Abstract: The invention relates to methods for pairwise sequencing of a polynucleotide template which result in the sequential determination of nucleotide sequence in two distinct and separate regions of the polynucleotide template.
Abstract: Provided are methods of adding adapters to nucleic acids. The methods include combining in a reaction mixture a template ribonucleic acid (RNA), a template switch oligonucleotide including a 3? hybridization domain and a sequencing platform adapter construct, a polymerase, and dNTPs. The reaction mixture components are combined under conditions sufficient to produce a product nucleic acid that includes the template RNA and the template switch oligonucleotide each hybridized to adjacent regions of a single product nucleic acid that includes a region polymerized from the dNTPs by the polymerase. Aspects of the invention further include compositions and kits.
Type:
Grant
Filed:
March 24, 2017
Date of Patent:
September 22, 2020
Assignee:
Takara Bio USA, Inc.
Inventors:
Craig Betts, Steve Oh, George G. Jokhadze, Nathalie Bolduc
Abstract: Disclosed are methods for lysis of cells, such as bacteria present in microbiomes, that combine three lysis steps—(1) heat, (2) detergent and (3) base—into a single step and that can be completed in a short period of time, e.g., a few minutes. The methods combine a normally incompatible detergent and base lysis, allows for simplified removal of detergent after lysis, and importantly, yields improved quantities of genomic DNA (gDNA) from difficult to lyse bacteria.
Abstract: 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:
Grant
Filed:
April 15, 2016
Date of Patent:
September 15, 2020
Assignee:
Five3 Genomics, LLC
Inventors:
John Zachary Sanborn, Charles Joseph Vaske, Stephen Charles Benz
Abstract: The invention relates to a method for genotyping individuals, through multiplexing genotyping, when samples carrying different loci of various individuals are pooled and genotyping is performed on this pool.
Abstract: A method and device for performing DNA sequencing and extracting structural information from unknown nucleic acid strands. The device includes a microwell structure, where identical DNA strands are immobilized within the microwell structure on a surface of a micro-bead, an active electrode or a porous polymer. The device further includes a CMOS-integrated semiconductor integrated circuit, where the CMOS-integrated semiconductor integrated circuit includes metal layers on a silicon substrate, where the metal layers form an active electrode biosensor. In addition, a sensing electrode is formed by creating openings in a passivation layer of the CMOS-integrated semiconductor integrated circuit to hold a single bead, on which the DNA strands are immobilized.
Type:
Grant
Filed:
April 12, 2016
Date of Patent:
August 11, 2020
Assignee:
Board of Regents, The University of Texas Systems
Abstract: Provided herein are reagents and kits for detection of multiple target sequences in a single-tube, single-color assay, and methods of use thereof. In particular, multiplex assays are provided for the detection of Mycobacterium tuberculosis complex target sequences (e.g., katG, rpoB, inhA promotor, pncA, etc.).
Type:
Grant
Filed:
November 18, 2014
Date of Patent:
August 11, 2020
Assignee:
Brandeis University
Inventors:
Lawrence J. Wangh, Kenneth E. Pierce, John E. Rice
Abstract: Methods and containers are provided for identifying a species, illustratively a bacterial species. Illustrative methods comprise amplifying various genes in the nucleic acid from the bacterial species in a single reaction mixture using pairs of outer first-stage primers designed to hybridize to generally conserved regions of the respective genes to generate a plurality of first-stage amplicons, dividing the reaction mixture into a plurality of second-stage reactions, each using a unique pair of second-stage primers, each pair of second-stage primers specific for a target bacterial species or subset of bacterial species, detecting which of the second-stage reactions amplified, and identifying the bacterial species based on second-stage amplification.
Type:
Grant
Filed:
July 26, 2017
Date of Patent:
July 28, 2020
Assignees:
BioFire Diagnostics, LLC, University of Utah Research Foundation
Inventors:
Mark Aaron Poritz, Anne Jeannette Blaschke-Bonkowsky
Abstract: Methods to simultaneously test and screen multiplexed, mixed cell populations, e.g., populations comprising genetically heterogeneous cancer cells, in common conditions.
Type:
Grant
Filed:
March 14, 2013
Date of Patent:
July 28, 2020
Assignees:
The Broad Institute, Inc., Dana Farber Cancer Institute, Inc.
Abstract: A method for tracking specific in situ hybridizations in biological samples using molecular barcodes is disclosed. Present invention specifically addresses the in suspension in situ hybridization protocols and makes it possible to track a mixed sample processed on a high throughput flow cytometer. Since the DNA probes selected for the molecular barcodes are naturally existing sequences on the chromosomes, each cell will have two copies of the molecular barcode as opposed to the single barcode provided by the other systems. Tracking is accomplished by following the florescence patterns emitted by the two, three, four or five fluorescent tags attached to the DNA probes. Alternatively, colorimetric system can be used for tracking by employing non-fluorescent tags and subsequent specific enzyme-substrate reactions.
