Patents Examined by Kenneth R. Horlick
  • Patent number: 11021758
    Abstract: Described herein are methods, compositions and kits directed to the detection of gene dysregulations such as those arising from gene fusions and/or chromosomal abnormalities, e.g., translocations, insertions, inversions and deletions. Samples containing dysregulated gene(s) of interest may show independent expression patterns for the 5? and 3? regions of the gene. The methods, compositions and kits are useful for detecting mutations that cause the differential expression of a 5? portion of a target gene relative to the 3? region of the target gene.
    Type: Grant
    Filed: December 9, 2019
    Date of Patent: June 1, 2021
    Assignee: Quest Diagnostics Investments LLC
    Inventors: Heather R. Sanders, Maher Albitar, Aurelia Meloni-Ehrig
  • Patent number: 11021744
    Abstract: Methods, devices, and kits are provided for performing PCR in <20 seconds per cycle, with improved efficiency and yield.
    Type: Grant
    Filed: November 2, 2018
    Date of Patent: June 1, 2021
    Assignee: University of Utah Research Foundation
    Inventors: Carl T. Wittwer, Jared Steven Farrar
  • Patent number: 11021738
    Abstract: A method of maintaining contiguity in chromosomal DNA following treatment with a tagmentase. Conditions are selected such that the tagmentase does not release from the DNA, and thus forms a bridge linking DNA segments that have the same relationship (haplotype) as occurred in the genomic DNA. Thus the tagmentase step can occur in bulk (before partitions are formed). The resulting tagmentase-bridged DNA segments can be added to partitions maintaining the bridged segments until they are introduced into different partitions. Once in partitions, the contiguous DNA segments can be barcoded with a partition-specific barcode, thereby allowing for later identification of contiguous DNA after sequencing in bulk (after partitions contents are merged).
    Type: Grant
    Filed: December 19, 2017
    Date of Patent: June 1, 2021
    Assignee: Bio-Rad Laboratories, Inc.
    Inventors: Ronald Lebofsky, Jeremy Agresti
  • Patent number: 11015187
    Abstract: The present disclosure relates to systems and methods for purifying nucleic acid. In particular, the present disclosure relates to systems and methods for purifying nucleic acids using metal or metal oxide compositions.
    Type: Grant
    Filed: November 22, 2019
    Date of Patent: May 25, 2021
    Assignee: ABBOTT MOLECULAR INC.
    Inventor: Gerard J. Gundling
  • Patent number: 11001837
    Abstract: The present invention provides a low-frequency mutation enrichment sequencing method for free target DNA in plasma, comprising plasma DNA extraction and library construction, general library TT COLD PCR amplification enrichment, probe enrichment capture, PCR and sequencing of captured products, and positive and negatice double-strand error-correction low-frequency information analysis.
    Type: Grant
    Filed: February 18, 2016
    Date of Patent: May 11, 2021
    Assignee: Geneplus—Beijing
    Inventors: Xiaoxing Lv, Xin Yi, Meiru Zhao, Yanfang Guan, Tao Liu, Ling Yang
  • Patent number: 11001899
    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: January 19, 2021
    Date of Patent: May 11, 2021
    Assignee: GUARDANT HEALTH, INC.
    Inventor: AmirAli Talasaz
  • Patent number: 11001896
    Abstract: The disclosed embodiments generally relate to a method and system to synthesize a target molecule within a droplet. In an exemplary embodiment, a first microfluidic device configured to contact a polynucleotide-containing component from a sample with lysis reagents to form a first droplet. The lysis reagents include an enzyme having protease activity. The first droplet is encapsulated with an immiscible carrier fluid. A collection reservoir is provided to receive and incubate the first droplet for a first duration of time. The first duration of time is sufficient to inactivate the enzyme of the lysis reagent. A second microfluidic device is provided to receive the first droplet and add nucleic acid synthesis reagent to thereby form a second nucleic acid synthesis droplet in the immiscible carrier fluid. Finally, a reaction chamber is provided to synthesize the target polynucleotide within the second nucleic acid synthesis droplet.
