Patents Assigned to The Translational Genomics Research Institute
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Patent number: 11993812Abstract: Embodiments of the invention include methods of identifying microorganisms and/or diagnosing infections in subjects cause by microorganisms. Embodiments of the invention may also include further characterizing (e.g., determining the presence of one or more antibiotic resistance markers) the microorganisms and determining a strain identity of the microorganisms.Type: GrantFiled: August 5, 2021Date of Patent: May 28, 2024Assignees: The Translational Genomics Research Institute, Arizona Board of Regents acting for and on behalf of Northern Arizona UniversityInventors: Elizabeth Driebe, Jolene Bowers, David Engelthaler, Paul Keim
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Patent number: 11987845Abstract: The present invention relates to a method of creating a biomarker profile, the method comprising the steps of: obtaining a sample of biofluid from a subject, wherein the sample is stored on a sample collection apparatus; removing the sample from the sample collection apparatus; extracting nucleic acids from the sample; sequencing the extracted nucleic acids to generate sequence data; and analyzing the sequence data using a two-step analytical methodology to create the biomarker profile. The present invention is also directed to methods of determining the sex of an in utero fetus, predicting onset of a migraine in a subject, and of tracking athletic performance in a subject.Type: GrantFiled: December 18, 2020Date of Patent: May 21, 2024Assignee: The Translational Genomics Research InstituteInventor: Matthew Huentelman
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Patent number: 11978535Abstract: A system is provided that considers allele fraction shifts as a function of copy number and clonal heterogeneity. The system leverages differences between allele frequencies to differentiate between somatic and normal variants in impure tumor samples. In solid tumors, stromal cells and infiltrating lymphocytes are typically interspersed among the tumor cells. The normal cell contamination in tumors can be leveraged to differentiate somatic from germline variants. We explicitly model allelic copy number and clonal sample fractions so that we can examine how these factors impact the power to detect somatic variants. The system models the copy number alterations, which can also affect the allele frequencies of both somatic and germline variants. The expected allele frequencies can be calculated. The expected allele frequencies for somatic and germline differ with tumor content for different copy number alterations.Type: GrantFiled: February 1, 2018Date of Patent: May 7, 2024Assignee: The Translational Genomics Research InstituteInventors: Rebecca Halperin, David Craig
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Patent number: 11926873Abstract: The present invention relates to a method of creating a biomarker profile, the method comprising the steps of: obtaining a sample of biofluid from a subject, wherein the sample is stored on a sample collection apparatus; removing the sample from the sample collection apparatus; extracting nucleic acids from the sample; sequencing the extracted nucleic acids to generate sequence data; and analyzing the sequence data using a two-step analytical methodology to create the biomarker profile. The present invention is also directed to methods of determining the sex of an in utero fetus, predicting onset of a migraine in a subject, and of tracking athletic performance in a subject.Type: GrantFiled: December 18, 2020Date of Patent: March 12, 2024Assignee: The Translational Genomics Research InstituteInventor: Matthew Huentelman
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Patent number: 11918350Abstract: An application running on a device to manage insulin site rotation may read a configuration file including a group, a plurality of sites in the group, and an image associated with the group. The application may detect an input selecting a site from the plurality of sites for administration of an insulin management device. The application may also set the selected site as unavailable for a predetermined duration in response to the input selecting the site. A log entry may be written to track usage of the site in response to the input selecting the site. A visual indicator on the selected site may show that the site is recently selected in response to detecting the input selecting the site within a predetermined duration. The insulin management device may be a pump, a syringe, or a glucose monitor.Type: GrantFiled: March 30, 2021Date of Patent: March 5, 2024Assignee: The Translational Genomics Research InstituteInventors: John Blanchard, Sampathkumar Rangasamy
