Patents Examined by John S. Brusca
  • Trait prediction coordination for genomic application environment
    Patent number: 10777300
    Abstract: Systems and methods are provided for trait prediction coordination. One embodiment is a method that includes launching a genomics application at a user device, receiving a command to present a partner application within the genomics application, selecting characteristics to predict for an individual, based on an identifier that distinguishes the partner application from other partner applications, operating polygenic models that generate predictions for the characteristics based on genetic records for the individual, acquiring media for the partner application, based on the predictions, and operating the partner application to update a display at the user device with the media, thereby providing the predictions in a format specific to the partner application.
    Type: Grant
    Filed: February 28, 2019
    Date of Patent: September 15, 2020
    Assignee: HELIX OPCO, LLC
    Inventors: Ryan Trunck, Rani Powers, Christopher M. Glode, Stewart Blanford, Daniel Shin
  • Pathogenicity scoring system for human clinical genetics
    Patent number: 10762981
    Abstract: Provided are methods and systems for determining the clinical significance of a genetic variant. The methods entail determining, for the variant, (a) a function score based on known impact of the variant on a biological function of a cell or protein, (b) a frequency score based on the frequency of the variant in a population, (c) a co-occurrence score based on how the variant co-occurs with a reference variant having known clinical significance relating to a clinical disease or condition, and (d) a family segregation score based on how the variant segregates with a disease or condition in a family; and aggregating, on a computer, the function score, the frequency score, the co-occurrence score, the family segregation score to generate a clinical significance score indicating the clinical significance of the genetic variant.
    Type: Grant
    Filed: October 22, 2014
    Date of Patent: September 1, 2020
    Assignee: ATHENA DIAGNOSTICS, INC.
    Inventors: Izabela Karbassi, Christopher Elzinga, Glenn Maston, Joseph Higgins, Sat Dev Batish, Christina Divincenzo, Michele McCarthy, Jennifer Lapierre, Felicita Dubois, Katelyn Medeiros, Jeffery Jones, Corey Braastad
  • Identification of microorganisms from genome sequencing data
    Patent number: 10752958
    Abstract: A diagnostic analysis method and system is provided for identifying a microorganism from a genome sequence. Partially or fully assembled microbial genomes or short reads from whole-genome sequencing of microbial genomes are processed into a 4 MB Boolean array while preserving 1% of the genomic information in a way that allows for rapid comparison of a query genome to a large reference database. This represents a critical savings in storage space and speed by which large reference libraries can be queried.
    Type: Grant
    Filed: May 11, 2017
    Date of Patent: August 25, 2020
    Assignee: Santa Clara University
    Inventors: David Hess, Farid Tadros, Michael Jared Lumpe, Eileen Wagner, Mark W. Pandori
  • mRNA sequences to control co-translational folding of proteins
    Patent number: 10724040
    Abstract: This invention relates to optimized heterologous production of properly folded and functional proteins. The present invention provides systems and methods involving determination of the optimal mRNA sequence, based on the underlying rates at which codons are translated and folding kinetic of nascent-protein, that maximizes co-translational protein folding of domains in order to maximize the proper folding and quality of the protein produced. The codon translation rates can be determined in a number of ways, including theoretical estimation and, preferably, through experimental data, such as ribosome profiling. The determination of an optimal mRNA sequence through the utilization of codon translation rates under a particular set of conditions allows for application of the method irrespective of the organism from which the protein in question was originally derived.
    Type: Grant
    Filed: July 15, 2016
    Date of Patent: July 28, 2020
    Assignee: The Penn State Research Foundation
    Inventors: Ajeet K. Sharma, Edward P. O'Brien
  • Systems and methods for identifying responders and non-responders to immune checkpoint blockade therapy
    Patent number: 10706954
    Abstract: Techniques for determining whether a subject is likely to respond to an immune checkpoint blockade therapy.
    Type: Grant
    Filed: November 26, 2019
    Date of Patent: July 7, 2020
    Assignee: BostonGene Corporation
    Inventors: Feliks Frenkel, Nikita Kotlov, Alexander Bagaev, Maksym Artomov, Ravshan Ataullakhanov
  • Modifications to polynucleotides for sequencing
    Patent number: 10689684
    Abstract: This disclosure describes techniques to improve the sequencing of polynucleotides by decreasing the likelihood of errors occurring during a sequencing calibration process. In implementations, regions of polynucleotides that are used for the calibration process can be modified to reduce a number of polynucleotides that have a same nucleotide at one or more positions of the calibration regions. In some cases, the calibration regions can be modified by adding a sequence to the polynucleotides that replaces the original calibration regions. Also, the calibration regions can be modified by rearranging the nucleotides at the different positions of the calibration regions. Additionally, the calibration regions can be modified by adding sequences of varying length to the polynucleotides being sequenced to produce polynucleotides having varying length with different calibration regions.
