Identifying A Library Member By Means Of A Tag, Label, Or Other Readable Or Detectable Entity Associated With The Library Member (e.g., Decoding Process, Etc.) Patents (Class 506/4)
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Patent number: 11993771Abstract: The present disclosure provides methods and compositions for cell free cloning and polynucleotide production. In illustrative aspects, the methods of the present disclosure comprise the use of molecular barcodes and a dilution step. Moreover, some aspects of the instant disclosure relate to systems and kits comprising molecular barcodes for use with methods of cell free cloning and polynucleotide production.Type: GrantFiled: June 16, 2023Date of Patent: May 28, 2024Assignee: Elegen CorporationInventor: Matthew Hill
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Patent number: 11987844Abstract: The present invention provides methods for detecting donor cell-free DNA in the circulation of an organ transplant recipient for the early identification of transplant rejection.Type: GrantFiled: January 29, 2019Date of Patent: May 21, 2024Assignee: 4BASES SAInventor: Valentina Favalli
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Patent number: 11946044Abstract: Disclosed herein are methods for isolating DNA, such as cell-free DNA (cfDNA) or DNA from a tissue sample, e.g., in which the DNA is partitioned into hypermethylated and hypomethylated partitions. After differential tagging of the partitions, portions of the hypomethylated partition are pooled with the hypermethylated partition or pooled separately. Epigenetic and sequence-variable target regions are captured from the pool comprising DNA from the hypermethylated and hypomethylated partitions, and sequence-variable target regions are captured from the pool comprising DNA from the hypomethylated partition. This approach can reduce costs and/or bandwidth by limiting sequencing of epigenetic target regions from the hypomethylated partition, which may be less informative than other DNA.Type: GrantFiled: July 29, 2021Date of Patent: April 2, 2024Assignee: Guardant Health, Inc.Inventors: Ariel Jaimovich, Sven Jeffrey Duenwald, Peter Vilem Grauman, Yupeng He, Charbel Said Eid, Haley Dara Axelrod
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Patent number: 11932901Abstract: Disclosed herein include systems, methods, compositions, and kits for performing targeted single cell mRNA sequencing assays. Capture oligonucleotides capable of specifically binding to target nucleic acid species are provided in some embodiments. Depletion oligonucleotides capable of specifically binding to undesirable nucleic acid species are provided in some embodiments. The method can comprise random priming and extension of barcoded transcripts followed by one or more enrichment and/or depletion steps using said capture oligonucleotides and/or depletion oligonucleotides. Immune repertoire profiling methods are also provided in some embodiments.Type: GrantFiled: July 12, 2021Date of Patent: March 19, 2024Assignee: Becton, Dickinson and CompanyInventors: Hye-Won Song, Margaret Nakamoto
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Patent number: 11859239Abstract: Provided is a nucleic acid sample-contained container including; a first nucleic acid molecule including an intended base sequence and a base sequence for detection different from the intended base sequence; and a second nucleic acid molecule free of the intended base sequence but including the base sequence for detection, wherein the nucleic acid sample-contained container includes the first nucleic acid molecule in a predetermined number. In a preferable mode, the copy number of the intended base sequence is less than 1,000, and the coefficient of variation (CV value) for the copy number is lower than 20%. In a more preferable mode, the nucleic acid molecules are artificially synthesized nucleic acid molecules. In a yet more preferable mode, the first nucleic acid molecule includes the intended base sequence in a plural number in the same molecule.Type: GrantFiled: March 18, 2019Date of Patent: January 2, 2024Assignee: Ricoh Company, Ltd.Inventors: Yudai Kawashima, Masayuki Yumoto, Satoshi Izumi, Manabu Seo
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Patent number: 11827930Abstract: The invention generally relates to sequencing library preparation methods. In certain embodiments, two template nucleic acids are joined together by a linking molecule, such as a PEG derivative. The linked template nucleic acids is amplified, creating linked amplicons.Type: GrantFiled: October 1, 2020Date of Patent: November 28, 2023Assignee: NCAN Genomics, Inc.Inventors: Milenko Despotovic, Joel Pel, Andrea Marziali
