Patents Examined by John S. Brusca
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Patent number: 11959128Abstract: The present invention relates to the field of noninvasive prenatal gene testing by high-through sequencing technologies. Particularly, the present application relates to a method for determining the content of cell-free fetal DNA in maternal peripheral blood.Type: GrantFiled: March 15, 2017Date of Patent: April 16, 2024Assignee: BERRY GENOMICS CO., LTD.Inventors: Xiaojie Zhang, Tao Cheng, Xiangbin Chen, Jianguang Zhang
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Patent number: 11935625Abstract: A computer-implemented method for processing and/or analyzing nucleic acid sequencing data comprises receiving a first data input and a second data input. The first data input comprises untargeted sequencing data generated from a first nucleic acid sample obtained from a subject. The second data input comprises target-specific sequencing data generated from a second nucleic acid sample obtained from the subject. Next, with the aid of a computer processor, the first data input and the second data input are combined to produce a combined data set. Next, an output derived from the combined data set is generated. The output is indicative of the presence or absence of one or more polymorphisms of the first nucleic acid sample and/or the second nucleic acid sample.Type: GrantFiled: November 19, 2020Date of Patent: March 19, 2024Assignee: PERSONALIS, INC.Inventors: Jason Harris, Mark R. Pratt, John West, Richard Chen, Ming Li
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Patent number: 11929145Abstract: Technology provided herein relates in part to methods, processes, machines and apparatuses for non-invasive assessment of genetic alterations. In particular, a method is provided for that includes obtaining a set of sequence reads. The sequence reads each include a single molecule barcode (SMB) sequence that is a non-random oligonucleotide sequence. The method further includes assigning the sequence reads to read groups according to a read group signature. The read group signature comprises an SMB sequence and a start and end position of a nucleic acid fragment from the circulating cell free sample nucleic acid. The sequence reads comprising start and end positions and an SMB sequence similar to the read group signature are assigned to a read group. The method further includes generating a consensus for each read group, and determining the presence or absence of a genetic alteration based on the consensus for each read group.Type: GrantFiled: January 22, 2018Date of Patent: March 12, 2024Assignee: SEQUENOM, INCInventors: Mostafa Azab, Michael Sykes, Youting Sun, Amin Mazloom, Taylor Jensen, Mathias Ehrich, Christopher Ellison
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Patent number: 11928614Abstract: Methods, systems and compositions that allow for treating a patient according to a patient customized therapeutic regimen are provided. Embodiments of the invention include obtaining dosage administration information from a patient and using the same to tailor a therapeutic regimen for the patient. Embodiments of the invention further include preparing and forwarding to the patient physical pharmaceutical dosages based on the customized therapeutic regimen.Type: GrantFiled: September 28, 2017Date of Patent: March 12, 2024Assignee: OTSUKA PHARMACEUTICAL CO., LTD.Inventors: Mark J. Zdeblick, Andrew Thompson, George M. Savage
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Patent number: 11929147Abstract: Described herein are methods for identifying quasispecies of genomes by clustering sequence reads for samples including the genomes based on the similarities of the sequence reads.Type: GrantFiled: September 12, 2018Date of Patent: March 12, 2024Assignee: Roche Sequencing Solutions, Inc.Inventors: Darya Filippova, Khai Luong, Garima Kushwaha
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Patent number: 11923046Abstract: Disclosed herein are methods, systems, and apparatus for detecting microamplifications or microdeletions in the genome of a fetus. In some embodiments, the method comprises receiving sequence tags for each of a plurality of DNA fragments in a biological sample; determining genomic positions for the sequence tags; determining whether the density of DNA in each of a plurality of genomic regions is aberrantly high or low; identifying as a microamplification a set of consecutive genomic regions having aberrantly high density; and identifying as a microdeletion a set of consecutive genomic regions having aberrantly low density. The biological sample may be a blood sample obtained noninvasively from a female subject pregnant with the fetus.Type: GrantFiled: February 7, 2020Date of Patent: March 5, 2024Assignee: The Chinese University of Hong KongInventors: Yuk Ming Dennis Lo, Kwan Chee Chan, Peiyong Jiang, Cheuk Yin Jandy Yu, Rossa Wai Kwun Chiu
