Applied Biosystems, LLC

United States of America

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2025 (YTD) 2
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IPC Class
C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids 86
C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides 46
C07H 21/04 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical 32
B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glasswareDroppers 30
C07H 21/02 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with ribosyl as saccharide radical 17
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NICE Class
01 - Chemical and biological materials for industrial, scientific and agricultural use 90
09 - Scientific and electric apparatus and instruments 64
05 - Pharmaceutical, veterinary and sanitary products 29
42 - Scientific, technological and industrial services, research and design 22
37 - Construction and mining; installation and repair services 13
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Status
Pending 14
Registered / In Force 338
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1.

AMPQUEST

      
Serial Number 99264348
Status Pending
Filing Date 2025-07-02
Owner Applied Biosystems, LLC ()
NICE Classes  ? 09 - Scientific and electric apparatus and instruments

Goods & Services

Scientific laboratory equipment and apparatus, namely, polymerase chain reaction (PCR) instrument

2.

PANGENOMEPRO

      
Serial Number 99054140
Status Pending
Filing Date 2025-02-24
Owner Applied Biosystems, LLC ()
NICE Classes  ?
  • 01 - Chemical and biological materials for industrial, scientific and agricultural use
  • 09 - Scientific and electric apparatus and instruments

Goods & Services

Kits consisting primarily of reagents and laboratory equipment, namely, microarrays sold as a unit for scientific research use Laboratory equipment, namely, microarrays

3.

INNOVIGENE

      
Application Number 1820534
Status Registered
Filing Date 2024-10-09
Registration Date 2024-10-09
Owner Applied Biosystems, LLC (USA)
NICE Classes  ? 09 - Scientific and electric apparatus and instruments

Goods & Services

Downloadable computer software for scientific analysis of genetic sequences.

4.

INNOVIGENE

      
Serial Number 98491302
Status Pending
Filing Date 2024-04-09
Owner Applied Biosystems, LLC ()
NICE Classes  ? 09 - Scientific and electric apparatus and instruments

Goods & Services

Downloadable computer software for scientific analysis of genetic sequences

5.

RESDNASEQ

      
Application Number 1780279
Status Registered
Filing Date 2023-10-23
Registration Date 2023-10-23
Owner APPLIED BIOSYSTEMS, LLC (USA)
NICE Classes  ? 01 - Chemical and biological materials for industrial, scientific and agricultural use

Goods & Services

Chemical reagents for non-medical purpose; diagnostic reagents and kits comprised of diagnostic reagents for scientific or research use.

6.

GOPURE

      
Serial Number 98360825
Status Pending
Filing Date 2024-01-17
Owner Applied Biosystems, LLC ()
NICE Classes  ? 09 - Scientific and electric apparatus and instruments

Goods & Services

(Based on Use in Commerce) Chromatography columns for laboratory use; Chromatography columns for laboratory use, namely, chromatography columns for the development of biologics; (Based on Intent To Use) Plastic laboratory consumables, namely 96-well plates having multi-well arrays that can be used in chemical analysis, biological analysis or patterning for laboratory use

7.

AB ASCEND

      
Serial Number 98327878
Status Pending
Filing Date 2023-12-22
Owner Applied Biosystems, LLC ()
NICE Classes  ? 37 - Construction and mining; installation and repair services

Goods & Services

Repair or maintenance of laboratory apparatus and instruments

8.

Miscellaneous Design

      
Serial Number 98217723
Status Pending
Filing Date 2023-10-10
Owner Applied Biosystems, LLC ()
NICE Classes  ? 01 - Chemical and biological materials for industrial, scientific and agricultural use

Goods & Services

Microbiological cell culture media, biological tissue in the nature of animal blood sera, mammalian and insect cells, mammalian and insect cell culture media and cell culture reagents; all of the foregoing goods for scientific or medical research use

9.

Miscellaneous Design

      
Serial Number 98215624
Status Pending
Filing Date 2023-10-09
Owner Applied Biosystems, LLC ()
NICE Classes  ? 09 - Scientific and electric apparatus and instruments

Goods & Services

Laboratory equipment, namely, plastic laboratory containers sold empty, all intended for use with liquid media, buffers, sera, reagents

10.

QUALTRAK

      
Application Number 1730548
Status Registered
Filing Date 2022-10-25
Registration Date 2022-10-25
Owner Applied Biosystems LLC (USA)
NICE Classes  ?
  • 05 - Pharmaceutical, veterinary and sanitary products
  • 10 - Medical apparatus and instruments

Goods & Services

Laboratory reagents, oligonucleotides, primers and probes, enzymes and enzyme mixes, nucleotide sets and nucleotide mixes, reference dyes, reaction buffers, detection labels, sold individually or as a kit, for nucleic acid genotyping, nucleic acid quantification and nucleic acid amplification including polymerase chain reaction and reverse transcription polymerase chain reaction for clinical and biopharmaceutical use. Probes.

11.

IDENTIFIND

      
Serial Number 97903715
Status Registered
Filing Date 2023-04-24
Registration Date 2024-08-13
Owner Applied Biosystems, LLC ()
NICE Classes  ? 42 - Scientific, technological and industrial services, research and design

Goods & Services

Providing online non-downloadable computer game software

12.

Reagents Useful for Synthesizing Rhodamine-Labeled Oligonucleotides

      
Application Number 17854220
Status Pending
Filing Date 2022-06-30
First Publication Date 2023-03-30
Owner Applied Biosystems, LLC (USA)
Inventor
  • Benson, Scott C.
  • Zou, Ruiming N.
  • Upadhya, Krishna G.
  • Kenney, Paul M.
  • Cassel, Jonathan M.

Abstract

The present disclosure provides reagents that can be used to label synthetic oligonucleotides with rhodamine dyes or dye networks that contain rhodamine dyes.

IPC Classes  ?

  • C07F 9/6561 - Heterocyclic compounds, e.g. containing phosphorus as a ring hetero atom containing systems of two or more relevant hetero rings condensed among themselves or condensed with a common carbocyclic ring or ring system, with or without other non-condensed hetero rings
  • C07F 9/6509 - Six-membered rings
  • C07F 9/24 - Esteramides
  • C07F 9/653 - Five-membered rings
  • C07F 9/655 - Heterocyclic compounds, e.g. containing phosphorus as a ring hetero atom having oxygen atoms, with or without sulfur, selenium, or tellurium atoms, as the only ring hetero atoms
  • C09B 11/24 - Phthaleins containing amino groups
  • C07H 21/04 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical
  • C07D 311/96 - Heterocyclic compounds containing six-membered rings having one oxygen atom as the only hetero atom, condensed with other rings spiro-condensed with carbocyclic rings or ring systems
  • C07H 19/04 - Heterocyclic radicals containing only nitrogen as ring hetero atom

13.

STERISEQ

      
Application Number 1717390
Status Registered
Filing Date 2023-02-09
Registration Date 2023-02-09
Owner Applied Biosystems, LLC (USA)
NICE Classes  ? 01 - Chemical and biological materials for industrial, scientific and agricultural use

Goods & Services

Real-time polymerase chain reaction kits, comprised primarily of reagents, for scientific laboratory use in the detection of bacteria and fungi contamination in bioprocess samples.

14.

QUALTRAK

      
Application Number 1697437
Status Registered
Filing Date 2022-10-25
Registration Date 2022-10-25
Owner Applied Biosystems LLC (USA)
NICE Classes  ? 09 - Scientific and electric apparatus and instruments

Goods & Services

Polymerase chain reaction (PCR) instruments for scientific, research, and biopharmaceutical use, namely, laboratory apparatus and instruments for amplifying DNA using polymerase chain reaction (PCR); scientific research instruments for use in measuring and quantifying DNA.

15.

STERISEQ

      
Serial Number 97545298
Status Registered
Filing Date 2022-08-11
Registration Date 2025-07-01
Owner Applied Biosystems, LLC ()
NICE Classes  ? 01 - Chemical and biological materials for industrial, scientific and agricultural use

Goods & Services

Real-time polymerase chain reaction kits, comprised primarily of reagents, for scientific laboratory use in the detection of bacteria and fungi contamination in bioprocess samples

16.

COMPOSITIONS, METHODS, AND KITS FOR AMPLIFYING NUCLEIC ACIDS

      
Application Number 17568066
Status Pending
Filing Date 2022-01-04
First Publication Date 2022-05-19
Owner APPLIED BIOSYSTEMS, LLC (USA)
Inventor
  • Dong, Shoulian
  • Stevens, Junko F.
  • Lee, Danny H.

Abstract

The present teachings are directed to compositions, methods, and kits for amplifying target nucleic acids while reducing non-specific fluorescence and undesired amplification products, sometimes referred to as secondary amplification products or spurious side-products. The enzyme inhibitors disclosed herein comprise a nucleotide sequence and at least one quencher. Complexes comprising an enzyme inhibitor associated with an enzyme, wherein at least one enzymatic activity of the enzyme is inhibited, are also provided. Methods for amplifying a target nucleic acid while reducing undesired amplification products are disclosed, as are methods for reducing non-specific fluorescence. Kits for expediting the performance of certain disclosed methods are also provided.

IPC Classes  ?

  • C12Q 1/6844 - Nucleic acid amplification reactions
  • C12Q 1/6848 - Nucleic acid amplification reactions characterised by the means for preventing contamination or increasing the specificity or sensitivity of an amplification reaction
  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides
  • G01N 21/64 - FluorescencePhosphorescence
  • C12N 15/115 - Aptamers, i.e. nucleic acids binding a target molecule specifically and with high affinity without hybridising therewith

17.

Method and System for Multiplex Genetic Analysis

      
Application Number 17537153
Status Pending
Filing Date 2021-11-29
First Publication Date 2022-05-19
Owner APPLIED BIOSYSTEMS, LLC (USA)
Inventor
  • Nordman, Eric S.
  • Oldham, Mark F.
  • Woudenberg, Timothy

Abstract

The present disclosure provides apparatus, systems and method for detecting separately and substantially simultaneously light emissions from a plurality of localized light-emitting analytes. A system according to exemplary embodiments of the present disclosure comprises a sample holder having structures formed thereon for spatially separating and constraining a plurality of light-emitting analytes each having a single nucleic acid molecule or a single nucleic acid polymerizing enzyme, a light source configured to illuminate the sample holder, an optical assembly configured to collect and detect separately and substantially simultaneously light emissions associated with the plurality of light emitting analytes. The system may further include a computer system configured to analyze the light emissions to determine the structures or properties of a target nucleic acid molecule associated with each analyte.

IPC Classes  ?

  • C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
  • C12Q 1/6869 - Methods for sequencing
  • G01N 21/64 - FluorescencePhosphorescence

18.

QUALTRAK

      
Serial Number 97380333
Status Pending
Filing Date 2022-04-25
Owner Applied Biosystems LLC ()
NICE Classes  ? 09 - Scientific and electric apparatus and instruments

Goods & Services

Polymerase chain reaction (PCR) instruments for scientific, research, and biopharmaceutical use, namely, laboratory apparatus and instruments for amplifying DNA using polymerase chain reaction (PCR); scientific research instruments for use in measuring and quantifying DNA, all the foregoing for use in connection with scientific research, biopharmaceutical drug development and genetic analysis, and not directly in connection with software and technology for experience management, customer, patient, student, product, and employee feedback analysis, natural language processing, market research, online reputation management, or surveys

19.

