Gene Sequence Determination Patents (Class 702/20)
  • Patent number: 11822541
    Abstract: Various techniques for accelerating Smith-Waterman sequence alignments are provided. For example, threads in a group of threads are employed to use an interleaved cell layout to store relevant data in registers while computing sub-alignment data for one or more local alignment problems. In another example, specialized instructions that reduce the number of cycles required to compute each sub-alignment score are utilized. In another example, threads are employed to compute sub-alignment data for a subset of columns of one or more local alignment problems while other threads begin computing sub-alignment data based on partial result data received from the preceding threads. After computing a maximum sub-alignment score, a thread stores the maximum sub-alignment score and the corresponding position in global memory.
    Type: Grant
    Filed: September 30, 2021
    Date of Patent: November 21, 2023
    Inventors: Maciej Piotr Tyrlik, Ajay Sudarshan Tirumala, Shirish Gadre
  • Patent number: 11821039
    Abstract: Provided herein is technology relating to detecting neoplasia and particularly, but not exclusively, to methods, compositions, and related uses for detecting premalignant and malignant neoplasms such as pancreatic and colorectal cancer.
    Type: Grant
    Filed: May 12, 2020
    Date of Patent: November 21, 2023
    Assignees: Mayo Foundation for Medical Education and Research, Exact Sciences Corporation
    Inventors: David A. Ahlquist, John B. Kisiel, William R. Taylor, Tracy C. Yab, Douglas W. Mahoney, Graham P. Lidgard, Hatim T. Allawi
  • Patent number: 11821031
    Abstract: Technical solutions for mapping long nucleic acid sequence reads to a target sequence are provided. A directed graph, representing all or some of a genome and comprising one or more nonlinear topological components, is obtained for an organism having a heterozygous genome. Each nonlinear topological component has an initiating node and a terminal node connected by at least a first branch and a second branch. One of these branches corresponds to the target sequence. The directed graph uses a plurality of sequence reads from a biological sample of the organism. The sequence reads are overlapped by an unrestricted overhang amount, provided there is a minimum consensus region between each two sequence reads. A query sequence, encompassing at least the initiating node or the terminal node of a first nonlinear topological component, is obtained. The directed graph is used to form a mapping of the query sequence to the directed graph.
    Type: Grant
    Filed: January 24, 2020
    Date of Patent: November 21, 2023
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Ivan Sović, James Drake
  • Patent number: 11817177
    Abstract: The present disclosure provides a method for enriching for multiple genomic regions using a first bait set that selectively hybridizes to a first set of genomic regions of a nucleic acid sample and a second bait set that selectively hybridizes to a second set of genomic regions of the nucleic acid sample. These bait set panels can selectively enrich for one or more nucleosome-associated regions of a genome, said nucleosome-associated regions comprising genomic regions having one or more genomic base positions with differential nucleosomal occupancy, wherein the differential nucleosomal occupancy is characteristic of a cell or tissue type of origin or disease state.
    Type: Grant
    Filed: November 14, 2022
    Date of Patent: November 14, 2023
    Assignee: Guardant Health, Inc.
    Inventors: Darya Chudova, Helmy Eltoukhy, Stefanie Ann Ward Mortimer, Diana Abdueva
  • Patent number: 11817191
    Abstract: The present invention relates to a system and methods for displaying genomic and clinical information. More specifically, the invention is directed to a system for collecting, displaying, and modeling an individual's genomic makeup, physiological characteristics, healthcare history, and lifestyle to enable personalized medicine, better understand the transition from health to disease, and identify additional risk factors for disease. Certain embodiments of the system facilitate generating and displaying a patient record on a graphical user interface. Additionally, embodiments of the invention allow users through the use of user interface to annotate, augment, and overall interact with the clinically more accurate and detailed user interface.
    Type: Grant
    Filed: January 8, 2021
    Date of Patent: November 14, 2023
    Assignee: Leap of Faith Technologies, Inc.
    Inventors: Frank Naeymi-Rad, Barbara Rapchak
  • Patent number: 11810305
    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 21, 2022
    Date of Patent: November 7, 2023
    Assignee: Ventana Medical Systems, Inc.
