Patents by Inventor Devin Locke
Devin Locke 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: 20240011074Abstract: The invention provides systems and methods for determining patterns of modification to a genome of a subject by representing the genome using a graph, such as a directed acyclic graph (DAG) with divergent paths for regions that are potentially subject to modification, profiling segments of the genome for evidence of epigenetic modification, and aligning the profiled segments to the DAG to determine locations and patterns of the epigenetic modification within the genome.Type: ApplicationFiled: June 5, 2023Publication date: January 11, 2024Applicant: Seven Bridges Genomics Inc.Inventors: Devin Locke, Wan-Ping Lee
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Publication number: 20230366046Abstract: The invention provides systems and methods for analyzing viruses by representing viral genetic diversity with a directed acyclic graph (DAG), which allows genetic sequencing technology to detect rare variations and represent otherwise difficult-to-document diversity within a sample. Additionally, a host-specific sequence DAG can be used to effectively segregate viral nucleic acid sequence reads from host sequence reads when a sample from a host is subject to sequencing. Known viral genomes can be represented using a viral reference DAG and the viral sequence reads from the sample can be compared to viral DAG to identify viral species or strains from which the reads were derived. Where the viral sequence reads indicate great genetic diversity in the virus that was infecting the host, those reads can be assembled into a DAG that itself properly represents that diversity.Type: ApplicationFiled: May 26, 2023Publication date: November 16, 2023Applicant: Seven Bridges Genomics Inc.Inventors: Devin Locke, Piotr Szamel
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Publication number: 20230357842Abstract: The invention provides methods of analyzing an individual's mtDNA by transforming available reference sequences into a directed graph that compactly represents all the information without duplication and comparing sequence reads from the mtDNA to the graph to identify the individual or describe their mtDNA. A directed graph can represent all of the genetic variation found among the mitochondrial genomes across all of a number of reference organisms while providing a single article to which sequence reads can be aligned or compared. Thus any sequence read or other sequence fragment can be compared, in a single operation, to the article that represents all of the reference mitochondrial sequences.Type: ApplicationFiled: April 7, 2023Publication date: November 9, 2023Applicant: Seven Bridges Genomics Inc.Inventors: Devin Locke, Piotr Szamel
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Publication number: 20230272483Abstract: The invention provides oncogenomic methods for detecting tumors by identifying circulating tumor DNA. A patient-specific reference directed acyclic graph (DAG) represents known human genomic sequences and non-tumor DNA from the patient as well as known tumor-associated mutations. Sequence reads from cell-free plasma DNA from the patient are mapped to the patient-specific genomic reference graph. Any of the known tumor-associated mutations found in the reads and any de novo mutations found in the reads are reported as the patient’s tumor mutation burden.Type: ApplicationFiled: November 30, 2022Publication date: August 31, 2023Applicant: Seven Bridges Genomics Inc.Inventors: Wan-Ping Lee, Devin Locke
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Patent number: 11702708Abstract: The invention provides systems and methods for analyzing viruses by representing viral genetic diversity with a directed acyclic graph (DAG), which allows genetic sequencing technology to detect rare variations and represent otherwise difficult-to-document diversity within a sample. Additionally, a host-specific sequence DAG can be used to effectively segregate viral nucleic acid sequence reads from host sequence reads when a sample from a host is subject to sequencing. Known viral genomes can be represented using a viral reference DAG and the viral sequence reads from the sample can be compared to viral DAG to identify viral species or strains from which the reads were derived. Where the viral sequence reads indicate great genetic diversity in the virus that was infecting the host, those reads can be assembled into a DAG that itself properly represents that diversity.Type: GrantFiled: July 24, 2020Date of Patent: July 18, 2023Assignee: Seven Bridges Genomics Inc.Inventors: Devin Locke, Piotr Szamel
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Patent number: 11697835Abstract: The invention provides systems and methods for determining patterns of modification to a genome of a subject by representing the genome using a graph, such as a directed acyclic graph (DAG) with divergent paths for regions that are potentially subject to modification, profiling segments of the genome for evidence of epigenetic modification, and aligning the profiled segments to the DAG to determine locations and patterns of the epigenetic modification within the genome.Type: GrantFiled: September 16, 2020Date of Patent: July 11, 2023Assignee: Seven Bridges Genomics Inc.Inventors: Devin Locke, Wan-Ping Lee
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Patent number: 11649495Abstract: The invention provides methods of analyzing an individual's mtDNA by transforming available reference sequences into a directed graph that compactly represents all the information without duplication and comparing sequence reads from the mtDNA to the graph to identify the individual or describe their mtDNA. A directed graph can represent all of the genetic variation found among the mitochondrial genomes across all of a number of reference organisms while providing a single article to which sequence reads can be aligned or compared. Thus any sequence read or other sequence fragment can be compared, in a single operation, to the article that represents all of the reference mitochondrial sequences.Type: GrantFiled: February 24, 2020Date of Patent: May 16, 2023Assignee: Seven Bridges Genomics Inc.Inventors: Devin Locke, Piotr Szamel
