Patents Assigned to Illumina, Inc.
  • Patent number: 11041196
    Abstract: Methods and compositions for characterizing a target polynucleotide, including, characterizing the sequence of the target polynucleotide, using the fractional translocation steps of the target polynucleotide's translocation through a pore.
    Type: Grant
    Filed: June 12, 2019
    Date of Patent: June 22, 2021
    Assignee: Illumina, Inc.
    Inventors: Eric Stava, Jens H. Gundlach, Jeffrey G. Mandell, Kevin L. Gunderson, Ian M. Derrington, Hosein Mohimani
  • Publication number: 20210179657
    Abstract: Provided is a method including detecting an incorporation of a labelled nucleotide into a nascent polynucleotide strand complementary to a template polynucleotide strand by a polymerase, wherein the polymerase is tethered to a solid support conductive channel by a tether and the labelled nucleotides is a compound of Formula I:
    Type: Application
    Filed: November 30, 2020
    Publication date: June 17, 2021
    Applicants: ILLUMINA, INC., ILLUMINA SINGAPORE PTE. LTD.
    Inventors: Jeffrey MANDELL, Silvia GRAVINA, Sergio PEISAJOVICH, Kaitlin PUGLIESE, Yin Nah TEO, Xiangyuan YANG, Maria Candelaria Rogert BACIGALUPO
  • Publication number: 20210172014
    Abstract: The present invention is concerned with compositions and methods for improving the rate of correct sample identification in indexed nucleic acid library preparations for multiplex next generation sequencing by modifying or blocking 5? and 3? ends of pooled indexed polynucleotides from multiple samples, with an optional exonuclease treatment, prior to amplification and sequencing.
    Type: Application
    Filed: February 22, 2021
    Publication date: June 10, 2021
    Applicants: Illumina, Inc., Illumina Cambridge Limited
    Inventors: Eric Hans Vermaas, Mahdieh Khosroheidari, Claire Bevis-Mott
  • Publication number: 20210172012
    Abstract: The application provides an agnostic, shotgun nucleic acid sequencing-based method for the detection of pathogens in samples from human patients, animals, or plants. The method includes dehosting the sample of the nucleic acid molecules of host origin and provides for the detection of pathogens without prior knowledge of their genome sequences.
    Type: Application
    Filed: December 2, 2020
    Publication date: June 10, 2021
    Applicant: ILLUMINA, INC.
    Inventors: Tong Liu, Fiona Kaper, Clifford Wang
  • Patent number: 11028436
    Abstract: The disclosed embodiments concern index oligonucleotides configured to identify sources of samples of nucleic acids and methods, apparatus, systems and computer program products for identifying and making the index oligonucleotides. In some implementations, the index oligonucleotides include a set of index sequences, a Hamming distance between any two index sequences of the set of index sequences meeting one or more criteria. System, apparatus, and computer program products are also provided for determining a sequence of interest using the index oligonucleotides.
    Type: Grant
    Filed: May 7, 2018
    Date of Patent: June 8, 2021
    Assignee: Illumina, Inc.
    Inventors: Tatjana Singer, Ryan Kelley, Gordon Bean, Eric Vermaas
  • Patent number: 11028435
    Abstract: The disclosed embodiments concern index oligonucleotides configured to identify sources of samples of nucleic acids and methods, apparatus, systems and computer program products for identifying and making the index oligonucleotides. In some implementations, the index oligonucleotides include a set of index sequences, a Hamming distance between any two index sequences of the set of index sequences meeting one or more criteria. System, apparatus, and computer program products are also provided for determining a sequence of interest using the index oligonucleotides.
    Type: Grant
    Filed: May 1, 2018
    Date of Patent: June 8, 2021
    Assignee: Illumina, Inc.
    Inventors: Ryan Kelley, Gordon Bean, Eric Vermaas
  • Patent number: 11031132
    Abstract: The present invention provides a novel approach for storing, analyzing, and/or accessing biological data in a cloud computing environment. Sequence data generated by a particular sequencing device may be uploaded to the cloud computing environment during a sequencing run, which reduces the on-site storage needs for the sequence data. Analysis of the data may also be performed in the cloud computing environment, and the instructions for such analysis may be set at the originating sequencing device. The sequence data in the cloud computing environment may be shared according to permissions. Further, the sequence data may be modified or annotated by authorized secondary users.
    Type: Grant
    Filed: January 28, 2019
    Date of Patent: June 8, 2021
    Assignee: Illumina, Inc.
