Patents by Inventor Caleb Kennedy
Caleb 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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Patent number: 11667965Abstract: 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: February 13, 2020Date of Patent: June 6, 2023Assignee: Invitae CorporationInventors: Gregory Porreca, Caleb Kennedy
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Publication number: 20230002823Abstract: 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: July 18, 2022Publication date: January 5, 2023Applicant: Invitae CorporationInventors: Gregory PORRECA, Caleb KENNEDY
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Patent number: 11390919Abstract: 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: February 13, 2020Date of Patent: July 19, 2022Assignee: Invitae CorporationInventors: Gregory Porreca, Caleb Kennedy
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Patent number: 11155863Abstract: 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: May 17, 2021Date of Patent: October 26, 2021Assignee: Invitae CorporationInventors: Gregory Porreca, Caleb Kennedy
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Patent number: 11149308Abstract: 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: May 17, 2021Date of Patent: October 19, 2021Assignee: Invitae CorporationInventors: Gregory Porreca, Caleb Kennedy
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Publication number: 20210269875Abstract: 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: May 17, 2021Publication date: September 2, 2021Applicant: Invitae CorporationInventors: Gregory PORRECA, Caleb KENNEDY
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Publication number: 20210269874Abstract: 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: May 17, 2021Publication date: September 2, 2021Applicant: Invitae CorporationInventors: Gregory PORRECA, Caleb KENNEDY
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Publication number: 20200181696Abstract: 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: February 13, 2020Publication date: June 11, 2020Inventors: Gregory Porreca, Caleb Kennedy
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Patent number: 10604799Abstract: 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: April 11, 2014Date of Patent: March 31, 2020Assignee: Molecular Loop Biosolutions, LLCInventors: Gregory Porreca, Caleb Kennedy
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Patent number: 10370710Abstract: 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: November 20, 2017Date of Patent: August 6, 2019Inventors: Gregory Porreca, Mark Umbarger, Caleb Kennedy
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Publication number: 20180298440Abstract: 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: November 20, 2017Publication date: October 18, 2018Inventors: Gregory Porreca, Mark Umbarger, Caleb Kennedy
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Patent number: 9822409Abstract: 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: December 30, 2015Date of Patent: November 21, 2017Assignee: Good Start Genetics, Inc.Inventors: Caleb Kennedy, Mark Umbarger, Gregory Porreca
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Patent number: 9535920Abstract: 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: December 4, 2015Date of Patent: January 3, 2017Assignee: Good Start Genetics, Inc.Inventors: Caleb Kennedy, Niru Chennagiri
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Publication number: 20160154795Abstract: 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: December 4, 2015Publication date: June 2, 2016Inventors: Caleb Kennedy, Niru Chennagiri
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Publication number: 20160115534Abstract: 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: December 30, 2015Publication date: April 28, 2016Inventors: Caleb Kennedy, Mark Umbarger, Gregory Porreca
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Patent number: 8976049Abstract: 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: August 22, 2014Date of Patent: March 10, 2015Assignee: Good Start Genetics, Inc.Inventors: Caleb Kennedy, Niru Chennagiri
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Publication number: 20140361911Abstract: 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: August 22, 2014Publication date: December 11, 2014Inventors: Caleb Kennedy, Niru Chennagiri
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Publication number: 20140255931Abstract: 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: April 11, 2014Publication date: September 11, 2014Applicant: GOOD START GENETICS, INC.Inventors: Gregory Porreca, Caleb Kennedy
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Publication number: 20140129201Abstract: The invention provides a method for validating a genetic test by introducing a simulated mutation into sequence reads. By editing the information in one or more sequence read files, a set of sequence reads can be manipulated to represent an expected genotype. An analysis of those sequence reads produces an observed genotype and concordance between the expected and observed genotypes validates the analysis. Thus, the invention provides methods for validating new genetic tests.Type: ApplicationFiled: October 1, 2013Publication date: May 8, 2014Applicant: GOOD START GENETICS, INC.Inventors: Caleb Kennedy, Gregory Porreca, Mark Umbarger
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Publication number: 20130324417Abstract: 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: June 4, 2012Publication date: December 5, 2013Applicant: Good Start Genetics, Inc.Inventors: Caleb Kennedy, Mark Umbarger, Greg Porreca