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Patent number: 11560598Abstract: The invention provides oncogenomic methods for detecting tumors by identifying circulating tumor DNA. A patient-specific reference directed acyclic graph (DAG) represents known human genomic sequences and non-tumor DNA from the patient as well as known tumor-associated mutations. Sequence reads from cell-free plasma DNA from the patient are mapped to the patient-specific genomic reference graph. Any of the known tumor-associated mutations found in the reads and any de novo mutations found in the reads are reported as the patient's tumor mutation burden.Type: GrantFiled: July 30, 2019Date of Patent: January 24, 2023Assignee: Seven Bridges Genomics Inc.Inventors: Wan-Ping Lee, Devin Locke
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Publication number: 20220254444Abstract: A method for screening for disease in a genomic sample is includes receiving a representation of a reference genome comprising a sequence of symbols. The presence of a predicted mutational event is identified in a location of the reference genome. An alternate path is created in the reference genome representing the predicted mutational event. A plurality of sequence reads are obtained from a genomic sample, wherein at least one sequence read comprises at least a portion of the predicted mutational event. The at least one sequence read is then mapped to the reference genome and a location is determined corresponding to the predicted mutational event. The predicted mutational event is then identified as present in the genomic sample. The method may be used to detect evidence of non-allelic homologous recombination (NAHR) occurring in genomic samples.Type: ApplicationFiled: February 11, 2022Publication date: August 11, 2022Applicant: Seven Bridges Genomics Inc.Inventor: Devin Locke
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Patent number: 11250931Abstract: A method for screening for disease in a genomic sample is includes receiving a representation of a reference genome comprising a sequence of symbols. The presence of a predicted mutational event is identified in a location of the reference genome. An alternate path is created in the reference genome representing the predicted mutational event. A plurality of sequence reads are obtained from a genomic sample, wherein at least one sequence read comprises at least a portion of the predicted mutational event. The at least one sequence read is then mapped to the reference genome and a location is determined corresponding to the predicted mutational event. The predicted mutational event is then identified as present in the genomic sample. The method may be used to detect evidence of non-allelic homologous recombination (NAHR) occurring in genomic samples.Type: GrantFiled: September 1, 2016Date of Patent: February 15, 2022Assignee: Seven Bridges Genomics Inc.Inventor: Devin Locke
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Publication number: 20200407778Abstract: The invention provides systems and methods for determining patterns of modification to a genome of a subject by representing the genome using a graph, such as a directed acyclic graph (DAG) with divergent paths for regions that are potentially subject to modification, profiling segments of the genome for evidence of epigenetic modification, and aligning the profiled segments to the DAG to determine locations and patterns of the epigenetic modification within the genome.Type: ApplicationFiled: September 16, 2020Publication date: December 31, 2020Applicant: Seven Bridges Genomics Inc.Inventors: Devin Locke, Wan-Ping Lee
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Publication number: 20200399719Abstract: The invention provides systems and methods for analyzing viruses by representing viral genetic diversity with a directed acyclic graph (DAG), which allows genetic sequencing technology to detect rare variations and represent otherwise difficult-to-document diversity within a sample. Additionally, a host-specific sequence DAG can be used to effectively segregate viral nucleic acid sequence reads from host sequence reads when a sample from a host is subject to sequencing. Known viral genomes can be represented using a viral reference DAG and the viral sequence reads from the sample can be compared to viral DAG to identify viral species or strains from which the reads were derived. Where the viral sequence reads indicate great genetic diversity in the virus that was infecting the host, those reads can be assembled into a DAG that itself properly represents that diversity.Type: ApplicationFiled: July 24, 2020Publication date: December 24, 2020Applicant: Seven Bridges Genomics Inc.Inventors: Devin Locke, Piotr Szamel
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Patent number: 10793895Abstract: The invention provides systems and methods for determining patterns of modification to a genome of a subject by representing the genome using a graph, such as a directed acyclic graph (DAG) with divergent paths for regions that are potentially subject to modification, profiling segments of the genome for evidence of epigenetic modification, and aligning the profiled segments to the DAG to determine locations and patterns of the epigenetic modification within the genome.Type: GrantFiled: January 27, 2016Date of Patent: October 6, 2020Assignee: Seven Bridges Genomics Inc.Inventors: Devin Locke, Wan-Ping Lee