    Type: Grant
    Filed: February 14, 2017
    Date of Patent: June 23, 2020
    Assignee: Microsoft Technology Licensing, LLC
    Inventors: Yuan-Jyue Chen, Karin Strauss, Luis H. Ceze, Lee Organick, Randolph Lopez, Georg Seelig
  • Methods for placing, accepting, and filling orders for products and services
    Patent number: 10689692
    Abstract: Methods and systems for ordering assays which detect SNPs or gene expression are provided. The methods use PCR and RT-PCR procedures. Collections of stock assays are assembled using pre- and post-manufacturing quality control procedures and made available to consumers via the Internet. In addition, custom assays are prepared upon order from the consumer and these assays are also prepared using pre- and post-manufacturing quality control procedures. The assays are then delivered to the consumer.
    Type: Grant
    Filed: September 6, 2016
    Date of Patent: June 23, 2020
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: Ryan T. Koehler, Kenneth J. Livak, Junko Stevens, Francisco M. De La Vega, Michael Rhodes, Laurent R. Bellon, Dawn Madden, Dennis A. Gilbert, Yu N. Wang, Eugene G. Spier, Xiaoqing You, Lily Xu, Jeremy Heil, Emily S. Winn-Deen, Ivy McMullen, Susan Eddins, Leila G. Smith
  • Genome compression and decompression
    Patent number: 10679727
    Abstract: The present invention relates to a method and apparatus for genome compression and decompression. In one embodiment of the present invention, there is a method for genome compression, including: selecting from a reference database a reference genome that matches the genome; building an index based on positions of the reference genome's multiple segments in the reference genome; aligning the genome with the reference genome based on the multiple segments so as to identify difference data between the genome and the reference genome; and generating a compressed genome, the compressed genome including at least the index and the difference data. In other embodiments, there is provided an apparatus for genome compression. Further, there is a method and apparatus for decompressing the genome that has been compressed using the above method and apparatus.
    Type: Grant
    Filed: October 11, 2014
    Date of Patent: June 9, 2020
    Assignee: International Business Machines Corporation
    Inventors: Jian Dong Ding, Min Gong, Yun Jie Qiu, Junchi Yan, Ya Nan Zhang
  • Biological sequence variant characterization
    Patent number: 10658069
    Abstract: Short fixed length sub-sequences, defined as reference sub-sequences, are extracted from a collection of reference sequences, and an index is constructed showing which short fixed length reference sub-sequence occurs in which reference sequences. Short fixed length sub-sequences, the same length as the reference sub-sequences and defined as source sub-sequences, are extracted from a collection of source sequences derived from a sample for which the signature is to be determined, and the short fixed length source sub-sequences are compiled to determine the frequency of each within the collection. The presence or absence of source sub-sequences in combination with the index is used to infer the presence or absence of reference sequences from the reference collection.
    Type: Grant
    Filed: October 10, 2014
    Date of Patent: May 19, 2020
    Assignee: International Business Machines Corporation
    Inventors: Thomas C. Conway, Kelly L Wyres
  • Resolving genome fractions using polymorphism counts
    Patent number: 10658070
    Abstract: Methods of reliably estimating genomic fraction (e.g., fetal fraction) from polymorphisms such as small base variations or insertions-deletions are disclosed. Sequenced data from a multigenomic source is used to determine allele counts for one or more of the polymorphisms. For one or more of the polymorphisms, zygosity is assigned, and genomic fraction is determined from the zygosity and allele counts. Certain embodiments employ SNPs as the relevant polymorphism. The disclosed methods can be applied as part of an intentional, pre-designed re-sequencing study targeted against known polymorphisms or can be used in a retrospective analysis of variations found by coincidence in overlapping sequences generated from maternal plasma (or any other setting where a mixture of DNA from several people are present).
    Type: Grant
    Filed: August 11, 2016
    Date of Patent: May 19, 2020
    Assignee: Verinata Health, Inc.
    Inventors: Richard P. Rava, Brian K. Rhees, John P. Burke
  • Systems and methods for generating, visualizing and classifying molecular functional profiles
    Patent number: 10650911
    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 a biological sample; determining a molecular-functional (MF) profile for a subject using the data; determining visual characteristics GUI elements using the data; generating a GUI personalized to the subject using the determined visual characteristics; and presenting the generated personalized GUI to a user.
