Patents by Inventor James Paul BROUGHTON
James Paul BROUGHTON has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Publication number: 20240139728Abstract: The application provides devices, kits and methods for a streamlined lateral flow assay for sample preparation, optional amplification, and detection of a target nucleic acid using programmable nuclease reagents.Type: ApplicationFiled: November 15, 2022Publication date: May 2, 2024Inventors: Maria-Nefeli TSALOGLOU, Janice Sha CHEN, James Paul BROUGHTON, Daniel Thomas DRZAL, Sarah Jane SHAPIRO, Clare Louise FASCHING, Carley Gelenter HENDRIKS, Jesus CHING, Sonal JAIN
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Publication number: 20240102084Abstract: Described herein are methods, devices, systems, and compositions for detecting a target nucleic acid using a programmable nuclease and a signal amplifier. Such methods, devices, systems, and compositions can comprise using signal amplifiers, such as catalytic oligonucleotides, which can be activated by programmable nucleases and be configured to cleave a reporter molecule upon activation. Signals can be generated and detected upon cleavage of reporter molecules.Type: ApplicationFiled: March 16, 2023Publication date: March 28, 2024Inventors: James Paul BROUGHTON, Janice Sha CHEN
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Publication number: 20240084401Abstract: Provided herein, in certain embodiments, are various methods, reagents, and devices for detection of multiple target nucleic acids in a sample, or multiple segments of a target nucleic acid in a sample, using a programmable nuclease. In certain embodiments, the present disclosure provides compositions of pools of guide nucleic acids, programmable nucleases, and detector nucleic acids and methods of using said compositions for detection of different segments of one target nucleic acid or different target nucleic acids in a sample.Type: ApplicationFiled: October 6, 2022Publication date: March 14, 2024Inventors: Matthew VEROSLOFF, Clare FASCHING, Carley Gelenter HENDRIKS, Xin MIAO, James Paul BROUGHTON, Lucas Benjamin HARRINGTON, Janice Sha CHEN
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Publication number: 20230332253Abstract: Described herein, in certain embodiments, are methods of assaying for a segment of a coronavirus target nucleic acid in a sample. In some embodiments, the target nucleic acid is from a gene of SARS-CoV-2, or a variant thereof. In some embodiments, methods described herein comprise a) contacting the sample to: i) a detector nucleic acid; and ii) a composition comprising a programmable nuclease and a non-naturally occurring guide nucleic acid, and b) assaying for a change in a signal, wherein the change in the signal is produced by cleavage of the detector nucleic acid by the programmable nuclease. Also provided herein are devices for performing the methods of assaying for a segment of a coronavirus target nucleic acid described herein.Type: ApplicationFiled: August 5, 2022Publication date: October 19, 2023Inventors: Maria-Nefeli TSALOGLOU, Clare FASCHING, Jesus CHING, Janice Sha CHEN, James Paul BROUGHTON, Daniel Thomas DRZAL, Sarah Jane SHAPIRO
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Publication number: 20230332218Abstract: The present disclosure provides compositions and methods of use for Type V CRISPR/Cas proteins. Type V CRISPR/Cas nucleases may be configured to bind nucleic acids in a sequence specific manner. Such a binding event may activate the Type V CRISPR/Cas nuclease for sequence non-specific trans-collateral cleavage of single-stranded nucleic acids. Provided herein are methods leveraging Type V CRISPR/Cas nuclease trans-collateral cleavage for identifying nucleic acid sequences.Type: ApplicationFiled: April 21, 2021Publication date: October 19, 2023Inventors: Benjamin RAUCH, William Douglass WRIGHT, Wiputra HARTONO, Lucas Benjamin HARRINGTON, Clarissa Oriel RHINES, Janice Sha CHEN, James Paul BROUGHTON, Aaron DELOUGHERY