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Patent number: 11807903Abstract: The present disclosure provides methods and compositions for tracking nucleic acid fragment origin by target-specific barcode tagging when original nucleic acid targets break into small fragments. Nucleic acid targets are captured in vitro on a solid support with clonally localized nucleic acid barcode templates. Many nucleic acid targets canbe processed simultaneously in a massively parallel fashion without partition. These nucleic acid target tracking methods can be used for a variety of applications in both whole genome sequencing and targeted sequencing in order to accurately identify genomic variants, haplotype phasing and assembly, for example.Type: GrantFiled: February 8, 2019Date of Patent: November 7, 2023Assignee: Universal Sequencing Technology CorporationInventors: Zhoutao Chen, Tsai-Chin Wu, Long Kim Pham, Yong Wang
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Patent number: 11808677Abstract: According to an aspect of the present disclosure, there is provided a polymerase chain reaction (PCR) patch which is provided as a gel type having a net-like structure forming micro-cavities, wherein at least a part of a plurality of reagents used in a PCR are contained in the micro-cavities, and when the patch contacts with an external region, the reagents contained in the micro-cavities move to at least a portion of the external region, and a PCR of a target DNA included in a sample located in the external region is performed.Type: GrantFiled: February 23, 2017Date of Patent: November 7, 2023Assignee: NOUL CO., LTD.Inventors: Dong Young Lee, Chan Yang Lim, Kyung Hwan Kim
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Patent number: 11795492Abstract: Aspects of the technology disclosed herein relate to methods of preparing and analyzing nucleic acids. In some embodiments, methods for preparing nucleic acids for sequence analysis (e.g., using next-generation sequencing) are provided herein.Type: GrantFiled: July 2, 2020Date of Patent: October 24, 2023Assignee: ArcherDX, LLC.Inventors: Joshua Stahl, Jason Myers, Brady Culver, Brian Kudlow
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Patent number: 11783918Abstract: Techniques for random access of particular DNA strands from a mixture of DNA strands are described. DNA strands that encode pieces of the same digital file are labeled with the same identification sequence. The identification sequence is used to selectively separate DNA strands that contain portions of the same digital file from other DNA strands. A DNA staple positions DNA strands with the identification sequence adjacent to sequencing adaptors. DNA ligase joins the molecules to create a longer molecule with the region encoding the digital file flanked by sequencing adaptors. DNA strands that include sequencing adaptors are sequenced and the sequence data is available for further analysis. DNA strands without the identification sequence are not joined to sequencing adaptors, and thus, are not sequenced. As a result, the sequencing data produced by the DNA sequencer comes from those DNA strands that included the identification sequence.Type: GrantFiled: October 30, 2017Date of Patent: October 10, 2023Assignee: Microsoft Technology Licensing, LLCInventors: Karin Strauss, Yuan-Jyue Chen
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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: 11613783Abstract: The present disclosure provides methods, systems, compositions, and kits for the high-throughput detection of multi-molecule biomarkers in a biological sample. The disclosed methods, systems, compositions, and kits utilize antibody-oligonucleotide tags to detect two or more molecules that are in close proximity.Type: GrantFiled: December 30, 2021Date of Patent: March 28, 2023Assignee: Tempus Labs, Inc.Inventor: Timothy Rand
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Patent number: 11590489Abstract: Sub-millimeter scale three-dimensional (3D) structures are disclosed with customizable chemical properties and/or functionality. The 3D structures are referred to as drop-carrier particles. The drop-carrier particles allow the selective association of one solution (i.e., a dispersed phased) with an interior portion of each of the drop-carrier particles, while a second non-miscible solution (i.e., a continuous phase) associates with an exterior portion of each of the drop-carrier particles due to the specific chemical and/or physical properties of the interior and exterior regions of the drop-carrier particles. The combined drop-carrier particle with the dispersed phase contained therein is referred to as a particle-drop. The selective association results in compartmentalization of the dispersed phase solution into sub-microliter-sized volumes contained in the drop-carrier particles. The compartmentalized volumes can be used for single-molecule assays as well as single-cell, and other single-entity assays.Type: GrantFiled: August 23, 2019Date of Patent: February 28, 2023Assignee: THE REGENTS OF THE UNIVERSITY OF CALIFORNIAInventors: Dino Di Carlo, Chueh-Yu Wu
