Patents Examined by Aaron A Priest
  • Patent number: 11410747
    Abstract: The invention relates to a method of estimating a nucleic acid copy number after amplification comprising the steps of providing a sample comprising nucleic acids of a to be determined number of copies; attaching variable labels to said nucleic acids; amplifying said nucleic acids with the labels with a nucleic acid duplication procedure, preferably PCR; determining amounts of amplified nucleic acid copies with a label, each amount is determined for nucleic acid copies with a different label; and providing an estimation of the nucleic acid copy number in the sample based on the determined amounts of amplified nucleic acid copies; as well as computer program products adapted for performing such methods.
    Type: Grant
    Filed: September 21, 2018
    Date of Patent: August 9, 2022
    Assignee: LEXOGEN GMBH
    Inventors: Andreas Turk, Michael Moldaschl
  • Patent number: 11408020
    Abstract: The present invention relates to methods of joining two or more double-stranded (ds) or single-stranded (ss) DNA molecules of interest in vitro, wherein the distal region of the first DNA molecule and the proximal region of the second DNA molecule of each pair share a region of sequence identity. The method allows the joining of a large number of DNA fragments, in a predetermined order and orientation, without the use of restriction enzymes. It can be used, e.g., to join synthetically produced sub-fragments of a gene or genome of interest. Kits for performing the method are also disclosed. The methods of joining DNA molecules may be used to generate combinatorial libraries useful to generate, for example, optimal protein expression through codon optimization, gene optimization, and pathway optimization.
    Type: Grant
    Filed: April 18, 2019
    Date of Patent: August 9, 2022
    Assignee: Codex DNA, Inc.
    Inventors: Daniel G. Gibson, Hamilton O. Smith, Clyde A. Hutchison, Lei Young, J. Craig Venter
  • Patent number: 11401546
    Abstract: The present invention relates to the detection of a target nucleic acid sequence by a PTOCE-E (PTO Cleavage and Extension-dependent Extension) assay. The PTOCE-E assay of the present invention can reduce the non-target signal and increase the target signal as compared with the conventional PTOCE and PCE-SH methods, thereby enabling more accurate detection of the target nucleic acid sequence.
    Type: Grant
    Filed: September 27, 2018
    Date of Patent: August 2, 2022
    Assignee: SEEGENE, INC.
    Inventors: Young Jo Lee, Han Bit Lee, Dae Young Kim
  • Patent number: 11396651
    Abstract: Methods and compositions for high-throughput, single cell analyses are provided. The methods and compositions can be used for analysis of genomes and transcriptomes, as well as antibody discovery, HLA typing, haplotyping and drug discovery.
    Type: Grant
    Filed: July 21, 2020
    Date of Patent: July 26, 2022
    Assignee: President and Fellows of Harvard College
    Inventors: George M. Church, Francois Vigneault
  • Patent number: 11384398
    Abstract: The disclosure is directed to kits and methods for amplifying and detecting human papilloma virus (HPV) of genotype 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, and/or 68 in a sample, which comprises a variety of combinations of forward oligonucleotide primers, reverse oligonucleotide primers, and oligonucleotide probes.
    Type: Grant
    Filed: December 18, 2019
    Date of Patent: July 12, 2022
    Assignee: ABBOTT MOLECULAR INC.
    Inventors: Wesley Grimm, Joshua Kostera, Robert Hillman, Hong Wang, Ning Tang, Shihai Huang, Klara Abravaya
  • Patent number: 11377688
    Abstract: This disclosure provides oligomers, combinations of oligomers, compositions, kits, uses, and methods for detecting a C1orf43 nucleic acid, such as C1orf43 mRNA, such as human C1orf43 mRNA, in a sample.
    Type: Grant
    Filed: November 15, 2018
    Date of Patent: July 5, 2022
    Assignee: Gen-Probe Incorporated
    Inventors: Siobhán M. Miick, Paul M. Darby, Jo Ann Jackson, Damon Kittredge Getman
  • Patent number: 11371084
    Abstract: Methods and systems described herein involve using long cell-free DNA fragments to analyze a biological sample from a pregnant subject. The status of methylated CpG sites and single nucleotide polymorphisms (SNPs) is often used to analyze DNA fragments of a biological sample. A CpG site and a SNP are typically separated from the nearest CpG site or SNP by hundreds or thousands of base pairs. Finding two or more consecutive CpG sites or SNPs on most cell-free DNA fragments is improbable or impossible. Cell-free DNA fragments longer than 600 bp may include multiple CpG sites and/or SNPs. The presence of multiple CpG sites and/or SNPs on long cell-free DNA fragments may allow for analysis than with short cell-free DNA fragments alone. The long cell-free DNA fragments can be used to identify a tissue of origin and/or to provide information on a fetus in a pregnant female.
