Patents Examined by Kaijiang Zhang
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Patent number: 11732301Abstract: The disclosure provides detection apparatus having one or more nanopores, methods for making apparatus having one or more nanopore and methods for using apparatus having one or more nanopores. Uses include, but are not limited to detection and sequencing of nucleic acids.Type: GrantFiled: March 1, 2021Date of Patent: August 22, 2023Assignee: Illumina, Inc.Inventors: Boyan Boyanov, Jeffrey G Mandell, Kevin L Gunderson, Jingwei Bai, Liangliang Qiang, Bradley Baas
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Patent number: 11732299Abstract: This disclosure relates to methods for spatial profiling of analytes present in a biological sample. Also provided are methods for using spatially barcoded arrays to detect a biological analyte in a cell comprising a small molecule.Type: GrantFiled: January 20, 2021Date of Patent: August 22, 2023Assignee: 10x Genomics, Inc.Inventor: Eswar Prasad Ramachandran Iyer
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Patent number: 11724244Abstract: Systems and methods for polynucleotide synthesis utilize electrochemical deprotection and novel redox chemistries compatible with advanced CMOS nodes, for highly reliable and massively scalable parallel construction of polynucleotide segments having a desired sequence or sequences. Via use of these exemplary techniques, low-cost and large-scale polynucleotide synthesis is facilitated, for example for data storage and retrieval applications.Type: GrantFiled: April 13, 2022Date of Patent: August 15, 2023Assignee: Avery Digital Data, Inc.Inventors: Barry Merriman, Ryan de Ridder, Matthew T. Holden, Tim Geiser
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Patent number: 11725305Abstract: Rapid methods, capable of being performed in a single reaction tube, are described herein for constructing libraries for high-throughput polynucleotide sequencing applications, such as next generation sequencing (NGS) applications. Oligonucleotide probes include chemically-active groups at their 5? or 3? ends, or both, to facilitate the cleavage of their 5? or 3? ends, or both, following their hybridization to the single-stranded ends of frayed template fragments. Cleavage of probe ends reveal single-stranded regions at the ends of the hybridized fragments. Adaptors, specific to these ends, are ligated to the hybridized probe/template fragments, and blunt end fragments are ligated to blunt ends of hybridized probe/template fragments, if present, to generate the adaptor-ligated fragments of the library.Type: GrantFiled: July 17, 2018Date of Patent: August 15, 2023Assignee: SEQONCE BIOSCIENCES, INC.Inventor: Joseph Dunham
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Patent number: 11725212Abstract: It is a first object of the present invention to provide a method for preparing a Tile vector, being a vector, which comprises a selectable marker and a coding polynucleotide, wherein said coding polynucleotide is immediately preceded and followed by a type IIs recognition sequence, wherein said preceding and following recognition sequences are recognized by a same type IIs restriction enzyme, but have an opposite orientation. More particularly, the position and orientation of said preceding and following type IIs recognition sequences provides for the cleavage of said Tile vector by a corresponding type IIs restriction enzyme resulting in the release of said coding polynucleotide sequence having at its respective ends overhang sequences with a known orientation and length, while lacking said preceding and following type IIs recognition sequences.Type: GrantFiled: December 19, 2017Date of Patent: August 15, 2023Assignees: Universiteit Gent, Katholieke Universiteit LeuvenInventors: Dennis Grimon, Hans Gerstmans, Yves Briers, Rob Lavigne
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Patent number: 11725238Abstract: The invention relates to a method for detection of analyte interaction with a channel molecule held in a membrane, comprising the optical detection of a modification in the flux of a signal molecule as it passes through the channel molecule by the action of a membrane potential, wherein the modification in the flux is caused by at least partial blockage of the channel molecule by the analyte. The invention further relates to bilayer arrays, components, methods of manufacture and use.Type: GrantFiled: July 20, 2020Date of Patent: August 15, 2023Assignee: OXFORD UNIVERSITY INNOVATION LIMITEDInventors: Mark Wallace, Hagan Bayley, Shuo Huang, Oliver Kieran Castell, Mercedes Romero-Ruiz
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Patent number: 11705218Abstract: In one embodiment, provided are a method for analyzing at least one nucleic acid that can conveniently and highly accurately analyze even a very small number of analyte at least one nucleic acid. In one embodiment, the present invention relates to a method for analyzing at least one nucleic acid, comprising: a library preparation step of preparing a library comprising at least one standard nucleic acid of specific copy number(s) and at least one analyte nucleic acid in a same system; a calibration curve data generation step of generating calibration curve data based on the copy number(s) of the at least one standard nucleic acid of specific copy number(s); and an analyte nucleic acid analysis step of identifying at least one nucleotide sequence of the analyte nucleic acid while identifying the number(s) of the at least one nucleotide sequence of the at least one analyte nucleic acid using the calibration curve data.Type: GrantFiled: December 18, 2019Date of Patent: July 18, 2023Assignees: Ricoh Company, Ltd., FASMAC CO., LTD.Inventors: Yusuke Osaki, Hirotaka Unno, Yudai Kawashima, Michie Hashimoto, Masayuki Yumoto, Satoshi Nakazawa, Yuki Yonekawa, Takahiro Matsudaira, Eri Nishiyama
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Patent number: 11702654Abstract: Methods and systems for decreasing amplification bias and primer-dimer formation in amplification reactions and for amplifying a plurality of target polynucleotides from a sample in a single reaction and for sequencing the target polynucleotides where samples can include forensic samples and where target polynucleotides can include identity- or ancestry-informative markers, short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs).Type: GrantFiled: June 13, 2018Date of Patent: July 18, 2023Assignee: ILLUMINA, INC.Inventors: Jon-Matthew Belton, Johann Felix Schlesinger, Siarhei Manakou, Amanda Garfinkel Young