    Inventors: Alexander G. Dickinson, Francisco Jose Garcia, Robert C. Kain, Scott D. Kahn, Andrew R. Nelson
  • Patent number: 11029513
    Abstract: A method for scanning a microarray, including (a) providing a microarray to an optical scanner, wherein the microarray includes a surface having features having different target molecules; (b) scanning the surface in the x or y direction to acquire optical signals from the features at sequential regions of the surface, wherein the focus setting between the optical scanner and the surface is dynamically controlled in real time by repeatedly (i) adding a predetermined focal offset, thereby introducing an error in the focus setting, and (ii) adjusting the focus setting to reduce the error in the focus setting, thereby acquiring the optical signals from different regions at different degrees of focus such that a subset of the regions that are scanned have an introduced focus error; and (c) analyzing the optical signals that are obtained at the different degrees of focus to identify the different target molecules.
    Type: Grant
    Filed: January 18, 2019
    Date of Patent: June 8, 2021
    Assignee: ILLUMINA, INC.
    Inventors: Darren Robert Segale, John Moon, Hongji Ren
  • Publication number: 20210168134
    Abstract: Flexible authentication technologies customized to particular tenants of a data center network can be implemented. For example, an administrator can specify a primary authentication server and specify at which data centers different applications are to be hosted for a given tenant. End users can be shielded from the complexities of implementing such configuration details. For example, single sign-on authentication can be implemented, even when applications are configured to be hosted in different data centers. Enterprise tenants can thus control where applications are hosted and enforce data containment scenarios without encumbering users with additional tasks. Collaboration and application-to-application authentication can be achieved.
    Type: Application
    Filed: August 10, 2020
    Publication date: June 3, 2021
    Applicant: Illumina, Inc.
    Inventors: Milan Karangutkar, Prabhu Palanisamy, Satnam Alag
  • Publication number: 20210164040
    Abstract: This disclosure provides a method of determining a sequence of nucleotides for a nucleic acid template. The method can include the steps of contacting the nucleic acid template with a conformationally labeled polymerase and at least four different nucleotide species under conditions wherein the conformationally labeled polymerase catalyzes sequential addition of the nucleotide species to form a nucleic acid complement of the nucleic acid template, wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase and wherein the rate or time duration for the conformational signal change is distinguishable for each different nucleotide species; detecting a series of changes in the signal from the conformationally labeled polymerase under the conditions; and determining the rates or time durations for the changes in the signal, thereby determining the sequence of nucleotides for the nucleic acid template.
    Type: Application
    Filed: November 6, 2020
    Publication date: June 3, 2021
    Applicant: Illumina, Inc.
    Inventors: Molly He, Cheng-Yao Chen, Eric Kool, Mostafa Ronaghi, Michael Previte, Rigo Pantoja
  • Publication number: 20210164027
    Abstract: This disclosure describes a hybridization buffer including a crowding agent, a method that includes using the hybridization buffer, and a kit including the hybridization buffer. This disclosure also describes blockers for use in hybrid capture methods, methods of using those blockers, and a kit including those blockers. Additionally, this disclosure describes a method of hybrid capture that does not include amplifying the library members using PCR prior to sequencing the library members.
    Type: Application
    Filed: August 13, 2019
    Publication date: June 3, 2021
    Applicants: Illumina, Inc., Illumina Cambridge Limited
    Inventors: Andrew F. Slatter, Junhua Zhao, Grace DeSantis, Stephen M. Gross, Hayley Marianne Hogan, Jian-Sen Li, Oliver Jon Miller
  • Patent number: 11020739
    Abstract: Imprinted substrates are often used to produce miniaturized devices for use in electrical, optic and biochemical applications. Imprinting techniques, such as nanoimprinting lithography, may leave residues in the surface of substrates that affect bonding and decrease the quality of the produced devices. An imprinted substrate with residue-free region, or regions with a reduced amount of residue for improved bonding quality is introduced. Methods to produce imprinted substrates without residues from the imprinting process are also introduced. Methods include physical exclusion methods, selective etching methods and energy application methods. These methods may produce residue-free regions in the surface of the substrate that can be used to produce higher strength bonding.
    Type: Grant
    Filed: September 11, 2017
    Date of Patent: June 1, 2021
    Assignee: Illumina, Inc.
    Inventors: Hui Han, Dajun A. Yuan, M. Shane Bowen
  • Patent number: 11021504
    Abstract: Embodiments of the present disclosure include methods and compositions for functionalizing molecules, such as oligonucleotides, with functional groups, including polyhistidine tags useful in affinity methods. Some embodiments include methods for modifying and purifying complex mixtures of molecules by exchange of functional tags.
    Type: Grant
    Filed: May 16, 2019
    Date of Patent: June 1, 2021
    Assignee: Illumina, Inc.
