Patents Examined by John S. Brusca
  • Patent number: 10832798
    Abstract: Methods for analyzing signal data generated by sequencing of a polynucleotide strand using a pH-based method of detecting nucleotide incorporation(s). In an embodiment, the method comprises formulating a function that models the output signal of a representative empty well of a reactor array. A time transformation is applied to the empty well function to obtain a time-warped empty well function. The time-warped empty well function is fitted to an output signal from the loaded well representative of a flow that results in a non-incorporation event in the loaded well. The fitted time-warped empty well function can then be used to analyze output signals from the loaded well for other flows.
    Type: Grant
    Filed: March 9, 2017
    Date of Patent: November 10, 2020
    Assignee: Life Technologies Corporation
    Inventor: Earl Hubbell
  • Patent number: 10825551
    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 27, 2016
    Date of Patent: November 3, 2020
    Assignee: THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
    Inventors: John Zachary Sanborn, David Haussler
  • Patent number: 10810239
    Abstract: A sequence data analyzer comprising: a read dictionary preparation unit creating a read sequence dictionary based on a concatenation string, the concatenation string constituted of a pair of a left sequence and a right sequence, which are obtained by sequencing a sample DNA fragment respectively from the left and right ends, and connecting characters connecting these sequences together; and a sample reconstruction unit extracting, as a sample sequence, a string up to a terminal character positioned in the string of a hit position of a query sequence in the read sequence dictionary, and extracting, as a mate sequence, the left sequence or right sequence until the appearance of a terminal character on the side where the hit position doesn't exist in the sample sequence.
    Type: Grant
    Filed: March 12, 2015
    Date of Patent: October 20, 2020
    Assignee: Hitachi High-Tech Corporation
    Inventor: Kouichi Kimura
  • Patent number: 10808243
    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: April 2, 2020
    Date of Patent: October 20, 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
  • Patent number: 10792421
    Abstract: This invention relates to automatic insulin delivery systems and methods of administering insulin. Preferably the systems and methods comprise a predictive feedforward control.
    Type: Grant
    Filed: October 5, 2017
    Date of Patent: October 6, 2020
    Assignee: Iowa State University Research Foundation, Inc.
    Inventors: Derrick K. Rollins, Sr., Yong Mei
  • Patent number: 10783984
    Abstract: Exemplary embodiments provide methods and systems for diploid genome assembly and haplotype sequence reconstruction. Aspects of the exemplary embodiment include generating a fused assembly graph from reads of both haplotypes, the fused assembly graph including identified primary contigs and associated contigs; generating haplotype-specific assembly graphs using phased reads and haplotype aware overlapping of the phased reads; merging the fused assembly graph and haplotype-specific assembly graphs to generate a merged assembly haplotype graph; removing cross-phasing edges from the merged assembly haplotype graph to generate a final haplotype-resolved assembly graph; and reconstructing haplotype-specific contigs from the final haplotype-resolved assembly graph resulting in haplotype-specific contigs.
    Type: Grant
    Filed: May 23, 2016
    Date of Patent: September 22, 2020
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Chen-Shan Chin, Paul Peluso, David Rank
  • Patent number: 10774379
    Abstract: This disclosure describes frameworks and techniques related to the random access of digital data encoded by polynucleotides. Digital data of a data file can be encoded as a series of nucleotides and one or more polynucleotide sequences can be generated that encode the digital data for the data file. The bits of the digital data can be segmented to produce multiple polynucleotide sequences that encode the bits of the digital data with each polynucleotide sequence encoding an individual segment of the digital data. The individual segments can be grouped together and associated with a group identifier. Each data file can be associated with a number of group identifiers and the number of segments in each group can be within a specified range. Primers corresponding to the group identifiers can be used to selectively access the polynucleotides that encode the digital data of a data file.
    Type: Grant
    Filed: March 15, 2017
    Date of Patent: September 15, 2020
    Assignee: Microsoft Technology Licensing, LLC
    Inventors: Yuan-Jyue Chen, Karin Strauss, Luis H. Ceze, Lee Organick
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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