Patents Examined by John S. Brusca
  • 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
  • Patent number: 11538557
    Abstract: Systems, methods, and analytical approaches for short read sequence assembly and for the detection of insertions and deletions (indels) in a reference genome. A method suitable for software implementation is presented in which indels may be readily identified in a computationally efficient manner.
    Type: Grant
    Filed: April 30, 2018
    Date of Patent: December 27, 2022
    Assignee: Applied Biosystems, LLC
    Inventor: Zheng Zhang
  • Patent number: 11538555
    Abstract: The technology disclosed relates to determining pathogenicity of nucleotide variants. In particular, the technology disclosed relates to specifying a particular amino acid at a particular position in a protein as a gap amino acid, and specifying remaining amino acids at remaining positions in the protein as non-gap amino acids. The technology disclosed further relates to generating a gapped spatial representation of the protein that includes spatial configurations of the non-gap amino acids, and excludes a spatial configuration of the gap amino acid, and determining a pathogenicity of a nucleotide variant based at least in part on the gapped spatial representation, and a representation of an alternate amino acid created by the nucleotide variant at the particular position.
    Type: Grant
    Filed: November 22, 2021
    Date of Patent: December 27, 2022
    Assignees: Illumina, Inc., Illumina Cambridge Limited
    Inventors: Tobias Hamp, Hong Gao, Kai-How Farh
  • Patent number: 11530454
    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: May 6, 2022
    Date of Patent: December 20, 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: 11515006
    Abstract: Embodiments are directed to systems and methods for pathogen detection using next-generation sequencing (NGS) analysis of a sample. Embodiments may apply alignment algorithms (e.g., SNAP and/or RAPSearch alignment algorithms) to align individual sequence reads from a sample in a next-generation sequencing (NGS) dataset against reference genome entries in a classified reference genome database. Embodiments of the present invention may include classifying, filtering, and displaying results to a clinician that can then quickly and easily obtain the results of the sequencing to identify a pathogen or other genetic material in a sample that is being tested. A negative sample and a corresponding database can be used to remove contaminants from a list of candidate pathogens. Thus, embodiments are directed to a system that is configured to filter the results of a sequencing alignment and classify a sample quickly.
    Type: Grant
    Filed: March 9, 2018
    Date of Patent: November 29, 2022
    Assignee: The Regents of the University of California
    Inventors: Charles Chiu, Samia Naccache, Scot Federman, Doug Stryke, Steve Miller, Erik Samayoa
  • Patent number: 11501851
    Abstract: The present disclosure provides methods of estimating a degree of ancestral relatedness between individuals. In an aspect, a method comprises receiving haplotype data comprising genetic markers shared among a population of individuals; dividing the haplotype data into segments based on the genetic markers; for each of the population of test individuals: (i) based on the genetic markers, matching segments of the haplotype data that are identical-by-descent between two individuals, (ii) for each of the matched segments: dividing the matched segment into discrete genomic intervals, scoring each of the discrete genomic intervals based on a degree of matching within or between the individuals, correcting the scores for consistency, and (iii) calculating a weighted sum over the discrete genomic intervals of the matched segment, based on the corrected scores and assigned weights; and (d) estimating the degree of ancestral relatedness between the individuals based on the weighted sums of the matched segments.
    Type: Grant
    Filed: January 6, 2022
    Date of Patent: November 15, 2022
    Assignee: Embark Veterinary, Inc.
    Inventors: Aaron J. Sams, Samuel H. Vohr, Adam S. Gardner, Matt Barton, Ryan Boyko, Adam R. Boyko
  • Patent number: 11492659
    Abstract: Provided herein are methods for determining fetal ploidy according to nucleic acid sequence reads. Nucleic acid sequence reads may be obtained from test sample nucleic acid comprising circulating cell-free nucleic acid from the blood of a pregnant female bearing a fetus. Fetal ploidy may be determined according to genomic section levels and a fraction of fetal nucleic acid in a test sample.
    Type: Grant
    Filed: December 10, 2018
    Date of Patent: November 8, 2022
    Assignee: Sequenom, Inc.
