Patents Examined by Kaijiang Zhang
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Patent number: 11867707Abstract: Embodiments of the present disclosure generally pertain to systems and methods for performing amplicon rescue multiplex polymerase chain reaction (arm-PCR). In one embodiment, the system comprises a processor and a reader coupled to a control element. The control element is configured to control the operation of the processor and the reader based on a variety of settings. The processor is configured to receive a self-contained cassette for performing PCR amplification of DNA and/or RNA obtained from an organic specimen. The processor engages with the cassette and manipulates reagents within the cassette in order to amplify and detect the DNA from the specimen. The processor also causes the cassette to deposit the DNA on a microarray within the cassette. The reader is configured to receive the cassette after it has been processed by the processor and to capture an image of the microarray for transmission to the control element as test data.Type: GrantFiled: December 22, 2020Date of Patent: January 9, 2024Assignee: iCubate, Inc.Inventors: Jeff Bertrand, Jian Han, Phillip Ewing
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Patent number: 11852628Abstract: The present disclosure provides methods of processing or analyzing a sample. A method for processing a sample may comprise hybridizing a probe molecule to a target region of a nucleic acid molecule (e.g., a ribonucleic acid (RNA) molecule), barcoding the probe-nucleic acid molecule complex, and performing extension, denaturation, and amplification processes. A method for processing a sample may comprise hybridizing first and second probes to adjacent or non-adjacent target regions of a nucleic acid molecule (e.g., an RNA molecule), linking the first and second probes to provide a probe-linked nucleic acid molecule, and barcoding the probe-linked nucleic acid molecule. One or more processes of the methods described herein may be performed within a partition, such as a droplet or well. One or more processes of the methods described herein may be performed on a cell, such as a permeabilized cell.Type: GrantFiled: March 16, 2023Date of Patent: December 26, 2023Assignee: 10X GENOMICS, INC.Inventors: Tarjei Sigurd Mikkelsen, Eswar Prasad Ramachandran Iyer, Andrew Kohlway, Luigi Jhon Alvarado Martinez, Katherine Pfeiffer, Andrew D. Price
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Patent number: 11834704Abstract: A method includes forming a patterned substrate including a plurality of base pads, using a nano-imprint lithography process. A capture substance is attached to each of the plurality of base pads, optionally through a linker, the capture substance being adapted to promote capture of a target molecule.Type: GrantFiled: December 7, 2020Date of Patent: December 5, 2023Assignee: Illumina, Inc.Inventors: M. Shane Bowen, Kevin L. Gunderson, Shengrong Lin, Maria Candelaria Rogert Bacigalupo, Kandaswamy Vijayan, Yir-Shyuan Wu, Bala Murali Venkatesan, James Tsay, John M. Beierle, Lorenzo Berti, Sang Ryul Park
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Patent number: 11834657Abstract: The disclosure provides for single amplification and double amplification methods for preparing nucleic acid samples for sequencing.Type: GrantFiled: June 12, 2018Date of Patent: December 5, 2023Assignees: University of Southern California, SeqOnce Biosciences Inc.Inventor: Joseph Dunham
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Patent number: 11820980Abstract: Methods and compositions are provided for preparing DNA libraries. Enzymes, adaptors, and sample nucleic acids are provided in a single reaction mixture to facilitate library preparation.Type: GrantFiled: April 27, 2020Date of Patent: November 21, 2023Assignee: Myriad Women's Health, Inc.Inventors: Henry H. Lai, Clement S. Chu
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Patent number: 11814619Abstract: This disclosure provides for devices, methods, and systems for generating a plurality of droplets within a collecting container at an extremely high rate (e.g., of at least 1 million droplets per minute, etc.), the plurality of droplets generated from an aqueous mixture comprising a set of single cells and a set of functionalized particles configured for a single cell assay. Upon generation, the plurality of droplets can be stabilized in position within a region of the collecting container, thereby providing a single-tube workflow for single cell analyses. Further, compositions implemented are structured to allow for overloading of partitions with functionalized particles, such that partitioned single-cells are co-localized with a subset of functionalized particles in a manner that allows for discernable tagging and downstream analyses.Type: GrantFiled: June 7, 2022Date of Patent: November 14, 2023Assignee: ENUMERIX, INC.Inventors: Eleen Yee Lam Shum, Janice Hoiyi Lai, Hei Mun Christina Fan, Stephen P. A. Fodor
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Patent number: 11808769Abstract: Provided herein are methods for preparing biological samples for spatial proteomic analysis, methods of determining a location of a protein analyte in a biological sample, and methods of determining a location of a protein analyte and a nucleic acid analyte in a biological sample.Type: GrantFiled: January 26, 2023Date of Patent: November 7, 2023Assignee: 10x Genomics, Inc.Inventors: Cedric Uytingco, James Michael Chell, Marlon Stoeckius, Albert Dale Kim, Dulce Ovando Morales, Andrej Hartnett, Yifeng Yin, Jennifer Chew
