Patents Examined by Sahana S Kaup
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Patent number: 11981891Abstract: Provided herein are methods for preparing a sequencing library that includes nucleic acids from a plurality of single cells. In one embodiment, the methods include linear amplification of the nucleic acids. In one embodiment, the sequencing library includes whole genome nucleic acids from the plurality of single cells. In one embodiment, the nucleic acids include three index sequences. Also provided herein are compositions, such as compositions that include the nucleic acids having three index sequences.Type: GrantFiled: May 17, 2019Date of Patent: May 14, 2024Assignees: Illumina, Inc., University of WashingtonInventors: Frank J. Steemers, Jay Shendure, Yi Yin
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Patent number: 11976276Abstract: The present invention is related to a method for recovering two or more genes, or gene products, or cDNAs, encoding for an immunoreceptor having two or more subunits, which two or more genes, or gene products, are comprised in a given source cell. The invention is further related to a method of creating a library of expressor cells, in which library each cell is capable of expressing two or more genes, or gene products, encoding for the subunits of the immunoreceptor. The invention is further related to a method of screening a library of expressor cells as created according to the above method, for one cell that expresses an immunoreceptor that has specificity for a given target molecule.Type: GrantFiled: November 5, 2021Date of Patent: May 7, 2024Assignee: Memo Therapeutics AGInventors: Martin Held, Christoph Esslinger
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Patent number: 11970786Abstract: The disclosed methods and kits are useful in processing and analyzing a multiplicity of samples in molecular biology workflows where there is an increased chance for sample cross-contamination or misidentification. Some embodiments of the methods and kits utilize at least one spike in control and at least one barcode per sample.Type: GrantFiled: February 15, 2019Date of Patent: April 30, 2024Assignee: BIOO Scientific CorporationInventors: Shannon Piehl, Josh Kinman
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Patent number: 11965891Abstract: Methods and compositions are described for single cell resolution, quantitative proteomic analysis using high throughput sequencing.Type: GrantFiled: December 29, 2016Date of Patent: April 23, 2024Assignee: Bio-Rad Laboratories, Inc.Inventors: Jeremy Agresti, Ronald Lebofsky
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Patent number: 11965208Abstract: Disclosed herein include systems, methods, compositions, and kits for associating single cell sequencing data with phenotypic data and/or agent exposure. In some embodiments, cell indexing oligonucleotides comprising cell indexing sequences are associated with cells. In some embodiments, synthetic particles are associated with stochastic labels comprising cell indexing sequences. Sequential hybridizing and imaging of probes annealing to a cell indexing sequence can generate a spatial index. The spatial index can be employed to identify of the partition from which a sequenced nucleic acid target molecule originated.Type: GrantFiled: April 15, 2020Date of Patent: April 23, 2024Assignee: Becton, Dickinson And CompanyInventors: Christina Chang, Sixing Li
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Patent number: 11965209Abstract: In one aspect, the present invention relates to a method for obtaining structural information about an encoded molecule. The encoded molecule may be produced by a reaction of a plurality of chemical entities and may be capable of being connected to an identifier oligonucleotide containing codons informative of the identity of the chemical entities which have participated in the formation of the encoded molecule. In a certain embodiment, primers are designed complementary to the codons appearing on the identifier oligonucleotide, and the presence, absence or relative abundance of a codon is evaluated by mixing a primer with the identifier oligonucleotide in the presence of a polymerase and substrate (deoxy)ribonucleotide triphosphates measuring the extension reaction. In another aspect, the invention provides a method for selecting compounds which binds to a target.Type: GrantFiled: September 9, 2021Date of Patent: April 23, 2024Assignee: NUEVOLUTION A/SInventors: Thomas Thisted, Mikkel Dybro Lundorf, Per-Ola Freskgard, Torben Ravn Rasmussen
