Abstract: The present invention relates to complexes of oligonucleotide-encoded libraries and methods of tagging and using such libraries. In particular, the oligonucleotides and methods can include complexes having at least one linkage for which a polymerase has reduced ability to read or translocate through.
Type:
Grant
Filed:
July 12, 2013
Date of Patent:
June 13, 2023
Assignee:
X-Chem, Inc.
Inventors:
Anthony D. Keefe, Alexander Litovchick, Matthew Clark
Abstract: A system, methods, and apparatus are described to collect and prepare single cells and groups of cells from microsamples of specimens and encode spatial information of the physical position of the cells in the specimen. In some embodiment, beads or surfaces with oligonucleotides containing spatial barcodes are used to analyze DNA or RNA. The spatial barcodes allow the position of the cell to be defined and the nucleic acid sequencing information, such as target sequencing, whole genome, gene expression, used to analyze the cells in a microsample for cell type, expression pattern, DNA sequence, and other information, in the context of the cell's physical position in the specimen. In other embodiment, markers such as isotopes are added to a microsample to encode spatial position with mass spectoscopy or other analysis. The spatial encoded information is then readout by analysis such as DNA sequencing, mass spectrometry, fluorescence, or other methods.
Abstract: Implementations of a method for seeding sequence libraries on a surface of a sequencing flow cell that allow for spatial segregation of the libraries on the surface are provided. The spatial segregation can be used to index sequence reads from individual sequencing libraries to increase efficiency of subsequent data analysis. In some examples, hydrogel beads containing encapsulated sequencing libraries are captured on a sequencing flow cell and degraded in the presence of a liquid diffusion barrier to allow for the spatial segregation and seeding of the sequencing libraries on the surface of the flow cell. Additionally, examples of systems, methods and compositions are provided relating to flow cell devices configured for nucleic acid library preparation and single cell sequencing. Some examples include flow cell devices having a hydrogel with genetic material disposed therein, and which is retained within the hydrogel during nucleic acid processing.
Type:
Grant
Filed:
April 13, 2022
Date of Patent:
May 16, 2023
Assignee:
ILLUMINA, INC.
Inventors:
Tarun Kumar Khurana, Yir-Shyuan Wu, Xi-Jun Chen, Filiz Gorpe-Yasar, Yan-You Lin, Victoria Popic, Erich B. Jaeger, Mostafa Ronaghi
Abstract: Embodiments of the present invention relate to analyzing components of a cell. In some embodiments, the present invention relate to analyzing components of a single cell. In some embodiments, the methods and compositions relate to sequencing nucleic acids. In some embodiments, the methods and compositions relate to identifying and/or quantitating nucleic acid, proteins, organelles, and/or cellular metabolites.
Type:
Grant
Filed:
February 10, 2016
Date of Patent:
April 25, 2023
Assignee:
ILLUMINA, INC.
Inventors:
Kevin L Gunderson, Frank J Steemers, Jeffrey S Fisher, Roberto Rigatti
Abstract: The present invention is directed to methods, compositions and systems for analyzing sequence information while retaining structural and molecular context of that sequence information.
Type:
Grant
Filed:
March 8, 2021
Date of Patent:
April 11, 2023
Assignee:
10X GENOMICS, INC.
Inventors:
Xinying Zheng, Serge Saxonov, Michael Schnall-Levin, Kevin Ness, Rajiv Bharadwaj
Abstract: Methods of analyzing cells, including interactions among different populations of cells. Methods include cell-containing liquid droplets with oligonucleotide-containing liquid droplets, hybridizing oligonucleotides to target nucleic acids from cells, extending the hybridized oligonucleotides on the target nucleic acids into cell identifier sequences on the target nucleic acids, and thereby identifying the type of cells initially present. The methods can be implemented in a high-throughput manner in a microfluidic system.
Type:
Grant
Filed:
October 25, 2019
Date of Patent:
March 21, 2023
Assignee:
Wisconsin Alumni Research Foundation
Inventors:
Ophelia S. Venturelli, Philip A. Romero, Ryan Hon Hean Hsu, Jin Wen Tan
Abstract: The present invention generally relates to droplet libraries and to systems and methods for the formation of libraries of droplets. The present invention also relates to methods utilizing these droplet libraries in various biological, chemical, or diagnostic assays.
Type:
Grant
Filed:
August 20, 2018
Date of Patent:
March 7, 2023
Assignee:
Bio-Rad Laboratories, Inc.
Inventors:
Darren Roy Link, John Brian Hutchison, Michael L. Samuels, Michael Weiner
Abstract: An electrowetting device includes a first substrate, a plurality of first electrodes formed on the first substrate, a dielectric layer formed on the plurality of first electrodes, a first water-repellent layer formed on the dielectric layer, a second substrate, a second electrode formed on the second substrate, and a second water-repellent layer formed on the second electrode. The first substrate and the second substrate are arranged with a gap between the first water-repellent layer and the second water-repellent layer. The first electrode includes an indium oxide-zinc oxide layer, the dielectric layer includes a silicon nitride layer, and the silicon nitride layer is formed directly on the indium oxide-zinc oxide layer.
Abstract: Described herein are methods of preparing dual-indexed nucleic acid libraries for methylation profiling using bisulfite conversion sequencing. In various embodiments, the methods use a two-step indexing process to tag bisulfite-treated DNA with unique molecular identifiers (UMIs).
Abstract: The present invention generally relates to droplet libraries and to systems and methods for the formation of libraries of droplets. The present invention also relates to methods utilizing these droplet libraries in various biological, chemical, or diagnostic assays.