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Patent number: 11892945Abstract: A method for storage of an item of information (210) is disclosed. The method comprises encoding bytes (720) in the item of information (210), and representing using a schema the encoded bytes by a DNA nucleotide to produce a DNA sequence (230). The DNA sequence (230) is broken into a plurality of overlapping DNA segments (240) and indexing information (250) added to the plurality of DNA segments. Finally, the plurality of DNA segments (240) is synthesized (790) and stored (795).Type: GrantFiled: October 29, 2021Date of Patent: February 6, 2024Assignee: EUROPEAN MOLECULAR BIOLOGY LABORATORYInventors: Nick Goldman, John Birney
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Patent number: 11875899Abstract: The invention provides a method for determining copy number variations (CNV) of a sequence of interest in a test sample that comprises a mixture of nucleic acids that are known or are suspected to differ in the amount of one or more sequence of interest. The method comprises a statistical approach that accounts for accrued variability stemming from process-related, interchromosomal and inter-sequencing variability. The method is applicable to determining CNV of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions. CNV that can be determined according to the method include trisomies and monosomies of any one or more of chromosomes 1-22, X and Y, other chromosomal polysomies, and deletions and/or duplications of segments of any one or more of the chromosomes, which can be detected by sequencing only once the nucleic acids of a test sample.Type: GrantFiled: September 18, 2019Date of Patent: January 16, 2024Assignee: Verinata Health, Inc.Inventors: Richard P. Rava, Brian K. Rhees
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Patent number: 11854669Abstract: The present invention relates to method for storing and transmitting information by employing a nucleic acid construct. The nucleic acid construct can include a lock region; a translation key region that corresponds to the identity of a key; and a message region including a nucleic sequence that corresponds to an encrypted message.Type: GrantFiled: July 16, 2019Date of Patent: December 26, 2023Assignee: National Technology & Engineering Solutions of Sandia, LLCInventors: George Bachand, Marlene Bachand, Andrew Gomez
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Patent number: 11837325Abstract: Provided is a method for identifying balanced translocation breakpoints and a carrying state for balanced translocations in embryos, comprising the following steps: amplifying and sequencing a sample; comparing the sequence which is obtained by means of sequencing with a reference genome and analyzing copy numbers; accurately determining the position of a translocation breakpoint; detecting single nucleotide polymorphisms (SNPs) around the breakpoint and genotyping the SNPs; analyzing an embryonic haplotype, and comprehensively determining a normal chromosome and a translocation chromosome haplotype; determining the embryonic carrying state and, according to the haplotype, selecting an embryo which does not carry a balanced translocation.Type: GrantFiled: March 2, 2018Date of Patent: December 5, 2023Assignee: YIKON GENOMICS (SHANGHAI) CO., LTDInventors: Shiping Bo, Zhen Zhang, Jun Ren, Yumei Gao, Sijia Lu
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Patent number: 11833164Abstract: Provided are methods of treating a patient diagnosed with Fabry disease and methods of enhancing ?-galactosidase A in a patient diagnosed with or suspected of having Fabry disease. Certain methods comprise administering to a patient a therapeutically effective dose of a pharmacological chaperone for ?-galactosidase A, wherein the patient has a mutation in the nucleic acid sequence encoding ?-galactosidase A. Also described are uses of pharmacological chaperones for the treatment of Fabry disease and compositions for use in the treatment of Fabry disease.Type: GrantFiled: August 7, 2020Date of Patent: December 5, 2023Assignee: Amicus Therapeutics, Inc.Inventors: Elfrida Benjamin, Xiaoyang Wu
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Patent number: 11789906Abstract: Method and systems for preparing and analyzing a DNA sample from a subject are provided herein. Also provided are methods and systems for obtaining, analyzing, and manipulating genomic and proteomic sequence data. In particular, methods and systems provided herein involve transformation of raw genetic or proteomic sequence into a compressed data set and transmission of the compressed data set using a fixed binary encoding scheme capable of compressing the data by up to 75%. An interface is in communication with the compression module and configured to display transmitted genomic and proteomic sequence data.Type: GrantFiled: November 19, 2015Date of Patent: October 17, 2023Assignee: ARC BIO, LLCInventors: Roberto Olivares-Amaya, David Andrew Sinclair, Alejandro Quiroz-Zarate, Thomas J. Watson, Jr.