    Inventors: Cosmin Deciu, Zeljko Dzakula, John Allen Tynan, Grant Hogg
  • Patent number: 11474070
    Abstract: A method for nucleic acid sequencing includes receiving a plurality of observed or measured signals indicative of a parameter observed or measured for a plurality of defined spaces; determining, for at least some of the defined spaces, whether the defined space comprises one or more sample nucleic acids; processing, for at least some of the defined spaces, the observed or measured signal to improve a quality of the observed or measured signal; generating, for at least some of the defined spaces, a set of candidate sequences of bases for the defined space using one or more metrics adapted to associate a score or penalty to the candidate sequences of bases; and selecting the candidate sequence leading to a highest score or a lowest penalty as corresponding to the correct sequence for the one or more sample nucleic acids in the defined space.
    Type: Grant
    Filed: November 20, 2018
    Date of Patent: October 18, 2022
    Assignee: Life Technologies Corporation
    Inventors: Marcin Sikora, Melville Davey, Christian Koller, Simon Cawley, Alan Williams, David Kulp
  • Patent number: 11464430
    Abstract: Methods and devices to detect analyte in body fluid are provided. Embodiments include processing sampled data from analyte sensor, determining a single, fixed, normal sensitivity value associated with the analyte sensor, estimating a windowed offset value associated with the analyte sensor for each available sampled data cluster, computing a time varying offset based on the estimated windowed offset value, and applying the time varying offset and the determined normal sensitivity value to the processed sampled data to estimate an analyte level for the sensor.
    Type: Grant
    Filed: September 28, 2018
    Date of Patent: October 11, 2022
    Assignee: Abbott Diabetes Care Inc.
    Inventor: Erwin Satrya Budiman
  • Patent number: 11459616
    Abstract: Methods are provided to improve the positive predictive value for cancer detection using cell-free nucleic acid samples. Various embodiments are directed to applications (e.g., diagnostic applications) of the analysis of the fragmentation patterns and size of cell-free DNA, e.g., plasma DNA and serum DNA, including nucleic acids from pathogens, including viruses. Embodiments of one application can determine if a subject has a particular condition. For example, a method of present disclosure can determine if a subject has cancer or a tumor, or other pathology. Embodiments of another application can be used to assess the stage of a condition, or the progression of a condition over time. For example, a method of the present disclosure may be used to determine a stage of cancer in a subject, or the progression of cancer in a subject over time (e.g., using samples obtained from a subject at different times).
    Type: Grant
    Filed: October 25, 2017
    Date of Patent: October 4, 2022
    Assignees: The Chinese University of Hong Kong, GRAIL, Inc.
    Inventors: Eugeni Namsaraev, Yuk-Ming Dennis Lo, Rossa Wai Kwun Chiu, Kwan Chee Chan, Peiyong Jiang, Kun Sun, Wai Kei Lam
  • Patent number: 11456058
    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: May 17, 2022
    Date of Patent: September 27, 2022
    Assignee: Personalis, Inc.
    Inventors: Jason Harris, Mark R. Pratt, John West, Richard Chen, Ming Li
  • Patent number: 11453912
    Abstract: A method of estimating a parameter related to sequencing of a sample nucleic acid template includes: receiving signal data relating to nucleotide incorporation events resulting from a series of flows of nucleotides onto an array of wells including (i) a first well containing the sample nucleic acid template and (ii) a plurality of other sample-containing wells; determining sequence information for the sample nucleic acid template using signal data from the first well; and constructing a phase-state model for a set of nucleotide flows that contributed at least in part to the sequence information, wherein the model includes a signal correction parameter that is determined using signal data from the plurality of other sample-containing wells.
    Type: Grant
    Filed: March 26, 2019
    Date of Patent: September 27, 2022
    Assignee: Life Technologies Corporation
    Inventors: Melville Davey, Michael Meyer, Marcin Sikora, Simon Cawley, Kirk Pastorian
  • Patent number: 11447833
    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: November 16, 2021
    Date of Patent: September 20, 2022
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: David M. Kurtz, Maximilian Diehn, Arash Ash Alizadeh
  • Patent number: 11450412
    Abstract: A system for smart pooling includes a computing device configured to obtain a feature datum, identify a predictive prevalence value as a function of the feature datum, wherein identifying the predictive prevalence value further comprises receiving a predictive training set correlating the feature datum with a probabilistic outcome, training a predictive machine-learning model as a function of the predictive training set, and identifying the predictive prevalence value as a function of the trained predictive machine-learning model and the feature datum, and determine an enhanced well count, wherein determining the enhanced well count further comprises generating a pooling threshold, and determining the enhanced well count as a function of the pooling threshold and the predictive prevalence value.
