/6806 ,  C12Q1/6844

CPC分类号： C12Q1/6874 ,  C12Q1/6844 ,  C12Q1/6806 ,  C12Q2600/154

摘要： Provided herein are methods for identifying a genetic characteristic, a fragment characteristic and an epigenetic characteristic of a double-stranded DNA molecule in a population of double-stranded DNA molecules by assaying both strands of the double-stranded DNA molecule.

公开(公告)号：US20240344125A1

公开(公告)日：2024-10-17

申请号：US18685199

申请日：2021-09-06

申请人： Hitachi High-Tech Corporation

发明人： Noriyuki SUMIDA ,  Hirokazu KATO ,  Michiru FUJIOKA

IPC分类号： C12Q1/6874 ,  C12Q1/6844

CPC分类号： C12Q1/6874 ,  C12Q1/6844

摘要： Provided is a nucleotide sequence identification method for analyzing a double-stranded DNA in one reaction system while reducing cost and labor. A method for identifying a nucleotide sequence in a target polynucleotide complementary pair constituting a double strand includes: a step of identifying, by using a first primer having a target recognition site configured to form a complementary pair with a part of one target polynucleotide of the target polynucleotide complementary pair, a nucleotide sequence in the one target polynucleotide; and a step of identifying, by using a second primer having a target recognition site configured to form a complementary pair with a part of the other target polynucleotide of the target polynucleotide complementary pair and a reaction stop site configured to stop a nucleotide extension reaction, a nucleotide sequence in the other target polynucleotide, in which a mobility of a second reaction product obtained by the second primer performing extension is smaller than a mobility of a first reaction product obtained by the first primer performing extension.

公开(公告)号：US12117438B2

公开(公告)日：2024-10-15

申请号：US16936121

申请日：2020-07-22

申请人： Element Biosciences, Inc.

发明人： Sinan Arslan ,  Molly He ,  Matthew Kellinger ,  Jake Levieux ,  Michael Previte ,  Junhua Zhao ,  Su Zhang

IPC分类号： G01N33/53 ,  C12Q1/6874 ,  G01N33/58

CPC分类号： G01N33/5308 ,  C12Q1/6874 ,  G01N33/582

摘要： Multivalent binding compositions including a particle-nucleotide conjugate having a plurality of copies of a nucleotide attached to the particle are described. The multivalent binding compositions allow one to localize detectable signals to active regions of biochemical interaction, e.g., sites of protein-protein interaction, protein-nucleic acid interaction, nucleic acid hybridization, or enzymatic reaction, and can be used to identify sites of base incorporation in elongating nucleic acid chains during polymerase reactions and to provide improved base discrimination for sequencing and array based applications.

公开(公告)号：US20240336959A1

公开(公告)日：2024-10-10

申请号：US18034595

申请日：2021-12-17

申请人： PIXELGEN TECHNOLOGIES AB

发明人： Simon FREDRIKSSON ,  Filip KARLSSON

IPC分类号： C12Q1/6841 ,  C12Q1/6806 ,  C12Q1/6874 ,  C12Q1/6876

CPC分类号： C12Q1/6841 ,  C12Q1/6806 ,  C12Q1/6874 ,  C12Q1/6876

摘要： Provided herein is a method for making a physical map of a population of barcoded particles. In some embodiments, the method may involve: producing a complex comprising: i. a population of barcoded particles, wherein the barcoded particles are uniquely barcoded by surface-tethered oligonucleotides that have unique particle identifier sequences; and ii. a population of bridging moieties that comprises oligonucleotide sequences; wherein the bridging moieties are hybridized directly or indirectly to complementary sites in the surface-tethered oligonucleotides; performing a ligation, polymerization and/or a gap-fill/ligation reaction on the complex, thereby producing reaction products that comprise pairs of unique particle identifier sequences or complements thereof from adjacent barcoded particles: sequencing the reaction products, analyzing the sequences to making one or more physical maps of the barcoded particles. Systems for practicing the method are also provided.

公开(公告)号：US12110552B2

公开(公告)日：2024-10-08

申请号：US16856924

申请日：2020-04-23

申请人： Natera, Inc.

