Patents Assigned to Genomed
  • Devices and systems incorporating acoustic ordering and methods of use thereof
    Patent number: 12186751
    Abstract: Devices, systems, and their methods of use, for generating droplets are provided. One or more geometric parameters of a microfluidic channel can be selected to generate droplets of a desired and predictable droplet size.
    Type: Grant
    Filed: June 29, 2020
    Date of Patent: January 7, 2025
    Assignee: 10x Genomics, Inc.
    Inventors: Alireza Salmanzadeh, Rajiv Bharadwaj
  • Methods and systems for analyte detection and analysis
    Patent number: 12188924
    Abstract: Provided are systems and methods for analyte detection and analysis. A system can comprise an open substrate configured to rotate. The open substrate can comprise an array of immobilized analytes. A solution comprising a plurality of probes may be directed, via centrifugal force, across the array during rotation of the substrate, 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 continuous rotational area scanning of the substrate.
    Type: Grant
    Filed: July 20, 2023
    Date of Patent: January 7, 2025
    Assignee: Ultima Genomics, Inc.
    Inventors: Kristopher Barbee, Nathan Beckett, Denis Pristinski, Derek Schulte, Avishai Bartov, Jamie Sullivan, Dumitru Brinza, Abizar Lakdawalla, Steven Menchen, Gilad Almogy, Mark Pratt
  • Multiplexed targeted amplification of polynucleotides
    Patent number: 12188088
    Abstract: Disclosed herein, inter alia, are compositions and methods for efficient amplification and sequencing of nucleic acid templates.
    Type: Grant
    Filed: June 15, 2023
    Date of Patent: January 7, 2025
    Assignee: Singular Genomics Systems, Inc.
    Inventors: Eli N. Glezer, Daan Witters, Tung Thanh Le
  • Three-dimensional spatial transcriptomics with sequencing readout
    Patent number: 12188085
    Abstract: In some embodiments described herein are methods for three-dimensional analysis of a biological sample, comprising migrating a population of spatial probes into the biological sample in each of three dimensions, wherein each spatial probe comprises a targeting domain and a migration domain. Also provided are kits and compositions for use according to any of the methods described herein.
    Type: Grant
    Filed: March 4, 2021
    Date of Patent: January 7, 2025
    Assignee: 10x Genomics, Inc.
    Inventor: Felice Alessio Bava
  • Bioinformatics methods of in silico validation and selection of circRNAs
    Patent number: 12188081
    Abstract: The present invention relates to bioinformatics methods of in silico validation of circRNA junctions and selection of circRNA junctions for further validation, more particularly detecting sequence reads supporting circRNA junction in a highly computationally efficient manner.
    Type: Grant
    Filed: January 24, 2020
    Date of Patent: January 7, 2025
    Assignee: The Translational Genomics Research Institute
    Inventors: Shobana Sekar, Winnie Liang, Jonathan Keats
  • Cleavable disulfide linkers and uses thereof
    Patent number: 12188089
    Abstract: Disclosed herein, inter alia, are methods and cleavable compounds that minimize byproduct formation following cleavage.
    Type: Grant
    Filed: February 12, 2024
    Date of Patent: January 7, 2025
    Assignee: Singular Genomics Systems, Inc.
    Inventors: Ronald Graham, Megha Cila
  • Sequential decoding of nucleic acids
    Patent number: 12188087
    Abstract: The present application provides compositions, systems, and methods for encoding and decoding nucleic acid molecules.
    Type: Grant
    Filed: November 29, 2021
    Date of Patent: January 7, 2025
    Assignee: 10x Genomics, Inc.
    Inventors: Malte Kühnemund, Toon Verheyen
  • SYSTEM AND METHOD FOR SEQUENCE IDENTIFICATION IN REASSEMBLY VARIANT
    Publication number: 20250006300
    Abstract: In one embodiment, a method for identifying candidate sequences for genotyping a genomic sample comprises obtaining a plurality of sequence reads mapping to a genomic region of interest. The plurality of sequence reads are assembled into a directed acyclic graph (DAG) comprising a plurality of branch sites representing variation present in the set of sequence reads, each branch site comprising two or more branches. A path through the DAG comprises a set of successive branches over two or more branch sites and represents a possible candidate sequence of the genomic sample. One or more paths through the DAG are ranked by calculating scores for one or more branch sites, wherein the calculated score comprises a number of sequence reads that span multiple branch sites in a given path. At least one path is selected as a candidate sequence based at least in part on its rank.
