Patents Examined by Steven W. Bailey
  • Patent number: 12367978
    Abstract: Computer implemented methods and computer systems are provided for estimating cancer cell fractions indicating proportions of cancer cells carrying one or more mutations of interest using one or more nucleic acid samples from a subject. The methods and systems provided herein implement processes that use a variational Bayesian mixture model to cluster initial cancer cell fractions and obtain the one or more final cancer cell fractions, the initial cancer cell fractions accounting for cancer purity and copy numbers. The disclosed methods and systems improve accuracy, validity, and reliability of tests for cancer clonality, and save time, materials, cost, and computer resources required for the tests, which can help design more affective cancer treatments.
    Type: Grant
    Filed: December 3, 2018
    Date of Patent: July 22, 2025
    Assignee: Illumina, Inc.
    Inventors: Vitor Ferreira Onuchic, Kristina M. Kruglyak
  • Patent number: 12210022
    Abstract: The present invention relates to a method of diagnosing over active bladder disorder (OAB), the method comprising: measuring the concentrations of adenosine triphosphate (ATP), acetylcholine (ACh), nitrite, monocyte chemoattractant protein 1 (MCP-1) and interleukin 5 (IL-5) in a sample obtained from a subject; normalising the concentrations to the concentration of creatinine (Cr) in the sample; range standardising the normalised concentrations and subject's age to the following values: Age to 120 years old; ATP/Cr to 0.000001 mole/mg×dl?1; ACh/Cr to 0.1 mole/mg×dl?1; Nitrite to 200 nM/mg×dl?1; MCP-1/Cr to 100 pg×ml?1/mg×dl?1; IL-5/Cr 100 pg×ml-mg×dl?1; applying the normalised and range standardised concentrations to the following formula: Logit (p)=?1.738±1.404±4.985±2.914×subject's age+3315.959±5435.254×[ATP]/[Cr]+(?25204.194±20268.337)×[ACh]/[Cr]+26.799±32.967×[nitrite]/[Cr]+6.755±25.132 [MCP-1]/[Cr]+(?61.838±148.
    Type: Grant
    Filed: February 18, 2019
    Date of Patent: January 28, 2025
    Assignee: UNIVERSITY OF PORTSMOUTH HIGHER EDUCATION CORPORATION
    Inventors: John S. Young, Sepinoud Firouzmand
  • Patent number: 12200042
    Abstract: A command center includes at least one network communications interface configured for two-way communications with a plurality of sites remote from the command center and at least one display screen and user interface. Each of the plurality of sites includes at least one forensic field test device configured to identify individuals using DNA samples from the individuals. The display screen and user interface are configured to depict aspects of forensic field test devices of the plurality of sites, wherein the aspects include a site identifier for each of the forensic field test devices and one or more additional aspects.
    Type: Grant
    Filed: September 30, 2020
    Date of Patent: January 14, 2025
    Inventors: Robert A. Schueren, David King, Chungsoo Charles Park, Arnaldo Barican, Charles David Troup
  • Patent number: 12157916
    Abstract: The present disclosure provides methods of identifying unreliable biological samples that may be mislabeled or contaminated, by determining the heteroplasmy and homoplasmy of mitochondrial DNA present in the biological samples.
    Type: Grant
    Filed: August 6, 2021
    Date of Patent: December 3, 2024
    Assignee: Regeneron Pharmaceuticals, Inc.
    Inventors: Ruoyu Zhang, Wei Keat Lim, Gurinder Atwal
  • Patent number: 12077818
    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: April 7, 2023
    Date of Patent: September 3, 2024
    Assignee: Life Technologies Corporation
    Inventors: Earl Hubbell, Christian Koller, Nils Homer
  • Patent number: 12057195
    Abstract: A method for prioritizing sequencing of nucleic acid molecules from two or more sources, comprising: (i) ligating one or more ends of each of a plurality of nucleic acid molecules to an adapter, wherein the adaptor is unique to each source and comprises a unique identifier nucleic acid sequence; (ii) pooling the nucleic acid molecules from each of the two or more sources; (iii) sequencing a plurality of nucleotides of an identifier nucleic acid sequence of an adapter; (iv) determining in real-time from which of the two or more sources the nucleic acid molecule being sequenced came; (v) determining, from a prioritization rule set and based on the determined source, a sequencing priority for the nucleic acid molecule; and (vi) allowing the sequencing process to proceed, or modifying the sequencing process, based on the determined sequencing priority.
    Type: Grant
    Filed: April 16, 2018
    Date of Patent: August 6, 2024
    Assignee: KONINKLIJKE PHILIPS N.V.
    Inventor: Brian David Gross
  • Patent number: 12031181
    Abstract: Provided herein are systems and methods for quantitating the HLA diversity in a solid tissue or circulating tumor DNA sample that is predictive of a patient's responsiveness to immune checkpoint inhibitory therapies.
    Type: Grant
    Filed: April 2, 2020
    Date of Patent: July 9, 2024
    Assignee: ILLUMINA, INC.
    Inventors: Bochao Zhang, Shile Zhang
  • Patent number: 12002551
    Abstract: The present invention discloses a method of constructing a pharmacophore to determine whether a molecule is a peroxisome proliferator-activated receptor ? full agonist, partial agonist or antagonist in terms of a binding energy or a free energy surface comprising: providing a protein receptor mimicking said peroxisome proliferator-activated receptor ? and a corresponding ligand; docking the corresponding ligand and the protein receptor to form a docked conformation; performing at least two rounds of molecular dynamic simulation to obtain at least one trajectory and at least one free energy surface; inputting the trajectory to construct at least one pharmacophore and obtaining the binding energy of the corresponding ligand; comparing the molecule with the corresponding ligand in terms of the binding energy thereof to the protein receptor in order to determine whether the molecule is the peroxisome proliferator-activated receptor ? full agonist, partial agonist or antagonist.
