Illumina Cambridge Limited

United Kingdom

Back to Profile

1-100 of 670 for Illumina Cambridge Limited Sort by
Query
Aggregations
Jurisdiction
        United States 317
        World 232
        Canada 121
Date
New (last 4 weeks) 4
2024 March (MTD) 3
2024 February 1
2024 January 6
2023 December 8
See more
IPC Class
C12Q 1/6869 - Methods for sequencing 198
C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids 158
C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay 115
C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH] 108
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA 81
See more
Status
Pending 188
Registered / In Force 482
Found results for  patents
  1     2     3     ...     7        Next Page

1.

FLOW CELLS

      
Application Number 18455090
Status Pending
Filing Date 2023-08-24
First Publication Date 2024-03-21
Owner ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Merkel, Timothy J.
  • George, Wayne N.
  • Brown, Andrew A.
  • Richez, Alexandre

Abstract

An example of a flow cell includes a base support, a reversibly swellable resin positioned over the base support, and a depression defined in the reversibly swellable resin. The reversibly swellable resin includes at least one hydrophilic monomer selected from the group consisting of a poly(ethylene glycol) based monomer, poly(propylene glycol) based monomer, and combinations thereof. The depression has a first opening dimension when the reversibly swellable resin is in a non-swelled stated and has a second opening dimension, that is smaller than the first opening dimension, when the reversibly swellable resin is in a swelled state.

IPC Classes  ?

  • B01L 9/00 - Supporting devices; Holding devices

2.

NANOPARTICLE WITH POLYNUCLEOTIDE BINDING SITE AND METHOD OF MAKING THEREOF

      
Application Number IB2023059187
Publication Number 2024/057280
Status In Force
Filing Date 2023-09-15
Publication Date 2024-03-21
Owner ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Szemjonov, Alexandra
  • La Rosa, Angelo
  • Artioli, Gianluca
  • Von Hatten, Xavier
  • Richez, Alexandre

Abstract

The present disclosure relates to a nanoparticle including a first layer including a first polymer and a first plurality of accessory oligonucleotides, a second layer including a second polymer and a single template site for bonding a template polynucleotide, and a third layer including a third polymer and a second plurality of accessory oligonucleotides. Also described herein is a method of making said nanoparticle, including "dip-coating," e.g., successively dipping a surface with wettable nanodomains in different polymer solutions. Further described herein is a method of making the nanoparticles by forming them in nanowells and subsequently releasing them from the nanowells. Also described herein is a method of attaching the nanoparticle to a substrate and amplifying the template polynucleotide using a polymerase.

IPC Classes  ?

  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12Q 1/6834 - Enzymatic or biochemical coupling of nucleic acids to a solid phase

3.

ADDING NUCLEOTIDES DURING SEQUENCE DETECTION

      
Application Number 18232127
Status Pending
Filing Date 2023-08-09
First Publication Date 2024-03-14
Owner ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Gatti-Lafranconi, Pietro
  • Balding, Philip

Abstract

Polynucleotide sequencing methods include incubating unlabeled nucleotides with a cluster of template polynucleotide strands having the same sequence when the identity of the previously added labeled nucleotide is being detected. The detection step provides time for the addition of the unlabeled nucleotides to be incorporated into the copy strands in which the previously added labeled nucleotide did not get incorporated. Thus, at the end of the detection step, all or most of the copy strands will be in phase and ready to incorporate the appropriate labeled nucleotide in the subsequence incorporate step.

IPC Classes  ?

  • 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 glassware; Droppers
  • C12Q 1/25 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving enzymes not classifiable in groups

4.

FLOW CELLS WITH SWELLABLE RESIN

      
Application Number EP2023073202
Publication Number 2024/042149
Status In Force
Filing Date 2023-08-24
Publication Date 2024-02-29
Owner ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Merkel, Timothy J.
  • George, Wayne N.
  • Brown, Andrew A.
  • Richez, Alexandre

Abstract

An example of a flow cell includes a base support, a reversibly swellable resin positioned over the base support, and a depression defined in the reversibly swellable resin. The reversibly swellable resin includes at least one hydrophilic monomer selected from the group consisting of a poly(ethylene glycol) based monomer, poly(propylene glycol) based monomer, and combinations thereof. The depression has a first opening dimension when the reversibly swellable resin is in a non-swelled stated and has a second opening dimension, that is smaller than the first opening dimension, when the reversibly swellable resin is in a swelled state.

IPC Classes  ?

  • B01J 19/00 - Chemical, physical or physico-chemical processes in general; Their relevant apparatus

5.

TAGMENTATION WORKFLOW

      
Application Number EP2023070845
Publication Number 2024/023219
Status In Force
Filing Date 2023-07-27
Publication Date 2024-02-01
Owner ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Kuna, Karolina
  • Morrell, Natalie
  • Gormley, Niall Anthony
  • Slatter, Andrew
  • Anastasi, Carole

Abstract

In an example of a method, a deoxyribonucleic acid sample is exposed to tagmentation in the presence of a tagmentation buffer including a divalent cation cofactor and a transposase enzyme to generate a tagmented DNA fragment complex. A chelator mixture is added to the tagmented DNA fragment complex. The chelator mixture includes a chelator of the divalent cation cofactor at a weight ratio that is at least 1:1 with the divalent cation cofactor; and has a pH ranging from 8 to 9. The tagmented DNA fragment complex is incubated in the chelator mixture at a temperature of at least 55°C for at least about 60 seconds, so that the transposase enzyme dissociates from a tagmented DNA fragment of the tagmented DNA fragment complex.

IPC Classes  ?

  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12Q 1/6869 - Methods for sequencing

6.

Methods of Preparing Directional Tagmentation Sequencing Libraries Using Transposon-Based Technology with Unique Molecular Identifiers for Error Correction

      
Application Number 18476719
Status Pending
Filing Date 2023-09-28
First Publication Date 2024-01-25
Owner
  • Illumina, Inc. (USA)
  • Illumina Cambridge Limited (United Kingdom)
Inventor
  • Verity, Susan C.
  • Kuersten, Robert Scott
  • Gormley, Niall Anthony
  • Kennedy, Andrew B.
  • Shultzaberger, Sarah E.
  • Slatter, Andrew
  • Bell, Emma
  • Ricoult, Sebastien Georg Gabriel
  • Desantis, Grace
  • Kaper, Fiona
  • Chuang, Han-Yu
  • Miller, Oliver Jon
  • Betley, Jason Richard
  • Gross, Stephen M.
  • Ekstrand, Mats

Abstract

Materials and methods for preparing nucleic acid libraries for next-generation sequencing are described herein. A variety of approaches are described relating to the use of unique molecular identifiers with transposon-based technology in the preparation of sequencing libraries. Also described herein are sequencing materials and methods for identifying and correcting amplification and sequencing errors.

IPC Classes  ?

  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA

7.

NANOIMPRINT LITHOGRAPHY RESIN COMPOSITION

      
Application Number 18343713
Status Pending
Filing Date 2023-06-28
First Publication Date 2024-01-18
Owner ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Szemjonov, Alexandra
  • Richez, Alexandre

Abstract

An example nanoimprint lithography (NIL) resin composition includes a total of three monomers, wherein two of the three monomers are selected from the group consisting of two different epoxy substituted silsesquioxane monomers; two different epoxy substituted cyclosiloxane monomers; and two different non-organosilicon epoxy monomers. A third of the three monomers is a fluorinated monomer that is present in an amount ranging from about from 0.5 mass % to about 4 mass %, based on a total solids content of the NIL resin composition. The NIL resin also includes a photoinitiator and a solvent.

IPC Classes  ?

  • C09D 163/00 - Coating compositions based on epoxy resins; Coating compositions based on derivatives of epoxy resins
  • C08G 59/36 - Epoxy compounds containing three or more epoxy groups together with mono-epoxy compounds
  • C08G 59/32 - Epoxy compounds containing three or more epoxy groups
  • C08G 59/68 - Macromolecules obtained by polymerising compounds containing more than one epoxy group per molecule using curing agents or catalysts which react with the epoxy groups characterised by the catalysts used
  • C09D 7/63 - Additives non-macromolecular organic
  • B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers

8.

MULTIBAND SCANNING AND FIBER BUNDLE TO ENABLE REDUCED LIGHT SOURCE INTENSITY AND IMPROVED IMAGING QUALITY

      
Application Number US2023026352
Publication Number 2024/006284
Status In Force
Filing Date 2023-06-27
Publication Date 2024-01-04
Owner
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
  • ILLUMINA, INC. (USA)
Inventor
  • Evans, Geraint
  • Lennon, Stephen
  • Condello, Danilo
  • Hong, Stanley
  • Watson, Dakota

Abstract

Some implementations of the disclosure describe an imaging system comprising: a camera including multiple image sensors that are spaced apart, each of the image sensors to capture an image of a respective sample location of multiple sample locations of a sample; and a fiber bundle comprising multiple fiber cores, each of the fiber cores to emit a light beam that is projected on a respective one of the sample locations.

IPC Classes  ?

  • G02B 21/06 - Means for illuminating specimen
  • G02B 6/04 - Light guides; Structural details of arrangements comprising light guides and other optical elements, e.g. couplings formed by bundles of fibres
  • G01N 21/64 - Fluorescence; Phosphorescence
  • G06T 7/00 - Image analysis
  • G02B 27/10 - Beam splitting or combining systems

9.

