Method Specially Adapted For Identifying A Library Member Patents (Class 506/2)
  • Patent number: 11661597
    Abstract: A population of nucleic acid adaptors is provided. In some embodiments, the population contains at least 50,000 different molecular barcode sequences, where the barcode sequences are double-stranded and at least 90% of the barcode sequences have an edit distance of at least 2. In certain cases, the adaptor may have an end in which the top and bottom strands are not complementary (i.e., may be in the form of a Y-adaptor). In some embodiments and depending on the how the adaptor is going to be employed, the other end of the adaptor may have a ligatable end or may be a transposon end sequence.
    Type: Grant
    Filed: April 13, 2016
    Date of Patent: May 30, 2023
    Assignee: THE BOARD OF TRUSTEES OF THE LELAND STANFORD JUNIOR UNIVERSITY
    Inventors: Billy Tsz Cheong Lau, Hanlee P. Ji
  • Patent number: 11643669
    Abstract: The present invention relates to systems and methods for recording and assaying cellular events, in particular gene expression. The invention provides hereto a method of determining a cellular event of interest in a cell comprising providing a cell comprising a CRISPR-Cas system, wherein the CRISPR-Cas system comprises a guide RNA that targets a selected DNA sequence and a Cas protein capable of modifying the selected DNA sequence; whereby a nucleic acid molecule encoding at least one of the guide RNA or Cas protein is operably connected in the cell with a regulatory element comprising a promoter responsive to the cellular event, and whereby expression of at least one CRISPR-Cas system component is driven by the promoter; and determining cellular event of interest based on detection of the modification of the selected DNA sequence.
    Type: Grant
    Filed: December 11, 2017
    Date of Patent: May 9, 2023
    Assignee: Massachusetts Institute of Technology
    Inventors: Alexander K. Shalek, Alethe Gaillard De Saint Germain
  • Patent number: 11639527
    Abstract: The present invention provides methods for sequencing and analysis of nucleic acids and determining that a subject is positive for a non-usual interstitial pneumonia subtype.
    Type: Grant
    Filed: March 30, 2021
    Date of Patent: May 2, 2023
    Assignee: Veracyte, Inc.
    Inventors: Giulia C. Kennedy, James Diggans, Jing Huang, Yoonha Choi, Su Yeon Kim, Daniel Pankratz, Moraima Pagan
  • Patent number: 11634774
    Abstract: A method for identifying one or more genomic variations in human genomic DNA, comprising employment of Alu, MIR and SVA sequence-based PCR primers and performing an inter-transposable-element (ITE) polymerase chain reaction on the assay mixture to produce an array of amplicons comprising the ITE genomic segments. Also provided the use of the method for identifying one or more genomic variants associated with a trait or a disease.
    Type: Grant
    Filed: May 18, 2018
    Date of Patent: April 25, 2023
    Assignee: PharmacoGenetics Limited
    Inventor: Hong Xue
  • Patent number: 11629382
    Abstract: Next Generation DNA sequencing promises to revolutionize clinical medicine and basic research. However, while this technology has the capacity to generate hundreds of billions of nucleotides of DNA sequence in a single experiment, the error rate of approximately 1% results in hundreds of millions of sequencing mistakes. These scattered errors can be tolerated in some applications but become extremely problematic when “deep sequencing” genetically heterogeneous mixtures, such as tumors or mixed microbial populations. To overcome limitations in sequencing accuracy, a method Duplex Consensus Sequencing (DCS) is provided. This approach greatly reduces errors by independently tagging and sequencing each of the two strands of a DNA duplex. As the two strands are complementary, true mutations are found at the same position in both strands. In contrast, PCR or sequencing errors will result in errors in only one strand.
    Type: Grant
    Filed: July 3, 2019
    Date of Patent: April 18, 2023
    Assignee: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATION
    Inventors: Jesse Salk, Lawrence A. Loeb, Michael Schmitt
  • Patent number: 11624062
    Abstract: Methods, systems and related compositions are provided to perform single-cell marking of a nucleic acid and/or protein in a sample based on in-cell or in-organelle barcoding of nucleic acid and/or protein complexes of the cell or organelle; the methods and systems herein described are configured to provide in-cell or in-organelle single-cell marked nucleic acid and/or protein complexes comprising a single-cell, cell-specific, or a single-cell organelle-specific marker.
