Patents Examined by Ethan C. Whisenant
  • Patent number: 11661629
    Abstract: Methods, assays, compositions and kits for the ligation of short polynucleotides are presented herein. The short polynucleotides are optionally no more than 7 nucleotides in length, and can be as short as 3 or 4 nucleotides in length. The ligation is optionally performed by CV ligase.
    Type: Grant
    Filed: October 28, 2019
    Date of Patent: May 30, 2023
    Assignee: Life Technologies Corporation
    Inventors: Stephen Hendricks, David J. King
  • Patent number: 11649481
    Abstract: Embodiments of the methods and compositions provided herein relate to the selective cleavage of target nucleic acids. Some embodiments include recombinase-mediated selective cleavage of target nucleic acids with single-stranded nucleic acid probes and a recombinase. Some embodiments also include the enrichment of non-target nucleic acids in a sample by selective cleavage of target nucleic acids in the sample, and removal of the cleaved target nucleic acids from the sample.
    Type: Grant
    Filed: March 15, 2019
    Date of Patent: May 16, 2023
    Assignee: Illumina, Inc.
    Inventor: Clifford Lee Wang
  • Patent number: 11643679
    Abstract: Disclosed herein, inter alia, are compositions and methods of use thereof for interrogating a cell.
    Type: Grant
    Filed: June 14, 2022
    Date of Patent: May 9, 2023
    Assignee: SINGULAR GENOMICS SYTEMS, INC.
    Inventors: Eli N. Glezer, Hu Cang, Zhenmin Hong
  • Patent number: 11634781
    Abstract: A method of processing a fecal sample from a human subject comprising removing a portion of a collected fecal sample and adding the removed portion of the sample to a buffer that prevents denaturation or degradation of blood proteins found in the sample, and detecting the presence of human blood in the removed portion of the fecal sample. The method further comprises stabilizing the remaining portion of the fecal sample.
    Type: Grant
    Filed: September 28, 2022
    Date of Patent: April 25, 2023
    Inventor: Joost Louwagie
  • Patent number: 11624084
    Abstract: Presented herein are methods and compositions for enhancing specific enrichment of target sequences in a nucleic acid library. Off-target hybridization probes may be used to reduce binding and/or capture of off-target regions of a nucleic acid library in a targeted sequencing workflow. The off-target hybridization probes may be specific for locations known to generate off-target sequencing reads for a particular set of hybridization probes.
    Type: Grant
    Filed: February 5, 2020
    Date of Patent: April 11, 2023
    Assignee: ILLUMINA, INC.
    Inventors: Li Teng, Chia-Ling Hsieh, Charles Lin, Han-Yu Chuang
  • Patent number: 11608520
    Abstract: Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample.
    Type: Grant
    Filed: December 15, 2021
    Date of Patent: March 21, 2023
    Assignee: 10x Genomics, Inc.
    Inventors: Christina Galonska, Marco Mignardi
  • Patent number: 11602752
    Abstract: The present invention relates to an apparatus for performing a nucleic acid amplification reaction and a fluorescence detection device for reaction analysis. The nucleic acid amplification apparatus of the present invention uses a plurality of blocks having different reaction temperatures by independent temperature control and the movement between the blocks is performed along sliding recesses formed in the blocks, enabling to greatly shorten the total amplification time (TAT). In the fluorescence detection device of the present invention, the positions of the light source and the photodetector are very unique for the reaction vessel in which an excitation light is provided and an emission light is generated.
    Type: Grant
    Filed: June 30, 2017
    Date of Patent: March 14, 2023
    Assignee: SEEGENE, INC.
