Biochemical Method (e.g., Using An Enzyme Or Whole Viable Micro-organism, Etc.) Patents (Class 506/26)
  • Patent number: 12281354
    Abstract: The present disclosure provides a method for monitoring residual disease in a subject. Generally, the method comprises determining a frequency of cancer mutations from a first sample obtained from a tumor biopsy from the subject; determining a frequency of the cancer mutations discovered in the first sample from a second sample comprising cell-free deoxyribonucleic acid (cfDNA) molecules that is obtained from the subject after the subject has undergone a course of treatment for cancer; and determining a presence or absence of cancer in the subject based on an analysis of the frequency of the cancer mutations from sequence data from the second sample, wherein adapters are ligated to at least 20% of the cfDNA molecules using more than a 10× molar excess of adapters relative to the cfDNA molecules in the population of cfDNA molecules.
    Type: Grant
    Filed: May 29, 2024
    Date of Patent: April 22, 2025
    Assignee: Guardant Health, Inc.
    Inventors: AmirAli Talasaz, Stefanie Ann Ward Mortimer
  • Patent number: 12270074
    Abstract: Methods and compositions for analyzing a library comprising a plurality of amplicons comprising identifier sequences are provided, for example, a library of amplicons in a cell or tissue sample attached to a solid support. For example, amplicons are sequenced using a polymerase to incorporate a plurality of cognate nucleotides into the sequencing primer or an extension product thereof to generate a plurality of extension products.
    Type: Grant
    Filed: February 27, 2024
    Date of Patent: April 8, 2025
    Assignee: 10X GENOMICS, INC.
    Inventors: Patrick J. Marks, Michael Schnall-Levin
  • Patent number: 12252734
    Abstract: Methods of uniquely labeling or barcoding molecules within a cell, a plurality of cells, and/or a tissue are provided. Kits for uniquely labeling or barcoding molecules within a cell, a plurality of cells, and/or a tissue are also provided. The molecules to be labeled may include, but are not limited to, RNAs, cDNAs, DNAs, proteins, peptides, and/or antigens.
    Type: Grant
    Filed: August 24, 2023
    Date of Patent: March 18, 2025
    Assignee: University of Washington
    Inventors: Georg Seelig, Richard Muscat, Alexander B. Rosenberg
  • Patent number: 12241059
    Abstract: The disclosure provides methods for creating long oligonucleotide reagents that include barcodes and other element for sequencing library preparation, where the oligonucleotides are created by multiple tiers of ligation of shorter oligos. The disclosed methods work to extend short oligos that are attached to particles, thereby allowing one to create particles that carry large number of long sample preparation oligonucleotides without being required to synthesize those full-length molecules with a polymerase.
    Type: Grant
    Filed: July 15, 2021
    Date of Patent: March 4, 2025
    Assignee: Illumina, Inc.
    Inventors: Robert Meltzer, Kristina Fontanez, Yi Xue
  • Patent number: 12227741
    Abstract: The invention provides methods of performing multi-parameter analysis of single cells. Specifically, the present invention is based, in part, on leveraging a separation of reaction volume scales to conduct high-throughput single cell multi-parameter measurements and library preparation on the same single cell using double emulsion micro-droplets and sorting using flow cytometry.
    Type: Grant
    Filed: July 1, 2019
    Date of Patent: February 18, 2025
    Assignees: CZ Biohub SF, LLC, The Board of Trustees of the Leland Stanford Junior University
    Inventors: Polly Fordyce, Kara Brower, Sandy Klemm, William Greenleaf
  • Patent number: 12215310
    Abstract: Described herein are probiotics, more particularly [to] the probiotic yeast Saccharomyces boulardii. Even more particularly described herein are enhanced probiotic potency S. boulardii. Also described here are mutant alleles useful to develop yeast strains with enhanced production of acetic acid. In addition, described here is the use of such yeast strains for the production of dietary supplements or pharmaceutical compositions to improve gastrointestinal comfort.
    Type: Grant
    Filed: September 14, 2018
    Date of Patent: February 4, 2025
    Assignees: VIB VZW, Katholieke Universiteit Leuven
    Inventors: Johan Thevelein, Benjamin Offei, Maria Remedios Foulquié Moreno, Paul Vandecruys
  • Patent number: 12186747
    Abstract: Single use cartridges for testing biological samples are provided that include multiple processing channels. A single use cartridge includes an aliquot staging well, a first amplification well, a second amplification well, an actuation port, and a fluid channel control valve assembly. The fluid channel control valve assembly is reconfigurable between a first fluid channel configuration and a second fluid channel configuration.