    Type: Grant
    Filed: September 25, 2018
    Date of Patent: April 11, 2023
    Assignee: CALIFORNIA INSTITUTE OF TECHNOLOGY
    Inventors: Rustem F. Ismagilov, Matthew S. Curtis, Mary Arrastia, David A. Selck, Mitchell Guttman
  • Patent number: 11615865
    Abstract: Factors affecting the fragmentation pattern of cell-free DNA (e.g., plasma DNA) and the applications, including those in molecular diagnostics, of the analysis of cell-free DNA fragmentation patterns are described. Various applications can use a property of a fragmentation pattern to determine a proportional contribution of a particular tissue type, to determine a genotype of a particular tissue type (e.g., fetal tissue in a maternal sample or tumor tissue in a sample from a cancer patient), and/or to identify preferred ending positions for a particular tissue type, which may then be used to determine a proportional contribution of a particular tissue type.
    Type: Grant
    Filed: September 10, 2019
    Date of Patent: March 28, 2023
    Assignee: The Chinese University of Hong Kong
    Inventors: Yuk-Ming Dennis Lo, Rossa Wai Kwun Chiu, Kwan Chee Chan, Peiyong Jiang
  • Patent number: 11608529
    Abstract: Next Generation DNA sequencing promises to revolutionize clinical medicine and basic research. However, while this technology has the capacity to generate hundreds of billions of nucleotides of DNA sequence in a single experiment, the error rate of approximately 1% results in hundreds of millions of sequencing mistakes. These scattered errors can be tolerated in some applications but become extremely problematic when “deep sequencing” genetically heterogeneous mixtures, such as tumors or mixed microbial populations. To overcome limitations in sequencing accuracy, a method Duplex Consensus Sequencing (DCS) is provided. This approach greatly reduces errors by independently tagging and sequencing each of the two strands of a DNA duplex. As the two strands are complementary, true mutations are found at the same position in both strands. In contrast, PCR or sequencing errors will result in errors in only one strand.
    Type: Grant
    Filed: June 28, 2021
    Date of Patent: March 21, 2023
    Assignee: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATION
    Inventors: Jesse Salk, Lawrence A. Loeb, Michael Schmitt
  • Patent number: 11605445
    Abstract: Factors affecting the fragmentation pattern of cell-free DNA (e.g., plasma DNA) and the applications, including those in molecular diagnostics, of the analysis of cell-free DNA fragmentation patterns are described. Various applications can use a property of a fragmentation pattern to determine a proportional contribution of a particular tissue type, to determine a genotype of a particular tissue type (e.g., fetal tissue in a maternal sample or tumor tissue in a sample from a cancer patient), and/or to identify preferred ending positions for a particular tissue type, which may then be used to determine a proportional contribution of a particular tissue type.
    Type: Grant
    Filed: September 10, 2019
    Date of Patent: March 14, 2023
    Assignee: The Chinese University of Hong Kong
    Inventors: Yuk-Ming Dennis Lo, Rossa Wai Kwun Chiu, Kwan Chee Chan, Peiyong Jiang
  • Patent number: 11603553
    Abstract: Provided herein are methods for enriching a biological sample for a target nucleic acid, and analyzing the nucleic acid. In some cases, a biological sample is enriched for target nucleic acids associated with a cancer or tumor. In some cases, a biological sample is enriched for target nucleic acids, and the target nucleic acids vary in length. In some cases, one or more probes are used to enrich the biological sample for the target nucleic acid. In some cases, one or more probes hybridize to one or more ends of a target nucleic acid.
    Type: Grant
    Filed: March 19, 2020
    Date of Patent: March 14, 2023
    Assignee: GRAIL, LLC
    Inventors: Eugeni Namsaraev, Maneesh Jain
  • Patent number: 11603564
    Abstract: The present invention relates to methods of predicting resistance to heart and skeletal muscle inflammation in salmonids, the method comprising determining the alleles present at a DNA polymorphism in the salmonid and predicting whether or not the salmonid is resistant to heart and skeletal muscle inflammation based on the determination of the alleles. The invention also relates to related methods of detecting, in a sample from a salmonid, the alleles present at a DNA polymorphism associated with resistance to heart and skeletal muscle inflammation, methods for obtaining an indication of risk of a salmonid developing heart and skeletal muscle inflammation, uses of such DNA polymorphisms, and methods of detecting, in a sample from a salmonid, one or more salmonid gene variants.
    Type: Grant
    Filed: January 30, 2018
    Date of Patent: March 14, 2023
    Assignee: AQUAGEN AS
    Inventors: Jacob Seilø Torgersen, Torkjel Bruheim, Vibeke Evenstad Emilsen, Thomas Moen, Nina Santi
  • Patent number: 11591656
    Abstract: Compositions and methods for the detection and treatment of ADHD are provided.