    Type: Grant
    Filed: July 30, 2021
    Date of Patent: September 20, 2022
    Assignee: Specialty Diagnostic (SDI) Laboratories, Inc.
    Inventors: Ozman Mohiuddin, William Henry Haase, Yashashree Shende, Sumi Thomas
  • Patent number: 11441185
    Abstract: The present invention provides assay systems and methods for determining the percent fetal contribution of cell-free DNA in a maternal sample from a pregnant female with an egg donor pregnancy. Further provided, are assay systems and methods for determining a statistical likelihood of the presence or absence of a fetal aneuploidy in a maternal sample using a determined percent fetal cell-free DNA in the sample.
    Type: Grant
    Filed: October 24, 2018
    Date of Patent: September 13, 2022
    Assignee: Roche Molecular Systems, Inc.
    Inventors: Arnold Oliphant, Eric Wang, Craig Struble
  • Patent number: 11430541
    Abstract: Disclosed are methods for determining copy number variation (CNV) known or suspected to be associated with a variety of medical conditions. In some embodiments, methods are provided for determining copy number variation of fetuses using maternal samples comprising maternal and fetal cell free DNA. In some embodiments, methods are provided for determining CNVs known or suspected to be associated with a variety of medical conditions. Some embodiments disclosed herein provide methods to improve the sensitivity and/or specificity of sequence data analysis by deriving a fragment size parameter. In some implementations, information from fragments of different sizes are used to evaluate copy number variations. In some implementations, one or more t-statistics obtained from coverage information of the sequence of interest is used to evaluate copy number variations. In some implementations, one or more fetal fraction estimates are combined with one or more t-statistics to determine copy number variations.
    Type: Grant
    Filed: August 31, 2018
    Date of Patent: August 30, 2022
    Assignee: Verinata Health, Inc.
    Inventors: Sven Duenwald, David A. Comstock, Catalin Barbacioru, Darya I. Chudova, Richard P. Rava, Keith W. Jones, Gengxin Chen, Dimitri Skvortsov
  • Patent number: 11421015
    Abstract: A system for selecting an immunogenic peptide composition comprising a processor and a memory storing processor-executable instructions that, when executed by the processor, cause the processor to create a first peptide set by selecting a plurality of base peptides, wherein at least one peptide of the plurality of base peptides is associated with a disease, create a second peptide set by adding to the first peptide set a modified peptide, wherein the modified peptide comprises a substitution of at least one residue of a base peptide selected from the plurality of base peptides, and create a third peptide set by selecting a subset of the second peptide set, wherein the selected subset of the second peptide set has a predicted vaccine performance, wherein the predicted vaccine performance has a population coverage above a predetermined threshold, and wherein the subset comprises at least one peptide of the second peptide set.
    Type: Grant
    Filed: July 30, 2021
    Date of Patent: August 23, 2022
    Assignee: Think Therapeutics, Inc.
    Inventors: David Gifford, Brandon Carter
  • Patent number: 11401556
    Abstract: A prognostic method, and a kit, for determining the risk of relapse of renal cancer of the clear cell renal carcinoma type, stages I and II, in a human subject; comprised of: (a) determining, in a tumor sample (biopsy) from the human subject, the levels of expression of the microRNAs hsa-miR-223, hsa-miR-103, hsa-miR-107, hsa-miR-425, hsa-miR-340, hsa-miR-130b, hsa-miR-652, hsa-miR-214, and hsa-miR-204; (b) determining a value which depends on the levels of expression of the microRNAs; and (c) determining the risk of relapse in renal cancer of the clear cell renal carcinoma type, in stages I and II, in the said human subject, by comparing the value obtained in step (b) with a cut-off value.
    Type: Grant
    Filed: September 23, 2016
    Date of Patent: August 2, 2022
    Assignees: FUNDACIÔN PARA LA INVESTIGACIÔN BIOMEDICA DEL HOSPITAL 12 DE OCTUBRE, FUNDACION PARA LA INVESTIGACION BIOMEDICA DEL HOSPITAL UNIVERSITARIO LA PAZ (FIBHULP)
    Inventors: Natalia Miranda Utrera, Felipe Villacampa Aubá, Daniel Castellano, Juan Angel Fresno Vara, Angelo Gámez Pozo