    Type: Grant
    Filed: April 11, 2019
    Date of Patent: May 11, 2021
    Assignee: The Regents of the University of California
    Inventors: Adam R. Abate, Dennis Jay Eastburn, Adam R. Sciambi
  • Patent number: 11001874
    Abstract: Methods of detecting aneuploidy in in vitro fertilized embryos are provided. A unique set of STR markers that can be rapidly and accurately quantified by multiplex PCR at the single cell level are used to analyze and select euploid embryos in an in vitro fertilization (IVF) setting. The markers include D13S284, D13S141, D18S54, D18S70, D21S266, D21S1951 and AMXY and are used to detect abnormalities in chromosomes 13, 18, 21 and the XY chromosomes.
    Type: Grant
    Filed: August 12, 2020
    Date of Patent: May 11, 2021
    Assignee: King Abdulaziz University
    Inventors: Aisha Elaimi, Ashraf Dallol, Adeel Chaudhary, Adel Abuzinadah, Muhammad Hussain Al-Qahtani
  • Patent number: 10995376
    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: January 11, 2021
    Date of Patent: May 4, 2021
    Assignee: GUARDANT HEALTH, INC.
    Inventor: AmirAli Talasaz
  • Patent number: 10988802
    Abstract: Methods are provided herein for identifying rare and/or unknown DNA sequences by next-generation sequencing approaches. Isolated double-stranded (ds), single-stranded (ss), or ds/ss DNA is fragmented and the fragments are polished, phosphorylated, and tailed, as necessary. Fragmentation can be enzymatic or mechanical. A universal adapter sequence is ligated to each fragment, wherein the adapter can have a top strand without a 5? phosphate, a 3? with an —H in place of the —OH, and/or a 3? extra base complementary to any base added to the polished fragments. The ligatamers may then serve as templates for amplification using a forward primer complementary to the adapter sequence and a reverse primer targeted to the fragment sequence. Compositions produced by these methods and kits adapted for performing these methods are also described herein.
    Type: Grant
    Filed: May 20, 2016
    Date of Patent: April 27, 2021
    Assignee: Sigma-Aldrich Co. LLC
    Inventor: Brian Ward
  • Patent number: 10988800
    Abstract: A PCR reaction vessel includes: a substrate; a channel formed on the substrate; a pair of filters, a first filter and a second filter, provided at respective ends of the channel; a pair of air communication ports, a first air communication port and a second air communication port, that communicate with the channel through the first filter and the second filter; a thermal cycle region formed between the first filter and the second filter in the channel; a branch point formed between the first filter and the second filter in the channel; a branched channel whose one end is connected to the branch point; and a sample introduction port formed at the other end of the branched channel.
    Type: Grant
    Filed: May 31, 2018
    Date of Patent: April 27, 2021
    Assignees: Nippon Sheet Glass Company, Limited, NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY, Go!Foton, Inc.
    Inventors: Takashi Fukuzawa, Hidenori Nagai, Naofumi Nishizawa
  • Patent number: 10982253
    Abstract: The present application is directed to biosensors and methods for detecting a microorganism target in a sample using a mechanically interlocked nucleic acid catanane, wherein an enzyme from the microorganism target or that is activated by a molecule from the microorganism target cleaves a linkage in a first single-stranded nucleic acid ring of the catanane structure, allowing rolling-circle amplification to occur and the presence of rolling-circle amplification products indicates the presence of the microorganism in the sample.
    Type: Grant
    Filed: December 12, 2016
    Date of Patent: April 20, 2021
    Assignee: McMaster University
    Inventors: Yingfu Li, John Brennan, Meng Liu
  • Patent number: 10968476
    Abstract: A workflow for direct qPCR quantification of unprocessed forensic casework samples is disclosed herein. 13pg of DNA has been detected by direct amplification from a paper substrate. Direct qPCR quantification of unprocessed forensic casework samples and direct STR amplification of unprocessed forensic casework samples collected on the same PE-swab will greatly increase forensic laboratory's efficiency and capability.
    Type: Grant
    Filed: May 3, 2019
    Date of Patent: April 6, 2021
    Assignee: LIFE TECHNOLOGIES CORPORATION
    Inventor: Jason Yingjie Liu
  • Patent number: 10968443
    Abstract: The disclosure provides methods for isolating nucleic acids from a biological fluid. In one aspect, the disclosure provides a method for isolating RNA. In another aspect, the disclosure provides a method for isolating DNA. In one aspect, the methods described herein utilize a protocol that combines a detergent-based initial denaturation, protease digestion, and organic extraction followed by column purification that maximizes RNA/DNA yield and preserves RNA/DNA integrity. In yet another aspect, the disclosure provides a kit for isolating RNA and/or DNA.