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Patent number: 10724110Abstract: The invention provides systems and methods for analyzing viruses by representing viral genetic diversity with a directed acyclic graph (DAG), which allows genetic sequencing technology to detect rare variations and represent otherwise difficult-to-document diversity within a sample. Additionally, a host-specific sequence DAG can be used to effectively segregate viral nucleic acid sequence reads from host sequence reads when a sample from a host is subject to sequencing. Known viral genomes can be represented using a viral reference DAG and the viral sequence reads from the sample can be compared to viral DAG to identify viral species or strains from which the reads were derived. Where the viral sequence reads indicate great genetic diversity in the virus that was infecting the host, those reads can be assembled into a DAG that itself properly represents that diversity.Type: GrantFiled: February 3, 2016Date of Patent: July 28, 2020Assignee: Seven Bridges Genomics Inc.Inventors: Devin Locke, Piotr Szamel
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Publication number: 20200232029Abstract: The invention provides methods of analyzing an individual's mtDNA by transforming available reference sequences into a directed graph that compactly represents all the information without duplication and comparing sequence reads from the mtDNA to the graph to identify the individual or describe their mtDNA. A directed graph can represent all of the genetic variation found among the mitochondrial genomes across all of a number of reference organisms while providing a single article to which sequence reads can be aligned or compared. Thus any sequence read or other sequence fragment can be compared, in a single operation, to the article that represents all of the reference mitochondrial sequences.Type: ApplicationFiled: February 24, 2020Publication date: July 23, 2020Applicant: Seven Bridges Genomics Inc.Inventors: Devin Locke, Piotr Szamel
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Publication number: 20200165683Abstract: The invention provides oncogenomic methods for detecting tumors by identifying circulating tumor DNA. A patient-specific reference directed acyclic graph (DAG) represents known human genomic sequences and non-tumor DNA from the patient as well as known tumor-associated mutations. Sequence reads from cell-free plasma DNA from the patient are mapped to the patient-specific genomic reference graph. Any of the known tumor-associated mutations found in the reads and any de novo mutations found in the reads are reported as the patient's tumor mutation burden.Type: ApplicationFiled: July 30, 2019Publication date: May 28, 2020Applicant: Seven Bridges Genomics Inc.Inventors: Wan-Ping Lee, Devin Locke
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Patent number: 10584380Abstract: The invention provides methods of analyzing an individual's mtDNA by transforming available reference sequences into a directed graph that compactly represents all the information without duplication and comparing sequence reads from the mtDNA to the graph to identify the individual or describe their mtDNA. A directed graph can represent all of the genetic variation found among the mitochondrial genomes across all of a number of reference organisms while providing a single article to which sequence reads can be aligned or compared. Thus any sequence read or other sequence fragment can be compared, in a single operation, to the article that represents all of the reference mitochondrial sequences.Type: GrantFiled: February 3, 2016Date of Patent: March 10, 2020Assignee: Seven Bridges Genomics Inc.Inventors: Devin Locke, Piotr Szamel
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Patent number: 10364468Abstract: The invention provides oncogenomic methods for detecting tumors by identifying circulating tumor DNA. A patient-specific reference directed acyclic graph (DAG) represents known human genomic sequences and non-tumor DNA from the patient as well as known tumor-associated mutations. Sequence reads from cell-free plasma DNA from the patient are mapped to the patient-specific genomic reference graph. Any of the known tumor-associated mutations found in the reads and any de novo mutations found in the reads are reported as the patient's tumor mutation burden.Type: GrantFiled: January 13, 2016Date of Patent: July 30, 2019Assignee: Seven Bridges Genomics Inc.Inventors: Wan-Ping Lee, Devin Locke
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Publication number: 20180060480Abstract: A method for screening for disease in a genomic sample is includes receiving a representation of a reference genome comprising a sequence of symbols. The presence of a predicted mutational event is identified in a location of the reference genome. An alternate path is created in the reference genome representing the predicted mutational event. A plurality of sequence reads are obtained from a genomic sample, wherein at least one sequence read comprises at least a portion of the predicted mutational event. The at least one sequence read is then mapped to the reference genome and a location is determined corresponding to the predicted mutational event. The predicted mutational event is then identified as present in the genomic sample. The method may be used to detect evidence of non-allelic homologous recombination (NAHR) occurring in genomic samples.Type: ApplicationFiled: September 1, 2016Publication date: March 1, 2018Inventor: Devin Locke
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Publication number: 20170199959Abstract: Genomes of different species may be embodied as a graph in which conserved parts of multiple genomes are stored at a fixed location in memory and accessed via spatial addressing. The graph branches into plural paths, each defined by pointers to other fixed locations in the memory, where the genomes diverge due to either divergent homology or non-homologous portions. The graph can represent whole genomic information for multiple species with the natural relationships among parts of the genomes being represented by the structure of the graph. Newly obtained sequences such as output from NGS instruments can be mapped onto the graph for assembly or identification.Type: ApplicationFiled: January 13, 2016Publication date: July 13, 2017Inventor: Devin Locke