Identifying A Library Member By Means Of A Tag, Label, Or Other Readable Or Detectable Entity Associated With The Library Member (e.g., Decoding Process, Etc.) Patents (Class 506/4)
  • Patent number: 10845308
    Abstract: An integrated circuit includes a photodetection region configured to receive incident photons. The photodetection region is configured to produce a plurality of charge carriers in response to the incident photons. The integrated circuit includes at least one charge carrier storage region. The integrated circuit also includes a charge carrier segregation structure configured to selectively direct charge carriers of the plurality of charge carriers directly into the at least one charge carrier storage region based upon times at which the charge carriers are produced.
    Type: Grant
    Filed: December 22, 2017
    Date of Patent: November 24, 2020
    Assignee: Quantum-Si Incorporated
    Inventors: Jonathan M. Rothberg, Keith G. Fife, David Boisvert
  • Patent number: 10832795
    Abstract: A method and apparatus for simultaneously determining multiple different biological molecule types in a sample include labeling each different biological molecule type in a biological sample with a unique combination of a plurality of labels. Each different biological molecule type is selected from a population of M different biological molecules types. The plurality of labels is selected from a population of L different labels; and, M is greater than L. Measurements are obtained of relative abundances of the L different labels in the sample. Relative abundance of up to M different biological molecule types in the sample are determined based on the measurements and a method of compressed sensing.
    Type: Grant
    Filed: March 22, 2017
    Date of Patent: November 10, 2020
    Assignee: THE BOARD OF TRUSTEES OF THE LELAND STANFORD JUNIOR UNIVERSITY
    Inventors: Karen Sachs, Mohammed N. AlQuraishi, Solomon Itani, Garry P. Nolan, Sean C. Bendall, Tyler J. Burns
  • Patent number: 10813935
    Abstract: Disclosed herein are compositions and methods for treating cancer. Further provided herein are compositions and methods for reducing, inhibiting, or preventing resistance of cancer to tyrosine kinase inhibitors. The methods may include administering an anti-resistance agent such as a CYP51A1 inhibitor or an agonist of miRNA-764 (SEQ ID NO: 4) to a subject. A tyrosine kinase inhibitor may also be administered to the subject in addition to the anti-resistance agent.
    Type: Grant
    Filed: February 23, 2018
    Date of Patent: October 27, 2020
    Assignees: TRANSGENEX NANOBIOTECH, INC., University of South Florida
    Inventors: Subhra Mohapatra, Shyam S. Mohapatra, Mark Howell, Rajesh Nair
  • Patent number: 10815523
    Abstract: The invention pertains to an assay that is capable of detecting a mutant polynucleotide in a plurality of polynucleotides. In one embodiment, the assay of the invention is capable of detecting one copy of a mutant polynucleotide in about 50,000 to about 100,000 copies of polynucleotides. The assay of the invention can be used to identify a mutant viral quasispecies or a mutant mRNA encoding an oncogenic protein from a tumor sample. The assay of the invention involves producing the single stranded complements of each of a plurality of polynucleotides containing the target sequence, wherein each of the single stranded complements contain a unique tag sequence and amplifying the single stranded complements by PCR using several sets of primers designed to introduce the sequences appropriate for a paired-end sequencing analysis of the amplified polynucleotides. The invention also pertains to kits for carrying out the assays of the invention.
    Type: Grant
    Filed: December 23, 2016
    Date of Patent: October 27, 2020
    Assignee: UNIVERSITY OF FLORIDA RESEARCH FOUNDATION, INCORPORATED
    Inventors: Gary P. Wang, Chak Kar (Eric) Li, Lin Liu
  • Patent number: 10774367
    Abstract: Presented are methods and compositions for preparing samples for amplification and sequencing. Particular embodiments relate to methods of preparing nucleic acid-containing cellular samples for library amplification, wherein the methods include providing nucleic acid containing-cellular samples from blood or FFPE samples, lysing cells of the sample to liberate nucleic acids, and performing tagmentation without purifying the liberated nucleic acids.