QUALTRAK

      
Serial Number 97380331
Status Pending
Filing Date 2022-04-25
Owner Applied Biosystems LLC ()
NICE Classes  ? 05 - Pharmaceutical, veterinary and sanitary products

Goods & Services

Biopharmaceutical laboratory reagents, oligonucleotides, primers and probes, enzymes and enzyme mixes, nucleotide sets and nucleotide mixes, fluorescent dye, all the foregoing for in-vitro medical, clinical or biopharmaceutical use, reaction buffers and sample detection labels in the form of strips of adhesive paper labels for laboratory use for nucleic acid genotyping tools, nucleic acid quantification and nucleic acid amplification including polymerase chain reactions, and reverse transcription polymerase chain reactions, for gene expression, genotyping, microbial testing applications all the foregoing for in-vitro medical, clinical or biopharmaceutical use; Kits comprised of laboratory reagents, oligonucleotides, primers and probes, enzymes and enzyme mixes, nucleotide sets and nucleotide mixes, fluorescent dye, all the foregoing for in-vitro medical, clinical, and biopharmaceutical use, reaction buffers and sample detection labels in the form of strips of adhesive paper labels for laboratory use for nucleic acid genotyping, nucleic acid quantification and nucleic acid amplification including polymerase chain reaction and reverse transcription polymerase chain reactions, all the foregoing for in-vitro medical, or biopharmaceutical use.

20.

VIC

      
Application Number 1644531
Status Registered
Filing Date 2021-11-02
Registration Date 2021-11-02
Owner Applied Biosystems, LLC (USA)
NICE Classes  ? 01 - Chemical and biological materials for industrial, scientific and agricultural use

Goods & Services

Reagents and reagent kits for scientific research use.

21.

APPARATUS, SYSTEM, AND METHOD USING IMMISCIBLE-FLUID-DISCRETE-VOLUMES

      
Application Number 17505085
Status Pending
Filing Date 2021-10-19
First Publication Date 2022-02-03
Owner APPLIED BIOSYSTEMS, LLC (USA)
Inventor
  • Lee, Linda G.
  • Woo, Sam L.
  • Ma, Congcong
  • Reel, Richard T.
  • Oldham, Mark F.
  • Cox, David M.
  • Schroeder, Benjamin G.
  • Sorenson, Jon M.
  • Wiyatno, Willy

Abstract

Various embodiments of the teachings relate to a system or method for sample preparation or analysis in biochemical or molecular biology procedures. The sample preparation can involve small volume processed in discrete portions or segments or slugs, herein referred to as discrete volumes. A molecular biology procedure can be nucleic acid analysis. Nucleic acid analysis can be an integrated DNA amplification/DNA sequencing procedure.

IPC Classes  ?

  • C12Q 1/6869 - Methods for sequencing
  • B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glasswareDroppers
  • F15C 5/00 - Manufacture of fluid-circuit elementsManufacture of assemblages of such elements
  • F16K 99/00 - Subject matter not provided for in other groups of this subclass
  • G01N 35/08 - Automatic analysis not limited to methods or materials provided for in any single one of groups Handling materials therefor using a stream of discrete samples flowing along a tube system, e.g. flow injection analysis
  • G01N 1/14 - Suction devices, e.g. pumpsEjector devices
  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
  • G01N 27/447 - Systems using electrophoresis

22.

Methods, compositions, and kits comprising linker probes for quantifying polynucleotides

      
Application Number 16947974
Grant Number 11891663
Status In Force
Filing Date 2020-08-26
First Publication Date 2020-12-31
Grant Date 2024-02-06
Owner APPLIED BIOSYSTEMS, LLC (USA)
Inventor
  • Chen, Caifu
  • Ridzon, Dana
  • Zhou, Zhaohui
  • Lao, Kai Qin
  • Straus, Neil A.

Abstract

The present invention is directed to methods, reagents, kits, and compositions for identifying and quantifying target polynucleotide sequences. A linker probe comprising a 3′ target specific portion, a loop, and a stem is hybridized to a target polynucleotide and extended to form a reaction product that includes a reverse primer portion and the stem nucleotides. A detector probe, a specific forward primer, and a reverse primer can be employed in an amplification reaction wherein the detector probe can detect the amplified target polynucleotide based on the stem nucleotides introduced by the linker probe. In some embodiments a plurality of short miRNAs are queried with a plurality of linker probes, wherein the linker probes all comprise a universal reverse primer portion a different 3′ target specific portion and different stems. The plurality of queried miRNAs can then be decoded in a plurality of amplification reactions.

IPC Classes  ?

  • C12Q 1/6876 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
  • C12N 9/00 - Enzymes, e.g. ligases (6.)ProenzymesCompositions thereofProcesses for preparing, activating, inhibiting, separating, or purifying enzymes
  • C07H 21/04 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical
  • C12Q 1/686 - Polymerase chain reaction [PCR]
  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides

23.

VERITIPRO

      
Application Number 1548667
Status Registered
Filing Date 2020-07-27
Registration Date 2020-07-27
Owner Applied Biosystems, LLC. (USA)
NICE Classes  ? 09 - Scientific and electric apparatus and instruments

Goods & Services

Laboratory equipment for scientific and research use, namely, thermal cycler.

24.

Reagents useful for synthesizing rhodamine-labeled oligonucleotides

      
Application Number 16776682
Grant Number 11407773
Status In Force
Filing Date 2020-01-30
First Publication Date 2020-08-27
Grant Date 2022-08-09
Owner Applied Biosystems, LLC (USA)
Inventor
  • Benson, Scott C.
  • Zou, Ruiming N.
  • Upadhya, Krishna G.
  • Kenney, Paul M.
  • Cassel, Jonathan M.

Abstract

The present disclosure provides reagents that can be used to label synthetic oligonucleotides with rhodamine dyes or dye networks that contain rhodamine dyes.

IPC Classes  ?

  • C07H 21/04 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical
  • C07H 19/04 - Heterocyclic radicals containing only nitrogen as ring hetero atom
  • C07F 9/6561 - Heterocyclic compounds, e.g. containing phosphorus as a ring hetero atom containing systems of two or more relevant hetero rings condensed among themselves or condensed with a common carbocyclic ring or ring system, with or without other non-condensed hetero rings
  • C07F 9/6509 - Six-membered rings
  • C07F 9/24 - Esteramides
  • C07F 9/653 - Five-membered rings
  • C07F 9/655 - Heterocyclic compounds, e.g. containing phosphorus as a ring hetero atom having oxygen atoms, with or without sulfur, selenium, or tellurium atoms, as the only ring hetero atoms
  • C09B 11/24 - Phthaleins containing amino groups
  • C07D 311/96 - Heterocyclic compounds containing six-membered rings having one oxygen atom as the only hetero atom, condensed with other rings spiro-condensed with carbocyclic rings or ring systems

25.

Device and method for making discrete volumes of a first fluid in contact with a second fluid, which are immiscible with each other

      
Application Number 16655911
Grant Number 11319585
Status In Force
Filing Date 2019-10-17
First Publication Date 2020-05-14
Grant Date 2022-05-03
Owner APPLIED BIOSYSTEMS, LLC (USA)
Inventor
  • Wiyatno, Willy K.
  • Lee, Linda
  • Cox, David
  • Nurse, James
  • Greiner, Douglas
  • Lehto, Dennis
  • Wojtowicz, Janusz
  • Woo, Sam
  • Reel, Richard

Abstract

A system may include a first conduit configured to form a first batch of discrete volumes of aqueous fluid separated by spacing liquid disposed between consecutive volumes of aqueous fluid, the spacing liquid being immiscible with the aqueous fluid volumes; a second conduit, fluidically coupled to the first conduit, the second conduit configured to statically hold the first batch of discrete volumes of aqueous fluid; and a third conduit configured to receive the first batch of discrete volumes of aqueous fluid from the second conduit. The third conduit can be configured to transfer the discrete volumes of aqueous fluid of the first batch for downstream processing.

IPC Classes  ?

  • G01N 1/14 - Suction devices, e.g. pumpsEjector devices
  • G01N 35/08 - Automatic analysis not limited to methods or materials provided for in any single one of groups Handling materials therefor using a stream of discrete samples flowing along a tube system, e.g. flow injection analysis
  • G01N 27/447 - Systems using electrophoresis
  • C12Q 1/6869 - Methods for sequencing
  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
  • B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glasswareDroppers
  • F15C 5/00 - Manufacture of fluid-circuit elementsManufacture of assemblages of such elements
  • F16K 99/00 - Subject matter not provided for in other groups of this subclass
  • B01L 3/02 - BurettesPipettes
  • B01L 7/00 - Heating or cooling apparatusHeat insulating devices

26.

Nanowire-based system for analysis of nucleic acids

      
Application Number 16570093
Grant Number 10961575
Status In Force
Filing Date 2019-09-13
First Publication Date 2020-05-07
Grant Date 2021-03-30
Owner APPLIED BIOSYSTEMS, LLC (USA)
Inventor
  • Sun, Hongye
  • Fung, Steven
  • Woo, Sam Lee

Abstract

A method for sequencing a nucleic acid template includes forming a nanowire assembly including a semiconductor nanowire and a probe covalently bound to the semiconductor nanowire; contacting the nanowire assembly with a template nucleic acid; contacting the nucleic acid duplexes with an extension nucleic acid, the extension nucleic acid joined to the probe; disrupting the nucleic acid duplexes; and measuring an electrical characteristic of a nanowire assembly of the set of nanowire assemblies.

IPC Classes  ?

  • G01N 27/30 - Electrodes, e.g. test electrodesHalf-cells
  • C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
  • C12Q 1/6811 - Selection methods for production or design of target specific oligonucleotides or binding molecules
  • C12Q 1/6869 - Methods for sequencing
  • G01N 27/327 - Biochemical electrodes
  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids

27.

Compositions, methods, and kits for amplifying nucleic acids

      
Application Number 16746216
Grant Number 11225686
Status In Force
Filing Date 2020-01-17
First Publication Date 2020-05-07
Grant Date 2022-01-18
Owner APPLIED BIOSYSTEMS, LLC (USA)
Inventor
  • Dong, Shoulian
  • Stevens, Junko F.
  • Lee, Danny H.

Abstract

The present teachings are directed to compositions, methods, and kits for amplifying target nucleic acids while reducing non-specific fluorescence and undesired amplification products, sometimes referred to as secondary amplification products or spurious side-products. The enzyme inhibitors disclosed herein comprise a nucleotide sequence and at least one quencher. Complexes comprising an enzyme inhibitor associated with an enzyme, wherein at least one enzymatic activity of the enzyme is inhibited, are also provided. Methods for amplifying a target nucleic acid while reducing undesired amplification products are disclosed, as are methods for reducing non-specific fluorescence. Kits for expediting the performance of certain disclosed methods are also provided.

IPC Classes  ?

  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides
  • C12N 15/115 - Aptamers, i.e. nucleic acids binding a target molecule specifically and with high affinity without hybridising therewith
  • C12Q 1/6844 - Nucleic acid amplification reactions
  • C12Q 1/6848 - Nucleic acid amplification reactions characterised by the means for preventing contamination or increasing the specificity or sensitivity of an amplification reaction
  • G01N 21/64 - FluorescencePhosphorescence

28.

DETECTION OF ANALYTES AND NUCLEIC ACIDS

      
Application Number 16575149
Status Pending
Filing Date 2019-09-18
First Publication Date 2020-04-02
Owner APPLIED BIOSYSTEMS, LLC (USA)
Inventor
  • Shannon, Mark
  • Ruff, David

Abstract

Methods of detecting at least one analyte and at least one nucleic acid in a sample are provided. Reagents for carrying out the methods are also provided.

IPC Classes  ?

29.

