Patents Examined by James Martinell
  • Compounds and method for representational selection of nucleic acids from complex mixtures using hybridization
    Patent number: 10538759
    Abstract: The invention provides a method of selecting a representational sample of nucleic acid sequences from a complex mixture. The method includes: (a) contacting a complex mixture of nucleic acids under conditions sufficient for hybridization with a population of capture probes complementary to one or more nucleic acids comprising a predetermined portion of the sequence collectively present in the complex mixture to form hybridization complexes of the one or more nucleic acids with the population of probes, the population of capture probes being attached to a solid support, and (b) removing unhybridized nucleic acids to select a representational sample of nucleic acids having a complexity of less than 10% but more than 0.
    Type: Grant
    Filed: November 20, 2017
    Date of Patent: January 21, 2020
    Assignee: Illumina, Inc.
    Inventors: John R. Stuelpnagel, David L. Barker, Jorge Velarde, Steven M. Barnard, Michael Graige
  • Exosomal biomarkers diagnostic of tuberculosis
    Patent number: 10526665
    Abstract: The disclosure provides a method for diagnosing an active mycobacterium tuberculosis infection by detecting certain RNA biomarkers present in secreted extracellular vesicles isolated from a bodily fluid. The RNA biomarkers in the secreted extracellular vesicles may include a certain mycobacterium RNAs as well as certain host cell RNAs. Also provided is an RNA signature of certain mycobacterium and host cell RNA present in secreted extracellular vesicles indicative of an active tuberculosis infection.
    Type: Grant
    Filed: March 3, 2017
    Date of Patent: January 7, 2020
    Assignee: University of Notre Dame du Lac
    Inventors: Jeffrey S. Schorey, Prachi Pratap Singh, Yong Cheng
  • Translocation and mutant ROS kinase in human non-small cell lung carcinoma
    Patent number: 10526661
    Abstract: In accordance with the invention, a novel gene translocation, (5q32, 6q22), in human non-small cell lung carcinoma (NSCLC) that results in a fusion proteins combining part of CD74 with Proto-oncogene Tyrosine Protein Kinase ROS Precursor (ROS) kinase has now been identified. The CD74-ROS fusion protein is anticipated to drive the proliferation and survival of a subgroup of NSCLC tumors. The invention therefore provides, in part, isolated polynucleotides and vectors encoding the disclosed mutant ROS kinase polypeptides, probes for detecting it, isolated mutant polypeptides, recombinant polypeptides, and reagents for detecting the fusion and truncated polypeptides.
    Type: Grant
    Filed: April 12, 2016
    Date of Patent: January 7, 2020
    Assignee: CELL SIGNALING TECHNOLOGY, INC.
    Inventors: Ting-Lei Gu, Ailan Guo
  • Identification of metastasis-specific miRNA and hypomethylation signatures in human colorectal cancer
    Patent number: 10519506
    Abstract: The present invention includes methods and biomarkers for diagnosing or detecting colorectal cancer metastasis in a human subject by comparing the Alu repeat methylation level in the biological sample to an Alu repeat methylation control level from a normal non-cancerous sample from the human subject, wherein a decrease in the Alu repeat methylation level is indicative of colorectal cancer and colorectal cancer metastasis.
    Type: Grant
    Filed: December 21, 2012
    Date of Patent: December 31, 2019
    Assignee: Baylor Research Institute
    Inventors: Ajay Goel, C. Richard Boland, Keun Hur
  • Methods for accurate sequence data and modified base position determination
    Patent number: 10515714
    Abstract: Disclosed herein are methods of determining the sequence and/or positions of modified bases in a nucleic acid sample present in a circular molecule with a nucleic acid insert of known sequence comprising obtaining sequence data of at least two insert-sample units. In some embodiments, the methods comprise obtaining sequence data using circular pair-locked molecules. In some embodiments, the methods comprise calculating scores of sequences of the nucleic acid inserts by comparing the sequences to the known sequence of the nucleic acid insert, and accepting or rejecting repeats of the sequence of the nucleic acid sample according to the scores of one or both of the sequences of the inserts immediately upstream or downstream of the repeats of the sequence of the nucleic acid sample.
    Type: Grant
    Filed: July 25, 2017
    Date of Patent: December 24, 2019
    Assignee: Industrial Technology Research Institute
    Inventors: Chao-Chi Pan, Jenn-Yeh Fann, Chung-Fan Chiou, Hung-Chi Chien, Hui-Ling Chen
  • Methods for synthesizing pools of probes
    Patent number: 10513722
    Abstract: Compositions, methods and kits are disclosed for synthesizing and amplifying pools of probes using precursor oligonucleotides. In some aspects the precursor is amplified and nicking enzymes are used to separate the full length probes from the amplification products. The methods enable the preparation of single stranded DNA probes of defined sequence and length that are suitable for use in target detection assays.
