Patents Examined by Carolyn L Greene
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Patent number: 11783918Abstract: Techniques for random access of particular DNA strands from a mixture of DNA strands are described. DNA strands that encode pieces of the same digital file are labeled with the same identification sequence. The identification sequence is used to selectively separate DNA strands that contain portions of the same digital file from other DNA strands. A DNA staple positions DNA strands with the identification sequence adjacent to sequencing adaptors. DNA ligase joins the molecules to create a longer molecule with the region encoding the digital file flanked by sequencing adaptors. DNA strands that include sequencing adaptors are sequenced and the sequence data is available for further analysis. DNA strands without the identification sequence are not joined to sequencing adaptors, and thus, are not sequenced. As a result, the sequencing data produced by the DNA sequencer comes from those DNA strands that included the identification sequence.Type: GrantFiled: October 30, 2017Date of Patent: October 10, 2023Assignee: Microsoft Technology Licensing, LLCInventors: Karin Strauss, Yuan-Jyue Chen
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Patent number: 11781169Abstract: One or more enzymes are used to repair damage in synthetic DNA molecules that encode digital information. The enzymes are included in a repair mixture containing one or more of DNA polymerase, DNA ligase, T4 Endonuclease, Endonuclease IV, Endonuclease VIII, and uracil glycosylase. The repair mixture may also contain one or more of a buffering solution, oxidized nicotinamide adenine dinucleotide (NAD+), and deoxyribose nucleoside triphosphates (dNTPs). The synthetic DNA molecules are incubated with the repair mixture for approximately four hours. Use of the repair solution allows recovery of the digital information from damaged DNA molecules.Type: GrantFiled: October 5, 2018Date of Patent: October 10, 2023Assignee: MICROSOFT TECHNOLOGY LICENSING, LLCInventors: Robert N. Grass, Alexander Xavier Christof Kohll, Weida Chen
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Patent number: 11781170Abstract: Means and methods for preparing double stranded target DNA molecules for sequencing. In embodiments double stranded backbone DNA molecules comprising 5? and 3? ends are provided that are: ligation compatible with 5? and 3? ends of the target DNA; form a first restriction enzyme recognition site when self-ligated; in a form that enables self-ligation. Methods may comprise providing, if not already present, the target DNA with 5? and 3? ends that are in a form that prevents self-ligation and that are ligation compatible with the backbone DNA 5? and 3? ends. Methods may further comprise ligating the target DNA to the backbone DNA in the presence of a ligase and a first restriction enzyme that cuts the first restriction enzyme recognition site, thereby producing at least one DNA circle comprising a backbone DNA molecule and a target DNA molecule.Type: GrantFiled: December 11, 2018Date of Patent: October 10, 2023Assignee: UMC Utrecht Holding B.V.Inventors: Wigard Pieter Kloosterman, Jeroen de Ridder, Alessio Marcozzi
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Patent number: 11761031Abstract: The subject invention pertains to the rapid amplification and real-time monitoring of nucleic acid sequences at a constant temperature. Specifically, fluorescent or electroactive-labeled loop probes and primers are designed to be specific to identified regions of a target nucleic acid sequences and subsequently amplify and permit the identification of the presence of the target sequence. In this method, a DNA polymerase with no 5? to 3? exonuclease activity is added to extend the primers and probes, while a nicking endonuclease is added to specifically identify the amplified nucleic acid product and cleave the label from the loop probe-extended DNA duplex.Type: GrantFiled: May 28, 2021Date of Patent: September 19, 2023Assignee: The Hong Kong University of Science and TechnologyInventors: I-Ming Hsing, Xiao Lu, Henson Lim Lee Yu
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Patent number: 11753679Abstract: The present disclosure provides a novel loop-de-loop method of detecting a target nucleic acid using a biosensor-labeled oligonucleotide. Further provided herein is a looped primer and a kit for use in the method.Type: GrantFiled: January 20, 2022Date of Patent: September 12, 2023Assignee: Uh-Oh Labs Inc.Inventor: Cameron Scott Ball
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Patent number: 11753687Abstract: The present invention provides methods for diagnosing melanoma and/or solar lentigo in a subject by analyzing nucleic acid molecules obtained from the subject. The present invention also provides methods for distinguishing melanoma from solar lentigo and/or dysplastic nevi and/or normal pigmented skin. The methods include analyzing expression or mutations in epidermal samples, of one or more skin markers. The methods can include the use of a microarray to analyze gene or protein profiles from a sample.Type: GrantFiled: March 8, 2021Date of Patent: September 12, 2023Assignee: DERMTECH, INC.Inventor: Sherman H. Chang
