Abstract: Disclosed herein, inter alia, are substrates, kits, and efficient methods of preparing and sequencing two or more regions of a double-stranded polynucleotide.
Type:
Grant
Filed:
October 21, 2022
Date of Patent:
October 17, 2023
Assignee:
Singular Genomics Systems, Inc.
Inventors:
Daan Witters, Eli N. Glezer, Allen Lipson
Abstract: Disclosed herein are methods, compositions, and devices for use in the early detection of cancer. The methods include preparing cell-free nucleic acid molecules from a subject for sequencing, sequencing a panel of regions in the cell-free nucleic acid molecules, and detecting one or more markers that are indicative of a cancer.
Abstract: Described herein are devices, systems, and methods for trapping single-cell lysates in sealed, microwells capable of printing RNA on glass or capturing RNA on beads. These provide efficient, inexpensive manipulation of RNA from individual cells suitable for single-cell transcriptomics on a large scale. Also described are dual barcode capture beads and merged barcode capture beads.
Type:
Grant
Filed:
November 27, 2018
Date of Patent:
October 17, 2023
Assignee:
The Trustees of Columbia University in the City of New York
Inventors:
Peter A. Sims, Sayantan Bose, Jinzhou Yuan
Abstract: The present invention relates to a microfluidic system including a temperature controller and a thermoplastic microfluidic chip that enables rapid PCR in a PCR chamber of the microfluidic chip. Thermal control of the PCR chamber is achieved by applying voltage to heater electrodes patterned directly onto one layer of the microfluidic chip. The temperature controller adjusts the voltage applied to the heater electrodes by changing temperature controller parameters selected to minimize duration of each PCR cycle. Furthermore, simple operation of the microfluidic chip is provided through using an integrated passive capillary valve, requiring minimum operator intervention and eliminating the need for fluidic interfacing, pumping, or metering during chip loading.
Type:
Grant
Filed:
July 13, 2020
Date of Patent:
October 3, 2023
Assignee:
University of Maryland
Inventors:
Donald DeVoe, Eric Kendall, Alex Sposito
Abstract: Methods of detecting the absence or presence of a micro-organism in a sample comprising: contacting the sample with a nucleic acid molecule which acts as a substrate for nucleic acid modifying activity of the micro-organism in the sample, incubating the thus contacted sample under conditions suitable for nucleic acid modifying activity; and specifically determining the absence or presence of a modified nucleic acid molecule resulting from the action of the nucleic acid modifying activity on the substrate nucleic acid molecule to indicate the absence or presence of the micro-organism. Corresponding kits are also provided.
Type:
Grant
Filed:
June 20, 2022
Date of Patent:
September 5, 2023
Assignee:
Momentum Bioscience Limited
Inventors:
Matthew A. Crow, Helen V. Bennett, Daniel S. Wratting, William H. Mullen
Abstract: Provided herein are compositions and methods of use thereof for screening a plurality of uniquely identifiable therapeutic moiety in vivo by identifying one or more reporters indicative of a cell state.
Abstract: The present invention provides a method for sequencing a nucleic acid using an immersion reaction protocol. The immersion reaction protocol comprises sequentially immersing a solid support having nucleic acid molecules immobilized thereon in different reaction containers to realize nucleic acid sequencing.
Type:
Grant
Filed:
August 1, 2017
Date of Patent:
July 4, 2023
Assignees:
MGI TECH CO., LTD., COMPLETE GENOMICS, INC.
Inventors:
Jin Yang, Xun Xu, Hui Wang, Bin Xie, Zhuokun Li, Shengming Zhao, Ao Chen, Chongjun Xu, Wenwei Zhang, Ming Ni
Abstract: Disclosed is a method for sequencing a nucleotide sequence of a target nucleic acid. The method comprises: providing a pool of amplicons, wherein the pool of amplicons is prepared by attaching a unique identifier to the target nucleic acid, and amplifying by PCR the target nucleic acid to which the unique identifier is attached; and sequencing the amplicons comprising the unique identifier and the target nucleic acid. In the method, a nucleotide sequence of the unique identifier comprises both a random nucleotide (N) and a predetermined nucleotide.
Abstract: The present invention discloses a Polymerase Chain Reaction (PCR) apparatus for real-time detecting of one or more fluorescent signals. According to the apparatus, the PCR is performed by controlling heating and cooling intervals of a reagent container receiving space. With the aid of an added specific probe and fluorescent material, as well as a light source and a spectrometer, a generated fluorescent signal is detected. Meanwhile, the apparatus is also pre-loaded with an algorithm configured to analyze and quantify the fluorescent signal in a real-time manner.
Abstract: This disclosure provides methods, compositions and kits for determining if nucleic acids detected in a sample such as a clinical sample are derived from contaminant pathogens or clinically-relevant pathogens.
Type:
Grant
Filed:
May 27, 2020
Date of Patent:
June 13, 2023
Assignee:
Karius, Inc.
Inventors:
Timothy A. Blauwkamp, Liza Huijse, Michael Rosen, Igor D. Vilfan
Abstract: The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease.
Type:
Grant
Filed:
August 6, 2021
Date of Patent:
June 6, 2023
Assignee:
Guardant Health, Inc.
