Patents by Inventor Mark Umbarger

Mark Umbarger 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).

  • Publication number: 20160210404
    Abstract: The present invention provides methods for validating results of a pre-implantation genetic screen. Methods of the invention increase the efficacy of the common PGS assay FAST-SeqS by taking advantage of single-nucleotide polymorphisms (SNPs) generated from the assay to confirm copy number calls, detect errors, identify samples, and recognize and identify sources of contamination. Methods of the invention increase the reliability of a PGS result, thereby making embryo selection more precise and improving outcomes of in vitro fertilization.
    Type: Application
    Filed: January 14, 2016
    Publication date: July 21, 2016
    Inventors: Mark Umbarger, Athurva Gore, Gregory Porreca
  • Publication number: 20160194692
    Abstract: The invention relates to carrier screening and methods for describing a structural variant, such as a large rearrangement or chromosomal abnormality, in a person's genome using probes that are designed to determine the person's genetic sequence and reveal substitution mutations and small structural variants. Identifying a structural variant may include exposing a nucleic acid to a plurality of probes. Each probe has a linked pair of targeting arms designed to hybridize upstream and downstream of a target in a genome. The method includes hybridizing two of the probes to the nucleic acid and attaching the two probes together to create an inter-probe product as well as detecting the inter-probe product and reporting a structural variant of the genome in the nucleic acid.
    Type: Application
    Filed: January 6, 2016
    Publication date: July 7, 2016
    Inventors: Athurva Gore, Mark Umbarger
  • Publication number: 20160115534
    Abstract: 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: Application
    Filed: December 30, 2015
    Publication date: April 28, 2016
    Inventors: Caleb Kennedy, Mark Umbarger, Gregory Porreca
  • Publication number: 20160068889
    Abstract: The invention generally relates to negative selection of nucleic acids. The invention provides methods and systems that remove unwanted segments of nucleic acid in a sample so that a target gene or region of interest may be analyzed without interference from the unwanted segments. A sample is obtained that includes single-stranded nucleic acid with one or more unwanted segments. Complementary nucleic acid is added to the single-stranded nucleic acid to create a double-stranded region that includes the unwanted segment. The double-stranded region is then digested, leaving single-stranded nucleic acid that includes the target gene or region of interest. This allows paralogs, pseudogenes, repetitive elements, and other segments of the genome that may be similar to the target gene or region of interest to be removed from the sample.
    Type: Application
    Filed: September 9, 2015
    Publication date: March 10, 2016
    Inventors: Jeff Gole, Athurva Gore, Mark Umbarger
  • Publication number: 20160003812
    Abstract: The invention generally relates to methods for maintaining the integrity and identification of a nucleic acid template in a multiplex sequencing reaction. In certain embodiments, methods of the invention involve obtaining a template nucleic acid, incorporating a pair of sequence identifiers into the template, and sequencing the template.
    Type: Application
    Filed: September 15, 2015
    Publication date: January 7, 2016
    Inventors: Gregory Porreca, Mark Umbarger, George Church
  • Patent number: 9228233
    Abstract: 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: Grant
    Filed: September 14, 2012
    Date of Patent: January 5, 2016
    Assignee: Good Start Genetics, Inc.
    Inventors: Caleb J. Kennedy, Mark Umbarger, Gregory Porreca
  • Publication number: 20150354003
    Abstract: The invention generally relates to methods for analyzing nucleic acids. In certain aspects, methods of the invention involve obtaining a sample including a nucleic acid template. A plurality of molecular inversion probes are tiled across a portion of the template. The probes are designed such that immediately adjacent probes hybridize to opposite strands of the nucleic acid template and probes on the same strand hybridize to the template in an overlapping manner. A region between targeting arms of a plurality of the molecular inversion probes is filled-in with nucleotides, and the filled-in region of a plurality of the probes is analyzed to obtain sequence information about the nucleic acid template.
    Type: Application
    Filed: August 14, 2015
    Publication date: December 10, 2015
    Inventor: Mark Umbarger
  • Patent number: 9163281
    Abstract: The invention generally relates to methods for maintaining the integrity and identification of a nucleic acid template in a multiplex sequencing reaction. In certain embodiments, methods of the invention involve obtaining a template nucleic acid, incorporating a pair of sequence identifiers into the template, and sequencing the template.
    Type: Grant
    Filed: April 7, 2011
    Date of Patent: October 20, 2015
    Assignee: Good Start Genetics, Inc.
    Inventors: Gregory Porreca, Mark Umbarger, George Church
  • Patent number: 9115387
    Abstract: The invention generally relates to methods for analyzing nucleic acids. In certain aspects, methods of the invention involve obtaining a sample including a nucleic acid template. A plurality of molecular inversion probes are tiled across a portion of the template. The probes are designed such that immediately adjacent probes hybridize to opposite strands of the nucleic acid template and probes on the same strand hybridize to the template in an overlapping manner. A region between targeting arms of a plurality of the molecular inversion probes is filled-in with nucleotides, and the filled-in region of a plurality of the probes is analyzed to obtain sequence information about the nucleic acid template.
    Type: Grant
    Filed: June 24, 2014
    Date of Patent: August 25, 2015
    Assignee: Good Start Genetics, Inc.
    Inventor: Mark Umbarger
  • Publication number: 20150111203
    Abstract: The invention generally relates to methods for determining carrier status with respect to a condition or disease. In certain embodiments, the method involves exposing a sample to a plurality of molecular inversion probes capable of capturing DNA from at least one genomic region suspected of having an altered copy number and at least one internal control DNA known or suspected to have a stable copy number, capturing and sequencing DNA that binds to the molecular inversion probes, and determining a copy number state of the at least one genomic region based on the sequence results.