    Inventors: Anindya Sarkar, Jim Martin
  • Patent number: 11810229
    Abstract: A graph display device includes: a display unit; and at least one processor, wherein the at least one processor is configured to convert a mathematical formula including two variables into a three-dimensional graph formula and display the three-dimensional graph formula on the display unit as a first three-dimensional graph.
    Type: Grant
    Filed: February 17, 2022
    Date of Patent: November 7, 2023
    Assignee: CASIO COMPUTER CO., LTD.
    Inventor: Hirokazu Tanaka
  • Patent number: 11804285
    Abstract: A method of detecting biomarkers using an artificial intelligence (AI) deep learning model for conversion data of nucleotide sequences and mutations of population genomes, the method including: collecting nucleotide sequences and mutations of population genomes; generating conversion data by reflecting mutations of diploid genomes in the collected nucleotide sequences; performing an artificial intelligence (AI) deep learning model with the generated conversion data; generating a fully connected network (FCN) by connecting the results obtained by the machine learning; and extracting biomarkers by the learned model.
    Type: Grant
    Filed: November 21, 2018
    Date of Patent: October 31, 2023
    Assignee: SYNTEKABIO, INC.
    Inventors: Jongsun Jung, Jaeyun Yoo, Jaemin Seol
  • Patent number: 11803777
    Abstract: Displaying an indication of ancestral data is disclosed. An indication that a genetic interval corresponds to a reference interval that has a likelihood of having one or more ancestral origins is received. One or more graphic display parameters are determined based at least in part on the indication. An indication of the one or more ancestral origins is visually displayed using the one or more graphic display parameters.
    Type: Grant
    Filed: March 8, 2023
    Date of Patent: October 31, 2023
    Assignee: 23andMe, Inc.
    Inventors: John Michael Macpherson, Brian Thomas Naughton, Joanna Louise Mountain
  • Patent number: 11782061
    Abstract: The present inventors have surprisingly found that a deoxyhypusine synthase (DHPS) gene, which was previously reported to correlate with prostate cancer and cervical cancer, is highly responsive to arteriosclerosis or digestive system cancer, whereby the gene can be used as a desired marker for arteriosclerosis or digestive system cancer. The present invention has been accomplished on the basis of this finding. Specifically, the present invention provides a method for determining arteriosclerosis or digestive system cancer, which method includes detecting expression of a deoxyhypusine synthase gene in a test sample (preferably a blood sample), and determining arteriosclerosis or digestive system cancer of a test subject from which the test sample has been obtained, on the basis of an increase in the gene expression as an index.
    Type: Grant
    Filed: November 5, 2015
    Date of Patent: October 10, 2023
    Assignees: FUJIKURA KASEI CO., LTD., National University Corporation Chiba University
    Inventors: Rika Nakamura, Hideyuki Kuroda, Go Tomiyoshi, Takaki Hiwasa, Masaki Takiguchi, Naokatsu Saeki
  • Patent number: 11776660
    Abstract: An information processing apparatus includes an input, a blood-relative list generator, a similar image searcher, and a suspect information generator. The input receives DNA information of a suspect and facial image relating to a plurality of facial images. The blood relative list generator generates a list of blood relatives who are presumed to be blood relatives of the suspect from a plurality of pieces of DNA information. The similar image searcher calculates degree of similarity between facial images of persons on the blood-relative list and each of the plurality of facial images, and searches for and retrieves a facial image resembling the image of the person on the blood-relative list based on the calculated degree of similarity. The suspect information generation part generates suspect information by associating information relating to the retrieved facial image with information relating to the person on the blood-relative list who resembles the retrieved facial image.