    Type: Grant
    Filed: March 12, 2020
    Date of Patent: June 4, 2024
    Assignee: Nanjing University
    Inventors: Hongling Liu, Laihao Shi
  • Patent number: 11959128
    Abstract: The present invention relates to the field of noninvasive prenatal gene testing by high-through sequencing technologies. Particularly, the present application relates to a method for determining the content of cell-free fetal DNA in maternal peripheral blood.
    Type: Grant
    Filed: March 15, 2017
    Date of Patent: April 16, 2024
    Assignee: BERRY GENOMICS CO., LTD.
    Inventors: Xiaojie Zhang, Tao Cheng, Xiangbin Chen, Jianguang Zhang
  • Patent number: 11935625
    Abstract: A computer-implemented method for processing and/or analyzing nucleic acid sequencing data comprises receiving a first data input and a second data input. The first data input comprises untargeted sequencing data generated from a first nucleic acid sample obtained from a subject. The second data input comprises target-specific sequencing data generated from a second nucleic acid sample obtained from the subject. Next, with the aid of a computer processor, the first data input and the second data input are combined to produce a combined data set. Next, an output derived from the combined data set is generated. The output is indicative of the presence or absence of one or more polymorphisms of the first nucleic acid sample and/or the second nucleic acid sample.
    Type: Grant
    Filed: November 19, 2020
    Date of Patent: March 19, 2024
    Assignee: PERSONALIS, INC.
    Inventors: Jason Harris, Mark R. Pratt, John West, Richard Chen, Ming Li
  • Patent number: 11929145
    Abstract: Technology provided herein relates in part to methods, processes, machines and apparatuses for non-invasive assessment of genetic alterations. In particular, a method is provided for that includes obtaining a set of sequence reads. The sequence reads each include a single molecule barcode (SMB) sequence that is a non-random oligonucleotide sequence. The method further includes assigning the sequence reads to read groups according to a read group signature. The read group signature comprises an SMB sequence and a start and end position of a nucleic acid fragment from the circulating cell free sample nucleic acid. The sequence reads comprising start and end positions and an SMB sequence similar to the read group signature are assigned to a read group. The method further includes generating a consensus for each read group, and determining the presence or absence of a genetic alteration based on the consensus for each read group.
    Type: Grant
    Filed: January 22, 2018
    Date of Patent: March 12, 2024
    Assignee: SEQUENOM, INC
    Inventors: Mostafa Azab, Michael Sykes, Youting Sun, Amin Mazloom, Taylor Jensen, Mathias Ehrich, Christopher Ellison
  • Patent number: 11928614
    Abstract: Methods, systems and compositions that allow for treating a patient according to a patient customized therapeutic regimen are provided. Embodiments of the invention include obtaining dosage administration information from a patient and using the same to tailor a therapeutic regimen for the patient. Embodiments of the invention further include preparing and forwarding to the patient physical pharmaceutical dosages based on the customized therapeutic regimen.
    Type: Grant
    Filed: September 28, 2017
    Date of Patent: March 12, 2024
    Assignee: OTSUKA PHARMACEUTICAL CO., LTD.
    Inventors: Mark J. Zdeblick, Andrew Thompson, George M. Savage
  • Patent number: 11923046
    Abstract: Disclosed herein are methods, systems, and apparatus for detecting microamplifications or microdeletions in the genome of a fetus. In some embodiments, the method comprises receiving sequence tags for each of a plurality of DNA fragments in a biological sample; determining genomic positions for the sequence tags; determining whether the density of DNA in each of a plurality of genomic regions is aberrantly high or low; identifying as a microamplification a set of consecutive genomic regions having aberrantly high density; and identifying as a microdeletion a set of consecutive genomic regions having aberrantly low density. The biological sample may be a blood sample obtained noninvasively from a female subject pregnant with the fetus.
    Type: Grant
    Filed: February 7, 2020
    Date of Patent: March 5, 2024
    Assignee: The Chinese University of Hong Kong
    Inventors: Yuk Ming Dennis Lo, Kwan Chee Chan, Peiyong Jiang, Cheuk Yin Jandy Yu, Rossa Wai Kwun Chiu
  • 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: 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: 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: 11783914
    Abstract: Embodiments of a system and method for characterizing a panel of conditions associated with a set of taxa related to microorganisms can include a taxonomic database including reference microbiome features for the set of taxa associated with the panel of conditions; a handling operable to collect a container including biological material from a user, the handling system comprising a sequencer system operable to determine a microorganism sequence dataset; and a panel characterization system operable to: determine user microbiome features for the set of taxa for the user based on the microorganism sequence dataset, generate a comparison between the user microbiome features and the reference microbiome features, and determine a panel characterization for the panel of conditions for the user based on the comparison; and a treatment system operable to promote a therapy for a condition of the panel of conditions based on the panel characterization.
    Type: Grant
    Filed: September 18, 2017
    Date of Patent: October 10, 2023
    Assignee: PSOMAGEN, INC.
    Inventors: Zachary Apte, Jessica Richman, Daniel Almonacid, Laurens Kraal, Francisco Ossandon, Juan Pablo Cardenas, Elisabeth Bik, Audrey Goddard
  • 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