    Type: Application
    Filed: May 29, 2024
    Publication date: January 2, 2025
    Applicant: Seven Bridges Genomics Inc.
    Inventor: Ivan Johnson
  • SELF-INCOMPATIBLE DIHAPLOID POTATO LINE AND PRODUCTION METHOD THEREFOR, AND HYBRID POTATO AND SEED PRODUCTION METHOD THEREFOR
    Publication number: 20250000046
    Abstract: Disclosed is a self-incompatible dihaploid potato and a production method therefor, and a hybrid potato and a seed production method therefor. The production method includes the following steps: haploid-inducing a diploid potato carrying one or more heterozygous self-compatibility genes by a haploid induction line, and screening haploid mutants; selecting a haploid mutant which does not contain any self-compatible gene; and performing chromosome doubling on the haploid mutant which does not contain any self-compatibility gene to obtain a self-incompatible dihaploid potato line. The self-incompatible dihaploid potato is used as a female parent for seed production, such that emasculation may be avoided, hybrids do not bear fruits, and the yield of the potato is increased.
    Type: Application
    Filed: September 15, 2024
    Publication date: January 2, 2025
    Applicants: Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences ( Shenzhen, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences
    Inventors: Chunzhi Zhang, Sanwen Huang, Pei Wang, Yanhui Zhu, Xinyu Jing
  • Flow cell receiver and methods of use
    Patent number: 12179208
    Abstract: The present disclosure relates to a flow cell receiver. The flow cell receiver can include at least one platen, having a plurality of ports. The flow cell receiver can include magnets. The flow cell receiver can be configured to automatically align, secure, and retain a flow cell carrier containing a flow cell.
    Type: Grant
    Filed: October 9, 2023
    Date of Patent: December 31, 2024
    Assignee: Singular Genomics Systems, Inc.
    Inventors: Sandor Kovacs, David Baranson, Eli N. Glezer
  • Device for tissue section immobilization and retention
    Patent number: 12181388
    Abstract: Disclosed herein, inter alia, are devices and methods for transfer and analyses of tissue sections using carrier substrates.
    Type: Grant
    Filed: April 1, 2024
    Date of Patent: December 31, 2024
    Assignee: Singular Genomics Systems, Inc.
    Inventors: Yuji Ishitsuka, Zhenmin Hong, Eli N. Glezer, Hu Cang, William Dempsey, Weiqiao Ding, Jaekyung Koh, Mohammad Vatankhah Varnosfaderani
  • Imaging system hardware
    Patent number: 12180543
    Abstract: A sample holder includes a first member featuring a first retaining mechanism configured to retain a first substrate that includes a sample, a second member featuring a second retaining mechanism configured to retain a second substrate that includes a reagent medium, and an alignment mechanism connected to at least one of the first and second members, and configured to align the first and second members such that the sample contacts at least a portion of the reagent medium when the first and second members are aligned.
    Type: Grant
    Filed: December 6, 2019
    Date of Patent: December 31, 2024
    Assignee: 10x Genomics, Inc.
    Inventors: Cedric Uytingco, Zachary Bent, Eswar Prasad Ramachandran Iyer, Fernandino Valdecanas, Meghan L. F. Frey, Steven William Short, Yifeng Yin, Rajiv Bharadwaj, Joakim Lundeberg, Augusto Manuel Tentori, David Maurice Cox, Jennifer Chew, Felice Alessio Bava, Linda Kvastad, Andrew D. Price
  • Methods for in SITU transcriptomics and proteomics
    Patent number: 12180542
    Abstract: Disclosed herein, inter alia, are compositions and methods of use thereof for interrogating a cell.
    Type: Grant
    Filed: August 2, 2022
    Date of Patent: December 31, 2024
    Assignee: Singular Genomics Systems, Inc.
    Inventors: Eli N. Glezer, Hu Cang, Zhenmin Hong
  • AP50 POLYMERASES AND USES THEREOF
    Publication number: 20240425913
    Abstract: The present disclosure relates in some aspects to recombinant Bacillus phage AP50 polymerases, modified AP50 polymerases, and compositions thereof. Also provided are methods of using the recombinant and/or modified AP50 polymerases for nucleic acid amplification (e.g., rolling circle amplification). In some aspects, the compositions and methods disclosed herein provide more robust amplification (e.g., RCA) reactions for improved in vitro and in situ analysis.
    Type: Application
    Filed: August 30, 2024
    Publication date: December 26, 2024
    Applicant: 10x Genomics, Inc.