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Patent number: 11761029Abstract: Described herein are devices, systems, fluidic devices, kits, and methods for detection of target nucleic acids associated with diseases, cancers, genetic disorders, a genotype, a phenotype, or ancestral origin. The devices, systems, fluidic devices, kits, and methods may comprise reagents of a guide nucleic acid targeting a target nucleic acid, a programmable nuclease, and a single stranded detector nucleic acid with a detection moiety. The target nucleic acid of interest may be indicative of a disease, and the disease may be communicable diseases, or of a cancer or genetic disorder. The target nucleic acid of interest may be indicative of a genotype, a phenotype, or ancestral origin.Type: GrantFiled: September 29, 2020Date of Patent: September 19, 2023Assignee: MAMMOTH BIOSCIENCES, INC.Inventors: Janice Sha Chen, Ashley Tehranchi, Andrew Besancon Lane, James Paul Broughton, Lucas Benjamin Harrington, Maria-Nefeli Tsaloglou, Xin Miao, Clare Louise Fasching, Jasmeet Singh, Pedro Patrick Draper Galarza
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Publication number: 20230159992Abstract: Disclosed herein are systems and methods for providing a high-throughput DETECTR assay in a single chamber. The single chamber may be one well of a microplate, and multiple assays may be conducted in a staggered fashion in separate chambers. The methods described herein implement a process including lysing a sample, isolating nucleic acid molecules, eluting the nucleic acid molecules, amplifying the nucleic acid molecules, and detecting a presence of a target nucleic acid.Type: ApplicationFiled: January 17, 2023Publication date: May 25, 2023Inventors: Timothy James PATNO, Jesus CHING, James Paul BROUGHTON, Xin MIAO, Janice Sha CHEN, Clare Louise FASCHING, Alexander HIRSCHI, Raymond Weibang MEI, Wesley Wendell ADDISON, II, Nazmiye Emel ALPAY, Farzaneh TONDNEVIS, Sara ANSALONI, Deepika VERMA
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Publication number: 20220411854Abstract: Described herein are devices, systems, fluidic devices, kits, and methods for detection of target nucleic acids associated with diseases, cancers, genetic disorders, a genotype, a phenotype, or ancestral origin. The devices, systems, fluidic devices, kits, and methods may comprise reagents of a guide nucleic acid targeting a target nucleic acid, a programmable nuclease, and a single stranded detector nucleic acid with a detection moiety. The target nucleic acid of interest may be indicative of a disease, and the disease may be communicable diseases, or of a cancer or genetic disorder. The target nucleic acid of interest may be indicative of a genotype, a phenotype, or ancestral origin.Type: ApplicationFiled: March 4, 2022Publication date: December 29, 2022Inventors: Janice Sha CHEN, Ashley TEHRANCHI, Andrew Besancon LANE, James Paul BROUGHTON, Lucas Benjamin HARRINGTON, Maria-Nefeli TSALOGLOU, Xin MIAO, Clare Louise FASCHING, Jasmeet SINGH, Pedro Patrick Draper GALARZA
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Publication number: 20220364159Abstract: Described herein are methods and systems for direct detection of DNA nucleic acids using a DNA-activated programmable RNA nuclease.Type: ApplicationFiled: July 22, 2020Publication date: November 17, 2022Inventors: James Paul Broughton, Janice Sha Chen, Lucas Benjamin Harrington
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Publication number: 20220325363Abstract: Described herein are devices, systems, fluidic devices, kits, and methods for detection of target nucleic acids.Type: ApplicationFiled: December 17, 2021Publication date: October 13, 2022Inventors: James Paul BROUGHTON, Jasmeet Singh, Clare Louise FASCHING, Maria-Nefeli TSALOGLOU, Pedro Patrick Draper GALARZA, Janice Sha CHEN, Xin MIAO, Lucas HARRINGTON, Daniel Thomas DRZAL, Sarah Jane Shapiro
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Publication number: 20220136038Abstract: Described herein are methods to detect nucleic acid modifications, such as methylated DNA or methylated RNA, using a programmable nuclease. The present disclosure further provides compositions and methods for generating and amplifying ssDNA from target nucleic acid sequences, or templates, for activation of programmable nucleases. Further provided herein are methods of coupling ssDNA amplification and activation of programmable nucleases with programmable nuclease systems, such as DETECTR systems, including trans cleavage of detector nucleic acids to produce a signal indicating the presence of the target nucleic acid sequence.Type: ApplicationFiled: July 1, 2021Publication date: May 5, 2022Inventors: Lucas Benjamin HARRINGTON, Janice Sha CHEN, James Paul BROUGHTON, Isaac Paterson WITTE