    Type: Grant
    Filed: June 12, 2018
    Date of Patent: May 12, 2020
    Assignee: BostonGene Corporation
    Inventors: Alexander Bagaev, Feliks Frenkel, Nikita Kotlov, Ravshan Ataullakhanov
  • Microbial strain improvement by a HTP genomic engineering platform
    Patent number: 10647980
    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: July 1, 2019
    Date of Patent: May 12, 2020
    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
  • Noninvasive prenatal molecular karyotyping from maternal plasma
    Patent number: 10643738
    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: March 15, 2013
    Date of Patent: May 5, 2020
    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
  • Methods and systems for predicting the risk of transgene silencing
    Patent number: 10633703
    Abstract: The present invention is based on the use of the H3K9me2 methylation levels in plant genomes to predict transgene silencing, transgene stability, and/or transgene expression level. Provided are methods and/or systems for generating whole-genome H3K9me2 maps and its use with an assigned threshold value for predicting gene silencing. The methods and/or systems provided herein can be used in high-throughput setting for screening large number of transformed event in a relatively short period of time as compared to existing technologies.
    Type: Grant
    Filed: October 25, 2016
    Date of Patent: April 28, 2020
    Assignee: Dow AgroSciences LLC
    Inventors: Pohao Wang, Shreedharan Sriram, Lakshmi Sastry-Dent
  • Generation and use of simulated genomic data
    Patent number: 10629292
    Abstract: Embodiments of the invention utilize a graph-based approach for simulating genomic datasets from large scale populations. Genomic data may be represented as a directed acyclic graph (DAG) that incorporates individual sample data including variant type, position, and zygosity. A simulator may operate on the DAG to generate variant datasets based on probabilistic traversal of the DAG. This probabilistic traversal reflects genomic variant types associated with the subpopulation used to build the DAG, and as a result, the generated variant datasets maintain statistical fidelity to the original sample data.
    Type: Grant
    Filed: December 19, 2016
    Date of Patent: April 21, 2020
    Assignee: SEVEN BRIDGES GENOMICS, INC.
    Inventors: Agata Foryciarz, Dennis A. Dean, II
  • Methods and processes for non-invasive assessment of genetic variations
    Patent number: 10622094
    Abstract: Provided herein are methods, processes, systems, machines and apparatuses for non-invasive assessment of genetic variations.
    Type: Grant
    Filed: June 20, 2014
    Date of Patent: April 14, 2020
    Assignee: Sequenom, Inc.
    Inventors: Sung K. Kim, Gregory Hannum, Jennifer Geis, Cosmin Deciu
  • Sequence assembly
    Patent number: 10604799
    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: April 11, 2014
    Date of Patent: March 31, 2020
    Assignee: Molecular Loop Biosolutions, LLC
    Inventors: Gregory Porreca, Caleb Kennedy
  • Robust variant identification and validation
    Patent number: 10607719
    Abstract: A non-transitory storage medium stores an assembled genetic sequence comprising aligned sequencing reads. An electronic processing device is configured to perform operations including: identifying a possible variant in the assembled genetic sequence; computing value of at least one read property for reads of the assembled genetic sequence; and calling the possible variant conditional upon the computed values of the at least one read property for sequencing reads of the assembled genetic sequence that include the possible variant satisfying an acceptance criterion. The electronic processing device may be further configured to select at least one region of the assembled genetic sequence for validation based on a non random selection criterion.
    Type: Grant
    Filed: December 3, 2012
    Date of Patent: March 31, 2020
    Assignee: Koninklijke Philips N.V.
    Inventors: Sunil Kumar, Randeep Singh, Biswaroop Chakrabarti, Subodh Kumar
  • Systems and methods for reconciling variants in sequence data relative to reference sequence data
    Patent number: 10600499
    Abstract: Techniques for identifying variations in sequence data relative to reference sequence data. The techniques include accessing information specifying multiple sets of variants in the sequence data relative to reference sequence data, each of the multiple sets of variants being generated by using a respective variant identification technique; and determining, using the information specifying the multiple sets of variants in the sequence data, a reconciled set of variants in the sequence data relative to the reference sequence data, the determining comprising: determining whether a first variant is present at a first position in the sequence data based, at least in part, on one or more variants at one or more other positions in the sequence data.
    Type: Grant
    Filed: July 13, 2016
    Date of Patent: March 24, 2020
    Inventor: Amit Jain
  • Detecting and classifying copy number variation
    Patent number: 10586610
    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: March 16, 2016
    Date of Patent: March 10, 2020
    Assignee: Verinata Health, Inc.
    Inventors: Richard P. Rava, Anupama Srinivasan