    Type: Grant
    Filed: April 26, 2022
    Date of Patent: October 3, 2023
    Inventor: Minoru Asogawa
  • Patent number: 11749384
    Abstract: A system and related method exchange medical information with a medical management system. The method comprises receiving, using a processor of a code point resolver, from the medical management system, medical text via a network interface. A code point is a single standardized medical terminology code (SMTC) that corresponds to a medical concept contained within the medical text. The method further applies rule-based logic to process the medical text to form a localized mapping of a text portion of the medical text to a plurality of candidate SMTCs (CSMTCs) that are related to at least one metathesaurus concept entity (MCE) in a metathesaurus, and to determines the code point from the CSMTCs. The method transmits, via the network interface, to the medical management system, the code point.
    Type: Grant
    Filed: January 29, 2021
    Date of Patent: September 5, 2023
    Inventors: Nicholas Todd Lawrence, Fernando Jose Suarez Saiz, Corey Sanders, Robert Louis Nielsen
  • Patent number: 11749381
    Abstract: A method for identifying a pathogen contained in a metagenomic sample and for identifying pathogenic markers in the genome of the pathogen includes: processing the sample to extract DNA from pathogens, sequencing the extracted DNA, thereby producing a set of reads, comparing the reads to a database of genomes of known pathogens to assign reads to the pathogens; producing a pool of reads and assembling them to produce contigs, comparing the contigs to a second database of markers to check whether they contain a marker. The method further includes the step of comparing the reads to the second database to assign reads to the markers, a read being assigned to a marker if it falls entirely into or is astride the marker, and the pool also includes the reads assigned to the markers, the contigs thereby being assembled from reads assigned to a pathogen and reads assigned to markers.
    Type: Grant
    Filed: October 12, 2017
    Date of Patent: September 5, 2023
    Assignee: BIOMÉRIEUX
    Inventors: Pierre Mahe, Maud Tournoud, Stéphane Schicklin, Ghislaine Guigon, Etienne Ruppe
  • Patent number: 11750629
    Abstract: An example device includes processing circuitry and a memory. The memory includes instructions that cause the device to perform various functions. The functions include receiving datastreams from a plurality of sensors of a high performance computing system, classifying each datastream of the each sensor to one of a plurality of datastream models, selecting an anomaly detection algorithm from a plurality of anomaly detection algorithms for each datastream, determining parameters of the each anomaly detection algorithm, determining an anomaly threshold for each datastream, and generating an indication that the sensor associated with the datastream is acting anomalously.
    Type: Grant
    Filed: September 18, 2020
    Date of Patent: September 5, 2023
    Assignee: Hewlett Packard Enterprise Development LP
    Inventors: Sergey Serebryakov, Tahir Cader, Nanjundaiah Deepak
  • Patent number: 11735323
    Abstract: A method, software, database and system for attribute partner identification and social network based attribute analysis are presented in which attribute profiles associated with individuals can be compared and potential partners identified. Connections can be formed within social networks based on analysis of genetic and non-genetic data. Degrees of attribute separation (genetic and non-genetic) can be utilized to analyze relationships and to identify individuals who might benefit from being connected.
    Type: Grant
    Filed: November 17, 2022
    Date of Patent: August 22, 2023
    Assignee: 23andMe, Inc.
    Inventors: Andrew Alexander Kenedy, Charles Anthony Eldering
  • Patent number: 11705217
    Abstract: Methods and systems for single molecule sequencing using concatemers of copies of sense and antisense strands. Concatemers are provided, for example, by carrying out rolling circle amplification on a circular molecule having sense and antisense regions to produce repeated copies of the sense and antisense regions connected by linking regions. The circular molecules can be produced by ligating hairpin adapters to each end of a double-stranded nucleic acid having a sense and antisense strand. The ligations can be carried out, for example using blunt end ligation. In some cases, a single molecule consensus sequence for a single template molecule is obtained. A single read from each template molecule can be obtained by comparing the sequence information of the sense and antisense regions.
