Gene Sequence Determination Patents (Class 702/20)
  • Patent number: 11031096
    Abstract: Various embodiments are described herein related to an assay, method and apparatus for performing an RNA Disruption Assay (RDA) for cellular RNA optionally in response to a cytotoxic treatment such as chemotherapy and/or radiation treatment. The method comprises obtaining at least one electropherogram dataset corresponding to a unique biological sample comprising the cellular RNA at a time point, optionally during or after the treatment; determining values for features from at least two shifted regions of the at least one electropherogram dataset, the shifting being due to the treatment; and optionally determining an RDA score based on a combination of the values of the features.
    Type: Grant
    Filed: April 24, 2013
    Date of Patent: June 8, 2021
    Assignee: RNA DIAGNOSTICS INC.
    Inventors: Kenneth Pritzker, Amadeo Mark Parissenti, Laura Pritzker, Mu Zhu, Xiaohui Wang, Stacey Santi, Rashmi Narendrula, Baoqing Guo
  • Patent number: 11031092
    Abstract: A computer-implemented method, computer program product, and computer processing system are provided for metagenomic pattern classification. The method includes pre-processing, by a processor, a taxonomy tree associated with a genome database to extract taxonomy related information therefrom. The genome database includes a plurality of genome sequences. The method further includes building, by the processor, a suffix tree on the genome database. The method also includes annotating, by the processor, nodes in the suffix tree, using a plurality of right maximal patterns derived from the extracted taxonomy related information as annotations, such that each of the plurality of right maximal patterns in the suffix tree points to a respective one of a plurality of nodes in the taxonomy tree and such that a leaf node in the taxonomy tree represents a respective sample organism. The annotations are configured to function as classifications for the plurality of genome sequences.
    Type: Grant
    Filed: November 1, 2017
    Date of Patent: June 8, 2021
    Assignee: INTERNATIONAL BUSINESS MACHINES CORPORATION
    Inventors: Laxmi Parida, Enrico Siragusa, Filippo Utro
  • Patent number: 11011252
    Abstract: The present invention provides algorithm-based molecular assays that involve measurement of expression levels of genes, or their co-expressed genes, from a biological sample obtained from a prostate cancer patient. The genes may be grouped into functional gene subsets for calculating a quantitative score useful to predict a likelihood of a clinical outcome for a prostate cancer patient.
    Type: Grant
    Filed: May 2, 2017
    Date of Patent: May 18, 2021
    Assignee: Genomic Health, Inc.
    Inventors: Steven Shak, Mark Lee, William F. Novotny, Tara Maddala, Michael R. Crager, Diana Cherbavaz, Robert J. Pelham, Carl L. Millward, Dejan Knezevic
  • Patent number: 10998084
    Abstract: A sequencing data analysis method, a device and a computer-readable medium for microsatellite instability. The present invention can use NGS sequencing results to determine whether the microsatellite instability is present. The sequencing data analysis method can significantly improve detection sensitivity without reducing specificity, and can quickly and automatically evaluate a stable or unstable status of each MSI locus with high throughput, high sensitivity, and high specificity. By combining the statuses for all MSI loci in each sample, the samples can be comprehensively evaluated as MSS, MSI-L, or MSI-H.
    Type: Grant
    Filed: June 6, 2018
    Date of Patent: May 4, 2021
    Assignee: NANJING SHIHE GENE BIOTECHNOLOGY CO., LTD.
    Inventors: Yang Shao, Xue Wu, Zhili Chang, Xiaonan Wang, Chongguang Yan, Shuyu Wu, Hua Bao, Xiaoling Tong
  • Patent number: 10990904
    Abstract: Embodiments in the present disclosure relate generally to computer network architectures for machine learning, artificial intelligence, and automated improvement and regularization of forecasting models, providing rapid improvement of the models. Embodiments may generate such rapid improvement of the models either occasionally on demand, or periodically, or as triggered by events such as an update of available data for such forecasts. Embodiments may indicate, after the improvement of the models, that various web applications using the models may be rerun to seek improved results for the web applications. Embodiments may include a combination of third-party databases to drive the forecasting models, including social media data, financial data, socio-economic data, medical data, search engine data, e-commerce site data, and other databases.
    Type: Grant
    Filed: July 27, 2020
    Date of Patent: April 27, 2021
    Assignee: CLARIFY HEALTH SOLUTIONS, INC.