Inventors:
AmirAli Talasaz, Stefanie Ann Ward Mortimer
Abstract: Methods and reagents for multiplex detection of antibodies are disclosed. In particular, the invention relates to multiplex detection of antibodies using antigen-DNA and antibody-binding agent-DNA conjugates carrying DNA barcodes for identifying and quantitating disease-relevant antibody isotypes, such as those involved in allergic responses, autoimmune diseases, infections, and inflammation.
Type:
Grant
Filed:
March 29, 2018
Date of Patent:
May 23, 2023
Assignee:
The Board of Trastees of the Leland Stanford Junior University
Inventors:
Carolyn Bertozzi, Stephen J. Galli, Kaori Mukai, Peter Robinson, Cheng-ting Tsai, Mindy Tsai
Abstract: Efficient methods are disclosed for the high throughput identification of mutations in genes in members of mutagenized populations. The methods comprise DNA isolation, pooling, amplification, creation of libraries, high throughput sequencing of libraries, preferably by sequencing-by-synthesis technologies, identification of mutations and identification of the member of the population carrying the mutation and identification of the mutation.
Type:
Grant
Filed:
December 18, 2019
Date of Patent:
May 16, 2023
Assignee:
Keygene N.V.
Inventors:
Michael Josephus Theresia Van Eijk, Adrianus Johannes Van Tunen
Abstract: Provided herein are compositions and methods for accurate and scalable Primary Template-Directed Amplification (PTA) nucleic acid amplification and sequencing methods, and their applications for research, diagnostics, and treatment.
Type:
Grant
Filed:
August 31, 2022
Date of Patent:
May 9, 2023
Assignee:
ST. JUDE CHILDREN'S RESEARCH HOSPITAL, INC.
Inventors:
Charles Gawad, John Easton, Veronica Gonzalez-Pena
Abstract: Disclosed herein are methods for use in detection of single nucleotide variants (SNVs) or indels. The methods may comprise enriching cell-free DNA molecules for a panel of genomic regions and deep sequencing the enriched cfDNA to detect the SNVs or indels.
Abstract: This disclosure relates to methods of determining quantification conditions for a microorganism and methods of quantifying microorganism concentration in a sample.
Abstract: Provided herein are methods, systems, and compositions for determining a base in a polynucleotide. In various aspects, the methods, systems, and compositions presented herein are useful for performing 4-base, 5-base, or 6-base sequencing of polynucleotide molecules, for example, from liquid biopsy samples or wherein the base is a low frequency mutation.
Type:
Grant
Filed:
March 21, 2022
Date of Patent:
March 21, 2023
Assignee:
Cambridge Epigenetix Limited
Inventors:
Shankar Balasubramanian, Jens Fullgrabe, Walraj Singh Gosal, Joanna Dawn Holbrook, Sidong Liu, David Morley, Oliver Nentwich, Tobias Ost, Michael Steward, Albert Vilella, Nicolas James Walker, Shirong Yu, Helen Rachel Bignell, Rita Santo San-Bento
Abstract: The invention is a method of identifying a cognate antigen for a T-cell receptor using neoantigens from a patient's tumor cells combined with the patient's T-cells and using cell sorting, genome sequencing, expressing TCR genes, presenting tumor neoantigens on MHC complex and uniquely barcoding the T-cells where TCR recognition occurs to tag all components of the TCR recognition complex.
Type:
Grant
Filed:
June 14, 2019
Date of Patent:
March 14, 2023
Assignees:
ROCHE SEQUENCING SOLUTIONS, INC., VENTANA MEDICAL SYSTEMS, INC.
Inventors:
Nelson R. Alexander, Aoune Barhoumi, Jan Berka, Rui Chen, Lisa L. Gallegos, Toumy Guettouche, Seoyoung Kim, Maeve E. O'Huallachain, Sedide Ozturk, Jigar Patel, Florian Rubelt, Stacey Stanislaw
Abstract: Provided herein are methods for enriching a biological sample for a target nucleic acid, and analyzing the nucleic acid. In some cases, a biological sample is enriched for target nucleic acids associated with a cancer or tumor. In some cases, a biological sample is enriched for target nucleic acids, and the target nucleic acids vary in length. In some cases, one or more probes are used to enrich the biological sample for the target nucleic acid. In some cases, one or more probes hybridize to one or more ends of a target nucleic acid.
Abstract: Provided herein is a method for analyzing polynucleotides such as genomic DNA. In certain embodiments, the method comprises: (a) treating chromatin isolated from a population of cells with an insertional enzyme complex to produce tagged fragments of genomic DNA; (b) sequencing a portion of the tagged fragments to produce a plurality of sequence reads; and (c) making an epigenetic map of a region of the genome of the cells by mapping information obtained from the sequence reads to the region. A kit for performing the method is also provided.
Type:
Grant
Filed:
June 6, 2022
Date of Patent:
March 7, 2023
Assignee:
The Board of Trustees of the Leland Stanford Junior University
Inventors:
Paul Giresi, Jason D. Buenrostro, Howard Y. Chang, William J. Greenleaf