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Patent number: 11584954Abstract: The present disclosure provides methods and systems for sample preparation and/or analysis. Samples may be cells, or may be derived from one or more cells. Sample preparation may comprise conducting one or more reactions on a target. Such reactions may be conducted in one or more partitions. One or more reactions may be performed in one or more successive operations.Type: GrantFiled: April 22, 2020Date of Patent: February 21, 2023Assignee: 10X GENOMICS, INC.Inventors: Zahra Kamila Belhocine, Josephine Lee, Francesca Meschi, Luz Montesclaros, Katherine Pfeiffer, Andrew D. Price, Jerald Sapida, David Sukovich, Tobias Daniel Wheeler, Yifeng Yin
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Patent number: 11549135Abstract: Provided herein are compositions and methods for simultaneously measuring target oligonucleotides and protein in single cells. Compositions comprise an antibody-tagged oligonucleotide, including an origin specific barcode handle sequence, a first primer handle sequence, a second primer handle sequence, and a target binding region. The composition may also include an adapter sequence, a unique molecular identifier (UMI), and a poly-A sequence. Methods for simultaneously measuring target oligonucleotides and protein in single cells generally involve delivering a mixture of the composition to a population of cells and encapsulating individual cells in an individual discrete volume comprising PCR primers on a bead.Type: GrantFiled: September 13, 2019Date of Patent: January 10, 2023Assignees: THE BROAD INSTITUTE, INC., PRESIDENT AND FELLOWS OF HARVARD COLLEGEInventor: Jesse Engreitz
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Patent number: 11542497Abstract: It is an object of the present invention to provide, for instance, a method for evaluating a function, such as transforming potential, of multiple different genes of interest, and a method capable of evaluating drug sensitivity of a subject having each gene of interest.Type: GrantFiled: March 30, 2018Date of Patent: January 3, 2023Assignee: The University of TokyoInventors: Hiroyuki Mano, Shinji Kohsaka, Masachika Ikegami
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Patent number: 11525157Abstract: Disclosed herein are methods and systems for correcting errors in sample amplification, including the errors occurred in determining the number of targets in samples. In some embodiments, the method comprises: stochastically barcoding a plurality of targets in the samples using oligonucleotides comprising stochastic barcodes to generate stochastically barcoded targets; contacting one or more defined barcoded primers with each of the one or more samples; and determining an amplification noise.Type: GrantFiled: December 26, 2018Date of Patent: December 13, 2022Assignee: Becton, Dickinson and CompanyInventor: Eleen Shum
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Patent number: 11520587Abstract: Systems and methods for instruction decoding using hash tables. An example method of constructing a decoding tree comprises: generating an aggregated vector of differentiating bit scores representing at least a subset of a set of processor instructions; identifying, based on the aggregated vector of differentiating bit scores, one or more opcode bit positions; and constructing a hash table implementing a current level of a decoding tree representing the subset of the set of processor instructions, wherein the hash table is indexed by one or more opcode bits identified by the one or more opcode bit positions.Type: GrantFiled: May 17, 2021Date of Patent: December 6, 2022Assignee: Parallels International GmbHInventors: Alexey Koryakin, Nikolay Dobrovolskiy
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Patent number: 11506608Abstract: A device for exciting objects with an excitation radiation and for detecting a photoluminescence radiation emitted by the objects after the absorption of the excitation radiation. The device includes a wall in contact with the objects, an organic light-emitting diode for emitting the excitation radiation and transparent to the photoluminescence radiation, an optical resonator tuned to the wavelength of the photoluminescence radiation and located on the side of the organic light-emitting diode opposite to the wall, and at least one sensor of the photoluminescence radiation arranged on the side of the optical resonator opposite to the organic light-emitting diode.Type: GrantFiled: October 29, 2020Date of Patent: November 22, 2022Assignee: Commissariat à l'Énergie Atomique et aux Énergies AlternativesInventors: Benoit Racine, Pierre Blandin, Etienne Quesnel