    Inventors: Jean P. Drouin, Samuel H. Bauknight, Todd Gottula, Yale Wang, Adam F. Rogow, Jeffrey D. Larson, Justin Warner
  • Patent number: 10978196
    Abstract: A system for personalized depression disorder treatment is disclosed herein. The system includes a server configured to communicate with existing healthcare resources and to receive patient data corresponding to a patient, the server including an analytics module. The system further includes a first database configured to store empirical patient outcomes, and further configured to communicate with the analytics module. Additionally, the system includes a user device having a graphical user interface (GUI) configured to communicate with the server and to display at least one output generated by the analytics module. The analytics module is configured to determine at least one of a personalized depression treatment and a personalized depression state prediction based on the empirical patient outcomes and the patient data.
    Type: Grant
    Filed: August 3, 2020
    Date of Patent: April 13, 2021
    Assignee: Tempus Labs, Inc.
    Inventors: Hailey B. Lefkofsky, Christopher N. Vlangos
  • Patent number: 10964408
    Abstract: Exemplary methods, procedures, computer-accessible medium, and systems for base-calling, aligning and polymorphism detection and analysis using raw output from a sequencing platform can be provided. A set of raw outputs can be used to detect polymorphisms in an individual by obtaining a plurality of sequence read data from one or more technologies (e.g., using sequencing-by-synthesis, sequencing-by-ligation, sequencing-by-hybridization, Sanger sequencing, etc.). For example, provided herein are exemplary methods, procedures, computer-accessible medium and systems, which can include and/or be configured for obtaining raw output from a sequencing platform configured to be used for reading fragment(s) of genomes, obtaining reference sequences for the genomes obtained independently from the raw output, and generating a base-call interpretation and/or alignment using the raw output and the reference sequences.
    Type: Grant
    Filed: April 27, 2010
    Date of Patent: March 30, 2021
    Assignee: New York University
    Inventors: Bhubaneswar Mishra, Giuseppe Narzisi
  • Patent number: 10949516
    Abstract: An information processing apparatus includes: a memory, and a processor configured to extract feature points from a biometric image of a living body, generate groups each including a certain number of feature points, obtain a first feature value of each of the groups, compares the first feature value with a second feature value which is a feature value of each of groups each including the certain number of feature points included in enrolled biometric information, specify, as a pair, two groups similar to each other, obtain a first degree of similarity between a first feature point included in a first group of the pair and a second feature point included in a second group of the pair in accordance with a number of groups similar to the first group of the pair, and authenticate the living body based on the degree of similarity.
    Type: Grant
    Filed: December 19, 2018
    Date of Patent: March 16, 2021
    Assignee: FUJITSU LIMITED
    Inventor: Kazuya Uno
  • Patent number: 10938415
    Abstract: Method for encoding of quality values of a data structure, whereby said data structure comprises a set of genomic reads, wherein the method comprises the following steps executable by a data processing system: ascertain the quality values of each read covering a certain index locus, —determine a codebook identifier identifying a specific codebook from a plurality of codebooks for said certain index locus based on the ascertained quality values of said certain index locus, whereby each code-book provides a mapping from a quality value of said quality value alphabet to a corresponding quantized quality value of a quantized quality value alphabet, —quantizing all ascertained quality values at said certain index locus using the specific codebook identified by the codebook identifier at said certain index locus in order to obtain for each quality value at said certain index locus a corresponding quantized quality value, and —encode all determined codebook identifiers using a first entropy encoder and encode all qu
    Type: Grant
    Filed: July 16, 2018
    Date of Patent: March 2, 2021
    Assignee: GOTTFRIED WILHELM LEIBNIZ UNIVERSITÄT HANNOVER
    Inventors: Jan Voges, Jörn Ostermann
  • Patent number: 10936746
    Abstract: Methods and systems are disclosed for genetic manipulation and for securing communication of genetic sequences. In one example, a sequence security system comprises a security device communicatively coupled to a separator module, the separator module comprising a first separator device and a second separator device. The security device may store instructions in non-transitory memory that are executable by a processor to receive a source sequence from the first separator device at a receiving module, receive manipulation instructions from the second separator device at the receiving module, and apply the manipulation instructions to the source sequence to form a target sequence via a transforming module. Thus, the source sequence and the manipulation instructions may be maintained separate from one another until the source sequence and the manipulation instructions are received at the receiving module, for example.
    Type: Grant
    Filed: December 11, 2017
    Date of Patent: March 2, 2021
    Assignee: SEROTINY, INC.
    Inventors: Justin Farlow, Colin Farlow
  • Patent number: 10918014
    Abstract: A fertilization precision control method for water and fertilizer integrated equipment and a control system thereof includes the following steps: step S1, establishing a fertilization precision control model of the water and fertilizer integrated equipment; and step S2, solving an optimal solution of the fertilization precision control model by adopting estimation of distribution algorithms.