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Patent number: 11959141Abstract: Methods of evaluating or providing a clonal profile of a subject interval, e.g., a subgenomic interval, or an expressed subgenomic interval (or of a cell containing the same), in a subject, are disclosed.Type: GrantFiled: December 4, 2015Date of Patent: April 16, 2024Assignee: Foundation Medicine, Inc.Inventors: Geoffrey Alan Otto, Michelle Nahas, Doron Lipson
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Patent number: 11959134Abstract: Methods of double-stranded nucleic acid sequence determination and assembly that are able to identify insertions, deletions, repeat region sizes and genomic rearrangements, for example, are disclosed herein, which can use relatively large labeled nucleic acid fragments to analyze the structure of even larger genetic regions. In some embodiments these methods involve the use of certain parameters which unexpectedly improve overall method performance. In some embodiments these methods involve sample labeling that does not result in the formation of single-stranded nucleic acid fragment labeling intermediaries.Type: GrantFiled: June 23, 2020Date of Patent: April 16, 2024Assignee: Bionano Genomics, Inc.Inventors: Michael G. Saghbini, Henry B. Sadowski, Goran Pljevaljcic, Alex R. Hastie, Han Cao
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Patent number: 11946043Abstract: The present disclosure provides methods for selectively tagging 5-methylcytosine in a DNA sample and using this approach for genome-wide profiling of 5-methylcytosine in a low input DNA sample such as circulating cell-free DNA.Type: GrantFiled: September 11, 2018Date of Patent: April 2, 2024Assignee: Ludwig Institute for Cancer Research LtdInventors: Chunxiao Song, Paulina Siejka
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Patent number: 11939574Abstract: The present invention provides ribosomal RNA origami nanostructures and in particular nanostructures comprising RNA staples, composition comprising such origami nanostructures as well as methods for manufacturing such origami structures.Type: GrantFiled: January 18, 2018Date of Patent: March 26, 2024Assignee: AUGMANITY NANO LTDInventors: Anastasia Shapiro, Ido Bachelet, Yaniv Amir, Erez Lavi, Danielle Karo-Atar
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Patent number: 11939626Abstract: Methods, devices, and systems for performing digital assays are provided. In certain aspects, the methods, devices, and systems can be used for the amplification and detection of nucleic acids. In certain aspects, the methods, devices, and systems can be used for the recognition, detection, and sizing of droplets in a volume. Also provided are compositions and kits suitable for use with the methods and devices of the present disclosure.Type: GrantFiled: July 19, 2022Date of Patent: March 26, 2024Assignee: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATIONInventors: Daniel T. Chiu, Jason E. Kreutz, Gloria S. Yen, Bryant S. Fujimoto
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Patent number: 11939573Abstract: Provided herein are methods, compositions, and kits for assays, many of which involve amplification reactions such as digital PCR or droplet digital PCR. The assays may be used for such applications as sequencing, copy number variation analysis, and others. In some cases, the assays involve subdividing a sample into multiple partitions (e.g., droplets) and merging the partitions with other partitions that comprise adaptors with barcodes.Type: GrantFiled: July 22, 2020Date of Patent: March 26, 2024Assignee: Bio-Rad Laboratories, Inc.Inventor: Serge Saxonov
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Patent number: 11939570Abstract: A microfluidic lab-on-a-chip system for DNA gene assembly that utilizes a DNA symbol library and a DNA linker library. The lab-on-a-chip has a fluidic platform with a plurality of arrays operably connected to a voltage source and a controller for the voltage source, a set of first inlets operably connected to the fluidic platform, each first inlet for one DNA symbol from a DNA symbol library, a set of second inlets operably connected to the fluidic platform, each second inlet for one DNA linker from a DNA linker library, and a mixing area operably connected to the fluidic platform and to the plurality of first inlets and the plurality of second inlets.Type: GrantFiled: April 23, 2020Date of Patent: March 26, 2024Assignee: SEAGATE TECHNOLOGY LLCInventors: Tim Rausch, Walter R Eppler, Gemma Mendonsa
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Patent number: 11919001Abstract: This invention generally relates to methods and systems for dispensing a droplet, in particular a picolitre volume droplet containing one or more entities.Type: GrantFiled: June 21, 2018Date of Patent: March 5, 2024Assignee: SPHERE FLUIDICS LIMITEDInventors: Dimitris Josephides, Marian Rehak, David Holmes, Frank F. Craig