    Type: Grant
    Filed: September 6, 2018
    Date of Patent: February 28, 2023
    Assignee: THE CHILDREN'S HOSPITAL OF PHILADELPHIA
    Inventors: Hakon Hakonarson, Berta Almoguera, Lyam Vazquez, Patrick Sleiman
  • Patent number: 11578366
    Abstract: The present invention includes a method for analyzing RNA fragments. In one aspect, the present invention includes a method of identifying a subject in need of therapeutic intervention to treat a disease or condition, disease recurrence, or disease progression comprises characterizing the identity of rRNA fragments. The invention also includes diagnosing, identifying or monitoring a disease or condition, and a method for identifying rRNA fragments. The invention also includes diagnosing, identifying or monitoring a glaucoma in a subject in need thereof by characterizing the identity of rRNA or tRNA fragments.
    Type: Grant
    Filed: December 22, 2017
    Date of Patent: February 14, 2023
    Assignee: Thomas Jefferson University
    Inventor: Isidore Rigoutsos
  • Patent number: 11578093
    Abstract: Protected fluorescent reagent compounds and their methods of synthesis are provided. The compounds are useful in various fluorescence-based analytical methods, including the analysis of highly multiplexed optical reactions in large numbers at high densities, such as single molecule real time nucleic acid sequencing reactions. The compounds contain fluorescent dye elements, that allow the compounds to be detected with high sensitivity at desirable wavelengths, binding elements, that allow the compounds to be recognized specifically by target biomolecules, and protective shield elements, that decrease undesirable contacts between the fluorescent dye elements and the bound target biomolecules and that therefore decrease photodamage of the bound target biomolecules by the fluorescent dye elements.
    Type: Grant
    Filed: August 28, 2020
    Date of Patent: February 14, 2023
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Lubomir Sebo, Jeremiah Hanes, Gene Shen, Louis Brogley, Stephen Yue, Frank Zheng, Yuri Lapin, John Lyle, Honey Osuna, Andrei Fedorov
  • Patent number: 11566285
    Abstract: Next Generation DNA sequencing promises to revolutionize clinical medicine and basic research. However, while this technology has the capacity to generate hundreds of billions of nucleotides of DNA sequence in a single experiment, the error rate of approximately 1% results in hundreds of millions of sequencing mistakes. These scattered errors can be tolerated in some applications but become extremely problematic when “deep sequencing” genetically heterogeneous mixtures, such as tumors or mixed microbial populations. To overcome limitations in sequencing accuracy, a method Duplex Consensus Sequencing (DCS) is provided. This approach greatly reduces errors by independently tagging and sequencing each of the two strands of a DNA duplex. As the two strands are complementary, true mutations are found at the same position in both strands. In contrast, PCR or sequencing errors will result in errors in only one strand.
    Type: Grant
    Filed: July 3, 2019
    Date of Patent: January 31, 2023
    Assignee: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATION
    Inventors: Jesse Salk, Lawrence A. Loeb, Michael Schmitt
  • Patent number: 11566286
    Abstract: Next Generation DNA sequencing promises to revolutionize clinical medicine and basic research. However, while this technology has the capacity to generate hundreds of billions of nucleotides of DNA sequence in a single experiment, the error rate of approximately 1% results in hundreds of millions of sequencing mistakes. These scattered errors can be tolerated in some applications but become extremely problematic when “deep sequencing” genetically heterogeneous mixtures, such as tumors or mixed microbial populations. To overcome limitations in sequencing accuracy, a method Duplex Consensus Sequencing (DCS) is provided. This approach greatly reduces errors by independently tagging and sequencing each of the two strands of a DNA duplex. As the two strands are complementary, true mutations are found at the same position in both strands. In contrast, PCR or sequencing errors will result in errors in only one strand.
    Type: Grant
    Filed: June 28, 2021
    Date of Patent: January 31, 2023
    Assignee: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATION
    Inventors: Jesse Salk, Lawrence A. Loeb, Michael Schmitt
  • Patent number: 11555218
    Abstract: The present invention relates to a sequencing method which allows for increased rates of sequencing and an increase in the density of sequencing data. The system may be based on next generation sequencing methods such as sequencing by synthesis (SBS) but uses multiple primers bound at different positions on the same nucleic acid strand.
    Type: Grant
    Filed: August 3, 2020
    Date of Patent: January 17, 2023
    Assignee: Illumina Cambridge Limited
    Inventor: Jonathan Mark Boutell
  • Patent number: 11542544
    Abstract: A method for enriching or amplifying a target nucleic acid including providing a system having a guide nucleic acid, and a Cas or Argonaute protein or a variant thereof. The guide nucleic acid contains a target-specific nucleotide region substantially complementary to a region of the target nucleic acid, and contacting the target nucleic acid with the system to form a complex.