    Type: Grant
    Filed: April 7, 2018
    Date of Patent: February 16, 2021
    Assignee: CAMCE WHU DESIGN & RESEARCH CO., LTD.
    Inventors: Lin Yang, Guangxing Wu, Zhengguang Wu, Tailai Li, Chonghua Mao
  • Patent number: 10909687
    Abstract: The present disclosure describes a method of foreground segmentation and nucleus ranking for scoring dual ISH images. The method has been developed to better identify those nuclei, within a selected field of view, that meet the criteria for dual ISH scoring.
    Type: Grant
    Filed: September 26, 2019
    Date of Patent: February 2, 2021
    Assignee: Ventana Medical Systems, Inc.
    Inventors: Anindya Sarkar, Jim Martin
  • Patent number: 10902936
    Abstract: The present invention provides for a method to identify a hospital acquired infection. The method includes computing the number of changes over time between an infection sample and at least a subset of the plurality of infection samples and determining if the number of changes over time is within an interval of an expected number of changes. If so, marking the infection sample as a hospital acquired infection.
    Type: Grant
    Filed: July 11, 2016
    Date of Patent: January 26, 2021
    Assignee: Koninklijke Philips N.V.
    Inventors: Henry Lin, Sitharthan Kamalakaran
  • Patent number: 10896742
    Abstract: Disclosed are techniques for predicting a trait of an individual and identifying a set of enriched record collections of a genetic community. To predict a trait of an individual, DNA features and non-DNA features of the individual are accessed to generate a feature vector that is inputted into a machine learning model. The machine learning model generates a prediction of the trait. The prediction may be based on an inheritance prediction and/or a community prediction. To identify a set of enriched record collections, individuals belonging to a genetic community are identified and a set of candidate record collections are accessed. A community count and a background count is determined for each candidate record collection. The set of enriched record collections are identified based on a comparison of the community count and the background count. The genetic community may be annotated using the set of enriched record collections.
    Type: Grant
    Filed: October 31, 2019
    Date of Patent: January 19, 2021
    Assignee: Ancestry.com DNA, LLC
    Inventors: Ahna R. Girshick, Natalie Telis, Julie M. Granka, Asher Keith Haug Baltzell, Shiya Song
  • Patent number: 10867693
    Abstract: The invention generally relates to genomic studies and specifically to improved methods for read mapping using identified nucleotides at known locations. The invention provides methods of using identified nucleotides at known places in a genome to guide the analysis of sequence reads from that genome by excluding potential mappings or assemblies that are not congruent with the identified nucleotides. Information about a plurality of SNPs in the subject's genome is used to identify candidate paths through a genomic directed acyclic graph (DAG). Sequence reads are mapped to the candidate paths.
    Type: Grant
    Filed: January 8, 2015
    Date of Patent: December 15, 2020
    Assignee: Seven Bridges Genomics Inc.
    Inventor: Deniz Kural
  • Patent number: 10861585
    Abstract: An information processing apparatus includes a memory and a processor coupled to the memory and configured to extract data having x times y bits from genome data in which a mutation pattern at each gene mutation position is represented as x bits, such that the extracted data is constituted by y data pieces each having x bits at y respective mutation positions, x and y being integers greater than or equal to 1, respectively, to refer to an addend table that stores a plurality of addend data associated with respective x-times-y-bit data to identify addend data corresponding to the extracted data, and to use an SIMD instruction to add the identified addend data to count data at positions corresponding to the y mutation positions in the genome data, the count data indicating counts of occurrences of mutation patterns in the genome data.
    Type: Grant
    Filed: September 11, 2017
    Date of Patent: December 8, 2020
    Assignee: FUJITSU LIMITED
    Inventors: Yoshifumi Ujibashi, Minoru Nakamura
  • Patent number: 10861203
    Abstract: Systems and methods for creating filtered data using graphical methodology. Stored data relationally-linked by an ontology are representable in rows and columns format. The system receives a first input selecting a first data source, displays a portion of the first data source in a first chart, receives a second input identifying a portion of the first chart, generates a first filter based on the identified portion, receives a third input selecting a linked object set, displays an indicator of the linked object set in a second sidebar, displays a portion of the linked object set in a second chart depicting information of the linked object set filtered by the first filter, receives a fourth input identifying a portion of the second chart, generates a second filter based on the identified portion, and displays fields of the linked object set, filtered by the first and second filter, in a third chart.
    Type: Grant
    Filed: February 12, 2019
    Date of Patent: December 8, 2020
    Assignee: PALANTIR TECHNOLOGIES INC.
