Patents Examined by Joyce Tung
  • Patent number: 9528160
    Abstract: The invention is directed to a method of selecting disease-correlated clonotypes that have a reduced likelihood of producing a false positive signal of relapse when, used to monitor minimal residual disease. In accordance with the invention, candidate correlating clonotype are obtained from a patient, the rarity of each is determined either by comparison with a clonotype database or a clonotype model, and one or more of the rarest of such clonotypes are used to monitor the minimal residual disease.
    Type: Grant
    Filed: March 15, 2013
    Date of Patent: December 27, 2016
    Assignee: Adaptive Biotechnolgies Corp.
    Inventors: Francois Pepin, Malek Faham, Martin Moorhead
  • Patent number: 9523129
    Abstract: The invention is directed to methods of generating sequence profiles of populations of nucleic acids, whose member nucleic acids contain regions of high variability, such as populations of nucleic acids encoding T cell receptors or B cell receptors. In one aspect, the invention provides pluralities of sets of primers for generating nested sets of templates from nucleic acids in such populations, thereby insuring the production of at least one template from which sequence reads are generated, despite such variability, or despite limited lengths or quality of sequence reads. In another aspect, members of such populations are bidirectionally sequenced so that further sequence information is obtained by analyzing overlapping sequence reads in the zones of highest variability.
    Type: Grant
    Filed: February 5, 2014
    Date of Patent: December 20, 2016
    Assignee: Adaptive Biotechnologies Corp.
    Inventors: Malek Faham, Martin Moorhead, Thomas Willis
  • Patent number: 9506119
    Abstract: The invention is directed to the use of sequence tags to improve sequence determination of amplicons of related sequences, particularly large and complex amplicons, such as those comprising recombined nucleic acids encoding immune receptor molecules. In one aspect, sequence reads having the same sequence tags are aligned after which final base calls are determined from a (possibly weighted) average base call from sequence read base calls at each position. Similarly, in another aspect, sequence reads comprising series of incorporation signals are aligned by common sequence tags and base calls in homopolymer regions are made as a function incorporation signal values at each “flow” position.
    Type: Grant
    Filed: March 15, 2013
    Date of Patent: November 29, 2016
    Assignee: Adaptive Biotechnologies Corp.
    Inventors: Malek Faham, Martin Moorhead, Thomas Willis, Jianbiao Zheng
  • Patent number: 9493830
    Abstract: The present invention provides methods for determining a nucleic acid sequence by performing successive cycles of duplex extension along a single stranded template. The cycles comprise steps of extension, ligation, and, preferably, cleavage. In certain embodiments the methods make use of extension probes containing phosphorothiolate linkages and employ agents appropriate to cleave such linkages. The invention provides methods of determining information about a sequence using at least two distinguishably labeled probe families. In certain embodiments the methods acquire less than 2 bits of information from each of a plurality of nucleotides in the template in each cycle. In certain embodiments the sequencing reactions are performed on templates attached to immobilized beads. The invention further provides sets of labeled extension probes containing phosphorothiolate linkages.
    Type: Grant
    Filed: October 18, 2013
    Date of Patent: November 15, 2016
    Assignee: Applied Biosystems, LLC
    Inventors: Kevin McKernan, Alan Blanchard, Lev Kotler, Gina Costa
  • Patent number: 9494520
    Abstract: The invention generally relates to droplet based digital PCR and methods for analyzing a target nucleic acid using the same. In certain embodiments, methods of the invention involve forming sample droplets containing, on average, a single target nucleic acid, amplifying the target in the droplets, excluding droplets containing amplicon from the target and amplicon from a variant of the target, and analyzing target amplicons.
    Type: Grant
    Filed: April 19, 2013
    Date of Patent: November 15, 2016
    Assignee: Raindance Technologies, Inc.
    Inventor: Darren R. Link
  • Patent number: 9494519
    Abstract: A fast, multiplexed PCR system is described that can rapidly generate amplified nucleic acid products, for example, a full STR profile, from a target nucleic acid. Such systems include, for example, microfluidic biochips and a custom built thermal cycler, which are also described. The resulting STR profiles can satisfy forensic guidelines for signal strength, inter-loci peak height balance, heterozygous peak height ratio, incomplete non-template nucleotide addition, and stutter.
    Type: Grant
    Filed: March 3, 2011
    Date of Patent: November 15, 2016
    Assignee: NetBio, Inc.
    Inventors: Richard F. Selden, Eugene Tan, Heung Chuan Lam, Heidi Susanne Giese, Gregory John Kellogg, John A. Wright
  • Patent number: 9458514
    Abstract: The present invention use of to a portion of the RPS7 gene or its corresponding mRNA in a diagnostic assay for fungal and yeast species and sequences for use in such assays and methods.
