Gene Sequence Determination Patents (Class 702/20)
  • Patent number: 11361842
    Abstract: Techniques are provided for detecting copy number variations. Each sequence read of a set of sequence reads is aligned with a portion of a reference sequence. A coverage vector is generated that includes a plurality of elements, each element in the plurality of elements indicating a number of the set of sequence reads that were aligned to a particular position within the reference sequence. A normalization vector is accessed that was generated based on performance of a component analysis on a set of other coverage vectors corresponding to a set of other subjects. An adjusted coverage vector is generated using the coverage vector and normalization vector. One or more subject-specific normalization values are generated based on the coverage vector. One or more copy number variations are identified that corresponding to the sample using the adjusted coverage vector and the subject-specific normalization values.
    Type: Grant
    Filed: August 4, 2021
    Date of Patent: June 14, 2022
    Assignee: Color Health, Inc.
    Inventors: Ryan Barrett, Nishant Bhat, Huy Hong, Katsuya Noguchi, Wendy McKennon, Krishna Pant, Taylor Sittler, Othman Laraki, Elad Gil
  • Patent number: 11345948
    Abstract: Provided is a method for detecting chromosomal Robertsonian translocation and the SNP (single nucleotide polymorphism) site and primer composition for use therein. The method is practical, simple, convenient and high in universality; moreover, a high-throughput sequencing technology is combined, so that the method has the advantages of low cost, and high sensitivity, specificity and accuracy.
    Type: Grant
    Filed: January 19, 2016
    Date of Patent: May 31, 2022
    Assignee: PEKING JABREHOO TECHNOLOGY CO. LTD
    Inventors: Tao Feng, Jia Fei
  • Patent number: 11347965
    Abstract: The technology disclosed relates to generating ground truth training data to train a neural network-based template generator for cluster metadata determination task. In particular, it relates to accessing sequencing images, obtaining, from a base caller, a base call classifying each subpixel in the sequencing images as one of four bases (A, C, T, and G), generating a cluster map that identifies clusters as disjointed regions of contiguous subpixels which share a substantially matching base call sequence, determining cluster metadata based on the disjointed regions in the cluster map, and using the cluster metadata to generate the ground truth training data for training the neural network-based template generator for the cluster metadata determination task.
    Type: Grant
    Filed: March 20, 2020
    Date of Patent: May 31, 2022
    Assignee: Illumina, Inc.
    Inventors: Anindita Dutta, Dorna Kashefhaghighi, Amirali Kia
  • Patent number: 11345724
    Abstract: The present invention relates to a compound of formula (I), wherein X is C?O, C?S or B—OH; Y is an electrophile and Z is a leaving group, or Y?Z is an electrophile; R1 comprises or consists of (a) (i) a first group binding to a proteolytic site of a proteasome, the first group being bound to X; and (ii) optionally a second group enhancing delivery; or (b) a group binding between subunits ?1 and ?2 of a proteasome; R2 and R3 are independently selected from H, methyl, methoxy, ethyl, ethenyl, ethynyl and cyano, wherein methyl and ethyl may be substituted with OH or halogen.
    Type: Grant
    Filed: June 6, 2017
    Date of Patent: May 31, 2022
    Assignee: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V.
    Inventors: Ashwin Chari, Holger Stark, Jil Schrader, Fabian Henneberg
  • Patent number: 11342048
    Abstract: A computer-based genomic annotation system, including a database configured to store genomic data, non-transitory memory configured to store instructions, and at least one processor coupled with the memory, the processor configured to implement the instructions in order to implement an annotation pipeline and at least one module filtering or analysis of the genomic data.
    Type: Grant
    Filed: March 12, 2019
    Date of Patent: May 24, 2022
    Assignee: THE SCRIPPS RESEARCH INSTITUTE
    Inventors: Ali Torkamani, Nicholas Schork
  • Patent number: 11314514
    Abstract: A data processing system 2 supporting vector processing operations uses scaling vector length querying instructions. The scaling vector length querying instructions return a result which is dependent upon a number of elements in a vector for a variable vector element size specified by the instruction and multiplied by a scaling value specified by the instruction. The scaling vector length querying instructions may be in the form of count instructions, increment instructions or decrement instructions. The instructions may include a pattern constraint applying a constraint, such as modulo(M) or power of 2 to the partial result value representing the number of vector elements provided for the register element size specified for the instruction.