    Inventors: Daniel Cervelli, Timothy Slatcher, Adam Storr
  • Patent number: 10854317
    Abstract: A method to align a next generation sequencing read to a reference sequence includes: (a) receiving a sequencing read; (b) performing a first alignment of the sequencing read to a reference sequence so as to identify a target sequence within the reference sequence whereto the sequencing read maps; (c) selecting a first and a second anchor sequence; (d) attaching the first anchor sequence to the upstream region of the sequencing read and the second anchor sequence to the downstream region of the sequencing read so as to generate an extended sequencing read; (e) attaching the first anchor sequence to the upstream region of the target sequence and the second anchor sequence to the downstream region of the target sequence, so as to generate an extended target sequence; (f) performing a second alignment of the extended sequencing read to the extended target sequence, so that the second alignment is more correctly mapped to the target sequence than the first alignment; (g) identifying a position where one or more b
    Type: Grant
    Filed: December 28, 2018
    Date of Patent: December 1, 2020
    Inventors: Ko-Wen Wu, Kun-Lin Li
  • Patent number: 10847250
    Abstract: This invention relates to a binomial calculation of copy number of data obtained from a mixed sample having a first source and a second source.
    Type: Grant
    Filed: February 10, 2014
    Date of Patent: November 24, 2020
    Assignee: Ariosa Diagnostics, Inc.
    Inventors: Craig Struble, John Stuelpnagel
  • Patent number: 10839940
    Abstract: Exemplary embodiments of the present disclosure relate generally to methods, computer-accessible medium and systems for assembling haplotype and/or genotype sequences of at least one genome, which can be based upon, e.g., consistent layouts of short sequence reads and long-range genome related data. For example, a processing arrangement can be configured to perform a procedure including, e.g., obtaining randomly located short sequence reads, using at least one score function in combination with constraints based on, e.g., the long range data, generating a layout of randomly located short sequence reads such that the layout is globally optimal with respect to the score function, obtained through searching coupled with score and constraint dependent pruning to determine the globally optimal layout substantially satisfying the constraints, generating a whole and/or a part of a genome wide haplotype sequence and/or genotype sequence, and converting a globally optimal layout into one or more consensus sequences.
    Type: Grant
    Filed: December 23, 2009
    Date of Patent: November 17, 2020
    Assignee: NEW YORK UNIVERSITY
    Inventors: Bhubaneswar Mishra, Giuseppe Narzisi
  • Patent number: 10832797
    Abstract: The invention includes methods for aligning reads (e.g., nucleic acid reads, amino acid reads) to a reference sequence construct, methods for building the reference sequence construct, and systems that use the alignment methods and constructs to produce sequences. The invention also includes methods and systems for evaluating the quality of the alignment between the reads and the reference sequence construct. The method is scalable, and can be used to align millions of reads to a construct thousands of bases or amino acids long. The invention additionally includes methods for identifying a disease or a genotype based upon alignment of nucleic acid reads to a location in the construct.
    Type: Grant
    Filed: October 17, 2014
    Date of Patent: November 10, 2020
    Assignee: Seven Bridges Genomics Inc.
    Inventor: Deniz Kural
  • Patent number: 10816537
    Abstract: Improved multi-cell nanopore-based sequencing chips and methods can employ formation, characterization, calibration, and/or normalization techniques. For example, various methods may include one or more steps of performing physical checks of cell circuitry, forming and characterizing a lipid layer on the cells, performing a zero point calibration of the cells, forming and characterizing nanopores on the lipid layers of each cell, performing a sequencing operation to accumulate sequencing signals from the cells, normalizing those sequencing signals, and determining bases based on the normalized sequencing signals.
    Type: Grant
    Filed: April 15, 2019
    Date of Patent: October 27, 2020
    Assignee: Roche Sequencing Solutions, Inc.
    Inventors: Morgan Mager, John Mannion
  • Patent number: 10803381
    Abstract: Techniques related to implementing neural networks for speech recognition systems are discussed. Such techniques may include processing a node of the neural network by determining a score for the node as a product of weights and inputs such that the weights are fixed point integer values, applying a correction to the score based on a correction value associated with at least one of the weights, and generating an output from the node based on the corrected score.