Abstract: This invention provides methods of determining the biological, pathological, genetic, epigenetic or disease status in a biological sample by determining the methylation status of a subpopulation of genomic DNA in the sample.
Abstract: Methods for detecting and quantifying an analyte employ a pair of proximity probes, each comprising a proteinaceous target-binding domain coupled to a nucleic acid domain (NAD), which NADs interact when the proximity probes have bound in proximity to their respective target; and a set of markers, wherein each marker is a nucleic acid molecule comprising a binding domain and a reporter domain giving a detectable signal, can interact with said NADs to form a nucleic acid molecule from which a detectable signal is generated, or with a nucleic acid molecule generated by interaction of said NADs, cannot interact with said NADs simultaneously with another marker in the set, generates a signal that is distinguishable from another marker signal, and is present in an amount capable of detecting analyte at a range of concentrations differing from the range of concentrations detectable by other markers.
Type:
Grant
Filed:
October 14, 2011
Date of Patent:
June 2, 2020
Assignee:
Navinci Diagnostics AB
Inventors:
Mats Gullberg, Irene Weibrecht, Carl-Magnus Clausson, Ola Söderberg
Abstract: The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences. In particular, the present invention provides methods and compositions for improving the efficiency of sequencing reactions by using fewer labels to distinguish between nucleotides and by detecting nucleotides at multiple detection positions in a target sequence.
Abstract: The invention provides an improved stem-loop target capture oligomer and methods of use. Such a target capture oligomer has a target-binding segment forming a loop flanked by stem segments forming a stem. The stem segments are of unequal length. Such probes show little or no binding to immobilized probes in the absence of a target nucleic acid but offer good target sensitivity. The probes are particularly useful in multiplex methods of detection in which multiple target capture oligomers are present for detecting of multiple target nucleic acids (for example, detecting multiple polymorphic forms of a target gene).
Type:
Grant
Filed:
February 1, 2013
Date of Patent:
May 19, 2020
Assignee:
GEN-PROBE INCORPORATED
Inventors:
James Carlson, Reinhold Pollner, Steven T. Brentano
Abstract: The present disclosure relates to a set of at least 100 single-stranded oligonucleotide probes directed against (or complementary to) portions of a genomic target sequence of interest. The present disclosure also relates to a method of detecting a genomic target sequence of interest using the set of oligonucleotide probes and a method of generating the set of oligonucleotide probes. Further the present disclosure relates to a kit comprising the set of oligonucleotide probes and at least one further component.
Type:
Grant
Filed:
April 22, 2016
Date of Patent:
May 5, 2020
Assignee:
Roche Molecular Systems, Inc.
Inventors:
Frank Bergmann, Walter Eberle, Thomas Fischer, Herbert von der Eltz
Abstract: The invention generally relates to a method for detecting a target nucleic acid in a sample. This invention is useful for detecting bacterial or viral agents in a sample, and is able to detect nucleic acids from a broad variety of, e.g., bacteria, rather than only one or a few different bacteria at a time.
Type:
Grant
Filed:
June 26, 2015
Date of Patent:
May 5, 2020
Assignee:
University of Florida Research Foundation, Inc.
Abstract: A device and method for collecting microorganisms from a fluid includes: a reaction module containing beads, fluid admission duct allowing entry into the module, fluid evacuating duct allowing outlet of the fluid passed through the module, retaining beads in the module, at least one channel for admission of reaction liquid, at least one channel for evacuation of the liquid(s), channels for admission and evacuation of the reaction liquid and the ducts for admission and evacuation of the fluid being positioned with: ducts for admission and evacuation of fluid facing and enclosing the module, in order to maximize contact between the fluid and beads, channels for the reaction liquid(s) being positioned respectively at opposite ends of the module, and channels for the reaction liquid(s) positioned in a plane, and ducts for admission and evacuation of fluid positioned along an axis, and in that the axis is roughly perpendicular to the plane.
Abstract: Disclosed herein are embodiments of a signaling conjugate, embodiments of a method of using the signaling conjugates, and embodiments of a kit comprising the signaling conjugate. The disclosed signaling conjugate comprises a latent reactive moiety and a chromogenic moiety that may further comprise a linker suitable for coupling the latent reactive moiety to the chromogenic moiety. The signaling conjugate may be used to detect one or more targets in a biological sample and are capable of being covalently deposited directly on or proximally to the target. Particular disclosed embodiments of the method of using the signaling conjugate comprise multiplexing methods.
Type:
Grant
Filed:
July 18, 2018
Date of Patent:
February 11, 2020
Assignee:
Ventana Medical Systems, Inc.
Inventors:
Nelson Alexander, William Day, Jerome W. Kosmeder, II, Mark Lefever, Larry Morrison, Anne M. Pedata, Stacey Stanislaw