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Patent number: 11486001Abstract: Disclosed herein, inter alia, are substrates, kits, and efficient methods of preparing and sequencing two or more regions of a double-stranded polynucleotide.Type: GrantFiled: February 7, 2022Date of Patent: November 1, 2022Assignee: Singular Genomics Systems, Inc.Inventors: Daan Witters, Eli N. Glezer, Allen Lipson
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Patent number: 11486008Abstract: The invention provides methods, systems, and computer readable medium for detecting ploidy of chromosome segments or entire chromosomes, for detecting single nucleotide variants and for detecting both ploidy of chromosome segments and single nucleotide variants. In some aspects, the invention provides methods, systems, and computer readable medium for detecting cancer or a chromosomal abnormality in a gestating fetus.Type: GrantFiled: June 21, 2018Date of Patent: November 1, 2022Assignee: Natera, Inc.Inventors: Joshua Babiarz, Tudor Pompiliu Constantin, Lane A. Eubank, George Gemelos, Matthew Micah Hill, Huseyin Eser Kirkizlar, Matthew Rabinowitz, Onur Sakarya, Styrmir Sigurjonsson, Bernhard Zimmermann
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Patent number: 11479819Abstract: The present invention pertains to a non-invasive method for monitoring transplanted organ status in organ-transplant recipients by determining the ratio of donor derived marker sequences to the marker sequences of the transplant recipient from circulating cell free DNA of the transplant recipients using digital droplet PCR. The invention also determined a normalized threshold value of the total circulating cell free nucleic acids healthy as well as in post-transplantation patients for assessing and monitoring transplanted organ status in organ-transplant recipients.Type: GrantFiled: December 14, 2018Date of Patent: October 25, 2022Assignee: ACRANNOLIFE GENOMICS PVT. LTD.Inventor: Avinash Ramani
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Patent number: 11479805Abstract: The present invention provides for single-molecule profiling of combinatorial protein modifications and single-molecule profiling of combinatorial protein modifications combined with single-molecule sequencing of protein/nucleic acids complexes. High-throughput single-molecule imaging was applied to decode combinatorial modifications on millions of individual nucleosomes from pluripotent stem cells and lineage-committed cells. Applicants identified bivalent nucleosomes with concomitant repressive and activating marks, as well as other combinatorial modification states whose prevalence varies with developmental potency. Applying genetic and chemical perturbations of chromatin enzymes show a preferential affect on nucleosomes harboring specific modification states. The present invention also combines this proteomic platform with single-molecule DNA sequencing technology to simultaneously determine the modification states and genomic positions of individual nucleosomes.Type: GrantFiled: August 19, 2016Date of Patent: October 25, 2022Assignees: The General Hospital Corporation, SEQLL LLCInventors: Efrat Shema-Yaacoby, Bradley Bernstein, Daniel Jones
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Patent number: 11479816Abstract: Comparison of common sequencing reads from sequencing based on partition-based barcoding can be used to improve sequencing results. Increased loading of barcodes per partition can also improve sequencing results.Type: GrantFiled: August 20, 2019Date of Patent: October 25, 2022Assignee: Bio-Rad Laboratories, Inc.Inventors: Ronald Lebofsky, Andrew Kohlway, Jennifer Chew, Zachary Burkett, Man Cheng
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Patent number: 11467157Abstract: Some embodiments disclosed herein provide a plurality of compositions each comprising a protein binding reagent conjugated with an oligonucleotide. The oligonucleotide comprises a unique identifier for the protein binding reagent it is conjugated with, and the protein binding reagent is capable of specifically binding to a protein target. Further disclosed are methods and kits for quantitative analysis of a plurality of protein targets in a sample and for simultaneous quantitative analysis of protein and nucleic acid targets in a sample. Also disclosed herein are systems and methods for preparing a labeled biomolecule reagent, including a labeled biomolecule agent comprising a protein binding reagent conjugated with an oligonucleotide.Type: GrantFiled: February 12, 2020Date of Patent: October 11, 2022Assignee: Becton, Dickinson and CompanyInventors: Christina Fan, Olaf Zoellner