    Type: Grant
    Filed: September 9, 2014
    Date of Patent: October 13, 2020
    Assignee: Intel Corporation
    Inventors: Piotr Rozen, Georg Stemmer
  • 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: 10748663
    Abstract: Techniques are disclosed for discovering, biological elements, functions and pathways, and environmental and nutritional factors related to diseases and medical syndromes. The techniques preprocess database query results and harmonize data using natural language processing before transforming them into the frequency space. The transformed results are analyzed with various categories of machine learning algorithms whose results are normalized, ranked and selectively combined, weighted or un-weighted, to produce a single result ranking the most important elements affecting a target disease or medical syndrome. The invention also uses alternative algorithms producing hypotheses on associations between medical topics, which are used as suggestions for exploratory medical research.
    Type: Grant
    Filed: April 30, 2018
    Date of Patent: August 18, 2020
    Inventor: Efthymios Kalafatis
  • Patent number: 10733701
    Abstract: Systems and methods for dynamic visualization of genomic data are provided in which a genomic visualization system adapts presentation of information content according to scale-relevant annotations within a sequence object.
    Type: Grant
    Filed: October 24, 2018
    Date of Patent: August 4, 2020
    Assignee: Five3 Genomics, LLC
    Inventors: Charles Joseph Vaske, John Zachary Sanborn, Stephen Charles Benz
  • Patent number: 10734105
    Abstract: A system for informed selection of prescriptive therapies. The system includes a computing device configured to receive compositional training data containing a plurality of unclassified data entries. The system is configured to retrieve a user biological profile and generate an unsupervised machine-learning model that utilizes a biological profile as an input and outputs a therapy response label. The system selects a therapy response model and receives from a remote device a proposed prescriptive therapy. The system creates a therapy response model and identifies a prescriptive therapy label for a proposed prescriptive therapy.
    Type: Grant
    Filed: November 30, 2019
    Date of Patent: August 4, 2020
    Inventor: Kenneth Neumann
  • Patent number: 10724110
    Abstract: The invention provides systems and methods for analyzing viruses by representing viral genetic diversity with a directed acyclic graph (DAG), which allows genetic sequencing technology to detect rare variations and represent otherwise difficult-to-document diversity within a sample. Additionally, a host-specific sequence DAG can be used to effectively segregate viral nucleic acid sequence reads from host sequence reads when a sample from a host is subject to sequencing. Known viral genomes can be represented using a viral reference DAG and the viral sequence reads from the sample can be compared to viral DAG to identify viral species or strains from which the reads were derived. Where the viral sequence reads indicate great genetic diversity in the virus that was infecting the host, those reads can be assembled into a DAG that itself properly represents that diversity.
    Type: Grant
    Filed: February 3, 2016
    Date of Patent: July 28, 2020
    Assignee: Seven Bridges Genomics Inc.
    Inventors: Devin Locke, Piotr Szamel
  • Patent number: 10726359
    Abstract: Embodiments in the present disclosure relate generally to computer network architectures for machine learning, artificial intelligence, and automated improvement and regularization of forecasting models, providing rapid improvement of the models. Embodiments may generate such rapid improvement of the models either occasionally on demand, or periodically, or as triggered by events such as an update of available data for such forecasts. Embodiments may indicate, after the improvement of the models, that various web applications using the models may be rerun to seek improved results for the web applications. Embodiments may include a combination of third-party databases to drive the forecasting models, including social media data, financial data, socio-economic data, medical data, search engine data, e-commerce site data, and other databases.
    Type: Grant
    Filed: August 6, 2019
    Date of Patent: July 28, 2020
    Assignee: Clarify Health Solutions, Inc.
    Inventors: Jean P. Drouin, Samuel H. Bauknight, Todd Gottula, Yale Wang, Adam F. Rogow, Jeffrey D. Larson, Justin Warner
  • Patent number: 10726946
    Abstract: A method for computing free energy difference between a reference molecule and a target molecule. The target molecule has the common set of atoms PAB and a set of atoms PB. The method includes applying a potential to restrain an interaction of the additional atomic component from the set of atoms PB with the common set of atoms PAB in the initial state. The method includes determining one or more transition states along a transformation path between the initial state and target state. The method includes scaling the restrain potential correspondingly along the transformation path until the potential becomes zero when a corresponding end state is reached, and calculating the free energy difference between the reference molecule and the target molecule using a value obtained along the transformation path from the initial state to the target state.
    Type: Grant
    Filed: August 22, 2017
    Date of Patent: July 28, 2020
    Assignee: Schrödinger, Inc.
