Patents Assigned to GenoMed, LLC
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Patent number: 12385035Abstract: The current invention provides a synthetic prokaryotic genome comprising 5 or fewer occurrences of one or more sense codons; and/or a synthetic prokaryotic genome derived from a parent genome, wherein the synthetic prokaryotic genome comprises less than 10%, 5%, 2%, 1%, 0.5%, 0.1% of the occurrences of one or more sense codons, relative to the parent genome; and/or a synthetic prokaryotic genome comprising 100 or more, 200 or more, or 1000 or more genes with no occurrences of one or more sense codons.Type: GrantFiled: May 14, 2020Date of Patent: August 12, 2025Assignees: United Kingdom Research and Innovation, Scarab Genomics, LLCInventors: Julius Fredens, Kaihang Wang, Daniel De La Torre, Louise F. H. Funke, Wesley E. Robertson, Jason W. Chin
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Patent number: 12378547Abstract: The current invention provides a synthetic prokaryotic genome comprising 5 or fewer occurrences of one or more sense codons; and/or a synthetic prokaryotic genome derived from a parent genome, wherein the synthetic prokaryotic genome comprises less than 10%, 5%, 2%, 1%, 0.5%, 0.1% of the occurrences of one or more sense codons, relative to the parent genome; and/or a synthetic prokaryotic genome comprising 100 or more, 200 or more, or 1000 or more genes with no occurrences of one or more sense codons.Type: GrantFiled: October 24, 2023Date of Patent: August 5, 2025Assignees: United Kingdom Research and Innovation, Scarab Genomics, LLCInventors: Julius Fredens, Kaihang Wang, Daniel De La Torre, Louise F. H. Funke, Wesley E. Robertson, Jason W. Chin
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Patent number: 12354709Abstract: Contemplated systems and methods employ chimeric reference sequences that include a plurality of viral genome sequences to identify/quantify integration and co-amplification events. Most typically, the viral genome sequences are organized in the chimeric reference sequences as single chromosomes and the chimeric reference sequences are in BAM format.Type: GrantFiled: September 5, 2019Date of Patent: July 8, 2025Assignee: Five3 Genomics, LLCInventors: John Zachary Sanborn, Charles Joseph Vaske, Stephen Charles Benz, Shahrooz Rabizadeh, Nicole Hensley, Patrick Soon-Shiong
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Publication number: 20240410025Abstract: Methods for rapidly and accurately detecting genetic material from hop latent viroid RNA (HLVd) that combines reverse transcription loop-mediated isothermal amplification (RT-LAMP) technology with specific oligonucleotide primers, fluorophore-labeled oligonucleotide primers, quencher-conjugated oligonucleotide primers, pH buffers, and enzymes, are described. The methods include at least one internal positive control targeting sequence, for minimizing false positive and false negative results, thereby allowing more certain interpretation of the results. The reaction can be performed at a single elevated temperature, can be completed in 1-1.5 hours, and the results can readily be interpreted by visually observing the fluorescence color of the reaction using ultraviolet light, or by using an electronic image acquisition system for viewing fluorescence results from one or more reactions.Type: ApplicationFiled: June 7, 2024Publication date: December 12, 2024Applicant: Colorado Genomics LLCInventors: Tassa K. Saldi, Erika L. Lasda, Alfonso Garrido-Lecca, Patrick K. Gonzales
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Publication number: 20240229167Abstract: Methods and a kit for detection of genetic material from SARS-CoV-2 that combines reverse transcription loop-mediated isothermal amplification (RT-LAMP) technology with specific oligonucleotide primers, fluorophore-labeled oligonucleotides, quencher technology, buffer components, enzymes, and enzyme ratios chosen to minimize false positive and false negative results, are described. The method includes internal positive control targeting sequences, allowing more certain interpretation of the results. The reaction can be performed at a single elevated temperature, can be completed in 1-2 hours, and the results can readily be interpreted by visually observing the fluorescence color of the reaction using ultraviolet light.Type: ApplicationFiled: June 16, 2023Publication date: July 11, 2024Applicant: Colorado Genomics LLCInventors: Tassa K. Saldi, Erika L. Lasda, Alfonso Garrido-Lecca, Patrick K. Gonzales
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Patent number: 11970725Abstract: Provided herein are E. coli host strains with improved capacity for producing recombinant proteins.Type: GrantFiled: April 12, 2023Date of Patent: April 30, 2024Assignee: Scarab Genomics LLCInventors: Frederick R. Blattner, Robert E. Novy, David A. Frisch, Charles Landry, Hyunsic Choi, Eric A. Steffen, John Brandon