    Type: Grant
    Filed: May 10, 2017
    Date of Patent: January 3, 2023
    Assignee: Illumina, Inc.
    Inventors: Jeffrey G. Mandell, Molly He
  • Patent number: 11535886
    Abstract: Provided includes methods and systems useful in array-based analysis of mixed nucleic acid populations, including for genotyping and copy number analysis of the various subpopulations of the mixed nucleic acid population. Also provided includes methods and systems useful in the diagnosis of genetic abnormalities in a mixed nucleic acid population taken from an organism.
    Type: Grant
    Filed: June 1, 2018
    Date of Patent: December 27, 2022
    Inventors: Jeanette Schmidt, Orna Mizrahi Man, Jiang Li
  • Patent number: 11535882
    Abstract: The present disclosure provide compositions, methods and kits for generating a set of combinatorial barcodes, and uses thereof for barcoding samples such as single cells or genomic DNA fragments. Some embodiments disclosed herein provide compositions comprising a set of component barcodes for producing a set of combinatorial barcodes. The set of component barcodes can comprise, for example, n×m unique component barcodes, wherein n and m are integers, each of the component barcodes comprises: one of n unique barcode subunit sequences; and one or two linker sequences or the complements thereof, wherein the component barcodes are configured to connect to each other through the one or two linker sequences or the complements thereof to produce a set of combinatorial barcodes.
    Type: Grant
    Filed: March 29, 2016
    Date of Patent: December 27, 2022
    Assignee: Becton, Dickinson and Company
    Inventors: Glenn Fu, Stephen P. A. Fodor
  • Patent number: 11531021
    Abstract: A method of using a sequencing cell includes applying an alternating signal across a nanopore of the sequencing cell. The method further includes acquiring a first set of voltage data during a first portion of a plurality of cycles of the alternating signal. The method further includes determining a shifted set of voltage data from the first set of voltage data, computing difference data values by computing differences between data points of the first set of voltage data and corresponding data points of the shifted set of voltage data, identifying a plurality of noise data points as data points having difference data values that are larger than a first threshold value, and removing the plurality of noise data points from the first set of voltage data.
    Type: Grant
    Filed: June 25, 2020
    Date of Patent: December 20, 2022
    Assignee: Roche Sequencing Solutions, Inc.
    Inventor: Kapil M. S. Bajaj
  • Patent number: 11519028
    Abstract: The present disclosure provides methods and compositions for sequencing nucleic acid molecules and identifying individual sample nucleic acid molecules using Molecular Index Tags (MITs). Furthermore, reaction mixtures, kits, and adapter libraries are provided.
    Type: Grant
    Filed: October 5, 2021
    Date of Patent: December 6, 2022
    Assignee: Natera, Inc.
    Inventors: Bernhard Zimmermann, Ryan Swenerton, Matthew Rabinowitz, Styrmir Sigurjonsson, George Gemelos, Apratim Ganguly, Himanshu Sethi
  • Patent number: 11519034
    Abstract: The present invention relates to a novel non-invasive method for the diagnosis of a non-alcoholic fatty liver disease, in particular non-alcoholic steatohepatitis, and/or liver fibrosis.
    Type: Grant
    Filed: September 14, 2018
    Date of Patent: December 6, 2022
    Assignee: Genfit
    Inventors: Remy Hanf, Genevieve Cordonnier, John Brozek
  • Patent number: 11512306
    Abstract: Temporal variations in one or more characteristics measured from a cell-free DNA sample are used to estimate a gestational age of a fetus. Example characteristics include the methylation level measured from the cell-free DNA sample, size of DNA fragments measured from the cell-free DNA sample (e.g., proportion of fetal-derived DNA fragments longer than a specified size), and ending patterns of the DNA fragments align to a reference genome.
    Type: Grant
    Filed: October 18, 2017
    Date of Patent: November 29, 2022
    Assignee: The Chinese University of Hong Kong
    Inventors: Yuk-Ming Dennis Lo, Rossa Wai Kwun Chiu, Kwan Chee Chan, Peiyong Jiang
  • Patent number: 11499180
    Abstract: The present invention is a method and compositions for primer extension target enrichment of nucleic acids and improvements thereto including simultaneously enriching for RNA and DNA and optionally sequencing the enriched products. An embodiment of the present invention includes a method comprising the steps of: hybridizing a target-specific primer to a target DNA or RNA, wherein the primer comprises a target-binding region and a region of complementarity to an adaptor; extending the primer with a DNA polymerase or reverse transcriptase to form a primer extension product; contacting the product with an adaptor comprising a longer strand with a 5?-overhang having complementarity to said primer and a shorter strand comprising a universal priming site; hybridizing the adaptor to the product; and ligating one strand of the adaptor to the product to form a ligation product.