    Inventors: Lingle Wang, Yuqing Deng, Yujie Wu, Byungchan Kim, Robert L. Abel
  • Patent number: 10705008
    Abstract: Particles such as blood cells can be categorized and counted by a digital image processor. A digital microscope camera can be directed into a flowcell defining a symmetrically narrowing flowpath in which the sample stream flows in a ribbon flattened by flow and viscosity parameters between layers of sheath fluid. A contrast pattern for autofocusing is provided on the flowcell, for example at an edge of a rear illumination opening. The image processor assesses focus accuracy from pixel data contrast. A positioning motor moves the microscope and/or flowcell along the optical axis for autofocusing on the contrast pattern target. The processor then displaces microscope and flowcell by a known distance between the contrast pattern and the sample stream, thus focusing on the sample stream. Blood cell images are collected from that position until autofocus is reinitiated, periodically, by input signal, or when detecting temperature changes or focus inaccuracy in the image data.
    Type: Grant
    Filed: March 17, 2014
    Date of Patent: July 7, 2020
    Assignee: Iris International, Inc.
    Inventors: Bart J. Wanders, Brett Jordan, Gregory A. Farrell, Thomas H. Adams, Warren Groner
  • Patent number: 10685740
    Abstract: Methods and systems for monitoring and determining antimicrobial resistance and antimicrobial treatment using genomic subtype information. Various embodiments utilize molecular epidemiology and next-generation sequencing technologies (NGS) to monitor multi-drug resistant pathogens and provide early insight into emergent microbial threats.
    Type: Grant
    Filed: March 10, 2016
    Date of Patent: June 16, 2020
    Assignee: Koninklijke Philips N.V.
    Inventors: Sitharthan Kamalakaran, Pramod Mayigowda, Henry Lin, Sonia Chothani
  • Patent number: 10622096
    Abstract: A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data includes an integrated circuit formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. One of the physical electrical interconnects forms an input to the integrated circuit that may be connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits may be arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the bioinformatics analysis on the reads of genomic data. Each subset of the hardwired digital logic circuits may be formed in a wired configuration to perform the one or more steps in the bioinformatics analysis.
    Type: Grant
    Filed: September 8, 2017
    Date of Patent: April 14, 2020
    Assignee: Edico Genome Corporation
    Inventors: Pieter van Rooyen, Michael Ruehle, Rami Mehio
  • 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
  • Patent number: 10600503
    Abstract: The present invention is directed to a platform (e.g., Web-based) that enables basic and clinical research activities by integrating patient characteristics and clinical outcome data with a variety of high-throughput research data in a unified environment. While several rich data repositories for high dimensional research data exist in the public domain, most focus on a single data type and do not support integration across multiple technologies. The present invention in at least one embodiment includes a broad collection of bioinformatics and systems biology tools for analysis and visualization of four major “omics” types: DNA, mRNA, microRNA, and metabolites, as well as next-generation sequencing. The present invention helps facilitate systems medicine by providing easy identification of trends and patterns in integrated datasets and hence facilitate the use of better targeted therapies for cancer.
    Type: Grant
    Filed: August 3, 2012
    Date of Patent: March 24, 2020
    Assignee: GEORGETOWN UNIVERSITY
    Inventors: Subha Madhavan, Michael A. Harris, Yuriy Gusev, Andrew Shinohara, David M. Tanenbaum, Kevin Rosso
  • Patent number: 10597711
    Abstract: A method for nucleic acid sequencing includes: disposing a plurality of template polynucleotide strands, sequencing primers, and polymerases in a plurality of defined spaces of a sensor array; exposing template polynucleotide strands to a series of flows of nucleotide species, the series comprising a sequence of random flows; and obtaining, for each of the series of flows of nucleotide species, a signal indicative of how many nucleotide incorporations occurred for that particular flow to determine a predicted sequence of nucleotides corresponding to the template polynucleotide strands.
    Type: Grant
    Filed: April 9, 2013
    Date of Patent: March 24, 2020
    Assignee: LIFE TECHNOLOGIES CORPORATION
    Inventors: Earl Hubbell, Jonathan Schultz
  • Patent number: 10597696
    Abstract: Provided herein are methods for detecting an increased probability or risk of neurodegeneration in a subject. In some embodiments the method comprises assaying a sample from the subject for lysozyme and/or cathepsin S and detecting the lysozyme and/or cathepsin S from the sample, wherein an increased lysozyme and/or cathepsin S compared to levels in a control subject sample indicate an increased probability or risk of neurodegeneration. Methods of treatment and screening assays for determining drug effectiveness are also provided herein.