    Type: Grant
    Filed: December 9, 2021
    Date of Patent: January 7, 2025
    Assignee: Amazon Technologies, Inc.
    Inventors: William Brian Greger, Aida Martin Galan, Manuela Alanis, Emanuel Elizalde, Luciano Braggio
  • Patent number: 12139751
    Abstract: The present disclosure relates in some aspects to methods and compositions for analysis of a target nucleic acid, such as in situ detection of a region of interest in a polynucleotide in a tissue sample. In some embodiments, provided herein are templated ligation probes (e.g., RNA-templated ligation probes) and selector probes for generation of a circularized ligated probe comprising an insertion sequence of a selector probe, wherein the circularized ligated probe is amplified in a rolling circle amplification reaction to generate a product that is detected in the sample.
    Type: Grant
    Filed: July 29, 2022
    Date of Patent: November 12, 2024
    Assignee: 10X GENOMICS, INC.
    Inventors: Jorge Iván Hernández Neuta, Malte Kühnemund, Jessica Östlin, Xiaoyan Qian, Toon Verheyen
  • Patent number: 12110560
    Abstract: The present disclosure provides a method for monitoring residual disease in a subject. Generally, the method comprises determining a frequency of cancer mutations from a first sample obtained from a tumor biopsy from the subject; determining a frequency of the cancer mutations discovered in the first sample from a second sample comprising cell-free deoxyribonucleic acid (cfDNA) molecules that is obtained from the subject after the subject has undergone a course of treatment for cancer; and determining a presence or absence of cancer in the subject based on an analysis of the frequency of the cancer mutations from sequence data from the second sample.
    Type: Grant
    Filed: March 4, 2024
    Date of Patent: October 8, 2024
    Assignee: Guardant Health, Inc.
    Inventor: AmirAli Talasaz
  • Patent number: 12104200
    Abstract: The present disclosure provides methods and systems for processing nucleic acid molecules from one or more cells. A cell may be comprised in a cell bead. Processing may comprise uniquely identifying nucleic acid molecules. Nucleic acid molecules may be identified by barcoding. Barcoding may be combinatorial barcoding. Combinatorial barcoding may allow for generation of a large number of barcodes, thereby uniquely identifying nucleic acids from a large number of single cells. Combinatorial barcoding may be performed in successive operations. Successive operations may be performed in partitions.
    Type: Grant
    Filed: June 7, 2019
    Date of Patent: October 1, 2024
    Assignee: 10X GENOMICS, INC
    Inventor: Michael Schnall-Levin
  • Patent number: 12098396
    Abstract: Provided herein relates to DNA polymerase variants and kits including the same, where the DNA polymerase variant has an improved function and activity of performing template-independent nucleic acids synthesis using canonical nucleotides and non-canonical nucleotide analogues in a thermotolerant manner.
    Type: Grant
    Filed: September 29, 2022
    Date of Patent: September 24, 2024
    Inventor: Cheng-Yao Chen
  • Patent number: 12091660
    Abstract: Compositions and methods are provided for detection of dynamic loci in a genome, where such loci may comprise structural variations as a result of DNA recombination; DNA duplication, insertions, deletions, transpositions, and epigenetic changes. The methods may utilize microfluidic platforms and functionalized polymer matrices to allow determination of mechanisms of cell-type-specific, programmed genomic heterogeneity. The method and compositions allow determination of mechanisms of cell-type-specific, programmed genomic heterogeneity.
    Type: Grant
    Filed: April 10, 2023
    Date of Patent: September 17, 2024
    Assignees: The Board of Trustees of the Leland Stanford Junior University, Board of Regents, The University of Texas System
    Inventors: Massa Shoura, Andrew Z. Fire, Stephen Levene
  • Patent number: 12087754
    Abstract: Provided is a method of fabricating a hybrid element, the method including forming a plurality of first elements on a first substrate, separating a plurality of second elements grown on a second substrate from the second substrate, a material of the second substrate being different from a material of the first substrate, and transferring the plurality of second elements, separated from the second substrate, onto the first substrate, wherein, in the transferring, the plurality of second elements are spaced apart from each other by a fluidic self-assembly method, and wherein each of the plurality of second elements includes a shuttle layer grown on the second substrate, an element layer grown on the shuttle layer, and an electrode layer on the element layer.