    Type: Application
    Filed: October 18, 2013
    Publication date: April 23, 2015
    Applicant: GOOD START GENETICS, INC.
    Inventors: Eric D. Boyden, Gregory Porreca, Mark Umbarger
  • Publication number: 20150111757
    Abstract: The invention generally relates to methods for determining carrier status with respect to a condition or disease. In certain embodiments, the method involves exposing a sample to a plurality of molecular inversion probes capable of capturing DNA from at least one genomic region suspected of having an altered copy number and at least one internal control DNA known or suspected to have a stable copy number, capturing and sequencing DNA that binds to the molecular inversion probes, and determining a copy number state of the at least one genomic region based on the sequence results.
    Type: Application
    Filed: December 18, 2013
    Publication date: April 23, 2015
    Applicant: GOOD START GENETICS, INC.
    Inventors: Eric D. Boyden, Gregory Porreca, Mark Umbarger
  • Publication number: 20150111208
    Abstract: The invention generally relates to method for assessing a genomic region of a subject. In certain embodiments, methods of the invention involve obtaining a sample including nucleic acid from a subject. The nucleic acid includes a target sequence from a target genomic region and a paralogous sequence from a non-target genomic region. The target sequence and the paralogous sequence are isolated from the sample. The target sequence and the paralogous sequence are sequenced to obtain sequence reads that include target sequence reads and paralogous sequence reads. The paralogous sequence reads are excluded, and the genomic region of the subject are assessed based on the target sequence reads.
    Type: Application
    Filed: October 13, 2014
    Publication date: April 23, 2015
    Inventors: Mark Umbarger, Gregory Porreca
  • Publication number: 20140308667
    Abstract: The invention generally relates to methods for analyzing nucleic acids. In certain aspects, methods of the invention involve obtaining a sample including a nucleic acid template. A plurality of molecular inversion probes are tiled across a portion of the template. The probes are designed such that immediately adjacent probes hybridize to opposite strands of the nucleic acid template and probes on the same strand hybridize to the template in an overlapping manner. A region between targeting arms of a plurality of the molecular inversion probes is filled-in with nucleotides, and the filled-in region of a plurality of the probes is analyzed to obtain sequence information about the nucleic acid template.
    Type: Application
    Filed: June 24, 2014
    Publication date: October 16, 2014
    Inventor: Mark Umbarger
  • Patent number: 8778609
    Abstract: The invention generally relates to methods for analyzing nucleic acids. In certain aspects, methods of the invention involve obtaining a sample including a nucleic acid template. A plurality of molecular inversion probes are tiled across a portion of the template. The probes are designed such that immediately adjacent probes hybridize to opposite strands of the nucleic acid template and probes on the same strand hybridize to the template in an overlapping manner. A region between targeting arms of a plurality of the molecular inversion probes is filled-in with nucleotides, and the filled-in region of a plurality of the probes is analyzed to obtain sequence information about the nucleic acid template.
    Type: Grant
    Filed: March 14, 2014
    Date of Patent: July 15, 2014
    Assignee: Good Start Genetics, Inc.
    Inventor: Mark Umbarger
  • Publication number: 20140129201
    Abstract: 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: Application
    Filed: October 1, 2013
    Publication date: May 8, 2014
    Applicant: GOOD START GENETICS, INC.
    Inventors: Caleb Kennedy, Gregory Porreca, Mark Umbarger
  • Publication number: 20140127688
    Abstract: Methods and systems for determining if a sample has been contaminated with other genetic material, for example, from another sample in a parallel workflow. The methods and systems compare measured allele fractions to predetermined distributions of allele fractions in order to calculate a likelihood that the sample has been contaminated.
    Type: Application
    Filed: November 6, 2013
    Publication date: May 8, 2014
    Applicant: GOOD START GENETICS, INC.
    Inventors: Mark Umbarger, Gregory Porreca
  • Publication number: 20130337447
    Abstract: Aspects of the invention relates to methods and compositions that are useful to reduce bias and increase the reproducibility of multiplex analysis of genetic loci. In some configurations, predetermined preparative steps and/or nucleic acid sequence analysis techniques are used in multiplex analyses for a plurality of genetic loci in a plurality of samples.
    Type: Application
    Filed: July 2, 2013
    Publication date: December 19, 2013
    Applicant: Good Start Genetics, Inc.
    Inventors: Gregory J. Porreca, Mark Umbarger
  • Publication number: 20130324417
    Abstract: 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: Application
    Filed: June 4, 2012
    Publication date: December 5, 2013
    Applicant: Good Start Genetics, Inc.
    Inventors: Caleb Kennedy, Mark Umbarger, Greg Porreca
  • Publication number: 20130288901
    Abstract: 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: Application
    Filed: September 14, 2012
    Publication date: October 31, 2013
    Applicant: GOOD START GENETICS, INC.
    Inventors: Caleb J. Kennedy, Mark Umbarger, Gregory Porreca
  • Publication number: 20130274146
    Abstract: The invention generally relates to methods of performing a capture reaction. In certain embodiments, the method involves obtaining a nucleic acid, fragmenting the nucleic acid, and capturing a target sequence on the nucleic acid fragment using a capture moiety, such as a molecular inversion probe.
    Type: Application
    Filed: April 17, 2012
    Publication date: October 17, 2013
    Applicant: GOOD START GENETICS, INC.
    Inventors: Mark Umbarger, Gregory Porreca, Charles Towne, George Church