Patents Examined by Teresa E Strzelecka
  • Patent number: 11555218
    Abstract: The present invention relates to a sequencing method which allows for increased rates of sequencing and an increase in the density of sequencing data. The system may be based on next generation sequencing methods such as sequencing by synthesis (SBS) but uses multiple primers bound at different positions on the same nucleic acid strand.
    Type: Grant
    Filed: August 3, 2020
    Date of Patent: January 17, 2023
    Assignee: Illumina Cambridge Limited
    Inventor: Jonathan Mark Boutell
  • Patent number: 11555222
    Abstract: The present invention provides a method of quantification of a target nucleic acid, using at least any two of the genes SYT10, EPHA3, PLEKHF1 and KBTBD4 as control genes. In particular, the combination of the genes SYT10, EPHA3, PLEKHF1 and KBTBD4, known as the 4Plex, is provided as a control for nucleic acid quantification. The 4Plex has particular utility as a control for nucleic acid quantification by methylation-specific droplet digital PCR.
    Type: Grant
    Filed: November 30, 2018
    Date of Patent: January 17, 2023
    Assignee: OSLO UNIVERSITETSSYKEHUS HF
    Inventors: Guro E. Lind, Marine Jeanmougin, Heidi D. Pharo, Kim Andresen, Ragnhild Lothe
  • Patent number: 11549154
    Abstract: Provided are compositions and methods useful to the determination of whether a microbial contaminant is present in a biological therapeutic production process. Specifically, an artificial positive amplification control plasmid and unique quantitative PCR detection probe are provided, which enables the rapid and real-time detection of a false positive result.
    Type: Grant
    Filed: April 22, 2020
    Date of Patent: January 10, 2023
    Assignee: Regeneron Pharmaceuticals, Inc.
    Inventors: Serge Monpoeho, Sheldon Mink, Paul Vescio
  • Patent number: 11549149
    Abstract: In one aspect, the invention features a combination of oligonucleotides comprising a forward primer oligonucleotide and a blocking oligonucleotide. The forward primer oligonucleotide has a 3? end region, where the 3? end region includes a portion complementary to a mutation positioned in a region within a polynucleotide. The blocking oligonucleotide contains a blocking moiety and has a 5? end region, where the 5? end region includes a portion complementary to a wild-type sequence of the region corresponding to the position of the mutation. In other aspects, the invention provides kits including the combination of primer oligonucleotides and methods of using the oligonucleotides to detect a mutation in a polynucleotide.
    Type: Grant
    Filed: January 23, 2018
    Date of Patent: January 10, 2023
    Assignee: The Broad Institute, Inc.
    Inventor: Edward F. Fritsch
  • Patent number: 11542548
    Abstract: A method for diagnosing or giving a prognosis for anxious temperament or trait-like anxiety in a human or non-human primate subject comprising the steps of (a) obtaining DNA from a blood or saliva sample from the subject and (b) quantifying methylation in a set of differentially methylated regions (DMRs) selected from SEQ ID NOs:1-75 or DMR-associated genes selected from DIP2C, GRB10, INPP5A, C17ORF97, PDXK, CACNA2D4, TRAPPC9, CRTC1, MEGF6, HIVEP3, OPCML, PITPNM2, ZFPM1, RAP1GAP2, NFATC1, RNF126, FSTL3, GNAS, SH3BP2, NEURL1B, MAD1L1, HSPA12B, IGF2, PEG10, PEG3, SLC16A3, SYTL1, and ZIM2, wherein a significant change methylation indicates the present of anxious temperament or trait-like anxiety, wherein the change is relative to DNA from a second human or non-human primate who does not have anxious temperament or trait-like anxiety. Also disclosed is a biomarker panel of DMR and DMR-associated genes for the diagnosis or prognosis of anxious temperament or trait-like anxiety.