NANOIMPRINT LITHOGRAPHY RESIN COMPOSITION

      
Application Number EP2023067577
Publication Number 2024/003104
Status In Force
Filing Date 2023-06-28
Publication Date 2024-01-04
Owner ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Szemjonov, Alexandra
  • Richez, Alexandre

Abstract

An example nanoimprint lithography (NIL) resin composition includes a total of three monomers, wherein two of the three monomers are selected from the group consisting of two different epoxy substituted silsesquioxane monomers; two different epoxy substituted cyclosiloxane monomers; and two different non-organosilicon epoxy monomers. A third of the three monomers is a fluorinated monomer that is present in an amount ranging from about from 0.5 mass% to about 4 mass%, based on a total solids content of the NIL resin composition. The NIL resin also includes a photoinitiator and a solvent.

IPC Classes  ?

  • C08L 83/06 - Polysiloxanes containing silicon bound to oxygen-containing groups
  • C08G 59/30 - Di-epoxy compounds containing atoms other than carbon, hydrogen, oxygen, and nitrogen
  • C08L 63/00 - Compositions of epoxy resins; Compositions of derivatives of epoxy resins

10.

SEQUENCING NANOPARTICLES AND METHODS OF MAKING THE SAME

      
Application Number 18343696
Status Pending
Filing Date 2023-06-28
First Publication Date 2024-01-04
Owner ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • El Fagui, Amani
  • George, Wayne N.

Abstract

An example of a sequencing nanoparticle includes a core of a negatively chargeable, hydrophobic polymer. Alternating layers of a positively charged acrylamide hydrogel and the negatively charged polymer are positioned on the core, wherein the positively charged acrylamide hydrogel forms an outer layer of the sequencing nanoparticle. A negatively charged primer set is attached to the outer layer.

IPC Classes  ?

  • 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 glassware; Droppers

11.

SEQUENCING NANOPARTICLES AND METHODS OF MAKING THE SAME

      
Application Number EP2023067570
Publication Number 2024/003100
Status In Force
Filing Date 2023-06-28
Publication Date 2024-01-04
Owner ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Amani, El Fagui
  • George, Wayne N.

Abstract

An example of a sequencing nanoparticle includes a core of a negatively chargeable, hydrophobic polymer. Alternating layers of a positively charged acrylamide hydrogel and the negatively charged polymer are positioned on the core, wherein the positively charged acrylamide hydrogel forms an outer layer of the sequencing nanoparticle. A negatively charged primer set is attached to the outer layer.

IPC Classes  ?

12.

ENHANCING CLUSTERING EFFICIENCY AND KINETICS

      
Application Number 18330298
Status Pending
Filing Date 2023-06-06
First Publication Date 2023-12-28
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Artioli, Gianluca Andrea
  • Beech, Timothy J.N.
  • Lessard-Viger, Mathieu
  • Turk-Macleod, Rebecca
  • Mather, Brian D.
  • Xi, Weixian
  • Von Hatten, Xavier

Abstract

A co-polymer includes a plurality of a first monomer including a terminal functional group that is to attach to at least two different primers; a plurality of a second monomer including a second functional group that is different from the terminal functional group, and that is selected from the group consisting of a phenyl group, methoxy propyl, glycosyl, vinyl pyrrolidone, and an imidazole group; and a plurality of a third monomer that is different from the first and second monomers. This co-polymer may be used in a flow cell, and may enhance the clustering efficiency and kinetics.

IPC Classes  ?

13.

FLUORESCENT DYES CONTAINING FUSED TETRACYCLIC BIS-BORON HETEROCYCLE AND USES IN SEQUENCING

      
Application Number 18342064
Status Pending
Filing Date 2023-06-27
First Publication Date 2023-12-28
Owner Illumina Cambridge Limited (United Kingdom)
Inventor
  • Callingham, Michael
  • Piekos, Justyna
  • Manni, Francesca

Abstract

The present application relates to dyes containing fused tetracyclic bis-boron containing heterocycle and their uses as fluorescent labels. These dyes may be used as fluorescent labels for nucleotides in nucleic acid sequencing applications.

IPC Classes  ?

  • C07F 5/02 - Boron compounds
  • C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
  • C12Q 1/6825 - Nucleic acid detection involving sensors

14.

METHODS OF ENRICHING A TARGET SEQUENCE FROM A SEQUENCING LIBRARY USING HAIRPIN ADAPTORS

      
Application Number 18025794
Status Pending
Filing Date 2022-09-10
First Publication Date 2023-12-28
Owner Illumina Cambridge Limited (United Kingdom)
Inventor Slatter, Andrew

Abstract

Disclosed herein is a method for enriching a sequencing library comprising double-stranded nucleic acid fragments comprising preparing a library of double-stranded fragments having one or more adaptors at ends of the double-stranded fragment; denaturing the double-stranded fragments to form single-stranded fragments; and hybridizing an extension primer that binds to a target sequence of at least one insert in the library of double-stranded fragments and that does not bind to non-target sequences. In an embodiment, the adaptor is a hairpin adaptor, and extension from the extension primer using a polymerase with 5′ to 3′ exonuclease activity removes all or part of a sequence of the hairpin adaptor that is at least partially complementary to the amplification primer sequence. Each fragment may comprise an insert comprising double-stranded nucleic acid and a hairpin adaptor at the 5′ end of one or both strands of the double-stranded fragments. Hairpin adaptors may comprise an amplification primer sequence and a sequence at least partially complementary to the amplification primer sequence.

IPC Classes  ?

  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA

15.

TIME-BASED CLUSTER IMAGING

      
Application Number 18204256
Status Pending
Filing Date 2023-05-31
First Publication Date 2023-12-21
Owner ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Morrell, Natalie
  • Slatter, Andrew
  • Thomson, Vicki

Abstract

In an example method, a series of time-based clustering images is generated for a plurality of library fragments from a genome sample. Each time-based clustering image in the series is sequentially generated. To generate each time-based clustering image in the series: i) a respective sample is introduced to a flow cell, the respective sample including contiguity preserved library fragments of the plurality of library fragments, wherein the contiguity preserved library fragments are attached to a solid support or are attached to each other; ii) the contiguity preserved library fragments are released from the solid support or from each other; iii) the contiguity preserved library fragments are amplified to generate a plurality of respective template strands; iv) the respective template strands are stained; and v) the respective template strands are imaged.

IPC Classes  ?

  • G06F 16/58 - Retrieval characterised by using metadata, e.g. metadata not derived from the content or metadata generated manually
  • G06V 10/26 - Segmentation of patterns in the image field; Cutting or merging of image elements to establish the pattern region, e.g. clustering-based techniques; Detection of occlusion
  • B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
  • B01L 7/00 - Heating or cooling apparatus; Heat insulating devices
  • C12Q 1/6844 - Nucleic acid amplification reactions
  • G06T 5/50 - Image enhancement or restoration by the use of more than one image, e.g. averaging, subtraction

16.

Sequencing Templates Comprising Multiple Inserts and Compositions and Methods for Improving Sequencing Throughput

      
Application Number 18303905
Status Pending
Filing Date 2023-04-20
First Publication Date 2023-12-21
Owner
  • Illumina, Inc. (USA)
  • Illumina Cambridge Limited (United Kingdom)
Inventor
  • Khurana, Tarun
  • Wu, Yir-Shyuan
  • Gormley, Niall Anthony
  • Boutell, Jonathan Mark

Abstract

Described herein is a polynucleotide for use as a sequencing template comprising multiple inserts. Also described herein are method of generating and using these polynucleotides and methods of use of such templates, including analysis of contiguity information. Further, sequencing templates comprising an insert sequence and a copy of the insert sequence can be used to correct for random errors generated during sequencing or amplification or to identify nucleobase damage or other mutation that leads to non-canonical base pairing in a double-stranded nucleic acid. Methods of performing methylation analysis are also described herein.

IPC Classes  ?

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

17.

ENHANCING CLUSTERING EFFICIENCY AND KINETICS

      
Application Number US2023068007
Publication Number 2023/240090
Status In Force
Filing Date 2023-06-06
Publication Date 2023-12-14
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Artioli, Gianluca, Andrea
  • Beech, Timothy, J., N.
  • Lessard-Viger, Mathieu
  • Turk-Macleod, Rebecca
  • Mather, Brian, D.
  • Xi, Weixian
  • Von Hatten, Xavier

Abstract

A co-polymer includes a plurality of a first monomer including a terminal functional group that is to attach to at least two different primers; a plurality of a second monomer including a second functional group that is different from the terminal functional group, and that is selected from the group consisting of a phenyl group, methoxy propyl, glycosyl, vinyl pyrrolidone, and an imidazole group; and a plurality of a third monomer that is different from the first and second monomers. This co-polymer may be used in a flow cell, and may enhance the clustering efficiency and kinetics.

IPC Classes  ?

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

18.

FLOW CELL INCLUDING A HETEROPOLYMER

      
Application Number 18233276
Status Pending
Filing Date 2023-08-11
First Publication Date 2023-12-07
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • George, Wayne N.
  • Vincent, Ludovic
  • Brown, Andrew A.
  • Lessard-Viger, Mathieu

Abstract

A flow cell includes a support and a heteropolymer attached to the support. The heteropolymer includes an acrylamide monomer including an attachment group to react with a functional group attached to a primer, and a monomer including a stimuli-responsive functional group. The monomer including the stimuli-responsive functional group may be pH-responsive, temperature-responsive, saccharide-responsive, nucleophile-responsive, and/or salt-responsive.

