Abstract: In some aspects, the present disclosure provides methods for enriching amplicons, or amplification products, comprising a concatemer of at least two or more copies of a target polynucleotide. In some embodiments, a method comprises sequencing the amplicons comprising at least two or more copies of a target polynucleotide. In some embodiments, the target polynucleotides comprise sequences resulting from chromosome rearrangement, including but not limited to point mutations, single nucleotide polymorphisms, insertions, deletions, and translocations including fusion genes. In some aspects, the present disclosure provides compositions and reaction mixtures useful in the described methods.
Abstract: Provided are vertical flow detection devices and related methods. The devices may comprise a membrane having a first surface and a second surface with a plurality of porous structures extending between the first and second surfaces to form fluid conduits from a first fluid chamber formed by the first surface and a second fluid chamber formed by the second fluid surface. A capture agent is immobilized on and/or in the membrane. A rigid porous membrane support mechanically supports the membrane and to provide a relatively uniform flow across the membrane. Various gaskets or holder elements are positioned around an outer edge of the membrane to prevent fluid leakage around the membrane. A fluid pump is configured to force a fluid sample flow in a direction from the first fluid chamber to the second fluid chamber.
Type:
Grant
Filed:
March 29, 2019
Date of Patent:
January 2, 2024
Assignee:
Arizona Board of Regents on Behalf of the University of Arizona
Abstract: There is disclosed a method of generating a massively parallel sequencing library comprising the steps of: a) providing a primary WGA DNA library (pWGAlib), including fragments comprising a WGA library universal sequence adapter; b) performing a single PCR cycle on the pWGAlib using a first primer (1PR) comprising from 5? to 3? a first sequencing adapter (1PR5SA) and a first primer 3? section (1PR3S) hybridizing to the reverse complementary of the WGA library universal sequence adapter; c) performing a single PCR cycle on the on the product of step b) using a second primer (2PR) comprising from 5? to 3? a second sequencing adapter (2PR5SA) different from the 1PR5SA, and a second primer 3? section (2PR3S) hybridizing to the WGA library universal sequence adapter reverse complementary; d) amplifying by PCR the product of step c) using a third primer comprising the 1PR5SA and a fourth primer comprising 2PR5SA.
Type:
Grant
Filed:
July 20, 2018
Date of Patent:
January 2, 2024
Assignee:
Menarini Silicon Biosystems S.p.A.
Inventors:
Valentina Del Monaco, Nicolò Manaresi, Genny Buson, Paola Tononi
Abstract: A method of identifying a polynucleic acid (PNA) is presented, including the steps of providing a PNA; modifying one or more nucleobases of the PNA by addition or removal of a hydrogen bonding partner, thereby altering the base pairing capacity of the one or more nucleobases; base pairing a complementary nucleic acid to the PNA, including base pairing to at least one modified nucleobase; identifying the sequence of the complementary nucleic acid at least at the position that is complementary to at least one modified nucleobase.
Type:
Grant
Filed:
February 18, 2022
Date of Patent:
January 2, 2024
Assignee:
IMBA—INSTITUT FÜR MOLEKULARE BIOTECHNOLOGIE GMBH
Inventors:
Stefan L. Ameres, Brian Reichholf, Veronika A. Herzog, Johannes Zuber, Matthias Muhar
Abstract: The invention provides methods, compositions, kits and devices for the detection of target molecules. In some embodiments, the invention allows for multiplexed target molecule detection.
Abstract: Systems and methods for rapid diagnostics related to the use of isothermal amplification reagents for detection of microbial species, including coronavirus, and methods of use, are provided.
Type:
Grant
Filed:
June 5, 2020
Date of Patent:
December 26, 2023
Assignees:
THE BROAD INSTITUTE, INC., MASSACHUSETTS INSTITUTE OF TECHNOLOGY
Inventors:
Feng Zhang, Jonathan Gootenberg, Omar Abudayyeh, Julia Joung, Alim Ladha, Han Altae-Tran, Guilhem Faure
Abstract: Methods for preparing enriched sequencing libraries from test samples that contain double-stranded deoxyribonucleic acid (dsDNA) are provided.
Abstract: Methods and apparatus relate to the synthesis of polynucleotides having a predefined sequence on a support. Assembly methods include primer extension to generate overlapping construction oligonucleotides and assembly of the polynucleotides of interest onto an anchor support-bound oligonucleotides. Methods and apparatus for selection of polynucleotides having the predefined sequence and/or length are disclosed.
Type:
Grant
Filed:
July 16, 2021
Date of Patent:
December 19, 2023
Assignee:
Gen9, Inc.
Inventors:
Joseph Jacobson, Li-Yun A. Kung, Andrew Kirk Wilson, Senthil Ramu, Daniel Schindler, Michael E. Hudson
Abstract: Provided herein, among other things, are various compositions and methods for analyzing chromatin. In some embodiments, the composition may comprise a mixture of a nicking enzyme, four dNTPs, at least one labeled dNTP and, optionally, a polymerase. In some embodiments, this method may comprise: obtaining a sample comprising chromatin, reacting the sample with the composition to selectively label the open chromatin in the sample, and analyzing the labeled sample.