    Inventors: Jong Yoon Chun, Seung Jae Lee
  • Patent number: 11597965
    Abstract: The present application provides methods for detecting a target nucleic acid molecule in a sample comprising contacting said sample with a ligatable probe comprising one or more parts and allowing said probe to hybridise to the target nucleic acid molecule, ligating any probe which has hybridised to the target nucleic acid molecule, amplifying the ligated probe, and detecting the amplification product, thereby to detect the target nucleic acid molecule, wherein said probes comprise at least one ribonucleotide at or near to a ligation site and/or wherein the probe or a probe part comprises an additional sequence 5? to a target-specific binding site which is not hybridised to the target nucleic acid molecule upon hybridisation of the probe to the target nucleic acid molecule and forms a 5? flap containing one or more nucleotides at its 3? end that is cleaved prior to ligation, and methods of synthesising a DNA molecule with Phi29 DNA polymerase using a template nucleic acid molecule comprising at least one ribo
    Type: Grant
    Filed: October 5, 2018
    Date of Patent: March 7, 2023
    Assignee: 10x Genomics, Inc.
    Inventors: Mats Nilsson, Malte K├╝hnemund, Tomasz Krzywkowski
  • Patent number: 11591636
    Abstract: Provided herein are methods and products for detecting analytes in a sample. The analytes may be rare analytes such as biomarkers in a biological sample. These methods make use of nucleic acid nanoswitches that adopt a particular conformation and have a particular length in the presence of an analyte.
    Type: Grant
    Filed: November 20, 2018
    Date of Patent: February 28, 2023
    Assignee: Children's Medical Center Corporation
    Inventors: Wesley Philip Wong, Johanna Blass, Darren Yang, Clinton H. Hansen
  • Patent number: 11584959
    Abstract: Methods are provided for reducing the complexity of a population of nucleic acids prior to performing an analysis of the nucleic acids, e.g., sequence analysis. The methods result in a subset of the initial population enriched for a target region, which is typically located within one or more target fragments. The methods are particularly useful for analyzing populations having a high degree of complexity, e.g., chromosomal-derived DNA, whole genomic DNA, or mRNA populations.
    Type: Grant
    Filed: March 24, 2020
    Date of Patent: February 21, 2023
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Thang Tat Pham, Yu-Chih Tsai, Jonas Korlach, Tyson A. Clark, Stephen Turner
  • Patent number: 11578359
    Abstract: In some aspects, the present disclosure provides methods for enriching amplicons, or amplification products, comprising a concatemer of at least two or more copies of a target polynucleotide. In some embodiments, a method comprises sequencing the amplicons comprising at least two or more copies of a target polynucleotide. In some embodiments, the target polynucleotides comprise sequences resulting from chromosome rearrangement, including but not limited to point mutations, single nucleotide polymorphisms, insertions, deletions, and translocations including fusion genes. In some aspects, the present disclosure provides compositions and reaction mixtures useful in the described methods.
    Type: Grant
    Filed: July 13, 2020
    Date of Patent: February 14, 2023
    Assignee: ACCURAGEN HOLDINGS LIMITED
    Inventors: Li Weng, Shengrong Lin, Ling Fung Tang
  • Patent number: 11560558
    Abstract: There is described herein, a method of capturing cell-free methylated DNA from a sample having less than 100 mg of cell-free DNA, comprising the steps of: subjecting the sample to library preparation to permit subsequent sequencing of the cell-free methylated DNA; adding a first amount of filler DNA to the sample, wherein at least a portion of the filler DNA is methylated; denaturing the sample; and capturing cell-free methylated DNA using a binder selective for methylated polynucleotides.
    Type: Grant
    Filed: November 4, 2021
    Date of Patent: January 24, 2023
    Assignees: UNIVERSITY HEALTH NETWORK, SINAI HEALTH SYSTEM
    Inventors: Daniel Diniz De Carvalho, Shu Yi Shen, Rajat Singhania
  • Patent number: 11560593
    Abstract: Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample using RNA-templated ligation.
    Type: Grant
    Filed: March 29, 2022
    Date of Patent: January 24, 2023
    Assignee: 10x Genomics, Inc.