IPC Classes  ?

  • C08L 33/08 - Homopolymers or copolymers of acrylic acid esters
  • C12Q 1/6869 - Methods for sequencing
  • C12Q 1/6853 - Nucleic acid amplification reactions using modified primers or templates
  • C08L 33/26 - Homopolymers or copolymers of acrylamide or methacrylamide

19.

Tagmentation Using Immobilized Transposomes With Linkers

      
Application Number 18327187
Status Pending
Filing Date 2023-06-01
First Publication Date 2023-12-07
Owner
  • Illumina, Inc. (USA)
  • Illumina Cambridge Limited (United Kingdom)
Inventor
  • Desantis, Grace
  • Gross, Stephen M.
  • Li, Jian-Sen
  • Morrell, Natalie
  • Slatter, Andrew
  • Shen, Kevin
  • Snow, Samantha

Abstract

The present disclosure relates to methods, compositions, and kits for treating target nucleic acids, including methods and compositions for fragmenting and tagging nucleic acid (e.g., DNA) using transposome complexes bound to a solid support.

IPC Classes  ?

  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C12N 11/06 - Enzymes or microbial cells immobilised on or in an organic carrier attached to the carrier via a bridging agent
  • C12Q 1/6869 - Methods for sequencing
  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay

20.

COMPOSITIONS AND METHODS FOR NUCLEIC ACID SEQUENCING

      
Application Number 18325610
Status Pending
Filing Date 2023-05-30
First Publication Date 2023-11-30
Owner
  • Illumina Cambridge Limited (United Kingdom)
  • Illumina Singapore Pte. Ltd. (Singapore)
  • Illumina, Inc. (USA)
  • Illumina Software, Inc. (USA)
Inventor
  • Wu, Xiaolin
  • Mccauley, Patrick
  • Dharmarwardana, Madushani
  • Nirantar, Saurabh
  • Golynskiy, Misha
  • Yang, Xiangyuan
  • Neelakandan, Ramesh
  • Mackworth, Benedict
  • Anastasi, Carole
  • Karunakaran, Aathavan
  • Vessere, Gery M.
  • Bracher, David

Abstract

Embodiments of the present disclosure relate to kits, compositions, and methods for nucleic acid sequencing, for example, two-channel nucleic acid sequencing by synthesis using blue and green light excitation. In particular, unlabeled nucleotides for incorporation may be used in conjunction with affinity reagents containing detectable labels excitable by blue and/or green lights, for specific binding to each type of nucleotides incorporated.

IPC Classes  ?

21.

3'-BLOCKED NUCLEOTIDES AND NANOPORE-BASED METHOD OF SYNTHESIZING POLYNUCLEOTIDES USING THE SAME

      
Application Number US2023022435
Publication Number 2023/229884
Status In Force
Filing Date 2023-05-16
Publication Date 2023-11-30
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
  • ILLUMINA SINGAPORE PTE. LTD. (Singapore)
Inventor
  • Mandell, Jeffrey
  • Teo, Yin Nah
  • Lukamto, Daniel
  • Yang, Xiangyuan
  • Richard, Jean-Alexandre
  • Lauw, Sherman
  • Ghomi, Hamed
  • Wu, Xiaolin
  • George, Wayne

Abstract

3'-blocked nucleotides, methods of deblocking the same, and methods of synthesizing polynucleotides using the same are provided herein. In some examples, a nucleotide is disposed within the aperture on the first side of a nanopore. The nucleotide may be coupled to a 3'-blocking group including a trigger. The trigger may be selectively activated using an initiator. The activated trigger may be used to remove the 3'-blocking group from the nucleotide.

IPC Classes  ?

  • C12Q 1/6869 - Methods for sequencing
  • C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C07H 19/10 - Pyrimidine radicals with the saccharide radical being esterified by phosphoric or polyphosphoric acids
  • C07H 19/20 - Purine radicals with the saccharide radical being esterified by phosphoric or polyphosphoric 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

22.

PREPARATION OF LONG READ NUCLEIC ACID LIBRARIES

      
Application Number US2023067468
Publication Number 2023/230553
Status In Force
Filing Date 2023-05-25
Publication Date 2023-11-30
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Meinholz, Heather
  • Gerhardt, Daniel
  • Burgess, Joshua
  • Monahan, Leigh G.
  • Dennin, Jennifer
  • Bruinsma, Stephen Paul
  • O'Meara, M. Maggie
  • Darling, Aaron Earl
  • Parker, Johnathan
  • Macarthur, Stewart
  • Raterman, Denise
  • Chen, Feng
  • Huang, Tina
  • Truong, Tiffany
  • Hawks, Brian
  • Musgrave-Brown, Esther
  • Verity, Susan
  • Slatter, Andrew
  • Tse, David

Abstract

Some embodiments of the methods and compositions provided herein relate to obtaining long read information from short reads of a target nucleic acid. Some embodiments include steps to selectively generate, mark, and amplify long nucleic acid fragments. Some embodiments include enriching for certain sequences in the long fragments with selection probes directed to certain pharmacogenetic (PGX) genes. Some embodiments also include fragmenting the long nucleic acid fragments into shorter fragments for sequencing, and informatically reconstructing a sequence of the target nucleic acid.

IPC Classes  ?

  • C12Q 1/6869 - Methods for sequencing
  • C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
  • C12N 9/22 - Ribonucleases
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA

23.

PREPARATION OF LONG READ NUCLEIC ACID LIBRARIES

      
Application Number US2023067471
Publication Number 2023/230556
Status In Force
Filing Date 2023-05-25
Publication Date 2023-11-30
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Meinholz, Heather
  • Gerhardt, Daniel
  • Burgess, Joshua
  • Monahan, Leigh G.
  • Dennin, Jennifer
  • Bruinsma, Stephen Paul
  • O'Meara, M. Maggie
  • Darling, Aaron Earl
  • Parker, Johnathan
  • Macarthur, Stewart
  • Raterman, Denise
  • Chen, Feng
  • Huang, Tina
  • Truong, Tiffany
  • Hawks, Brian
  • Musgrave-Brown, Esther
  • Verity, Susan
  • Slatter, Andrew
  • Tse, David

Abstract

Some embodiments of the methods and compositions provided herein relate to obtaining long read information from short reads of a target nucleic acid. Some embodiments include steps to selectively generate, mark, and amplify long nucleic acid fragments. Some embodiments include enriching for certain sequences in the long fragments with selection probes directed to major histocompatibility complex (MHC) genes. Some embodiments also include fragmenting the long nucleic acid fragments into shorter fragments for sequencing, and informatically reconstructing a sequence of the target nucleic acid.

IPC Classes  ?

  • C12Q 1/6869 - Methods for sequencing
  • C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
  • C12N 9/22 - Ribonucleases
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA

24.

DEEP LEARNING-BASED VARIANT CLASSIFIER

      
Application Number 18314638
Status Pending
Filing Date 2023-05-09
First Publication Date 2023-11-30
Owner
  • Illumina, Inc. (USA)
  • Illumina Cambridge Limited (United Kingdom)
Inventor
  • Schulz-Trieglaff, Ole
  • Cox, Anthony James
  • Farh, Kai-How

Abstract

The technology disclosed directly operates on sequencing data and derives its own feature filters. It processes a plurality of aligned reads that span a target base position. It combines elegant encoding of the reads with a lightweight analysis to produce good recall and precision using lightweight hardware. For instance, one million training examples of target base variant sites with 50 to 100 reads each can be trained on a single GPU card in less than 10 hours with good recall and precision. A single GPU card is desirable because it a computer with a single GPU is inexpensive, almost universally within reach for users looking at genetic data. It is readily available on could-based platforms.

IPC Classes  ?

  • G16B 40/20 - Supervised data analysis
  • G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
  • G06F 18/214 - Generating training patterns; Bootstrap methods, e.g. bagging or boosting
  • G06F 18/2431 - Multiple classes
  • G06N 3/045 - Combinations of networks
  • G16B 40/00 - ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
  • G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
  • G06F 9/38 - Concurrent instruction execution, e.g. pipeline, look ahead
  • G06N 3/04 - Architecture, e.g. interconnection topology
  • G06N 3/084 - Backpropagation, e.g. using gradient descent

25.

SEPARATING POLYNUCLEOTIDE FRAGMENTS

      
Application Number 18447800
Status Pending
Filing Date 2023-08-10
First Publication Date 2023-11-30
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Bacigalupo, Maria Candelaria Rogert
  • Steemers, Frank
  • Fisher, Jeffrey
  • Slatter, Andrew
  • Kraft, Lewis
  • Gormley, Niall
  • Bowen, M. Shane

Abstract

Provided is a method, including stretching a polynucleotide over a substrate including a plurality of equally spaced cleavage regions including a plurality of transposases, cleaving the polynucleotide with two or more of the plurality of transposases to form a plurality of polynucleotide fragments, and separating, within the plurality of polynucleotide fragments, a population of longer polynucleotide fragments from a population of shorter polynucleotide fragments. Also provided is a method including stretching a polynucleotide over a substrate including a plurality of equally spaced cleavage regions including a plurality of transposases, cleaving the polynucleotide with two or more of the plurality of transposases to form a plurality of polynucleotide fragments, and separating, within the plurality of polynucleotide fragments, a population of longer polynucleotide fragments from a population of shorter polynucleotide fragments.