    Type: Grant
    Filed: March 9, 2021
    Date of Patent: June 28, 2022
    Assignee: The Chinese University of Hong Kong
    Inventors: Yuk-Ming Dennis Lo, Rossa Wai Kwun Chiu, Kwan Chee Chan, Peiyong Jiang, Suk Hang Cheng, Cheuk Yin Yu, Yee Ting Cheung, Wenlei Peng
  • Patent number: 11359232
    Abstract: The invention relates to the amplification of specific target nucleic acids. The invention provides methods, reagents, and kits for carrying out such amplification via the autoligation chain reaction (ACR).
    Type: Grant
    Filed: October 11, 2019
    Date of Patent: June 14, 2022
    Inventor: Ricardo Mancebo
  • Patent number: 11352674
    Abstract: Provided herein is reagent mixture comprising multiplexed amplification reagents and flap assay reagents for detecting, in a single reaction, mutant copies of the KRAS gene that contain any of the 34A, 34C, 34T, 35A, 35C, 35T or 38A point mutations. Methods that employ the reagent mix and kits for performing the same are also provided.
    Type: Grant
    Filed: March 10, 2020
    Date of Patent: June 7, 2022
    Assignee: Exact Sciences Development Company, LLC
    Inventors: Rebecca Oldham-Haltom, Hatim Allawi, Hongzhi Zou, Michael J. Domanico, Graham P. Lidgard
  • Patent number: 11352622
    Abstract: Described herein are methods and compositions that provide highly efficient nucleic acid amplification. In some embodiments, this allows a 3-fold or greater increase of amplification product for each amplification cycle and therefore increased sensitivity and speed over conventional PCR. Modified bases can be employed in primers to provide this base-3 or greater amplification with satisfactory PCR cycle times, which are improved, as compared to those observed in the absence of modified bases.
    Type: Grant
    Filed: October 29, 2019
    Date of Patent: June 7, 2022
    Assignee: CEPHEID
    Inventor: Russell Higuchi
  • Patent number: 11345947
    Abstract: A microfluidic device includes a plurality of reaction wells; and a plurality of solid supports, and each of the solid supports has a reagent attached thereto. The reagent is attached to the solid support via a labile reagent/support bond such that the reagent is configured to be cleaved from the support via a cleaving operation.
    Type: Grant
    Filed: February 28, 2017
    Date of Patent: May 31, 2022
    Assignee: The University of North Carolina at Chapel Hill
    Inventors: John Michael Ramsey, William Henley, Emily Oblath
  • Patent number: 11326206
    Abstract: The present disclosure provides compositions, methods and systems for quantifying target sequences and identifying target sequence variants.
    Type: Grant
    Filed: April 6, 2017
    Date of Patent: May 10, 2022
    Assignee: PACIFIC BIOSCIENCES OF CALIFORNIA, INC.
    Inventors: Yi Zhang, Steven Brentano, Eugene Tu, Kandaswamy Vijayan
  • Patent number: 11322224
    Abstract: The present disclosure provides methods for determining the ploidy status of a chromosome in a gestating fetus from genotypic data measured from a mixed sample of DNA comprising DNA from both the mother of the fetus and from the fetus, and optionally from genotypic data from the mother and father. The ploidy state is determined by using a joint distribution model to create a plurality of expected allele distributions for different possible fetal ploidy states given the parental genotypic data, and comparing the expected allelic distributions to the pattern of measured allelic distributions measured in the mixed sample, and choosing the ploidy state whose expected allelic distribution pattern most closely matches the observed allelic distribution pattern. The mixed sample of DNA may be preferentially enriched at a plurality of polymorphic loci in a way that minimizes the allelic bias, for example using massively multiplexed targeted PCR.
    Type: Grant
    Filed: November 4, 2014
    Date of Patent: May 3, 2022
    Assignee: Natera, Inc.
    Inventors: Matthew Rabinowitz, George Gemelos, Milena Banjevic, Allison Ryan, Zachary Demko, Matthew Hill, Bernhard Zimmermann, Johan Baner
  • Patent number: 11319581
    Abstract: The present invention relates to improved methods for epigenetic blood and immune cell counting, and respective uses and kits.
