Patents by Inventor Caleb J. Kennedy
Caleb J. Kennedy 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: 20210089581Abstract: The invention relates to using a graph database in genetic analyses to link mutation data to extrinsic data. Entities such as mutations, patients, samples, alleles, and clinical information are individually represented and stored as nodes and relationships between entities are also individually represented and stored. Each node and relationship can be stored using a fixed-size record and nodes can be flexibly invoked to represent any entity without disrupting the existing data. Systems and methods of the invention may be used for obtaining data representing a mutation in an individual and using a node in a graph database to store a description of the mutation. The node has stored within it a pointer to an adjacent node that provides information about a clinical significance of the variant. The graph database can be queried to provide a report of the clinical significance of the mutation.Type: ApplicationFiled: August 21, 2020Publication date: March 25, 2021Inventors: Alexander FRIEDEN, Caleb J. KENNEDY, Xavier S. HAURIE
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Publication number: 20210057045Abstract: The present invention generally relates to determining the clinical significance of a variant nucleic acid sequence. The invention can involve sequencing a nucleic acid to generate at least one sequence read, identifying a variant sequence within the sequence read, determining the equivalent insertion/deletion region (EIR) of the variant sequence, identifying a functional region including at least a portion of the EIR, and associating the EIR with the identified functional region, thereby to determine the clinical significance of the variant.Type: ApplicationFiled: August 19, 2020Publication date: February 25, 2021Inventors: Caleb J. KENNEDY, Mark UMBARGER, Gregory PORRECA
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Patent number: 10706017Abstract: The present invention generally relates to storing sequence read data. The invention can involve obtaining a plurality of sequence reads from a sample, identifying one or more sets of duplicative sequence reads within the plurality of sequence reads, and storing only one of the sequence reads from each set of duplicative sequence reads in a text file using nucleotide characters.Type: GrantFiled: January 3, 2017Date of Patent: July 7, 2020Assignee: Good Start Genetics, Inc.Inventors: Caleb J. Kennedy, Niru Chennagiri
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Publication number: 20170116216Abstract: The present invention generally relates to storing sequence read data. The invention can involve obtaining a plurality of sequence reads from a sample, identifying one or more sets of duplicative sequence reads within the plurality of sequence reads, and storing only one of the sequence reads from each set of duplicative sequence reads in a text file using nucleotide characters.Type: ApplicationFiled: January 3, 2017Publication date: April 27, 2017Inventors: Caleb J. Kennedy, Niru Chennagiri
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Patent number: 9292527Abstract: The present invention generally relates to storing sequence read data. The invention can involve obtaining a plurality of sequence reads from a sample, identifying one or more sets of duplicative sequence reads within the plurality of sequence reads, and storing only one of the sequence reads from each set of duplicative sequence reads in a text file using nucleotide characters.Type: GrantFiled: January 23, 2015Date of Patent: March 22, 2016Assignee: Good Start Genetics, Inc.Inventors: Caleb J. Kennedy, Niru Chennagiri
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Publication number: 20160048608Abstract: The invention relates to using a graph database in genetic analyses to link mutation data to extrinsic data. Entities such as mutations, patients, samples, alleles, and clinical information are individually represented and stored as nodes and relationships between entities are also individually represented and stored. Each node and relationship can be stored using a fixed-size record and nodes can be flexibly invoked to represent any entity without disrupting the existing data. Systems and methods of the invention may be used for obtaining data representing a mutation in an individual and using a node in a graph database to store a description of the mutation. The node has stored within it a pointer to an adjacent node that provides information about a clinical significance of the variant. The graph database can be queried to provide a report of the clinical significance of the mutation.Type: ApplicationFiled: August 14, 2015Publication date: February 18, 2016Inventors: Alexander Frieden, Caleb J. Kennedy, Xavier S. Haurie
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Patent number: 9228233Abstract: The invention generally relates to methods for analyzing nucleic acids to identify novel mutations associated with diseases. In certain embodiments, methods of the invention involve obtaining nucleic acid from a subject having a disease, identifying at least one mutation in the nucleic acid, and comparing the mutation to a database of mutations known to be associated with the disease, wherein mutations that do not match to the database are identified as novel mutations.Type: GrantFiled: September 14, 2012Date of Patent: January 5, 2016Assignee: Good Start Genetics, Inc.Inventors: Caleb J. Kennedy, Mark Umbarger, Gregory Porreca
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Patent number: 9218352Abstract: The present invention generally relates to storing sequence read data. The invention can involve obtaining a plurality of sequence reads from a sample, identifying one or more sets of duplicative sequence reads within the plurality of sequence reads, and storing only one of the sequence reads from each set of duplicative sequence reads in a text file using nucleotide characters.Type: GrantFiled: January 23, 2015Date of Patent: December 22, 2015Assignee: Good Start Genetics, Inc.Inventors: Caleb J. Kennedy, Niru Chennagiri
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Publication number: 20150149510Abstract: The present invention generally relates to storing sequence read data. The invention can involve obtaining a plurality of sequence reads from a sample, identifying one or more sets of duplicative sequence reads within the plurality of sequence reads, and storing only one of the sequence reads from each set of duplicative sequence reads in a text file using nucleotide characters.Type: ApplicationFiled: January 23, 2015Publication date: May 28, 2015Inventors: Caleb J. Kennedy, Niru Chennagiri
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Patent number: 8847799Abstract: The present invention generally relates to storing sequence read data. The invention can involve obtaining a plurality of sequence reads from a sample, identifying one or more sets of duplicative sequence reads within the plurality of sequence reads, and storing only one of the sequence reads from each set of duplicative sequence reads in a text file using nucleotide characters.Type: GrantFiled: June 2, 2014Date of Patent: September 30, 2014Assignee: Good Start Genetics, Inc.Inventors: Caleb J. Kennedy, Niru Chennagiri
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Patent number: 8738300Abstract: The invention relates to assembly of sequence reads. The invention provides a method for identifying a mutation in a nucleic acid involving sequencing nucleic acid to generate a plurality of sequence reads. Reads are assembled to form a contig, which is aligned to a reference. Individual reads are aligned to the contig. Mutations are identified based on the alignments to the reference and to the contig.Type: GrantFiled: June 12, 2012Date of Patent: May 27, 2014Assignee: Good Start Genetics, Inc.Inventors: Gregory Porreca, Caleb J. Kennedy
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Publication number: 20130288901Abstract: The invention generally relates to methods for analyzing nucleic acids to identify novel mutations associated with diseases. In certain embodiments, methods of the invention involve obtaining nucleic acid from a subject having a disease, identifying at least one mutation in the nucleic acid, and comparing the mutation to a database of mutations known to be associated with the disease, wherein mutations that do not match to the database are identified as novel mutations.Type: ApplicationFiled: September 14, 2012Publication date: October 31, 2013Applicant: GOOD START GENETICS, INC.Inventors: Caleb J. Kennedy, Mark Umbarger, Gregory Porreca
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Publication number: 20130268206Abstract: The invention relates to assembly of sequence reads. The invention provides a method for identifying a mutation in a nucleic acid involving sequencing nucleic acid to generate a plurality of sequence reads. Reads are assembled to form a contig, which is aligned to a reference. Individual reads are aligned to the contig. Mutations are identified based on the alignments to the reference and to the contig.Type: ApplicationFiled: June 12, 2012Publication date: October 10, 2013Applicant: Good Start Genetics, Inc.Inventors: Gregory Porreca, Caleb J. Kennedy