Patents by Inventor Athurva Gore
Athurva Gore 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: 20240417795Abstract: 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: ApplicationFiled: June 16, 2023Publication date: December 19, 2024Inventors: Athurva Gore, Mark Umbarger
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Patent number: 11965157Abstract: The present disclosure relates to methods for constructing polynucleotide libraries and/or polynucleotide sequencing. Related kits and devices are also disclosed. The present disclosure also relates to compositions, kits, devices, and methods for conducting genetic and genomic analysis, for example, by polynucleotide sequencing. In particular aspects, provided herein are compositions, kits, and methods for constructing libraries with improved ligation efficiency and conversion rate during sequencing. In certain embodiments, the compositions, kits, and methods herein are useful for analyzing polynucleotide fragments, such as circulating polynucleotide fragments in the body of a subject, including circulating tumor DNA.Type: GrantFiled: April 18, 2018Date of Patent: April 23, 2024Assignee: Singlera Genomics, Inc.Inventors: Jeffrey A Gole, Athurva Gore, Rui Liu
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Patent number: 11680284Abstract: 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: GrantFiled: August 30, 2018Date of Patent: June 20, 2023Assignee: Moledular Loop Biosciences, Inc.Inventors: Athurva Gore, Mark Umbarger
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Publication number: 20220333160Abstract: 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: ApplicationFiled: July 1, 2022Publication date: October 20, 2022Inventors: Jeff Gole, Athurva Gore, Mark Umbarger
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Patent number: 11408024Abstract: 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: GrantFiled: September 9, 2015Date of Patent: August 9, 2022Assignee: Molecular Loop Biosciences, Inc.Inventors: Jeff Gole, Athurva Gore, Mark Umbarger
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Publication number: 20210292821Abstract: The invention generally relates to methods for determining aneuploidy of cells with respect to a control sample. In certain embodiments, the method involves exposing a sample to a plurality of probes capable of capturing DNA from at least one chromosome suspected of having an altered copy number, and at least one control DNA sample known or suspected to have a stable copy number, capturing and sequencing DNA that binds to the probes, calculating a chromosomal read fraction; determining a sample specific scaling factor; scaling the chromosomal read fractions, normalizing the scaled read fractions, and determining a copy number state of at least one chromosome.Type: ApplicationFiled: June 4, 2021Publication date: September 23, 2021Applicant: Good Start Genetics, Inc.Inventor: Athurva GORE
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Patent number: 11053548Abstract: The invention generally relates to methods for determining aneuploidy of cells with respect to a control sample. In certain embodiments, the method involves exposing a sample to a plurality of probes capable of capturing DNA from at least one chromosome suspected of having an altered copy number, and at least one control DNA sample known or suspected to have a stable copy number, capturing and sequencing DNA that binds to the probes, calculating a chromosomal read fraction; determining a sample specific scaling factor; scaling the chromosomal read fractions, normalizing the scaled read fractions, and determining a copy number state of at least one chromosome.Type: GrantFiled: May 12, 2015Date of Patent: July 6, 2021Assignee: Good Start Genetics, Inc.Inventor: Athurva Gore
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Publication number: 20210090687Abstract: 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: ApplicationFiled: August 5, 2020Publication date: March 25, 2021Inventors: Mark UMBARGER, Athurva GORE, Gregory PORRECA
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Publication number: 20200123538Abstract: The present disclosure relates to methods for constructing polynucleotide libraries and/or polynucleotide sequencing. Related kits and devices are also disclosed. The present disclosure also relates to compositions, kits, devices, and methods for conducting genetic and genomic analysis, for example, by polynucleotide sequencing. In particular aspects, provided herein are compositions, kits, and methods for constructing libraries with improved ligation efficiency and conversion rate during sequencing.Type: ApplicationFiled: April 18, 2018Publication date: April 23, 2020Applicant: Singlera Genomics, Inc.Inventors: Jeffrey A GOLE, Athurva GORE, Rui LIU
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Patent number: 10445543Abstract: The invention generally relates to devices and systems for individually barcoding sample vessels. In certain embodiments, the devices comprise an attachment member and an extension member, where the extension member can accommodate an identifier, such as a barcode. When loaded into a substrate, the barcoded vials are scanned by a barcode reader.Type: GrantFiled: August 24, 2018Date of Patent: October 15, 2019Assignee: Good Start Genetics, Inc.Inventors: Gregory Porreca, Mark Umbarger, Athurva Gore
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Publication number: 20190295690Abstract: Methods for improving variant protection are provided. The methods include the steps of generating an in silico genome map that includes a primary path, and a secondary path comprising variants that were missed or incorrectly called in a sequence assembly simulation, aligning the secondary path to the primary path, convoluting the second path to the primary path, and identifying the variants based upon reads that align with the secondary path but not the primary path. All of method steps can be carried out using a computer. Systems incorporated these methods are also included.Type: ApplicationFiled: February 3, 2017Publication date: September 26, 2019Inventors: Athurva Gore, Eric Tsung, Gregory Porreca
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Publication number: 20180371533Abstract: 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: ApplicationFiled: August 30, 2018Publication date: December 27, 2018Inventors: Athurva Gore, Mark Umbarger
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Publication number: 20180365458Abstract: The invention generally relates to devices and systems for individually barcoding sample vessels. In certain embodiments, the devices comprise an attachment member and an extension member, where the extension member can accommodate an identifier, such as a barcode. When loaded into a substrate, the barcoded vials are scanned by a barcode reader.Type: ApplicationFiled: August 24, 2018Publication date: December 20, 2018Inventors: Gregory Porreca, Mark Umbarger, Athurva Gore
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Patent number: 10066259Abstract: 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: GrantFiled: January 6, 2016Date of Patent: September 4, 2018Assignee: Good Start Genetics, Inc.Inventors: Athurva Gore, Mark Umbarger
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Patent number: 10061953Abstract: The invention generally relates to devices and systems for individually barcoding sample vessels. In certain embodiments, the devices comprise an attachment member and an extension member, where the extension member can accommodate an identifier, such as a barcode. When loaded into a substrate, the barcoded vials are scanned by a barcode reader.Type: GrantFiled: January 13, 2016Date of Patent: August 28, 2018Assignee: Good Start Genetics, Inc.Inventors: Gregory Porreca, Mark Umbarger, Athurva Gore
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Publication number: 20160210486Abstract: The invention generally relates to devices and systems for individually barcoding sample vessels. In certain embodiments, the devices comprise an attachment member and an extension member, where the extension member can accommodate an identifier, such as a barcode. When loaded into a substrate, the barcoded vials are scanned by a barcode reader.Type: ApplicationFiled: January 13, 2016Publication date: July 21, 2016Inventors: Gregory Porreca, Mark Umbarger, Athurva Gore
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Publication number: 20160210404Abstract: 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: ApplicationFiled: January 14, 2016Publication date: July 21, 2016Inventors: Mark Umbarger, Athurva Gore, Gregory Porreca
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Publication number: 20160194692Abstract: 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: ApplicationFiled: January 6, 2016Publication date: July 7, 2016Inventors: Athurva Gore, Mark Umbarger
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Publication number: 20160068889Abstract: 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: ApplicationFiled: September 9, 2015Publication date: March 10, 2016Inventors: Jeff Gole, Athurva Gore, Mark Umbarger
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Patent number: D773070Type: GrantFiled: February 24, 2015Date of Patent: November 29, 2016Assignee: Good Start Genetics, Inc.Inventors: Gregory Porreca, Mark Umbarger, Athurva Gore