VERITIPRO

      
Serial Number 88775062
Status Registered
Filing Date 2020-01-27
Registration Date 2021-01-05
Owner Applied Biosystems, LLC. ()
NICE Classes  ? 09 - Scientific and electric apparatus and instruments

Goods & Services

Laboratory equipment for scientific and research use, namely, thermal cycler

30.

siRNA sequence-independent modification formats for reducing off-target phenotypic effects in RNAI, and stabilized forms thereof

      
Application Number 16409689
Grant Number 10900038
Status In Force
Filing Date 2019-05-10
First Publication Date 2019-12-12
Grant Date 2021-01-26
Owner APPLIED BIOSYSTEMS, LLC (USA)
Inventor
  • Puri, Nitin
  • Charles, Irudaya
  • Magdaleno, Susan Maylin
  • Vlassov, Alexander
  • Burnett, Christopher

Abstract

Modification formats having modified nucleotides are provided for siRNA. Short interfering RNA having modification formats and modified nucleotides provided herein reduce off-target effects in RNA interference of endogenous genes. Further modification formatted siRNAs are demonstrated to be stabilized to nuclease-rich environments. Unexpectedly, increasing or maintaining strand bias, while necessary to maintain potency for endogenous RNA interference, is not sufficient for reducing off-target effects in cell biology assays.

IPC Classes  ?

  • C12N 15/113 - Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides
  • C12N 15/11 - DNA or RNA fragmentsModified forms thereof

31.

Electrowetting dispensing devices and related methods

      
Application Number 16258515
Grant Number 10739307
Status In Force
Filing Date 2019-01-25
First Publication Date 2019-09-26
Grant Date 2020-08-11
Owner APPLIED BIOSYSTEMS, LLC (USA)
Inventor
  • Vann, Charles S.
  • Banerjee, Debjyoti
  • Geiser, Timothy G.
  • Nurse, James C.
  • Beard, Nigel P.

Abstract

A method for dispensing liquid for use in biological analysis may comprise positioning liquid to be dispensed via electrowetting. The positioning may comprise aligning the liquid with a plurality of predetermined locations. The method may further comprise dispensing the aligned liquid from the plurality of predetermined locations through a plurality of openings respectively aligned with the predetermined locations. The dispensing may be via electrowetting.

IPC Classes  ?

  • G01N 27/453 - Cells therefor
  • G01N 27/447 - Systems using electrophoresis
  • B01L 3/02 - BurettesPipettes
  • B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glasswareDroppers
  • B01J 4/00 - Feed devicesFeed or outlet control devices

32.

Systems and methods for electronic detection with nanoFETs

      
Application Number 16247069
Grant Number 11175258
Status In Force
Filing Date 2019-01-14
First Publication Date 2019-07-18
Grant Date 2021-11-16
Owner Applied Biosystems, LLC (USA)
Inventor
  • Oldham, Mark F.
  • Nordman, Eric S.

Abstract

There is disclosed a system for electrical charge detection comprising a nanoFET device. Also disclosed is a method of electrical charge detection for single molecule sequencing. The method includes attaching a macromolecule or assemblies thereof to a gate of a nanoFET device and flowing in a solution of charge tags, where a charge tag includes a nucleotide attached to a charge complex. The method also includes incorporating one charge tag into the macromolecule or assemblies thereof and cleaving the charge tags from the macromolecule or assemblies thereof. The method further includes detecting at least one of current and voltage from the nanoFET device.

IPC Classes  ?

  • G01N 27/414 - Ion-sensitive or chemical field-effect transistors, i.e. ISFETS or CHEMFETS
  • B82Y 15/00 - Nanotechnology for interacting, sensing or actuating, e.g. quantum dots as markers in protein assays or molecular motors
  • C12Q 1/6825 - Nucleic acid detection involving sensors
  • G01N 33/543 - ImmunoassayBiospecific binding assayMaterials therefor with an insoluble carrier for immobilising immunochemicals

33.

Amplification and detection of ribonucleic acids

      
Application Number 16363508
Grant Number 10829808
Status In Force
Filing Date 2019-03-25
First Publication Date 2019-07-11
Grant Date 2020-11-10
Owner Applied Biosystems, LLC (USA)
Inventor Kuersten, R. Scott

Abstract

Compositions, methods, and kits for detecting one or more species of RNA molecules are disclosed. In one embodiment, a first adaptor and a second adaptor are ligated to the RNA molecule using a polypeptide comprising double-strand specific RNA ligase activity, without an intervening purification step. The ligated product is reverse transcribed, then at least some of the ribonucleosides in the reverse transcription product are removed. Primers are added and amplified products are generated. In certain embodiments, the sequence of at least part of at least one species of amplified product is determined and at least part of the corresponding RNA molecule is determined. In some embodiments, at least some of the amplified product species are detected, directly or indirectly, allowing the presence and/or quantity of the RNA molecule of interest to be determined.

IPC Classes  ?

  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides
  • C12Q 1/6855 - Ligating adaptors
  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay

34.

MYCOSEQ

      
Application Number 1473054
Status Registered
Filing Date 2019-05-06
Registration Date 2019-05-06
Owner Applied Biosystems, LLC (USA)
NICE Classes  ? 01 - Chemical and biological materials for industrial, scientific and agricultural use

Goods & Services

Real-time polymerase chain reaction kits, comprised primarily of reagents, for scientific laboratory use in the detection of bacterial contamination in bioprocess samples.

35.

PROTEINSEQ

      
Application Number 1471173
Status Registered
Filing Date 2019-05-06
Registration Date 2019-05-06
Owner Applied Biosystems, LLC (USA)
NICE Classes  ? 01 - Chemical and biological materials for industrial, scientific and agricultural use

Goods & Services

Kits comprised of reagents and buffers for scientific laboratory use to detect contamination in bioprocess samples.

36.

Apparatus, system, and method using immiscible-fluid-discrete-volumes

      
Application Number 16054391
Grant Number 11162137
Status In Force
Filing Date 2018-08-03
First Publication Date 2019-03-21
Grant Date 2021-11-02
Owner APPLIED BIOSYSTEMS LLC (USA)
Inventor
  • Lee, Linda G.
  • Woo, Sam L.
  • Ma, Congcong
  • Reel, Richard T.
  • Oldham, Mark F.
  • Cox, David M.
  • Schroeder, Benjamin G.
  • Sorenson, Jon M.
  • Wiyatno, Willy

Abstract

Various embodiments of the teachings relate to a system or method for sample preparation or analysis in biochemical or molecular biology procedures. The sample preparation can involve small volume processed in discrete portions or segments or slugs, herein referred to as discrete volumes. A molecular biology procedure can be nucleic acid analysis. Nucleic acid analysis can be an integrated DNA amplification/DNA sequencing procedure.

IPC Classes  ?

  • C12Q 1/6869 - Methods for sequencing
  • B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glasswareDroppers
  • F15C 5/00 - Manufacture of fluid-circuit elementsManufacture of assemblages of such elements
  • F16K 99/00 - Subject matter not provided for in other groups of this subclass
  • G01N 35/08 - Automatic analysis not limited to methods or materials provided for in any single one of groups Handling materials therefor using a stream of discrete samples flowing along a tube system, e.g. flow injection analysis
  • G01N 1/14 - Suction devices, e.g. pumpsEjector devices
  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
  • G01N 27/447 - Systems using electrophoresis
  • B01L 3/02 - BurettesPipettes
  • B01L 7/00 - Heating or cooling apparatusHeat insulating devices

37.

System and methods for indel identification using short read sequencing

      
Application Number 15966145
Grant Number 11538557
Status In Force
Filing Date 2018-04-30
First Publication Date 2018-12-06
Grant Date 2022-12-27
Owner Applied Biosystems, LLC (USA)
Inventor Zhang, Zheng

Abstract

Systems, methods, and analytical approaches for short read sequence assembly and for the detection of insertions and deletions (indels) in a reference genome. A method suitable for software implementation is presented in which indels may be readily identified in a computationally efficient manner.

IPC Classes  ?

  • G16B 30/20 - Sequence assembly
  • G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
  • G16B 30/10 - Sequence alignmentHomology search

38.

MYCOSEQ

      
Serial Number 88184066
Status Registered
Filing Date 2018-11-06
Registration Date 2019-06-11
Owner Applied Biosystems, LLC ()
NICE Classes  ? 01 - Chemical and biological materials for industrial, scientific and agricultural use

Goods & Services

Real-time polymerase chain reaction kits, comprised primarily of reagents, for scientific laboratory use in the detection of bacterial contamination in bioprocess samples

39.

PROTEINSEQ

      
Serial Number 88184082
Status Registered
Filing Date 2018-11-06
Registration Date 2019-06-11
Owner Applied Biosystems, LLC ()
NICE Classes  ? 01 - Chemical and biological materials for industrial, scientific and agricultural use

Goods & Services

kits comprised of reagents and buffers for scientific laboratory use to detect contamination in bioprocess samples

40.

Differential dissociation and melting curve peak detection

      
Application Number 15965380
Grant Number 11257570
Status In Force
Filing Date 2018-04-27
First Publication Date 2018-11-01
Grant Date 2022-02-22
Owner Applied Biosystems, LLC (USA)
Inventor Cheng, Francis T.

Abstract

Systems and methods are provided for processing a melting or dissociation curve of a DNA or other sample, for example, during PCR processing. In some embodiments, detection of the melting point and melting curve behavior can be enhanced by taking a derivative of the curve, and detecting peaks in the differential dissociation curve. In some embodiments, the derivative operation can comprise the use of edge-processing, or other detection algorithms. In some embodiments, the dissociation analysis can comprise removing low-frequency (or pedestal) components of the differential dissociation curve. In some embodiments, the differential dissociation curve can exhibit a smoothed or more regular appearance than the raw detected data.

IPC Classes  ?

  • G16B 40/10 - Signal processing, e.g. from mass spectrometry [MS] or from PCR
  • G16B 45/00 - ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
  • G16B 99/00 - Subject matter not provided for in other groups of this subclass
  • C12Q 1/6844 - Nucleic acid amplification reactions

41.

AMPFLSTR

      
Application Number 1420214
Status Registered
Filing Date 2018-06-29
Registration Date 2018-06-29
Owner Applied Biosystems, LLC (USA)
NICE Classes  ? 01 - Chemical and biological materials for industrial, scientific and agricultural use

Goods & Services

DNA typing kits consisting primarily of reagents for scientific use.

42.

QUANTIFILER

      
Application Number 1419387
Status Registered
Filing Date 2018-06-29
Registration Date 2018-06-29
Owner Applied Biosystems, LLC (USA)
NICE Classes  ? 01 - Chemical and biological materials for industrial, scientific and agricultural use

Goods & Services

Reagents for scientific or research use; reagents for forensics, paternity, and human identification use.

43.

YFILER

      
Application Number 1419615
Status Registered
Filing Date 2018-06-29
Registration Date 2018-06-29
Owner APPLIED BIOSYSTEMS, LLC (USA)
NICE Classes  ? 01 - Chemical and biological materials for industrial, scientific and agricultural use

Goods & Services

Reagents for scientific or medical research use; reagents for forensics and paternity use.

44.

Electrowetting dispensing devices and related methods

      
Application Number 15614601
Grant Number 10215730
Status In Force
Filing Date 2017-06-05
First Publication Date 2018-05-10
Grant Date 2019-02-26
Owner APPLIED BIOSYSTEMS, LLC (USA)
Inventor
  • Vann, Charles S.
  • Banerjee, Debjyoti
  • Geiser, Timothy G.
  • Nurse, James C.
  • Beard, Nigel P.

Abstract

A method for dispensing liquid for use in biological analysis may comprise positioning liquid to be dispensed via electrowetting. The positioning may comprise aligning the liquid with a plurality of predetermined locations. The method may further comprise dispensing the aligned liquid from the plurality of predetermined locations through a plurality of openings respectively aligned with the predetermined locations. The dispensing may be via electrowetting.

IPC Classes  ?

