Patents Examined by John S. Brusca
  • Patent number: 10349877
    Abstract: Methods and apparatus for providing data processing and control for use in a medical communication system are provided.
    Type: Grant
    Filed: April 3, 2015
    Date of Patent: July 16, 2019
    Assignee: Abbott Diabetes Care inc.
    Inventors: Gary Alan Hayter, Benjamin Jay Feldman
  • Patent number: 10347365
    Abstract: A visualization system comprising a persistent memory, storing a dataset, and a non-persistent memory implements a pattern visualizing method. The dataset contains discrete attribute values for each first entity in a plurality of first entities for each second entity in a plurality of second entities. The dataset is compressed by blocked compression and represents discrete attribute values in both compressed sparse row and column formats. The discrete attribute values are clustered to assign each second entity to a cluster in a plurality of clusters. Differences in the discrete attribute values for the first entity across the second entities of a given cluster relative to the discrete attribute value for the same first entity across the other clusters are computed thereby deriving differential values. A heat map of these differential values for each first entity for each cluster is displayed to reveal the pattern in the dataset.
    Type: Grant
    Filed: February 8, 2018
    Date of Patent: July 9, 2019
    Assignee: 10X GENOMICS, INC.
    Inventors: Alexander Y. Wong, Jeffrey Mellen, Kevin Wu, Paul Ryvkin
  • Patent number: 10336998
    Abstract: The present disclosure provides a HTP microbial genomic engineering platform that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition. The HTP genomic engineering platform described herein is microbial strain host agnostic and therefore can be implemented across taxa. Furthermore, the disclosed platform can be implemented to modulate or improve any microbial host parameter of interest.
    Type: Grant
    Filed: March 16, 2018
    Date of Patent: July 2, 2019
    Assignee: Zymergen Inc.
    Inventors: Zach Serber, Erik Jedediah Dean, Shawn Manchester, Katherine Gora, Michael Flashman, Erin Shellman, Aaron Kimball, Shawn Szyjka, Barbara Frewen, Thomas Treynor, Kenneth S. Bruno
  • Patent number: 10329608
    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: October 8, 2013
    Date of Patent: June 25, 2019
    Assignee: Life Technologies Corporation
    Inventors: Earl Hubbell, Christian Koller, Nils Homer
  • Patent number: 10331849
    Abstract: Techniques for construction of internal controls for improved accuracy and sensitivity of DNA testing include obtaining first data and determining weights over real numbers for a normalization function in less than a day. The first data indicates a measured amount of reference sequences for nucleic acids from training samples. The reference sequences include a target, for which an abundance is indicative of a condition of interest, and covariates not correlated with the condition of interest. The normalization function involves a sum of abundances of the covariates, as internal controls, each multiplied by a corresponding one of the weights. The weights are determined based on minimizing variance of a Taylor expansion of a ratio of a measured amount of the target divided by a value of the normalization function evaluated with measured amounts of the covariates over a portion of the first data in which the condition is absent.
    Type: Grant
    Filed: May 11, 2015
    Date of Patent: June 25, 2019
    Assignee: ECHELON DIAGNOSTICS, INC.
    Inventors: John Burke, Stephen Healy Sanders
  • Patent number: 10323280
    Abstract: The invention encompasses methods for increasing genetic progress in livestock, and for genetic dissemination, including the use of amniocentesis to obtain fetal amniocytes for use in genomic evaluation and cloning.
    Type: Grant
    Filed: October 14, 2016
    Date of Patent: June 18, 2019
    Assignee: Inguran, LLC
    Inventors: Juan F. Moreno, John Dobrinsky, David Kendall, Claas Heuer
  • Patent number: 10323268
    Abstract: Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations.
    Type: Grant
    Filed: May 6, 2016
    Date of Patent: June 18, 2019
    Assignee: Sequenom, Inc.