    Type: Grant
    Filed: December 31, 2015
    Date of Patent: April 6, 2021
    Assignee: THE ROCKEFELLER UNIVERSITY
    Inventors: Klaas Max, Karl Bertram, Kemal Akat, Thomas H. Tuschl, Jenny Li, Kimberly Bogardus
  • Patent number: 10961592
    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: December 10, 2019
    Date of Patent: March 30, 2021
    Assignee: GUARDANT HEALTH, INC.
    Inventor: AmirAli Talasaz
  • Patent number: 10947584
    Abstract: This disclosure describes related novel methods for Recombinase-Polymerase Amplification (RPA) of a target DNA that exploit the properties of recombinase and related proteins, to invade double-stranded DNA with single stranded homologous DNA permitting sequence specific priming of DNA polymerase reactions. The disclosed methods have the advantage of not requiring thermocycling or thermophilic enzymes, thus offering easy and affordable implementation and portability relative to other amplification methods. Further disclosed are conditions to enable real-time monitoring of RPA reactions, methods to regulate RPA reactions using light and otherwise, methods to determine the nature of amplified species without a need for gel electrophoresis, methods to improve and optimize signal to noise ratios in RPA reactions, methods to optimize oligonucleotide primer function, methods to control carry-over contamination, and methods to employ sequence-specific third ‘specificity’ probes.
    Type: Grant
    Filed: June 14, 2019
    Date of Patent: March 16, 2021
    Assignee: ABBOTT DIAGNOSTICS SCARBOROUGH, INC.
    Inventors: Olaf Piepenburg, Colin H. Williams, Niall A. Armes, Derek L. Stemple
  • Patent number: 10947600
    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: October 12, 2020
    Date of Patent: March 16, 2021
    Assignee: GUARDANT HEALTH, INC.
    Inventor: AmirAli Talasaz
  • Patent number: 10941436
    Abstract: Methods for the high-throughput analysis of transgenic events are herein disclosed. The methods use libraries of sheared genomic DNA ligated to specialized adapters and pooled for sequence analysis and comparison to known genomic and insert sequence. The method finds use in detecting characterizing insertion site, transgene integrity, and transgene copy number.
    Type: Grant
    Filed: October 10, 2019
    Date of Patent: March 9, 2021
    Inventors: Mary Beatty, Kevin Hayes, Jenna Hoffman, Haining Lin, Gina Marie Zastrow-Hayes
  • Patent number: 10934596
    Abstract: A method for automated microbial detection includes collecting air particles into a solid-state sampler, the air particles including microbes, charging the air particles using a plasma field generated by propulsion electrodes, focusing the charged air particles toward a sample well of a microfluidic testing cartridge, tagging the charged air particles with a fluorescence marker, and detecting a quantity of the microbes using a fluorescence detector.
    Type: Grant
    Filed: April 10, 2018
    Date of Patent: March 2, 2021
    Assignee: UChicago Argonne, LLC
    Inventors: Jack Gilbert, Charles Catlett, Peter Beckman
  • Patent number: 10894980
    Abstract: Methods are provided for nucleic acid amplification including contacting a double stranded nucleic acid with transposases bound to transposon DNA, wherein the transposon DNA includes a transposase binding site and an RNA polymerase promoter sequence, wherein the transposases/transposon DNA complex bind to target locations along the double stranded nucleic acid and cleave the double stranded nucleic acid into a plurality of double stranded fragments, with each double stranded fragment having the transposon DNA bound to each 5? end of the double stranded fragment, extending the double stranded fragments along the transposon DNA to make double stranded extension products having double stranded RNA polymerase promoter sequences at each end, contacting the double stranded extension products with an RNA polymerase to make a plurality of RNA transcripts of each double stranded extension product, reverse transcribing the RNA transcripts into single stranded copy DNA, forming complementary strands to the single strand
    Type: Grant
    Filed: July 15, 2016
    Date of Patent: January 19, 2021
    Assignee: President and Fellows of Harvard College
    Inventors: Chongyi Chen, Dong Xing, Xiaoliang Sunney Xie