    Type: Grant
    Filed: January 19, 2018
    Date of Patent: July 18, 2023
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Kevin Travers, Geoff Otto, Stephen Turner, Cheryl Heiner, Congcong Ma
  • Patent number: 11676686
    Abstract: Methods and computer apparatuses are disclosed for processing genomic data in at least partially automated workflows of modules. A method comprises: specifying a source from which nucleic acid sequence(s) are to be obtained; selecting module(s) for processing data, including at least one module for processing the one or more nucleic acid sequences; presenting, in a graphical user interface, graphical components representing the source and the module(s) as nodes within a workspace; receiving, via the graphical user interface, inputs arranging the source and the module(s) as a workflow comprising a series of nodes, the series indicating, for each particular module, that output from one of the source or another particular module is to be input into the particular module; generating an output for the workflow based upon the nucleic acid sequence(s) by processing each module in an order indicated by the series.
    Type: Grant
    Filed: June 23, 2021
    Date of Patent: June 13, 2023
    Assignee: Palantir Technologies Inc.
    Inventors: Lekan Wang, Hyunghoon Cho, Abimanyu Raja, Elizabeth Caudill
  • Patent number: 11644470
    Abstract: The present systems and methods are directed to de novo identification of peptide sequences from tandem mass spectrometry data. The systems and methods uses unconverted mass spectrometry data from which features are extracted. Using unconverted mass spectrometry data reduces the loss of information and provides more accurate sequencing of peptides. The systems and methods combine deep learning and neural networks to sequencing of peptides.
    Type: Grant
    Filed: April 13, 2020
    Date of Patent: May 9, 2023
    Inventors: Rui Qiao, Ngoc Hieu Tran, Lei Xin, Xin Chen, Baozhen Shan, Ali Ghodsi, Ming Li
  • Patent number: 11646102
    Abstract: Disclosed herein are systems and methods for performing secondary analyses of nucleotide sequencing data in a time-efficient manner. Some embodiments include performing a secondary analysis iteratively while sequence reads are generated by a sequencing system. Secondary analyses can encompass both alignment of sequence reads to a reference sequence (e.g., the human reference genome sequence) and utilization of this alignment to detect differences between a sample and the reference. Secondary analysis can enable detection of genetic differences, variant detection and genotyping, identification of single nucleotide polymorphisms (SNPs), small insertions and deletion (indels) and structural changes in the DNA, such as copy number variants (CNVs) and chromosomal rearrangements.
    Type: Grant
    Filed: October 6, 2017
    Date of Patent: May 9, 2023
    Inventors: Francisco Jose Garcia, Come Raczy, Aaron Day, Michael J. Carney
  • Patent number: 11646101
    Abstract: A method for global mapping between a first sequence Xp and a second sequence Xg.
    Type: Grant
    Filed: June 5, 2019
    Date of Patent: May 9, 2023
    Inventors: Xin Gao, Renmin Han, Sheng Wang, Yu Li
  • Patent number: 11636952
    Abstract: A method of measuring body fluid content, the method comprising computer executed steps, the steps comprising: receiving a value of a temperature of a body part of a subject, and generating corrective data based on the received measured temperature value and on previously gathered data, the corrective data being usable for correcting a measurement of content of a fluid sample taken from the body part.
    Type: Grant
    Filed: June 30, 2018
    Date of Patent: April 25, 2023
    Assignee: AZURE VAULT LTD.
    Inventor: Ze'ev Russak
  • Patent number: 11632125
    Abstract: A method of compressive read mapping. A high-resolution homology table is created for the reference genomic sequence, preferably by mapping the reference to itself. Once the homology table is created, the reads are compressed to eliminate full or partial redundancies across reads in the dataset. Preferably, compression is achieved through self-mapping of the read dataset. Next, a coarse mapping from the compressed read data to the reference is performed. Each read link generated represents a cluster of substrings from one or more reads in the dataset and stores their differences from a locus in the reference. Preferably, read links are further expanded to obtain final mapping results through traversal of the homology table, and final mapping results are reported. As compared to prior techniques, substantial speed-up gains are achieved through the compressive read mapping technique due to efficient utilization of redundancy within read sequences as well as the reference.