    Type: Grant
    Filed: October 17, 2018
    Date of Patent: September 15, 2020
    Assignee: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Louise Fraser, Paula Kokko-Gonzales, Andrew Slatter
  • Patent number: 10767223
    Abstract: Aspects of the present invention include analyzing nucleic acids from single cells using methods that include using tagged polynucleotides containing multiplex identifier sequences.
    Type: Grant
    Filed: May 12, 2020
    Date of Patent: September 8, 2020
    Assignee: 10X Genomics, Inc.
    Inventors: Sydney Brenner, Gi Mikawa, Robert Osborne, Andrew Slatter
  • Patent number: 10746742
    Abstract: Disclosed herein are methods of high-throughput mapping of viral neutralizing antibody epitopes. Also disclosed are in vitro immunoprecipitation-based adenoassociated virus Barcode-Seq-based methods of mapping viral neutralizing antibody epitopes. In some embodiments, a method of high-throughput mapping of viral NtAb conformational epitopes can be utilized, which may comprise HP scanning of mutant viral libraries, immunoprecipitation (IP), and/or next-generation sequencing (NGS) technology. In some embodiments, a method of identifying one or more dominant epitopes in a viral vector may comprise contacting a mutant capsid of a virus with serum from a subject previously exposed to the virus and immunopredpitating serum immunoglobulins from the serum. In various embodiments, the viral vector may be an AAV vector.
    Type: Grant
    Filed: April 24, 2015
    Date of Patent: August 18, 2020
    Assignee: OREGON HEALTH & SCIENCE UNIVERSITY
    Inventors: Hiroyuki Nakai, Kei Adachi
  • Patent number: 10738352
    Abstract: The present invention relates to a method of analyzing a composition of nucleic acids derived from a single cell using a microplate including a plurality of reaction wells, the microplate having one bead arranged in one reaction well, the one bead having bound thereto a plurality of molecules of single-stranded oligonucleotides, the single-stranded oligonucleotides each having a nucleic acid capture sequence exposed at the 3? end and a barcode sequence on the 5? side of the nucleic acid capture sequence, the barcode sequence including a base sequence that differs from bead to bead.
    Type: Grant
    Filed: April 7, 2015
    Date of Patent: August 11, 2020
    Assignee: IDAC THERANOSTICS, INC.
    Inventors: Shin-ichi Hashimoto, Shuichi Kaneko, Kouji Matsushima
  • Patent number: 10718011
    Abstract: This invention provides methods of using labeled primers or probes for nucleic acid target detection and to detect the identity or presence of a nucleotide at certain positions in nucleic acid sequences with single molecule sensitivity using nanopore detection, and sets of oligonucleotide primers for use in such methods, as well as methods of quantitative PCR coupled with nanopore detection.
    Type: Grant
    Filed: February 12, 2015
    Date of Patent: July 21, 2020
    Assignee: The Trustees of Columbia University in the City of New York
    Inventors: Chuanjuan Tao, Shiv Kumar, Minchen Chien, Jingyue Ju
  • Patent number: 10711269
    Abstract: A method for making an asymmetrically-tagged sequencing library is provided. In some embodiments, the method may comprise: obtaining a symmetrically-tagged library of cDNA or genomic DNA fragments, hybridizing a tailed first primer to the 3? sequence tag of the library and extending the same to produce primer extension products, and amplifying the primer extension products using a pair of tailed primers to produce asymmetrically-tagged library.
    Type: Grant
    Filed: January 18, 2017
    Date of Patent: July 14, 2020
    Assignee: Agilent Technologies, Inc.
    Inventors: Brian Jon Peter, David Taussig, Bahram Arezi, Robert A. Ach, Nicholas M. Sampas
  • Patent number: 10697013
    Abstract: Aspects of the present invention include analyzing nucleic acids from single cells using methods that include using tagged polynucleotides containing multiplex identifier sequences.
    Type: Grant
    Filed: March 12, 2020
    Date of Patent: June 30, 2020
    Assignee: 10X Genomics, Inc.