    Inventors: Cosmin Deciu, Zeljko Jovan Dzakula, Mathias Ehrich, Sung Kyun Kim
  • Patent number: 10318704
    Abstract: Disclosed are methods for determining copy number variation (CNV) known or suspected to be associated with a variety of medical conditions, including syndromes related to CNV of subchromosomal regions. In some embodiments, methods are provided for determining CNV of fetuses using maternal samples comprising maternal and fetal cell free DNA. Some embodiments disclosed herein provide methods to improve the sensitivity and/or specificity of sequence data analysis by removing within-sample GC-content bias. In some embodiments, removal of within-sample GC-content bias is based on sequence data corrected for systematic variation common across unaffected training samples. In some embodiments, syndrome related biases in sample data are also removed to increase signal to noise ratio. Also disclosed are systems for evaluation of CNV of sequences of interest.
    Type: Grant
    Filed: May 29, 2015
    Date of Patent: June 11, 2019
    Assignee: Verinata Health, Inc.
    Inventors: Darya I. Chudova, Diana Abdueva
  • Patent number: 10311967
    Abstract: Various methods, systems, computer readable media, and graphical user interfaces (GUIs) are presented and described that enable a subject, doctor, or user to characterize or classify various types of cancer precisely. Additionally, described herein are methods, systems, computer readable media, and GUIs that enable more effective specification of treatment and improved outcomes for patients with identified types of cancer. Some embodiments of the methods, systems, computer readable media, and GUIs described herein comprise obtaining RNA expression data and/or whole exome sequencing (WES) data for biological samples; determining a respective plurality of molecular-functional (MF) profiles for a plurality of subjects; clustering the plurality of MF profiles to obtain MF profile clusters; determining a molecular-functional (MF) profile for an additional subject; and identifying, from among the MF profile clusters, a particular MF profile cluster with which to associate the MF profile for the subject.
    Type: Grant
    Filed: June 12, 2018
    Date of Patent: June 4, 2019
    Assignee: BostonGene Corporation
    Inventors: Alexander Bagaev, Feliks Frenkel, Nikita Kotlov, Ravshan Ataullakhanov
  • Patent number: 10294518
    Abstract: The invention discloses methods and apparatuses for the detection and diagnostics of genetic alterations/mutations in a target sample, which may be a solid tissue or a bodily fluid. A reference sample is also acquired, and the target and reference samples are replicated into multiple target and reference replicates. The replicates are sequenced, and the sequence data is analyzed based on a statistical test. The statistical test compares the measurements between the target and reference replicates at respective allelic indices. True positive calls are then made based on the results of the statistical testing, and the desired genetic alterations/mutations are identified at the base-pair level. The invention may be used for diagnostics related to cancer, auto-immune disease, organ transplant rejection, genetic fetal abnormalities and pathogens.
    Type: Grant
    Filed: September 16, 2016
    Date of Patent: May 21, 2019
    Assignee: Fluxion Biosciences, Inc.
    Inventors: Nicholas Kamps-Hughes, Cristian Ionescu-Zanetti
  • Patent number: 10275568
    Abstract: Methods and software products for analysis of alternative splicing are disclosed. In general the methods involve normalizing probe set or exon intensity to an expression level measurement of the gene. The methods may be used to identify tissue-specific alternative splicing events.
    Type: Grant
    Filed: March 27, 2012
    Date of Patent: April 30, 2019
    Assignee: Affymetrix, Inc.
    Inventors: Alan Williams, Simon Cawley, John E. Blume, Hui Wang, Tyson Clark
  • Patent number: 10273540
    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: August 15, 2013
    Date of Patent: April 30, 2019
    Assignee: Life Technologies Corporation
    Inventors: Melville Davey, Michael Meyer, Marcin Sikora, Simon Cawley, Kirk Pastorian
  • Patent number: 10267777
    Abstract: Methods are described herein for small molecule biochemical profiling of an individual subject for diagnosis of a disease or disorder, facilitating diagnosis of a disease or disorder, and/or identifying an increased risk of developing a disease or disorder in the individual subject. Aberrant levels of small molecules present in a sample from an individual subject are identified and diagnostic information relevant to the individual subject is obtained based on the identified aberrant levels. The obtained diagnostic information includes one or more of an identification of at least one biochemical pathway associated with the identified subset of the small molecules having aberrant levels, an identification at least one disease or disorder associated with the identified subset of the small molecules having aberrant levels, and an identification of at least one recommended follow up test associated with the identified subset of the small molecules having aberrant levels.
    Type: Grant
    Filed: October 7, 2016
    Date of Patent: April 23, 2019
    Assignee: Metabolon, Inc.
