Patents Examined by Mary K Zeman
  • Patent number: 11139046
    Abstract: Embodiments include methods, systems, and computer program products for analyzing genomic data. Aspects include receiving genomic data for an organism, sample phenotypes, and a plurality of gene sets. Aspects include, for each of the gene sets, determining a set of genes G corresponding to genes in the gene set and a set of genes G? corresponding to genes outside the gene set for the phenotypes R and R?. Aspects also include determining a set of mutated genes M and a set of non-mutated genes M? for R and R? and a mutation enrichment score. Aspects also include determining a set of differentiated genes D a set of non-differentiated genes D? for R and R?. Aspects also include identifying an enriched gene set GE based at least in part upon the mutation enrichment score and the differentiation enrichment score.
    Type: Grant
    Filed: December 1, 2017
    Date of Patent: October 5, 2021
    Assignee: INTERNATIONAL BUSINESS MACHINES CORPORATION
    Inventors: Chaya Levovitz, Laxmi Parida, Kahn Rhrissorrakrai
  • Patent number: 11124831
    Abstract: Methods are provided for analyzing one or more genetic samples, comprising procuring one or more genetic samples comprising genetic material from one or more individuals and sequencing the genetic material using non-targeted, ultra-low coverage sequencing to obtain genetic information for individual associated with the one or more genetic samples. Personal and genetic information associated with the individuals is stored in a database for retrieval and manipulation.
    Type: Grant
    Filed: August 10, 2017
    Date of Patent: September 21, 2021
    Assignee: NEW YORK GENOME CENTER
    Inventors: Joseph K. Pickrell, Tomaz Berisa, Suma Jaini, Brian Houck-Loomis, Kaja Wasik
  • Patent number: 11069434
    Abstract: An insulin delivery supervisor (IDS) with a safety analysis and supervision function that can reside between the insulin request and the insulin delivery and can intercept any excessive insulin requests before the insulin was delivered. The IDS can be implemented in any system based on insulin pump or pen and will work with either SMBG or CGM modes of blood glucose monitoring.
    Type: Grant
    Filed: March 11, 2011
    Date of Patent: July 20, 2021
    Assignee: UNIVERSITY OF VIRGINIA PATENT FOUNDATION
    Inventors: Marc D. Breton, Stephen D. Patek, Boris P. Kovatchev, Colleen S. Hughes
  • Patent number: 11054361
    Abstract: A method for analyzing sample cells reacting with at least one specific marker, includes providing a reference sample and an active sample and providing a set (E+) of cells declared positive from among the active sample cells. The method further includes determining a vector coefficient (?) from the active sample and from the set (E+) and determining at least one set of positive cells in the reference sample as a function of the vector coefficient (?). A rate of false positives (?) is calculated in the reference sample from the number of positive cells of the reference sample.
    Type: Grant
    Filed: December 11, 2015
    Date of Patent: July 6, 2021
    Assignee: COMMISSARIAT A L'ENERGIE ATOMIQUE ET AUX ENERGIES ALTERNATIVES
    Inventors: Josselin Garnier, Françoise Poggi, Gilles Defaux, Antonio Cosma, Robert Quach
  • Patent number: 11024414
    Abstract: A system and method for converting static/still medical images of a particular patient into dynamic and interactive images interacting with medical tools including medical devices by coupling a model of tissue dynamics and tool characteristics to the patient specific imagery for simulating a medical procedure in an accurate and dynamic manner by coupling a model of tissue dynamics to patient specific imagery for simulating cerebral aneurysm clipping surgery.
    Type: Grant
    Filed: October 16, 2017
    Date of Patent: June 1, 2021
    Assignee: SURGICAL THEATER, INC.
    Inventor: Mordechai Avisar
  • Patent number: 11004540
    Abstract: A method for determining false positives calls in a biological data plot is provided. The method includes identifying a first data cluster as non-amplification data points within the biological data plot and identifying a second data cluster as wild-type positives within the biological data plot. The method further includes estimating a position in the biological data plot of a center of the first and second data clusters. The method further includes determining, for each data point within the first data cluster, a probability of belonging to the first data cluster and determining, for each data point within the second data cluster, a probability of belonging to the second data cluster. The method includes applying a probability threshold for each data point within the first and second data cluster to identify false positives.
    Type: Grant
    Filed: June 3, 2016
    Date of Patent: May 11, 2021
    Assignee: LIFE TECHNOLOGIES CORPORATION
    Inventors: Nivedita Sumi Majumdar, Thomas Wessel
  • Patent number: 10957423
    Abstract: Apparatuses and methods are disclosed for comparing a first biosequence string with a second biosequence string to assess similarity between those biosequence strings. For example, a field programmable gate array (FPGA) can be used to (1) detect substrings of the second biosequence string that are matches to substrings of the first biosequence string, and (2) map the detected substrings of the second biosequence string to corresponding positions in the first biosequence string where the detected substrings are located based on a data structure that links substrings of the first biosequence string to positions in the first biosequence string where the substrings of the first biosequence string are located. These operations can be used to seed an alignment between the first and second biosequence strings that permits comparisons to be performed over longer substrings of the first and second biosequence strings so that similarities between those longer substrings can be quantified.