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Patent number: 11795450Abstract: Array-based enzymatic oligonucleotide synthesis creates a large number of polynucleotides using an uncontrolled and template independent polymerase such as terminal deoxynucleotidyl transferase (TdT). Spatial control of reaction conditions on the surface of the array allows creation of polynucleotides with a variety of arbitrary sequences. Spatial control may be implemented by removing protecting groups attached to nucleotides only at a selected location on the array or by other techniques such as location-specific regulation of enzymatic activity. The ratio of polynucleotides with protecting groups to unprotected polynucleotides used during a cycle of synthesis is adjusted to control the length of homopolymers created by the polymerase. Digital information may be encoded in the enzymatically synthesized polynucleotides.Type: GrantFiled: September 6, 2019Date of Patent: October 24, 2023Assignee: MICROSOFT TECHNOLOGY LICENSING, LLCInventors: Bichlien Nguyen, Sergey Yekhanin, Karin Strauss
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Patent number: 11788137Abstract: The present invention is related to a Template Switch Oligo construct and its use into a ligase free diagnostic and/or sequencing method and to the kit for performing the method of the invention.Type: GrantFiled: September 30, 2020Date of Patent: October 17, 2023Assignee: DIAGENODE S.A.Inventors: Gilles Brocart, CĂ©line Sabatel, Florence Durieux
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Patent number: 11788136Abstract: A method of capturing a population of T-Cell receptor and/or immunoglobulin sequences with variable regions within a patient sample, the method comprising: extracting and/or preparing DNA fragments from the patient sample; ligating a nucleic acid adapter to the DNA fragments, the nucleic acid adapter suitable for recognition by a pre-selected nucleic acid probe; capturing DNA fragments existing in the patient sample using a collection of nucleic acid hybrid capture probes, wherein each capture probe is designed to hybridize to a known V gene segment and/or a J gene segment within the T cell receptor and/or immunoglobulin genomic loci.Type: GrantFiled: May 29, 2018Date of Patent: October 17, 2023Assignee: University Health NetworkInventors: Trevor John Pugh, David Thomas Mulder, Etienne Raymond G. A. Mahe
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Patent number: 11781132Abstract: Disclosed are a method for DNA extraction in a sample for next generation sequencing (NGS) and a method of constructing a NGS library using the extracted DNA. The method for DNA extraction includes: preparing a mixture by mixing a biological sample with a buffer; applying microwaves to the mixture; and recovering DNA. The method of constructing a NGS library includes: extracting DNA according to the method for DNA extraction; amplifying a target DNA using primers; and purifying the amplified product and subjecting the purified product to library pooling.Type: GrantFiled: March 26, 2020Date of Patent: October 10, 2023Assignees: MACROGEN, INC., PSOMAGEN, INC.Inventors: Joshua Sungwoo Yang, Jaekyung Chon, Ik Jung Choi, Hyun Min Park, Jieun Park, Jeongsun Seo, Changhoon Kim, Jong Yeon Shin, Han Sol Seo, Jiwon Shin, In Hee Hwang, Seon Hye Sim, Chang Woo Cho, Kyuin Hwang, In Seon Kim, Hyung Il Lee, Jung Hyun Cho
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Patent number: 11773388Abstract: The present disclosure provides a method for enrichment of at least one target nucleic acid in a library of nucleic acids. A first oligonucleotide is hybridized to a target nucleic acid in library of nucleic acids having first and second adapters. The hybridized first oligonucleotide is extended with a first polymerase, thereby producing a first primer extension complex including the target nucleic acid and the extended first oligonucleotide. The first primer extension complex is captured, enriched relative to the library of nucleic acids, and a second oligonucleotide is hybridized to the target nucleic acid. The hybridized second oligonucleotide is extended with a second polymerase, thereby producing a second primer extension complex including the target nucleic acid and the extended second oligonucleotide, and further liberating the extended first oligonucleotide from the first primer extension complex.Type: GrantFiled: June 22, 2020Date of Patent: October 3, 2023Assignees: Roche Sequencing Solutions, Inc., Kapa Biosystems, Inc.Inventors: Daniel Burgess, Brian Christopher Godwin, Alexander Lovejoy, Bronwen Miller, Jo-Anne Elizabeth Penkler, Joseph Platzer
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Patent number: 11767557Abstract: Modifications to both hardware and enzymatic reactions used in single cell analyses such as but not limited to Seq-well that enable significant increases in the yield of transcripts per cell, portability and ease of use, increased scalability of the assay, and linkage of transcript information to other measurements made in the picowell arrays are disclosed.Type: GrantFiled: December 7, 2018Date of Patent: September 26, 2023Assignee: Massachusetts Institute of TechnologyInventors: J. Christopher Love, Todd Michael Gierahn, Alexander K. Shalek, Marc Havens Wadsworth, Travis K. Hughes