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Publication number: 20220119788Abstract: Disclosed herein are compositions, kits, and methods related to improved Cas activity. Through compositions and kits disclosed herein and practice of methods disclosed herein, one attains improved Cas activity such as Cas12 activity relative to Cas proteins in the art such as LbCas12. Further described herein are methods to detect target nucleic acid using a programmable nuclease system. Often, the target nucleic acids are present in at low frequency in the sample. Provided herein are methods for enriching these target nucleic acids for detection. Also described herein are methods to insert a PAM sequence into a target sequence of interest for use in a detection comprising a programmable nuclease.Type: ApplicationFiled: October 6, 2021Publication date: April 21, 2022Inventors: Lucas Benjamin HARRINGTON, Janice Sha CHEN, James Paul BROUGHTON, Pedro Patrick Draper GALARZA, Wiputra J. HARTONO, Isaac Paterson WITTE, Jasmeet SINGH
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Publication number: 20220099662Abstract: Described herein are devices, systems, fluidic devices, kits, and methods for detection of target nucleic acids associated with diseases, cancers, genetic disorders, a genotype, a phenotype, or ancestral origin. The devices, systems, fluidic devices, kits, and methods may comprise reagents of a guide nucleic acid targeting a target nucleic acid, a programmable nuclease, and a single stranded detector nucleic acid with a detection moiety. The target nucleic acid of interest may be indicative of a disease, and the disease may be communicable diseases, or of a cancer or genetic disorder. The target nucleic acid of interest may be indicative of a genotype, a phenotype, or ancestral origin.Type: ApplicationFiled: September 30, 2020Publication date: March 31, 2022Inventors: Janice Sha CHEN, Ashley TEHRANCHI, Andrew Besancon LANE, James Paul BROUGHTON, Lucas Benjamin HARRINGTON, Maria-Nefeli TSALOGLOU, Xin MIAO, Clare Louise FASCHING, Jasmeet SINGH, Pedro Patrick Draper GALARZA
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Patent number: 11273442Abstract: Described herein are devices, systems, fluidic devices, kits, and methods for detection of target nucleic acids associated with diseases, cancers, genetic disorders, a genotype, a phenotype, or ancestral origin. The devices, systems, fluidic devices, kits, and methods may comprise reagents of a guide nucleic acid targeting a target nucleic acid, a programmable nuclease, and a single stranded detector nucleic acid with a detection moiety. The target nucleic acid of interest may be indicative of a disease, and the disease may be communicable diseases, or of a cancer or genetic disorder. The target nucleic acid of interest may be indicative of a genotype, a phenotype, or ancestral origin.Type: GrantFiled: September 29, 2020Date of Patent: March 15, 2022Assignee: MAMMOTH BIOSCIENCES, INC.Inventors: Janice Sha Chen, Ashley Tehranchi, Andrew Besancon Lane, James Paul Broughton, Lucas Benjamin Harrington, Maria-Nefeli Tsaloglou, Xin Miao, Clare Louise Fasching, Jasmeet Singh, Pedro Patrick Draper Galarza
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Publication number: 20220072537Abstract: Described herein are devices, systems, fluidic devices, kits, and methods for detection of target nucleic acids associated with diseases, cancers, genetic disorders, a genotype, a phenotype, or ancestral origin. The devices, systems, fluidic devices, kits, and methods may comprise reagents of a guide nucleic acid targeting a target nucleic acid, a programmable nuclease, and a single stranded detector nucleic acid with a detection moiety. The target nucleic acid of interest may be indicative of a disease, and the disease may be communicable diseases, or of a cancer or genetic disorder. The target nucleic acid of interest may be indicative of a genotype, a phenotype, or ancestral origin.Type: ApplicationFiled: September 29, 2020Publication date: March 10, 2022Inventors: Janice Sha CHEN, Ashley TEHRANCHI, Andrew Besancon LANE, James Paul BROUGHTON, Lucas Benjamin HARRINGTON, Maria-Nefeli TSALOGLOU, Xin MIAO, Clare Louise FASCHING, Jasmeet SINGH, Pedro Patrick Draper GALARZA