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Patent number: 11459618Abstract: A panel of gene expression markers for gastric cancer patient treated or to be treated by cetuximab is provided. Methods and compositions are also provided, e.g., kits, for evaluating gene expression levels of the markers and methods of using such gene expression levels to predict a gastric cancer patient's response to cetuximab.Type: GrantFiled: March 28, 2018Date of Patent: October 4, 2022Assignee: CROWN BIOSCIENCE, INC. (TAICANG)Inventors: Binchen Mao, Sheng Guo, Henry Qixiang Li
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Patent number: 11447818Abstract: The disclosed embodiments concern methods, systems and computer program products for determining sequences of interest using unique molecular indexes (UMIs) that are uniquely associable with individual polynucleotide fragments, including sequences with low allele frequencies or long sequence length. In some implementations, the UMIs include variable-length nonrandom UMIs (vNRUMIs). Methods and systems for making and using sequencing adapters comprising vNRUMIs are also provided.Type: GrantFiled: September 12, 2018Date of Patent: September 20, 2022Assignee: Illumina, Inc.Inventors: Chen Zhao, Kevin Wu, Han-Yu Chuang, Jennifer Lococo, Alex So, Dwight Baker, Tatjana Singer
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Patent number: 11447827Abstract: The invention provides methods, systems, and computer readable medium for detecting ploidy of chromosome segments or entire chromosomes, for detecting single nucleotide variants and for detecting both ploidy of chromosome segments and single nucleotide variants. In some aspects, the invention provides methods, systems, and computer readable medium for detecting cancer or a chromosomal abnormality in a gestating fetus.Type: GrantFiled: June 21, 2018Date of Patent: September 20, 2022Assignee: Natera, Inc.Inventors: Joshua Babiarz, Tudor Pompiliu Constantin, Lane A. Eubank, George Gemelos, Matthew Micah Hill, Huseyin Eser Kirkizlar, Matthew Rabinowitz, Onur Sakarya, Styrmir Sigurjonsson, Bernhard Zimmermann
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Patent number: 11441179Abstract: This disclosure provides methods and compositions for sample processing, particularly for sequencing applications. Included within this disclosure are bead compositions, such as diverse libraries of beads attached to large numbers of oligonucleotides containing barcodes. Often, the beads provides herein are degradable. For example, they may contain disulfide bonds that are susceptible to reducing agents. The methods provided herein include methods of making libraries of barcoded beads as well as methods of combining the beads with a sample, such as by using a microfluidic device.Type: GrantFiled: April 9, 2020Date of Patent: September 13, 2022Assignee: 10X GENOMICS, INC.Inventors: Christopher Hindson, Michael Schnall-Levin, Andrew Price, Paul Hardenbol, Yuan Li
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Patent number: 11414709Abstract: The invention provides methods, systems, and computer readable medium for detecting ploidy of chromosome segments or entire chromosomes, for detecting single nucleotide variants and for detecting both ploidy of chromosome segments and single nucleotide variants. In some aspects, the invention provides methods, systems, and computer readable medium for detecting cancer or a chromosomal abnormality in a gestating fetus.Type: GrantFiled: March 20, 2019Date of Patent: August 16, 2022Assignee: Natera, Inc.Inventors: Joshua Babiarz, Tudor Pompiliu Constantin, Lane A. Eubank, George Gemelos, Matthew Micah Hill, Huseyin Eser Kirkizlar, Matthew Rabinowitz, Onur Sakarya, Styrmir Sigurjonsson, Bernhard Zimmermann
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Patent number: 11414699Abstract: According to various embodiments, a system and method for characterizing protein and nucleic acid content of a plurality of individual particles. The method includes encapsulating individual particles into compartments also containing analyte specific binding complements with oligonucleotide tags comprising a unique molecular identifier sequence, a sequence to identify the analyte specific binding complement, and a homology domain sequence. Allowing the oligonucleotide tags to hybridize on homology domain to form initial tag pairs, amplifying the tag pairs, using an enzyme to cut at the homology domain, allowing tags to re-hybridize, pooling the compartments, and sequencing. Finally, predicting co-encapsulated analytes by computational identification of clusters based on more frequently found oligonucleotide tag pairs.Type: GrantFiled: May 15, 2019Date of Patent: August 16, 2022Assignee: MANTRA BIO, INC.Inventors: Terry Alden Gaige, Chi-Chih (Ginny) Kang, Catherine RoseMary Planey, Dragan Sebisanovic