    Type: Grant
    Filed: June 11, 2020
    Date of Patent: January 3, 2023
    Assignees: Wisconsin Alumni Research Foundation;, Emory University
    Inventors: Reid Spencer Alisch, Pankaj Chopra
  • Patent number: 11542561
    Abstract: Provided herein is a real-time PCR-based method of detecting, in a sample, an agent causing onychodystrophy, wherein the agent causing onychodystrophy belongs to a secondary clade member including one or more primary clade members. Also provided are compositions and kits that finds use in implementing the present method.
    Type: Grant
    Filed: February 20, 2020
    Date of Patent: January 3, 2023
    Assignee: BAKOTIC PATHOLOGY ASSOCIATES, LLC
    Inventors: Idowu Akinsanmi, Lori Bennett, Liquan Yang, Marianna Agassandian, Rama Murthy Sakamuri, Erik Gustafson, Lilly Kong, Kiran Madanahally Divakar
  • Patent number: 11535884
    Abstract: The present invention relates to a method for enrichment of target DNA with high GC content based on target sequence capture and multiple displacement amplification, as well as a kit suitable for this method. The present invention also relates to a method for constructing a sequencing library of target DNA with high GC content based on the enrichment method of the present invention.
    Type: Grant
    Filed: February 7, 2018
    Date of Patent: December 27, 2022
    Assignee: BERRY GENOMICS CO., LTD.
    Inventors: Ziwei Qu, Tao Yu, Fangming Wang, Nannan Zhang, Jianguang Zhang
  • Patent number: 11535886
    Abstract: Provided includes methods and systems useful in array-based analysis of mixed nucleic acid populations, including for genotyping and copy number analysis of the various subpopulations of the mixed nucleic acid population. Also provided includes methods and systems useful in the diagnosis of genetic abnormalities in a mixed nucleic acid population taken from an organism.
    Type: Grant
    Filed: June 1, 2018
    Date of Patent: December 27, 2022
    Inventors: Jeanette Schmidt, Orna Mizrahi Man, Jiang Li
  • Patent number: 11525164
    Abstract: The present disclosure provides for a method of determining microbial identities and/or abundances in a biological sample. The method may comprise: (a) immobilizing the biological sample in a matrix; (b) fracturing/breaking the matrix (that comprises the biological sample) into clusters; and (c) determining identities and/or abundances of microbes in the clusters.
    Type: Grant
    Filed: March 27, 2019
    Date of Patent: December 13, 2022
    Assignee: The Trustees of Columbia University in the City of New York
    Inventors: Harris H. Wang, Ravi Sheth
  • Patent number: 11519016
    Abstract: The invention features methods panels, cartridges, and systems for detecting pathogens and for diagnosing and treating diseases, including bacteremia and sepsis.
    Type: Grant
    Filed: January 20, 2017
    Date of Patent: December 6, 2022
    Assignee: T2 Biosystems, Inc.
    Inventors: Ulrich Hans Thomann, Lori Anne Neely, Heidi Susanne Giese, Jessica Ann Townsend, Rahul Krishan Dhanda, Thomas Jay Lowery, Jr., Urvi Ved, Brendan Manning, Nu Ai Phung, Joanne Lawton Garver, Benjamin B. Stone
  • Patent number: 11519021
    Abstract: The present invention relates to methods and kits for identifying microsatellite instability (MSI) in a sample. In particular it relates to identifying microsatellite instability in a tumor sample, which may be from a subject suspected of having colorectal cancer or Lynch syndrome. The methods and kits can be used to identify mismatch repair defects. More particularly the invention relates to a panel of markers for a sequencing based MSI test, that can differentiate between MSI-H and MSS CRCs. The invention also allows for determination of biological significance, differentiating between PCR and sequencing errors and MSI induced indels/mutations.