    Type: Grant
    Filed: February 8, 2022
    Date of Patent: September 10, 2024
    Assignee: SAMSUNG ELECTRONICS CO., LTD.
    Inventors: Kyungwook Hwang, Junsik Hwang, Dongho Kim, Hyunjoon Kim, Joonyong Park, Seogwoo Hong
  • Patent number: 12077814
    Abstract: A method for low frequency somatic cell mutation identification and quantification, relating specifically to a method for transposon copy number and genome location identification. Specific sites of different transposon families are used, transposon insertion sequences are specifically enriched via library construction, high-throughput sequencing and bioinformatics analysis are used, and genome locations, copy numbers and types of transposons within samples are accurately identified. The method economically and accurately identifies copy numbers and genome locations of transposons.
    Type: Grant
    Filed: July 23, 2018
    Date of Patent: September 3, 2024
    Assignee: PEKING UNIVERSITY
    Inventors: Liping Wei, Boxun Zhao, Yue Huang, Qixi Wu, Yongxin Ye, Xianing Zheng
  • Patent number: 12071654
    Abstract: Provided herein are methods of normalizing nucleic acid libraries. The method uses nucleic acid probes with nucleic acid sequences that are complementary to one or more of these adaptor sequences are added to the nucleic acids libraries. The probes can hybridize to the adaptor sequences in the single stranded nucleic acid molecules derived from the libraries to form hybridization complexes. The probes are conjugated to a first binding member, which can interact with a second binding member that is conjugated to solid supports. The solid supports can then be collected and the single stranded nucleic acid molecules can be recovered in a volume of elution buffer to reach a desired concentration. As compared to standard methods, the methods are more efficient and cost-effective.
    Type: Grant
    Filed: April 1, 2020
    Date of Patent: August 27, 2024
    Assignee: SEQUENOM, INC
    Inventors: Tricia Zwiefelhofer, Jason Nathanson
  • Patent number: 12071656
    Abstract: Compositions, kits and methods are described that comprise one or more constructs, each construct comprising a ligand attached or conjugated to a polymer construct, e.g., an oligonucleotide sequence, by a linker, each ligand binding specifically to a single target located in or on the surface of a cell. The polymer construct comprises a) an Amplification Handle; b) a Barcode that specifically identifies a single ligand; c) an optional Unique Molecular Identifier that is positioned adjacent to the Barcode on its 5? or 3? end; and d) an Anchor for hybridizing to a complementary sequence, e.g., for generation of a double-stranded oligonucleotide. These compositions are used in methods, including high throughput methods, for detecting one or more targets or epitopes in a biological sample. These compositions are also used in a high throughput method for characterizing a cell by simultaneous detection of one or more epitopes located in or on the cell and its transcriptome.
    Type: Grant
    Filed: April 30, 2021
    Date of Patent: August 27, 2024
    Assignee: New York Genome Center, Inc.
    Inventors: Marlon Stoeckius, Peter Smibert, Brian Houck-Loomis
  • Patent number: 12065697
    Abstract: Disclosed herein is a specific B-family DNA polymerase variants that exhibit an improved incorporation of nucleotide analogues for synthesizing polynucleotides and sequencing the associated nucleic acid template. More particularly, the DNA sequencing-by-synthesis method can be efficiently performed by said B-family DNA polymerase variants with a normal nucleic acid template and reversible dye-terminator nucleotides to precisely determine the sequence of associated nucleic acid template.
    Type: Grant
    Filed: June 28, 2022
    Date of Patent: August 20, 2024
    Inventor: Cheng-Yao Chen
  • Patent number: 12054773
    Abstract: The present disclosure provides methods and systems for producing full-length sequencing information of transcriptomes from single cells or from the bulk. Random ligation and circularization of barcoded or non-barcoded complementary deoxyribonucleic molecules can be used to provide a circular template for amplification and subsequent sequencing.
    Type: Grant
    Filed: August 26, 2020
    Date of Patent: August 6, 2024
    Assignee: 10X GENOMICS, INC.
