Patents Examined by John S. Brusca
  • Patent number: 11892945
    Abstract: A method for storage of an item of information (210) is disclosed. The method comprises encoding bytes (720) in the item of information (210), and representing using a schema the encoded bytes by a DNA nucleotide to produce a DNA sequence (230). The DNA sequence (230) is broken into a plurality of overlapping DNA segments (240) and indexing information (250) added to the plurality of DNA segments. Finally, the plurality of DNA segments (240) is synthesized (790) and stored (795).
    Type: Grant
    Filed: October 29, 2021
    Date of Patent: February 6, 2024
    Assignee: EUROPEAN MOLECULAR BIOLOGY LABORATORY
    Inventors: Nick Goldman, John Birney
  • Patent number: 11875899
    Abstract: The invention provides a method for determining copy number variations (CNV) of a sequence of interest in a test sample that comprises a mixture of nucleic acids that are known or are suspected to differ in the amount of one or more sequence of interest. The method comprises a statistical approach that accounts for accrued variability stemming from process-related, interchromosomal and inter-sequencing variability. The method is applicable to determining CNV of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions. CNV that can be determined according to the method include trisomies and monosomies of any one or more of chromosomes 1-22, X and Y, other chromosomal polysomies, and deletions and/or duplications of segments of any one or more of the chromosomes, which can be detected by sequencing only once the nucleic acids of a test sample.
    Type: Grant
    Filed: September 18, 2019
    Date of Patent: January 16, 2024
    Assignee: Verinata Health, Inc.
    Inventors: Richard P. Rava, Brian K. Rhees
  • Patent number: 11854669
    Abstract: The present invention relates to method for storing and transmitting information by employing a nucleic acid construct. The nucleic acid construct can include a lock region; a translation key region that corresponds to the identity of a key; and a message region including a nucleic sequence that corresponds to an encrypted message.
    Type: Grant
    Filed: July 16, 2019
    Date of Patent: December 26, 2023
    Assignee: National Technology & Engineering Solutions of Sandia, LLC
    Inventors: George Bachand, Marlene Bachand, Andrew Gomez
  • Patent number: 11837325
    Abstract: Provided is a method for identifying balanced translocation breakpoints and a carrying state for balanced translocations in embryos, comprising the following steps: amplifying and sequencing a sample; comparing the sequence which is obtained by means of sequencing with a reference genome and analyzing copy numbers; accurately determining the position of a translocation breakpoint; detecting single nucleotide polymorphisms (SNPs) around the breakpoint and genotyping the SNPs; analyzing an embryonic haplotype, and comprehensively determining a normal chromosome and a translocation chromosome haplotype; determining the embryonic carrying state and, according to the haplotype, selecting an embryo which does not carry a balanced translocation.
    Type: Grant
    Filed: March 2, 2018
    Date of Patent: December 5, 2023
    Assignee: YIKON GENOMICS (SHANGHAI) CO., LTD
    Inventors: Shiping Bo, Zhen Zhang, Jun Ren, Yumei Gao, Sijia Lu
  • Patent number: 11833164
    Abstract: Provided are methods of treating a patient diagnosed with Fabry disease and methods of enhancing ?-galactosidase A in a patient diagnosed with or suspected of having Fabry disease. Certain methods comprise administering to a patient a therapeutically effective dose of a pharmacological chaperone for ?-galactosidase A, wherein the patient has a mutation in the nucleic acid sequence encoding ?-galactosidase A. Also described are uses of pharmacological chaperones for the treatment of Fabry disease and compositions for use in the treatment of Fabry disease.
    Type: Grant
    Filed: August 7, 2020
    Date of Patent: December 5, 2023
    Assignee: Amicus Therapeutics, Inc.
    Inventors: Elfrida Benjamin, Xiaoyang Wu
  • Patent number: 11789906
    Abstract: Method and systems for preparing and analyzing a DNA sample from a subject are provided herein. Also provided are methods and systems for obtaining, analyzing, and manipulating genomic and proteomic sequence data. In particular, methods and systems provided herein involve transformation of raw genetic or proteomic sequence into a compressed data set and transmission of the compressed data set using a fixed binary encoding scheme capable of compressing the data by up to 75%. An interface is in communication with the compression module and configured to display transmitted genomic and proteomic sequence data.
    Type: Grant
    Filed: November 19, 2015
    Date of Patent: October 17, 2023
    Assignee: ARC BIO, LLC
    Inventors: Roberto Olivares-Amaya, David Andrew Sinclair, Alejandro Quiroz-Zarate, Thomas J. Watson, Jr.
