Patents Assigned to SEVEN BRIDGES GENOMICS INC.
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Publication number: 20240096450Abstract: Systems and methods for analyzing genomic information can include obtaining a sequence read including genetic information; identifying, within a graph representing a reference genome, a plurality of candidate mapping positions that relate to the genetic information, the graph comprising nodes representing genetic sequences and edges connecting pairs of nodes; determining, by means of a computer system, whether an alignment with the graph surrounding each of the plurality of candidate mapping positions is advanced or basic; and performing for each candidate mapping position, by means of the computer system, a local alignment based on whether the local alignment is advanced or basic. The advanced local alignment can include a first-local-alignment algorithm, and the basic local alignment includes a second-local-alignment algorithm. Based on the local alignments, the mapped position of the sequence read can be identified within the genome.Type: ApplicationFiled: September 11, 2023Publication date: March 21, 2024Applicant: Seven Bridges Genomics Inc.Inventors: Kaushik Ghose, Wan-Ping Lee
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Publication number: 20240062850Abstract: The invention provides methods for identifying rare variants near a structural variation in a genetic sequence, for example, in a nucleic acid sample taken from a subject. The invention additionally includes methods for aligning reads (e.g., nucleic acid reads) to a reference sequence construct accounting for the structural variation, methods for building a reference sequence construct accounting for the structural variation or the structural variation and the rare variant, and systems that use the alignment methods to identify rare variants. The method is scalable, and can be used to align millions of reads to a construct thousands of bases long, or longer.Type: ApplicationFiled: October 25, 2023Publication date: February 22, 2024Applicant: Seven Bridges Genomics Inc.Inventor: Deniz Kural
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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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Patent number: 11837328Abstract: The invention provides methods for identifying rare variants near a structural variation in a genetic sequence, for example, in a nucleic acid sample taken from a subject. The invention additionally includes methods for aligning reads (e.g., nucleic acid reads) to a reference sequence construct accounting for the structural variation, methods for building a reference sequence construct accounting for the structural variation or the structural variation and the rare variant, and systems that use the alignment methods to identify rare variants. The method is scalable, and can be used to align millions of reads to a construct thousands of bases long, or longer.Type: GrantFiled: September 19, 2022Date of Patent: December 5, 2023Assignee: Seven Bridges Genomics Inc.Inventor: Deniz Kural
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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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Patent number: 11810648Abstract: Systems and methods for analyzing genomic information can include obtaining a sequence read including genetic information; identifying, within a graph representing a reference genome, a plurality of candidate mapping positions that relate to the genetic information, the graph comprising nodes representing genetic sequences and edges connecting pairs of nodes; determining, by means of a computer system, whether an alignment with the graph surrounding each of the plurality of candidate mapping positions is advanced or basic; and performing for each candidate mapping position, by means of the computer system, a local alignment based on whether the local alignment is advanced or basic. The advanced local alignment can include a first-local-alignment algorithm, and the basic local alignment includes a second-local-alignment algorithm. Based on the local alignments, the mapped position of the sequence read can be identified within the genome.Type: GrantFiled: October 24, 2019Date of Patent: November 7, 2023Assignee: Seven Bridges Genomics Inc.Inventors: Kaushik Ghose, Wan-Ping Lee
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Patent number: 11756652Abstract: The invention provides methods for comparing one set of genetic sequences to another without discarding any information within either set. A set of genetic sequences is represented using a directed acyclic graph (DAG) avoiding any unwarranted reduction to a linear data structure. The invention provides a way to align one sequence DAG to another to produce an alignment that can itself be stored as a DAG. DAG-to-DAG alignment is a natural choice wherever a set of genomic information consisting of more than one string needs to be compared to any non-linear reference. For example, a subpopulation DAG could be compared to a population DAG in order to compare the genetic features of that subpopulation to those of the population.Type: GrantFiled: November 2, 2020Date of Patent: September 12, 2023Assignee: Seven Bridges Genomics Inc.Inventor: Deniz Kural