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Patent number: 11866789Abstract: Various embodiments provide compositions and methods for detecting cancers containing an NRG1 fusion event and treating a patient with a therapeutic agent that is targeted to the NRG1 fusion. Exemplary compositions for treating cancers containing the NRG1 fusion may comprise therapeutic agents inhibiting Epidermal Growth Factor Receptor and/or ERBB2 such as cetuximab, panitumumab, Sym004, MM-151, mAb 806, mAb 528, MEHD794A, gefitinib, erlotinib, lapatinib, afatinib, PD153035, AG1478, trastuzumab, and pertuzumab. In some embodiments, the therapeutic agent may be a combination of trastuzumab, and pertuzumab.Type: GrantFiled: August 25, 2021Date of Patent: January 9, 2024Assignee: The Translational Genomics Research InstituteInventors: Sara Byron, Jessica Aldrich, John Carpten, David Craig, Mitesh Borad, Alan Bryce, Michael Barrett, George Vasmatzis, Keith Stewart
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Patent number: 11844816Abstract: Embodiments of the invention provide a method of reducing colonization of a subject's anterior nares and/or nasal cavity by a microorganism (e.g., Staphylococcus aureus). In some aspects, the method may include administering a pharmaceutical composition to the subject, wherein the pharmaceutical composition comprises a therapeutically effective amount of at least one probiotic.Type: GrantFiled: July 20, 2022Date of Patent: December 19, 2023Assignees: The Translational Genomics Research Institute, Arizona Board of Regents on behalf of Northern Arizona UniversityInventors: Cindy Liu, Lance B. Price
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Publication number: 20230213521Abstract: The application discloses in vitro methods for diagnosing lung cancer in a subject, wherein the method comprises detecting at least one biomarker selected from the group consisting of Rho GDP dissociation inhibitor beta (ARHGDIB), alpha-tubulin 4A (TUBA4A), glutathione S-transferase omega 1 (GSTO1), filamin A (FLNA), peroxiredoxin 6 (PRDX6) and cadherin 13 (CDH13) in a biological sample from the subject, and kits for measuring said at least one biomarker.Type: ApplicationFiled: April 28, 2021Publication date: July 6, 2023Applicants: Luxembourg Institute of Health (LIH), Fred Hutchinson Cancer Center, The Translational Genomics Research Institute (TGEN)Inventors: Victoria EL KHOURY, Anna Elisabeth SCHRITZ, Yeoun Jin KIM, Guy BERCHEM, Amanda PAULOVICH, Jeffrey WHITEAKER, Konstantinos PETRITIS, Patrick PIRROTTE, Tony TEGELER
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Publication number: 20230207068Abstract: Methods are provided to classify and identify features in mass spectral data using neural network algorithms. A convolutional neural network (CNN) was trained to identify amino acids from an unknown protein sample. The CNN was trained using known peptide sequences to predict amino acid presence, diversity, and frequency, peptide length, subsequences of amino acids classified by features include aliphatic/aromatic, hydrophobic/hydrophilic, positive/negative charge, and combinations thereof. Mass spectra data of a sample unknown to the trained CNN was discretized into a one-dimensional vector and input into the CNN. The CNN models can potentially be integrated to determine the complete peptide sequence from a spectrum, thereby improving the yield of identifiable protein sequences from mass spec analysis.Type: ApplicationFiled: February 20, 2023Publication date: June 29, 2023Applicant: THE TRANSLATIONAL GENOMICS RESEARCH INSTITUTEInventors: Patrick Pirrotte, Gil Speyer, Ritin Sharma, Krystine Garcia-Mansfield
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Patent number: 11634761Abstract: The present invention provides a method of determining integrity and/or quantity of cell free DNA (cfDNA) in a biological sample comprising amplifying target sequences with at least a first primer/probe set and at least a second primer probe/set, amplifying the target sequences of differing lengths, and monitoring for detection of the labels of the oligonucleotide probes, and determining the integrity and/or quantity of the cfDNA based on the level of detection of the label of the oligonucleotide probe from the first primer/probe set compared to the level detection of the label of the oligonucleotide probe from the second primer/probe set. The present invention also provides methods for generating a library with the cfDNA for sequencing and analysis.Type: GrantFiled: May 20, 2020Date of Patent: April 25, 2023Assignee: The Translational Genomics Research InstituteInventors: Muhammed Murtaza, Tania Contente-Cuomo