  • G01N 27/453 - Cells therefor
  • G01N 27/447 - Systems using electrophoresis
  • B01L 3/02 - BurettesPipettes
  • B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glasswareDroppers
  • B01J 4/00 - Feed devicesFeed or outlet control devices

45.

siRNA sequence-independent modification formats for reducing off-target phenotypic effects in RNAi, and stabilized forms thereof

      
Application Number 15696172
Grant Number 10329564
Status In Force
Filing Date 2017-09-05
First Publication Date 2018-03-01
Grant Date 2019-06-25
Owner APPLIED BIOSYSTEMS, LLC (USA)
Inventor
  • Puri, Nitin
  • Charles, Irudaya
  • Magdaleno, Susan Maylin
  • Vlassov, Alexander
  • Burnett, Christopher

Abstract

Modification formats having modified nucleotides are provided for siRNA. Short interfering RNA having modification formats and modified nucleotides provided herein reduce off-target effects in RNA interference of endogenous genes. Further modification formatted siRNAs are demonstrated to be stabilized to nuclease-rich environments. Unexpectedly, increasing or maintaining strand bias, while necessary to maintain potency for endogenous RNA interference, is not sufficient for reducing off-target effects in cell biology assays.

IPC Classes  ?

  • C12N 15/113 - Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides
  • C12N 15/11 - DNA or RNA fragmentsModified forms thereof

46.

Amplification and detection of ribonucleic acids

      
Application Number 15803609
Grant Number 10240191
Status In Force
Filing Date 2017-11-03
First Publication Date 2018-02-22
Grant Date 2019-03-26
Owner Applied Biosystems, LLC (USA)
Inventor Kuersten, R. Scott

Abstract

Compositions, methods, and kits for detecting one or more species of RNA molecules are disclosed. In one embodiment, a first adaptor and a second adaptor are ligated to the RNA molecule using a polypeptide comprising double-strand specific RNA ligase activity, without an intervening purification step. The ligated product is reverse transcribed, then at least some of the ribonucleosides in the reverse transcription product are removed. Primers are added and amplified products are generated. In certain embodiments, the sequence of at least part of at least one species of amplified product is determined and at least part of the corresponding RNA molecule is determined. In some embodiments, at least some of the amplified product species are detected, directly or indirectly, allowing the presence and/or quantity of the RNA molecule of interest to be determined.

IPC Classes  ?

  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides
  • C12Q 1/6855 - Ligating adaptors
  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay

47.

Nucleic acid terminators incorporating a cationic moiety and methods for their use

      
Application Number 14501507
Grant Number RE046683
Status In Force
Filing Date 2014-09-30
First Publication Date 2018-01-23
Grant Date 2018-01-23
Owner Applied Biosystems, LLC (USA)
Inventor
  • Rosenblum, Barnett
  • Menchen, Steven
  • Khan, Shaheer
  • Kenney, Paul

Abstract

Disclosed are methods and kits applicable to sequencing methods, such as Sanger dideoxy sequencing methods. The methods and kits disclosed utilize a cationically charged nucleic acid terminator in combination with a discriminatory polymerase.

IPC Classes  ?

  • C07H 21/00 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids

48.

Methods of detecting target nucleic acids

      
Application Number 15614606
Grant Number 10196680
Status In Force
Filing Date 2017-06-05
First Publication Date 2017-09-28
Grant Date 2019-02-05
Owner APPLIED BIOSYSTEMS, LLC (USA)
Inventor
  • Sharaf, Muhammad A.
  • Woudenberg, Timothy
  • Mullah, Khairuzzaman Bashar

Abstract

The present disclosure relates to methods of identifying target nucleic acids by using coded molecules and its analysis by translocation through a nanopore. Generally, coded molecules are subject to a target polynucleotide dependent modification. The modified coded molecule is detected by isolating the modified coded molecules from the unmodified coded molecules prior to analysis through the nanopore or by detecting a change in the signal pattern of the coded molecule when analyzed through the nanopore.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
  • C12Q 1/6825 - Nucleic acid detection involving sensors
  • C12Q 1/6816 - Hybridisation assays characterised by the detection means
  • C12Q 1/6876 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
  • C12Q 1/6823 - Release of bound markers
  • C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
  • C12Q 1/6832 - Enhancement of hybridisation reaction
  • G01N 27/447 - Systems using electrophoresis

49.

Method of making a paired tag library for nucleic acid sequencing

      
Application Number 15495333
Grant Number 10190164
Status In Force
Filing Date 2017-04-24
First Publication Date 2017-08-10
Grant Date 2019-01-29
Owner APPLIED BIOSYSTEMS, LLC (USA)
Inventor
  • Li, Bin
  • Xi, Lei
  • Ranade, Swati
  • Wang, Yangzhou

Abstract

The present disclosure relates to methods and compositions for making paired tags and paired tag libraries.

IPC Classes  ?

  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides
  • C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]

50.

Nanowire-based system for analysis of nucleic acids

      
Application Number 15449889
Grant Number 10415090
Status In Force
Filing Date 2017-03-03
First Publication Date 2017-06-22
Grant Date 2019-09-17
Owner APPLIED BIOSYSTEMS, LLC (USA)
Inventor
  • Sun, Hongye
  • Fung, Steven
  • Woo, Sam Lee

Abstract

A method for sequencing a nucleic acid template includes forming a nanowire assembly including a semiconductor nanowire and a probe covalently bound to the semiconductor nanowire; contacting the nanowire assembly with a template nucleic acid; contacting the nucleic acid duplexes with an extension nucleic acid, the extension nucleic acid joined to the probe; disrupting the nucleic acid duplexes; and measuring an electrical characteristic of a nanowire assembly of the set of nanowire assemblies.

IPC Classes  ?

  • G01N 27/30 - Electrodes, e.g. test electrodesHalf-cells
  • C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
  • C12Q 1/6811 - Selection methods for production or design of target specific oligonucleotides or binding molecules
  • C12Q 1/6869 - Methods for sequencing
  • G01N 27/327 - Biochemical electrodes
  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids

51.

Amplification and detection of ribonucleic acids

      
Application Number 15450675
Grant Number 09834816
Status In Force
Filing Date 2017-03-06
First Publication Date 2017-06-22
Grant Date 2017-12-05
Owner APPLIED BIOSYSTEMS, LLC (USA)
Inventor Kuersten, R. Scott

Abstract

Compositions, methods, and kits for detecting one or more species of RNA molecules are disclosed. In one embodiment, a first adaptor and a second adaptor are ligated to the RNA molecule using a polypeptide comprising double-strand specific RNA ligase activity, without an intervening purification step. The ligated product is reverse transcribed, then at least some of the ribonucleosides in the reverse transcription product are removed. Primers are added and amplified products are generated. In certain embodiments, the sequence of at least part of at least one species of amplified product is determined and at least part of the corresponding RNA molecule is determined. In some embodiments, at least some of the amplified product species are detected, directly or indirectly, allowing the presence and/or quantity of the RNA molecule of interest to be determined.

IPC Classes  ?

  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides
  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA

52.

Reagents, methods, and libraries for bead-based sequencing

      
Application Number 15291982
Grant Number 10323277
Status In Force
Filing Date 2016-10-12
First Publication Date 2017-03-23
Grant Date 2019-06-18
Owner APPLIED BIOSYSTEMS, LLC (USA)
Inventor
  • Mckernan, Kevin
  • Blanchard, Alan
  • Kotler, Lev
  • Costa, Gina

Abstract

The present invention provides methods for determining a nucleic acid sequence by performing successive cycles of duplex extension along a single stranded template. The cycles comprise steps of extension, ligation, and, preferably, cleavage. In certain embodiments the methods make use of extension probes containing phosphorothiolate linkages and employ agents appropriate to cleave such linkages. The invention provides methods of determining information about a sequence using at least two distinguishably labeled probe families. In certain embodiments the methods acquire less than 2 bits of information from each of a plurality of nucleotides in the template in each cycle. In certain embodiments the sequencing reactions are performed on templates attached to immobilized beads. The invention further provides sets of labeled extension probes containing phosphorothiolate linkages In addition, the invention includes performing multiple sequencing reactions on a single template by removing initializing oligonucleotides and extended strands and performing subsequent reactions using different initializing oligonucleotides.

IPC Classes  ?

  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides
  • C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
  • B82Y 15/00 - Nanotechnology for interacting, sensing or actuating, e.g. quantum dots as markers in protein assays or molecular motors
  • B82Y 30/00 - Nanotechnology for materials or surface science, e.g. nanocomposites
  • C12Q 1/6837 - Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
  • C12Q 1/6844 - Nucleic acid amplification reactions
  • C12Q 1/6869 - Methods for sequencing

53.

Methods of detecting target nucleic acids

      
Application Number 15241711
Grant Number 09677126
Status In Force
Filing Date 2016-08-19
First Publication Date 2016-12-08
Grant Date 2017-06-13
Owner APPLIED BIOSYSTEMS, LLC (USA)
Inventor
  • Sharaf, Muhammad A.
  • Woudenberg, Timothy
  • Mullah, Khairuzzaman Bashar

Abstract

The present disclosure relates to methods of identifying target nucleic acids by using coded molecules and its analysis by translocation through a nanopore. Generally, coded molecules are subject to a target polynucleotide dependent modification. The modified coded molecule is detected by isolating the modified coded molecules from the unmodified coded molecules prior to analysis through the nanopore or by detecting a change in the signal pattern of the coded molecule when analyzed through the nanopore.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
  • G01N 27/447 - Systems using electrophoresis

54.

Amplification and detection of ribonucleic acids

      
Application Number 15209090
Grant Number 09624534
Status In Force
Filing Date 2016-07-13
First Publication Date 2016-10-27
Grant Date 2017-04-18
Owner APPLIED BIOSYSTEMS, LLC (USA)
Inventor Kuersten, R. Scott

Abstract

Compositions, methods, and kits for detecting one or more species of RNA molecules are disclosed. In one embodiment, a first adaptor and a second adaptor are ligated to the RNA molecule using a polypeptide comprising double-strand specific RNA ligase activity, without an intervening purification step. The ligated product is reverse transcribed, then at least some of the ribonucleosides in the reverse transcription product are removed. Primers are added and amplified products are generated. In certain embodiments, the sequence of at least part of at least one species of amplified product is determined and at least part of the corresponding RNA molecule is determined. In some embodiments, at least some of the amplified product species are detected, directly or indirectly, allowing the presence and/or quantity of the RNA molecule of interest to be determined.

IPC Classes  ?

  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides
  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA

55.

Adaptive thermal block temperature control method and system

      
Application Number 15155371
Grant Number 10493419
Status In Force
Filing Date 2016-05-16
First Publication Date 2016-09-08
Grant Date 2019-12-03
Owner Applied Biosystems, LLC (USA)
Inventor
  • Lim, Chee Kiong
  • Ching, Chee Wee

Abstract

Aspects of the present teachings describe a method and apparatus for automatically controlling a block temperature to reduce undershooting and overshooting of the temperatures of a sample contained in the block and participating in a polymerase chain reaction (PCR). The adaptive thermal block temperature control begins when a sample temperature enters a sample window region between a preliminary setpoint temperature and a target setpoint temperature for the sample. Based on thermodynamic behavior of the sample and the predetermined phase of PCR, predicting a time period measured subsequent to the preliminary setpoint temperature when the sample will reach the target setpoint suitable for the predetermined phase of PCR. During this time period, varying the block temperature ramp rate with a series of cooling and heating changes to ensure the block temperature reaches the target setpoint temperature at approximately the same time as the sample reaches the same. Synchronizing the block temperature and sample temperature to the target setpoint temperature reduces undershooting and overshooting of the sample temperature and increases the speed and efficiency of the overall PCR process as it relates to the thermal cycling operations.