    Inventors: Frank J Steemers, Kevin L Gunderson, Kerri York, Ryan Christopher Smith
  • Publication number: 20210155987
    Abstract: The present invention includes methods and materials for use in the detection preeclampsia and/or determining an increased risk for preeclampsia in a pregnant female, the method including identifying in a biosample obtained from the pregnant women a plurality of circulating RNA (C-RNA) molecules.
    Type: Application
    Filed: November 20, 2020
    Publication date: May 27, 2021
    Applicant: ILLUMINA, INC.
    Inventors: Sarah E. Shultzaberger, Fiona Kaper, Sarah Kinnings, Suzanne Rohrback, Carlo Randise-Hinchliff
  • Publication number: 20210154667
    Abstract: An apparatus for directing fluid into and out of a fluidic device includes two or more fluid prime channels connected to a fluid inlet of the fluidic device, a flow control valve for each fluid prime channel to control flow between the fluid prime channel and the fluid inlet, one or more outlet channels connected to a fluid outlet of the fluidic device, and a flow control valve for each outlet channel to control flow between the fluid outlet and the associated outlet channel. An apparatus for delivering fluids to a fluid inlet includes a plate that is rotatable about an axis of rotation and a plurality of fluid compartments disposed on the plate, each compartment having a fluid exit port disposed at a common radial distance from the axis of rotation and positioned to align with the fluid inlet as the plate rotates about the axis of rotation.
    Type: Application
    Filed: February 2, 2021
    Publication date: May 27, 2021
    Applicants: Illumina, Inc., Illumina Cambridge Limited
    Inventors: Wesley A. Cox-Muranami, Darren Robert Segale, Oliver Jon Miller, Jennifer Olivia Foley, Tarun Kumar Khurana, Paul Crivelli, Gary Watts
  • Patent number: 11016008
    Abstract: An analysis instrument may perform analytical operations on an analyte that is combined with multiple reagents prior to being introduced into a flow cell. The instrument may include a nozzle sipper that aspirates reagents from a recipient, along with an analyte. The reagents may be directed to a volume and may be repeatedly moved into and out of the volume by cycling of a pump. The reagents may be ejected into a destination recipient with the nozzle sipper promoting vorticity in the recipient to enhance mixing. The repeated aspiration and ejection through the nozzle sipper effectively mixes the reagents and the template in an automated or semi-automated fashion.
    Type: Grant
    Filed: December 13, 2017
    Date of Patent: May 25, 2021
    Assignee: ILLUMINA, INC.
    Inventors: Bradley Kent Drews, Michael Dai Wang, Umberto Ulmanella, James Michael Osmus, Stephen Wayne Clark, Johanna Lynn Whitacre, Steven Scott Phelps, Michelle L. Alvarez, Michael Adalbert Niziolek, Debra Sue Bryan, Joshua Augustin Darland
  • Patent number: 11014089
    Abstract: Sample carrier includes a thermal-control block having an active surface and an outer surface that face in opposite directions. The active surface has a series of mounting areas that are distributed along a length of the thermal-control block. The sample carrier also includes chamber cells that are configured to be disposed over respective mounting areas of the series of mounting areas. The sample carrier also includes a removable cover body that is configured to be coupled to the thermal-control block with the chamber cells therebetween. The thermal-control block and the chamber cells are shaped to form corresponding reaction chambers therebetween. The cover body and the thermal-control block are in fixed positions with respect to each other to form a unitary structure. The reaction chambers have corresponding inlets that open in a common direction to an exterior of the sample carrier.
    Type: Grant
    Filed: May 26, 2016
    Date of Patent: May 25, 2021
    Assignee: Illumina, Inc.
    Inventors: Darryl Donovan, Antoni Murcia
  • Publication number: 20210147927
    Abstract: Presented herein are polymerase enzymes for improved incorporation of nucleotide analogues, in particular nucleotides which are modified at the 3? sugar hydroxyl, as well as methods and kits using the same.
    Type: Application
    Filed: July 15, 2020
    Publication date: May 20, 2021
    Applicant: ILLUMINA, INC.
    Inventors: Erin Bomati, Molly He, Cheng-Yao Chen, Sergio Peisajovich
  • Patent number: D923197
    Type: Grant
    Filed: December 19, 2019
    Date of Patent: June 22, 2021
    Assignee: Illumina, Inc.
    Inventors: Erik Allegoren, Erik Williamson, Jack Godfrey-Wood
  • Patent number: D923198
    Type: Grant
    Filed: December 19, 2019
    Date of Patent: June 22, 2021
    Assignee: Illumina, Inc.
    Inventors: Erik Allegoren, Erik Williamson, Jack Godfrey-Wood