    Type: Grant
    Filed: December 14, 2007
    Date of Patent: October 4, 2016
    Assignee: National University of Ireland, Galway
    Inventors: Thomas Gerard Barry, Terence James Smith, Majella Maher
  • Patent number: 9458516
    Abstract: A kit for detecting Bovine leukemia virus (BLV) according to the present invention includes: a first PCR primer being oligonucleotide including successive 20 bases or more in the base sequence denoted by SEQ ID NO: 1, the first PCR primer being oligonucleotide having 50 bases or less; and second PCR primer being including successive 20 bases or more in the base sequence denoted by SEQ ID NO: 2, the second PCR primer being oligonucleotide having 50 bases or less is included.
    Type: Grant
    Filed: October 21, 2011
    Date of Patent: October 4, 2016
    Assignee: RIKEN
    Inventors: Yoko Aida, Shin-nosuke Takeshima, Mayuko Jimba, Daiji Endoh
  • Patent number: 9447465
    Abstract: The present invention provides a method of sequencing a single polynucleotide in which the nucleotide base and/or probe which is incorporated during sequencing is labelled with a bead which is detected to identity the base and/or probe which has bound to the single polynucleotide. Particularly, the detection of the bead may be carried out using an apparatus comprising a surface provided with a means for detecting a bead e.g. with one or more light sensitive elements.
    Type: Grant
    Filed: September 30, 2011
    Date of Patent: September 20, 2016
    Assignee: GENESEQUE AS
    Inventor: Jarle Kotsbak
  • Patent number: 9441266
    Abstract: The invention generally relates to droplet based digital PCR and methods for analyzing a target nucleic acid using the same. In certain embodiments, methods of the invention involve forming sample droplets containing, on average, a single target nucleic acid, amplifying the target in the droplets, excluding droplets containing amplicon from the target and amplicon from a variant of the target, and analyzing target amplicons.
    Type: Grant
    Filed: February 22, 2013
    Date of Patent: September 13, 2016
    Assignee: Raindance Technologies, Inc.
    Inventors: Jonathan William Larson, Qun Zhong, Darren Roy Link
  • Patent number: 9434984
    Abstract: This invention provides novel compositions and processes for analyte detection, quantification and amplification. Nucleic acid arrays and libraries of analytes are usefully incorporated into such compositions and processes. Universal detection elements, signaling entities and the like are employed to detect and if necessary or desirable, to quantify analytes. Amplification of target analytes are also provided by the compositions and processes of this invention.
    Type: Grant
    Filed: July 29, 2004
    Date of Patent: September 6, 2016
    Assignee: Enzo Life Sciences, Inc.
    Inventors: Elazar Rabbani, Jannis G. Stavrianopoulos, James J. Donegan, Jack Coleman
  • Patent number: 9428797
    Abstract: This invention provides novel compositions and processes for analyte detection, quantification and amplification. Nucleic acid arrays and libraries of analytes are usefully incorporated into such compositions and processes. Universal detection elements, signaling entities and the like are employed to detect and if necessary or desirable, to quantify analytes. Amplification of target analytes are also provided by the compositions and processes of this invention.
    Type: Grant
    Filed: July 29, 2004
    Date of Patent: August 30, 2016
    Assignee: Enzo Life Sciences, Inc.
    Inventors: Elazar Rabbani, Jannis G. Stavrianopoulos, James J. Donegan, Jack Coleman
  • Patent number: 9399797
    Abstract: The invention generally relates to droplet based digital PCR and methods for analyzing a target nucleic acid using the same. In certain embodiments, a method for determining the nucleic acid make-up of a sample is provided.
    Type: Grant
    Filed: April 30, 2012
    Date of Patent: July 26, 2016
    Assignee: Raindance Technologies, Inc.
    Inventors: John Brian Hutchison, Jeffrey Charles Olson, Darren Roy Link
  • Patent number: 9394332
    Abstract: The present application is directed to a method for performing a bisulfite reaction to determine methylation positions in a nucleic acid, i.e. methylated and non-methylated cytosines, whereby the nucleic acid is bound to a solid phase during the deamination and/or desulfonation step of the bisulfite reaction. The solid phase is preferably a material comprising glass or silica, more preferably a glass fleece, glass membrane or a magnetic glass particle. Further, the use of a solid phase for binding a nucleic acid during the deamination and/or desulfonation step of the bisulfite reaction is disclosed and a kit containing a bisulfite reagent and a solid phase.