    Inventors: Vijay Kumar Sreenivasa Gopalan, Paul Ryvkin, Zachary Bent, Jessica Michele Terry, David Jaffe, Patrick Marks, Tarjei Sigurd Mikkelsen
  • Patent number: 12057195
    Abstract: A method for prioritizing sequencing of nucleic acid molecules from two or more sources, comprising: (i) ligating one or more ends of each of a plurality of nucleic acid molecules to an adapter, wherein the adaptor is unique to each source and comprises a unique identifier nucleic acid sequence; (ii) pooling the nucleic acid molecules from each of the two or more sources; (iii) sequencing a plurality of nucleotides of an identifier nucleic acid sequence of an adapter; (iv) determining in real-time from which of the two or more sources the nucleic acid molecule being sequenced came; (v) determining, from a prioritization rule set and based on the determined source, a sequencing priority for the nucleic acid molecule; and (vi) allowing the sequencing process to proceed, or modifying the sequencing process, based on the determined sequencing priority.
    Type: Grant
    Filed: April 16, 2018
    Date of Patent: August 6, 2024
    Assignee: KONINKLIJKE PHILIPS N.V.
    Inventor: Brian David Gross
  • Patent number: 12024566
    Abstract: An anti-SIRP? antibody that can be used as a tumor agent and an anti-tumor agent comprising the antibody as an active ingredient. An antibody that binds specifically to human SIRP? to inhibit binding of human SIRP? to CD47.
    Type: Grant
    Filed: July 9, 2019
    Date of Patent: July 2, 2024
    Assignees: NATIONAL UNIVERSITY CORPORATION KOBE UNIVERSITY, DAIICHI SANKYO COMPANY, LIMITED
    Inventors: Takashi Matozaki, Mayumi Sue, Kensuke Nakamura, Chigusa Yoshimura
  • Patent number: 12018302
    Abstract: Glycerol-free enzyme formulations are described. In some embodiments, a glycerol-free enzyme formulation is stabilized by high salt concentration. The glycerol free enzyme formulation may comprise a reverse transcriptase enzyme.
    Type: Grant
    Filed: February 23, 2022
    Date of Patent: June 25, 2024
    Assignee: Thermo Fisher Scientific Baltics, UAB
    Inventors: Juozas Siurkus, Darius Kavaliauskas, Daumantas Matulis, Lina Baranauskiene
  • Patent number: 12019015
    Abstract: The present invention discloses devices for independently-controllable, multi-chamber cuvettes for rapid, concurrent spectral analyses, embodied applications of same, and methods therein. Devices include: a multi-chamber cuvette having contiguous analysis chambers forming a single continuous inner cavity configured to contain a liquid in an inner-cavity volume, wherein each chamber is configured to serve as a measurement zone for the liquid in the inner cavity when the volume is filled with the liquid by regulation of hydrostatic pressure in the inner cavity in order to prevent fluid flow from a given chamber to another chamber, and wherein each volume in each zone is designated a zone volume; thermal-contact windows positioned in a chamber to enable independent temperature control of a zone volume in a zone; and cuvette optical windows, positioned in each chamber to provide independent optical access to each zone, adapted to enable analysis of each zone volume in each zone.
    Type: Grant
    Filed: September 23, 2023
    Date of Patent: June 25, 2024
    Inventor: Daniel N. J. Halbert
  • Patent number: 12006547
    Abstract: A process for analysing chromosome regions and interactions relating to ALS and Huntington's disease.
    Type: Grant
    Filed: October 1, 2018
    Date of Patent: June 11, 2024
    Assignee: Oxford BioDynamics PLC
    Inventors: Alexandre Akoulitchev, Aroul Selvam Ramadass, Ewan Hunter, Matthew Salter
  • Patent number: 11999994
    Abstract: Described herein are compositions and methods for the production and quantification of barcoded or unique molecular identifier (UMI)-labeled substrates. In one aspect, the substrate is a bead comprising a template oligonucleotide that is elongated by successive extension reactions to provide a bead with an oligonucleotide comprising a plurality of barcodes and conserved anchor regions. Methods are also described for quantifying the amount of template oligonucleotide loaded onto the substrate and the products of the extension reaction after each round and after the final extension.
    Type: Grant
    Filed: January 13, 2022
    Date of Patent: June 4, 2024
    Assignee: INTEGRATED DNA TECHNOLOGIES, INC.
    Inventors: Joseph Dobosy, Scott D. Rose, Jeffrey A. Manthey, Shawn D. Allen, Steven A. Henck, Mark Behlke
  • Patent number: 11986823
    Abstract: A microfluidic device includes an array unit and a nanostructure connected to the array unit, wherein the array unit comprises array cells with substances for a polymerase chain reaction. The array cells include nucleotides with stop properties according to the Sanger sequencing method and primers for an asymmetric polymerase chain reaction. The nanostructure is configured to determine lengths of nucleotide strands formed by the polymerase chain reaction.