    Inventors: Sydney Brenner, Gi Mikawa, Robert Osborne, Andrew Slatter
  • Patent number: 10683536
    Abstract: The invention provides improved methods for synthesizing polynucleotides, such as DNA and RNA, using renewable initiators coupled to a solid support. Using the methods of the invention, specific sequences of polynucleotides can be synthesized de novo, base by base, in an aqueous environment, without the use of a nucleic acid template.
    Type: Grant
    Filed: August 18, 2015
    Date of Patent: June 16, 2020
    Assignee: Molecular Assemblies, Inc.
    Inventor: J. William Efcavitch
  • Patent number: 10670578
    Abstract: Improved resolution and detection of nanoparticles are achieved when a nanopore connecting liquid compartments in a device running on the Coulter principle is provided with fluid coatings such as lipid walls. Fluid lipid walls are made of a lipid bilayer, and preferably include lipid anchored mobile ligands as part of the lipid bilayer. By varying the nature and concentration of the mobile ligand in the lipid bilayer, multifunctional coatings of lipids are provided.
    Type: Grant
    Filed: April 8, 2019
    Date of Patent: June 2, 2020
    Assignee: THE REGENTS OF THE UNIVERSITY OF MICHIGAN
    Inventors: Michael Mayer, Erik Yusko, Jerry Yang
  • Patent number: 10605733
    Abstract: The present disclosure relates to systems and methods for cellular imaging and identification through the use of a light sheet flow cytometer. In one implementation, a light sheet flow cytometer may include a light source configured to emit light having one or more wavelengths, at least one optical element configured to form a light sheet from the emitted light, a microfluidic channel configured to hold a sample, and an imaging device. The imaging device may be adapted to forming 3-D images of the sample such that identification tags attached to the sample are visible.
    Type: Grant
    Filed: December 6, 2017
    Date of Patent: March 31, 2020
    Assignee: Verily Life Sciences LLC
    Inventors: Cheng-Hsun Wu, Brian M. Rabkin, Supriyo Sinha, John D. Perreault, Chinmay Belthangady, James Higbie, Seung Ah Lee
  • Patent number: 10601852
    Abstract: Provided is an information processing device that includes a processor and has a capability to detect abnormalities on an in-vehicle network that may be caused by an attack. The processor receives input of data elements to be used as training data, normalizes the training data so as to be distributed within a first region, divides a multi-dimensional second region that encompasses the first region into third regions that are hypercubes of equal sizes, obtains S data elements that are contained by each of the third regions, and for each third region that includes a number of data elements that is less than a first threshold value T, adds noise elements that are vectors with a uniform distribution to the third regions, generates noise-added training data including the vectors in the second region, and generates and outputs Isolation Forest learning model data by using the generated noise-added training data.
    Type: Grant
    Filed: January 24, 2019
    Date of Patent: March 24, 2020
    Assignee: PANASONIC INTELLECTUAL PROPERTY CORPORATION OF AMERICA
    Inventors: Ryota Takahashi, Takamitsu Sasaki
  • Patent number: 10519035
    Abstract: The invention provides a method to form and functionalize monolayers on a silicon-rich silicon nitride surface or a silicon surface formed by a nanopore fabrication method known as dielectric breakdown. Thermal, photochemical and radical processing can be used to hydrosilylate nascent silicon and silicon nitride surfaces with various reagents. The conventional need for hydrofluoric acid etching prior to coupling functional groups to the surfaces is thereby completely avoided.
    Type: Grant
    Filed: February 20, 2018
    Date of Patent: December 31, 2019
    Assignee: Rhode Island Council On Postsecondary Education
    Inventors: Jason R. Dwyer, Y. M. Nuwan D. Y. Bandara, Buddini Iroshika Karawdeniya, Julie C. Whelan
  • Patent number: 10519499
    Abstract: The disclosure provides detection apparatus having one or more nanopores, methods for making apparatus having one or more nanopore and methods for using apparatus having one or more nanopores. Uses include, but are not limited to detection and sequencing of nucleic acids.
    Type: Grant
    Filed: July 29, 2015
    Date of Patent: December 31, 2019
    Assignee: Illumina, Inc.