  • Patent number: 11769597
    Abstract: Disclosed herein are methods and compositions for associating a genetic variant with intraretinal fluid. Also disclosed herein are methods and compositions for associating a genetic variant with visual acuity, anatomic outcomes or treatment frequency.
    Type: Grant
    Filed: June 1, 2018
    Date of Patent: September 26, 2023
    Assignee: Regeneron Pharmaceuticals, Inc.
    Inventors: Lorah Perlee, Sara Hamon, Charles Paulding
  • Patent number: 11697846
    Abstract: The invention provides a method for determining copy number variations (CNV) of a sequence of interest in a test sample that comprises a mixture of nucleic acids that are known or are suspected to differ in the amount of one or more sequence of interest. The method comprises a statistical approach that accounts for accrued variability stemming from process-related, interchromosomal and inter-sequencing variability. The method is applicable to determining CNV of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions. CNV that can be determined according to the method include trisomies and monosomies of any one or more of chromosomes 1-22, X and Y, other chromosomal polysomies, and deletions and/or duplications of segments of any one or more of the chromosomes, which can be detected by sequencing only once the nucleic acids of a test sample.
    Type: Grant
    Filed: July 26, 2019
    Date of Patent: July 11, 2023
    Assignee: Verinata Health, Inc.
    Inventors: Richard P. Rava, Brian K. Rhees
  • Patent number: 11694768
    Abstract: Technology provided herein relates in part to non-invasive classification of one or more genetic copy number variations (CNVs) for a test sample. Technology provided herein is useful for classifying a genetic CNV for a sample as part of non-invasive pre-natal (NIPT) testing and oncology testing, for example.
    Type: Grant
    Filed: January 24, 2018
    Date of Patent: July 4, 2023
    Inventors: John A. Tynan, Amin Mazloom, Yijin Wu, Mark Whidden, Mathias Ehrich
  • Patent number: 11667965
    Abstract: The invention relates to assembly of sequence reads. The invention provides a method for identifying a mutation in a nucleic acid involving sequencing nucleic acid to generate a plurality of sequence reads. Reads are assembled to form a contig, which is aligned to a reference. Individual reads are aligned to the contig. Mutations are identified based on the alignments to the reference and to the contig.
    Type: Grant
    Filed: February 13, 2020
    Date of Patent: June 6, 2023
    Assignee: Invitae Corporation
    Inventors: Gregory Porreca, Caleb Kennedy
  • Patent number: 11657900
    Abstract: Methods for estimating genomic copy number and loss of heterozygosity using Hidden Markov Model based estimation are disclosed.
    Type: Grant
    Filed: January 10, 2019
    Date of Patent: May 23, 2023
    Assignee: AFFYMETRIX, INC.
    Inventor: Srinka Ghosh
  • Patent number: 11655500
    Abstract: A method for sequencing a nucleic acid template includes: (a) performing a first sequencing process including flowing nucleotides and/or reagents to the nucleic acid template according to a first predetermined ordering of nucleotides and/or reagents to obtain a first sequencing result; (b) after the first sequencing process, performing a second sequencing process including flowing nucleotides and/or reagents to the nucleic acid template according to a second predetermined ordering of nucleotides and/or reagents to obtain a second sequencing result, the second predetermined ordering of nucleotides and/or reagents being different from the first predetermined ordering of nucleotides and/or reagents and at least one of the first and second predetermined orderings of nucleotides and/or reagents being designed for repeat sequencing; and (c) determining a sequence of bases corresponding to at least a portion of the nucleic acid template using both the first sequencing result and the second sequencing result.
    Type: Grant
    Filed: June 3, 2019
    Date of Patent: May 23, 2023
    Assignee: Life Technologies Corporation
    Inventors: Earl Hubbell, Christian Koller, Nils Homer
  • Patent number: 11634779
    Abstract: Processes and materials to detect cancer from a biopsy are described. In some cases, cell-free nucleic acids can be sequenced, and the sequencing result can be utilized to detect sequences derived from a neoplasm. Detection of somatic variants occurring in phase can indicate the presence of cancer in a diagnostic scan and a clinical intervention can be performed.
    Type: Grant
    Filed: May 2, 2022
    Date of Patent: April 25, 2023
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: David M. Kurtz, Maximilian Diehn, Arash Ash Alizadeh
  • Patent number: 11636919
    Abstract: A method for evaluating variant likelihood includes: providing a plurality of template polynucleotide strands, sequencing primers, and polymerase in a plurality of defined spaces disposed on a sensor array; exposing the plurality of template polynucleotide strands, sequencing primers, and polymerase to a series of flows of nucleotide species according to a predetermined order; obtaining measured values corresponding to an ensemble of sequencing reads for at least some of the template polynucleotide strands in at least one of the defined spaces; and evaluating a likelihood that a variant sequence is present given the measured values corresponding to the ensemble of sequencing reads, the evaluating comprising: determining a measurement confidence value for each read in the ensemble of sequencing reads and modifying at least some model-predicted values using a first bias for forward strands and a second bias for reverse strands.