    Type: Grant
    Filed: May 2, 2019
    Date of Patent: May 21, 2024
    Assignee: Robert Bosch GmbH
    Inventor: Franz Laermer
  • Patent number: 11981966
    Abstract: The present technology relates to methods for determining whether a patient diagnosed with breast cancer, colorectal cancer, melanoma or lung cancer will benefit from or is predicted to be responsive to treatment with an individual therapeutic agent or a specific combination of therapeutic agents. These methods are based on screening a patient's solid tumors and detecting alterations in target nucleic acid sequences corresponding to a specific set of cancer-related genes. Kits for use in practicing the methods are also provided.
    Type: Grant
    Filed: May 8, 2020
    Date of Patent: May 14, 2024
    Assignee: Quest Diagnostics Investments LLC
    Inventors: Heather Sanders, Kevin Qu, James Prentice, Frederic Waldman
  • Patent number: 11970736
    Abstract: The present disclosure relates to a next generation DNA sequencing method and use for accurate and massively parallel quantification of one or more nucleic acid targets, for example in large volumes of unpurified sample material. More particularly, the disclosed embodiments is related to a method and a kit comprising probes for detecting and quantifying genetic targets in complex samples. The disclosed embodiments includes two target-specific nucleic acid probes per genetic target, a barcode loop oligo and a bridge oligo or bridge oligo complex.
    Type: Grant
    Filed: August 31, 2022
    Date of Patent: April 30, 2024
    Assignee: Genomill Health Oy
    Inventors: Juha-Pekka Pursiheimo, Tatu Hirvonen, Anttoni Korkiakoski, Manu Tamminen
  • Patent number: 11952626
    Abstract: Provided herein are systems and methods for processing biomolecules (e.g., nucleic acid molecules, proteins) from a sample. A method for processing biomolecules may comprise hybridizing a probe molecule to a target region of a nucleic acid molecule (e.g., a ribonucleic acid (RNA) molecule) and barcoding the probe-nucleic acid molecule complex or derivatives thereof. Such a method can comprise performing a nucleic acid reaction, e.g., extension, denaturation, and amplification. A method for processing a sample may comprise hybridizing probes to (i) target regions of a nucleic acid molecule (e.g., RNA molecule) and (ii) a reporter oligonucleotide of a feature binding group, and barcoding the probe-associated molecules. One or more processes of the methods described herein may be performed within a partition, such as a droplet or well.
    Type: Grant
    Filed: August 22, 2023
    Date of Patent: April 9, 2024
    Assignee: 10X GENOMICS, INC.
    Inventors: Katherine Pfeiffer, Andrew Scott Kohlway, Andrew John Hill, Paul Eugene Lund
  • Patent number: 11946101
    Abstract: The invention provides improved methods, compositions, and kits for detecting ploidy of chromosome regions, e.g. for detecting cancer or a chromosomal abnormality in a gestating fetus. The methods can utilize a set of more than 200 SNPs that are found within haploblocks and can include analyzing a series of target chromosomal regions related to cancer or a chromosomal abnormality in a gestating fetus. Finally the method may use knowledge about chromosome crossover locations or a best fit algorithm for the analysis. The compositions may comprise more than 200 primers located within haplotype blocks known to show CNV.
    Type: Grant
    Filed: June 21, 2022
    Date of Patent: April 2, 2024
    Assignee: Natera, Inc.
    Inventors: Huseyin Eser Kirkizlar, Raheleh Salari, Styrmir Sigurjonsson, Bernhard Zimmermann, Allison Ryan, Naresh Vankayalapati
  • Patent number: 11920123
    Abstract: A cell analyzing device includes a control circuit. The control circuit acquires data of an observation image. The control circuit specifies a colony of a cultured cell in the observation image. The control circuit calculates a ratio at which the cultured cell occupies a predetermined range included in the observation image as an occupancy rate. The control circuit calculates a size of the colony. The control circuit determines a state of the cultured cell based on the occupancy rate and the size of the colony.
    Type: Grant
    Filed: July 15, 2020
    Date of Patent: March 5, 2024
    Assignee: Evident Corporation
    Inventors: Yasunobu Iga, Taiji Mine, Yoshinobu Akahori
  • Patent number: 11905553
    Abstract: Provided herein are compositions and methods for accurate and scalable Primary Template-Directed Amplification (PTA) nucleic acid amplification and sequencing methods, and their applications for research, diagnostics, and treatment.