    Inventors: Boyan Boyanov, Jeffrey G Mandell, Kevin L Gunderson, Jingwei Bai, Liangliang Qiang, Bradley Baas
  • Patent number: 10486153
    Abstract: The present disclosure provides flow cells and methods of fabricating flow cells. The method includes combining three portions: a first substrate, a second substrate, and microfluidic channels between the first substrate and the second substrate having walls of a photoresist dry film. Through-holes for inlet and outlet are formed in the first substrate or the second substrate. Patterned capture sites are stamped on the first substrate and the second substrate by a nanoimprint lithography process. In other embodiments, parts of the patterned capture sites are selectively attached to a surface chemistry pattern formed of silicon oxide islands each disposed on an outcrop of a soft bottom layer.
    Type: Grant
    Filed: May 23, 2017
    Date of Patent: November 26, 2019
    Assignee: ILLUMINA, INC.
    Inventors: Shang-Ying Tsai, Li-Min Hung, Jung-Huei Peng
  • Patent number: 10487345
    Abstract: Novel methods that may be used for the manufacture of plant alkaloid compounds and novel polynucleotide compounds are provided. The plant alkaloid compounds are useful as medicinal compounds.
    Type: Grant
    Filed: April 27, 2015
    Date of Patent: November 26, 2019
    Assignee: Epimeron Inc.
    Inventor: Peter James Facchini
  • Patent number: 10480028
    Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing.
    Type: Grant
    Filed: December 19, 2017
    Date of Patent: November 19, 2019
    Assignee: 10X GENOMICS, INC.
    Inventors: Benjamin Hindson, Christopher Hindson, Michael Schnall-Levin, Kevin Ness, Mirna Jarosz, Serge Saxonov
  • Patent number: 10358731
    Abstract: This invention relates to a metal catalyst, a manufacturing method of the metal catalyst, and an electrochemical reduction method. The metal catalyst is manufactured by a method comprising providing a conductor to one side of an insulator, providing a fluid including a metal ion and an electron mediator to the other side of the insulator and providing a voltage to the conductor. The electrochemical reduction method comprises providing a conductor to one side of an insulator, providing a fluid including reduction material and an electron mediator to the other side of the insulator and providing a voltage to the conductor.
    Type: Grant
    Filed: November 23, 2016
    Date of Patent: July 23, 2019
    Assignee: Seoul National University R&DB Foundation
    Inventors: Taekdong Chung, Jinyoung Lee
  • Patent number: 10295551
    Abstract: Identification and use of proteins fluorescently labeled and that undergo a change in fluorescence index upon binding bilirubin are described. Probes are disclosed which are labeled at a cysteine or lysine residue and also probes labeled at both cysteine and lysine with two different fluorophores. These probes are useful for determination of unbound bilirubin levels in a fluid sample.
    Type: Grant
    Filed: November 17, 2016
    Date of Patent: May 21, 2019
    Assignee: Alan Marc Kleinfeld
    Inventor: Alan Marc Kleinfeld
  • Patent number: 10266876
    Abstract: Methods and systems are provided for creating molecular barcodes or indicia for cellular constituents within single cells and for resolving such barcodes or indicia with super-resolution technologies such as super-resolution microscopy. By this approach, numerous molecular species that can be measured simultaneously in single cells. It has been demonstrated that multiple mRNA transcripts can be labeled with a spatially ordered sequence of fluorophores, and that barcodes can be resolved. In addition, alternative splicing events can be characterized by identifying and quantifying mRNA isoforms in an individual cell.
    Type: Grant
    Filed: December 21, 2012
    Date of Patent: April 23, 2019
    Assignee: CALIFORNIA INSTITUTE OF TECHNOLOGY
    Inventors: Long Cai, Eric Lubeck
  • Patent number: 10253364
    Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing.
    Type: Grant
    Filed: May 15, 2018
    Date of Patent: April 9, 2019
    Assignee: 10X GENOMICS, INC.
    Inventors: Benjamin Hindson, Christopher Hindson, Michael Schnall-Levin, Kevin Ness, Mima Jarosz, Serge Saxonov, Paul Hardenbol, Rajiv Bharadwaj, Xinying Zheng, Phillip Belgrader
  • Patent number: 10240197
    Abstract: Aspects of the present invention include analyzing nucleic acids from single cells using methods that include using tagged polynucleotides containing multiplex identifier sequences.