IPC Classes  ?

  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA

26.

PREPARATION OF LONG READ NUCLEIC ACID LIBRARIES

      
Application Number US2023067465
Publication Number 2023/230550
Status In Force
Filing Date 2023-05-25
Publication Date 2023-11-30
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Meinholz, Heather
  • Gerhardt, Daniel
  • Burgess, Joshua
  • Monahan, Leigh G.
  • Dennin, Jennifer
  • Bruinsma, Stephen Paul
  • O'Meara, M. Maggie
  • Darling, Aaron Earl
  • Parker, Johnathan
  • Macarthur, Stewart
  • Raterman, Denise
  • Chen, Feng
  • Huang, Tina
  • Truong, Tiffany
  • Hawks, Brian
  • Musgrave-Brown, Esther
  • Verity, Susan
  • Slatter, Andrew
  • Tse, David

Abstract

Some embodiments of the methods and compositions provided herein relate to obtaining long read information from short reads of a target nucleic acid. Some embodiments include steps to selectively generate, mark, and amplify long nucleic acid fragments. Some embodiments include enriching for certain sequences in the long fragments with selection probes directed to an American College of Medical Genetics (ACMG) panel of genes. Some embodiments also include fragmenting the long nucleic acid fragments into shorter fragments for sequencing, and informatically reconstructing a sequence of the target nucleic acid.

IPC Classes  ?

  • C12Q 1/6869 - Methods for sequencing
  • C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
  • C12N 9/22 - Ribonucleases
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA

27.

PREPARATION OF LONG READ NUCLEIC ACID LIBRARIES

      
Application Number US2023067466
Publication Number 2023/230551
Status In Force
Filing Date 2023-05-25
Publication Date 2023-11-30
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Meinholz, Heather
  • Gerhardt, Daniel
  • Burgess, Joshua
  • Monahan, Leigh G.
  • Dennin, Jennifer
  • Bruinsma, Stephen Paul
  • O'Meara, M. Maggie
  • Darling, Aaron Earl
  • Parker, Johnathan
  • Macarthur, Stewart
  • Raterman, Denise
  • Chen, Feng
  • Huang, Tina
  • Truong, Tiffany
  • Musgrave-Brown, Esther
  • Verity, Susan
  • Slatter, Andrew
  • Shin, Yoon Hye
  • Tse, David

Abstract

Some embodiments of the methods and compositions provided herein relate to obtaining long read information from short reads of a target nucleic acid. Some embodiments include steps to selectively generate, mark, and amplify long nucleic acid fragments. Some embodiments include enriching for certain sequences in the long fragments with selection probes directed to certain challenging medically relevant genes (CMRG). Some embodiments also include fragmenting the long nucleic acid fragments into shorter fragments for sequencing, and informatically reconstructing a sequence of the target nucleic acid.

IPC Classes  ?

  • C40B 30/06 - Methods of screening libraries by measuring effects on living organisms, tissues or cells
  • C12Q 1/686 - Polymerase chain reaction [PCR]

28.

PREPARATION OF LONG READ NUCLEIC ACID LIBRARIES

      
Application Number US2023067467
Publication Number 2023/230552
Status In Force
Filing Date 2023-05-25
Publication Date 2023-11-30
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
  • ILLUMINA SOFTWARE, INC. (USA)
Inventor
  • Meinholz, Heather
  • Gerhardt, Daniel
  • Burgess, Joshua
  • Monahan, Leigh G.
  • Dennin, Jennifer
  • Bruinsma, Stephen Paul
  • O'Meara, M. Maggie
  • Darling, Aaron Earl
  • Parker, Johnathan
  • Krueger, Chateen
  • Ross, Brian
  • Macarthur, Stewart
  • Lusk, Ryan
  • Halpern, Aaron L.
  • Gross, Stephen M.
  • Raterman, Denise
  • Chen, Feng
  • Hawks, Brian
  • Schalembier, Angelica
  • Musgrave-Brown, Esther
  • Verity, Susan
  • Slatter, Andrew

Abstract

Some embodiments of the methods and compositions provided herein relate to obtaining long read information from short reads of a target nucleic acid. Some embodiments include steps to selectively generate, mark, and amplify long nucleic acid fragments. Some embodiments include enriching for certain sequences in the long fragments with selection probes directed to certain genes throughout the genome and expressed regions with low mappability. Some embodiments also include fragmenting the long nucleic acid fragments into shorter fragments for sequencing, and informatically reconstructing a sequence of the target nucleic acid.

IPC Classes  ?

  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C12N 11/06 - Enzymes or microbial cells immobilised on or in an organic carrier attached to the carrier via a bridging agent
  • C12Q 1/6837 - Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
  • G16B 25/20 - Polymerase chain reaction [PCR]; Primer or probe design; Probe optimisation

29.

PREPARATION OF SIZE-CONTROLLED NUCLEIC ACID FRAGMENTS

      
Application Number US2023022553
Publication Number 2023/225095
Status In Force
Filing Date 2023-05-17
Publication Date 2023-11-23
Owner
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
  • ILLUMINA, INC. (USA)
Inventor
  • Gormley, Niall, Anthony
  • Slatter, Andrew
  • Gross, Stephen
  • Busby, Kayla
  • Yunghans, Allison
  • Roos, Morgan
  • Kuersten, Robert Scott

Abstract

A transposome complex capable of producing size-controlled nucleic acid fragments is described herein. In some embodiments, the transposome complex includes multiple inactive transposomes with active transposomes on both ends of the multiple inactive transposomes. Applications, uses, and variations of the disclosed transposome complex include, but are not limited to, library preparation for a nucleic acid and tuning the length of the transposome complex to produce nucleic acid fragments of predetermined or desired lengths.

IPC Classes  ?

  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA

30.

REAGENT CARTRIDGES AND RELATED SYSTEMS AND METHODS FOR CONTROLLING REAGENT TEMPERATURE

      
Application Number 18002448
Status Pending
Filing Date 2022-03-02
First Publication Date 2023-11-09
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Rosas, Elisabet
  • Balding, Philip
  • Delattre, Cyril
  • Weir, Jacqueline
  • Vega, Ramir
  • Foley, Jennifer
  • Sangiorgio, Paul
  • Segale, Darren
  • Gatti Lafranconi, Pietro
  • Khurana, Tarun
  • Ruden, Jacob
  • Hetherington, Craig

Abstract

Reagent cartridges and related systems and methods for controlling reagent temperature are disclosed. In accordance with an implementation, an apparatus includes a system and a reagent cartridge. The system includes a reagent cartridge receptacle, a non-contact temperature controller, a processor operatively coupled to the temperature controller. The reagent cartridge is receivable within the reagent cartridge receptacle and includes a flow cell assembly, a plurality of reagent reservoirs, and a manifold assembly. The manifold assembly includes a common fluidic line and a plurality of reagent fluidic lines. Each of the plurality of reagent fluidic lines is adapted to be fluidically coupled to a corresponding reagent reservoir and selectively couplable to the common fluidic line. The processor is to cause the temperature controller to change a temperature of at least one of the common fluidic line or one or more of the reagent fluidic lines.

IPC Classes  ?

  • B01L 7/00 - Heating or cooling apparatus; Heat insulating devices

31.

POLYMERASES, COMPOSITIONS, AND METHODS OF USE

      
Application Number 18120639
Status Pending
Filing Date 2023-03-13
First Publication Date 2023-11-09
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
  • ILLUMINA SINGAPORE PTE. LTD. (Singapore)
Inventor
  • Klausing, Kay
  • Ghomi, Hamed Tabatabaei
  • Golynskiy, Misha
  • Nirantar, Saurabh
  • Mcdonald, Seth
  • Peisajovich, Sergio

Abstract

Presented herein are altered polymerase enzymes for improved incorporation of nucleotides and nucleotide analogues, in particular altered polymerases that maintain high fidelity under reduced incorporation times, as well as methods and kits using the same.

IPC Classes  ?

  • C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)

32.

COMPOSITIONS AND METHODS FOR IMPROVING SEQUENCING SIGNALS

      
Application Number 18192288
Status Pending
Filing Date 2023-03-29
First Publication Date 2023-11-09
Owner
  • Illumina, Inc. (USA)
  • Illumina Cambridge Limited (United Kingdom)
Inventor
  • You, Huihong
  • Caber, Samuel
  • Chesney, Michael
  • Mao, Jie
  • Richez, Alexandre
  • Macleod, Rebecca
  • Welch, Emily
  • Mei, Zhong
  • Wu, Xiaolin
  • Anastasi, Carole
  • Fuhrmann, Alexander

Abstract

Embodiments of the present disclosure relate to compositions and kits for use in sequencing by synthesis to improve fluorescent signal intensity and reduce signal decay caused by short wavelength light source during the imaging events. Methods of sequencing using the compositions and kits described herein are also provided.

IPC Classes  ?

  • C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
  • C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay

33.

SHORT PENDANT ARM LINKERS FOR NUCLEOTIDES IN SEQUENCING APPLICATIONS

      
Application Number 18313227
Status Pending
Filing Date 2023-05-05
First Publication Date 2023-11-02
Owner Illumina Cambridge Limited (United Kingdom)
Inventor
  • Cressina, Elena
  • Francais, Antoine
  • Liu, Xiaohai

Abstract

The present disclosure relates to new nucleotide and oligonucleotide compounds and their use in nucleic acid sequencing applications.