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Patent number: 11414688Abstract: This disclosure provides methods for preparing a sequencing library including the steps of providing a template nucleic acid sequence, dNTPs, dUTP, a primer, a polymerase, a dUTP excising enzyme, and a plurality of beads including oligonucleotide adapter sequence segments; amplifying the template nucleic acid with the polymerase, dNTPs, dUTP and random hexamer to provide a complementary nucleic acid sequence including occasional dUTPs; and excising the incorporated dUTPs with the dUTP excising enzyme to provide nicks in the complementary nucleic acid sequence to provide a sequencing library.Type: GrantFiled: December 17, 2019Date of Patent: August 16, 2022Assignee: 10X GENOMICS, INC.Inventors: Paul Hardenbol, Pranav Patel, Benjamin Hindson, Paul William Wyatt, Keith Bjornson, Indira Wu, Zahra Kamila Belhocine
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Patent number: 11401561Abstract: The present invention provides a primer composition for analyzing intestinal flora, a detection kit composed thereof, and an application of the same. The present invention employs two-step amplification to obtain a sequencing library, and the primer composition comprises a random base.Type: GrantFiled: December 31, 2017Date of Patent: August 2, 2022Assignee: SUZHOU PRECISION GENE CO. LTD.Inventors: Yongliang Zhu, Yanzhao Mu
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Patent number: 11392846Abstract: Applying a local-adapted minority oversampling strategy technique to an imbalanced dataset including positive samples belonging to a minority class and negative samples belonging to a majority class, the minority class being less prevalent than the majority class, wherein each sample from the dataset includes a plurality of features. The local-adapted minority oversampling strategy includes determining a local imbalance for each positive sample from the minority class corresponding to a number of other positive samples and/or negative samples within a neighborhood of each positive sample. The local-adapted minority oversampling strategy also includes calculating a local-adapted oversampling ratio based on the local imbalance estimated for each positive sample and replicating each positive sample using the local-adapted oversampling ratio to generate a new dataset.Type: GrantFiled: May 24, 2019Date of Patent: July 19, 2022Assignee: Canon U.S.A., Inc.Inventors: Xiwu Cao, Samuel Schrader
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Patent number: 11385218Abstract: The present disclosure provides compositions, methods, and systems for identifying marked hydrocarbon fluids. These compositions, methods, and systems utilize a gas chromatography marker including a pyrrolidinone. The methods and systems can identify the presence or absence of the gas chromatography marker and/or the pyrrolidinone. The compositions, methods, and systems can optionally utilize a spectroscopic marker.Type: GrantFiled: November 14, 2019Date of Patent: July 12, 2022Assignee: UNITED COLOR MANUFACTURING, INC.Inventors: Michael P. Hinton, Justin J. Frederico
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Patent number: 11371094Abstract: Provided herein are compositions, systems and methods for tagging molecular events, reactions, species, etc., but without the need for complex, highly diverse libraries of tagging molecules. Provided are tagging moieties that can have a smaller number, a few, or even a single original “tagging” structure that may be transformed or transformable, in situ, into a collection of larger numbers of unique tagging or “barcode” moieties.Type: GrantFiled: March 13, 2020Date of Patent: June 28, 2022Assignee: 10X Genomics, Inc.Inventors: Paul Ryvkin, Jason Underwood, Michael Schnall-Levin, Tarjei Mikkelsen, Benjamin Hindson
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Patent number: 11371095Abstract: The invention relates to a high-throughput method for characterizing the genome-wide activity of editing nucleases in vitro.Type: GrantFiled: February 3, 2021Date of Patent: June 28, 2022Assignee: St. Jude Children's Research Hospital, Inc.Inventors: Shengdar Q. Tsai, Cicera R. Lazzarotto