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Patent number: 11702693Abstract: This disclosure relates to compositions and methods for analyzing single cells using cell printing and spatial analysis.Type: GrantFiled: January 19, 2021Date of Patent: July 18, 2023Assignee: 10x Genomics, Inc.Inventor: Rajiv Bharadwaj
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Patent number: 11702649Abstract: 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: GrantFiled: October 23, 2018Date of Patent: July 18, 2023Assignees: The Broad Institute, Inc., Massachusetts Institute of TechnologyInventors: Paul Blainey, Navpreet Ranu, Todd Gierahn, J. Christopher Love
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Patent number: 11697839Abstract: The present invention relates to a method of identifying a target genomic nucleic acid sequence including hybridizing a set of probes to the target genomic nucleic acid sequence, wherein the set of probes has a unique associated barcode sequence for identification of the target genomic nucleic acid sequence, wherein each probe of the set includes (1) a complementary sequence complementary to a first strand of the target genomic nucleic acid sequence and (2) the associated barcode sequence or a portion of the associated barcode sequence, sequencing the associated barcode sequence from probes hybridized to the target genomic nucleic acid sequence using a fluorescence-based sequencing method, and identifying the target genomic nucleic acid sequence by the sequenced barcode sequence.Type: GrantFiled: October 13, 2020Date of Patent: July 11, 2023Assignee: President and Fellows of Harvard CollegeInventors: Evan R. Daugharthy, Son C. Nguyen, Chao-ting Wu, George M. Church
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Patent number: 11692219Abstract: The invention pertains to construction of next-generation DNA sequencing (NGS) libraries for whole genome sequencing, targeted resequencing, sequencing-based screening assays, metagenomics, or any other application requiring sample preparation for NGS.Type: GrantFiled: January 5, 2021Date of Patent: July 4, 2023Assignee: INTEGRATED DNA TECHNOLOGIES, INC.Inventors: Zachary Zwirko, Yu Zheng, Mirna Jarosz, Caifu Chen, Joseph Walder
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Patent number: 11661626Abstract: Provided herein are methods of identifying a methylation status of an analyte in a biological sample. Also provided herein are methods that combine identifying the methylation status with spatial technology to identify the location of a methylation status in a biological sample.Type: GrantFiled: August 5, 2022Date of Patent: May 30, 2023Assignee: 10x Genomics, Inc.Inventors: Layla Katiraee, Michael Schnall-Levin, Christina Galonska, Marlon Stoeckius
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Patent number: 11649499Abstract: This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions.Type: GrantFiled: November 23, 2022Date of Patent: May 16, 2023Assignee: Personalis, Inc.Inventors: Gabor T. Bartha, Gemma Chandratillake, Richard Chen, Sarah Garcia, Hugo Yu Kor Lam, Shujun Luo, Mark R. Pratt, John West
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Patent number: 11649497Abstract: Disclosed herein include systems, methods, compositions, and kits for determining expressions of proteins and genes simultaneously, and for sample indexing. The method can comprise extending a cellular component-binding reagent specific oligonucleotide hybridized to an oligonucleotide barcode to generate an extended cellular component-binding reagent specific oligonucleotide. The extended cellular component-binding reagent specific oligonucleotide can be separated from the oligonucleotide barcodes. The separated extended cellular component-binding reagent specific oligonucleotide can be amplified separately from barcoded cDNA.Type: GrantFiled: January 12, 2021Date of Patent: May 16, 2023Assignee: Becton, Dickinson and CompanyInventors: Dennis Prosen, Katherine Lazaruk
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Patent number: 11643685Abstract: This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions.Type: GrantFiled: May 18, 2022Date of Patent: May 9, 2023Assignee: Personalis, Inc.Inventors: John West, Christian Haudenschild, Richard Chen
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Patent number: 11639928Abstract: 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: February 24, 2022Date of Patent: May 2, 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: 11634765Abstract: The present disclosure is concerned with compositions and methods for the paired-end sequencing of target nucleic acids, and more particularly to obtaining nucleotide sequence information from two separate regions of target nucleic acids using amplification sites having a single type of surface primer.Type: GrantFiled: December 17, 2019Date of Patent: April 25, 2023Assignee: ILLUMINA CAMBRIDGE LIMITEDInventors: Jonathan Mark Boutell, Pietro Gatti-Lafranconi
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Patent number: 11635427Abstract: 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: GrantFiled: July 24, 2020Date of Patent: April 25, 2023Assignee: Bio-Rad Laboratories, Inc.Inventors: Michael L. Samuels, Darren Roy Link
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Patent number: 11629377Abstract: A series of hybridisations is performed for forming a target double-stranded nucleic acid from initial fragments, where each further hybridisation step hybridises the direct products of a pair of earlier hybridisation steps. For at least one further hybridisation step HF, both of the corresponding pair of earlier hybridisation steps HE comprise an error-detecting type of hybridisation step, which includes an error detecting operation to detect whether the hybridised fragments formed in the error-detecting type of hybridisation step HE comprise at least one erroneous hybridised fragment, and discarding at least part of the erroneous fragment to exclude it from a subsequent further hybridisation step. By detecting and removing erroneous fragments throughout a staged and controlled hybridisation process, erroneous fragments are prevented from diluting the pool of error-free fragments at each hybridisation step, to improve yield.Type: GrantFiled: September 27, 2018Date of Patent: April 18, 2023Assignee: EVONETIX LTDInventors: Matthew James Hayes, Raquel Maria Sanches-Kuiper, Daniel Adrian Bygrave