Patents Assigned to Applied Biosystems, LLC.
  • Patent number: 11538557
    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.
    Type: Grant
    Filed: April 30, 2018
    Date of Patent: December 27, 2022
    Assignee: Applied Biosystems, LLC
    Inventor: Zheng Zhang
  • Publication number: 20220389499
    Abstract: A method for forming discrete volumes of aqueous fluid may comprise flowing aqueous fluid into a first conduit from a supply of aqueous fluid and flowing into the first conduit a spacing liquid supplied from a second conduit, the spacing liquid being immiscible with the aqueous fluid. The flowing of the aqueous fluid and the spacing liquid into the first conduit forms discrete volumes of the aqueous fluid, with consecutive discrete volumes of the aqueous fluid separated by the spacing liquid. The method may further comprise transferring the discrete volumes of the aqueous fluid and spacing liquid from the first conduit to a third conduit for processing.
    Type: Application
    Filed: April 25, 2022
    Publication date: December 8, 2022
    Applicant: APPLIED BIOSYSTEMS, LLC
    Inventors: Willy K. Wiyatno, Linda Lee, David Cox, James Nurse, Douglas Greiner, Dennis Lehto, Janusz Wojtowicz, Sam Woo, Richard Reel
  • Patent number: 11407773
    Abstract: The present disclosure provides reagents that can be used to label synthetic oligonucleotides with rhodamine dyes or dye networks that contain rhodamine dyes.
    Type: Grant
    Filed: January 30, 2020
    Date of Patent: August 9, 2022
    Assignee: Applied Biosystems, LLC
    Inventors: Scott C. Benson, Ruiming N. Zou, Krishna G. Upadhya, Paul M. Kenney, Jonathan M. Cassel
  • Patent number: 11319585
    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.
    Type: Grant
    Filed: October 17, 2019
    Date of Patent: May 3, 2022
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: Willy K. Wiyatno, Linda Lee, David Cox, James Nurse, Douglas Greiner, Dennis Lehto, Janusz Wojtowicz, Sam Woo, Richard Reel
  • Patent number: 11257570
    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.
    Type: Grant
    Filed: April 27, 2018
    Date of Patent: February 22, 2022
    Assignee: Applied Biosystems, LLC
    Inventor: Francis T. Cheng
  • Publication number: 20220033896
    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.
    Type: Application
    Filed: October 19, 2021
    Publication date: February 3, 2022
    Applicant: APPLIED BIOSYSTEMS, LLC
    Inventors: Linda G. LEE, Sam L. WOO, Congcong MA, Richard T. REEL, Mark F. OLDHAM, David M. COX, Benjamin G. SCHROEDER, Jon M. SORENSON, Willy WIYATNO
  • Patent number: 11225686
    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.
    Type: Grant
    Filed: January 17, 2020
    Date of Patent: January 18, 2022
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: Shoulian Dong, Junko F. Stevens, Danny H. Lee
  • Patent number: 11175258
    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.
    Type: Grant
    Filed: January 14, 2019
    Date of Patent: November 16, 2021
    Assignee: Applied Biosystems, LLC
    Inventors: Mark F. Oldham, Eric S. Nordman
  • Patent number: 11162137
    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.
    Type: Grant
    Filed: August 3, 2018
    Date of Patent: November 2, 2021
    Assignee: APPLIED BIOSYSTEMS LLC
    Inventors: Linda G. Lee, Sam L. Woo, Congcong Ma, Richard T. Reel, Mark F. Oldham, David M. Cox, Benjamin G. Schroeder, Jon M. Sorenson, Willy Wiyatno
  • Patent number: 11111525
    Abstract: This invention is directed to methods, kits, non-nucleotide probes as well as other compositions pertaining to the suppression of binding of detectable nucleic acid probes to undesired nucleotide sequences of genomic nucleic acid in assays designed to determine target genomic nucleic acid.
    Type: Grant
    Filed: March 19, 2018
    Date of Patent: September 7, 2021
    Assignees: Applied Biosystems, LLC, Agilent Technologies, Inc.
    Inventors: Kirsten Vang Nielsen, Jens Hyldig-Nielsen, Brett F. Williams
  • Patent number: 10961575
    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.
    Type: Grant
    Filed: September 13, 2019
    Date of Patent: March 30, 2021
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: Hongye Sun, Steven Fung, Sam Lee Woo
  • Patent number: 10900038
    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.
    Type: Grant
    Filed: May 10, 2019
    Date of Patent: January 26, 2021
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: Nitin Puri, Irudaya Charles, Susan Maylin Magdaleno, Alexander Vlassov, Christopher Burnett
  • Publication number: 20200392571
    Abstract: Methods and systems for ordering assays which detect SNPs or gene expression are provided. The methods use PCR and RT-PCR procedures. Collections of stock assays are assembled using pre- and post-manufacturing quality control procedures and made available to consumers via the Internet. In addition, custom assays are prepared upon order from the consumer and these assays are also prepared using pre- and post-manufacturing quality control procedures. The assays are then delivered to the consumer.