    Type: Grant
    Filed: February 28, 2020
    Date of Patent: March 23, 2021
    Assignee: WASHINGTON UNIVERSITY
    Inventors: Jeremy Daniel Buhler, Roger Dean Chamberlain, Mark Allen Franklin, Kwame Gyang, Arpith Chacko Jacob, Praveen Krishnamurthy, Joseph Marion Lancaster
  • Patent number: 10957421
    Abstract: Methods and systems for characterizing two or more nucleic acids in a sample. The method can include the steps of providing a hybrid machine learning approach that enables rapid and automated deconvolution of DNA mixtures of multiple contributors. The input is analyzed by an expert system which is implemented in the form of a rule set. The rule set establishes requirements based on expectations on the biology and methods used. The methods and systems also include a machine learning algorithm that is either incorporated into the expert system, or utilizes the output of the expert system for analysis. The machine learning algorithm can be any of a variety of different algorithms or combinations of algorithms used to perform classification in a complex data environment.
    Type: Grant
    Filed: December 3, 2015
    Date of Patent: March 23, 2021
    Assignee: Syracuse University
    Inventors: Michael Marciano, Jonathan Adelman
  • Patent number: 10936626
    Abstract: Databases and data processing systems for use with a network-based personal genetics services platform may include member information pertaining to a plurality of members of the network-based personal genetics services platform. The member information may include genetic information, family history information, environmental information, and phenotype information of the plurality of members. A data processing system may determine, based at least in part on the member information, a model for predicting a phenotype from genetic information, family history information, and environmental information, wherein determining the model includes training the model using the member information pertaining to a set of the plurality of members.
    Type: Grant
    Filed: May 14, 2020
    Date of Patent: March 2, 2021
    Assignee: 23andMe, Inc.
    Inventors: Brian Thomas Naughton, Chuong Do, John Michael Macpherson
  • Patent number: 10913986
    Abstract: A computer-implemented method of preparing a set of differentially informative methylated positions (DIMPs) or differentially informative methylated regions (DIMRs) from a sample methylome of an animal or plant having a phenotypic characteristic different from a wild-type of the same species of animal or plant, and the characteristic is associate with differences in methylation of the genome, comprises: providing a computer with the sample methylome, and a reference methylome of the wild-type of the same species of animal or plant; calculating with the computer a divergence between a plurality of cytosine positions of the sample methylome and the reference methylome; and selecting with the computer a set of DIMPs or DIMRs. Each DIMP or DIMR is selected based on an approximation of the energy required to produce the divergence between methylation levels of the plurality of cytosine positions of the sample methylome as compared to the wild-type methylome.
    Type: Grant
    Filed: February 1, 2017
    Date of Patent: February 9, 2021
    Assignee: The Board of Regents of the University of Nebraska
    Inventors: Sally A. Mackenzie, Robersy Sanchez
  • Patent number: 10872681
    Abstract: Computer software products, methods, and systems are described which provide functionality to a user conducting experiments designed to detect and/or identify genetic sequences and other characteristics of a genetic sample, such as, for instance, gene copy number and aberrations thereof. The presently described software allows the user to interact with a graphical user interface which depicts the genetic information obtained from the experiment. The presently disclosed methods and software are related to bioinformatics and biological data analysis. Specifically, provided are methods, computer software products and systems for analyzing and visually depicting genotyping data on a screen or other visual projection. The presently disclosed methods and software allow the user conducting the experiment to differentially filter complex genetic data and information by varying genetic parameters and removing or highlighting visually various regions of genetic data of interest (CytoRegions).
    Type: Grant
    Filed: September 22, 2017
    Date of Patent: December 22, 2020
    Assignee: Affymetrix, Inc.
    Inventors: Carl A. Dowds, Jody C. McIntyre, Edgar E. Erwin, Garret D. Wilson, Pragna B. Parmar, Breck S. Ohlson, Richard D. Shippy, Francisco J. Cifuentes
  • Patent number: 10854318
    Abstract: Inferring a characteristic of an individual is disclosed. An indication that a first user and a second user have at least one shared chromosomal segment is received. Information about the second user is obtained. A characteristic of the first user is inferred based at least in part on the information about the second user.
    Type: Grant
    Filed: July 31, 2017
    Date of Patent: December 1, 2020
    Assignee: 23andMe, Inc.
    Inventors: John Michael Macpherson, Brian Thomas Naughton, Joanna Louise Mountain
  • Patent number: 10854316
    Abstract: A system configured to characterize a ratio of contributors to a DNA mixture within a sample, the system including: a sample preparation module configured to generate initial data about the DNA mixture within the sample; a processor comprising a ratio of contributors determination module configured to: (i) receive the generated initial data; (ii) analyze the generated initial data to determine the ratio of contributors to the DNA mixture within the sample; and an output device configured to receive the determined ratio of contributors from the processor, and further configured to output information about the received determined ratio of contributors.