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Patent number: 11174470Abstract: Disclosed herein are compositions, kits, and methods related to improved Cas activity. Through compositions and kits disclosed herein and practice of methods disclosed herein, one attains improved Cas activity such as Cas12 activity relative to Cas proteins in the art such as LbCas12. Further described herein are methods to detect target nucleic acid using a programmable nuclease system. Often, the target nucleic acids are present in at low frequency in the sample. Provided herein are methods for enriching these target nucleic acids for detection. Also described herein are methods to insert a PAM sequence into a target sequence of interest for use in a detection comprising a programmable nuclease.Type: GrantFiled: September 29, 2020Date of Patent: November 16, 2021Assignee: MAMMOTH BIOSCIENCES, INC.Inventors: Lucas Benjamin Harrington, Janice Sha Chen, James Paul Broughton, Pedro Patrick Draper Galarza, Wiputra J. Hartono, Isaac Paterson Witte, Jasmeet Singh
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Publication number: 20210102242Abstract: Described herein are devices, systems, fluidic devices, kits, and methods for detection of target nucleic acids associated with diseases, cancers, genetic disorders, a genotype, a phenotype, or ancestral origin. The devices, systems, fluidic devices, kits, and methods may comprise reagents of a guide nucleic acid targeting a target nucleic acid, a programmable nuclease, and a single stranded detector nucleic acid with a detection moiety. The target nucleic acid of interest may be indicative of a disease, and the disease may be communicable diseases, or of a cancer or genetic disorder. The target nucleic acid of interest may be indicative of a genotype, a phenotype, or ancestral origin.Type: ApplicationFiled: September 29, 2020Publication date: April 8, 2021Inventors: Janice Sha CHEN, Ashley TEHRANCHI, Andrew Besancon LANE, James Paul BROUGHTON, Lucas Benjamin HARRINGTON, Maria-Nefeli TSALOGLOU, Xin MIAO, Clare Louise FASCHING, Jasmeet SINGH, Pedro Patrick Draper GALARZA
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Publication number: 20210078002Abstract: Described herein are devices, systems, fluidic devices, kits, and methods for detection of target nucleic acids associated with diseases, cancers, genetic disorders, a genotype, a phenotype, or ancestral origin. The devices, systems, fluidic devices, kits, and methods may comprise reagents of a guide nucleic acid targeting a target nucleic acid, a programmable nuclease, and a single stranded detector nucleic acid with a detection moiety. The target nucleic acid of interest may be indicative of a disease, and the disease may be communicable diseases, or of a cancer or genetic disorder. The target nucleic acid of interest may be indicative of a genotype, a phenotype, or ancestral origin.Type: ApplicationFiled: September 30, 2020Publication date: March 18, 2021Inventors: Janice Sha CHEN, Ashley TEHRANCHI, Andrew Besancon LANE, James Paul BROUGHTON, Lucas Benjamin HARRINGTON, Maria-Nefeli TSALOGLOU, Xin MIAO, Clare Louise FASCHING, Jasmeet SINGH, Pedro Patrick Draper GALARZA
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Publication number: 20210009974Abstract: Disclosed herein are compositions, kits, and methods related to improved Cas activity. Through compositions and kits disclosed herein and practice of methods disclosed herein, one attains improved Cas activity such as Cas12 activity relative to Cas proteins in the art such as LbCas12. Further described herein are methods to detect target nucleic acid using a programmable nuclease system. Often, the target nucleic acids are present in at low frequency in the sample. Provided herein are methods for enriching these target nucleic acids for detection. Also described herein are methods to insert a PAM sequence into a target sequence of interest for use in a detection comprising a programmable nuclease.Type: ApplicationFiled: September 29, 2020Publication date: January 14, 2021Inventors: Lucas Benjamin HARRINGTON, Janice Sha CHEN, James Paul BROUGHTON, Pedro Patrick Draper GALARZA, Wiputra J. HARTONO, Isaac Paterson WITTE, Jasmeet SINGH