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Patent number: 11769597Abstract: Disclosed herein are methods and compositions for associating a genetic variant with intraretinal fluid. Also disclosed herein are methods and compositions for associating a genetic variant with visual acuity, anatomic outcomes or treatment frequency.Type: GrantFiled: June 1, 2018Date of Patent: September 26, 2023Assignee: Regeneron Pharmaceuticals, Inc.Inventors: Lorah Perlee, Sara Hamon, Charles Paulding
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Patent number: 11697846Abstract: The invention provides a method for determining copy number variations (CNV) of a sequence of interest in a test sample that comprises a mixture of nucleic acids that are known or are suspected to differ in the amount of one or more sequence of interest. The method comprises a statistical approach that accounts for accrued variability stemming from process-related, interchromosomal and inter-sequencing variability. The method is applicable to determining CNV of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions. CNV that can be determined according to the method include trisomies and monosomies of any one or more of chromosomes 1-22, X and Y, other chromosomal polysomies, and deletions and/or duplications of segments of any one or more of the chromosomes, which can be detected by sequencing only once the nucleic acids of a test sample.Type: GrantFiled: July 26, 2019Date of Patent: July 11, 2023Assignee: Verinata Health, Inc.Inventors: Richard P. Rava, Brian K. Rhees
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Patent number: 11694768Abstract: Technology provided herein relates in part to non-invasive classification of one or more genetic copy number variations (CNVs) for a test sample. Technology provided herein is useful for classifying a genetic CNV for a sample as part of non-invasive pre-natal (NIPT) testing and oncology testing, for example.Type: GrantFiled: January 24, 2018Date of Patent: July 4, 2023Inventors: John A. Tynan, Amin Mazloom, Yijin Wu, Mark Whidden, Mathias Ehrich
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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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Patent number: 11657900Abstract: Methods for estimating genomic copy number and loss of heterozygosity using Hidden Markov Model based estimation are disclosed.Type: GrantFiled: January 10, 2019Date of Patent: May 23, 2023Assignee: AFFYMETRIX, INC.Inventor: Srinka Ghosh
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Patent number: 11655500Abstract: A method for sequencing a nucleic acid template includes: (a) performing a first sequencing process including flowing nucleotides and/or reagents to the nucleic acid template according to a first predetermined ordering of nucleotides and/or reagents to obtain a first sequencing result; (b) after the first sequencing process, performing a second sequencing process including flowing nucleotides and/or reagents to the nucleic acid template according to a second predetermined ordering of nucleotides and/or reagents to obtain a second sequencing result, the second predetermined ordering of nucleotides and/or reagents being different from the first predetermined ordering of nucleotides and/or reagents and at least one of the first and second predetermined orderings of nucleotides and/or reagents being designed for repeat sequencing; and (c) determining a sequence of bases corresponding to at least a portion of the nucleic acid template using both the first sequencing result and the second sequencing result.Type: GrantFiled: June 3, 2019Date of Patent: May 23, 2023Assignee: Life Technologies CorporationInventors: Earl Hubbell, Christian Koller, Nils Homer
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Patent number: 11634779Abstract: Processes and materials to detect cancer from a biopsy are described. In some cases, cell-free nucleic acids can be sequenced, and the sequencing result can be utilized to detect sequences derived from a neoplasm. Detection of somatic variants occurring in phase can indicate the presence of cancer in a diagnostic scan and a clinical intervention can be performed.Type: GrantFiled: May 2, 2022Date of Patent: April 25, 2023Assignee: The Board of Trustees of the Leland Stanford Junior UniversityInventors: David M. Kurtz, Maximilian Diehn, Arash Ash Alizadeh
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Patent number: 11636919Abstract: A method for evaluating variant likelihood includes: providing a plurality of template polynucleotide strands, sequencing primers, and polymerase in a plurality of defined spaces disposed on a sensor array; exposing the plurality of template polynucleotide strands, sequencing primers, and polymerase to a series of flows of nucleotide species according to a predetermined order; obtaining measured values corresponding to an ensemble of sequencing reads for at least some of the template polynucleotide strands in at least one of the defined spaces; and evaluating a likelihood that a variant sequence is present given the measured values corresponding to the ensemble of sequencing reads, the evaluating comprising: determining a measurement confidence value for each read in the ensemble of sequencing reads and modifying at least some model-predicted values using a first bias for forward strands and a second bias for reverse strands.Type: GrantFiled: May 9, 2018Date of Patent: April 25, 2023Assignee: LIFE TECHNOLOGIES CORPORATIONInventors: Earl Hubbell, Sowmi Utiramerur