    Type: Grant
    Filed: June 8, 2021
    Date of Patent: April 18, 2023
    Inventors: Bonnie Berger Leighton, Deniz Yorukoglu, Jian Peng
  • Patent number: 11610645
    Abstract: There is a need for more effective and efficient predictive data analysis solutions for processing genetic sequencing data. This need can be addressed by, for example, techniques for performing predictive data analysis based on genetic sequences that utilize at least one of cross-variant polygenic risk modeling using genetic risk profiles, cross-variant polygenic risk modeling using functional genetic risk profiles, per-condition polygenic clustering operations, cross-condition polygenic predictive inferences, and cross-condition polygenic diagnoses.
    Type: Grant
    Filed: April 30, 2020
    Date of Patent: March 21, 2023
    Assignee: Optum Services (Ireland) Limited
    Inventors: Kenneth Bryan, Megan O'Brien, David S. Monaghan, Chirag Chadha
  • Patent number: 11610648
    Abstract: The method includes compressing numbers of reads data for targeted genes of a gene expression assay performed on a test sample. The targeted genes are organized into categories. Each category represents a functional context associated with the targeted genes in that category. The numbers of reads corresponding to targeted genes each category is compressed to form a compressed value for the category. The compressed value is compared to a baseline value for the category to determine an enrichment or a loss of a signature corresponding to the functional context of the category. The method may include analyzing information from multiple assays performed on the test sample, assigning a score value to each assay result and predicting a response to immune-oncology treatment based on the assigned scores.
    Type: Grant
    Filed: April 17, 2020
    Date of Patent: March 21, 2023
    Assignee: Life Technologies Corporation
    Inventors: Fiona Hyland, Asha Kamat, Timothy Looney
  • Patent number: 11600360
    Abstract: Polynucleotide sequencing generates multiple reads of a polynucleotide molecule. Many or all of the reads contain errors. Trace reconstruction takes multiple reads generated by a polynucleotide sequencer and uses those multiple reads to reconstruct accurately the nucleotide sequence of the polynucleotide molecule. Some reads may contain errors that cannot be corrected. Thus, there may be reads that can be used throughout their entire length and other reads that have indeterminant errors which cannot be corrected. Rather than discarding the entire read when an indeterminant error is found, the portion of the read with the error is skipped and the sequence of the read following the error is used to reconstruct the trace. The amount of the read skipped is determined by the location of subsequence after the error that matches a consensus sequence of the other reads. Analysis resumes at a location determined by the location of the match.
    Type: Grant
    Filed: August 20, 2018
    Date of Patent: March 7, 2023
    Assignee: Microsoft Technology Licensing, LLC
    Inventors: Sergey Mikhailovich Yekhanin, Miklos Zoltan Racz
  • Patent number: 11561196
    Abstract: In one embodiment, a sample surface of a biosensor includes pixel areas and holds a plurality of clusters during a sequence of sampling events such that the clusters are distributed unevenly over the pixel areas. In another embodiment, a biosensor has a sample surface that includes pixel areas and an array of wells overlying the pixel areas, the biosensor including two wells and two clusters per pixel area. The two wells per pixel area include a dominant well and a subordinate well. The dominant well has a larger cross section over the pixel area than the subordinate well. In yet another embodiment, an illumination system is coupled to a biosensor that illuminates the pixel areas with different angles of illumination during a sequence of sampling events, including, for a sampling event, illuminating each of the wells with off-axis illumination to produce asymmetrically illuminated well regions in each of the wells.
    Type: Grant
    Filed: January 7, 2019
    Date of Patent: January 24, 2023
    Assignee: Illumina, Inc.
    Inventors: Dietrich Dehlinger, Ali Agah, Tracy Helen Fung, Emrah Kostem, Craig Hetherington
  • Patent number: 11556724
    Abstract: A nervous system emulator engine includes working computational models of the vertebrate nervous system to generate lifelike animal behavior in a robot. These models include functions representing several anatomical features of the vertebrate nervous system, such as spinal cord, brainstem, basal ganglia, thalamus and cortex. The emulator engine includes a hierarchy of controllers in which controllers at higher levels accomplish goals by continuously specifying desired goals for lower-level controllers. The lowest levels of the hierarchy reflect spinal cord circuits that control muscle tension and length. Moving up the hierarchy into the brainstem and midbrain/cortex, progressively more abstract perceptual variables are controlled. The nervous system emulator engine may be used to build a robot that generates the majority of animal behavior, including human behavior. The nervous system emulator engine may also be used to build working models of nervous system functions for clinical experimentation.