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Patent number: 11913952Abstract: Provided herein are compositions and methods for detecting the binding of a peptide to an MHC molecule, and the binding of a peptide:MHC complex to a TCR. In preferred embodiments, the compositions and methods are in a highly-multiplexed way. The compositions and methods disclosed herein can be used to provide direct information on which peptides are bound to an MHC molecule. Also provided is a method for simultaneously detecting a large number of peptides for binding to an MHC molecule and/or a T cell. A method for detecting competitive binding of a large number of peptides to an MHC molecule and/or a T cell is also disclosed. Also provided herein is a method for simultaneously detecting a large number of specific TCRs. The compositions and methods of the present invention are useful for vaccine design, research and monitoring of autoimmune and infectious disease, immunogenicity testing of therapeutics, and tissue typing.Type: GrantFiled: November 22, 2021Date of Patent: February 27, 2024Assignee: Prognosys Biosciences, Inc.Inventors: John Andrew Altin, Mark S. Chee
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Patent number: 11898209Abstract: This disclosure relates to new assay methods for analysis of circulating tumor cells (CTCs) in blood samples for detection, e.g., early detection, and/or monitoring of disease, e.g., cancer. The methods provide ultra-high sensitivity and specificity, and include the use of microfluidic isolation of CTCs and digital detection of RNA derived from the CTCs.Type: GrantFiled: October 8, 2020Date of Patent: February 13, 2024Assignee: The General Hospital CorporationInventors: Daniel A. Haber, Ravi Kapur, Mehmet Toner, Shyamala Maheswaran, Xin Hong, David Tomoaki Miyamoto, Tanya Todorova, Sarah Javaid
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Patent number: 11878302Abstract: System, including methods and apparatus, for spacing droplets from each other and for detection of spaced droplets.Type: GrantFiled: September 2, 2021Date of Patent: January 23, 2024Assignee: Bio-Rad Laboratories, Inc.Inventors: George Carman, Thomas H. Cauley, III, David P. Stumbo
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Patent number: 11873528Abstract: The present invention is directed to methods, compositions and systems for analyzing sequence information while retaining structural and molecular context of that sequence information.Type: GrantFiled: September 12, 2022Date of Patent: January 16, 2024Assignee: 10x Genomics, Inc.Inventors: Xinying Zheng, Serge Saxonov, Michael Schnall-Levin, Kevin Ness, Rajiv Bharadwaj
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Patent number: 11872533Abstract: The invention relates to a device (1) for generating droplets (30) comprising a plurality of channels (20), wherein each channel (20) extends from an inlet (201) along a respective longitudinal axis (L) to an outlet (202), wherein said device (1) comprises a plurality of layers (10) of a substrate material arranged in a stack (100), wherein each layer (10) comprises a first side (101) and a second side (102) facing away from each other, and wherein said first side (101) of each layer (10) comprises a plurality of grooves (103), wherein said channels (20) are formed by said grooves (103) of said first side (101) of a respective layer (10) of said stack (100) and said second side (102) of a respective adjacent layer (10) of said stack (100). The invention further relates to a method for generating droplets (30) and a fabrication method of the device (1).Type: GrantFiled: March 22, 2018Date of Patent: January 16, 2024Assignee: ETH ZURICHInventors: André R. Studart, Alessandro Ofner, Pascal Schwendimann
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Patent number: 11866777Abstract: The disclosed embodiments concern methods, apparatus, systems and computer program products for determining sequences of interest using unique molecular index (UMI) sequences that are uniquely associable with individual polynucleotide fragments, including sequences with low allele frequencies and long sequence length. In some implementations, the UMIs include both physical UMIs and virtual UMIs. In some implementations, the unique molecular index sequences include non-random sequences. System, apparatus, and computer program products are also provided for determining a sequence of interest implementing the methods disclosed.Type: GrantFiled: October 21, 2020Date of Patent: January 9, 2024Assignee: Illumina, Inc.Inventors: Sante Gnerre, Byoungsok Jung, Emrah Kostem, Alex Aravanis, Alex So, Xuyu Cai, Zhihong Zhang, Frank J. Steemers