IPC Classes  ?

  • C12Q 1/6869 - Methods for sequencing
  • C07H 19/06 - Pyrimidine radicals
  • 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 19/16 - Purine radicals
  • C07H 19/20 - Purine radicals with the saccharide radical being esterified by phosphoric or polyphosphoric acids
  • C07H 19/10 - Pyrimidine radicals with the saccharide radical being esterified by phosphoric or polyphosphoric acids
  • C07H 19/073 - Pyrimidine radicals with 2-deoxyribosyl as the saccharide radical
  • C07H 19/14 - Pyrrolo-pyrimidine radicals
  • 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 1/6809 - Methods for determination or identification of nucleic acids involving differential detection
  • C12Q 1/6816 - Hybridisation assays characterised by the detection means

34.

METHODS AND SYSTEMS FOR ENCAPSULATING LYOPHILISED MICROSPHERES

      
Application Number 18307376
Status Pending
Filing Date 2023-04-26
First Publication Date 2023-11-02
Owner ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Ricoult, Sébastien
  • Plitzko, Matthias
  • Luy, Bernhard

Abstract

The present disclosure relates to a method, including providing one or more lyophilised microspheres in a mixing vessel at a first temperature and generating a fluidized bed of the one or more lyophilised microspheres in the mixing vessel, under conditions effective to encapsulate the one or more lyophilised microspheres with a coating formulation. In an example, the fluidized bed has a fluidization rate of between about 1 cubic meters per hour (m3/h) and about 30 m3/h. In another example, the fluidized bed has an environmental humidity of between about 10% and about 20%. In still another example, the coating formulation is applied at a spray rate of between about 1.5 grams per minute (g/min) and about 10 g/min. In yet another example, the coating formulation is applied at an atomizing rate of between about 0.5 bar and about 1.5 bar. In a further example, the fluidized bed is in a Wurster configuration, a top spray configuration, or a combination thereof. The present disclosure also relates to a system, including one or more lyophilised microspheres, a mixing vessel configured for holding the one or more lyophilised microspheres, a mixer for generating a fluidized bed of the one or more lyophilised microspheres in the mixing vessel at a location, and at least one spray nozzle configured to introduce a shell formulation into the mixing vessel at the location.

IPC Classes  ?

  • C12Q 1/6869 - Methods for sequencing
  • B01J 13/22 - Coating
  • B05C 19/02 - Apparatus specially adapted for applying particulate materials to surfaces using fluidised-bed technique

35.

METHODS AND SYSTEMS FOR ENCAPSULATING LYOPHILISED MICROSPHERES

      
Application Number IB2023054319
Publication Number 2023/209606
Status In Force
Filing Date 2023-04-26
Publication Date 2023-11-02
Owner ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Ricoult, Sébastien
  • Plitzko, Matthias
  • Luy, Bernhard

Abstract

The present disclosure relates to a method, including providing one or more lyophilised microspheres in a mixing vessel at a first temperature and generating a fluidized bed of the one or more lyophilised microspheres in the mixing vessel, under conditions effective to encapsulate the one or more lyophilised microspheres with a coating formulation. In an example, the fluidized bed has a fluidization rate of between about 1 cubic meters per hour (m3/h) and about 30 m3/h. In another example, the fluidized bed has an environmental humidity of between about 10% and about 20%. In still another example, the coating formulation is applied at a spray rate of between about 1.5 grams per minute (g/min) and about 10 g/min. In yet another example, the coating formulation is applied at an atomizing rate of between about 0.5 bar and about 1.5 bar. In a further example, the fluidized bed is in a Wurster configuration, a top spray configuration, or a combination thereof. The present disclosure also relates to a system, including one or more lyophilised microspheres, a mixing vessel configured for holding the one or more lyophilised microspheres, a mixer for generating a fluidized bed of the one or more lyophilised microspheres in the mixing vessel at a location, and at least one spray nozzle configured to introduce a shell formulation into the mixing vessel at the location.

IPC Classes  ?

  • B01J 13/04 - Making microcapsules or microballoons by physical processes, e.g. drying, spraying
  • B01J 8/18 - Chemical or physical processes in general, conducted in the presence of fluids and solid particles; Apparatus for such processes with fluidised particles

36.

DNA ORIGAMI STRUCTURE AND PROTEIN NANOPORE CONSTRUCT

      
Application Number US2023019596
Publication Number 2023/211818
Status In Force
Filing Date 2023-04-24
Publication Date 2023-11-02
Owner ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Garcia, Miguel Angel Aleman
  • Richez, Alexandre

Abstract

The present application discloses a novel DNA origami structure and a nanopore construct associated with the DNA origami structure. The DNA origami structure includes a first hydrophilic section at a first end of the DNA origami structure, a stopper section adjacent the first hydrophilic section, a second hydrophilic section at a second end of the DNA origami structure, a hydrophobic section between the stopper section and the second hydrophilic section, and an open cavity running through the DNA origami structure from the first end to the second end. The stopper section is configured to lay against the membrane when the DNA origami structure is inserted through the membrane.

IPC Classes  ?

  • C12Q 1/6869 - Methods for sequencing
  • B82Y 30/00 - Nanotechnology for materials or surface science, e.g. nanocomposites

37.

Complex Surface-Bound Transposome Complexes

      
Application Number 18316575
Status Pending
Filing Date 2023-05-12
First Publication Date 2023-10-26
Owner Illumina Cambridge Limited (United Kingdom)
Inventor
  • Slatter, Andrew
  • Musgrave-Brown, Esther
  • Verity, Susan C.
  • Gormley, Niall Anthony

Abstract

The present disclosure relates to methods, compositions, and kits for generating a library of tagged nucleic acid fragments without using PCR amplification, including methods and compositions for fragmenting and tagging nucleic acids (e.g., DNA) using transposome complexes immobilized on solid support.

IPC Classes  ?

  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12Q 1/6834 - Enzymatic or biochemical coupling of nucleic acids to a solid phase
  • C12Q 1/6869 - Methods for sequencing

38.

METHODS AND ARRAYS FOR PRODUCING AND SEQUENCING MONOCLONAL CLUSTERS OF NUCLEIC ACID

      
Application Number 18320122
Status Pending
Filing Date 2023-05-18
First Publication Date 2023-10-26
Owner Illumina Cambridge Limited (United Kingdom)
Inventor
  • Gunderson, Kevin L.
  • Bai, Jingwei
  • Kellinger, Matthew William
  • Beierle, John M.
  • Boutell, Jonathan Mark
  • Rigatti, Roberto
  • Rogert Bacigalupo, Maria Candelaria
  • Boyanov, Boyan
  • Maisinger, Klaus

Abstract

The present disclosure relates to the field of molecular biology and more specifically to microarrays and methods.

IPC Classes  ?

  • C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
  • B01J 19/00 - Chemical, physical or physico-chemical processes in general; Their relevant apparatus
  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12Q 1/6837 - Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
  • C12Q 1/6853 - Nucleic acid amplification reactions using modified primers or templates
  • C40B 40/06 - Libraries containing nucleotides or polynucleotides, or derivatives thereof
  • C40B 50/14 - Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creation; Particular methods of cleavage from the solid support

39.

POLARIZATION BASED SENSING

      
Application Number US2023066004
Publication Number 2023/205729
Status In Force
Filing Date 2023-04-20
Publication Date 2023-10-26
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Rezaei, Mohsen
  • Hetherington, Craig
  • Sangiorgio, Paul
  • Ciesla, Craig
  • Evans, Geraint
  • Hong, Stanley
  • Emadi, Arvin

Abstract

There is set forth herein, in one example, an apparatus. The apparatus can comprise, for example: a first reaction site and a second reaction site associated to a common pixel, wherein the pixel comprises a pixel sensor.

IPC Classes  ?

  • G01N 21/64 - Fluorescence; Phosphorescence
  • G01N 21/21 - Polarisation-affecting properties
  • G01J 4/04 - Polarimeters using electric detection means

40.

FLOW CELLS

      
Application Number 18317865
Status Pending
Filing Date 2023-05-15
First Publication Date 2023-10-19
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Fisher, Jeffrey S.
  • Mather, Brian D.
  • Rogert Bacigalupo, Maria Candelaria
  • Fullerton, Justin
  • Vincent, Ludovic
  • Kraft, Lewis J.
  • Hong, Sahngki
  • Boyanov, Boyan
  • Bowen, M. Shane
  • Park, Sang
  • George, Wayne N.
  • Brown, Andrew A.

Abstract

An example of a flow cell includes a substrate; a first primer set attached to a first region on the substrate, the first primer set including an un-cleavable first primer and a cleavable second primer; and a second primer set attached to a second region on the substrate, the second primer set including a cleavable first primer and an un-cleavable second primer.

IPC Classes  ?

41.

APTAMER DYNAMIC RANGE COMPRESSION AND DETECTION TECHNIQUES

      
Application Number US2023017778
Publication Number 2023/196528
Status In Force
Filing Date 2023-04-06
Publication Date 2023-10-12
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Slatter, Andrew
  • Randise-Hinchliff, Carlo
  • Price, Andrew
  • Gormley, Niall Anthony
  • Manzo, Andrea
  • Subramanian, Nithya
  • Kaper, Fiona
  • Jones, David
  • Norberg, Steven

Abstract

Aptamer detection techniques with dynamic range compression are described that permit removal of a portion of more abundant aptamers in an aptamer-based assay. In an embodiment, a mixture of tagged probes and dummy probes can be used such that the dummy probes bind abundant aptamers and in turn are not captured or amplified for detection in downstream steps. Other techniques are also contemplated, including targeted removal of or cleavage of probes that bind to excess aptamers.