Type:
Grant
Filed:
November 9, 2021
Date of Patent:
December 12, 2023
Assignee:
New England Biolabs, Inc.
Inventors:
Chaithanya Ponnaluri, Hang-Gyeong Chin, Pierre O. Esteve, Sriharsa Pradhan
Abstract: A method for determining a mutation in genomic DNA is described. The method is characterized in that the mutation analysis is performed with genomic DNA, in which at least a part of the cytosines contained therein has previously been converted into uracil or another base with a base pairing behavior or molecular weight distinguishable from that of cytosine.
Abstract: The methods and reagents are provided for barcoding and analysis of DNA samples using partition (e.g., droplet) technology while avoiding performing amplification in droplets.
Abstract: The present invention is directed to treatment of nucleic acid molecules that are attached or associated with solid supports for biochemical analysis, including nucleic acid sequencing. After loading on the solid support, the nucleic acid molecules are treated with a composition comprising a condensing agent, a volume excluding agent, or both, then treated with a composition comprising a protein.
Abstract: The present disclosure provides methods and systems for detecting multiple different nucleotides in a sample. In particular, the disclosure provides for detection of multiple different nucleotides in a sample utilizing fewer detection moieties than the number of nucleotides being detected and/or fewer imaging events than the number of nucleotides being detected.
Type:
Grant
Filed:
January 20, 2021
Date of Patent:
November 28, 2023
Assignee:
Illumina, Inc.
Inventors:
Robert C. Kain, Xiaohai Liu, Wenyi Feng, Bernard Hirschbein, Helmy A. Eltoukhy, Xiaolin Wu, Geoffrey Paul Smith, Jonathan Mark Boutell, Thomas Joseph, Randall Smith, Min-Jui Richard Shen, Carolyn Tregidgo, Kay Klausing
Abstract: A probe for detecting hepatitis B virus and a method for detecting an insertion site of hepatitis B virus at high efficiency based on the analysis method of next-generation sequencing using the probe is disclosed. A probe can be provided that is capable of confirming the insertion site of HBV in the human genome with a possibility of developing into liver cancer. In addition, by applying the probe to the analysis method of next-generation sequencing, HBV insertion sites in the human genome can be analyzed at low cost and high efficiency.
Type:
Grant
Filed:
November 4, 2020
Date of Patent:
November 14, 2023
Assignee:
THE CATHOLIC UNIVERSITY OF KOREA INDUSTRY-ACADEMIC COOPERATION FOUNDATION
Inventors:
Jeong Won Jang, Hye Seon Kim, Jin Seoub Kim, Eung Ryoung Lee
Abstract: The present disclosure relates to methods of identifying RNA targets of RNA binding proteins. In aspects, the disclosure relates to a method of identifying RNA molecules bound by RNA binding proteins. Some embodiments of the present disclosure relate to a method that can definitively identify direct RNA-target interactions with targeted proteins without the requirement for immunoprecipitation or gel extraction. In some embodiments, the method may include combining multiple antibodies in the same sample.
Abstract: Compositions and methods, systems, and kits for detecting and quantifying variations in numbers of molecules, particularly variations in gene dosage, e.g., due to gene duplication, or to variations from the normal euploid complement of chromosomes, e.g., trisomy of one or more chromosomes that are normally found in diploid pairs, without digital sequencing.
Type:
Grant
Filed:
December 7, 2021
Date of Patent:
October 17, 2023
Assignee:
Enumera Molecular, Inc.
Inventors:
Matthew Sekedat, Jeffrey Buis, Ronald David Beaubien, Sharat Singh, Jeff Perry
Abstract: Systems and methods for performing simultaneous nucleic acid amplification and detection. The systems and methods comprise methods for managing a plurality of protocols in conjunction with directing a sensor array across each of a plurality of reaction chambers. In certain embodiments, the protocols comprise thermocycling profiles and the methods may introduce offsets and duration extensions into the thermocycling profiles to achieve more efficient detection behavior.
Type:
Grant
Filed:
September 21, 2020
Date of Patent:
October 17, 2023
Assignee:
Becton, Dickinson and Company
Inventors:
Thomas Catalino Gubatayao, Kalyan Handique, Karthik Ganesan, Daniel M. Drummond
Abstract: Methods of determining the origin of cell free DNA (cfDNA), for detecting death of a cell type or tissue in a subject, for determining a cellular state of a cell as it died, and combinations thereof, are provided. As are computer program products for doing same.
Type:
Grant
Filed:
March 13, 2019
Date of Patent:
October 10, 2023
Assignee:
YISSUM RESEARCH DEVELOPMENT COMPANY OF THE HEBREW UNIVERSITY OF JERUSALEM LTD.
Abstract: The invention provides methods, compositions, kits and devices for the detection of target molecules. In some embodiments, the invention allows for multiplexed target molecule detection.