    Type: Grant
    Filed: November 16, 2018
    Date of Patent: March 26, 2019
    Assignee: 10X GENOMICS, INC.
    Inventors: Sydney Brenner, Gi Mikawa, Robert Osborne, Andrew Slatter
  • Patent number: 10155980
    Abstract: In some aspects, the present disclosure provides methods for identifying sequence variants in a nucleic acid sample. In some embodiments, a method comprises identifying sequence differences between sequencing reads and a reference sequence, and calling a sequence difference that occurs in at least two different circular polynucleotides, such as two circular polynucleotides having different junctions, or two different sheared polynucleotides as the sequence variant. In some aspects, the present disclosure provides compositions and systems useful in the described methods.
    Type: Grant
    Filed: November 1, 2017
    Date of Patent: December 18, 2018
    Assignee: ACCURAGEN HOLDINGS LIMITED
    Inventors: Li Weng, Zhaohui Sun, Shengrong Lin
  • Patent number: 10155981
    Abstract: Aspects of the present invention include analyzing nucleic acids from single cells using methods that include using tagged polynucleotides containing multiplex identifier sequences.
    Type: Grant
    Filed: August 15, 2017
    Date of Patent: December 18, 2018
    Assignee: 10X GENOMICS, INC.
    Inventors: Sydney Brenner, Gi Mikawa, Robert Osborne, Andrew Slatter
  • Patent number: 10150995
    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: July 24, 2018
    Date of Patent: December 11, 2018
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Paul Giresi, Jason D. Buenrostro, Howard Y. Chang, William J. Greenleaf
  • Patent number: 10106789
    Abstract: Methods and systems are provided for massively parallel genetic analysis of single cells in emulsion droplets or reaction containers. Genetic loci of interest are targeted in a single cell using a set of probes, and a fusion complex is formed by molecular linkage and amplification techniques. Methods are provided for high-throughput, massively parallel analysis of the fusion complex in a single cell in a population of at least 10,000 cells. Also provided are methods for tracing genetic information back to a cell using barcode sequences.
    Type: Grant
    Filed: February 13, 2017
    Date of Patent: October 23, 2018
    Assignee: GigaGen, Inc.
    Inventors: David Scott Johnson, Everett Hurteau Meyer
  • Patent number: 10011871
    Abstract: The present disclosure provides compositions and methods for accurately detecting mutations by uniquely tagging double stranded nucleic acid molecules with dual cyphers such that sequence data obtained from a sense strand can be linked to sequence data obtained from an anti-sense strand when sequenced, for example, by massively parallel sequencing methods.
    Type: Grant
    Filed: February 15, 2013
    Date of Patent: July 3, 2018
    Assignee: Fred Hutchinson Cancer Research Center
    Inventor: Jason H. Bielas
  • Patent number: 9938578
    Abstract: The present disclosure generally pertains to a multiplex method for analyzing samples comprising using polynucleotide amplification to produce amplified products wherein one or more target sequences are tagged with a non-interfering, non-canceling target-specific polynucleotide identification tag, pyrosequencing the amplified products through the non-canceling target-specific polynucleotide identification tag sequence to detect the presence of one or more specific polynucleotide identification tags. The presence of a specific polynucleotide identification tag being correlated with the presence of a specific target sequence.
    Type: Grant
    Filed: September 24, 2013
    Date of Patent: April 10, 2018
    Assignee: iRepertoire, Inc.
    Inventors: Jian Han, Chunlin Wang
  • Patent number: 9897532
    Abstract: A system is disclosed that enables the automated measurement of cellular mechanical parameters at high throughputs. The microfluidic device uses intersecting flows to create an extensional flow region where the cells undergo controlled stretching. Cells are focused into streamlines prior to entering the extensional flow region. In the extensional region, each cell's deformation is measured with an imaging device. Automated image analysis extracts a range of independent biomechanical parameters from the images. These may include cell size, deformability, and circularity. The single cell data that is obtained may then be used to in a variety of ways. Scatter density plots of deformability and circularity may be developed and displayed for the user. Mechanical parameters such as deformability and circularity may be gated or thresholded to identify certain cells of interest or sub-populations of interest. Similarly, the mechanical data obtained using the device may be used as cell signatures.