    Type: Grant
    Filed: September 1, 2018
    Date of Patent: January 17, 2023
    Inventor: Joseph William Barter
  • Patent number: 11543340
    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: September 18, 2019
    Date of Patent: January 3, 2023
    Assignee: Iris International, Inc.
    Inventors: Bart J. Wanders, Brett Jordan, Gregory A. Farrell, Thomas H. Adams, Warren Groner
  • Patent number: 11536709
    Abstract: Platelet cell data may be obtained from analysis of a blood sample by a hematology analyzer or like device. Systems and apparatus may process the platelet cell data in accordance with platelet parameter thresholds selected by a user. The platelet cell data may then be categorized and displayed in one or more useful forms for medical diagnostic and/or research purposes. The platelet cell data may be categorized and displayed in, e.g., tabular and/or graphical form based on the user-selected platelet parameter thresholds. Methods of processing platelet cell data for categorizing and displaying the platelet cell data in one or more useful forms are also provided, as are other aspects.
    Type: Grant
    Filed: March 30, 2016
    Date of Patent: December 27, 2022
    Assignee: Siemens Healthcare Diagnostics Inc.
    Inventors: Frederick Stelling, Val Jones, William Canfield
  • Patent number: 11501851
    Abstract: The present disclosure provides methods of estimating a degree of ancestral relatedness between individuals. In an aspect, a method comprises receiving haplotype data comprising genetic markers shared among a population of individuals; dividing the haplotype data into segments based on the genetic markers; for each of the population of test individuals: (i) based on the genetic markers, matching segments of the haplotype data that are identical-by-descent between two individuals, (ii) for each of the matched segments: dividing the matched segment into discrete genomic intervals, scoring each of the discrete genomic intervals based on a degree of matching within or between the individuals, correcting the scores for consistency, and (iii) calculating a weighted sum over the discrete genomic intervals of the matched segment, based on the corrected scores and assigned weights; and (d) estimating the degree of ancestral relatedness between the individuals based on the weighted sums of the matched segments.
    Type: Grant
    Filed: January 6, 2022
    Date of Patent: November 15, 2022
    Assignee: Embark Veterinary, Inc.
    Inventors: Aaron J. Sams, Samuel H. Vohr, Adam S. Gardner, Matt Barton, Ryan Boyko, Adam R. Boyko
  • Patent number: 11488688
    Abstract: The invention provides methods for identifying rare variants near a structural variation in a genetic sequence, for example, in a nucleic acid sample taken from a subject. The invention additionally includes methods for aligning reads (e.g., nucleic acid reads) to a reference sequence construct accounting for the structural variation, methods for building a reference sequence construct accounting for the structural variation or the structural variation and the rare variant, and systems that use the alignment methods to identify rare variants. The method is scalable, and can be used to align millions of reads to a construct thousands of bases long, or longer.
    Type: Grant
    Filed: June 17, 2019
    Date of Patent: November 1, 2022
    Assignee: Seven Bridges Genomics Inc.
    Inventor: Deniz Kural
  • Patent number: 11475683
    Abstract: An object classification system for classifying objects is described. The system comprises an imaging region adapted for irradiating an object of interest, an arrayed detector, and a mixing unit configured for mixing the irradiation stemming from the object of interest by reflecting or scattering on average at least three times the irradiation after its interaction with the object of interest and prior to said detection.
    Type: Grant
    Filed: May 26, 2018
    Date of Patent: October 18, 2022
    Inventors: Peter Bienstman, Alessio Lugnan, Floris Laporte
  • Patent number: 11436429
    Abstract: The technology disclosed processes a first input through a first neural network and produces a first output. The first input comprises first image data derived from images of analytes and their surrounding background captured by a sequencing system for a sequencing run. The technology disclosed processes the first output through a post-processor and produces metadata about the analytes and their surrounding background. The technology disclosed processes a second input through a second neural network and produces a second output. The second input comprises third image data derived by modifying second image data based on the metadata. The second image data is derived from the images of the analytes and their surrounding background. The second output identifies base calls for one or more of the analytes at one or more sequencing cycles of the sequencing run.