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Patent number: 11767558Abstract: Polynucleotide sequencing methods include incubating unlabeled nucleotides with a cluster of template polynucleotide strands having the same sequence when the identity of the previously added labeled nucleotide is being detected. The detection step provides time for the addition of the unlabeled nucleotides to be incorporated into the copy strands in which the previously added labeled nucleotide did not get incorporated. Thus, at the end of the detection step, all or most of the copy strands will be in phase and ready to incorporate the appropriate labeled nucleotide in the subsequence incorporate step.Type: GrantFiled: December 5, 2019Date of Patent: September 26, 2023Assignee: Illumina Cambridge LimitedInventors: Pietro Gatti-Lafranconi, Philip Balding
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Patent number: 11761037Abstract: The present invention discloses a probe applicable to high-throughput sequencing and a method of enriching a target region using the probe. The probe includes, in an order from a 5? end, a ligation arm, a masking sequence 1, a UID sequence 1, an Illumina Tag1 sequence, a dU region, an Illumina Tag2 sequence, a UID sequence 2, a masking sequence 2 and an extension arm; wherein the masking sequence 1, the masking sequence 2, the dU region, the UID sequence 1, and the UID sequence 2 may be 0 bp. When sequencing is performed by using a library built by the probe of the present invention, it is not necessary to add a sequencing primer additionally, and adopting the method of the present invention may directly use an RNA as a template to capture a target region, so as to simplify the experiment procedure.Type: GrantFiled: July 18, 2018Date of Patent: September 19, 2023Assignee: AMOY DIAGNOSTICS CO., LTD.Inventors: Linhua Zhang, Xuchao Li, Huijuan Ge, Baolei Jin, Ning Chen, Li Ruan, Limou Zheng
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Patent number: 11760997Abstract: Compositions, systems, and methods for the display of analytes such as biomolecules are described. Display of analytes is achieved by coupling of the analytes to displaying molecules that are configured to associate with surfaces or interfaces. Arrays of analytes may be formed from the described systems for utilization in assays and other methods.Type: GrantFiled: October 28, 2022Date of Patent: September 19, 2023Assignee: Nautilus Subsidiary, Inc.Inventors: Tural Aksel, Stephen Hendricks, Elvis Ikwa, Pierre Indermuhle, Sadie Ingle, Christina Inman, Parag Mallick, Torri Elise Rinker, Steven Tan
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Patent number: 11752483Abstract: The present disclosure provides methods, compositions, and kits for methods that can improve techniques nucleic acid analysis, and can allow for more reliable and accurate targeted, multiplexed, high throughput sequencing. The methods, compositions, and kits can be used for sequencing target loci of nucleic acid. The methods, compositions, and kits disclosed herein can be used for assisted de novo targeted sequencing. The methods, compositions, and kits disclosed herein can also be used for library labeling for de novo sequencing and phasing.Type: GrantFiled: August 10, 2020Date of Patent: September 12, 2023Assignee: The Scripps Research InstituteInventors: Steven Robert Head, Phillip T. Ordoukhanian, Daniel R. Salomon
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Patent number: 11739380Abstract: A method of analyzing a molecule is disclosed. A lipid bilayer is formed such that it divides a first reservoir characterized by a first reservoir osmolarity from a second reservoir characterized by a second reservoir osmolarity. An electrolyte solution is flowed to the first reservoir that tends to make a first change to a ratio of the first reservoir osmolarity to the second reservoir osmolarity. A voltage is applied across the lipid bilayer, wherein the lipid bilayer is inserted with a nanopore, and wherein a net transfer of ions between the first reservoir and the second reservoir tends to make a second change to the ratio of the first reservoir osmolarity to the second reservoir osmolarity, and wherein the first change to the ratio and the second change to the ratio tends to counter-balance each other.Type: GrantFiled: March 12, 2021Date of Patent: August 29, 2023Assignee: Roche Sequencing Solutions, Inc.Inventors: Geoffrey Barrall, Jason Komadina, Marcin Rojek
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Patent number: 11739440Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and analyte characterization from a single cell. Such polynucleotide processing may be useful for a variety of applications. The compositions, methods, systems, and devices disclosed herein generally describe barcoded oligonucleotides, which can be bound to a bead, such as a gel bead, useful for characterizing one or more analytes including, for example, protein (e.g., cell surface or intracellular proteins) and chromatin (e.g., accessible chromatin).Type: GrantFiled: June 9, 2020Date of Patent: August 29, 2023Assignee: 10X GENOMICS, INC.Inventors: Jason Bell, Geoffrey McDermott, Francesca Meschi, Katherine Pfeiffer, Michael Schnall-Levin, Xinying Zheng
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Patent number: 11732253Abstract: The present invention provides methods for repurposing beads and other solid supports for separately capturing RNA and DNA without a loss of binding capacity by using a surfactant.Type: GrantFiled: February 2, 2021Date of Patent: August 22, 2023Assignee: Tecan Genomics, Inc.Inventors: Douglas A. Amorese, David Ruff