    Type: Grant
    Filed: August 23, 2017
    Date of Patent: December 6, 2022
    Inventors: John Burn, Mohammed Ghanim Mehdi Alhilal, Francisco Mauro Santibanez-Koref, Lisa Redford, Michael Stewart Jackson
  • Patent number: 11499184
    Abstract: Biomarkers and methods for identifying, verifying and confirming circulating serum-based microRNAs. The microRNAs (PARKmiRs) can be used to differentiate patient's suffering from Parkinson's disease (PD) from non-PD patients.
    Type: Grant
    Filed: February 3, 2017
    Date of Patent: November 15, 2022
    Assignee: ST. JOHN'S UNIVERSITY
    Inventors: Simon Geir Moller, Indranil Basak, Ketan Patil, Jan Petter Larsen
  • Patent number: 11499193
    Abstract: Disclosed are formulations, including both liquid and lyophilized formulations, comprising a far-red dye probe and a non-linear surfactant or foamban. Also disclosed are related methods for preparing a lyophilized far-red dye probe formulation as well as related kits and diagnostic products.
    Type: Grant
    Filed: February 6, 2019
    Date of Patent: November 15, 2022
    Assignee: Gen-Probe Incorporated
    Inventors: Sheila Aubin-Walker, Mehrdad R. Majlessi, Jimmykim Pham, Joshua Bousquet
  • Patent number: 11499179
    Abstract: A cleavage-based real-time PCR assay method is provided. In general terms, the assay method includes subjecting a reaction mixture comprising a) PCR reagents for amplifying a nucleic acid target, and b) flap cleavage reagents for performing a flap cleavage assay on the amplified nucleic acid target to two sets of thermocycling conditions. No additional reagents are added to the reaction between said first and second sets of cycles and, in each cycle of the second set of cycles, cleavage of a flap probe is measured.
    Type: Grant
    Filed: February 12, 2020
    Date of Patent: November 15, 2022
    Assignee: Exact Sciences Development Company, LLC
    Inventors: Rebecca Oldham-Haltom, Hongzhi Zou, Graham P. Lidgard, Michael J. Domanico, Hatim Allawi
  • Patent number: 11486008
    Abstract: The invention provides methods, systems, and computer readable medium for detecting ploidy of chromosome segments or entire chromosomes, for detecting single nucleotide variants and for detecting both ploidy of chromosome segments and single nucleotide variants. In some aspects, the invention provides methods, systems, and computer readable medium for detecting cancer or a chromosomal abnormality in a gestating fetus.
    Type: Grant
    Filed: June 21, 2018
    Date of Patent: November 1, 2022
    Assignee: Natera, Inc.
    Inventors: Joshua Babiarz, Tudor Pompiliu Constantin, Lane A. Eubank, George Gemelos, Matthew Micah Hill, Huseyin Eser Kirkizlar, Matthew Rabinowitz, Onur Sakarya, Styrmir Sigurjonsson, Bernhard Zimmermann
  • Patent number: 11473145
    Abstract: The inventors initially participated to the identification of LPIN1 mutations as a cause for massive rhabdomyolysis episodes in children, triggered by febrile illness. The inventors have suggested that TLR9 antagonists would be suitable for the treatment of rhabdomyolysis (WO2017085115). The inventors thus treated 2 patients with lipin-1 disease by a TRL9 antagonist (hydroxychloroquine). They showed that the accumulation of mtDNA in plasma of the two patients before treatment decreases under treatment. When the treatment was stopped, the accumulation of mtDNA reappeared, then normalized when treatment was resumed. Accordingly, the present invention relates to a method for determining whether a patient suffering from rhabdomyolysis achieves a response with a TLR9 antagonist comprising determining the amount of mitochondrial DNA (mtDNA) in a blood sample obtained from the patient (e.g. by PCR).