    Type: Grant
    Filed: June 23, 2016
    Date of Patent: April 26, 2022
    Assignee: Arm Limited
    Inventors: Nigel John Stephens, Grigorios Magklis, Alejandro Martinez Vicente, Nathanael Premillieu
  • Patent number: 11302418
    Abstract: The current invention concerns a computer-implemented method, a computer system and a tangible non-transitory computer-readable data carrier comprising a computer program product for aligning a query nucleic acid sequence against a reference nucleic acid sequence. An optimal alignment score of the query sequence against the reference sequence is determined by a dynamic programming algorithm. The algorithm is configured for locally optimizing a partial alignment score based on a nucleotide substitution cost, a gap insertion cost, an amino acid substitution cost, as well as a frameshift penalty.
    Type: Grant
    Filed: May 31, 2018
    Date of Patent: April 12, 2022
    Assignee: Emweb bvba
    Inventor: Koen Deforche
  • Patent number: 11255813
    Abstract: A method for nucleic acid sequencing includes receiving a plurality of signals indicative of a parameter measured for a plurality of defined spaces, at least some of the defined spaces including one or more sample nucleic acids, the signals being responsive to a plurality of nucleotide flows introducing nucleotides to the defined spaces; determining, for at least some of the defined spaces, whether the defined space includes a sample nucleic acid; processing, for at least some of the defined spaces determined to include a sample nucleic acid, the received signals to improve a quality of the received signals; and predicting a plurality of nucleotide sequences corresponding to respective sample nucleic acids for the defined spaces based on the processed signals and the nucleotide flows.
    Type: Grant
    Filed: February 11, 2019
    Date of Patent: February 22, 2022
    Assignee: Life Technologies Corporation
    Inventors: Melville Davey, Simon Cawley, Alan Williams
  • Patent number: 11250932
    Abstract: Disclosed herein are methods of identifying infections, such as methods of identifying bacterial infections which utilize whole metagenome sequence analysis to sequence the entire wound microbiome of clinical samples. The disclosed methods use fast k-mer based sequence analysis, predictive modeling, and Bayesian network analysis, to analyze bacterial metagenomic sequence compositions in conjunction with clinical factors to stratify communities of bacteria into healing versus non-healing clusters. The methods of identifying infections can include performing molecular analysis of a patient wound sample, preparing the data obtained from the molecular analysis, diagnosing the wound sample and/or prognosing the wound sample. The disclosed methods can also be used to identify protein function as well as novel biomarkers.
    Type: Grant
    Filed: February 18, 2015
    Date of Patent: February 15, 2022
    Assignee: Arizona Board of Regents on Behalf of the University of Arizona
    Inventors: George S. Watts, Bonnie L. Hurwitz
  • Patent number: 11205501
    Abstract: Determination of a frequency distribution of nucleotide sequence variants—differing from a nucleotide reference by at least one intermediate part—of a sample is disclosed. A reference set of sequence read data is generated by performing a plurality of reference sequence reads (each having a read start site, RSS) for each sequence reference variant of a reference variant list. It is determined (for each RSS and for the intermediate part of each sequence reference variant) whether the intermediate part is detectable by corresponding reference sequence read. A sample set of sequence read data is generated by performing sample sequence reads for the sample, and a total number of occurrences in the sample set is determined for each RSS and for the intermediate part of each sequence reference variant. The frequency distribution of the plurality of nucleotide sequence variants is determined based on the number of occurrences determined for an RSS where the intermediate part is detectable.