IPC Classes  ?

  • C12Q 1/6816 - Hybridisation assays characterised by the detection means
  • C12Q 1/6869 - Methods for sequencing
  • C12Q 1/6876 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes

42.

ALTERED CYTIDINE DEAMINASES AND METHODS OF USE

      
Application Number US2023017846
Publication Number 2023/196572
Status In Force
Filing Date 2023-04-07
Publication Date 2023-10-12
Owner
  • ILLUMINA SINGAPORE PTE. LTD. (Singapore)
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Toh, Dewei Joel
  • Beh, Leslie Yee Ming
  • Tan, Shu Ting
  • Traczyk, Anna
  • Nirantar, Saurabh
  • Brustad, Eric
  • Ghomi, Hamed Tabatabaei
  • Fahmi, Zahra
  • Ravichandraprabhu, Lekha
  • Brown, Colin
  • Busby, Kayla
  • Gross, Stephen
  • Karadeema, Rebekah
  • Lam, Huy
  • Mathonet, Pascale
  • Shultzaberger, Sarah E.
  • Tzeng, Kathleen
  • Yunghans, Allison Kathleen

Abstract

The present disclosure is concerned with proteins, methods, compositions, and kits for mapping of methylation status of nucleic acids, including 5-methylcytosine and 5-hydroxymethyl cytosine (5hmC). In one embodiment, proteins are provided that selectively act on certain modified cytosines of target nucleic acids and converts them to thymidine or modified thymidine analogues. In another embodiment, proteins are provided that selectively act on certain modified cytosines of target nucleic acids and converts them to uracil or thymidine and selectively do not act on other certain modified cytosines of target nucleic acids. Also provided are compositions and kits that include one or more of the proteins and methods for using one or more of the proteins.

IPC Classes  ?

  • C12N 9/78 - Hydrolases (3.) acting on carbon to nitrogen bonds other than peptide bonds (3.5)
  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12Q 1/6869 - Methods for sequencing

43.

SYSTEMS AND METHODS OF SEQUENCING POLYNUCLEOTIDES

      
Application Number US2023016388
Publication Number 2023/192163
Status In Force
Filing Date 2023-03-27
Publication Date 2023-10-05
Owner
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
  • ILLUMINA, INC. (USA)
Inventor
  • Callingham, Michael
  • Burek, Michael, John
  • Winnard, Christopher
  • Miller, Oliver, Jon

Abstract

The application relates to DNA sequencing systems and methods. Systems and methods for determining the nucleotide sequence of a polynucleotide include attaching three different fluorescent dyes to three different nucleotides during incorporation. In particular, long Stokes shifted dyes may be used to determine the sequence of polynucleotides in a sequencing by synthesis system.

IPC Classes  ?

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

44.

LABELED AVIDIN AND METHODS FOR SEQUENCING

      
Application Number EP2023057854
Publication Number 2023/186815
Status In Force
Filing Date 2023-03-27
Publication Date 2023-10-05
Owner ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Wu, Xiaolin
  • Mccauley, Patrick
  • Dharmarwardana, Madushani

Abstract

Embodiments of the present disclosure relate to compositions and methods for improving the intensity of the fluorescent signals during nucleic acid sequencing. In particular, at least one biotin-binding site of the labeled streptavidin is blocked to reduce fluorescent signal deflation.

IPC Classes  ?

45.

CHROMENOQUINOLINE DYES AND USES IN SEQUENCING

      
Application Number EP2023057863
Publication Number 2023/186819
Status In Force
Filing Date 2023-03-27
Publication Date 2023-10-05
Owner ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Callingham, Michael
  • Hynes, Niall
  • Romanov, Nikolai Nikolaevich

Abstract

The present application relates to chromenoquinoline dyes and their uses as fluorescent labels. For example, these dyes may be used to label nucleotides for nucleic acid sequencing.

IPC Classes  ?

  • C09B 57/00 - Other synthetic dyes of known constitution
  • C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
  • G01N 33/50 - Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing

46.

PAIRED-END RE-SYNTHESIS USING BLOCKED P5 PRIMERS

      
Application Number EP2023058307
Publication Number 2023/187061
Status In Force
Filing Date 2023-03-30
Publication Date 2023-10-05
Owner ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Ma, Xiaoyu
  • Lessard-Viger, Mathieu
  • Brustad, Eric
  • Fisher, Jeffrey
  • Boutell, Jonathan
  • Chang, Weihua

Abstract

The present disclosure is generally directed to strategies for template capture and amplification during sequencing. In some examples, a solid support is used for template capture and amplification.

IPC Classes  ?

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

47.

AMPHIPHILIC BLOCK-CO-POLYMERS CROSS-LINKED WITH DIFFERENT CROSS-LINKERS CONSECUTIVELY FORMING A CROSS-LINKING HIERARCHY

      
Application Number EP2023058396
Publication Number 2023/187112
Status In Force
Filing Date 2023-03-30
Publication Date 2023-10-05
Owner ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Conde-Gonzalez, Antonio
  • Richez, Alexandre
  • Garoldini, Davide
  • Uttley, Oliver
  • Vacogne, Charlotte

Abstract

Barriers including molecules covalently bonded to amphiphilic molecules, and methods of making the same, are provided herein. In some examples, a barrier between first and second fluids includes one or more layers comprising a plurality of amphiphilic molecules; and a first layer comprising a plurality of molecules covalently bonded to amphiphilic molecules of the plurality of amphiphilic molecules.

IPC Classes  ?

  • B01D 67/00 - Processes specially adapted for manufacturing semi-permeable membranes for separation processes or apparatus
  • B01D 69/02 - Semi-permeable membranes for separation processes or apparatus characterised by their form, structure or properties; Manufacturing processes specially adapted therefor characterised by their properties
  • B01D 69/12 - Composite membranes; Ultra-thin membranes
  • B01D 69/14 - Dynamic membranes
  • B01D 71/80 - Block polymers
  • C12Q 1/6869 - Methods for sequencing

48.

COMPOSITIONS AND METHODS FOR IMPROVING SEQUENCING SIGNALS

      
Application Number EP2023058142
Publication Number 2023/186982
Status In Force
Filing Date 2023-03-29
Publication Date 2023-10-05
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • You, Huihong
  • Caber, Samuel
  • Chesney, Michael
  • Mao, Jie
  • Macleod, Rebecca
  • Welch, Emily
  • Mei, Zhong
  • Richez, Alexandre
  • Wu, Xiaolin
  • Anastasi, Carole
  • Fuhrmann, Alexander

Abstract

Embodiments of the present disclosure relate to compositions and kits for use in sequencing by synthesis to improve fluorescent signal intensity and reduce signal decay caused by short wavelength light source during the imaging events. Methods of sequencing using the compositions and kits described herein are also provided.

IPC Classes  ?

49.

METHODS FOR CHEMICAL CLEAVAGE OF SURFACE-BOUND POLYNUCLEOTIDES

      
Application Number EP2023057956
Publication Number 2023/186872
Status In Force
Filing Date 2023-03-28
Publication Date 2023-10-05
Owner ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Miller, Oliver
  • Marafini, Pietro
  • Kwasniewska, Alix

Abstract

Embodiments of the present disclosure relate to modified extension primers for use in generating clustered polynucleotides for sequencing by synthesis. In particular, the disclosure relates to methods of chemically linearizing clustered polynucleotides in preparation for sequencing by cleavage of one or more strands of double-stranded polynucleotides immobilized on a solid support by a periodate salt.

IPC Classes  ?

50.

DEVICES INCLUDING OSMOTICALLY BALANCED BARRIERS, AND METHODS OF MAKING AND USING THE SAME

      
Application Number EP2023058184
Publication Number 2023/187001
Status In Force
Filing Date 2023-03-29
Publication Date 2023-10-05
Owner ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Von Hatten, Xavier
  • Conde-Gonzalez, Antonio
  • Kocsis, Istvan
  • Richez, Alexandre

Abstract

Devices including osmotically balanced barriers, and methods of making and using the same, are provided herein. A fluidic well may include a barrier having first and second sides. A first fluid within the fluidic well may contact the first side of the barrier, and may have a first composition including a first concentration of a salt. A second fluid within the fluidic well may contact the second side of the barrier and may have a second composition including a second concentration of the salt that is different than the first concentration. The difference between the first and second concentrations of the salt may generate a first osmotic pressure across the barrier. The second composition further may include a concentration of a compound other than the salt. The concentration of the compound may generate a second osmotic pressure across the barrier that opposes and substantially balances the first osmotic pressure.

IPC Classes  ?

  • C12Q 1/6869 - Methods for sequencing
  • G01N 33/487 - Physical analysis of biological material of liquid biological material

51.