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Patent number: 11725252Abstract: The present disclosure relates to a PCR detection kit for rapidly identifying Salmonella of specific serotypes. The kit includes primers for detecting tcpS gene, the primers for detecting the tcpS gene including a forward primer having a nucleotide sequence as set forth in SEQ ID NO. 1 and a reverse primer having a nucleotide sequence as set forth in SEQ ID NO. 2. The kit can identify Salmonella of enteritidis, pullorum/gallinarum, and dublin serotypes rapidly and in a high throughput, which can be used as an auxiliary method for the conventional serotyping of Salmonella.Type: GrantFiled: November 18, 2016Date of Patent: August 15, 2023Assignee: YANGZHOU UNIVERSITYInventors: Xinan Jiao, Zhiming Pan, Dan Xiong, Li Song, Yang Jiao, Lin Sun, Xiang Chen, Shizhong Geng, Jinlin Huang, Yuelan Yin
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Patent number: 11718870Abstract: Molecules may be analyzed (e.g., sequencing of nucleic acid molecules) by tunneling recognition at a tunneling junction. Embodiments of the present invention may allow detecting individual nucleotides and the sequencing of a nucleic acid molecule using a tunneling junction. By labeling a specific nucleotide with a moiety, tunneling junctions may generate a signal with a suitable signal-to-noise ratio. The tunneling recognition uses a tunneling current that is mostly through the moiety rather than mostly through the nucleotide or a portion of the molecule of interest. Because a single nucleotide can be detected with a signal with a suitable signal-to-noise ratio resulting from the tunneling current passing through the moiety, embodiments of the present invention may allow for fast detection of nucleotides using a tunneling current.Type: GrantFiled: June 19, 2019Date of Patent: August 8, 2023Assignee: Roche Sequencing Solutions, Inc.Inventors: Yann Astier, Juraj Topolancik, Hannes Kuchelmeister, Frank Bergmann, Dieter Heindl, Nikolaus Klaus-Peter Stengele
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Patent number: 11708614Abstract: Assays and methods for detecting resistance to beta-lactam antibiotics including detection of multiple ?-lactamase family specific gene targets by polymerase chain reaction or microarray. One or more kits including primers and/or probes for identification of ?-lactamase genes selected from the group consisting of one or more of the following: MOX-like, FOX-like, ACC-like, ACT/MIR-like, CMY-2-like, DHA-like, CTX-M-14-like, CTX-M-15-like, VIM-like, NDM-like, IMP-like, KPC-like, and OXA-48-like, OXA-51-like, OXA-143-like, OXA-58-like, OXA-23-like, OXA-24/40-like, TEM-like, and SHV-like. A kit may also include one or more primers and/or probes for the identification a non-beta lactamase gene family which confers antibiotic resistance, such as the MCR-1 gene.Type: GrantFiled: June 15, 2017Date of Patent: July 25, 2023Assignees: STRECK LLC, CREIGHTON UNIVERSITYInventors: Maria Torres-Gonzalez, Nancy Hanson, Joel Lechner, Stephanie Cossette, Cathy Scheer, Matthew R. Kreifels, Stacey Morrow, Christopher Connelly, Laura R. Porter, Randy Fowler
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Patent number: 11667968Abstract: Provided herein is a polymerase-free enzyme mix (FRAG) for fragmenting double-stranded DNA. In some embodiments the enzyme mix may comprise a double-stranded DNA nickase and at least one of a DNA ligase capable of sealing a nick within a DNA, and a single-strand specific DNA nuclease. Methods for fragmenting double-stranded DNA are also provided.Type: GrantFiled: April 8, 2022Date of Patent: June 6, 2023Assignee: New England Biolabs, Inc.Inventors: Lynne Apone, Brittany S. Sexton, Margaret Heider, Louise J S Williams, Eileen T. Dimalanta
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Patent number: 11667960Abstract: Disclosed are methods and systems for detecting RNA and sequencing RNA in a wide range of samples such as samples with low concentrations of nucleic acid, samples with degraded nucleic acid, samples that would not otherwise be amenable to conventional sequencing or RNA detection methods, poor quality samples, high quality samples in which rare mutations are sought, formalin-fixed paraffin-embedded samples, blood samples, etc. The methods of the present invention may use paired, large panels of primers to amplify many short fragments that overlap between but not within each panel. Each panel's amplicon set may fill the gaps between those of the opposing panel, thereby providing complete gene or genomic coverage. A preliminary, multiplex amplification step amplifies target nucleic acid for all downstream reactions such as Sanger sequencing, cloning, and Next Generation Sequencing (NGS).Type: GrantFiled: April 20, 2017Date of Patent: June 6, 2023Assignee: ARIZONA BOARD OF REGENTS ON BEHALF OF THE UNIVERSITY OF ARIZONAInventors: Michael Worobey, Thomas Watts
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Patent number: 11649479Abstract: Provided herein are compositions, methods and uses that relate to an easy, accurate and reliable dual or duplex assay that determines both protein and nucleic acid amounts in a viral preparation in a single container and further determines full versus empty virion content.Type: GrantFiled: March 22, 2019Date of Patent: May 16, 2023Assignee: LIFE TECHNOLOGIES CORPORATIONInventors: Yixin Li, Bharti Solanki, Sheung-Mei Shih, Peter Bell, Darick Dayne