    Inventor: Shankar SHASTRY
  • METHODS OF SELECTING AND TREATING CANCER SUBJECTS THAT ARE CANDIDATES FOR TREATMENT USING INHIBITORS OF PARP
    Publication number: 20240425934
    Abstract: The technology relates in part to methods of selecting for and/or treating subjects having cancer, where the subjects are identified as having at least one genetic structural variant that renders them suitable candidates for a treatment method that includes the administration of at least one homologous recombination deficient direct therapy, such as an inhibitor of a polyadenosine diphosphate-ribose polymerase (PARP) enzyme.
    Type: Application
    Filed: September 5, 2024
    Publication date: December 26, 2024
    Applicant: Arima Genomics, Inc.
    Inventors: Anthony Schmitt, Kristin Sikkink
  • Sequencing using non-natural nucleotides
    Patent number: 12173365
    Abstract: The present disclosure provides methods and systems for nucleic acid sequencing. Such systems and methods may achieve context-independent incorporation, have reduced context-dependence or have context-dependence that is amenable to calibration and modeling. Such systems and methods may also reduce misincorporation.
    Type: Grant
    Filed: April 5, 2022
    Date of Patent: December 24, 2024
    Assignee: Ultima Genomics, Inc.
    Inventors: Gilad Almogy, Linda Lee
  • Systems and methods for analyzing viral nucleic acids
    Patent number: 12173374
    Abstract: The invention provides systems and methods for analyzing viruses by representing viral genetic diversity with a directed acyclic graph (DAG), which allows genetic sequencing technology to detect rare variations and represent otherwise difficult-to-document diversity within a sample. Additionally, a host-specific sequence DAG can be used to effectively segregate viral nucleic acid sequence reads from host sequence reads when a sample from a host is subject to sequencing. Known viral genomes can be represented using a viral reference DAG and the viral sequence reads from the sample can be compared to viral DAG to identify viral species or strains from which the reads were derived. Where the viral sequence reads indicate great genetic diversity in the virus that was infecting the host, those reads can be assembled into a DAG that itself properly represents that diversity.
    Type: Grant
    Filed: May 26, 2023
    Date of Patent: December 24, 2024
    Assignee: Seven Bridges Genomics Inc.
    Inventors: Devin Locke, Piotr Szamel
  • CAPTURING OLIGONUCLEOTIDES IN SPATIAL TRANSCRIPTOMICS
    Publication number: 20240416315
    Abstract: Disclosed are extended and/or branched oligonucleotide capture probe assemblies for use in spatial transcriptomics systems, and methods for making the capture probe assemblies.
    Type: Application
    Filed: August 29, 2024
    Publication date: December 19, 2024
    Applicant: 10X Genomics, Inc.
    Inventor: Felice Alessio Bava
  • High resolution spatial genomic analysis of tissues and cell aggregates
    Patent number: 12168226
    Abstract: Provided are devices and methods for capturing template sample nucleic acids in a spatially specific manner that is coordinated with the original location of the templates in a tissue sample. By preserving spatial information regarding a given sample, the disclosed technology allows for improved diagnostics as well as improved therapeutic decision making for patient care and therapy.
    Type: Grant
    Filed: October 17, 2017
    Date of Patent: December 17, 2024
    Assignee: BioSkryb Genomics, Inc.
    Inventors: Jason A. A. West, Kyle Hukari
  • Hybrid/capture probe designs for full-length cDNA
    Patent number: 12168801
    Abstract: Systems and methods for identifying and using hybrid/capture probes are provided. cDNA sequences from poly-adenylated mRNA are obtained. Each cDNA sequence in a first subset maps to a gene in a plurality of genes. Each cDNA sequence in a second subset maps to a reference genome portion not represented by the plurality of genes. Each gene has a corresponding plurality of transcripts. The cDNA sequences are exposed to at least 2×103 nucleic acid baits between K1 and K2 residues long, forming nucleic acid bait—sequence read complexes. Each nucleic acid bait that hybridizes to a cDNA sequence mapping to a gene selectively hybridizes to a first subset or another subset of transcripts corresponding to the gene. Each transcript of each gene is hybridizable to a nucleic acid bait in the at least 2×103 nucleic acid baits. The nucleic acid bait—sequence read complexes are captured and analyzed.
    Type: Grant
    Filed: July 2, 2021
    Date of Patent: December 17, 2024
    Assignee: 10X Genomics, Inc.
    Inventors: Andrew John Hill, Katherine Pfeiffer, Andrew Scott Kohlway