COMPOSITIONS INCLUDING AQUEOUS AMINE BORANE COMPLEXES AND POLYNUCLEOTIDES, AND METHODS OF USING THE SAME TO DETECT METHYLCYTOSINE OR HYDROXYMETHYLCYTOSINE

      
Application Number EP2023058202
Publication Number 2023/187012
Status In Force
Filing Date 2023-03-29
Publication Date 2023-10-05
Owner ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Cressina, Elena
  • Vybornyi, Mykhailo
  • Hofer, Alexandre
  • Anastasi, Carole

Abstract

Disclosed herein are aqueous compositions that include a pyridine complex and a polynucleotide. The compositions can be used to detect methylcytosine and/or hydroxymethylcytosine in the polynucleotide. In some examples, the compositions may be used as part of a TET-assisted borane sequencing workflow.

IPC Classes  ?

  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12Q 1/6869 - Methods for sequencing

52.

METHODS FOR INSERTING NANOPORES INTO POLYMERIC MEMBRANES USING CHAOTROPIC SOLVENTS

      
Application Number EP2023058343
Publication Number 2023/187081
Status In Force
Filing Date 2023-03-30
Publication Date 2023-10-05
Owner ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Kocsis, Istvan
  • Vacogne, Charlotte
  • Uttley, Oliver
  • Conde-Gonzalez, Antonio
  • Richez, Alexandre

Abstract

Methods of inserting a nanopore into a polymeric membrane are provided herein. The membrane may be destabilized using a chaotropic solvent. The nanopore may be inserted into the destabilized polymer membrane. The chaotropic solvent may be removed to stabilize the polymer membrane with the nanopore inserted therein.

IPC Classes  ?

53.

NANOPORE DEVICES INCLUDING BARRIERS USING DIBLOCK OR TRIBLOCK COPOLYMERS, AND METHODS OF MAKING THE SAME

      
Application Number EP2023058383
Publication Number 2023/187104
Status In Force
Filing Date 2023-03-30
Publication Date 2023-10-05
Owner ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Richez, Alexandre
  • Conde-Gonzalez, Antonio
  • Uttley, Oliver
  • Vacogne, Charlotte
  • Garoldini, Davide
  • Aleman Garcia, Miguel Angel
  • Vyborna, Yuliia

Abstract

Nanopore devices including barriers using diblock or triblock copolymers, and methods of making the same, are provided herein. In some examples, a barrier between first and second fluids is suspended by a barrier support defining an aperture. The barrier may include one or more layers suspended across the aperture and including molecules of a block copolymer. Each molecule of the block copolymer may include one or more hydrophilic blocks having an approximate length A and one or more hydrophobic blocks having an approximate length B. The hydrophilic blocks may form outer surfaces of the barrier and the hydrophobic blocks may be located within the barrier. The hydrophobic blocks may include a polymer selected from the group consisting of poly(dimethylsiloxane) (PDMS), polybutadiene (PBd), polyisoprene, polymyrcene, polychloroprene, hydrogenated polydiene, fluorinated polyethylene, polypeptide, and poly(isobutylene) (PIB).

IPC Classes  ?

54.

BARRIERS INCLUDING CROSS-LINKED AMPHIPHILIC MOLECULES, AND METHODS OF MAKING THE SAME

      
Application Number EP2023058387
Publication Number 2023/187106
Status In Force
Filing Date 2023-03-30
Publication Date 2023-10-05
Owner ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Conde-Gonzalez, Antonio
  • Vacogne, Charlotte
  • Kocsis, Istvan
  • Richez, Alexandre
  • Uttley, Oliver
  • Aleman Garcia, Miguel Angel
  • Vyborna, Yuliia

Abstract

Barriers including crosslinked amphiphilic molecules, and methods of making the same, are provided herein. In some examples, a barrier between first and second fluids includes at least one layer comprising a plurality of amphiphilic molecules. Amphiphilic molecules of the plurality of amphiphilic molecules are crosslinked to one another.

IPC Classes  ?

55.

AMPHIPHILIC POLYMERS TO BE USED IN BARRIERS AND PREPARATION THEREOF, BARRIERS WITH NANOPORES AND PREPARATION THEREOF

      
Application Number EP2023058393
Publication Number 2023/187110
Status In Force
Filing Date 2023-03-30
Publication Date 2023-10-05
Owner ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Conde-Gonzalez, Antonio
  • Vacogne, Charlotte
  • Uttley, Oliver
  • Kocsis, Istvan
  • Richez, Alexandre

Abstract

Nanopore devices including barriers using amphiphilic units, and methods of making the same, are provided herein. In some examples, a barrier between first and second fluids includes a first layer comprising a first plurality of amphiphilic units, a second layer comprising a second plurality of the amphiphilic units and contacting the first plurality of amphiphilic units. The amphiphilic units may be substantially the same size as one another. The amphiphilic units respectively may include hydrophobic blocks and hydrophilic blocks coupled to the hydrophobic blocks.

IPC Classes  ?

  • B01D 69/02 - Semi-permeable membranes for separation processes or apparatus characterised by their form, structure or properties; Manufacturing processes specially adapted therefor characterised by their properties
  • B01D 69/14 - Dynamic membranes
  • B01D 71/80 - Block polymers
  • B01D 71/82 - Macromolecular material not specifically provided for in a single one of groups characterised by the presence of specified groups, e.g. introduced by chemical after-treatment
  • C08G 77/28 - Polysiloxanes containing silicon bound to organic groups containing atoms other than carbon, hydrogen, and oxygen sulfur-containing groups
  • C08L 83/08 - Polysiloxanes containing silicon bound to organic groups containing atoms other than carbon, hydrogen, and oxygen
  • C12Q 1/6869 - Methods for sequencing
  • C08G 81/00 - Macromolecular compounds obtained by interreacting polymers in the absence of monomers, e.g. block polymers
  • C09D 187/00 - Coating compositions based on unspecified macromolecular compounds, obtained otherwise than by polymerisation reactions only involving unsaturated carbon-to-carbon bonds

56.

BARRIERS INCLUDING BIOLOGICAL NANOPORE FOR DNA SEQUENCING, THE BARRIERS BEING MADE OF CO-POLYMERS WITH END AND/OR MIDDLE GROUPS, AND METHODS OF MAKING THE SAME

      
Application Number EP2023058395
Publication Number 2023/187111
Status In Force
Filing Date 2023-03-30
Publication Date 2023-10-05
Owner ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Uttley, Oliver
  • Garoldini, Davide
  • Kocsis, Istvan
  • Vacogne, Charlotte
  • Conde-Gonzalez, Antonio
  • Richez, Alexandre
  • Aleman Garcia, Miguel Angel
  • Vyborna, Yuliia

Abstract

Nanopore devices including barriers using polymers with end groups, and methods of making the same, are provided herein. In some examples, a barrier between first and second fluids is provided. The barrier may be suspended by a barrier support defining an aperture. The barrier may include one or more layers suspended across the aperture and including molecules of a block copolymer. Each molecule of the block copolymer may include one or more hydrophilic blocks having an approximate length A and one or more hydrophilic blocks having an approximate length B. The hydrophilic blocks may form outer surfaces of the barrier and the hydrophobic blocks being located within the barrier. End groups may be coupled to ends of the hydrophilic blocks that form outer surfaces of the barrier. The end groups may have a different hydrophilicity than the hydrophilic blocks.

IPC Classes  ?

  • B01D 69/02 - Semi-permeable membranes for separation processes or apparatus characterised by their form, structure or properties; Manufacturing processes specially adapted therefor characterised by their properties
  • B01D 69/14 - Dynamic membranes
  • C08G 77/28 - Polysiloxanes containing silicon bound to organic groups containing atoms other than carbon, hydrogen, and oxygen sulfur-containing groups
  • C08G 81/00 - Macromolecular compounds obtained by interreacting polymers in the absence of monomers, e.g. block polymers
  • C09D 187/00 - Coating compositions based on unspecified macromolecular compounds, obtained otherwise than by polymerisation reactions only involving unsaturated carbon-to-carbon bonds
  • C12Q 1/6869 - Methods for sequencing

57.

METHODS FOR MAKING FLOW CELL SURFACES

      
Application Number EP2023056729
Publication Number 2023/180161
Status In Force
Filing Date 2023-03-16
Publication Date 2023-09-28
Owner ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Szemjonov, Alexandra
  • Edge, Phillippa
  • Richez, Alexandre

Abstract

In an example method, an initial depression is defined in a first resin layer of a multi-layer stack including the first resin layer over a second resin layer or a base support. The first resin layer is resistant to silanization in an organic solvent, the second resin layer or the base support is reactive toward silanization in the organic solvent, and the first resin layer and the second resin layer or the base support are orthogonally etchable. A remaining portion of the first resin layer at the initial depression is anisotropically etched, using air or O2 plasma, through to expose a surface of the second resin layer or the base support and to form a depression. The multi-layer stack is exposed to a silane in the organic solvent to selectively silanizing the surface of the second resin layer or the base support at the depression.

IPC Classes  ?

  • G03F 7/00 - Photomechanical, e.g. photolithographic, production of textured or patterned surfaces, e.g. printed surfaces; Materials therefor, e.g. comprising photoresists; Apparatus specially adapted therefor
  • B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers

58.

SUBSTRATE WITH ORTHOGONALLY FUNCTIONAL NANODOMAINS

      
Application Number US2023064690
Publication Number 2023/183764
Status In Force
Filing Date 2023-03-20
Publication Date 2023-09-28
Owner ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Szemjonov, Alexandra
  • George, Wayne N.
  • Richez, Alexandre

Abstract

Embodiments of the present disclosure also relate to methods of fabricating flow cell substrates. Some exemplary workflows exploit orthogonal chemistries of substrate layers such that the process does not include polishing steps. Substrates prepared by the method described herein can include a first primer set and a second primer set compatible with simultaneous paired-end sequencing methods.