    Type: Grant
    Filed: March 21, 2020
    Date of Patent: September 6, 2022
    Assignee: Illumina, Inc.
    Inventors: Kishore Jaganathan, Anindita Dutta, Dorna Kashefhaghighi, John Randall Gobbel, Amirali Kia
  • Patent number: 11430131
    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: December 21, 2020
    Date of Patent: August 30, 2022
    Assignee: Ventana Medical Systems, Inc.
    Inventors: Anindya Sarkar, Jim Martin
  • Patent number: 11426731
    Abstract: A cartridge for digital real-time Polymerase chain reaction (PCR) includes a microfluidic chamber, a well array, a CMOS photo sensor array and a PCB. The microfluidic chamber includes an inlet formed for injection of a liquid sample, the microfluidic chamber being capable of injection molding. The well array includes a plurality of microwells through which upper and lower portions are perforated and being attached to a lower surface of the microfluidic chamber. The CMOS photo sensor array is disposed below the well array to capture a response image of a sample filled in microwells of the well array. The PCB has a vent formed for vacuum processing of micro flow path formed in the microfluidic chamber, a space formed between the well array and the microfluidic chamber, and a microwell formed in the well array as the liquid sample is injected through the inlet.
    Type: Grant
    Filed: April 22, 2019
    Date of Patent: August 30, 2022
    Inventors: Sergiy Oleksandrov, Do Young Lee, Min Sik Song, Kyung Hak Choi
  • Patent number: 11410745
    Abstract: Techniques are described that facilitate determining potential cancer gene therapy targets by joint modeling of cancer survival events. In one embodiment, a computer-implemented comprises employing, by a device operatively coupled to a processor, a multi-task learning model to determine active genetic factors respectively associated with different types of cancer based on cancer survival data and patient genomic data for groups of patients that respectively survived the different types of cancer. The computer-implemented method further comprises, determining, by the device, common active genetic factors of the active genetic factors that are shared between two or more types of cancer of the different types of cancer.
    Type: Grant
    Filed: June 18, 2018
    Date of Patent: August 9, 2022
    Inventors: Zhaonan Sun, Zach Shahn, Ping Zhang, Fei Wang, Jianying Hu
  • Patent number: 11390914
    Abstract: The disclosure provides for methods, compositions, systems, devices, and kits for whole transcriptome amplification using stochastic barcodes.
    Type: Grant
    Filed: April 21, 2016
    Date of Patent: July 19, 2022
    Assignee: Becton, Dickinson and Company
    Inventors: Glenn Fu, Craig Betts, Christina Fan, Gretchen Yinbon Lam
  • Patent number: 11378544
    Abstract: A biosensor for base calling is provided. The biosensor comprises a sampling device, which includes a sample surface that has an array of pixel areas and a solid-state imager that has an array of sensors. Each sensor generates pixel signals in each base calling cycle. Each pixel signal represents light gathered in one base calling cycle from one or more clusters in a corresponding pixel area of the sample surface. The biosensor further comprises a signal processor configured for connection to the sampling device. The signal processor receives and processes the pixel signals from the sensors for base calling in a base calling cycle, and uses the pixel signals from fewer sensors than a number of clusters base called in the base calling cycle. The pixel signals from the fewer sensors include at least one pixel signal representing light gathered from at least two clusters in the corresponding pixel area.
    Type: Grant
    Filed: January 7, 2019
    Date of Patent: July 5, 2022
    Assignee: Illumina, Inc.
    Inventors: Dietrich Dehlinger, Ali Agah, Tracy Helen Fung, Emrah Kostem
  • 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: 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: 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
    Inventors: Tao Feng, Jia Fei
  • 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
    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
    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