    Type: Grant
    Filed: December 2, 2016
    Date of Patent: December 1, 2020
    Assignee: Syracuse University
    Inventors: Michael Marciano, Jonathan D. Adelman, Laura C. Haarer
  • Patent number: 10846371
    Abstract: The invention relates to methods and kits for determining and optimizing a personalized treatment regimen for a subject suffering from a pathologic disorder based on calculating the value of M, that indicates the ability of said subject to eliminate said disorder. The invention specifically relates to optimization of interferon treatment of viral disorders.
    Type: Grant
    Filed: April 2, 2015
    Date of Patent: November 24, 2020
    Assignee: YISSUM RESEARCH DEVELOPMENT COMPANY OF THE HEBREW UNIVERSITY OF JERUSALM LTD.
    Inventor: Yoav Smith
  • Patent number: 10825552
    Abstract: The present invention relates to methods for evaluating and/or predicting the outcome of a clinical condition, such as cancer, metastasis, AIDS, autism, Alzheimer's, and/or Parkinson's disorder. The methods can also be used to monitor and track changes in a patient's DNA and/or RNA during and following a clinical treatment regime. The methods may also be used to evaluate protein and/or metabolite levels that correlate with such clinical conditions. The methods are also of use to ascertain the probability outcome for a patient's particular prognosis.
    Type: Grant
    Filed: May 12, 2017
    Date of Patent: November 3, 2020
    Assignee: THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
    Inventors: John Zachary Sanborn, David Haussler
  • Patent number: 10777304
    Abstract: The redundancy in genomic sequence data is exploited by compressing sequence data in such a way as to allow direct computation on the compressed data using methods that are referred to herein as “compressive” algorithms. This approach reduces the task of computing on many similar genomes to only slightly more than that of operating on just one. In this approach, the redundancy among genomes is translated into computational acceleration by storing genomes in a compressed format that respects the structure of similarities and differences important to analysis. Specifically, these differences are the nucleotide substitutions, insertions, deletions, and rearrangements introduced by evolution. Once such a compressed library has been created, analysis is performed on it in time proportional to its compressed size, rather than having to reconstruct the full data set every time one wishes to query it.
    Type: Grant
    Filed: July 24, 2017
    Date of Patent: September 15, 2020
    Inventors: Michael H. Baym, Bonnie Berger Leighton, Po-Ru Loh
  • Patent number: 10777302
    Abstract: Processing genetic information comprises: receiving an input that includes information pertaining to a specific genetic variant; and identifying, in a database comprising genotype information of a plurality of candidate individuals, a matching individual imputed to have the specific genetic variant. The genotype information of the matching individual corresponding to the specific genetic variant is not directly assayed.
    Type: Grant
    Filed: September 2, 2016
    Date of Patent: September 15, 2020
    Assignee: 23andMe, Inc.
    Inventors: Arnab Chowdry, Geoffrey Benton, Brian Thomas Naughton
  • Patent number: 10726945
    Abstract: A differential sequence object is constructed on the basis of alignment of sub-strings via incremental synchronization of sequence strings using known positions of the sub-strings relative to a reference genome sequence. An output file is then generated that comprises only relevant changes with respect to the reference genome.
    Type: Grant
    Filed: March 31, 2017
    Date of Patent: July 28, 2020
    Assignee: THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
    Inventors: John Zachary Sanborn, David Haussler
  • Patent number: 10720229
    Abstract: System, computer program products, and methods are disclosed for estimating a degree of ancestral relatedness between two individuals. The haplotype data for a population of individuals is divided into segment windows based on genetic markers, and matched segments for the haplotype data are generated. Each matched segment having a first cM width that exceeds a threshold cM width is included in counting the matched segments in each segment window. A weight associated with each segment window is estimated based on the count of matched segments in the associated segment window. A weighted sum of per-window cM widths for each matched segment is calculated based on the first cM width and the weights associated with the segment windows of the matched segment. The weighted sum of per-window cM widths are used to estimate a degree of ancestral relatedness between two individuals.
    Type: Grant
    Filed: October 14, 2015
    Date of Patent: July 21, 2020
    Assignee: Ancestry.com DNA, LLC
    Inventors: Mathew J Barber, Yong Wang, Keith D. Noto, Kenneth G. Chahine, Catherine Ann Ball
  • Patent number: 10718003
    Abstract: Accurate measurements of the presence or absence of an analyte (e.g., MRSA) in a sample are provided. For example, the sample can be subjected to an activation reagent (potentially after an initial reagent has already been added), which can cause a flash signal that increases and then decreases over time. Signal data points can be measured from the flash signal using a detector. A quadratic regression function that fits the signal data points can be determined. An accuracy of the quadratic fit can be determined, as well as a signal-to-background ratio. A difference between a signal-to-background term and an accuracy term can be used as a score that is compared to a threshold to determine whether the analyte is present in the sample.
    Type: Grant
    Filed: December 19, 2016
    Date of Patent: July 21, 2020
    Assignee: Roche Molecular Systems, Inc.
    Inventors: Diego Ariel Rey, Paul Hayter, Manoj Sharma, Nick Reinig