    Type: Grant
    Filed: August 23, 2019
    Date of Patent: November 15, 2022
    Assignee: Roche Sequencing Solutions, Inc.
    Inventors: Brian Christopher Godwin, Sedide Ozturk
  • Patent number: 11473138
    Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing. In some cases, this disclosure provides methods for the generation of polynucleotide barcode libraries, and for the attachment of such polynucleotides to target polynucleotides.
    Type: Grant
    Filed: November 27, 2019
    Date of Patent: October 18, 2022
    Assignee: 10X GENOMICS, INC.
    Inventors: Benjamin Hindson, Mirna Jarosz, Paul Hardenbol, Michael Schnall-Levin, Kevin Ness, Serge Saxonov
  • Patent number: 11466319
    Abstract: Labeled nucleotide analogs comprising at least one avidin protein, at least one dye-labeled compound, and at least one nucleotide compound are provided. The analogs are useful in various fluorescence-based analytical methods, including the analysis of highly multiplexed optical reactions in large numbers at high densities, such as single molecule real time nucleic acid sequencing reactions. The analogs are detectable with high sensitivity at desirable wavelengths. They contain structural components that modulate the interactions of the analogs with DNA polymerase, thus decreasing photodamage and improving the kinetic and other properties of the analogs in sequencing reactions. Also provided are nucleotide and dye-labeled compounds of the subject analogs, as well as intermediates useful in the preparation of the compounds and analogs. Compositions comprising the compounds, methods of synthesis of the intermediates, compounds, and analogs, and mutant DNA polymerases are also provided.
    Type: Grant
    Filed: August 28, 2020
    Date of Patent: October 11, 2022
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Lubomir Sebo, Gene Shen, Stephen Yue, Honey Osuna, Yuri Lapin, Louis Brogley, Andrei Fedorov
  • Patent number: 11459609
    Abstract: Described herein are methods of generating a coupled sequencing read pair for a polynucleotide, and methods of analyzing the coupled sequencing read pair. The coupled sequencing read pair can be analyzed to detect polynucleotide variants, including at loci that are not directly sequenced within the coupled sequencing read pair. Other analytical methods can include using coupled sequencing read pairs to construct or validate a consensus sequence. The coupled sequencing read pair may be generated for a polynucleotide by generating sequencing data for a first region by extending a primer using labeled nucleotides; further extending the primer through a second region using nucleotides provided in a second region flow order, wherein primer extension through the second region is faster than primer extension through the first region; and generating sequencing data associated with a sequence of a third region of the polynucleotide by further extending the primer using labeled nucleotides.
    Type: Grant
    Filed: November 3, 2021
    Date of Patent: October 4, 2022
    Assignee: Ultima Genomics, Inc.
    Inventors: Mark Pratt, Gilad Almogy, Dumitru Brinza, Eliane Trepagnier, Omer Barad, Yoav Etzioni, Florian Oberstrass
  • Patent number: 11447829
    Abstract: Provided herein are methods and systems for identifying chimeric nucleic acid fragments, e.g., organism-pathogen chimeric nucleic acid fragments and chromosomal rearrangement chimeric nucleic acid fragments. Also provided herein are methods and systems relating to determining a pathogen integration profile or a chromosomal rearrangement in a biological sample and determining a classification of pathology based at least in part on a pathogen integration profile or a chromosomal rearrangement in a biological sample. In certain aspects of the present disclosure, cell-free nucleic acid molecules from a biological sample are analyzed.
    Type: Grant
    Filed: June 28, 2019
    Date of Patent: September 20, 2022
    Assignee: GRAIL, LLC
    Inventors: Yuk-Ming Dennis Lo, Rossa Wai Kwun Chiu, Kwan Chee Chan, Peiyong Jiang, Wai Kei Lam, Haiqiang Zhang
  • Patent number: 11441240
    Abstract: Provided herein are methods that enable parallel evaluation of multiple functional nucleic acids in individual cells or subpopulations of cells, in the context of incubation with other types of single cells. The key insight is concurrent measurement of polynucleic acids derived from small populations of at least two different cell types, such that function in one cell type is linked to the clonal identity of another cell. These methods simultaneously process thousands, millions, or more single cells or small populations of cells. The method integrates molecular, algorithmic, and engineering approaches. This invention has broad and useful application in a number of biological and medical fields, including immunology and drug discovery.