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Patent number: 11352714Abstract: Provided herein are methods for identification of an expression profile, a transcriptional profile, and/or an epigenetic profile from a cell-containing sample. Also provided are compositions for use in the disclosed methods.Type: GrantFiled: March 5, 2019Date of Patent: June 7, 2022Assignee: VERILY LIFE SCIENCES LLCInventors: Jerrod Schwartz, Ci Chu, Charles Kim, Bi Yu Li, Xiaomi Du
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Patent number: 11322413Abstract: Methods of forming an integrated device, and in particular forming one or more sample wells in an integrated device, are described. The methods may involve forming a metal stack over a cladding layer, forming an aperture in the metal stack, forming first spacer material within the aperture, and forming a sample well by removing some of the cladding layer to extend a depth of the aperture into the cladding layer. In the resulting sample well, at least one portion of the first spacer material is in contact with at least one layer of the metal stack.Type: GrantFiled: August 29, 2019Date of Patent: May 3, 2022Assignee: Quantum-Si IncorporatedInventors: Gerard Schmid, James Beach
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Patent number: 11280745Abstract: A sensing device can use electromagnetic resonance to detect properties of a sample. For example, the sensing device can be immersed into a sample, placed in proximity to a sample, or otherwise located within sensing range of a sample. The sensing device can transmit a signal onto the sample and receive a reflected signal using a resonating structure. The sensing device can analyze the reflected signal to detect a constituent in the sample, such as a concentration of the constituent in the sample.Type: GrantFiled: July 4, 2019Date of Patent: March 22, 2022Assignee: Mezent CorporationInventors: Perry Allen MacDonald, Daniel Joseph Denninghoff
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Patent number: 11279929Abstract: The present invention relates to antisense oligonucleotides that are capable of modulating expression of Tau in a target cell. The oligonucleotides hybridize to MAPT mRNA. The present invention further relates to conjugates of the oligonucleotide and pharmaceutical compositions and methods for treatment of Tauopathies, Alzheimzer's disease, fronto-temporal dementia (FTD), FTDP-17, progressive supranuclear palsy (PSP), chronic traumatic encephalopathy (CTE), corticobasal ganglionic degeneration (CBD), epilepsy, Dravet syndrome, depression, seizure disorders and movement disorders.Type: GrantFiled: July 3, 2019Date of Patent: March 22, 2022Assignee: Hoffmann-La Roche, Inc.Inventors: Peter Hagedorn, Anja Mølhart Høg, Marianne L. Jensen, Richard E. Olson
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Patent number: 11274334Abstract: Methods of preparing a plurality of sample-barcoded anchor-domain-flanked gene specific deoxyribonucleic acid (DNA) fragments from a template nucleic acid, e.g., ribonucleic acid (RNA), sample are provided. Aspects of the methods include employing a set of gene specific primer pairs, wherein each pair of gene specific primers is made up of a forward primer and a reverse primer, at least one of which includes a sample barcode domain. The methods find use in a variety of different applications, including high-throughput sequencing, e.g., expression profiling, applications, including of small biological samples, e.g., single-cells.Type: GrantFiled: August 16, 2019Date of Patent: March 15, 2022Assignee: Cellecta, Inc.Inventors: Alex Chenchik, Costa Frangou, Mikhail Makhanov, Russell Paul Darst, IV, Donato Tedesco, Lester Kobzik
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Patent number: 11248267Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and analyte characterization. Such polynucleotide processing may be useful for a variety of applications, including analyte characterization by polynucleotide sequencing. 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), genomic DNA, and RNA (e.g., mRNA or CRISPR guide RNAs). Also described herein, are barcoded labelling agents and oligonucleotide molecules useful for “tagging” analytes for characterization.Type: GrantFiled: February 12, 2021Date of Patent: February 15, 2022Assignee: 10X GENOMICS, INC.Inventors: Phillip Belgrader, Josephine Harada, Tarjei Sigurd Mikkelsen, Katherine Pfeiffer, Serge Saxonov, John R. Stuelpnagel
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Patent number: 11236387Abstract: Provided herein are methods and compositions for improved sequencing techniques using, for example, polymeric particles and/or three-dimensional structures.Type: GrantFiled: September 24, 2020Date of Patent: February 1, 2022Assignee: Singular Genomics Systems, Inc.Inventors: Eli N. Glezer, Mohammad Vatankhah Varnosfaderani, Daan Witters, Vahid Karimkhani