IPC Classes  ?

  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides
  • B01J 19/00 - Chemical, physical or physico-chemical processes in generalTheir relevant apparatus
  • B01L 7/00 - Heating or cooling apparatusHeat insulating devices
  • G05D 23/32 - Automatic controllers with an auxiliary heating device affecting the sensing element, e.g. for anticipating change of temperature with provision for adjustment of the effect of the auxiliary heating device, e.g. as a function of time

56.

APPLIED BIOSYSTEMS

      
Serial Number 87141415
Status Registered
Filing Date 2016-08-17
Registration Date 2018-04-24
Owner Applied Biosystems, LLC ()
NICE Classes  ? 10 - Medical apparatus and instruments

Goods & Services

Medical laboratory instruments for diagnostic use and medical diagnostic instruments, namely, nucleic acid sequencers and synthesizers, genetic analyzers, fragment analyzers, electrophoresis machines, linkage analyzers, genetic mappers, thermal cyclers, cytometer, chemical reaction mixture containment apparatus and structural parts thereof, protein and peptide synthesizers, mass spectrometer and chromatograph, high-throughput instruments for preparation of nucleic acid samples; laboratory medical and diagnostic supplies, namely, plastic consumables, namely, reaction trays and well plates, racks, vials, caps and septa for use with laboratory glassware for diagnostic purposes, needles, bottles, flask, filters for processing samples and fluids, storage tubes, and seals for laboratory glassware and plastic goods, plastic tray covers for holding microplates, microplate, pipette tips, reagent reservoir, optical heat field covers, plastic cards for sample collection, and plastic capillary arrays, all for diagnostic and medical use

57.

siRNA sequence-independent modification formats for reducing off-target phenotypic effects in RNAI, and stabilized forms thereof

      
Application Number 15015912
Grant Number 09771583
Status In Force
Filing Date 2016-02-04
First Publication Date 2016-08-11
Grant Date 2017-09-26
Owner APPLIED BIOSYSTEMS, LLC (USA)
Inventor
  • Puri, Nitin
  • Charles, Irudaya
  • Magdaleno, Susan
  • Vlassov, Alexander
  • Burnett, Christopher

Abstract

Modification formats having modified nucleotides are provided for siRNA. Short interfering RNA having modification formats and modified nucleotides provided herein reduce off-target effects in RNA interference of endogenous genes. Further modification formatted siRNAs are demonstrated to be stabilized to nuclease-rich environments. Unexpectedly, increasing or maintaining strand bias, while necessary to maintain potency for endogenous RNA interference, is not sufficient for reducing off-target effects in cell biology assays.

IPC Classes  ?

  • C12N 15/113 - Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides
  • C12N 15/11 - DNA or RNA fragmentsModified forms thereof

58.

Compositions for in situ nucleic acid analysis

      
Application Number 15041648
Grant Number 10501780
Status In Force
Filing Date 2016-02-11
First Publication Date 2016-08-11
Grant Date 2019-12-10
Owner APPLIED BIOSYSTEMS, LLC (USA)
Inventor
  • Fekete, Richard A.
  • Nguyen, Annalee

Abstract

Sample preparation processes for in situ RNA or DNA analysis, methods and compositions therefor are provided. Processes provided herein allow DNA or RNA analysis to be carried out in the same tube or on an aliquot of the prepared sample without centrifugation or extraction. The preparation process can be carried out at room temperature in as little as seven minutes and is amenable to high throughput processing using manual or robotic platforms.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
  • C12Q 1/6841 - In situ hybridisation
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C12Q 1/6844 - Nucleic acid amplification reactions
  • C12Q 1/686 - Polymerase chain reaction [PCR]

59.

BIGDYE

      
Application Number 179399200
Status Registered
Filing Date 2016-08-02
Registration Date 2018-11-28
Owner APPLIED BIOSYSTEMS, LLC (USA)
NICE Classes  ? 01 - Chemical and biological materials for industrial, scientific and agricultural use

Goods & Services

(1) Reagents for scientific and research purposes in the field of genetic analysis.

60.

Apparatus, system, and method using immiscible-fluid-discrete-volumes

      
Application Number 14925656
Grant Number 10041113
Status In Force
Filing Date 2015-10-28
First Publication Date 2016-07-07
Grant Date 2018-08-07
Owner Applied Biosystems, LLC (USA)
Inventor
  • Lee, Linda G.
  • Woo, Sam L.
  • Ma, Congcong
  • Reel, Richard T.
  • Oldham, Mark F.
  • Cox, David M.
  • Schroeder, Benjamin G.
  • Sorenson, Jon M.
  • Wiyatno, Willy

Abstract

Various embodiments of the teachings relate to a system or method for sample preparation or analysis in biochemical or molecular biology procedures. The sample preparation can involve small volume processed in discrete portions or segments or slugs, herein referred to as discrete volumes. A molecular biology procedure can be nucleic acid analysis. Nucleic acid analysis can be an integrated DNA amplification/DNA sequencing procedure.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides
  • C12Q 1/6869 - Methods for sequencing
  • B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glasswareDroppers
  • F15C 5/00 - Manufacture of fluid-circuit elementsManufacture of assemblages of such elements
  • F16K 99/00 - Subject matter not provided for in other groups of this subclass
  • G01N 35/08 - Automatic analysis not limited to methods or materials provided for in any single one of groups Handling materials therefor using a stream of discrete samples flowing along a tube system, e.g. flow injection analysis
  • G01N 1/14 - Suction devices, e.g. pumpsEjector devices
  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
  • G01N 27/447 - Systems using electrophoresis
  • B01L 3/02 - BurettesPipettes
  • B01L 7/00 - Heating or cooling apparatusHeat insulating devices

61.

Nanowire-based system for analysis of nucleic acids

      
Application Number 14997669
Grant Number 09587277
Status In Force
Filing Date 2016-01-18
First Publication Date 2016-05-12
Grant Date 2017-03-07
Owner Applied Biosystems, LLC (USA)
Inventor
  • Sun, Hongye
  • Fung, Steven
  • Woo, Sam Lee

Abstract

A method for sequencing a nucleic acid template includes forming a nanowire assembly including a semiconductor nanowire and a probe covalently bound to the semiconductor nanowire; contacting the nanowire assembly with a template nucleic acid; contacting the nucleic acid duplexes with an extension nucleic acid, the extension nucleic acid joined to the probe; disrupting the nucleic acid duplexes; and measuring an electrical characteristic of a nanowire assembly of the set of nanowire assemblies.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
  • C12Q 1/00 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions

62.

Biological analysis systems, devices, and methods

      
Application Number 14997956
Grant Number 10184149
Status In Force
Filing Date 2016-01-18
First Publication Date 2016-05-12
Grant Date 2019-01-22
Owner APPLIED BIOSYSTEMS, LLC (USA)
Inventor
  • Lehto, Dennis
  • Boege, Steven J.

Abstract

A device for performing biological sample reactions may include a plurality of flow cells configured to be mounted to a common microscope translation stage, wherein each flow cell is configured to receive at least one sample holder containing biological sample. Each flow cell also may be configured to be selectively placed in an open position for positioning the at least one sample holder into the flow cell and a closed position for reacting biological sample contained in the at least one sample holder. The plurality of flow cells may be configured to be selectively placed in the open position and the closed position independently of each other.

IPC Classes  ?

  • B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glasswareDroppers
  • B01L 7/00 - Heating or cooling apparatusHeat insulating devices
  • C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
  • G01N 21/05 - Flow-through cuvettes
  • G03B 27/42 - Projection printing apparatus, e.g. enlarger, copying camera for automatic sequential copying of the same original
  • B01L 9/00 - Supporting devicesHolding devices
  • G01N 15/14 - Optical investigation techniques, e.g. flow cytometry
  • G01N 21/03 - Cuvette constructions

63.

Device and method for making discrete volumes of a first fluid in contact with a second fluid, which are immiscible with each other

      
Application Number 14844279
Grant Number 10450604
Status In Force
Filing Date 2015-09-03
First Publication Date 2016-04-07
Grant Date 2019-10-22
Owner Applied Biosystems, LLC (USA)
Inventor
  • Wiyatno, Willy
  • Lee, Linda
  • Cox, David
  • Nurse, James
  • Greiner, Douglas
  • Lehto, Dennis
  • Wojtowicz, Janusz
  • Woo, Sam
  • Reel, Richard

Abstract

A method for generating, within a conduit, discrete volumes of one or more fluids that are immiscible with a second fluid. The discrete volumes can be used for biochemical or molecular biology procedures involving small volumes, for example, microliter-sized volumes, nanoliter-sized volumes, or smaller. The discrete volumes are separated from one another by a liquid that is immiscible with the fluid(s) of the discrete volumes, for example, aqueous immiscible-fluid-discrete volumes separated by an oil.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
  • C12Q 1/6869 - Methods for sequencing
  • B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glasswareDroppers
  • F15C 5/00 - Manufacture of fluid-circuit elementsManufacture of assemblages of such elements
  • F16K 99/00 - Subject matter not provided for in other groups of this subclass
  • G01N 35/08 - Automatic analysis not limited to methods or materials provided for in any single one of groups Handling materials therefor using a stream of discrete samples flowing along a tube system, e.g. flow injection analysis
  • G01N 1/14 - Suction devices, e.g. pumpsEjector devices
  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
  • G01N 27/447 - Systems using electrophoresis
  • B01L 3/02 - BurettesPipettes
  • B01L 7/00 - Heating or cooling apparatusHeat insulating devices

64.

Systems and methods for generating automated software workflow for biological testing

      
Application Number 14859001
Grant Number 10769559
Status In Force
Filing Date 2015-09-18
First Publication Date 2016-03-24
Grant Date 2020-09-08
Owner Applied Biosystems, LLC (USA)
Inventor
  • Desimas, Bruce
  • Dow, Leslie

Abstract

The workflow application integrates with a research software application associated with a laboratory instrument to provide a user with step-by-step instructions on how to follow the workflow steps of a laboratory experiment. The instructions are dynamically tailored, according to the nature of the workflow, the samples being experimented upon and/or the operating states of the instrument and/or the research software application. The workflow application significantly reduces the learning curve to operate sophisticated laboratory instruments. In a genetic testing instrument the workflow application can prescribe the need for control samples and can optimize the layout of samples within the instrument's sample receiving plate or fixture.

IPC Classes  ?

  • G06G 7/48 - Analogue computers for specific processes, systems, or devices, e.g. simulators
  • G06F 15/00 - Digital computers in generalData processing equipment in general
  • G06Q 10/06 - Resources, workflows, human or project managementEnterprise or organisation planningEnterprise or organisation modelling
  • C12Q 1/686 - Polymerase chain reaction [PCR]

65.

BIGDYE

      
Application Number 1290141
Status Registered
Filing Date 2015-12-18
Registration Date 2015-12-18
Owner Applied Biosystems, LLC (USA)
NICE Classes  ? 01 - Chemical and biological materials for industrial, scientific and agricultural use

Goods & Services

Reagents for scientific or research use.

66.

Compositions, methods, and kits for amplifying nucleic acids

      
Application Number 14876711
Grant Number 10604796
Status In Force
Filing Date 2015-10-06
First Publication Date 2016-01-28
Grant Date 2020-03-31
Owner Applied Biosystems, LLC (USA)
Inventor
  • Dong, Shoulian
  • Stevens, Junko F.
  • Lee, Danny H.