    Type: Grant
    Filed: May 6, 2016
    Date of Patent: December 24, 2019
    Inventors: Yuker Wang, Keith W. Jones, Ronald J. Sapolsky
  • Control preparation for fish methods in microbiology
    Patent number: 10508302
    Abstract: The invention relates to a control preparation (e.g. comprising microorganism control cells embedded in a cold polymerising resin or plastic) for use in a method for detection of a target microorganism in microbiological pathology, comprising a plurality of section bodies joint by a joining polymer, wherein each section body comprises a matrix polymer (e.g. a cold polymerising resin or plastic). A first section body comprises a nucleic acid sequence specific for the target microorganism (e.g. microorganism cells used as positive control). A second section body comprises a second nucleic acid sequence, which in comparison to said first nucleic acid sequence, contains a deletion, an additional nucleoside or a different nucleoside in one, two, three or four positions of said second nucleic acid sequence and which does not hybridize to said first nucleic acid sequence under stringent conditions (e.g.
    Type: Grant
    Filed: January 27, 2016
    Date of Patent: December 17, 2019
    Assignee: CHARITE UNIVERSITATSMEDIZIN BERLIN
    Inventor: Annette Moter
  • Method of predicting a response to an anti-tumor treatment
    Patent number: 10508310
    Abstract: The invention provides an in vitro method for determining the likelihood for a patient affected with a tumor to respond to a treatment with a pro-apoptotic peptide able to disrupt interaction between caspase 9 and PP2A, which method comprises determining expression level of at least each of VIM, MK167, TCF7L2, NEK2, BIRC5, MCL1, and PLK1 genes, in a biological sample of said patient.
    Type: Grant
    Filed: December 9, 2014
    Date of Patent: December 17, 2019
    Assignees: SORBONNE UNIVERSITE, INSTITUT CURIE
    Inventors: Angelita Rebollo Garcia, Fariba Nemati, Didier Decaudin
  • Spatially encoded biological assays
    Patent number: 10494667
    Abstract: The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.
    Type: Grant
    Filed: June 11, 2019
    Date of Patent: December 3, 2019
    Assignee: Prognosys Biosciences, Inc.
    Inventor: Mark S. Chee
  • Compositions and methods for screening T cells with antigens for specific populations
    Patent number: 10481158
    Abstract: Compositions and methods for isolating patient-derived antigen-specific T cells include an antigen complex having a polynucleotide barcoded nanoparticle sorting agent complexed with a peptide-loaded streptavidin major histocompatability complex (MHC) tetramer, the barcoding technology allowing for high fidelity screening of a library of the antigen complexes to readily isolate and identify antigen-specific T cells.
    Type: Grant
    Filed: June 1, 2016
    Date of Patent: November 19, 2019
    Assignee: California Institute of Technology
    Inventors: James R. Heath, Songming Peng
  • Spatially encoded biological assays
    Patent number: 10480022
    Abstract: The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.
    Type: Grant
    Filed: February 14, 2019
    Date of Patent: November 19, 2019
    Assignee: Prognosys Biosciences, Inc.
    Inventor: Mark S. Chee
  • Rotationally sequestered translators
    Patent number: 10479994
    Abstract: Provided are nucleic acid translators capable of carrying out logic operations with improved efficiency, maximized output and reduced off-target effects, in particular in a biological system. Methods of using these translators to transduce signal are also provided.
    Type: Grant
    Filed: March 27, 2017
    Date of Patent: November 19, 2019
    Assignee: Emerald Therapeutics, Inc.
    Inventors: Daniel J. Kleinbaum, Brian M. Frezza, Brad Bond, Jonathan Leung, George W. Fraser
  • Spatially encoded biological assays
    Patent number: 10472669
    Abstract: The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.
    Type: Grant
    Filed: May 2, 2019
    Date of Patent: November 12, 2019
    Assignee: Prognosys Biosciences, Inc.
    Inventor: Mark S. Chee
  • Biomarker RNF6 for colorectal cancer
    Patent number: 10457993
    Abstract: The present invention provides a method for diagnosing of colorectal cancer in a subject and a method for determining risk of recurrence of colorectal cancer among colorectal cancer patients by detecting overexpression of the RNF6 gene, which in some cases is due to a higher than normal copy number of the genomic sequence of this gene. A kit and device useful for such methods are also provided. In addition, the present invention provides a method for treating colon cancer by suppressing RNF6 gene expression or activity.