    Inventors: James Michael Chell, Marlon Stoeckius, Jonathan Alles, Caroline Julie Gallant, Christina Galonska, Felice Alessio Bava, Layla Katiraee
  • Patent number: 11542542
    Abstract: The present disclosure relates to improved methods for detecting nucleic acids using DNA fingerloop stem loop structures, wherein the DNA fingerloop stem loop structures diminish base pairing of a detection probe to a mismatched target nucleic acid. The present disclosure also relates to improved methods for amplifying nucleic acids. Further disclosed are chimeric fingerloop DNAs for use in methods for modulating protein expression levels and/or RNA stability.
    Type: Grant
    Filed: July 18, 2018
    Date of Patent: January 3, 2023
    Assignee: Ohio State Innovation Foundation
    Inventor: Richard A. Lease
  • Patent number: 11536715
    Abstract: The present disclosure provides, inter alia, methods and compositions (e.g., conjugates) for imaging, at high spatial resolution, targets of interest.
    Type: Grant
    Filed: September 3, 2019
    Date of Patent: December 27, 2022
    Assignee: President and Fellows of Harvard College
    Inventors: Ralf Jungmann, Peng Yin, Mingjie Dai, Maier S. Avendano Amado, Johannes B. Woehrstein
  • Patent number: 11531020
    Abstract: Disclosed herein are methods and compositions relating to synthesized nanopores. The synthesized nanopores can be used for detecting a target molecule (e.g. RNA, DNA, or peptide).
    Type: Grant
    Filed: January 17, 2018
    Date of Patent: December 20, 2022
    Inventors: Kang Zhang, Rui Hou
  • Patent number: 11530435
    Abstract: Disclosed herein are compositions and methods for detecting RNA binding sites and RNA interacting partners involving the use of a modified capture oligonucleotide having a dual toehold design.
    Type: Grant
    Filed: May 15, 2019
    Date of Patent: December 20, 2022
    Assignee: Yale University
    Inventors: Martin Machyna, Matthew Simon
  • Patent number: 11512356
    Abstract: Described herein are systems and methods for multiplexed analysis of two or more targets in a test sample including a first set of particles including a first set of target-specific reagents and a first optically detectable identifier capable of emitting a first wavelength indicative of a first target, and at least one second set of particles including a second set of target-specific reagents and a second optically detectable identifier capable of emitting a second wavelength indicative of a second target; and at least one optically detectable reporter probe capable of constitutively emitting a third wavelength in response to reaction of the first set of target-specific reagents with the first target in the test sample and/or reaction of the second set of target-specific reagents with the second target in the test sample, wherein the first wavelength, the second wavelength, and the third wavelength are optically discernable from one another.
    Type: Grant
    Filed: November 8, 2018
    Date of Patent: November 29, 2022
    Assignee: Tokitae LLC
    Inventors: Samantha A. Byrnes, Kevin Paul Flood Nichols, Bernhard Hans Weigl
  • Patent number: 11505819
    Abstract: This present disclosure describes hybridization probes modularly constructed from several oligonucleotides with a pattern of designed complementary interactions, allowing the probes to sequence-specifically capture or analyze nucleic acid target sequences that are long and/or complex.
    Type: Grant
    Filed: September 22, 2017
    Date of Patent: November 22, 2022
    Assignee: William Marsh Rice University
    Inventors: David Zhang, Juexiao Wang, Yan Yan
  • Patent number: 11499181
    Abstract: Method of haplotype analysis. In an exemplary method, an aqueous phase containing nucleic acid may be partitioned into a plurality of discrete volumes. At least one allele sequence may be amplified in the volumes from each of a first polymorphic locus and a second polymorphic locus that exhibit sequence variation in the nucleic acid. At least one measure of co-amplification of allele sequences from both loci in the same volumes may be determined. A haplotype of the first and second loci may be selected based on the at least one measure of co-amplification.
    Type: Grant
    Filed: December 28, 2018
    Date of Patent: November 15, 2022
    Assignee: Bio-Rad Laboratories, Inc.
    Inventors: John F. Regan, Serge Saxonov, Michael Y. Lucero, Benjamin J. Hindson, Phillip Belgrader, Simant Dube, Austin P. So, Jeffrey C. Mellen, Nicholas J. Heredia, Kevin D. Ness, Billy W. Colston, Jr.