    Type: Grant
    Filed: January 28, 2019
    Date of Patent: February 20, 2024
    Assignee: ST. JUDE CHILDREN'S RESEARCH HOSPITAL, INC.
    Inventors: Charles Gawad, John Easton, Veronica Gonzalez-Pena
  • Patent number: 11898205
    Abstract: This disclosure relates to methods for increasing capture efficiency of a spatial array using rolling circle amplification of a padlock probe that hybridizes to a capture probe. Also provided are methods for using such spatial arrays to detect a biological analyte in a biological sample.
    Type: Grant
    Filed: February 2, 2021
    Date of Patent: February 13, 2024
    Assignee: 10x Genomics, Inc.
    Inventor: Felice Alessio Bava
  • Patent number: 11900595
    Abstract: Disclosed herein, inter alia, are methods and systems of image analysis useful for identifying and/or quantifying features in patterns.
    Type: Grant
    Filed: May 5, 2021
    Date of Patent: February 13, 2024
    Assignee: Singular Genomics Systems, Inc.
    Inventors: Fedor Trintchouk, Eli N. Glezer
  • Patent number: 11859249
    Abstract: There is disclosed a method of generating a massively parallel sequencing library comprising the steps of: a) providing a primary WGA DNA library (pWGAlib), including fragments comprising a WGA library universal sequence adapter; b) performing a single PCR cycle on the pWGAlib using a first primer (1PR) comprising from 5? to 3? a first sequencing adapter (1PR5SA) and a first primer 3? section (1PR3S) hybridizing to the reverse complementary of the WGA library universal sequence adapter; c) performing a single PCR cycle on the on the product of step b) using a second primer (2PR) comprising from 5? to 3? a second sequencing adapter (2PR5SA) different from the 1PR5SA, and a second primer 3? section (2PR3S) hybridizing to the WGA library universal sequence adapter reverse complementary; d) amplifying by PCR the product of step c) using a third primer comprising the 1PR5SA and a fourth primer comprising 2PR5SA.
    Type: Grant
    Filed: July 20, 2018
    Date of Patent: January 2, 2024
    Assignee: Menarini Silicon Biosystems S.p.A.
    Inventors: Valentina Del Monaco, Nicolò Manaresi, Genny Buson, Paola Tononi
  • Patent number: 11845084
    Abstract: Provided are methods and related devices for preparing a cell and tissue culture, including a hanging drop culture. Microwells are specially loaded with cell mixtures using a removable reservoir and forcing cells into the underlying microwells. The removable reservoir is removed and the cells partitioned into the individual microwells and covered by an immiscible layer of fluid. The microwells and immiscible layer is inverted and the cells in the microwells cultured. The microwells may have shape-controlling elements to control the three-dimensional shape of the culture.
    Type: Grant
    Filed: May 4, 2021
    Date of Patent: December 19, 2023
    Assignees: The Board of Trustees of the University of Illinois, Mayo Foundation for Medical Education and Research
    Inventors: Anurup Ganguli, Rashid Bashir, Panagiotis Z. Anastasiadis, George Vasmatzis
  • Patent number: 11845984
    Abstract: A method for sequencing a biological molecule, such as a nucleic acid molecule, and a method for detecting and/or correcting sequencing error(s) in the sequencing results are provided. Kits and systems based on the above methods are also provided.
    Type: Grant
    Filed: July 13, 2020
    Date of Patent: December 19, 2023
    Assignee: CYGNUS BIOSCIENCES (BEIJING) CO., LTD.
    Inventors: Yanyi Huang, Zitian Chen, Wenxiong Zhou, Haifeng Duan, Li Kang, Shuo Qiao
  • Patent number: 11795496
    Abstract: A method of determining responsiveness to therapy for rheumatoid arthritis.
    Type: Grant
    Filed: June 24, 2016
    Date of Patent: October 24, 2023
    Assignee: Oxford Biodynamics PLC
    Inventors: Aroul Ramadass, Ewan Hunter, Alexandre Akoulitchev
  • Patent number: 11783917
    Abstract: The technology disclosed processes input data through a neural network and produces an alternative representation of the input data. The input data includes per-cycle image data for each of one or more sequencing cycles of a sequencing run. The per-cycle image data depicts intensity emissions of one or more analytes and their surrounding background captured at a respective sequencing cycle. The technology disclosed processes the alternative representation through an output layer and producing an output and base calls one or more of the analytes at one or more of the sequencing cycles based on the output.
