Abstract: A digital droplet PCR method of analyzing the methylation status of methylation sites of a double-stranded DNA molecule which comprises at least two methylation sites per single strand of the double-stranded DNA molecule is disclosed.
Type:
Grant
Filed:
July 13, 2018
Date of Patent:
October 11, 2022
Assignees:
YISSUM RESEARCH DEVELOPMENT COMPANY OF THE HEBREW UNIVERSITY OF JERUSALEM LTD., HADASIT MEDICAL RESEARCH SERVICES AND DEVELOPMENT LTD.
Inventors:
Yuval Dor, Ruth Shemer, Benjamin Glaser, Judith Magenheim
Abstract: The present application is generally directed to systems, methods, and devices for diagnostics for sensing and/or identifying pathogens, genomic materials, proteins, and/or other small molecules or biomarkers. In some implementations, a small footprint low cost device provides rapid and robust sensing and identification. Such a device may utilize microfluidics, biochemistry, and electronics to detect one or more targets at once in the field and closer to or at the point of care.
Type:
Grant
Filed:
September 20, 2017
Date of Patent:
October 11, 2022
Assignee:
ALVEO TECHNOLOGIES, INC.
Inventors:
Shad Pierson, Timothy D. Meehan, Kyle William Montgomery, Daniel J. Wade, Jess M. Sustarich, Brenna Hearn Lord, Ronald Phillip Chiarello
Abstract: The present invention provides, among other things, methods for purifying high quality messenger RNA (mRNA) suitable for clinical use, without using any caustic or flammable solvents. The present invention is, in part, based on surprising discovery that mRNA can be successfully purified by selective precipitation and washing without using ethanol while maintaining integrity and high purity of mRNA. Thus, the present invention provides an effective, reliable, and safer method of purifying RNA from large scale manufacturing process therapeutic applications without using any caustic or inflammable solvents.
Type:
Grant
Filed:
May 15, 2020
Date of Patent:
September 27, 2022
Assignee:
Translate Bio, Inc.
Inventors:
Jonathan Abysalh, Frank DeRosa, Jorel E. Vargas, Cameron M. Smith
Abstract: The inventions cover systems and methods for generation of emulsions having suitable clarity without requiring refractive index matching between emulsion components. Systems can include: a substrate including a set of openings; a reservoir facing the substrate at a first side and containing a sample fluid configured for droplet formation upon interacting with the set of openings of the substrate; and a collecting container facing the substrate at a second side and containing a set of fluid layers configured with a density gradient and suitable immiscibility characteristics. One or more components of the system(s) can support methods for emulsion generation, in relation to enabling interactions between multiple continuous phases and a dispersed droplet phase to generate clear emulsions. Applications of the inventions(s) can include performance of droplet-based digital PCR in an improved manner (e.g., without requiring implementation of correction factors based upon Poisson statistics).
Type:
Grant
Filed:
December 23, 2021
Date of Patent:
September 20, 2022
Assignee:
Enumerix, Inc.
Inventors:
Hei Mun Christina Fan, Eleen Yee Lam Shum, Janice Hoiyi Lai, Stephen P. A. Fodor
Abstract: The invention relates to control compositions for a quantitative polymerase chain reaction. More particularly, the invention relates to control compositions for a quantitative polymerase chain reaction having at least one barcode sequence fragment and at least a first and a second primer binding site fragment, and to methods of their use.
Abstract: This disclosure provides methods and compositions for sample processing, particularly for sequencing applications. Included within this disclosure are bead compositions, such as diverse libraries of beads attached to large numbers of oligonucleotides containing barcodes. Often, the beads provides herein are degradable. For example, they may contain disulfide bonds that are susceptible to reducing agents. The methods provided herein include methods of making libraries of barcoded beads as well as methods of combining the beads with a sample, such as by using a microfluidic device.
Type:
Grant
Filed:
April 9, 2020
Date of Patent:
September 13, 2022
Assignee:
10X GENOMICS, INC.
Inventors:
Christopher Hindson, Michael Schnall-Levin, Andrew Price, Paul Hardenbol, Yuan Li
Abstract: Ultraspecific, programmable nucleic acid sensors capable of detecting and preferentially amplifying target DNA molecules comprising a particular SNP or mutation are provided. In some cases, the ultraspecific programmable nucleic acid sensors are useful for detecting SNP-containing DNA molecules indicative of cancer such as cell-free DNA circulating in the blood or indicative of organ transplant rejection Also provided are methods for construction of such ultraspecific nucleic acid sensors and methods for preferential amplification of target DNA molecules containing a mutation of interest, as well as testing systems for early cancer screening and routine monitoring of circulating cancer DNA using liquid biological samples such as serum, plasma, or saliva.
Type:
Grant
Filed:
November 15, 2017
Date of Patent:
September 6, 2022
Assignee:
ARIZONA BOARD OF REGENTS ON BEHALF OF ARIZONA STATE UNIVERSITY
Inventors:
Alexander Green, Fan Hong, Soma Chaudhary, Anli Tang, Hao Yan
Abstract: The present invention concerns processes for barcoding nucleic acids from single cells and processes for genotyping single cells having a phenotype of interest.
Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing.
Type:
Grant
Filed:
April 20, 2020
Date of Patent:
August 23, 2022
Assignee:
10X GENOMICS, INC.