    Type: Grant
    Filed: September 18, 2014
    Date of Patent: March 24, 2020
    Assignee: University of Notre Dame du Lac
    Inventors: Kasturi Haldar, Md. Suhail Alam
  • Patent number: 10586609
    Abstract: A method and apparatus for determining similarity among gene sequences, for compressing a gene sequence, and for decompressing a gene sequence. The method for determining similarity between a first gene sequence and a second gene sequence includes: moving a sliding window of a predefined length on the first gene sequence and the second gene sequence respectively; extracting a first part String1i of the first gene sequence within the sliding window, and a second part String2i of the second gene sequence within the sliding window during the ith movement of the sliding window; and determining similarity between the first gene sequence and the second gene sequence based on the first part String1i and the second part String2i. Also provided is an apparatus for the above method.
    Type: Grant
    Filed: October 29, 2015
    Date of Patent: March 10, 2020
    Assignee: International Business Machines Corporation
    Inventors: Jian Dong Ding, Sheng Huang, Junchi Yan, Ya Nan Zhang, Jun Zhu
  • Patent number: 10564123
    Abstract: A system and method for continuously monitoring as well as identifying and quantifying intracellular components in a cell culture such as microalgal culture of a bioreactor is described. This is done to determine an optimum concentration of intracellular components of interest, such as lipids. The method may be integrated directly with the cultivation chamber to conduct real-time measurements to quickly obtain accurate and continuous information that may be used as feedback to control the cultivation growth conditions. Such characterization may provide highly relevant data to determine if the culture is ready for biofuel processing. If the culture is not ready for biofuel processing, the data allows for the modification of the growth condition in the microalgae culture in order to achieve the desired concentration of the microalgal intracellular component of interest for biofuel processing.
    Type: Grant
    Filed: May 11, 2018
    Date of Patent: February 18, 2020
    Assignee: UNITED ARAB EMIRATES UNIVERSITY
    Inventors: Mahmoud F. Y. Al Ahmad, Hina Laghari
  • Patent number: 10557821
    Abstract: In one exemplary embodiment, a method for detecting variants in electropherogram data is provided. The method includes receiving electropherogram data from an instrument and analyzing the electropherogram data to identify mixed bases in the electropherogram data. The method further includes validating the identified mixed bases. Then the method includes determining variants in the electropherogram data based on the validated mixed bases.
    Type: Grant
    Filed: February 1, 2019
    Date of Patent: February 11, 2020
    Assignee: LIFE TECHNOLOGIES CORPORATION
    Inventors: David Denny, David Woo, Manjula Aliminati, Siva Kumar Samsani, Stephanie Schneider, Yoke Peng Lim, Sylvia Chang
  • Patent number: 10540324
    Abstract: Disclosed is a human haplotyping method. The method includes: collecting a sequence of a gene to be analyzed; matching and aligning reads of the collected sequence to a reference stored in a database; electing candidate alleles from among alleles of the reference; and selecting a final allele from among the candidate alleles.
    Type: Grant
    Filed: January 9, 2019
    Date of Patent: January 21, 2020
    Assignee: SYNTEKABIO CO., LTD.
    Inventors: Jongsun Jung, Sunho Lee, Sojeong Ka, Jonghui Hong, Yangrae Cho
  • Patent number: 10515450
    Abstract: Embodiments of the present disclosure provide for methods and systems for preparing chromosomal spread for a selected cell so that chromosomal spreads and/or translocations can be correlated with the selected cell.
    Type: Grant
    Filed: October 20, 2017
    Date of Patent: December 24, 2019
    Assignee: University of Florida Research Foundation, Inc.
    Inventors: Tanmay P. Lele, Wallace Gregory Sawyer
  • Patent number: 10501779
    Abstract: Novel methods and compositions for identifying one or more factors associated with a nucleic acid sequence (e.g., DNA and/or RNA) of interest are provided.
    Type: Grant
    Filed: May 11, 2012
    Date of Patent: December 10, 2019
    Assignee: President and Fellows of Harvard College
    Inventors: Chao-ting Wu, Brian Beliveau
  • Patent number: 10503967
    Abstract: A system includes an interface configured to receive time series data representing information from a plurality of sensors, and a processor configured to construct a behavior model based on the time series data. The processor identifies features in the time series data, divides the time series data of each of the identified features into segments, and extracts feature components from the segments. The processor further constructs a plurality of state graphs, each state graph including components connected by weighted edges, constructs a behavior graph, wherein the state graphs form vertices of the behavior graph, clusters the state graphs in the behavior graph; and selects a representative state graph from each cluster, wherein the behavior model includes the selected state graphs.