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Publication number: 20240132977Abstract: Methods and a kit for detection of genetic material from SARS-CoV-2 that combines reverse transcription loop-mediated isothermal amplification (RT-LAMP) technology with specific oligonucleotide primers, fluorophore-labeled oligonucleotides, quencher technology, buffer components, enzymes, and enzyme ratios chosen to minimize false positive and false negative results, are described. The method includes internal positive control targeting sequences, allowing more certain interpretation of the results. The reaction can be performed at a single elevated temperature, can be completed in 1-2 hours, and the results can readily be interpreted by visually observing the fluorescence color of the reaction using ultraviolet light.Type: ApplicationFiled: June 15, 2023Publication date: April 25, 2024Applicant: Colorado Genomics LLCInventors: Tassa K. Saldi, Erika L. Lasda, Alfonso Garrido-Lecca, Patrick K. Gonzales
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Patent number: 11932907Abstract: The disclosure relates to methods, compositions, and kits for the early determination of the sex of a fetus. The disclosure also provides methods, compositions, and kits for detecting fetal nucleic acids in biological samples (e.g., cell-free fetal DNA). An embodiment includes a method of improving the accuracy of fetal sex determination by reducing a level of contaminating DNA in a blood sample from a pregnant human subject, comprising obtaining a capillary blood sample collected from the upper arm using a push-button blood collection device, thereby reducing a level of contaminating DNA from a non-maternal and non-fetal source in the capillary blood sample as compared to a blood sample collected from a site on the finger or hand of the subject, and detecting the presence or absence of fetal Y-chromosome to determine the sex of the fetus.Type: GrantFiled: April 26, 2023Date of Patent: March 19, 2024Assignee: Gateway Genomics, LLCInventor: Christopher Jacob
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Patent number: 11807896Abstract: Disclosed herein are compositions, systems, kits and methods related to preserving physical linkage information of isolated DNA subject to DNA damage, and identifying a nucleic acid preservative. Physical linkage information and DNA integrity may be preserved by methods relating to reassembly of chromatin onto isolated DNA molecules so as to protect the nucleic acids, preserve physical linkage information, or size select molecules of interest. Nucleic acid compositions produced by methods disclosed herein are preserved so as to be analyzed, for example, by high throughput sequencing methods.Type: GrantFiled: March 25, 2016Date of Patent: November 7, 2023Assignee: Dovetail Genomics, LLCInventors: Brandon J. Rice, David Haussler
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Patent number: 11600361Abstract: Disclosed herein are compositions, systems and methods related to sequence assembly, such as nucleic acid sequence assembly of single reads and contigs into larger contigs and scaffolds through the use of read pair sequence information, such as read pair information indicative of nucleic acid sequence phase or physical linkage.Type: GrantFiled: February 13, 2019Date of Patent: March 7, 2023Assignee: Dovetail Genomics, LLCInventors: Nicholas H. Putnam, Jonathan C. Stites, Brandon J. Rice
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Patent number: 11361844Abstract: Contemplated systems and methods employ chimeric reference sequences that include a plurality of viral genome sequences to identify/quantify integration and co-amplification events. Most typically, the viral genome sequences are organized in the chimeric reference sequences as single chromosomes and the chimeric reference sequences are in BAM format.Type: GrantFiled: July 11, 2018Date of Patent: June 14, 2022Assignee: Five3 Genomics, LLCInventors: John Zachary Sanborn, Charles Joseph Vaske, Stephen Charles Benz, Shahrooz Rabizadeh, Nicole Hensley, Patrick Soon-Shiong
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Patent number: 11268885Abstract: A sampling device having a lower portion with a sample container. A cap is moveably attached with the lower portion and includes a cutting edge configured for cutting a leaf. When the cap is attached to the lower portion with a leaf there between, a leaf sample is deposited into the sample container of the lower portion. The cap includes a vent in fluid communication with the sample container such that the leaf sample is dried. A detachable label can extend from the lower portion.Type: GrantFiled: November 25, 2019Date of Patent: March 8, 2022Assignee: Orion Genomics LLCInventors: Jacob Paul Hendrickx, Michael Sylvester Botzet, Nathan D. Lakey, Anthony D. Favello
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Patent number: 11183269Abstract: Systems and methods of genomic analysis are presented that provide a framework to determine a tumor's clonality, the number and proportion of all major clones, and the variants that distinguish them. Contemplated systems and methods also allow phasing mutations to parental alleles to so time their emergence within the population of tumor cells, and provide an accurate estimate of the amount of contaminating normal tissue that was present in the tumor biopsy.Type: GrantFiled: November 7, 2013Date of Patent: November 23, 2021Assignee: Five3 Genomics, LLCInventor: John Zachary Sanborn