    Type: Grant
    Filed: March 30, 2016
    Date of Patent: October 29, 2019
    Assignee: The Chinese University of Hong Kong
    Inventors: Jun Yu, Joseph Jao Yiu Sung
  • Method of nucleic acid fragment detection
    Patent number: 10460828
    Abstract: A method of nucleic acid fragment detection includes capturing a target nucleic acid fragment by an oligonucleotide probe to form a hybridised double strand. The oligonucleotide probe has an identification sequence complementary to the target nucleic acid fragment and a reproducible sequence. The hybridised double strand is removed to expose the reproducible sequence of the oligonucleotide probe. The repeats of the reproducible sequence are produced. The repeats of the reproducible sequence are labelled by a detection probe for identification and quantitation.
    Type: Grant
    Filed: September 25, 2017
    Date of Patent: October 29, 2019
    Assignee: Lifeos Genomics Corporation
    Inventors: Timothy Z. Liu, Ching-Jou Huang
  • Personalized genetic testing
    Patent number: 10450611
    Abstract: The present disclosure provides methods and systems for personalized genetic testing of a subject. In some embodiments, a sequencing assay is performed on a biological sample from the subject, which then leads to genetic information related to the subject. Next, nucleic acid molecules are array-synthesized or selected based on the genetic information derived from data of the sequencing assay. At least some of the nucleic acid molecules may then be used in an assay which may provide additional information on one or more biological samples from the subject or a biological relative of the subject.
    Type: Grant
    Filed: October 25, 2017
    Date of Patent: October 22, 2019
    Assignee: Personalis, Inc.
    Inventors: John West, Christian Haudenschild, Richard Chen
  • Methods for non-invasive detection of transplant health or rejection
    Patent number: 10435750
    Abstract: The present invention relates to the technical field of organ and tissue transplantation and specifically to methods allowing rejection of transplanted organs and tissues by a transplant patient. The present invention provides methods for non-invasive and ex vivo or in vitro detection of the presence or absence of transplant rejection, i.e. transplant health or rejection. The present methods allow for effective and continuous monitoring of transplant status with a minimal or absent discomfort for a transplant patient.
    Type: Grant
    Filed: July 3, 2015
    Date of Patent: October 8, 2019
    Assignee: MULTIPLICOM N.V.
    Inventors: Dirk Goossens, Joachim De Schrijver, Jurgen Del Favero
  • Prognostic method for individuals with prostate cancer
    Patent number: 10428385
    Abstract: The present invention relates generally to the detection and identification of various forms of genetic markers, and various forms of proteins, which have the potential utility as diagnostic markers. By determining the level of a plurality of biomarkers and genetic markers in a patient sample, and combining the obtained values according to a predefined formula, it is possible to forecast if it is likely that the prostate cancer patient will require active therapy like radiation therapy or surgery. A method based on a redundantly designed combination of data is disclosed for estimating if prostate cancer is aggressive or indolent. Said method combines SNP data to form a composite value, wherein at least 5% of the SNPs can be disregarded.
    Type: Grant
    Filed: November 20, 2013
    Date of Patent: October 1, 2019
    Assignee: PHADIA AB
    Inventors: Henrik Grönberg, Martin Eklund
  • Method for indicating a presence or non-presence of aggressive prostate cancer
    Patent number: 10431326
    Abstract: The present invention relates generally to the detection and identification of various forms of genetic markers, and various forms of proteins, which have the potential utility as diagnostic markers. By determining the level of a plurality of biomarkers and genetic markers in a patient sample, and combining the obtained values according to a predefined formula, it is possible to determine if it is likely that the patient suffers from aggressive prostate cancer. The present invention is particularly applicable only for patients having a body mass index value greater than 25.
    Type: Grant
    Filed: November 20, 2013
    Date of Patent: October 1, 2019
    Assignee: PHADIA AB
    Inventors: Henrik Grönberg, Martin Eklund
  • Diagnostic method for distinguishing forms of esophageal eosinophilia
    Patent number: 10422004
    Abstract: The invention provides methods for diagnosing eosinophilic esophagitis in a patient using a biomarker based assay directed to KCNJ2/Kir2.1 and related compositions, kits, and computer program products.
    Type: Grant
    Filed: August 10, 2015
    Date of Patent: September 24, 2019
    Assignees: CHILDREN'S HOSPITAL MEDICAL CENTER, THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
    Inventors: Marc E. Rothenberg, Ting Wen, Seema Aceves