    Inventors: Michael V. Milburn, John A. Ryals, Lining Guo, Andrea Eckhart, Jacob Wulff, Adam D. Kennedy, Thomas J. Jönsson, Ryan Douglas Michalek, Bryan Wittmann, Matthew Mitchell
  • Patent number: 10229244
    Abstract: Methods for estimating genomic copy number and loss of heterozygosity using Hidden Markov Model based estimation are disclosed.
    Type: Grant
    Filed: June 20, 2008
    Date of Patent: March 12, 2019
    Assignee: Affymetrix, Inc.
    Inventor: Srinka Ghosh
  • Patent number: 10215743
    Abstract: Methods, system and device are provided for detection and quantitative and qualitative analysis of components in a gaseous mixture distinguished by high selectivity and high resolution. The influence of individual gases may be distinguished through detection of changes associated with a sensor's sensitive layer that interacts with the components of the gaseous mixture. Through periodic variations of parameters or conditions of the sensor, the characteristics of the gas components may be derived. For example, the concentration of a gas or multiple gases in a mixture may be determined with a high degree of accuracy. Non-invasive detection of biological off-gases may be implemented. Other uses abound.
    Type: Grant
    Filed: September 29, 2015
    Date of Patent: February 26, 2019
    Inventors: Pavel Nosovitskiy, Gennadiy Nosovitskiy
  • Patent number: 10198552
    Abstract: The present invention relates to a new diagnosis method in the field of hepatology, combining measurement of serum markers and of liver elasticity.
    Type: Grant
    Filed: November 30, 2012
    Date of Patent: February 5, 2019
    Assignees: ASSISTANCE PUBLIQUE—HOPITAUX DE PARIS, BIOPREDICTIVE
    Inventor: Thierry Poynard
  • Patent number: 10196681
    Abstract: Provided herein are methods, processes and apparatuses for determining the fraction of fetal nucleic acid in a test sample derived from a pregnant female with improved accuracy and/or precision. Also, provided herein are methods, processes and apparatuses for determining the presence or absence of a genetic variation in a fetus with improved accuracy and/or precision. Certain methods include using fetal fraction measurements for the determination of a fetal genetic variation.
    Type: Grant
    Filed: March 14, 2013
    Date of Patent: February 5, 2019
    Assignee: Sequenom, Inc.
    Inventors: Cosmin Deciu, Zeljko Dzakula, John Allen Tynan, Grant Hogg
  • Patent number: 10194685
    Abstract: The present invention provides a computer program for determining the optimum diet of an animal, determining what nutritional deficiencies exist in that diet, and formulating a supplement to correct those deficiencies. It allows the creation of a nutritionally complete and balanced diet with a sufficient but not excessive quantity of water, energy, protein, fat, carbohydrate, amino acids, fatty acids, vitamins, minerals, and vitamin-like nutrients. The specific compositions of supplements generated using the computer program are also claimed.
    Type: Grant
    Filed: February 27, 2015
    Date of Patent: February 5, 2019
    Inventor: Sean Delaney
  • Patent number: 10192027
    Abstract: Contemplated systems and methods integrate genomic/exomic data with transcriptomic data by correlating a cancer associated mutation in the genome/exome with the transcription level of the affected gene carrying the mutation, particularly where the mutation is a 3-terminal nonsense mutation.
    Type: Grant
    Filed: March 25, 2015
    Date of Patent: January 29, 2019
    Assignee: FIVE3 GENOMICS, LLC
    Inventor: John Zachary Sanborn
  • Patent number: 10186332
    Abstract: A determination device for enabling a computer to carry out a process including the steps of: obtaining an analysis result on methylation status of a CpG site located in a promoter region of at least one gene selected from HOXB4 (Homeobox B4) and ZSCAN31 (zinc finger and SCAN domain containing 31) in a DNA sample derived from a subject; and outputting a determination result as information on lung cancer in the subject based on the resulting analysis result is provided. A computer readable medium and a marker for obtaining information on lung cancer are also provided.
    Type: Grant
    Filed: July 9, 2015
    Date of Patent: January 22, 2019
    Assignees: SYSMEX CORPORATION, THE UNIVERSITY OF TOKYO
    Inventors: Kaya Tai, Genta Nagae, Hiroyuki Aburatani