    Type: Grant
    Filed: November 24, 2014
    Date of Patent: February 20, 2018
    Assignee: THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
    Inventors: Dino Di Carlo, Daniel R. Gossett, Henry T. K. Tse
  • Patent number: 9896683
    Abstract: Methods for isolating circulating small RNAs, e.g., microRNA (miRNA), from plasma samples, e.g., that comprise using an alkaline phenol:chloroform extraction, and methods of use thereof, including for the detection, prognosis, and/or monitoring of disease in a subject.
    Type: Grant
    Filed: July 29, 2015
    Date of Patent: February 20, 2018
    Assignees: University of Massachusetts, Firefly BioWorks
    Inventors: Victor Ambros, Rosalind Lee, Anthony Patrick Fusco
  • Patent number: 9816088
    Abstract: Provided herein are methods and composition for immune repertoire sequencing and single cell barcoding. In some aspects, such methods may comprise steps of: (a) forming a plurality of first vessels each comprising: (i) a single cell, and (ii) a single solid support; (b) copying onto the single solid support: (i) a first copy of a first cell polynucleotide from the single cell, and (ii) a second copy of a second cell polynucleotide from the single cell; (c) forming a plurality of second vessels each comprising (i) a single solid support from the plurality of first vessels, and (ii) a barcoded polynucleotide; and (d) amplifying (i) the first copy and the second copy with a first primer set, and (ii) the barcode with a second primer set, wherein a primer of the first primer set is complementary to a primer of the second set; and (e) forming first and second single cell barcoded sequences.
    Type: Grant
    Filed: March 14, 2014
    Date of Patent: November 14, 2017
    Assignee: AbVitro LLC
    Inventors: Francois Vigneault, Adrian Wrangham Briggs
  • Patent number: 9725765
    Abstract: The invention generally relates to methods for obtaining a sequence, such as a consensus sequence or a haplotype sequence. In certain embodiments, methods of the invention involve determining an amount of amplifiable nucleic acid present in a sample, partitioning the nucleic acid based upon results of the determining step such that each partitioned portion includes, on average, a subset of unique sequences, sequencing the nucleic acid to obtain sequence reads, and assembling a consensus sequence from the reads.
    Type: Grant
    Filed: September 10, 2012
    Date of Patent: August 8, 2017
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Dmitry Pushkarev, Stephen R. Quake, Ayelet Voskoboynik, Michael Kertesz
  • Patent number: 9670526
    Abstract: Methods and related products are disclosed that improve the probability of interaction between a target molecule and a nanopore by capturing the target molecule on a surface comprising the nanopore. The captured target molecule, the nanopore, or both, are able to move relative to each other along the surface. When the leader of the target molecule is in proximity with the nanopore, interaction of the target portion of the target molecule with the nanopore occurs, thereby permitting sensing of the target portion. Confining the target molecule and nanopore in this manner leads to significantly enhanced interaction with the nanopore.
    Type: Grant
    Filed: November 8, 2013
    Date of Patent: June 6, 2017
    Assignee: Stratos Genomics, Inc.
    Inventors: Mark Stamatios Kokoris, Robert N. McRuer
  • Patent number: 9605311
    Abstract: The present invention relates to compositions, methods and systems for analyzing the methylation state of nucleic acids. Some embodiments relate to a compositions, methods and systems for analyzing the methylation state of DNA with a gene array.
    Type: Grant
    Filed: July 10, 2014
    Date of Patent: March 28, 2017
    Assignee: Illumina, Inc.
    Inventor: Henri A. Kester
  • Patent number: 9523128
    Abstract: The present invention provides nucleic acids and peptides, and methods of using the nucleic acids and peptides to identify subjects at risk for a TDP-43 proteinopathy. The invention also provides for an array comprising the nucleic acids and peptides of the invention.