    Type: Grant
    Filed: May 16, 2019
    Date of Patent: September 13, 2022
    Assignee: GigaGen, Inc.
    Inventors: David Scott Johnson, Adam Shultz Adler, Matthew James Spindler, Rena Aviva Mizrahi
  • Patent number: 11427933
    Abstract: Provided herein are methods that enable parallel evaluation of multiple functional nucleic acids in individual cells or subpopulations of cells, in the context of incubation with other types of single cells. The key insight is concurrent measurement of polynucleic acids derived from small populations of at least two different cell types, such that function in one cell type is linked to the clonal identity of another cell. These methods simultaneously process thousands, millions, or more single cells or small populations of cells. The method integrates molecular, algorithmic, and engineering approaches. This invention has broad and useful application in a number of biological and medical fields, including immunology and drug discovery.
    Type: Grant
    Filed: August 3, 2021
    Date of Patent: August 30, 2022
    Assignee: GigaGen, Inc.
    Inventors: David Scott Johnson, Adam Shultz Adler, Matthew James Spindler, Rena Aviva Mizrahi
  • Patent number: 11430543
    Abstract: Embodiments of a method and/or system can include generating a set of target-associated molecules (e.g., spike-in molecules) associated with one or more biological targets; generating one or more spike-in mixtures based on processing the set of target-associated molecules with one or more samples including the one or more biological targets; performing one or more Sanger sequencing operations on the one or more spike-in mixtures; determining one or more abundance metrics based on chromatogram-related outputs from the one or more Sanger sequencing operations; and/or facilitating characterization of one or more medical conditions based on the one or more abundance metrics.
    Type: Grant
    Filed: August 6, 2018
    Date of Patent: August 30, 2022
    Assignee: BillionToOne, Inc.
    Inventors: David Tsao, Oguzhan Atay
  • Patent number: 11427870
    Abstract: A method for estimating a risk for a subject suffering from encapsulating peritoneal sclerosis is provided, including measuring an expression level of at least one microRNA from a sample of the subject, and the microRNA is selected from miR-17, miR-100, miR-155, miR-202, miR-422a, and miR-483; comparing the expression level of the microRNA in the sample to that of a same miRNA of a control, when the expression level of miRNA in the sample is lower than that of the control, the subject is estimated having the risk of encapsulating peritoneal sclerosis. A kit for estimating a risk for a subject suffering from encapsulating peritoneal sclerosis is also provided, including at least one agent for identifying the at least one microRNA as above mentioned from the sample of the subject.
    Type: Grant
    Filed: July 9, 2020
    Date of Patent: August 30, 2022
    Assignee: National Central University
    Inventors: Nian-Han Ma, Chiu-Chin Huang, Jin-Bor Chen, Chin-Chung Tseng, I-Kuan Wang, Chien-Lung Chen, An-Lun Li
  • Patent number: 11419949
    Abstract: Provided herein are variant adeno-associated virus (AAV) capsid proteins having one or more modifications in amino acid sequence relative to a parental AAV capsid protein, which, when present in an AAV virion, confer increased infectivity of one or more types of retinal cells as compared to the infectivity of the retinal cells by an AAV virion comprising the unmodified parental AAV capsid protein. Also provided are recombinant AAV virions and pharmaceutical compositions thereof comprising a variant AAV capsid protein as described herein, methods of making these rAAV capsid proteins and virions, and methods for using these rAAV capsid proteins and virions in research and in clinical practice, for example in, e.g., the delivery of nucleic acid sequences to one or more cells of the retina for the treatment of retinal disorders and diseases.
    Type: Grant
    Filed: January 29, 2021
    Date of Patent: August 23, 2022
    Assignee: 4D Molecular Therapeutics Inc.
    Inventors: David H. Kirn, Melissa Kotterman, David Schaffer
  • Patent number: 11414710
    Abstract: The present technology provides polynucleotide compositions and methods of using the same to detect circulating tumor DNA (ctDNA) in a patient. Kits for use in practicing the methods are also provided.
    Type: Grant
    Filed: December 27, 2017
    Date of Patent: August 16, 2022
    Assignee: Quest Diagnostics Investments LLC
    Inventors: Suzzette Arnal, Taraneh Angeloni
  • Patent number: 11414700
    Abstract: Disclosed herein are systems, methods, and compositions useful for profiling T cell receptor (TCR) and B cell receptor (BCR) repertoire using next-generation sequencing (NGS) methods. In certain embodiments, the methods include enriching a sample for TCR/BCR RNA sequences, and determining the TCR/BCR profile of a subject using five different oligonucleotide pools. Also disclosed herein are systems and methods for diagnosing, treating, or predicting infection, disease, medical conditions, therapeutic outcome, or therapeutic efficacy based on the TCR/BCR profile data from a subject in need thereof.
