Patents Examined by Joyce Tung
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Patent number: 9528160Abstract: 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: GrantFiled: March 15, 2013Date of Patent: December 27, 2016Assignee: Adaptive Biotechnolgies Corp.Inventors: Francois Pepin, Malek Faham, Martin Moorhead
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Patent number: 9523129Abstract: 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: GrantFiled: February 5, 2014Date of Patent: December 20, 2016Assignee: Adaptive Biotechnologies Corp.Inventors: Malek Faham, Martin Moorhead, Thomas Willis
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Patent number: 9506119Abstract: 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: GrantFiled: March 15, 2013Date of Patent: November 29, 2016Assignee: Adaptive Biotechnologies Corp.Inventors: Malek Faham, Martin Moorhead, Thomas Willis, Jianbiao Zheng
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Patent number: 9494519Abstract: 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: GrantFiled: March 3, 2011Date of Patent: November 15, 2016Assignee: NetBio, Inc.Inventors: Richard F. Selden, Eugene Tan, Heung Chuan Lam, Heidi Susanne Giese, Gregory John Kellogg, John A. Wright
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Patent number: 9494520Abstract: 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: GrantFiled: April 19, 2013Date of Patent: November 15, 2016Assignee: Raindance Technologies, Inc.Inventor: Darren R. Link
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Patent number: 9493830Abstract: 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: GrantFiled: October 18, 2013Date of Patent: November 15, 2016Assignee: Applied Biosystems, LLCInventors: Kevin McKernan, Alan Blanchard, Lev Kotler, Gina Costa
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Patent number: 9458516Abstract: 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: GrantFiled: October 21, 2011Date of Patent: October 4, 2016Assignee: RIKENInventors: Yoko Aida, Shin-nosuke Takeshima, Mayuko Jimba, Daiji Endoh
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Patent number: 9458514Abstract: 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: GrantFiled: December 14, 2007Date of Patent: October 4, 2016Assignee: National University of Ireland, GalwayInventors: Thomas Gerard Barry, Terence James Smith, Majella Maher
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Patent number: 9447465Abstract: 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: GrantFiled: September 30, 2011Date of Patent: September 20, 2016Assignee: GENESEQUE ASInventor: Jarle Kotsbak
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Patent number: 9441266Abstract: 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: GrantFiled: February 22, 2013Date of Patent: September 13, 2016Assignee: Raindance Technologies, Inc.Inventors: Jonathan William Larson, Qun Zhong, Darren Roy Link
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Patent number: 9434984Abstract: 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: GrantFiled: July 29, 2004Date of Patent: September 6, 2016Assignee: Enzo Life Sciences, Inc.Inventors: Elazar Rabbani, Jannis G. Stavrianopoulos, James J. Donegan, Jack Coleman
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Patent number: 9428797Abstract: 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: GrantFiled: July 29, 2004Date of Patent: August 30, 2016Assignee: Enzo Life Sciences, Inc.Inventors: Elazar Rabbani, Jannis G. Stavrianopoulos, James J. Donegan, Jack Coleman
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Patent number: 9399797Abstract: 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: GrantFiled: April 30, 2012Date of Patent: July 26, 2016Assignee: Raindance Technologies, Inc.Inventors: John Brian Hutchison, Jeffrey Charles Olson, Darren Roy Link
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Patent number: 9394566Abstract: 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: GrantFiled: July 1, 2013Date of Patent: July 19, 2016Assignee: Bayer CropScience N.V.Inventors: Linda Trolinder, Veerle Habex
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Patent number: 9394332Abstract: 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: GrantFiled: August 25, 2003Date of Patent: July 19, 2016Assignee: Epigenomics AGInventors: Christine Markert-Hahn, Dirk Block
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Patent number: 9394567Abstract: 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: GrantFiled: April 9, 2013Date of Patent: July 19, 2016Assignee: ADAPTIVE BIOTECHNOLOGIES CORPORATIONInventors: Thomas Asbury, Victoria Carlton, Malek Faham, Stephen C. Macevicz, Martin Moorhead, Thomas Willis, Jianbiao Zheng
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Patent number: 9382550Abstract: 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: GrantFiled: July 18, 2012Date of Patent: July 5, 2016Assignee: BAYER CROPSCIENCE N.V.Inventors: Linda Trolinder, Sofie Moens, Dimitri Paelinck, Veerle Habex, Hans Van Herck
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Patent number: 9376707Abstract: 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: GrantFiled: May 23, 2014Date of Patent: June 28, 2016Assignee: BIOVICA INTERNATIONAL ABInventor: J. Simon Gronowitz
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Patent number: 9376724Abstract: 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: GrantFiled: February 16, 2012Date of Patent: June 28, 2016Assignee: GENETIC ANALYSIS ASInventors: Knut Rudi, Heidi Cecilie Vebø, Monika Sekelja, Morten Isaksen
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Patent number: 9366632Abstract: 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: GrantFiled: April 19, 2013Date of Patent: June 14, 2016Assignee: Raindance Technologies, Inc.Inventors: Darren R. Link, Qun Zhong, Andrew Watson