    Type: Grant
    Filed: November 23, 2015
    Date of Patent: December 10, 2019
    Assignee: THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
    Inventors: Majid Sarrafzadeh, Foad Dabiri, Hyduke Noshadi
  • Patent number: 10495561
    Abstract: Particles such as blood cells can be categorized and counted by a digital image processor. A digital microscope camera can be directed into a flowcell defining a symmetrically narrowing flowpath in which the sample stream flows in a ribbon flattened by flow and viscosity parameters between layers of sheath fluid. A contrast pattern for autofocusing is provided on the flowcell, for example at an edge of a rear illumination opening. The image processor assesses focus accuracy from pixel data contrast. A positioning motor moves the microscope and/or flowcell along the optical axis for autofocusing on the contrast pattern target. The processor then displaces microscope and flowcell by a known distance between the contrast pattern and the sample stream, thus focusing on the sample stream. Blood cell images are collected from that position until autofocus is reinitiated, periodically, by input signal, or when detecting temperature changes or focus inaccuracy in the image data.
    Type: Grant
    Filed: March 17, 2014
    Date of Patent: December 3, 2019
    Assignee: Iris International, Inc.
    Inventors: Bart J. Wanders, Brett Jordan, Gregory A. Farrell, Thomas H. Adams, Warren Groner
  • Patent number: 10475190
    Abstract: The present disclosure describes a method of foreground segmentation and nucleus ranking for scoring dual ISH images. The method has been developed to better identify those nuclei, within a selected field of view, that meet the criteria for dual ISH scoring.
    Type: Grant
    Filed: July 25, 2017
    Date of Patent: November 12, 2019
    Assignee: VENTANA MEDICAL SYSTEMS, INC.
    Inventors: Anindya Sarkar, Jim Martin
  • Patent number: 10467749
    Abstract: The present disclosure provides a method and a system for processing an image. The method includes: an image pre-processing step, including analyzing an image input to be processed so as to obtain a first image; and a spot detecting step, including analyzing the first image so as to compute a spot determining threshold; analyzing the first image so as to acquire a candidate pixel spot, and judging whether the candidate pixel spot is the spot according to the spot determining threshold; computing a sub-pixel center coordinate of the spot and an intensity value of the sub-pixel center coordinate if yes; and discarding the candidate pixel spot if no. According to the method, the image is denoised in the image pre-processing step, such that a calculation in the spot detecting step may be reduced. In addition, the accuracy of determining the image spot may be improved.
    Type: Grant
    Filed: October 5, 2017
    Date of Patent: November 5, 2019
    Assignee: GENEMIND BIOSCIENCES COMPANY LIMITED
    Inventors: Weibin Xu, Huan Jin, Qin Yan, Zefei Jiang, Zhiliang Zhou
  • Patent number: 10428367
    Abstract: A portable detector is disclosed for detecting certain analytes of interest, such as genetic material (e.g., nucleic acids). The detector includes a reading component for the detection of the analytes, and control circuitry for controlling operation of the reading component. Processing circuitry may be included to perform both primary analysis of acquired data, and where desired, secondary analysis. Where desired, some or all of the computationally intensive tasks may be off-loaded to enhance the portability and speed of the device. The device may incorporate various types of interface, technologies for reading and analysis, positioning system interfaces, and so forth. A number of exemplary use cases and methods are also disclosed.
    Type: Grant
    Filed: July 13, 2016
    Date of Patent: October 1, 2019
    Assignee: ILLUMINA, INC.
    Inventors: Robert C. Kain, Min-Jui Richard Shen, John A. Moon, Helmy A. Eltoukhy
  • Patent number: 10373707
    Abstract: Embodiments of the present invention include method, systems and computer program products for algebraic phasing of polyploids. Aspects of the invention include receiving a matrix including a set of two or more single-nucleotide poloymorphisms (SNPs) for two or more sample organisms. Each row of the matrix is set to a ploidy based on a number of ploidies present in the two or more sample organisms. Each allele in the set of two or more SNPs is represented as a binary number. A set of algebraic rules is received, wherein the set of algebraic rules include an algebraic phasing algorithm. And the set of algebraic rules are applied to the matrix to determine a haplotype of a parent of the two or more sample organisms.
    Type: Grant
    Filed: December 31, 2018
    Date of Patent: August 6, 2019
    Assignee: INTERNATIONAL BUSINESS MACHINES CORPORATION
    Inventors: Laxmi P. Parida, Filippo Utro
  • Patent number: 10364465
    Abstract: The disclosure provides a plurality of nucleic acid sequences comprising multiple variants of a reference sequence. The disclosure further provides plasmids, cells, methods and kits comprising the same.
    Type: Grant
    Filed: August 15, 2014
    Date of Patent: July 30, 2019
    Assignee: Life Technologies Corporation
    Inventors: Mona Shahbazian, Kara Norman, Aron Lau, Nakul Nataraj