    Type: Grant
    Filed: March 20, 2020
    Date of Patent: October 10, 2023
    Inventors: Kishore Jaganathan, John Randall Gobbel, Amirali Kia
  • Patent number: 11759761
    Abstract: Methods of generating a nucleic acid signature for identifying particles associated in a partition are provided. In one aspect, the method comprises: partitioning a sample into a plurality of partitions comprising a particle comprising a solid support surface, the solid support surface having a plurality of oligonucleotide primers conjugated thereon, wherein the oligonucleotide primers comprise a barcode sequence, and wherein the partitions have 0, 1, or more than 1 particles per partition; providing in a partition a substrate comprising a barcode sequence or repeating clonal barcode sequences; and in the partition, associating a first particle conjugated to oligonucleotide primers comprising a first barcode sequence and a second particle conjugated to oligonucleotide primers comprising a second barcode sequence to a barcode sequence from the substrate, thereby generating a nucleic acid signature for the particles in the partition.
    Type: Grant
    Filed: July 20, 2021
    Date of Patent: September 19, 2023
    Assignee: Bio-Rad Laboratories, Inc.
    Inventors: Ronald Lebofsky, Nicholas Heredia
  • Patent number: 11739373
    Abstract: Provided herein, in some embodiments, are systems, methods, compositions, and kits for detecting and quantifying analytes using a primary analyte binding molecule conjugated to a nucleic acid template.
    Type: Grant
    Filed: February 5, 2019
    Date of Patent: August 29, 2023
    Assignee: G1 Sciences, LLC
    Inventor: Sudha Haran
  • Patent number: 11702649
    Abstract: The present invention relates to the analysis of complex single cell sequencing libraries. Disclosed are methods for enrichment of library members based on the presence of cell-of origin barcodes to identify and concentrate DNA that is relevant to interesting cells or components that would be expensive or difficult to study otherwise. Also, disclosed are methods of capturing cDNA library molecules by use of CRISPR systems, hybridization or PCR. The present invention allows for identifying the properties of rare cells in single cell RNA-seq data and accurately profile them through clustering approaches. Further information on transcript abundances from subpopulations of single cells can be analyzed at a lower sequencing effort. The methods also allow for linking TCR alpha and beta chains at the single cell level.
    Type: Grant
    Filed: October 23, 2018
    Date of Patent: July 18, 2023
    Assignees: The Broad Institute, Inc., Massachusetts Institute of Technology
    Inventors: Paul Blainey, Navpreet Ranu, Todd Gierahn, J. Christopher Love
  • Patent number: 11687791
    Abstract: According to some embodiments of the present disclosure, a device is disclosed. In embodiments, the device stores a computer program comprised of a set of encoded executable instructions; a genomic differentiation object and genomic regulation instructions (GRI) that were used to encode the set of encoded executable instructions. The device further includes a processing system comprising a VDAX and a set of processing cores. The VDAX is configured to: receive encoded instructions to be executed from the set of encoded executable instructions and decode the encoded instructions into decoded executable instruction based on a modified genomic differentiation object and sequences extracted from metadata associated with the encoded instructions. In these embodiments, the modified genomic differentiation object is modified from the genomic differentiation object using the GRI.
    Type: Grant
    Filed: February 10, 2022
    Date of Patent: June 27, 2023
    Assignee: Quantum Digital Solutions Corporation
    Inventors: William C. Johnson, Karen Ispiryan, Gurgen Khachatryan
  • Patent number: 11655499
    Abstract: Provided herein are methods and systems for establishing the presence of a sequence element in nucleic acid molecules. The sequence element may comprise a fused gene, a reporter gene, or another useful sequence for cell and tissue engineering, such as those used for labeling cells, identifying successfully transfected or transduced cells, etc. A method provided herein may additionally allow for barcoding of nucleic acid molecules and analysis of libraries of barcoded nucleic acid molecules.
    Type: Grant
    Filed: February 25, 2020
    Date of Patent: May 23, 2023
    Assignee: 10X GENOMICS, INC.
    Inventor: Katherine Pfeiffer
  • Patent number: 11643682
    Abstract: Provided herein are compositions and methods for accurate and scalable Primary Template-Directed Amplification (PTA) nucleic acid amplification and sequencing methods, and their applications for research, diagnostics, and treatment.