    Type: Grant
    Filed: October 14, 2014
    Date of Patent: December 20, 2016
    Assignee: WASHINGTON UNIVERSITY
    Inventors: Nigel J. Cairns, Robert H. Baloh, Alan Pestronk, Michael A. Gitcho, Alison M. Goate
  • Patent number: 9395359
    Abstract: Arrays of single molecules and methods of producing an array of single molecules are described. Arrays with defined volumes between 10 attoliters and 50 picoliters enable single molecule detection and quantitation.
    Type: Grant
    Filed: March 4, 2015
    Date of Patent: July 19, 2016
    Assignee: Trustees of Tufts College
    Inventors: David R. Walt, David M. Rissin
  • Patent number: 9376691
    Abstract: The present invention provides for a modified host cell comprising a heterologous pinene synthase (PS), or enzymatically active fragment or variant thereof, and optionally a geranyl pyrophosphate synthase (GPPS), or enzymatically active fragment or variant thereof, or a fusion protein comprising: (a) a PS and (b) a GPPS linked by a linker.
    Type: Grant
    Filed: November 27, 2013
    Date of Patent: June 28, 2016
    Assignee: The Regents of the University of California
    Inventors: Pamela P. Peralta-Yahya, Jay D. Keasling
  • Patent number: 9347929
    Abstract: Improved resolution and detection of nanoparticles are achieved when a nanopore connecting liquid compartments in a device running on the Coulter principle is provided with fluid lipid walls. The fluid lipid walls are made of a lipid bilayer, and preferably include lipid anchored mobile ligands as part of the lipid bilayer. By varying the nature and concentration of the mobile ligand in the lipid bilayer, multifunctional coatings of lipids are provided.
    Type: Grant
    Filed: February 20, 2012
    Date of Patent: May 24, 2016
    Assignee: The Regents Of The University Of Michigan
    Inventors: Michael Mayer, Erik Yusko, Jerry Yang
  • Patent number: 9297048
    Abstract: The present invention relates to an antibiotic resistance profile for Neisseria gonorrhoeae by assessing the presence of mutations (e.g., SNP) in antibiotic resistant genes that confer bacterial resistance against antibiotics such as penicillin, tetracycline, fluoroquinolones, cephalosporin, macrolides and spectinomycin. There is provided a method and a kit for generating an antibiotic resistance profile for Neisseria gonorrhoeae by utilizing a multiplex PCR to amplify segments of antibiotic-resistant genes, allele-specific primer extension to detect gene mutation, and detection of such gene mutations with gel electrophoresis, capillary electrophoresis, or DNA microarray. The present method provides useful information to physicians relating the antibiotic susceptibility of Neisseria gonorrhoeae against different classes of antibiotics.
    Type: Grant
    Filed: June 2, 2011
    Date of Patent: March 29, 2016
    Assignee: Medical Diagnostic Laboratories, LLC
    Inventors: Sergey Balashov, Eli Mordechai, Martin E. Adelson, Scott E. Gygax
  • Patent number: 9267174
    Abstract: The invention provides a non-invasive technique for the differential detection of multiple genotypes and/or mutations for a plurality of target genes in a biological sample containing genetic material from different genomic sources. Methods are conducted using multiplex amplification of a plurality of target sequences from the biological sample, and sequencing is used to detect and enumerate genetic mutations and chromosomal abnormalities at the single nucleotide level.
    Type: Grant
    Filed: October 26, 2011
    Date of Patent: February 23, 2016
    Assignee: Stanford University
    Inventors: Stephen R. Quake, Wei Gu, Hei-Mun Christina Fan
  • Patent number: 9193997
    Abstract: Methods are provided for the detection and analysis of clonality in a cell population, where parallel sequencing is applied to a nucleic acid sample obtained from the cell population, optionally a population of lymphocytes. Replicate samples are amplified, and sequenced, where identification of coincident sequences in two or more replicates is indicative of clonal expansion.