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Patent number: 11639527Abstract: The present invention provides methods for sequencing and analysis of nucleic acids and determining that a subject is positive for a non-usual interstitial pneumonia subtype.Type: GrantFiled: March 30, 2021Date of Patent: May 2, 2023Assignee: Veracyte, Inc.Inventors: Giulia C. Kennedy, James Diggans, Jing Huang, Yoonha Choi, Su Yeon Kim, Daniel Pankratz, Moraima Pagan
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Patent number: 11634770Abstract: This invention relates to methods and compositions for detecting the presence or absence of a Respiratory Syncytial Virus target nucleic acid in a biological sample using isothermal nucleic acid amplification.Type: GrantFiled: August 30, 2018Date of Patent: April 25, 2023Assignee: IONIAN TECHNOLOGIES, LLCInventors: Honghua Zhang, Richard Roth
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Patent number: 11613775Abstract: Provided herein are systems and methods for high-resolution mapping of DNA polymerase fidelity using nucleotide imbalances and next-generation sequencing.Type: GrantFiled: December 21, 2018Date of Patent: March 28, 2023Assignee: Northwestern UniversityInventors: Alexandra M. de Paz, Keith E.J. Tyo
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Patent number: 11591660Abstract: Methods and oligonucleotide reagents for diagnosing chikungunya virus and Zika virus infections are described. In particular, the invention relates to quantitative assays that can detect all lineages of chikungunya virus and Zika virus and distinguish chikungunya virus and Zika virus from each other as well as dengue virus and other arbovirus pathogens.Type: GrantFiled: January 14, 2017Date of Patent: February 28, 2023Assignee: THE BOARD OF TRUSTEES OF THE LELAND STANFORD JUNIOR UNIVERSITYInventors: Benjamin A. Pinsky, Jesse Waggoner
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Patent number: 11578358Abstract: Integrated devices that include a sample preparation component integrated with a detection component are disclosed. The sample preparation component may be a digital microfluidics module or a surface acoustic wave module which modules are used for combing a sample droplet with a reagent droplet and for performing additional sample preparation step leading to a droplet that contains beads/particles/labels that indicate presence or absence of an analyte of interest in the sample. The beads/particles/labels may be detected by moving the droplet to the detection component of the device, which detection component includes an array of wells. The detection modules disclosed here can be used for detecting analytes of interest which analytes may have been enriched by amplification, isolation, or other techniques.Type: GrantFiled: September 14, 2017Date of Patent: February 14, 2023Inventors: Mark A. Hayden, Jeffrey B. Huff, Sophie Laurenson, Andrew Fischer, John Robinson, Shelley R. Holets-McCormack
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Patent number: 11578357Abstract: The invention relates to reagents and methods for improving the efficiency of multiplex nucleic acid amplification, in particular where overlapping amplicons are to be generated. The invention also relates to reagents and methods for improving the efficiency of multistep nucleic acid amplification, in particular the performance of two separate amplification reactions designed to occur in sequence in the same reaction mixture or vessel. The invention further relates to reagents and methods for improving multistep nucleic acid amplification reactions by controlling the output of the first amplification reaction. In particular, primers are provided that minimise the formation of aberrant amplification products. Such primers are particularly useful where first and second amplification reactions take place in a single reaction mixture or vessel.Type: GrantFiled: November 15, 2017Date of Patent: February 14, 2023Assignee: AGILENT TECHNOLOGIES, INC.Inventors: Jurgen Peter Lode Del Favero, Lien Heyrman, Bart Tegenbos, Dirk Goossens, Joachim De Schrijver
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Patent number: 11578332Abstract: The present invention generally relates to improved methods of assembly of two or more DNA fragments, methods of rapid ligation-independent cloning, and kits for rapid ligation-independent cloning and their uses.Type: GrantFiled: June 5, 2017Date of Patent: February 14, 2023Inventor: Philippe Valadon
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Patent number: 11542547Abstract: This invention discloses multi-part primers for primer-dependent nucleic acid amplification methods. Also disclosed are multiplex assay methods, related reagent kits, and oligonucleotides for such methods.Type: GrantFiled: April 5, 2017Date of Patent: January 3, 2023Assignee: RUTGERS, THE STATE UNIVERSITY OF NEW JERSEYInventors: Salvatore A. E. Marras, Diana Vargas-Gold, Sanjay Tyagi, Fred Russell Kramer