发明人： Matthew Rabinowitz ,  Matthew Micah Hill ,  Bernhard Zimmermann ,  Johan Baner ,  George Gemelos ,  Milena Banjevic ,  Allison Ryan ,  Styrmir Sigurjonsson ,  Zachary Demko

IPC分类号： C12Q1/68 ,  C12Q1/6809 ,  C12Q1/6811 ,  C12Q1/6844 ,  C12Q1/6848 ,  C12Q1/6851 ,  C12Q1/6855 ,  C12Q1/6869 ,  C12Q1/6874 ,  C12Q1/6883

CPC分类号： C12Q1/6883 ,  C12Q1/6809 ,  C12Q1/6811 ,  C12Q1/6844 ,  C12Q1/6848 ,  C12Q1/6851 ,  C12Q1/6855 ,  C12Q1/6869 ,  C12Q1/6874 ,  C12Q2600/156 ,  C12Q1/6848 ,  C12Q2527/107 ,  C12Q2537/143 ,  C12Q1/6809 ,  C12Q2527/107 ,  C12Q2537/143 ,  C12Q1/6851 ,  C12Q2531/113 ,  C12Q2535/122 ,  C12Q2537/143 ,  C12Q2563/159

摘要： The invention provides methods for simultaneously amplifying multiple nucleic acid regions of interest in one reaction volume as well as methods for selecting a library of primers for use in such amplification methods. The invention also provides library of primers with desirable characteristics, such as minimal formation of amplified primer dimers or other non-target amplicons.

公开(公告)号：US12110550B2

公开(公告)日：2024-10-08

申请号：US18588765

申请日：2024-02-27

申请人： Singular Genomics Systems, Inc.

发明人： Daan Witters ,  Allen Lipson ,  Eli N. Glezer

IPC分类号： C12Q1/68 ,  C12Q1/6874

CPC分类号： C12Q1/6874

摘要： Disclosed herein, inter alia, are complexes, kits, and efficient methods of sequencing two strands of a double stranded polynucleotide.

公开(公告)号：US12110548B2

公开(公告)日：2024-10-08

申请号：US17165802

申请日：2021-02-02

申请人： 10x Genomics, Inc.

发明人： Felice Alessio Bava

IPC分类号： C12Q1/6874 ,  C12Q1/6876

CPC分类号： C12Q1/6874 ,  C12Q1/6876

摘要： In some aspects, provided herein are methods for analyzing a nucleic acid comprising first and second regions of interest flanking an adaptor region, comprising hybridizing an anchor to the adaptor region, analyzing the first region of interest from one end of the anchor using probe ligation (e.g., sequencing-by-ligation), and binding a polymerase to the other end of the anchor and optionally incorporating a nucleotide and/or analog thereof into the anchor by the polymerase using the second region of interest or a probe bound thereto as a template. In some embodiments, the second region of interest is used as a template for sequencing-by-synthesis. In some embodiments, spatially resolved detections of analytes are performed at a cellular or sub-cellular resolution which involve correlating signals associated with analytes with specific spatial locations in a biological sample.

公开(公告)号：US20240327910A1

公开(公告)日：2024-10-03

申请号：US18618509

申请日：2024-03-27

申请人： Illumina, Inc.

发明人： Justyna Piekos ,  Mykhailo Vybornyi ,  Michael Callingham

IPC分类号： C12Q1/6874 ,  C07D221/14 ,  C07D401/04 ,  C07D401/14 ,  C07D471/06 ,  C09B57/08

CPC分类号： C12Q1/6874 ,  C07D221/14 ,  C07D401/04 ,  C07D401/14 ,  C07D471/06 ,  C09B57/08

摘要： The present application relates to dyes containing a naphthalimide core and their uses as fluorescent labels. These dyes may be used as fluorescent labels for nucleotides in nucleic acid sequencing applications.

公开(公告)号：US20240327897A1

公开(公告)日：2024-10-03

申请号：US18589293

申请日：2024-02-27

申请人： Becton, Dickinson and Company

发明人： Hye-Won Song

IPC分类号： C12Q1/6806 ,  C12N9/22 ,  C12Q1/68 ,  C12Q1/6874

CPC分类号： C12Q1/6806 ,  C12N9/22 ,  C12Q1/68 ,  C12Q1/6874 ,  C12Q2565/1025 ,  C12Q2600/154

摘要： Disclosed herein include systems, methods, kits, and compositions for labeling nuclear target-associated DNA in a cell. Some embodiments provide digestion compositions comprising a DNA digestion enzyme and a binding reagent capable of specifically binding to the nuclear target. Some embodiments provide conjugates comprising a transposome and a binding reagent capable of specifically binding to a nuclear target. The transposome can comprise a transposase (e.g., Tn5 transposase), a first adaptor having a first 5′ overhang, and a second adaptor having a second 5′ overhang. The methods can comprise contacting a permeabilized cell comprising a nuclear target associated with dsDNA, such as genomic DNA (gDNA), with the compositions provided herein to generate a plurality of nuclear target-associated dsDNA fragments (e.g., nuclear target-associated gDNA fragments) each comprising the one or two single-stranded overhangs.