    Type: Grant
    Filed: April 2, 2019
    Date of Patent: December 21, 2021
    Assignee: TIGERQ AB
    Inventors: David Yudovich, Jonas Larsson
  • Patent number: 11193175
    Abstract: Values for tumor mutation burden from different samples can be made more comparable to each other or control standards by a normalization regime that takes into account the minor allele fraction of highly rated mutations in a sample. Such analysis can provide an indication where the tumor mutation burden of a test sample lies on a distribution of tumor mutation burdens in a control population, and thus, whether the individual providing the test sample is likely to be amenable to immunotherapy to treat cancer.
    Type: Grant
    Filed: May 4, 2020
    Date of Patent: December 7, 2021
    Assignee: GUARDANT HEALTH, INC.
    Inventor: Darya Chudova
  • Patent number: 11193878
    Abstract: Techniques are disclosed relating to fluorescence-based flow cytometry. A flow cytometer may include a partially-reflective surface configured to reflect a first portion of fluorescent emissions from a sample to a first optical sensor and direct a second, greater portion of fluorescent emissions from the sample to a second optical sensor and a controller configured to determine a value representing the intensity of the fluorescent emissions based on a first measurement taken by the first optical sensor, a second measurement taken by the second optical sensor, or both. A flow cytometer may include a baseplate with a first side and a second, opposing side with a flow cell, a laser, and a reflective surface disposed above the first side and an optical sensor and isolating material disposed below the second side. The reflective surface receives fluorescent emissions and reflects at least a portion through the baseplate to the optical sensor.
    Type: Grant
    Filed: October 29, 2020
    Date of Patent: December 7, 2021
    Assignee: Chandlertec Inc.
    Inventor: Van S. Chandler
  • Patent number: 11135699
    Abstract: Systems and methods of providing run-time quality control and monitoring of a single or multiple sequencing runs are provided herein. In some embodiments, the run-time system includes or is in communication with a processor capable of determining various types of run-time information relating to the quality, progress, etc. of various sequencing runs. In some embodiments, the system can also be in communication with a user interface, for example, a GUI, capable of representing and communicating various types of information to a user regarding the quality of the individual or multiple runs, the functioning of the instrument, an error event, etc. Additionally, the system can capable of receiving actionable information from a user via the GUI thereby allowing the user to terminate or repeat various sequencing steps in a particular run, terminate a entire run, terminate all runs, allow a run to proceed, etc.
    Type: Grant
    Filed: July 18, 2017
    Date of Patent: October 5, 2021
    Assignee: Life Technologies Corporation
    Inventors: Yerramalli Subramaniam, Puneet Suri, Sylvia Chang, Chengyong Yang
  • 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: 11094397
    Abstract: Techniques for securely encoding, communicating, and comparing genomic information using probabilistic data structures are provided. In some embodiments, genomic information in a secure computing environment may be encoded and/or anonymized by building a probabilistic data structure that represents sub-strings of the genomic information as members of a set; the probabilistic data structure may then be securely transmitted outside the secure computing environment. In some embodiments, a probabilistic data structure representing sub-strings of sensitive genomic information as members of a set may be received in an unsecure computing environment and may be queried to generate output data indicating whether reference sub-strings are probable members of the set.
    Type: Grant
    Filed: May 11, 2018
    Date of Patent: August 17, 2021
    Assignee: NOBLIS, INC.
    Inventor: Tyler W. Barrus
  • Patent number: 11041199
    Abstract: Provided herein and methods and apparatuses for sequencing nucleic acids. For example, provided is an analytical detection apparatus, including (a) a stage configured to support a flow cell; (b) a detector configured to observe a detection channel of the flow cell when the flow cell is supported by the stage; (c) a plurality of fluid delivery channels, wherein each of the fluid delivery channels fluidically connects a reservoir to the detection channel of the flow cell; and (d) a first heater configured to heat the plurality of fluid delivery channels.
    Type: Grant
    Filed: December 19, 2019
    Date of Patent: June 22, 2021
    Assignee: Omniome, Inc.
    Inventors: Michael John Erickstad, Eric Villarreal, Vyshnavi Balakrishnan, Xenia Aparicio, Rebecca McGinley, Arnold Oliphant
  • 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: 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: 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: 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: 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: 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: 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: 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: 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