    Type: Grant
    Filed: February 8, 2018
    Date of Patent: May 3, 2022
    Assignee: Precision for Medicine GmbH
    Inventor: Sven Olek
  • Patent number: 11306365
    Abstract: The present invention provides a molecular marker C42257 for rapidly identifying genetic sex of Marsupenaeus japonicus and applications thereof. The nucleotide sequence of the molecular marker C42257 is shown in SEQ ID NO:1. The nucleotide sequences of the primer pair of molecular marker C42257 used for detection are C42257F: GGGGGACAA ACAGAGACA (SEQ ID NO: 2) and C42257R: ATCGGGGTGGATTTAGAA (SEQ ID NO: 3), respectively. The molecular marker C42257 is not affected by the tissue specificity of M. japonicus and the environment, and the steps are simple and the results are obvious. The genomic DNA of M. japonicus and the primer pair are subjected to PCR reaction and electrophoresis detection. If a target band appears at 183 bp, it is a female M. japonicus. The molecular marker can also promote the establishment of the seedling breeding technology of all-female or high-female-ratio M. japonicus. Therefore, it has a broad application prospect.
    Type: Grant
    Filed: September 2, 2021
    Date of Patent: April 19, 2022
    Assignee: Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences
    Inventors: Xianyun Ren, Jianjian Lv, Weikang Lan, Ling Jin, Ping Liu, Jian Li
  • Patent number: 11306357
    Abstract: The present disclosure provides methods for determining the ploidy status of a chromosome in a gestating fetus from genotypic data measured from a sample of DNA from the mother of the fetus and from the fetus, and from genotypic data from the mother and optionally also from the father. The ploidy state is determined by using a joint distribution model to create a set of expected allele distributions for different possible fetal ploidy states given the parental genotypic data, and comparing the expected allelic distributions to the pattern of measured allelic distributions measured in the mixed sample, and choosing the ploidy state whose expected allelic distribution pattern most closely matches the observed allelic distribution pattern. In an embodiment, the mixed sample of DNA may be preferentially enriched at a plurality of polymorphic loci in a way that minimizes the allelic bias.
    Type: Grant
    Filed: February 12, 2014
    Date of Patent: April 19, 2022
    Assignee: Natera, Inc.
    Inventors: Matthew Rabinowitz, George Gemelos, Milena Banjevic, Allison Ryan, Zachary Demko, Matthew Hill, Bernhard Zimmerman, Johan Baner
  • Patent number: 11306349
    Abstract: The present invention relates to the detection of a target nucleic acid sequence by a PTOCE (PTO Cleavage and Extension) assay. The present invention detects a target nucleic acid sequence in which the PTO (Probing and Tagging Oligonucleotide) hybridized with the target nucleic acid sequence is cleaved to release a fragment and the fragment is hybridized with the CTO (Capturing and Templating Oligonucleotide) to form an extended duplex, followed by detecting the presence of the extended duplex. The extended duplex provides signals (generation, increase, extinguishment or decrease of signals) from labels indicating the presence of the extended duplex and has adjustable Tm value, which are well adoptable for detection of the presence of the target nucleic acid sequence.
    Type: Grant
    Filed: December 2, 2019
    Date of Patent: April 19, 2022
    Assignee: SEEGENE, INC.
    Inventors: Jong Yoon Chun, Young Jo Lee
  • Patent number: 11306348
    Abstract: The present disclosure relates to methods, compositions, and kits for generating a library of tagged nucleic acid fragments without using PCR amplification, including methods and compositions for fragmenting and tagging nucleic acids (e.g., DNA) using transposome complexes immobilized on solid support.
    Type: Grant
    Filed: May 3, 2021
    Date of Patent: April 19, 2022
    Assignee: Illumina Cambridge Limited
    Inventors: Andrew Slatter, Esther Musgrave-Brown, Susan C. Verity, Niall Anthony Gormley
  • Patent number: 11299770
    Abstract: A method for analyzing planar sample is provided. In some cases the method comprises: (a) incubating the planar sample with a capture agent that is linked to an oligonucleotide, wherein the capture agent specifically binds to complementary sites in the planar sample; (b) reading a fluorescent signal caused by extension of a primer that is hybridized to the oligonucleotide, using fluorescence microscopy. Several implementations of the method, and multiplexed versions of the same, are also provided.
    Type: Grant
    Filed: January 4, 2019
    Date of Patent: April 12, 2022
    Assignee: THE BOARD OF TRUSTEES OF THE LELAND STANFORD JUNIOR UNIVERSITY
    Inventors: Nikolay Samusik, Garry P. Nolan, Yury Goltsev
  • Patent number: 11299766
    Abstract: Provided herein is technology relating to the amplification-based detection of bisulfite-treated DNAs and particularly, but not exclusively, to methods and compositions for multiplex amplification of low-level sample DNA prior to further characterization of the sample DNA. The technology further provides methods for isolating DNA from blood or blood product samples, e.g., plasma samples.
    Type: Grant
    Filed: May 29, 2020
    Date of Patent: April 12, 2022
    Assignee: Exact Sciences Corporation
    Inventors: Graham P. Lidgard, Hatim Allawi