Abstract: A method is described for recovering resources from a microbe supporting environment such as a water treatment system, comprising the steps of using microbial DNA sequencing to analyze the microbiome of the microbe supporting environment and identifying adjustments to the microbial content of the microbiome that will be useful in extracting resources from the microbe supporting environment such as a water treatment system, wherein the resources extracted can include, for example, methane released by microbes, nitrogen, phosphorus, or other contaminants generated by microbes, and/or clean water obtained by removing contaminants in a water treatment system.
Abstract: The present invention relates to methods for detecting, enriching, and analyzing rare cells that are present in the blood, e.g. fetal cells. The invention further features methods of analyzing rare cell(s) to determine the presence of an abnormality, disease or condition in a subject, e.g. a fetus by analyzing a cellular sample from the subject.
Type:
Grant
Filed:
October 7, 2019
Date of Patent:
March 1, 2022
Assignees:
The General Hospital Corporation, Verinata Health, Inc., GPB Scientific, LLC
Inventors:
Ravi Kapur, Mehmet Toner, Zihua Wang, Martin Fuchs
Abstract: Provided herein are, inter alia, nucleic acids, methods, and kits for detecting unmethylated DNA in body fluid sample of a subject. The disclosure includes compositions, methods, and kits for detecting unmethylation at a CpG site in an insulin gene promoter of a subject.
Type:
Grant
Filed:
July 8, 2019
Date of Patent:
March 1, 2022
Assignee:
City of Hope
Inventors:
Kevin Ferreri, Mohamed I. Husseiny Elsayed
Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.
Type:
Grant
Filed:
August 19, 2019
Date of Patent:
February 22, 2022
Assignee:
Illumina, Inc.
Inventors:
Min-Jui Richard Shen, Jonathan Mark Boutell, Kathryn M. Stephens, Mostafa Ronaghi, Kevin L. Gunderson, Bala Murali Venkatesan, M. Shane Bowen, Kandaswamy Vijayan
Abstract: Techniques, systems, and devices are disclosed for non-thermal cycling of polymerase chain reaction (PCR). In one aspect, a method for cycling PCR includes receiving an electrolytic fluid including ions, primers, polymerase enzymes, nucleotides, and a double-stranded nucleic acid in a fluid chamber having a first electrode and a second electrode, applying an electric field across the first and the second electrodes to generate a first pH level of the electrolytic fluid to denature the double-stranded nucleic acid to at least partial single strands, and applying a second electric field across the first and second electrodes to produce a second pH level of the electrolytic fluid, in which the second pH level enables binding of a polymerase enzyme and a primer with a corresponding segment of the single strands.
Type:
Grant
Filed:
December 3, 2019
Date of Patent:
February 22, 2022
Assignee:
THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
Abstract: A method for quantifying labels on a substrate is performed by an electronic device with one or more processors and memory. The method includes obtaining digital data corresponding to a multi-dimensional measurement over the substrate; identifying a first set of sub-portions of the digital data; and, for a respective sub-portion of the first set of sub-portions of the digital data: increasing a quantity of labels, and subtracting a reference signal distribution from the respective sub-portion to obtain subtracted sub-portion data. The method also includes obtaining subtracted digital data. The subtracted digital data includes the subtracted sub-portion data for the respective sub-portion. The method further includes identifying a second set of one or more sub-portions of the subtracted digital data; and, for a respective sub-portion of the second set of one or more sub-portions of the subtracted digital data, increasing a quantity of labels.
Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and analyte characterization. Such polynucleotide processing may be useful for a variety of applications, including analyte characterization by polynucleotide sequencing. The compositions, methods, systems, and devices disclosed herein generally describe barcoded oligonucleotides, which can be bound to a bead, such as a gel bead, useful for characterizing one or more analytes including, for example, protein (e.g., cell surface or intracellular proteins), genomic DNA, and RNA (e.g., mRNA or CRISPR guide RNAs). Also described herein, are barcoded labelling agents and oligonucleotide molecules useful for “tagging” analytes for characterization.