    Type: Grant
    Filed: April 21, 2021
    Date of Patent: August 16, 2022
    Assignee: Tempus Labs, Inc.
    Inventors: Jason Perera, Taylor Harding, Brittany Mineo, Aly A. Khan, Richard Blidner, Jenna L. Malinauskas
  • Patent number: 11408033
    Abstract: 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: Grant
    Filed: October 23, 2020
    Date of Patent: August 9, 2022
    Assignee: Personalis, Inc.
    Inventors: Gabor T. Bartha, Gemma Chandratillake, Richard Chen, Sarah Garcia, Hugo Yu Kor Lam, Shujun Luo, Mark R. Pratt, John West
  • Patent number: 11408037
    Abstract: 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: Grant
    Filed: February 28, 2019
    Date of Patent: August 9, 2022
    Assignee: 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
  • Patent number: 11401316
    Abstract: The present invention pertains to novel high avidity antigen recognizing constructs against Human Papilloma Virus antigens. The invention provides novel T cell receptor (TCR) based molecules which are selective and specific for HPV 16/18 proteins E5, E6 and E7. The TCR of the invention, and HPV antigen-binding fragments derived therefrom, are of use for the diagnosis, treatment and prevention of HPV infection, as well as for the diagnosis, treatment and prevention of HPV infection mediated secondary diseases as HPV infection caused cancers, such as cervical, nasopharyngeal or head and neck cancer. Further provided are nucleic acids encoding the proteins of the invention, and recombinant cells expressing the same.
    Type: Grant
    Filed: October 13, 2016
    Date of Patent: August 2, 2022
    Assignee: MAX-DELBRUECK-CENTRUM FUER MOLEKULARE MEDIZIN IN DER HELMHOLTZ-GEMEINSCHAFT
    Inventors: Thomas Blankenstein, Gerald Willimsky
  • Patent number: 11390916
    Abstract: The invention provides methods for simultaneously amplifying multiple nucleic acid regions of interest in one reaction volume as well as methods for selecting a library of primers for use in such amplification methods. The invention also provides library of primers with desirable characteristics, such as minimal formation of amplified primer dimers or other non-target amplicons.
    Type: Grant
    Filed: January 24, 2020
    Date of Patent: July 19, 2022
    Assignee: Natera, Inc.
    Inventors: Bernhard Zimmermann, Matthew Hill, Philippe Lacroute, Michael Dodd, Alexander Wong
  • Patent number: 11384377
    Abstract: The invention provides improved methods for synthesizing polynucleotides, such as DNA and RNA, using renewable initiators coupled to a solid support. Using the methods of the invention, specific sequences of polynucleotides can be synthesized de novo, base by base, in an aqueous environment, without the use of a nucleic acid template.
    Type: Grant
    Filed: April 6, 2020
    Date of Patent: July 12, 2022
    Assignee: Molecular Assemblies, Inc.
    Inventors: J. William Efcavitch, Kim Albizati, Natasha Paul, Sanjay Agarwalla
  • Patent number: 11377699
    Abstract: The present disclosure provides a method for diagnosing a head and neck cancer in a subject. The method comprises the steps of: a) measuring an expression level of miR-125b or miR-342 and miR-125b in a sample from the subject; b) measuring an expression level of a normalizing miR in the sample and normalizing the measured expression level of miR-125b or miR-342 and miR-125b using the measured expression level of the normalizing miR; and c) diagnosing a head and neck cancer in a subject having a normalized measured expression level of miR-125b elevated relative to a reference expression level of miR-125b or having a ratio of normalized measured expression level of miR-342 to normalized measured expression level of miR-125b reduced relative to a reference ratio of expression level of miR-342 to expression level of miR-125b. Uses and kits associated with the herein disclosed methods are also disclosed.
    Type: Grant
    Filed: November 30, 2018
    Date of Patent: July 5, 2022
    Assignee: PROVINCIAL HEALTH SERVICES AUTHORITY
    Inventors: Catherine Garnis, Martial Guillaud
  • Patent number: 11371100
    Abstract: 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: Grant
    Filed: February 28, 2019
    Date of Patent: June 28, 2022
    Assignee: 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
  • Patent number: 11374124
    Abstract: Described examples include integrated circuits, drain extended transistors and fabrication methods in which a silicide block material or other protection layer is formed on a field oxide structure above a drift region to protect the field oxide structure from damage during deglaze processing. Further described examples include a shallow trench isolation (STI) structure that laterally surrounds an active region of a semiconductor substrate, where the STI structure is laterally spaced from the oxide structure, and is formed under gate contacts of the transistor.