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Publication number: 20230094433Abstract: Methods, kits, and oligonucleotides used in the detection of the coronavirus strain, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), are disclosed. In some aspects, the oligonucleotides are primers or probes used in the described methods or kits. The oligonucleotide consists of 40 or less nucleotides and has a nucleotide sequence that consists essentially of, or is a variant of, the nucleotide sequence of: SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, or SEQ ID NO:10.Type: ApplicationFiled: September 30, 2022Publication date: March 30, 2023Applicant: THE TRANSLATIONAL GENOMICS RESEARCH INSTITUTEInventors: William Tanner Porter, Erin Kelley, Jolene Bowers, David Engelthaler
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Patent number: 11587644Abstract: Methods are provided to classify and identify features in mass spectral data using neural network algorithms. A convolutional neural network (CNN) was trained to identify amino acids from an unknown protein sample. The CNN was trained using known peptide sequences to predict amino acid presence, diversity, and frequency, peptide length, subsequences of amino acids classified by features include aliphatic/aromatic, hydrophobic/hydrophilic, positive/negative charge, and combinations thereof. Mass spectra data of a sample unknown to the trained CNN was discretized into a one-dimensional vector and input into the CNN. The CNN models can potentially be integrated to determine the complete peptide sequence from a spectrum, thereby improving the yield of identifiable protein sequences from mass spec analysis.Type: GrantFiled: July 30, 2018Date of Patent: February 21, 2023Assignee: The Translational Genomics Research InstituteInventors: Patrick Pirrotte, Gil Speyer, Ritin Sharma, Krystine Garcia-Mansfield
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Patent number: 11572591Abstract: The present invention provides a method of detecting Staphylococcus aureus in a subject, by contacting a sample obtained from the subject with at least one detectably labeled probe of the invention or detecting in the sample identity to a sequence of the invention. The invention is also directed to kits, microarrays and detectable Staphylococcus aureus polynucleotide probes useful in detecting the presence of Staphylococcus aureus.Type: GrantFiled: April 26, 2018Date of Patent: February 7, 2023Assignees: The Translational Genomics Research Institute, Arizona Board of Regents on behalf of Northern Arizona University, Centers for Disease Control and PreventionInventors: Elizabeth Driebe, Jolene Bowers, David Engelthaler, Paul Keim, Brandi Limbago, James K. Rasheed, Linda McDougal, Valerie S. Albrecht
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Patent number: 11446353Abstract: The present invention comprises methods of treating an infection using a pharmaceutical composition comprising an active ingredient selected from Table 1. In some aspects, the infection can be caused by one or more pathogens, including fungal pathogens. For example, the infection may be Valley Fever.Type: GrantFiled: July 6, 2020Date of Patent: September 20, 2022Assignees: The Translational Genomics Research Institute, Arizona Board of Regents on behalf of Northern Arizona UniversityInventors: David Engelthaler, Elizabeth Driebe, Hongwei “Holly” Yin, Michael Valentine, Donald Chow, Jolene Bowers, Paul Keim, Bridget Barker
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Patent number: 11406671Abstract: Embodiments of the invention provide a method of reducing colonization of a subject's anterior nares and/or nasal cavity by a microorganism (e.g., Staphylococcus aureus). In some aspects, the method may include administering a pharmaceutical composition to the subject, wherein the pharmaceutical composition comprises a therapeutically effective amount of at least one probiotic.Type: GrantFiled: April 25, 2016Date of Patent: August 9, 2022Assignee: The Translational Genomics Research InstituteInventors: Cindy Liu, Lance B. Price
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Patent number: 11386977Abstract: An Amplicon Sequencing Analysis Pipeline (ASAP) system (120, 600) characterizes a genetic sample. The ASAP system (120, 600) receives assay configuration data individually associating reference sequences and genetic characteristics. The ASAP system (120, 600) processes amplicon sequencing data and the reference sequences to characterize the genetic sample based on the individual associations between the reference sequences and the genetic characteristics in the assay configuration data. The ASAP (120, 600) system transfers genetic data indicating the genetic characteristics for the genetic sample and indicating interpretation metrics for amplicon sequencing read depth and quality related to the genetic characteristics.Type: GrantFiled: May 23, 2016Date of Patent: July 12, 2022Assignees: The Translational Genomics Research Institute, Arizona Board of Regents for and on behalf of Northern Arizona UniversityInventors: Darrin Lemmer, Jolene Bowers, Erin Kelley, David Engelthaler, Elizabeth Driebe, Paul Keim