Abstract

The present teachings are directed to compositions, methods, and kits for amplifying target nucleic acids while reducing non-specific fluorescence and undesired amplification products, sometimes referred to as secondary amplification products or spurious side-products. The enzyme inhibitors disclosed herein comprise a nucleotide sequence and at least one quencher. Complexes comprising an enzyme inhibitor associated with an enzyme, wherein at least one enzymatic activity of the enzyme is inhibited, are also provided. Methods for amplifying a target nucleic acid while reducing undesired amplification products are disclosed, as are methods for reducing non-specific fluorescence. Kits for expediting the performance of certain disclosed methods are also provided.

IPC Classes  ?

  • C12Q 1/6844 - Nucleic acid amplification reactions
  • C12N 15/115 - Aptamers, i.e. nucleic acids binding a target molecule specifically and with high affinity without hybridising therewith
  • G01N 21/64 - FluorescencePhosphorescence

67.

Systems and methods for electronic detection with nanofets

      
Application Number 14864372
Grant Number 10180428
Status In Force
Filing Date 2015-09-24
First Publication Date 2016-01-14
Grant Date 2019-01-15
Owner APPLIED BIOSYSTEMS, LLC (USA)
Inventor
  • Oldham, Mark F.
  • Nordman, Eric S.

Abstract

There is disclosed a system for electrical charge detection comprising a nanoFET device. Also disclosed is a method of electrical charge detection for single molecule sequencing. The method includes attaching a macromolecule or assemblies thereof to a gate of a nanoFET device and flowing in a solution of charge tags, where a charge tag includes a nucleotide attached to a charge complex. The method also includes incorporating one charge tag into the macromolecule or assemblies thereof and cleaving the charge tags from the macromolecule or assemblies thereof. The method further includes detecting at least one of current and voltage from the nanoFET device.

IPC Classes  ?

  • G01N 27/414 - Ion-sensitive or chemical field-effect transistors, i.e. ISFETS or CHEMFETS
  • G01N 33/543 - ImmunoassayBiospecific binding assayMaterials therefor with an insoluble carrier for immobilising immunochemicals
  • B82Y 15/00 - Nanotechnology for interacting, sensing or actuating, e.g. quantum dots as markers in protein assays or molecular motors
  • C12Q 1/6825 - Nucleic acid detection involving sensors

68.

Multiplex compositions and methods for quantification of human nuclear DNA and human male DNA and detection of PCR inhibitors

      
Application Number 14744095
Grant Number 09481909
Status In Force
Filing Date 2015-06-19
First Publication Date 2015-12-17
Grant Date 2016-11-01
Owner APPLIED BIOSYSTEMS, LLC (USA)
Inventor
  • Shewale, Jaiprakash
  • Furtado, Manohar
  • Brzoska, Pius
  • Barbisin, Maura
  • Fang, Rixun
  • Malicdem, Michael
  • O'Shea, Cristin

Abstract

The invention relates to a method for simultaneous quantification of human nuclear DNA and human male DNA in a biological sample while also detecting the presence of PCR inhibitors in a single reaction. The multiplex quantification method also provides a ratio of human nuclear and male DNA present in a biological sample. Such sample characterization is useful for achieving efficient and accurate results in downstream molecular techniques such as genotyping.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides

69.

Electrowetting dispensing devices and related methods

      
Application Number 14817573
Grant Number 09671365
Status In Force
Filing Date 2015-08-04
First Publication Date 2015-11-26
Grant Date 2017-06-06
Owner Applied Biosystems, LLC (USA)
Inventor
  • Vann, Charles S.
  • Banerjee, Debjyoti
  • Geiser, Timothy G.
  • Nurse, James C.
  • Beard, Nigel P.

Abstract

A method for dispensing liquid for use in biological analysis may comprise positioning liquid to be dispensed via electrowetting. The positioning may comprise aligning the liquid with a plurality of predetermined locations. The method may further comprise dispensing the aligned liquid from the plurality of predetermined locations through a plurality of openings respectively aligned with the predetermined locations. The dispensing may be via electrowetting.

IPC Classes  ?

  • G01N 27/453 - Cells therefor
  • G01N 27/447 - Systems using electrophoresis
  • B01L 3/02 - BurettesPipettes
  • B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glasswareDroppers
  • B01J 4/00 - Feed devicesFeed or outlet control devices

70.

Method of making a paired tag library for nucleic acid sequencing

      
Application Number 14798558
Grant Number 09657291
Status In Force
Filing Date 2015-07-14
First Publication Date 2015-11-05
Grant Date 2017-05-23
Owner APPLIED BIOSYSTEMS, LLC (USA)
Inventor
  • Li, Bin
  • Xi, Lei
  • Ranade, Swati
  • Wang, Yangzhou

Abstract

The present disclosure relates to methods and compositions for making paired tags and paired tag libraries.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA

71.

Methods of detecting target nucleic acids

      
Application Number 14790369
Grant Number 09434982
Status In Force
Filing Date 2015-07-02
First Publication Date 2015-10-29
Grant Date 2016-09-06
Owner Applied Biosystems LLC (USA)
Inventor
  • Sharaf, Muhammad A.
  • Woudenberg, Timothy
  • Mullah, Khairuzzaman Bashar

Abstract

The present disclosure relates to methods of identifying target nucleic acids by using coded molecules and its analysis by translocation through a nanopore. Generally, coded molecules are subject to a target polynucleotide dependent modification. The modified coded molecule is detected by isolating the modified coded molecules from the unmodified coded molecules prior to analysis through the nanopore or by detecting a change in the signal pattern of the coded molecule when analyzed through the nanopore.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids

72.

Compositions, systems, and methods for immiscible fluid discrete volume manipulation

      
Application Number 12036037
Grant Number 09152150
Status In Force
Filing Date 2008-02-22
First Publication Date 2015-10-06
Grant Date 2015-10-06
Owner Applied Biosystems, LLC (USA)
Inventor
  • Lee, Linda G.
  • Oldham, Mark F.
  • Woo, Sam L.
  • Cox, David M.
  • Reel, Richard T.
  • Ma, Peter N.
  • Johnson, Ben F.
  • Letho, Dennis

Abstract

Systems and methods of manipulating discrete volumes of a first fluid in a second fluid are provided. In some embodiments, discrete volumes can be formed in a conduit. In other embodiments, addition fluid can be added to a discrete volume in a first conduit by injecting the addition fluid at a relatively higher pressure. In some embodiments, discrete volumes that normally would not coalesce can be manipulated to be merged together.

IPC Classes  ?

  • G05D 11/00 - Control of flow ratio
  • G05D 7/06 - Control of flow characterised by the use of electric means
  • B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glasswareDroppers
  • B01F 13/00 - Other mixers; Mixing plant, including combinations of dissimilar mixers
  • G01N 35/08 - Automatic analysis not limited to methods or materials provided for in any single one of groups Handling materials therefor using a stream of discrete samples flowing along a tube system, e.g. flow injection analysis
  • B01L 3/02 - BurettesPipettes

73.

Analyzing messenger RNA and micro RNA in the same reaction mixture

      
Application Number 14627741
Grant Number 09422603
Status In Force
Filing Date 2015-02-20
First Publication Date 2015-08-20
Grant Date 2016-08-23
Owner Applied Biosystems, LLC (USA)
Inventor
  • Lao, Kai Qin
  • Straus, Neil A.

Abstract

The present teachings provide methods, compositions, and kits for performing primer extension reactions on at least two target polynucleotides in the same reaction mixture. In some embodiments, a reverse transcription reaction is performed on a first target polynucleotide with a hot start primer comprising a self-complementary stem and a loop, and extension products form at high temperatures but extension products form less so at low temperatures since the self-complementary stem of the hot start primer prevents hybridization of the target specific region to the target. However, non-hot start primers with free target specific regions can hybridize to their corresponding targets at the low temperature and extension can happen at the low temperature.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides

74.

Reagents useful for synthesizing rhodamine-labeled oligonucleotides

      
Application Number 14702499
Grant Number 09783560
Status In Force
Filing Date 2015-05-01
First Publication Date 2015-08-20
Grant Date 2017-10-10
Owner Applied Biosystems, LLC (USA)
Inventor
  • Benson, Scott C.
  • Zou, Ruiming N.
  • Upadhya, Krishna G.
  • Kenney, Paul M.
  • Cassel, Jonathan M.

Abstract

The present disclosure provides reagents that can be used to label synthetic oligonucleotides with rhodamine dyes or dye networks that contain rhodamine dyes.

IPC Classes  ?

  • C07D 311/96 - Heterocyclic compounds containing six-membered rings having one oxygen atom as the only hetero atom, condensed with other rings spiro-condensed with carbocyclic rings or ring systems
  • C07H 19/04 - Heterocyclic radicals containing only nitrogen as ring hetero atom
  • C07F 9/6561 - Heterocyclic compounds, e.g. containing phosphorus as a ring hetero atom containing systems of two or more relevant hetero rings condensed among themselves or condensed with a common carbocyclic ring or ring system, with or without other non-condensed hetero rings
  • C07H 21/04 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical

75.

System for genetic surveillance and analysis

      
Application Number 14566651
Grant Number 10181010
Status In Force
Filing Date 2014-12-10
First Publication Date 2015-07-30
Grant Date 2019-01-15
Owner APPLIED BIOSYSTEMS, LLC (USA)
Inventor
  • Patel, Chirag
  • Fuernkranz, Hans
  • Greenstein, Michael

Abstract

A genetic surveillance system comprises a communications network and at least one reader-analyzer instrument. The reader-analyzer instrument has a communication interface to communicate over the network. The reader-analyzer instrument is adapted to perform genetic assay analysis of a sample obtained from a member of a population and to generate detection-related data based upon the analysis. The reader-analyzer instrument is adapted to associate qualifying information with the detection-related data and to communicate the associated qualifying information and detection-related data over the network.

IPC Classes  ?

  • G06F 19/00 - Digital computing or data processing equipment or methods, specially adapted for specific applications (specially adapted for specific functions G06F 17/00;data processing systems or methods specially adapted for administrative, commercial, financial, managerial, supervisory or forecasting purposes G06Q;healthcare informatics G16H)
  • G06F 19/20 - for hybridisation or gene expression, e.g. microarrays, sequencing by hybridisation, normalisation, profiling, noise correction models, expression ratio estimation, probe design or probe optimisation
  • G06F 19/22 - for sequence comparison involving nucleotides or amino acids, e.g. homology search, motif or Single-Nucleotide Polymorphism [SNP] discovery or sequence alignment
  • G06F 19/28 - for programming tools or database systems, e.g. ontologies, heterogeneous data integration, data warehousing or computing architectures
  • G16H 10/40 - ICT specially adapted for the handling or processing of patient-related medical or healthcare data for data related to laboratory analysis, e.g. patient specimen analysis
  • G16H 50/80 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for detecting, monitoring or modelling epidemics or pandemics, e.g. flu

76.

Use of antibody-surrogate antigen systems for detection of analytes

      
Application Number 14074931
Grant Number 09575069
Status In Force
Filing Date 2013-11-08
First Publication Date 2015-07-16
Grant Date 2017-02-21
Owner APPLIED BIOSYSTEMS, LLC (USA)
Inventor
  • Menchen, Steven
  • Lam, Joe Y.
  • Ma, Zhaochun
  • Mullah, Khairuzzaman Bashar

Abstract

Compositions, methods and kits for labeling proteins and uses in reporter systems for detecting, quantifying and/or characterizing analytes.

IPC Classes  ?

  • G01N 33/58 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing involving labelled substances
  • C07D 311/88 - Nitrogen atoms
  • G01N 33/532 - Production of labelled immunochemicals

77.