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Patent number: 11232539Abstract: A method includes exciting, at a first time period, a first set of pixels in an excitation array, wherein the first set of pixels comprises more than one pixel, and no pixel in the first set of pixels is adjacent to another pixel in the first set of pixels. The method also includes exciting, at a second time period, a second set of pixels in the excitation array wherein the second set of pixels comprises more than one pixel, and no pixel in the second set of pixels is adjacent to another pixel in the second set of pixels. The method retrieves excitation data, wherein the excitation data is comprised of data from the first set of pixels and data from the second set of pixels, and the excitation data is capable of being combined to reconstruct an image of a target object for rendering on a display.Type: GrantFiled: November 27, 2019Date of Patent: January 25, 2022Assignee: THE BOEING COMPANYInventor: Morteza Safai
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Patent number: 11214794Abstract: The invention provides methods, compositions, kits and devices for the detection of target molecules. In some embodiments, the invention allows for multiplexed target molecule detection.Type: GrantFiled: November 6, 2018Date of Patent: January 4, 2022Assignee: Roche Sequencing Solutions, Inc.Inventor: Garry P. Nolan
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Patent number: 11209381Abstract: A medical detection substrate and a manufacturing method thereof, a medical detection chip and a medical detection system are provided. The medical detection substrate includes: a substrate, and a detection unit on the substrate; the detection unit includes two groups of test electrodes, the substrate includes a plurality of recessed portions, and the at least two groups of test electrodes are located in the plurality of recessed portions and spaced apart by insulation bank portions. The two groups of test electrodes are insulated and spaced apart by the insulation bank portions, so as to effectively avoid a transverse interference electric field to be generated between the two groups of test electrodes, thereby effectively improving the detection accuracy and sensitivity of the medical detection substrate, and providing a reliable basis for disease diagnosis.Type: GrantFiled: February 2, 2018Date of Patent: December 28, 2021Assignees: BEIJING BOE OPTOELECTRONICS TECHNOLOGY CO., LTD., BOE TECHNOLOGY GROUP CO., LTD.Inventors: Zhenyu Xie, Zhenyu Hao, Yuekai Gao, Lijun Mao, Tiansheng Li
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Patent number: 11200383Abstract: Material in a supply chain is tracked by a method of applying a DNA taggant set to a first batch of the material produced by a first supplier of the material. The DNA taggant set corresponds to a tag string corresponding to the first supplier. The first batch is aggregated with a second batch to create an aggregated lot. A sample is selected from the aggregated lot and tested to determine a DNA taggant set of the sample. After selecting a sample from the aggregated lot, the sample may be labeled with a grade and then placed in a receptacle corresponding to the grade.Type: GrantFiled: August 28, 2019Date of Patent: December 14, 2021Inventors: Antonios Zografos, Laurie M. Clotilde
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Patent number: 11180801Abstract: In various aspects, the present disclosure provides methods, compositions, reactions mixtures, kits, and systems for sequencing both RNA and DNA from a single source sample. In some embodiments, RNA is treated so as to differentiate RNA sequences from DNA sequences derived from the same sample. In some embodiments, the RNA and DNA are cell-free polynucleotides.Type: GrantFiled: October 31, 2018Date of Patent: November 23, 2021Assignee: GRAIL, LLCInventors: Matthew Larson, H. John Kim, Nick Eattock, Arash Jamshidi
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Patent number: 11168320Abstract: Provided herein are methods and systems for structure-assisted evolution of multivalent aptamers using a single stranded DNA or single-stranded RNA nanostructure as a structural support. Also provided herein are methods for constructing ssDNA or ssRNA nanostructures as structural supports suitable for structure-assisted evolution of multivalent aptamers.Type: GrantFiled: August 9, 2017Date of Patent: November 9, 2021Assignee: Arizona Board of Regents on behalf of Arizona State UniversityInventor: Hao Yan