Type:
Grant
Filed:
February 12, 2021
Date of Patent:
February 15, 2022
Assignee:
10X GENOMICS, INC.
Inventors:
Phillip Belgrader, Josephine Harada, Tarjei Sigurd Mikkelsen, Katherine Pfeiffer, Serge Saxonov, John R. Stuelpnagel
Abstract: Provided are methods and systems useful for screening large libraries of effector molecules. Such methods and systems are particularly useful in microfluidic systems and devices. The methods and systems provided herein utilize encoded effectors to screen large libraries of effectors.
Type:
Grant
Filed:
November 5, 2020
Date of Patent:
February 15, 2022
Assignee:
1859, Inc.
Inventors:
Devon Cayer, Andrew MacConnell, Pavel Chubukov, Ramesh Ramji, Sean Stromberg
Abstract: Provided is a method for isolating exosomal DNA, the method comprising: (i) providing a sample, wherein the sample comprises a blood sample from peripheral blood of a pregnant woman; and (ii) subjecting the sample to isolating, thus obtaining the exosomal DNA. Also provided are a method for detecting a blood sample, a method for constructing a sequencing library on a blood sample, a method for high-throughput sequencing an exosomal DNA sequencing library, a method for non-invasive prenatal gene detection, a device for non-invasive prenatal gene detection, and a kit for detecting a blood sample and use thereof.
Type:
Grant
Filed:
July 23, 2019
Date of Patent:
February 8, 2022
Assignees:
BGI SHENZHEN, MGI TECH CO., LTD.
Inventors:
Ya Gao, Sen Lu, Jia Zhao, Peng Zeng, Fang Chen, Hui Jiang
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:
April 14, 2021
Date of Patent:
February 8, 2022
Assignee:
ENUMERIX, INC.
Inventors:
Hei Mun Christina Fan, Eleen Yee Lam Shum, Janice Hoiyi Lai, Stephen P. A. Fodor
Abstract: Next Generation DNA sequencing promises to revolutionize clinical medicine and basic research. However, while this technology has the capacity to generate hundreds of billions of nucleotides of DNA sequence in a single experiment, the error rate of approximately 1% results in hundreds of millions of sequencing mistakes. These scattered errors can be tolerated in some applications but become extremely problematic when “deep sequencing” genetically heterogeneous mixtures, such as tumors or mixed microbial populations. To overcome limitations in sequencing accuracy, a method Duplex Consensus Sequencing (DCS) is provided. This approach greatly reduces errors by independently tagging and sequencing each of the two strands of a DNA duplex. As the two strands are complementary, true mutations are found at the same position in both strands. In contrast, PCR or sequencing errors will result in errors in only one strand.
Type:
Grant
Filed:
August 30, 2018
Date of Patent:
February 8, 2022
Assignee:
UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATION
Inventors:
Jesse Salk, Lawrence A. Loeb, Michael Schmitt
Abstract: The present invention relates to technology for preparing oligonucleotides for detecting a target nucleic acid molecule in a sample. Unlike the conventional methods, the present invention provides a first oligonucleotide candidate group designed appropriately for the first selected nucleotide sequence of the target nucleic acid molecule as a standard instead of simultaneously referring to all of the sequences exhibiting the genetic diversity. Then, an optimal oligonucleotide capable of accurately detecting a target nucleic acid molecule exhibiting genetic diversity in a sample is provided by using the first oligonucleotide candidate group.
Type:
Grant
Filed:
September 29, 2017
Date of Patent:
January 11, 2022
Assignee:
SEEGENE, INC.
Inventors:
Gi-Seok Yoon, Jun-Seo Lee, Kwang-Il Lee
Abstract: The disclosure provides methods and systems for analyzing fluid samples comprising obtaining fluid samples in at least one cavity of a substrate and introducing also buffers and/or reagents in the cavity, performing nucleic acid extraction and/or purification in the cavity, and performing nucleic acid amplification in the same cavity.