    Type: Application
    Filed: June 5, 2020
    Publication date: December 17, 2020
    Applicant: APPLIED BIOSYSTEMS, LLC
    Inventors: Ryan T. KOEHLER, Kenneth J. LIVAK, Junko STEVENS, Francisco M. DE LA VEGA, Michael RHODES, Laurent R. BELLON, Dawn MADDEN, Dennis A. GILBERT, Yu N. WANG, Eugene G. SPIER, Xiaoqing YOU, Lily XU, Jeremy HEIL, Emily S. WINN-DEEN, Ivy McMULLEN, Susan EDDINS, Leila G. SMITH
  • Patent number: 10829808
    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.
    Type: Grant
    Filed: March 25, 2019
    Date of Patent: November 10, 2020
    Assignee: Applied Biosystems, LLC
    Inventor: R. Scott Kuersten
  • Patent number: 10808288
    Abstract: This invention is related to novel PNA probes, probe sets, methods and kits pertaining to the detection of one or more species of Candida yeast. Non-limiting examples of probing nucleobase sequences that can be used for the probes of this invention can be selected from the group consisting of: AGA-GAG-CAG-CAT-GCA (Seq. Id. No. 1), AGA-GAG-CAA-CAT-GCA (Seq. Id. No. 2), ACA-GCA-GAA-GCC-GTG (Seq. Id. No. 3), CAT-AAA-TGG-CTA-CCA-GA (Seq. Id. No. 4), CAT-AAA-TGG-CTA-CCC-AG (Seq. Id. No. 5), ACT-TGG-AGT-CGA-TAG (Seq. Id. No. 6), CCA-AGG-CTT-ATA-CTC-GC (Seq. Id. No. 7), CCC-CTG-AAT-CGG-GAT (Seq. Id. No. 8), GAC-GCC-AAA-GAC-GCC (Seq. Id. No. 9), ATC-GTC-AGA-GGC-TAT-AA (Seq. Id. No. 10), TAG-CCA-GAA-GAA-AGG (Seq. Id. No. 11), CAT-AAA-TGG-CTA-GCC-AG (Seq. Id. No. 12), CTC-CGA-TGT-GAC-TGC-G (Seq. Id. No. 13), TCC-CAG-ACT-GCT-CGG (Seq. Id. No. 14), TCC-AAG-AGG-TCG-AGA (Seq. Id. No. 15), GCC-AAG-CCA-CAA-GGA (Seq. Id. No. 16), GCC-GCC-AAG-CCA-CA (Seq. Id. No. 17), GGA-CTT-GGG-GTT-AG (Seq. Id. No.
    Type: Grant
    Filed: August 28, 2017
    Date of Patent: October 20, 2020
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: Jens J. Hyldig-Nielsen, Henrik Stender, Kenneth M. Oliveira, Susan Rigby
  • Patent number: 10781486
    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.
    Type: Grant
    Filed: April 18, 2017
    Date of Patent: September 22, 2020
    Assignee: Applied Biosystems, LLC
    Inventors: Caifu Chen, Dana Ridzon, Zhaohui Zhou, Kai Qin Lao, Neil A. Straus
  • Patent number: 10768110
    Abstract: An apparatus and method are provided for differentiating multiple detectable signals by excitation wavelength. The apparatus can include a light source that can emit respective excitation light wavelengths or wavelength ranges towards a sample in a sample retaining region, for example, in a well. The sample can contain two or more detectable markers, for example, fluorescent dyes, each of which can be capable of generating increased detectable emissions when excited in the presence of a target component. The detectable markers can have excitation wavelength ranges and/or emission wavelength ranges that overlap with the ranges of the other detectable markers. A detector can be arranged for detecting an emission wavelength or wavelength range emitted from a first marker within the overlapping wavelength range of at least one of the other markers.
    Type: Grant
    Filed: December 18, 2009
    Date of Patent: September 8, 2020
    Assignee: Applied Biosystems, LLC
    Inventors: Howard G. King, Steven J. Boege, Eugene F. Young, Mark F. Oldham
  • Patent number: 10769559
    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.
    Type: Grant
    Filed: September 18, 2015
    Date of Patent: September 8, 2020
    Assignee: Applied Biosystems, LLC
    Inventors: Bruce DeSimas, Leslie Dow
  • Publication number: 20200270287
    Abstract: The present disclosure provides reagents that can be used to label synthetic oligonucleotides with rhodamine dyes or dye networks that contain rhodamine dyes.
    Type: Application
    Filed: January 30, 2020
    Publication date: August 27, 2020
    Applicant: Applied Biosystems, LLC
    Inventors: Scott C. Benson, Ruiming N. Zou, Krishna G. Upadhya, Paul M. Kenney, Jonathan M. Cassel
  • Patent number: 10739307
    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.
    Type: Grant
    Filed: January 25, 2019
    Date of Patent: August 11, 2020
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: Charles S. Vann, Debjyoti Banerjee, Timothy G. Geiser, James C. Nurse, Nigel P. Beard