    Type: Grant
    Filed: June 28, 2018
    Date of Patent: June 28, 2022
    Assignee: Texas Instruments Incorporated
    Inventors: James Robert Todd, Xiaoju Wu, Henry Litzmann Edwards, Binghua Hu
  • Patent number: 11371084
    Abstract: Methods and systems described herein involve using long cell-free DNA fragments to analyze a biological sample from a pregnant subject. The status of methylated CpG sites and single nucleotide polymorphisms (SNPs) is often used to analyze DNA fragments of a biological sample. A CpG site and a SNP are typically separated from the nearest CpG site or SNP by hundreds or thousands of base pairs. Finding two or more consecutive CpG sites or SNPs on most cell-free DNA fragments is improbable or impossible. Cell-free DNA fragments longer than 600 bp may include multiple CpG sites and/or SNPs. The presence of multiple CpG sites and/or SNPs on long cell-free DNA fragments may allow for analysis than with short cell-free DNA fragments alone. The long cell-free DNA fragments can be used to identify a tissue of origin and/or to provide information on a fetus in a pregnant female.
    Type: Grant
    Filed: March 9, 2021
    Date of Patent: June 28, 2022
    Assignee: The Chinese University of Hong Kong
    Inventors: Yuk-Ming Dennis Lo, Rossa Wai Kwun Chiu, Kwan Chee Chan, Peiyong Jiang, Suk Hang Cheng, Cheuk Yin Yu, Yee Ting Cheung, Wenlei Peng
  • Patent number: 11365408
    Abstract: The disclosure provides DNA library preparation methods that do not require a purification between adapter ligation and PCR amplification. Adaptors are added to DNA fragments to form oligonucleotide extension products and the oligonucleotide extension products are amplified without stopping or interruption for a cleanup step. Excess materials, such as enzymes, adaptors, or co-factors, from the adaptor addition step do not interfere with the amplification step and the amplification step proceeds without regards to the presence of reagents from the ligation step. In preferred embodiments, the ligation and amplification step make use of a common priming sequence e.g., in the form of one of the adaptor oligos.
    Type: Grant
    Filed: February 6, 2019
    Date of Patent: June 21, 2022
    Assignee: NUGEN TECHNOLOGIES, INC.
    Inventors: Bin Li, Benjamin G. Schroeder, Manqing Hong, Maureen Peterson
  • Patent number: 11359239
    Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing.
    Type: Grant
    Filed: May 7, 2021
    Date of Patent: June 14, 2022
    Assignee: 10X GENOMICS, INC.
    Inventors: Benjamin Hindson, Kevin Ness, Serge Saxonov, Paul Hardenbol
  • Patent number: 11359248
    Abstract: Disclosed herein are methods for use in detection of single nucleotide variants (SNVs) or indels. The methods may comprise enriching cell-free DNA molecules for a panel of genomic regions and deep sequencing the enriched cfDNA to detect the SNVs or indels.
    Type: Grant
    Filed: October 21, 2021
    Date of Patent: June 14, 2022
    Assignee: GUARDANT HEALTH, INC.
    Inventors: Stefanie Ann Ward Mortimer, Amirali Talasaz, Darya Chudova, Helmy Eltoukhy
  • Patent number: 11345968
    Abstract: Disclosed herein are methods for use in detection of molecular residual disease. The methods may comprise deep sequencing a panel of genomic regions in cell-free DNA molecules and computer processing sequence reads to detect variants that are indicative of molecular residual disease.
    Type: Grant
    Filed: July 2, 2021
    Date of Patent: May 31, 2022
    Assignee: GUARDANT HEALTH, INC.
    Inventors: Stefanie Ann Ward Mortimer, AmirAli Talasaz, Darya Chudova, Helmy Eltoukhy
  • Patent number: 11332787
    Abstract: The present invention provides methods, compositions, and systems for distributing molecules and complexes into reaction sites. In particular, the methods, compositions, and systems of the present invention result in loading of polymerase enzyme complexes into a predetermined number of reaction sites, including nanoscale wells.
    Type: Grant
    Filed: June 28, 2019
    Date of Patent: May 17, 2022
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Jaime Juan Benitez-Marzan, Natasha Popovich, Lei Sun