    Type: Grant
    Filed: August 25, 2003
    Date of Patent: July 19, 2016
    Assignee: Epigenomics AG
    Inventors: Christine Markert-Hahn, Dirk Block
  • Patent number: 9394567
    Abstract: The invention is directed to methods for detecting and quantifying nucleic acid contamination in a tissue sample of an individual containing T cells and/or B cells, which is used for generating a sequence-based clonotype profile. In one aspect, the invention is implemented by measuring the presence and/or level of an endogenous or exogenous nucleic acid tag by which nucleic acid from an intended individual can be distinguished from that of unintended individuals. Endogenous tags include genetic identity markers, such as short tandem repeats, rare clonotypes or the like, and exogenous tags include sequence tags employed to determine clonotype sequences from sequence reads.
    Type: Grant
    Filed: April 9, 2013
    Date of Patent: July 19, 2016
    Assignee: ADAPTIVE BIOTECHNOLOGIES CORPORATION
    Inventors: Thomas Asbury, Victoria Carlton, Malek Faham, Stephen C. Macevicz, Martin Moorhead, Thomas Willis, Jianbiao Zheng
  • Patent number: 9394566
    Abstract: The invention provides specific transgenic cotton plants, plant material and seeds, characterized in that these products harbor a specific transformation event at a specific location in the cotton genome. Tools are also provided which allow rapid and unequivocal identification of the event in biological samples.
    Type: Grant
    Filed: July 1, 2013
    Date of Patent: July 19, 2016
    Assignee: Bayer CropScience N.V.
    Inventors: Linda Trolinder, Veerle Habex
  • Patent number: 9382550
    Abstract: The invention provides specific transgenic cotton plants, plant material and seeds, characterized in that these products harbor a specific transformation event at a specific location in the cotton genome. Tools are also provided which allow rapid and unequivocal identification of the event in biological samples.
    Type: Grant
    Filed: July 18, 2012
    Date of Patent: July 5, 2016
    Assignee: BAYER CROPSCIENCE N.V.
    Inventors: Linda Trolinder, Sofie Moens, Dimitri Paelinck, Veerle Habex, Hans Van Herck
  • Patent number: 9376724
    Abstract: The invention provides a method for identifying a neonatal subject at risk for NEC, said method comprising (a) profiling the microbiota in a sample from the GI tract of said subject prior to a conclusive diagnosis of NEC and/or prior to full onset of NEC, (b1) comparing said profile to a standard microbiota profile obtained from corresponding samples from neonatal subjects with NEC or subjects which later developed NEC and determining the degree of correlation between said profile and the standard profile(s), and/or (b2) comparing said profile to a standard microbiota profile obtained from corresponding samples from neonatal subjects which did not develop NEC and determining the degree of correlation between said profile and the standard profile, and (c) identifying the subject as being at risk of NEC if significant correlation is observed in (b1) and/or significant correlation is not seen in (b2).
    Type: Grant
    Filed: February 16, 2012
    Date of Patent: June 28, 2016
    Assignee: GENETIC ANALYSIS AS
    Inventors: Knut Rudi, Heidi Cecilie Vebø, Monika Sekelja, Morten Isaksen
  • Patent number: 9376707
    Abstract: An assay kit for determination of thymidine kinase (TK) activity in a biological sample, such as blood, serum, plasma, Cerebral Spinal Fluid (CSF), pleural fluid, ascites, tissues, cells and extracts thereof, is described. The assay kit can used in a method that comprises contacting, in a buffer, a Basic Reaction Mixture comprising: solid surface-attached primer and/or template, a modified deoxy nucleoside, such as BromodeoxyUridine, IododeoxyUridine, FluorodeoxyUridine or VinyldexoyThymidine as a kinase enzyme substrate, a phosphate donor, a nucleotide polymerizing enzyme, and a kinase enzyme source devoid of TK activity, such as a yeast extract, with the biological sample. After incubation the amount of modified deoxy nucleoside that has been incorporated into the solid surface-attached primer and/or template, is determined and the TK activity present in the biological sample is directly proportional to the amount of incorporated modified deoxy nucleoside.
    Type: Grant
    Filed: May 23, 2014
    Date of Patent: June 28, 2016
    Assignee: BIOVICA INTERNATIONAL AB
    Inventor: J. Simon Gronowitz
  • Patent number: 9366632
    Abstract: The invention generally relates to droplet based digital PCR and methods for analyzing a target nucleic acid using the same. In certain embodiments, methods of the invention involve forming sample droplets containing, on average, a single target nucleic acid, amplifying the target in the droplets, excluding droplets containing amplicon from the target and amplicon from a variant of the target, and analyzing target amplicons.
    Type: Grant
    Filed: April 19, 2013
    Date of Patent: June 14, 2016
    Assignee: Raindance Technologies, Inc.
    Inventors: Darren R. Link, Qun Zhong, Andrew Watson