Abstract: Next Generation DNA sequencing promises to revolutionize clinical medicine and basic research. However, while this technology has the capacity to generate hundreds of billions of nucleotides of DNA sequence in a single experiment, the error rate of approximately 1% results in hundreds of millions of sequencing mistakes. These scattered errors can be tolerated in some applications but become extremely problematic when “deep sequencing” genetically heterogeneous mixtures, such as tumors or mixed microbial populations. To overcome limitations in sequencing accuracy, a method Duplex Consensus Sequencing (DCS) is provided. This approach greatly reduces errors by independently tagging and sequencing each of the two strands of a DNA duplex. As the two strands are complementary, true mutations are found at the same position in both strands. In contrast, PCR or sequencing errors will result in errors in only one strand.
Type:
Grant
Filed:
August 30, 2018
Date of Patent:
December 14, 2021
Assignee:
UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATION
Inventors:
Jesse Salk, Lawrence A. Loeb, Michael Schmitt
Abstract: A manually actuated chromatography device comprising a chamber for receiving a liquid sample, a pump with a metering valve, and a chromatography element, wherein the pump moves a predetermined volume of liquid from the sample chamber to the chromatography element.
Type:
Grant
Filed:
October 31, 2016
Date of Patent:
November 30, 2021
Assignees:
ALERE SAN DIEGO, INC., ALERE SWITZERLAND GMBH
Inventors:
Daniel Nicholas Haworth, John Paul Palmer-Felgate
Abstract: The present invention relates to a biomarker and uses thereof for liver cancer diagnosis or prognosis prediction. The biomarker according to the present invention may be used as a marker for liver cancer diagnosis and prognosis prediction with improved specificity and sensitivity. Thus, the biomarker may be used not only to diagnose or prognose liver cancer with high accuracy and reliability, but also to effectively screen a liver cancer treatment agent.
Type:
Grant
Filed:
April 27, 2017
Date of Patent:
November 23, 2021
Assignee:
THE CATHOLIC UNIVERSITY OF KOREA INDUSTRY-ACADEMIC COOPERATION FOUNDATION
Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and analyte characterization. Such polynucleotide processing may be useful for a variety of applications, including analyte characterization by polynucleotide sequencing. The compositions, methods, systems, and devices disclosed herein generally describe barcoded oligonucleotides, which can be bound to a bead, such as a gel bead, useful for characterizing one or more analytes including, for example, protein (e.g., cell surface or intracellular proteins), genomic DNA, and RNA (e.g., mRNA or CRISPR guide RNAs). Also described herein, are barcoded labelling agents and oligonucleotide molecules useful for “tagging” analytes for characterization.
Type:
Grant
Filed:
October 29, 2020
Date of Patent:
November 23, 2021
Assignee:
10X GENOMICS, INC
Inventors:
Michael Ybarra Lucero, Tarjei Sigurd Mikkelsen, Katherine Pfeiffer, Stephane Claude Boutet
Abstract: The invention is a novel method of making and using a library such as a sequencing library of single stranded circular nucleic acid templates via splint ligation.
Type:
Grant
Filed:
March 9, 2020
Date of Patent:
November 9, 2021
Assignee:
Roche Sequencing Solutions, Inc.
Inventors:
Michael George, Jenny A. Johnson, Duylinh Nguyen, Ulrich Schlecht
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:
April 22, 2021
Date of Patent:
November 2, 2021
Assignees:
Spatial Transcriptomics AB, Illumina, Inc.
Inventors:
Jonas Frisen, Patrik Stahl, Joakim Lundeberg, Gordon M. Cann, Leila Bazargan, Alex Aravanis
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:
April 14, 2021
Date of Patent:
November 2, 2021
Inventors:
Hei Mun Christina Fan, Eleen Yee Lam Shum, Janice Hoiyi Lai, Stephen P. A. Fodor