    Type: Grant
    Filed: December 15, 2011
    Date of Patent: November 24, 2015
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Andrew Fire, Scott D. Boyd, Jason Merker, Kyunga Seo, Eleanor L. Marshall
  • Patent number: 9139874
    Abstract: In some embodiments, methods for obtaining sequence information from a nucleic acid template linked to a support include hybridizing a first primer to a template strand linked to a support, sequencing a portion of the nucleic acid template, thereby forming an extended first primer product that is complementary to a portion of the nucleic acid template. In some embodiments, the method further includes introducing a nick into a portion of the template strand that is hybridized to the extended first primer product, degrading a portion of the template strand from the nick using a degrading agent, where a portion of the extended first primer remains hybridized to an undegraded portion of the template strand, and sequencing at least some of the single-stranded portion of the extended first primer by synthesis.
    Type: Grant
    Filed: July 6, 2012
    Date of Patent: September 22, 2015
    Assignee: Life Technologies Corporation
    Inventors: Jason Myers, Zhoutao Chen, Devin Dressman, Theo Nikiforov
  • Publication number: 20150148241
    Abstract: The present invention relates to a high throughput method for the identification and detection of molecular markers wherein restriction fragments are generated and suitable adaptors comprising (sample-specific) identifiers are ligated. The adapter-ligated restriction fragments may be selectively amplified with adaptor compatible primers carrying selective nucleotides at their 3? end. The amplified adapter-ligated restriction fragments are, at least partly, sequenced using high throughput sequencing methods and the sequence parts of the restriction fragments together with the sample-specific identifiers serve as molecular markers.
    Type: Application
    Filed: February 4, 2015
    Publication date: May 28, 2015
    Applicant: Keygene N.V.
    Inventors: Michael Josephus Theresia VAN EIJK, Taco Peter JESSE
  • Publication number: 20150148240
    Abstract: This invention provides methods of derivatizing a double-stranded DNA comprising contacting double-stranded DNA with a CpG methyltransferase and an s-adenosylmethionine analog. This invention also provides methods of sequencing DNA to determine methylation patterns.
    Type: Application
    Filed: December 19, 2014
    Publication date: May 28, 2015
    Applicant: The Trustees of Columbia University in the City of New York
    Inventors: Timothy H. Bestor, John R. Edwards, Jingyue Ju, Xiaoxu Li
  • Publication number: 20150141270
    Abstract: Provided is a single-stranded nucleic acid aptamer specifically binding to Klebsiella pneumoniae, and a method for detecting Klebsiella pneumoniae by using the same. The aptamer of the present disclosure, and a method, a composition, a kit or a sensor of using the same may be used to specifically detect Klebsiella pneumoniae present in an aqueous environment, foods, and medical samples and also be applied in fields such as sanitary conditions of foods and medical diagnosis.
    Type: Application
    Filed: July 30, 2014
    Publication date: May 21, 2015
    Applicant: KOREA INSTITUTE OF SCIENCE AND TECHNOLOGY
    Inventors: Byoung Chan KIM, Yeon Seok KIM, Jin Yang CHUNG, Jong Soo JURNG, Min Young SONG
  • Publication number: 20150133320
    Abstract: A nucleic acid molecule can be annealed to an appropriate immobilized primer. The primer can then be extended and the molecule and the primer can be separated from one another. The extended primer can then be annealed to another immobilized primer and the other primer can be extended. Both extended primers can then be separated from one another and can be used to provide further extended primers. The process can be repeated to provide amplified, immobilized nucleic acid molecules. These can be used for many different purposes, including sequencing, screening, diagnosis, in situ nucleic acid synthesis, monitoring gene expression, nucleic acid fingerprinting, etc.
    Type: Application
    Filed: January 20, 2015
    Publication date: May 14, 2015
    Applicant: ILLUMINA, INC.
    Inventors: Eric H. Kawashima, Laurent Farinelli, Pascal Mayer
  • Publication number: 20150133318
    Abstract: The instant invention is based, at least in part, on the identification of novel methods for the enzymatic enrichment of capped RNAs. The invention provides, e.g., methods for enrichment of capped RNAs, kits for making such capped RNAs, and compositions of enriched RNAs or cDNA libraries derived therefrom.
    Type: Application
    Filed: April 24, 2014
    Publication date: May 14, 2015
    Applicant: UNIVERSITY OF MASSACHUSETTS
    Inventors: Craig C. MELLO, Weifeng GU