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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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Publication number: 20230044434Abstract: The invention provides methods for identifying rare variants near a structural variation in a genetic sequence, for example, in a nucleic acid sample taken from a subject. The invention additionally includes methods for aligning reads (e.g., nucleic acid reads) to a reference sequence construct accounting for the structural variation, methods for building a reference sequence construct accounting for the structural variation or the structural variation and the rare variant, and systems that use the alignment methods to identify rare variants. The method is scalable, and can be used to align millions of reads to a construct thousands of bases long, or longer.Type: ApplicationFiled: September 19, 2022Publication date: February 9, 2023Applicant: Seven Bridges Genomics Inc.Inventor: Deniz Kural
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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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Patent number: 11558487Abstract: A method for stream-processing biomedical data includes receiving, by a file system on a computing device, a first request for access to at least a first portion of a file stored on a remotely located storage device. The method includes receiving, by the file system, a second request for access to at least a second portion of the file. The method includes determining, by a pre-fetching component executing on the computing device, whether the first request and the second request are associated with a sequential read operation. The method includes automatically retrieving, by the pre-fetching component, a third portion of the requested file, before receiving a third request for access to least the third portion of the file, based on a determination that the first request and the second request are associated with the sequential read operation.Type: GrantFiled: March 3, 2021Date of Patent: January 17, 2023Assignee: SEVEN BRIDGES GENOMICS INC.Inventor: Nemanja Zbiljic
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Publication number: 20220411881Abstract: The invention includes methods and systems for identifying diseased-induced mutations by producing multi-dimensional reference sequence constructs that account for variations between individuals, different diseases, and different stages of those diseases. Once constructed, these reference sequence constructs can be used to align sequence reads corresponding to genetic samples from patients suspected of having a disease, or who have had the disease and are in suspected remission. The reference sequence constructs also provide insight to the genetic progression of the disease.Type: ApplicationFiled: June 29, 2022Publication date: December 29, 2022Applicant: Seven Bridges Genomics Inc.Inventor: Deniz Kural
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Patent number: 11488688Abstract: The invention provides methods for identifying rare variants near a structural variation in a genetic sequence, for example, in a nucleic acid sample taken from a subject. The invention additionally includes methods for aligning reads (e.g., nucleic acid reads) to a reference sequence construct accounting for the structural variation, methods for building a reference sequence construct accounting for the structural variation or the structural variation and the rare variant, and systems that use the alignment methods to identify rare variants. The method is scalable, and can be used to align millions of reads to a construct thousands of bases long, or longer.Type: GrantFiled: June 17, 2019Date of Patent: November 1, 2022Assignee: Seven Bridges Genomics Inc.Inventor: Deniz Kural
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Patent number: 11447828Abstract: The invention includes methods and systems for identifying diseased-induced mutations by producing multi-dimensional reference sequence constructs that account for variations between individuals, different diseases, and different stages of those diseases. Once constructed, these reference sequence constructs can be used to align sequence reads corresponding to genetic samples from patients suspected of having a disease, or who have had the disease and are in suspected remission. The reference sequence constructs also provide insight to the genetic progression of the disease.Type: GrantFiled: August 21, 2018Date of Patent: September 20, 2022Assignee: Seven Bridges Genomics Inc.Inventor: Deniz Kural
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Publication number: 20220261384Abstract: Methods of the invention include representing biological data in a memory subsystem within a computer system with a data structure that is particular to a location in the memory subsystem and serializing the data structure into a stream of bytes that can be deserialized into a clone of the data structure. In a preferred genomic embodiment, the biological data comprises genomic sequences and the data structure comprises a genomic directed acyclic graph (DAG) in which objects have adjacency lists of pointers that indicate the location of any object adjacent to that object. After serialization and deserialization, the clone genomic DAG has the same structure as the original to represent the same sequences and relationships among them as the original.Type: ApplicationFiled: April 26, 2022Publication date: August 18, 2022Applicant: Seven Bridges Genomics Inc.Inventor: Vladimir Semenyuk
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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