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Patent number: 11359251Abstract: A method of detecting Enterovirus D68 is provided. The method may include adding to a mixture containing the sample from the subject, (a) a first forward primer comprising SEQ ID NO: 1, (b) a second forward primer comprising SEQ ID NO: 2, (c) a third forward primer comprising SEQ ID NO: 3, (d) a first reverse primer comprising SEQ ID NO: 4, and (e) a second reverse primer comprising SEQ ID NO: 5, subjecting the mixture to conditions that allow nucleic acid amplification, and detecting the presence or absence of Enterovirus D68 by analyzing the nucleic acid amplification products. The forward primers may include a first universal tail sequence and reverse primers may include a second universal tail sequence. The nucleic acid amplification products may be sequenced using next-generation sequencing.Type: GrantFiled: July 20, 2018Date of Patent: June 14, 2022Assignee: The Translational Genomics Research InstituteInventors: David Engelthaler, Jolene Bowers
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Patent number: 11345969Abstract: The present invention relates to method of detecting and characterizing one or more Borrelia species causing Lyme Disease or tick-borne relapsing fever within a sample from a subject, the method comprising: a) subjecting DNA and/or RNA from the sample to a PCR amplification reaction using primer pairs targeting at least one region of Borrelia 16S rRNA and at least one region of flaB, ospA, ospB, ospC, glpQ, 16S-23S intergenic spacer (IGS1), 5S-23S intergenic spacer (IGS2), bbk32, dbpA, dbpB, and/or p66; and b) analyzing amplification products resulting from the PCR amplification reaction to detect the one or more Borrelia species.Type: GrantFiled: February 11, 2017Date of Patent: May 31, 2022Assignees: The Translational Genomics Research Institute, Arizona Board of Regents on behalf of Northern Arizona UniversityInventors: Elizabeth Driebe, Paul S. Keim, David Engelthaler, Jolene Bowers, Nathan C. Nieto
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Patent number: 11248270Abstract: The present invention provides a method of detecting one or more Klebsiella species within a sample from a subject, the method comprising: subjecting DNA and/or RNA from the sample to a PCR amplification reaction using primer pairs targeting species-specific canonical single nucleotide polymorphisms (canSNPs); and analyzing amplification products resulting from the PCR amplification reaction to detect the one or more Klebsiella species. The present invention also provides a kit for detection of one or more Klebsiella species, Klebsiella clonal groups, AMR genes, and/or virulence genes, the kit comprising primer pairs targeting species-specific canSNPs, K. pneumoniae genes M1 and M2, clonal group-specific canSNPs, AMR genes, and/or virulence genes.Type: GrantFiled: March 14, 2017Date of Patent: February 15, 2022Assignees: The Translational Genomics Research Institute, Arizona Board of Regents on behalf of Northern Arizona UniversityInventors: Jolene Bowers, Elizabeth Driebe, David Engelthaler, Paul Keim, Darrin Lemmer
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Publication number: 20220042112Abstract: Various embodiments provide compositions and methods for detecting cancers containing an NRG1 fusion event and treating a patient with a therapeutic agent that is targeted to the NRG1 fusion. Exemplary compositions for treating cancers containing the NRG1 fusion may comprise therapeutic agents inhibiting Epidermal Growth Factor Receptor and/or ERBB2 such as cetuximab, panitumumab, Sym004, MM-151, mAb 806, mAb 528, MEHD794A, gefitinib, erlotinib, lapatinib, afatinib, PD153035, AG1478, trastuzumab, and pertuzumab. In some embodiments, the therapeutic agent may be a combination of trastuzumab, and pertuzumab.Type: ApplicationFiled: August 25, 2021Publication date: February 10, 2022Applicants: THE TRANSLATIONAL GENOMICS RESEARCH INSTITUTE, MAYO FOUNDATION FOR MEDICAL EDUCATION AND RESEARCHInventors: Sara Byron, Jessica Aldrich, John Carpten, David Craig, Mitesh Borad, Alan Bryce, Michael Barrett, George Vasmatzis, Keith Stewart