Type:
Grant
Filed:
October 11, 2016
Date of Patent:
December 27, 2022
Assignee:
Bio-Rad Laboratories, Inc.
Inventors:
Darren Link, John Brian Hutchison, Michael Samuels, Michael Weiner
Abstract: Embodiments provided herein relate to methods and compositions for preparing nucleic acid libraries. Some embodiments include preparing libraries from nucleic acids obtained from degraded samples, such as ancient samples and fixed samples.
Type:
Grant
Filed:
October 12, 2020
Date of Patent:
November 29, 2022
Assignee:
Illumina, Inc.
Inventors:
Raquel Maria Sanches-Kuiper, Vincent Peter Smith, Sean Humphray
Abstract: The present invention generally relates to droplet libraries and to systems and methods for the formation of libraries of droplets. The present invention also relates to methods utilizing these droplet libraries in various biological, chemical, or diagnostic assays.
Type:
Grant
Filed:
October 25, 2021
Date of Patent:
November 29, 2022
Assignee:
Bio-Rad Laboratories, Inc.
Inventors:
Darren Roy Link, John Brian Hutchison, Michael L. Samuels, Michael Weiner
Abstract: Disclosed herein are antigenic peptide-MHC complexes, termed comPACT polypeptides and comPACT polynucleotides, and methods of producing such complexes. Also discloses herein are methods of producing libraries of comPACT polynucleotides and polypeptides, and their exemplary use in capturing cancer neoepitope-reactive T cells with high accuracy. Dual particle detection approaches for detection of neoantigen specific T cells with improved sensitivity and specificity are provided. Signal to noise ratio analysis of isolated T cells for detection of neoantigen-specific T cells with improved T cells is also provided.
Type:
Grant
Filed:
February 12, 2020
Date of Patent:
November 29, 2022
Assignee:
PACT PHARMA, INC.
Inventors:
Songming Peng, Boi Bryant Quach, Duo An, Xiaoyan Robert Bao, Alex Franzusoff, Barbara Sennino, Olivier Dalmas, Stefanie Mandl-Cashman
Abstract: The present disclosure is directed to a single-end sequencing method for improved detection of genomic rearrangements such as deletions, insertions, inversions, and translocations that are present in a polynucleotide. A first priming event allows for sequencing of a target sequence, and a second priming event on an adapter allows for identification of the sequences amplified and tagged by selective amplification. The combination of priming events in the same direction facilitates read alignment and the identification of any genomic rearrangements.
Abstract: A novel method for preparing sequence-verified oligonucleotides is disclosed. In particular, the invention relates to a simple, affordable, and scalable method that combines high-throughput mating of yeast clones, a unique selectable system for combining DNA sequences in yeast, and next-generation sequencing. This method allows sequence-verified oligonucleotides to be readily isolated from complex libraries.
Type:
Grant
Filed:
August 19, 2020
Date of Patent:
November 22, 2022
Assignee:
The Board of Trustees of the Leland Stanford Junior University
Inventors:
Robert P. St. Onge, Ulrich Schlecht, Sasha F. Levy, Ronald W. Davis, Joseph Horecka
Abstract: The present invention provides for single-molecule profiling of combinatorial protein modifications and single-molecule profiling of combinatorial protein modifications combined with single-molecule sequencing of protein/nucleic acids complexes. High-throughput single-molecule imaging was applied to decode combinatorial modifications on millions of individual nucleosomes from pluripotent stem cells and lineage-committed cells. Applicants identified bivalent nucleosomes with concomitant repressive and activating marks, as well as other combinatorial modification states whose prevalence varies with developmental potency. Applying genetic and chemical perturbations of chromatin enzymes show a preferential affect on nucleosomes harboring specific modification states. The present invention also combines this proteomic platform with single-molecule DNA sequencing technology to simultaneously determine the modification states and genomic positions of individual nucleosomes.
Type:
Grant
Filed:
August 19, 2016
Date of Patent:
October 25, 2022
Assignees:
The General Hospital Corporation, SEQLL LLC
Inventors:
Efrat Shema-Yaacoby, Bradley Bernstein, Daniel Jones
Abstract: The present invention is directed to methods, compositions and systems for analyzing sequence information while retaining structural and molecular context of that sequence information.
Type:
Grant
Filed:
November 14, 2018
Date of Patent:
October 18, 2022
Assignee:
10X GENOMICS, INC.
Inventors:
Xinying Zheng, Serge Saxonov, Michael Schnall-Levin, Kevin Ness, Rajiv Bharadwaj
Abstract: Methods, devices, and systems for performing digital assays are provided. In certain aspects, the methods, devices, and systems can be used for the amplification and detection of nucleic acids. In certain aspects, the methods, devices, and systems can be used for the recognition, detection, and sizing of droplets in a volume. Also provided are compositions and kits suitable for use with the methods and devices of the present disclosure.
Type:
Grant
Filed:
March 6, 2020
Date of Patent:
August 30, 2022
Assignee:
UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATION
Inventors:
Daniel T. Chiu, Jason E. Kreutz, Gloria S. Yen, Bryant S. Fujimoto
Abstract: A method for the synthesis of a chimeric conjugate molecule by micellar catalysis that may form part of DNA-encoded compound libraries. A DNA-coupled organic starter molecule may be reacted with another organic compound, using a catalyst located within a micelle, to form a conjugate of an organic candidate compound coupled to a DNA identifier tag.