Amplification and detection of ribonucleic acids

      
Application Number 14571142
Grant Number 09416406
Status In Force
Filing Date 2014-12-15
First Publication Date 2015-04-09
Grant Date 2016-08-16
Owner Applied Biosystems, LLC (USA)
Inventor Kuersten, R. Scott

Abstract

Compositions, methods, and kits for detecting one or more species of RNA molecules are disclosed. In one embodiment, a first adaptor and a second adaptor are ligated to the RNA molecule using a polypeptide comprising double-strand specific RNA ligase activity, without an intervening purification step. The ligated product is reverse transcribed, then at least some of the ribonucleosides in the reverse transcription product are removed. Primers are added and amplified products are generated. In certain embodiments, the sequence of at least part of at least one species of amplified product is determined and at least part of the corresponding RNA molecule is determined. In some embodiments, at least some of the amplified product species are detected, directly or indirectly, allowing the presence and/or quantity of the RNA molecule of interest to be determined.

IPC Classes  ?

  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides
  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA

78.

Axial illumination for capillary electrophoresis

      
Application Number 14340298
Grant Number 09285316
Status In Force
Filing Date 2014-07-24
First Publication Date 2015-02-19
Grant Date 2016-03-15
Owner Applied Biosystems, LLC (USA)
Inventor
  • Reel, Richard
  • Nordman, Eric

Abstract

System and method for fluorescent light excitation and detection from samples to enhance the numerical aperture and/or reduce the cross-talk of the fluorescent light. The system for analyzing samples comprising: a light source that provides a non-coherent excitation light; at least one housing, wherein the housing transports samples and propagates the non-coherent excitation light by total internal reflection; a coupling optical element configured to introduce the non-coherent excitation light into the at least one housing through a wall of the at least one housing; and at least one NA enhancing optical element to collect an emitted fluorescence, wherein the NA enhancing optical element is constructed of a first material and the housing is constructed of a second material, wherein the first material has a greater index of refraction than the second material.

IPC Classes  ?

79.

Sample preparation for in situ nucleic acid analysis, methods and compositions therefor

      
Application Number 14459805
Grant Number 09279152
Status In Force
Filing Date 2014-08-14
First Publication Date 2015-02-19
Grant Date 2016-03-08
Owner Applied Biosystems, LLC (USA)
Inventor
  • Fekete, Richard
  • Nguyen, Annalee

Abstract

Sample preparation processes for in situ RNA or DNA analysis, methods and compositions therefor are provided. Processes provided herein allow DNA or RNA analysis to be carried out in the same tube or on an aliquot of the prepared sample without centrifugation or extraction. The preparation process can be carried out at room temperature in as little as seven minutes and is amenable to high throughput processing using manual or robotic platforms.

IPC Classes  ?

  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides
  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA

80.

Electrowetting dispensing devices and related methods

      
Application Number 14479824
Grant Number 09132400
Status In Force
Filing Date 2014-09-08
First Publication Date 2015-01-08
Grant Date 2015-09-15
Owner Applied Biosystems, LLC (USA)
Inventor
  • Vann, Charles S.
  • Banerjee, Debjyoti
  • Geiser, Timothy G.
  • Nurse, James C.
  • Beard, Nigel P.

Abstract

A method for dispensing liquid for use in biological analysis may comprise positioning liquid to be dispensed via electrowetting. The positioning may comprise aligning the liquid with a plurality of predetermined locations. The method may further comprise dispensing the aligned liquid from the plurality of predetermined locations through a plurality of openings respectively aligned with the predetermined locations. The dispensing may be via electrowetting.

IPC Classes  ?

  • G01N 27/453 - Cells therefor
  • B01J 4/00 - Feed devicesFeed or outlet control devices
  • B01L 3/02 - BurettesPipettes
  • B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glasswareDroppers

81.

Electrowetting dispensing devices and related methods

      
Application Number 14479188
Grant Number 09126169
Status In Force
Filing Date 2014-09-05
First Publication Date 2014-12-25
Grant Date 2015-09-08
Owner Applied Biosystems, LLC (USA)
Inventor
  • Vann, Charles S.
  • Banerjee, Debjyoti
  • Geiser, Timothy G.
  • Nurse, James C.
  • Beard, Nigel P.

Abstract

A method for dispensing liquid for use in biological analysis may comprise positioning liquid to be dispensed via electrowetting. The positioning may comprise aligning the liquid with a plurality of predetermined locations. The method may further comprise dispensing the aligned liquid from the plurality of predetermined locations through a plurality of openings respectively aligned with the predetermined locations. The dispensing may be via electrowetting.

IPC Classes  ?

  • G01N 27/453 - Cells therefor
  • B01J 4/00 - Feed devicesFeed or outlet control devices
  • B01L 3/02 - BurettesPipettes
  • B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glasswareDroppers

82.

Methods for bead-based sequencing

      
Application Number 13737534
Grant Number 09217177
Status In Force
Filing Date 2013-01-09
First Publication Date 2014-11-20
Grant Date 2015-12-22
Owner APPLIED BIOSYSTEMS, LLC (USA)
Inventor
  • Mckernan, Kevin
  • Blanchard, Alan
  • Kotler, Lev
  • Costa, Gina

Abstract

The present invention provides methods for determining a nucleic acid sequence by performing successive cycles of duplex extension along a single stranded template. The cycles comprise steps of extension, ligation, and, preferably, cleavage. In certain embodiments the methods make use of extension probes containing phosphorothiolate linkages and employ agents appropriate to cleave such linkages. The invention provides methods of determining information about a sequence using at least two distinguishably labeled probe families. In certain embodiments the methods acquire less than 2 bits of information from each of a plurality of nucleotides in the template in each cycle. In certain embodiments the sequencing reactions are performed on templates attached to beads. The invention further provides sets of labeled extension probes containing phosphorothiolate linkages. In addition, the invention includes performing multiple sequencing reactions on a single template by removing initializing oligonucleotides and extended strands and performing subsequent reactions using different initializing oligonucleotides.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
  • B82Y 15/00 - Nanotechnology for interacting, sensing or actuating, e.g. quantum dots as markers in protein assays or molecular motors
  • B82Y 30/00 - Nanotechnology for materials or surface science, e.g. nanocomposites

83.

Differential dissociation and melting curve peak detection

      
Application Number 14259057
Grant Number 09977860
Status In Force
Filing Date 2014-04-22
First Publication Date 2014-11-20
Grant Date 2018-05-22
Owner Applied Biosystems, LLC (USA)
Inventor Cheng, Francis T.

Abstract

Systems and methods are provided for processing a melting or dissociation curve of a DNA or other sample, for example, during PCR processing. In some embodiments, detection of the melting point and melting curve behavior can be enhanced by taking a derivative of the curve, and detecting peaks in the differential dissociation curve. In some embodiments, the derivative operation can comprise the use of edge-processing, or other detection algorithms. In some embodiments, the dissociation analysis can comprise removing low-frequency (or pedestal) components of the differential dissociation curve. In some embodiments, the differential dissociation curve can exhibit a smoothed or more regular appearance than the raw detected data.

IPC Classes  ?

  • G06F 19/10 - Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology (in silico methods of screening virtual chemical libraries C40B 30/02;in silico or mathematical methods of creating virtual chemical libraries C40B 50/02)
  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids

84.

Fluorescent dye compounds, conjugates and uses thereof

      
Application Number 14229663
Grant Number 09745336
Status In Force
Filing Date 2014-03-28
First Publication Date 2014-10-09
Grant Date 2017-08-29
Owner Applied Biosystems, LLC (USA)
Inventor
  • Graham, Ronald
  • Zou, Ruiming
  • Upadhya, Krishna
  • Benson, Scott

Abstract

The present teachings generally relate to fluorescent dyes, linkable forms of fluorescent dyes, energy transfer dyes, reagents labeled with fluorescent dyes and uses thereof.

IPC Classes  ?

  • C07H 19/04 - Heterocyclic radicals containing only nitrogen as ring hetero atom
  • C07H 21/00 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
  • C07D 219/06 - Oxygen atoms
  • C09B 15/00 - Acridine dyes
  • C09K 11/06 - Luminescent, e.g. electroluminescent, chemiluminescent, materials containing organic luminescent materials
  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
  • G01N 33/58 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing involving labelled substances

85.

Electrowetting dispensing devices and related methods

      
Application Number 14262921
Grant Number 09061262
Status In Force
Filing Date 2014-04-28
First Publication Date 2014-09-11
Grant Date 2015-06-23
Owner Applied Biosystems, LLC (USA)
Inventor
  • Vann, Charles S.
  • Banerjee, Debjyoti
  • Geiser, Timothy G.
  • Nurse, James C.
  • Beard, Nigel P.

Abstract

A device having a first substrate and a second substrate separated from the first substrate to form a volume between the first and second substrates, electrodes disposed on the first and second substrates and facing the volume, each substrate comprising at least one electrode, and a first insulating layer disposed on the first substrate and a second insulating layer disposed on the second substrate to separate the electrodes from the volume.

IPC Classes  ?

  • B01J 4/00 - Feed devicesFeed or outlet control devices
  • B01L 3/02 - BurettesPipettes
  • B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glasswareDroppers

86.

Reagents, methods, and libraries for bead-based sequencing

      
Application Number 14057055
Grant Number 09493830
Status In Force
Filing Date 2013-10-18
First Publication Date 2014-09-04
Grant Date 2016-11-15
Owner Applied Biosystems, LLC (USA)
Inventor
  • Mckernan, Kevin
  • Blanchard, Alan
  • Kotler, Lev
  • Costa, Gina

Abstract

The present invention provides methods for determining a nucleic acid sequence by performing successive cycles of duplex extension along a single stranded template. The cycles comprise steps of extension, ligation, and, preferably, cleavage. In certain embodiments the methods make use of extension probes containing phosphorothiolate linkages and employ agents appropriate to cleave such linkages. The invention provides methods of determining information about a sequence using at least two distinguishably labeled probe families. In certain embodiments the methods acquire less than 2 bits of information from each of a plurality of nucleotides in the template in each cycle. In certain embodiments the sequencing reactions are performed on templates attached to immobilized beads. The invention further provides sets of labeled extension probes containing phosphorothiolate linkages. In addition, the invention includes performing multiple sequencing reactions on a single template by removing initializing oligonucleotides and extended strands and performing subsequent reactions using different initializing oligonucleotides.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides
  • B82Y 15/00 - Nanotechnology for interacting, sensing or actuating, e.g. quantum dots as markers in protein assays or molecular motors
  • B82Y 30/00 - Nanotechnology for materials or surface science, e.g. nanocomposites

87.

N-vinylamide)s and their use in capillary electrophoresis

      
Application Number 14148401
Grant Number 09671367
Status In Force
Filing Date 2014-01-06
First Publication Date 2014-07-31
Grant Date 2017-06-06
Owner Applied Biosystems, LLC (USA)
Inventor Lau, Aldrich N. K.

Abstract

The invention relates generally to polymers and copolymers comprising N-vinylamide-type monomers, their preparation, and compositions, such as electrophoresis separation media, containing the same; to supports, such as capillaries, containing these polymers; and methods for separating a mixture of biomolecules, especially polynucleotides, using capillary electrophoresis. Separation media comprising such polymers yield advantageous performance in the analysis and separation of biomolecules by capillary electrophoresis.

IPC Classes  ?

88.

Methods of detecting target nucleic acids

      
Application Number 14137376
Grant Number 09074252
Status In Force
Filing Date 2013-12-20
First Publication Date 2014-06-19
Grant Date 2015-07-07
Owner Applied Biosystems, LLC (USA)
Inventor
  • Sharaf, Muhammad A.
  • Woudenberg, Timothy
  • Mullah, Khairuzzaman Bashar

Abstract

The present disclosure relates to methods of identifying target nucleic acids by using coded molecules and its analysis by translocation through a nanopore. Generally, coded molecules are subject to a target polynucleotide dependent modification. The modified coded molecule is detected by isolating the modified coded molecules from the unmodified coded molecules prior to analysis through the nanopore or by detecting a change in the signal pattern of the coded molecule when analyzed through the nanopore.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids

89.