    Type: Grant
    Filed: July 26, 2018
    Date of Patent: October 18, 2022
    Assignees: INSERM (INSTITUT NATIONAL DE LA SANTÉ ET DE LA RECHERCHE MÉDICALE), FOUNDATION IMAGING, ASSISTANCE PUBLIQUE-HÔPITAUX DE PARIS (APHP), CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE (CNRS), UNIVERSITÉ DE PARIS
    Inventors: Pascale De Lonlay-Debeney, Peter Van Endert, Marine Madrange, Yamina Hamel, François-Xavier Mauvais
  • Patent number: 11466327
    Abstract: The present invention relates to the use of the value of the expression of at least one gene selected from the group comprising: GBP 1 gene, HLF gene, CXCL13 gene and SULT1E1 gene, for the estimation of prognosis of distant relapse-free survival or overall survival of a patient with triple negative breast cancer (TNBC) having received a neoadjuvant chemotherapy (NACT).
    Type: Grant
    Filed: July 3, 2017
    Date of Patent: October 11, 2022
    Assignees: ISTITUTO EUROPEO DI ONCOLOGIA (IEO), INSTITUT GUSTAVE ROUSSY
    Inventors: Michiels Stefan, Mohamed Amine Bayar, Fabrice Andre, Carmen Criscitiello, Giuseppe Curigliano
  • Patent number: 11459611
    Abstract: The identification of mutations that are present in a small fraction of DNA templates is essential for progress in several areas of biomedical research. Though massively parallel sequencing instruments are in principle well-suited to this task, the error rates in such instruments are generally too high to allow confident identification of rare variants. We here describe an approach that can substantially increase the sensitivity of massively parallel sequencing instruments for this purpose. One example of this approach, called “Safe-SeqS” for (Safe-Sequencing System) includes (i) assignment of a unique identifier (UID) to each template molecule; (ii) amplification of each uniquely tagged template molecule to create UID-families; and (iii) redundant sequencing of the amplification products. PCR fragments with the same UID are truly mutant (“super-mutants”) if ?95% of them contain the identical mutation.
    Type: Grant
    Filed: May 21, 2019
    Date of Patent: October 4, 2022
    Assignee: The Johns Hopkins University
    Inventors: Bert Vogelstein, Kenneth W. Kinzler, Nickolas Papadopoulos, Isaac A. Kinde
  • Patent number: 11453917
    Abstract: The methods and compositions provided herein relate to the discovery of 13 STR markers, found on the human Y chromosome, having surprisingly high mutation rates when compared with 173 other Y-STR markers known today. The set of RM-Y-STRs may overcome the current dilemma of Y-chromosome analysis in forensic applications due to their extraordinary mutation properties. Embodiments of the invention include methods for allelic determination of rapidly-mutating Y-STR markers, amplification primers for the analysis of rapidly-mutating Y-STR markers, allelic ladders for analysis of rapidly-mutating Y-STR markers, and kits for the analysis of rapidly-mutating Y-STR markers.
    Type: Grant
    Filed: April 3, 2020
    Date of Patent: September 27, 2022
    Inventors: Rixun Fang, Manohar Furtado, Manfred Kayser, Kaye Ballantyne
  • Patent number: 11453913
    Abstract: The identification of mutations that are present in a small fraction of DNA templates is essential for progress in several areas of biomedical research. Though massively parallel sequencing instruments are in principle well-suited to this task, the error rates in such instruments are generally too high to allow confident identification of rare variants. We here describe an approach that can substantially increase the sensitivity of massively parallel sequencing instruments for this purpose. One example of this approach, called “Safe-SeqS” for (Safe-Sequencing System) includes (i) assignment of a unique identifier (UID) to each template molecule; (ii) amplification of each uniquely tagged template molecule to create UID-families; and (iii) redundant sequencing of the amplification products. PCR fragments with the same UID are truly mutant (“super-mutants”) if ?95% of them contain the identical mutation.
    Type: Grant
    Filed: May 19, 2021
    Date of Patent: September 27, 2022
    Assignee: The Johns Hopkins University
    Inventors: Bert Vogelstein, Kenneth W. Kinzler, Nickolas Papadopoulos, Isaac A. Kinde