    Type: Grant
    Filed: August 31, 2022
    Date of Patent: May 9, 2023
    Assignee: ST. JUDE CHILDREN'S RESEARCH HOSPITAL, INC.
    Inventors: Charles Gawad, John Easton, Veronica Gonzalez-Pena
  • Patent number: 11634766
    Abstract: Provided herein include methods and compositions for analyzing nucleic acid in individual cells. In some embodiments, the methods herein include generating, within individual cells, fragmented cellular genomic DNA and cDNA copies of cellular RNA molecules, barcoding the fragmented genomic DNA and the cDNA within each cell such that the genomic DNA and the cDNA from the same cell receive the same unique barcode sequence, isolating the barcoded genomic DNA and cDNA, and characterizing one or more features of the individual cells based, at least in part, on sequencing of the isolated barcoded genomic DNA and the cDNA.
    Type: Grant
    Filed: February 4, 2020
    Date of Patent: April 25, 2023
    Assignees: The Broad Institute, Inc., Massachusetts Institute of Technology, President and Fellows of Harvard College
    Inventors: Jason Daniel Buenrostro, Sai Ma, Aviv Regev
  • Patent number: 11635427
    Abstract: The invention generally relates to performing sandwich assays in droplets. In certain embodiments, the invention provides methods for detecting a target analyte that involve forming a compartmentalized portion of fluid including a portion of a sample suspected of containing a target analyte and a sample identifier, a first binding agent having a target identifier, and a second binding agent specific to the target analyte under conditions that produce a complex of the first and second binding agents with the target analyte, separating the complexes, and detecting the complexes, thereby detecting the target analyte.
    Type: Grant
    Filed: July 24, 2020
    Date of Patent: April 25, 2023
    Assignee: Bio-Rad Laboratories, Inc.
    Inventors: Michael L. Samuels, Darren Roy Link
  • Patent number: 11623219
    Abstract: Air-matrix digital microfluidics (DMF) apparatuses and methods of using them to prevent or limit evaporation and surface fouling of the DMF apparatus. In particular, described herein are air-matrix DMF apparatuses and methods of using them including thermally controllable regions with a wax material that may be used to selectively encapsulate a reaction droplet in the air gap of the apparatus; additional aqueous droplets may be combined with the encapsulated droplet even after separating from the wax, despite residual wax coating, by merging with an aqueous droplet having a coating of a secondary material (e.g., an oil or other hydrophobic material) that may remove the wax from the droplet and/or allow combining of the droplets.
    Type: Grant
    Filed: April 4, 2018
    Date of Patent: April 11, 2023
    Assignee: mirOculus Inc.
    Inventors: Mais J. Jebrail, Alexandra Judy Cho, Foteini Christodoulou
  • Patent number: 11624064
    Abstract: Provided herein are methods of enriching mutated cell free nucleic acids for detection and diagnosis of cancer. Also provided are methods using a CRISPR-Cas system to target and deplete unwanted more abundant cell free nucleic acid sequences thereby enriching for less abundant sequences.
    Type: Grant
    Filed: June 13, 2017
    Date of Patent: April 11, 2023
    Assignee: GRAIL, LLC
    Inventors: Gordon Cann, Alex Aravanis, Arash Jamshidi, Rick Klausner, Richard Rava
  • Patent number: 11618808
    Abstract: Some embodiments described herein relate to a substrate with a surface comprising a silane or a silane derivative covalently attached to optionally substituted cycloalkene or optionally substituted heterocycloalkene for direct conjugation with a functionalized molecule of interest, such as a polymer, a hydrogel, an amino acid, a nucleoside, a nucleotide, a peptide, a polynucleotide, or a protein. In some embodiments, the silane or silane derivative contains optionally substituted norbornene or norbornene derivatives. Method for preparing a functionalized surface and the use in DNA sequencing and other diagnostic applications are also disclosed.
    Type: Grant
    Filed: March 5, 2021
    Date of Patent: April 4, 2023
    Assignee: Illumina, Inc.
    Inventors: Lorenzo Berti, Andrew A. Brown, Wayne N. George
  • Patent number: 11608494
    Abstract: This invention relates to, in part, compositions of beta-lactamases and methods of using these enzymes in, for example, gastrointestinal tract (GI tract) disorders such as C. difficile infection (CDI).
    Type: Grant
    Filed: December 8, 2021
    Date of Patent: March 21, 2023
    Assignee: Theriva Biologics, Inc.
    Inventors: Michael Kaleko, Sheila Connelly