Systems and methods for multiple analyte detection

      
Application Number 14093933
Grant Number 09714444
Status In Force
Filing Date 2013-12-02
First Publication Date 2014-06-12
Grant Date 2017-07-25
Owner APPLIED BIOSYSTEMS, LLC (USA)
Inventor
  • Yue, Min
  • Liu, David M.
  • Roy, Joy
  • Chiang, Yuh-Min
  • Yang, Joon Mo
  • Lehto, Dennis
  • Vann, Charles S.
  • Beard, Nigel P.
  • Harding, Ian A.
  • Van Camp, John R.
  • Dromaretsky, Alexander
  • Ermakov, Sergey V.
  • Oldham, Mark F.
  • Shariati, Maryam
  • Ulmanella, Umberto

Abstract

Systems and methods for multiple analyte detection include a system for distribution of a biological sample that includes a substrate, wherein the substrate includes a plurality of sample chambers, a sample introduction channel for each sample chamber, and a venting channel for each sample chamber. The system may further include a preloaded reagent contained in each sample chamber and configured for nucleic acid analysis of a biological sample that enters the substrate and a sealing instrument configured to be placed in contact with the substrate to seal each sample chamber so as to substantially prevent sample contained in each sample chamber from flowing out of each sample chamber. The substrate can be constructed of detection-compatible and assay-compatible materials.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
  • B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glasswareDroppers
  • G01N 35/02 - Automatic analysis not limited to methods or materials provided for in any single one of groups Handling materials therefor using a plurality of sample containers moved by a conveyor system past one or more treatment or analysis stations

90.

Methods, compositions, and kits for detecting protein aggregates

      
Application Number 13975056
Grant Number 09518296
Status In Force
Filing Date 2013-08-23
First Publication Date 2014-05-15
Grant Date 2016-12-13
Owner APPLIED BIOSYSTEMS LLC (USA)
Inventor
  • Ruff, David
  • Shannon, Mark
  • Livak, Kenneth
  • Guegler, Karl
  • Hennessy, Kevin

Abstract

The present teachings provide methods, compositions, and kits for detecting the presence of protein aggregates. In some embodiments, the protein aggregate is treated with a labeled precursor, and the labeled precursor is incorporated into the protein aggregate to form a labeled protein aggregate. The labeled protein aggregate is then measured, thus detecting the presence of the protein aggregate. In some embodiments, the labeled protein aggregate is detected by interaction of labeled precursors, for example by a proximity ligation assay.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
  • C07K 14/47 - Peptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from animalsPeptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from humans from vertebrates from mammals

91.

Sample preparation for in situ nucleic acid analysis, methods and compositions therefor

      
Application Number 14136685
Grant Number 08828664
Status In Force
Filing Date 2013-12-20
First Publication Date 2014-05-08
Grant Date 2014-09-09
Owner Applied Biosystems, LLC. (USA)
Inventor
  • Fekete, Richard
  • Nguyen, Annalee

Abstract

Sample preparation processes for in situ RNA or DNA analysis, methods and compositions therefor are provided. Processes provided herein allow DNA or RNA analysis to be carried out in the same tube or on an aliquot of the prepared sample without centrifugation or extraction. The preparation process can be carried out at room temperature in as little as seven minutes and is amenable to high throughput processing using manual or robotic platforms.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides

92.

Method for direct amplification from crude nucleic acid samples

      
Application Number 13914478
Grant Number 09057110
Status In Force
Filing Date 2013-06-10
First Publication Date 2014-05-01
Grant Date 2015-06-16
Owner APPLIED BIOSYSTEMS LLC (USA)
Inventor
  • Chang, Chien-Wei
  • Hennessy, Lori
  • Wang, Dennis

Abstract

The present teachings relate to improved methods, kits, and reaction mixtures for amplifying nucleic acids. In some embodiments a novel direct buffer formulation is provided which allows for the direct amplification of the nucleic acids in a crude sample with minimal sample purification.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids

93.

Method of automated calibration and diagnosis of laboratory instruments

      
Application Number 14023111
Grant Number 09482652
Status In Force
Filing Date 2013-09-10
First Publication Date 2014-05-01
Grant Date 2016-11-01
Owner Applied Biosystems, LLC (USA)
Inventor
  • Desimas, Bruce E.
  • Dow, Leslie A.

Abstract

Method and system providing an automated workflow for installing and/or calibrating laboratory equipment. The workflow empowers an end user to perform installation and calibration thereby reducing the costs associated with such activities. The automated workflow taught herein, can greatly reduce the incidence of calibration error by providing for verification of certain events during the calibration process.

IPC Classes  ?

  • G01N 3/00 - Investigating strength properties of solid materials by application of mechanical stress
  • G01N 33/00 - Investigating or analysing materials by specific methods not covered by groups
  • G01N 31/00 - Investigating or analysing non-biological materials by the use of the chemical methods specified in the subgroupsApparatus specially adapted for such methods
  • G01D 18/00 - Testing or calibrating apparatus or arrangements provided for in groups

94.

SiRNA sequence-independent modification formats for reducing off-target phenotypic effects in RNAi, and stabilized forms thereof

      
Application Number 13975136
Grant Number 09273312
Status In Force
Filing Date 2013-08-23
First Publication Date 2014-04-03
Grant Date 2016-03-01
Owner Applied Biosystems, LLC (USA)
Inventor
  • Puri, Nitin
  • Charles, Irudaya
  • Magdaleno, Susan
  • Vlassov, Alexander
  • Burnett, Christopher

Abstract

Modification formats having modified nucleotides are provided for siRNA. Short interfering RNA having modification formats and modified nucleotides provided herein reduce off-target effects in RNA interference of endogenous genes. Further modification formatted siRNAs are demonstrated to be stabilized to nuclease-rich environments. Unexpectedly, increasing or maintaining strand bias, while necessary to maintain potency for endogenous RNA interference, is not sufficient for reducing off-target effects in cell biology assays.

IPC Classes  ?

  • C12N 15/113 - Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides
  • C12N 15/11 - DNA or RNA fragmentsModified forms thereof

95.

Electrowetting-based valving and pumping systems

      
Application Number 14028199
Grant Number 09011663
Status In Force
Filing Date 2013-09-16
First Publication Date 2014-03-20
Grant Date 2015-04-21
Owner Applied Biosystems, LLC (USA)
Inventor Ulmanella, Umberto

Abstract

The present teachings relate to microfluidic valves and pumping systems, which may be suitable for controlling and facilitating liquid flow. Electrodes are disposed proximately to volumes containing a liquid. The liquid flow can be facilitated by electrowetting forces. Processes for controlling the flow of liquids, as well as for pumping liquids, are also disclosed.

IPC Classes  ?

  • G01N 27/453 - Cells therefor
  • F16K 31/02 - Operating meansReleasing devices electricOperating meansReleasing devices magnetic
  • G05D 7/06 - Control of flow characterised by the use of electric means
  • B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glasswareDroppers
  • F16K 99/00 - Subject matter not provided for in other groups of this subclass

96.

Electrowetting dispensing devices and related methods

      
Application Number 13892141
Grant Number 09044724
Status In Force
Filing Date 2013-05-10
First Publication Date 2014-01-02
Grant Date 2015-06-02
Owner Applied Biosystems, LLC (USA)
Inventor
  • Vann, Charles S.
  • Banerjee, Debjyoti
  • Geiser, Timothy G.
  • Nurse, James C.
  • Beard, Nigel P.

Abstract

A method for dispensing liquid for use in biological analysis may comprise positioning liquid to be dispensed via electrowetting. The positioning may comprise aligning the liquid with a plurality of predetermined locations. The method may further comprise dispensing the aligned liquid from the plurality of predetermined locations through a plurality of openings respectively aligned with the predetermined locations. The dispensing may be via electrowetting.

IPC Classes  ?

  • B01J 4/00 - Feed devicesFeed or outlet control devices
  • B01L 3/02 - BurettesPipettes
  • B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glasswareDroppers

97.

Chimeric oligonucleotides for ligation-enhanced nucleic acid detection, methods and compositions therefor

      
Application Number 13871827
Grant Number 08889355
Status In Force
Filing Date 2013-04-26
First Publication Date 2013-12-19
Grant Date 2014-11-18
Owner Applied Biosystems, LLC (USA)
Inventor
  • Kuersten, R. Scott
  • Pasloske, Brittan

Abstract

Ligation-enhanced nucleic acid detection assay embodiments for detection of RNA or DNA are described. The assay embodiments rely on ligation of chimeric oligonucleotide probes to generate a template for amplification and detection. The assay embodiments are substantially independent of the fidelity of a polymerase for copying compromised nucleic acid. Very little background amplification is observed and as few as 1000 copies of target nucleic acid can be detected. Method embodiments are particularly adept for detection of RNA from compromised samples such as formalin-fixed and paraffin-embedded samples. Heavily degraded and cross-linked nucleic acids of compromised samples, in which classic quantitative real time PCR assays typically fail to adequately amplify signal, can be reliably detected and quantified.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
  • C07H 21/00 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
  • C07H 21/02 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with ribosyl as saccharide radical
  • C07H 21/04 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical

98.

Amplification and detection of ribonucleic acids

      
Application Number 13960780
Grant Number 08932816
Status In Force
Filing Date 2013-08-06
First Publication Date 2013-12-12
Grant Date 2015-01-13
Owner Applied Biosystems, LLC (USA)
Inventor Kuersten, R. Scott

Abstract

Compositions, methods, and kits for detecting one or more species of RNA molecules are disclosed. In one embodiment, a first adaptor and a second adaptor are ligated to the RNA molecule using a polypeptide comprising double-strand specific RNA ligase activity, without an intervening purification step. The ligated product is reverse transcribed, then at least some of the ribonucleosides in the reverse transcription product are removed. Primers are added and amplified products are generated. In certain embodiments, the sequence of at least part of at least one species of amplified product is determined and at least part of the corresponding RNA molecule is determined. In some embodiments, at least some of the amplified product species are detected, directly or indirectly, allowing the presence and/or quantity of the RNA molecule of interest to be determined.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA

99.

Modified surfaces as solid supports for nucleic acid purification

      
Application Number 13850275
Grant Number 09464315
Status In Force
Filing Date 2013-03-25
First Publication Date 2013-11-14
Grant Date 2016-10-11
Owner Applied Biosystems, LLC (USA)
Inventor
  • Latham, Gary
  • Fang, Xingwang
  • Conrad, Richard
  • Kemppainen, Jon
  • Setterquist, Robert
  • Pasloske, Brittan

Abstract

The invention relates to methods of separating polynucleotides, such as DNA, RNA and PNA, from solutions containing polynucleotides by reversibly binding the polynucleotides to a solid surface, such as a magnetic microparticle.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA

100.

Alternative nucleic acid sequencing methods

      
Application Number 13860769
Grant Number 09404155
Status In Force
Filing Date 2013-04-11
First Publication Date 2013-11-14
Grant Date 2016-08-02
Owner Applied Biosystems, LLC (USA)
Inventor Bortner, Scott

Abstract

Embodiments are provided that provide for parallel sequencing of nucleic acid segments. In some embodiments, a single sequence is sequenced by at least two different sequencing techniques and the results compared, allowing for deficiencies or strengths of one technique to be complemented by the second technique.

IPC Classes  ?

  • C40B 20/08 - Direct analysis of the library members per se by physical methods, e.g. spectroscopy
  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
  • G06F 19/22 - for sequence comparison involving nucleotides or amino acids, e.g. homology search, motif or Single-Nucleotide Polymorphism [SNP] discovery or sequence alignment
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