Inventors:
Benjamin Hindson, Serge Saxonov, Kevin Ness, Paul Hardenbol, Michael Schnall-Levin, Mirna Jarosz
Abstract: In certain embodiments, the present invention provides a method to identify driver mutations in a tumor and its cancer cell subpopulations. The method of the present invention is used to design treatment strategies for cancer patients.
Abstract: Methods and systems for digital measurements are provided. In an embodiment, the method includes producing a plurality of droplets, wherein at least one of the droplets of the plurality of droplets contains an analyte molecule from a sample; measuring at least a first portion of the plurality of droplets to determine individual volumes of droplets in the first portion of the plurality of droplets; analyzing at least a second portion of the plurality of droplets to determine a number of droplets in the second portion of the plurality of droplets that contain the analyte molecule; and using individual volumes of the droplets in the first portion of the plurality of droplets and the number of droplets in the second portion of the plurality of droplets that contain the analyte molecule to determine the concentration of the analyte molecule in the sample.
Type:
Grant
Filed:
February 5, 2020
Date of Patent:
August 2, 2022
Assignee:
University of Washington through its Center for Commercialization
Inventors:
Daniel T. Chiu, Bryant S. Fujimoto, Alexander R. Gansen, Gloria S. Yen, Robert M. Lorenz
Abstract: Methods, sample vessels, and instruments are provided for melting curve analysis. A sample is amplified by thermal cycling the sample well between at least an annealing temperature and a denaturation temperature through n cycles, where each cycle includes an in-cycle denaturation step. Fluorescent data is collected during the in-cycle denaturation step of n cycles where n is at least two. Then a composite melting curve is generated using the fluorescent data collected during the denaturation step of each of the n cycles, and the sample is called using the composite melting curve, where the call is a positive or a negative call.
Type:
Grant
Filed:
June 21, 2018
Date of Patent:
July 26, 2022
Assignee:
BIOFIRE DIAGNOSTICS, LLC
Inventors:
Benjamin William Galvin, Thomas Charles Robbins, Charles Benjamin Cox
Abstract: The invention provides compositions and methods for making closed nucleic acid structures in which one or both strands are continuous. The closed nucleic acid structures can be used as sequencing templates among other applications.
Abstract: The present invention is directed to methods and compositions for long fragment read sequencing. The present invention encompasses methods and compositions for preparing long fragments of genomic DNA, for processing genomic DNA for long fragment read sequencing methods, as well as software and algorithms for processing and analyzing sequence data.
Type:
Grant
Filed:
October 10, 2016
Date of Patent:
July 19, 2022
Assignee:
Complete Genomics, Inc.
Inventors:
Radoje Drmanac, Brock A. Peters, Andrei Alexeev, Peter Hong
Abstract: Compositions are provided for 3? adapters and methods of use are provided that include methods requiring a plurality of ligation steps involving a single-stranded target polynucleotide and 3? and 5? adapters. Embodiments of the 3? adapters comprise a cleavable linker positioned between a single-stranded region and a double-stranded region. Upon ligating the 3? adapters, the single-stranded region is released by cleaving the cleavable linker.
Abstract: A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.
Type:
Grant
Filed:
March 11, 2022
Date of Patent:
July 19, 2022
Assignees:
Spatial Transcriptomics AB, Illumina, Inc.
Inventors:
Jonas Frisen, Patrik Stahl, Joakim Lundeberg, Gordon M. Cann, Leila Bazargan, Alex Aravanis
Abstract: Infectious diseases have been sources of large-scale epidemics and pandemics resulting in millions of casualties worldwide. Detection of these biological agents normally involves several lab processes including sample preparation, nucleic acid separation and amplification, and diagnostic analysis. These steps, either performed manually or automated by high-throughput machinery, are tedious, expensive, and highly susceptible to cross-contamination. The present system is an integrated lab-on-a-device designed, developed, and tested in compatibility with a mechanical fixture for sample-to-answer biological analysis of infectious diseases.
Type:
Grant
Filed:
March 20, 2019
Date of Patent:
July 19, 2022
Assignee:
CHARLES R. DREW UNIVERSITY OF MEDICINE AND SCIENCE
Inventors:
Benjamin Liu, Eva McGhee, Robin Liu, Miguel Nava
Abstract: Nucleic acid constructs and methods that provide superior prevention of primer-dimers and other artifacts of false priming events are disclosed. In particular, there is disclosed a hairpin primer having a target-specific primer region, wherein the target-specific region comprises a target-binding dependent cleavage sequence; a first stem forming region 5? of the target-specific primer region; and a second stem forming region 3? of the target-specific primer region, wherein the second stem forming region is complementary to the first stem forming region. Methods of using the hairpin primer to amplify a target nucleic acid are also disclosed.
Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing.
Type:
Grant
Filed:
May 7, 2021
Date of Patent:
June 14, 2022
Assignee:
10X GENOMICS, INC.
Inventors:
Benjamin Hindson, Kevin Ness, Serge Saxonov, Paul Hardenbol
Abstract: Nucleic acid oligonucleotide sequences are disclosed which include amplification oligomers and probe oligomers which are useful for detecting multiple types of human papillomaviruses (HPV) associated with cervical cancer. Methods for detecting multiple HPV types in biological specimens by amplifying HPV nucleic acid sequences in vitro and detecting the amplified products are disclosed.
Type:
Grant
Filed:
February 10, 2020
Date of Patent:
June 14, 2022
Assignee:
GEN-PROBE INCORPORATED
Inventors:
Sylvia A. Norman, Jennifer J. Bungo, William L. Hanna, Neeraj P. Rao