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Patent number: 11168367Abstract: The disclosure pertains to materials and methods for capturing a target genomic region, comprising hybridizing an extension probe and a ligation probe to target sequences that flank the target genomic region; elongating the 3? end of the extension probe until the 3? end of the elongated extension probe is adjacent to the 5? end of the ligation probe; and ligating the 3? end of the elongated extension probe with the 5? end of the ligation probe to produce a ligated probe. The ligated probe can be PCR amplified to produce copies of the target genomic region that can be detected or sequenced. Certain embodiments of the invention also provide methods of producing double stranded probes suitable for capturing and analyzing both strands of a target genomic region in a double stranded genomic DNA. The invention also provides kits for performing the methods disclosed herein.Type: GrantFiled: May 29, 2020Date of Patent: November 9, 2021Assignee: RAPiD Genomics LLCInventors: Leandro Gomide Neves, Adam Payton
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Patent number: 10961586Abstract: Contemplated systems and methods allow for computational genomic analysis using paired-end sequence analysis and split read refinement to thereby identify high-confidence breakpoints associated with high copy numbers and orientation of rearrangements, which is then the basis for full reconstruction of double minutes (DM). In especially preferred aspects, the DM will also include an oncogene or tumor suppressor gene, and/or may be found in blood or blood derived fluids.Type: GrantFiled: February 22, 2017Date of Patent: March 30, 2021Assignee: Five3 Genomics, LLCInventors: John Zachary Sanborn, Charles Joseph Vaske, Stephen Charles Benz
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Patent number: 10774384Abstract: Contemplated systems and methods allow for computational genomic analysis using paired-end sequence analysis and split read refinement to thereby identify high-confidence breakpoints associated with high copy numbers and orientation of rearrangements, which is then the basis for full reconstruction of double minutes (DM). In especially preferred aspects, the DM will also include an oncogene or tumor suppressor gene, and/or may be found in blood or blood derived fluids.Type: GrantFiled: April 15, 2016Date of Patent: September 15, 2020Assignee: Five3 Genomics, LLCInventors: John Zachary Sanborn, Charles Joseph Vaske, Stephen Charles Benz
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Patent number: 10772318Abstract: A composition and method for generating reagents and the composition of these reagents for the stabilization and preservation of viability of cancer tissue which has been surgically excised and the suspension and/or termination of apoptosis (cell death) by significant modulation of cell metabolism by low molar concentrations of synergistic chemistries and hormonal growth enhancers while maintaining normal gene expression patterns of the surgically excised tissue.Type: GrantFiled: February 13, 2017Date of Patent: September 15, 2020Assignee: Truckee Applied Genomics, LLCInventor: Tony K. Baker
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Patent number: 10733701Abstract: Systems and methods for dynamic visualization of genomic data are provided in which a genomic visualization system adapts presentation of information content according to scale-relevant annotations within a sequence object.Type: GrantFiled: October 24, 2018Date of Patent: August 4, 2020Assignee: Five3 Genomics, LLCInventors: Charles Joseph Vaske, John Zachary Sanborn, Stephen Charles Benz
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Publication number: 20200216798Abstract: Methods and compositions for long term continuous flow fermentation using a two vessel continuous culture fermentation apparatus are described.Type: ApplicationFiled: March 19, 2020Publication date: July 9, 2020Applicant: Scarab Genomics, LLCInventor: Frederick R. BLATTNER
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Patent number: 10685738Abstract: Cancer types (e.g., organ/tissue of origin and/or cancer subtype for an organ/tissue) can be distinguished by applying statistical methods to data samples consisting of counts of somatic single nucleotide variations (SNVs) across a tumor genome of a patient. For example, a factor loading matrix for each cancer type to be distinguished can be computed using a set of training data samples for which the cancer type is known. To determine the cancer type for a testing (or diagnostic) data sample, a regression analysis over the set of factor loading matrices yields statistical parameters that can be used to identify the cancer type.Type: GrantFiled: September 19, 2017Date of Patent: June 16, 2020Assignee: Quantigic Genomics LLCInventor: Zurab Kakushadze