    Type: Grant
    Filed: May 9, 2018
    Date of Patent: April 25, 2023
    Assignee: LIFE TECHNOLOGIES CORPORATION
    Inventors: Earl Hubbell, Sowmi Utiramerur
  • Patent number: 11636920
    Abstract: We describe systems and methods for generating and training convolutional neural networks using biological sequences and relevance scores derived from structural, biochemical, population and evolutionary data. The convolutional neural networks take as input biological sequences and additional information and output molecular phenotypes. Biological sequences may include DNA, RNA and protein sequences. Molecular phenotypes may include protein-DNA interactions, protein-RNA interactions, protein-protein interactions, splicing patterns, polyadenylation patterns, and microRNA-RNA interactions, which may be described using numerical, categorical or ordinal attributes. Intermediate layers of the convolutional neural networks are weighted using relevance score sequences, for example, conservation tracks.
    Type: Grant
    Filed: December 21, 2018
    Date of Patent: April 25, 2023
    Assignee: Deep Genomics Incorporated
    Inventors: Hui Yuan Xiong, Brendan Frey
  • Patent number: 11587642
    Abstract: Techniques for determining one or more cell composition percentages from expression data. The techniques include obtaining expression data for a biological sample, the biological sample previously obtained from a subject, the expression data including first expression data associated with a first set of genes associated with a first cell type; determining a first cell composition percentage for the first cell type using the expression data and one or more non-linear regression models including a first non-linear regression model, wherein the first cell composition percentage indicates an estimated percentage of cells of the first cell type in the biological sample, wherein determining the first cell composition percentage for the first cell type comprises: processing the first expression data with the first non-linear regression model to determine the first cell composition percentage for the first cell type; and outputting the first cell composition percentage.
    Type: Grant
    Filed: March 29, 2022
    Date of Patent: February 21, 2023
    Assignee: BostonGene Corporation
    Inventors: Aleksandr Zaitsev, Maksim Chelushkin, Ilya Cheremushkin, Ekaterina Nuzhdina, Vladimir Zyrin, Daniiar Dyikanov, Alexander Bagaev, Ravshan Ataullakhanov, Boris Shpak
  • Patent number: 11587645
    Abstract: Amino acid sequences of antibodies can be generated using a generative adversarial network that includes a first generating component that generates amino acid sequences of antibody light chains and a second generating component generates amino acid sequences of antibody heavy chains. Amino acid sequences of antibodies can be produced by combining the respective amino acid sequences produced by the first generating component and the second generating component. The training of the first generating component and the second generating component can proceed at different rates. Additionally, the antibody amino acids produced by combining amino acid sequences from the first generating component and the second generating component may be evaluated according to complentarity-determining regions of the antibody amino acid sequences.
    Type: Grant
    Filed: May 19, 2020
    Date of Patent: February 21, 2023
    Assignee: Just-Evotec Biologics, Inc.
    Inventors: Tileli Amimeur, Randal Robert Ketchem, Jeremy Martin Shaver, Rutilio H. Clark, John Alex Taylor
  • Patent number: 11574702
    Abstract: The present disclosure describes methods for determining the functional consequences of mutations. The methods include the use of machine learning to identify and quantify features of all atom molecular dynamics simulations to obtain the disruptive severity of genetic variants on molecular function.
    Type: Grant
    Filed: December 19, 2018
    Date of Patent: February 7, 2023
    Assignee: George Mason University
    Inventors: Mohsin Saleet Jafri, Matthew McCoy
  • Patent number: 11566281
    Abstract: Systems and methods for analyzing overlapping sequence information can obtain first and second overlapping sequence information for a polynucleotide, align the first and second sequence information, determine a degree of agreement between the first and second sequence information for a location along the polynucleotide, and determine a base call and a quality value for the location.
    Type: Grant
    Filed: September 28, 2018
    Date of Patent: January 31, 2023
    Assignee: Life Technologies Corporation
    Inventors: Sowmi Utiramerur, Simon Cawley, Yongming Sun, Fiona Hyland
  • Patent number: 11560586
    Abstract: Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations.
    Type: Grant
    Filed: April 26, 2019
    Date of Patent: January 24, 2023
    Assignee: SEQUENOM, INC.
    Inventors: Cosmin Deciu, Zeljko Jovan Dzakula, Mathias Ehrich, Sung Kyun Kim