IPC Classes  ?

  • B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
  • G01N 21/64 - Fluorescence; Phosphorescence
  • G03F 7/00 - Photomechanical, e.g. photolithographic, production of textured or patterned surfaces, e.g. printed surfaces; Materials therefor, e.g. comprising photoresists; Apparatus specially adapted therefor

59.

METHODS AND COMPOSITIONS FOR CLUSTER GENERATION BY BRIDGE AMPLIFICATION

      
Application Number 18139689
Status Pending
Filing Date 2023-04-26
First Publication Date 2023-09-21
Owner ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Boutell, Jonathan Mark
  • Miller, Oliver

Abstract

The present disclosure is concerned with compositions and methods for reducing the steps used in the generation of monoclonal clusters by combining the enzymes used for linearization and removal of unused surface primers.

IPC Classes  ?

  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12N 9/22 - Ribonucleases
  • C12Q 1/6844 - Nucleic acid amplification reactions
  • C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]

60.

METHODS OF PREPARING LOOP FORK LIBRARIES

      
Application Number EP2023056641
Publication Number 2023/175021
Status In Force
Filing Date 2023-03-15
Publication Date 2023-09-21
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
  • ILLUMINA SOFTWARE, INC. (USA)
Inventor
  • Carrami, Eli
  • Boutell, Jonathan
  • Miller, Oliver
  • Karunakaran, Aathavan
  • Bruinsma, Stephen
  • Gormley, Niall

Abstract

The invention relates to methods and kits for use in nucleic acid sequencing, in particular methods for use in concurrent sequencing, and in particular concurrent sequencing of tandem insert libraries.

IPC Classes  ?

  • C12Q 1/6869 - Methods for sequencing
  • C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
  • G16B 40/10 - Signal processing, e.g. from mass spectrometry [MS] or from PCR

61.

METHODS OF DETERMINING SEQUENCE INFORMATION

      
Application Number EP2023056653
Publication Number 2023/175026
Status In Force
Filing Date 2023-03-15
Publication Date 2023-09-21
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
  • ILLUMINA SOFTWARE, INC. (USA)
Inventor
  • Boutell, Jonathan
  • Gormley, Niall
  • Vessere, Gery
  • Karunakaran, Aathavan
  • Carrami, Eli
  • Miller, Oliver
  • Bruinsma, Stephen
  • Sridharan, Shagesh
  • Saraf, Nileshi

Abstract

A method of determining sequence information from two or more polynucleotide sequence portions, the method comprising: selecting one of a plurality of classifications based on first and second intensity data, wherein each classification represents one or more possible combinations of respective nucleobases of the two or more polynucleotide sequence portions, and wherein at least one classification represents more than one possible combination of respective nucleobases.

IPC Classes  ?

  • G16B 40/10 - Signal processing, e.g. from mass spectrometry [MS] or from PCR
  • C12Q 1/6869 - Methods for sequencing
  • C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]

62.

CONCURRENT SEQUENCING OF FORWARD AND REVERSE COMPLEMENT STRANDS ON SEPARATE POLYNUCLEOTIDES FOR METHYLATION DETECTION

      
Application Number EP2023056665
Publication Number 2023/175037
Status In Force
Filing Date 2023-03-15
Publication Date 2023-09-21
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
  • ILLUMINA SOFTWARE, INC. (USA)
  • ILLUMINA SINGAPORE PTE. LTD. (Singapore)
Inventor
  • Karunakaran, Aathavan
  • Sridharan, Shagesh
  • Boutell, Jonathan
  • Vessere, Gery

Abstract

The invention relates to methods and associated products for preparing polynucleotide sequences for detection of modified cytosines and sequencing said polynucleotides to detect modified cytosines. The methods comprise treatment of the target polynucleotide with a conversion reagent that is configured to convert a modified cytosine to thymine or a nucleobase which is read as thymine/uracil, and/or configured to convert an unmodified cytosine to uracil or a nucleobase which is read as thymine/uracil. In particular embodiments, portions of both strands of the treated target are sequenced concurrently.

IPC Classes  ?

  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
  • C12Q 1/6869 - Methods for sequencing

63.

CONCURRENT SEQUENCING OF FORWARD AND REVERSE COMPLEMENT STRANDS ON CONCATENATED POLYNUCLEOTIDES FOR METHYLATION DETECTION

      
Application Number EP2023056668
Publication Number 2023/175040
Status In Force
Filing Date 2023-03-15
Publication Date 2023-09-21
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
  • ILLUMINA SOFTWARE, INC. (USA)
  • ILLUMINA SINGAPORE PTE. LTD. (Singapore)
Inventor
  • Gormley, Niall
  • Boutell, Jonathan
  • Karunakaran, Aathavan

Abstract

The invention relates to methods of detecting modified cytosines in nucleic acid sequences.

IPC Classes  ?

  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
  • C12Q 1/6869 - Methods for sequencing

64.

METHODS OF BASE CALLING NUCLEOBASES

      
Application Number EP2023056672
Publication Number 2023/175043
Status In Force
Filing Date 2023-03-15
Publication Date 2023-09-21
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
  • ILLUMINA SOFTWARE, INC. (USA)
Inventor
  • Vessere, Gery
  • Karunakaran, Aathavan
  • Raczy, Come
  • Gau, Jeff
  • Boutell, Jonathan
  • Andres, Roberto
  • Burek, Michael
  • Carrami, Eli

Abstract

A method of base calling nucleobases of two or more polynucleotide sequence portions, wherein said polynucleotide sequence portions have been selectively processed such that an intensity of the signals obtained based upon the respective first nucleobase is greater than an intensity of the signals obtained based upon the respective second nucleobase.

IPC Classes  ?

  • C12Q 1/6869 - Methods for sequencing
  • C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
  • G16B 40/10 - Signal processing, e.g. from mass spectrometry [MS] or from PCR

65.

METHODS FOR PREPARING SIGNALS FOR CONCURRENT SEQUENCING

      
Application Number EP2023056626
Publication Number 2023/175013
Status In Force
Filing Date 2023-03-15
Publication Date 2023-09-21
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
  • ILLUMINA SOFTWARE, INC. (USA)
Inventor
  • Vessere, Gery
  • Karunakaran, Aathavan
  • Raczy, Come
  • Gau, Jeff
  • Boutell, Jonathan
  • Andres, Roberto
  • Burek, Michael
  • Carrami, Eli

Abstract

The invention relates to methods for use in nucleic acid sequencing, in particular methods for use in concurrent sequencing.

IPC Classes  ?

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

66.

CONCURRENT SEQUENCING OF FORWARD AND REVERSE COMPLEMENT STRANDS ON SEPARATE POLYNUCLEOTIDES

      
Application Number EP2023056634
Publication Number 2023/175018
Status In Force
Filing Date 2023-03-15
Publication Date 2023-09-21
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
  • ILLUMINA SOFTWARE, INC. (USA)
Inventor
  • Carrami, Eli
  • Boutell, Jonathan
  • Miller, Oliver
  • Karunakaran, Aathavan
  • Bruinsma, Stephen
  • Gormley, Niall

Abstract

The invention relates to methods of detecting mismatched base pairs in nucleic acid sequences.

IPC Classes  ?

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

67.

PAIRED-END SEQUENCING

      
Application Number EP2023056648
Publication Number 2023/175024
Status In Force
Filing Date 2023-03-15
Publication Date 2023-09-21
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
  • ILLUMINA SOFTWARE, INC. (USA)
Inventor
  • Karunakaran, Aathavan
  • Saraf, Nileshi
  • Leong, Samantha Antonio
  • Vega, Ramir Villa
  • Vessere, Gery

Abstract

Systems and methods of identifying nucleobases in a template polynucleotide are disclosed. In one embodiment, such a method may include providing a substrate comprising a plurality of double stranded template polynucleotides in a cluster. Each double stranded template polynucleotide may comprise a first strand and a second strand. The method may further include contacting the plurality of double stranded template polynucleotides with first primers which bind to the first strand and second primers which bind to the second strand. The method may further include extending the first primers and the second primers by contacting the cluster with labeled nucleobases to form first labeled primers and second labeled primers. The method may further include stimulating light emissions from the first and second labeled primers, wherein an amplitude of the signal generated by the first labeled primers is greater than an amplitude of the signal generated by the second labeled primers. The method may further include identifying the labeled nucleobases added to the first primers and the second primers based on the amplitude of the signal generated by the labeled nucleobases.

IPC Classes  ?

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

68.

CONCURRENT SEQUENCING OF HETERO N-MER POLYNUCLEOTIDES

      
Application Number EP2023056656
Publication Number 2023/175029
Status In Force
Filing Date 2023-03-15
Publication Date 2023-09-21
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
  • ILLUMINA SOFTWARE, INC. (USA)
Inventor
  • Vessere, Gery
  • Karunakaran, Aathavan
  • Boutell, Jonathan
  • Andres, Roberto
  • Burek, Michael

Abstract

The invention relates to methods for use in nucleic acid sequencing, in particular methods for use in concurrent sequencing.

IPC Classes  ?

  • C12Q 1/6869 - Methods for sequencing
  • C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
  • G16B 40/10 - Signal processing, e.g. from mass spectrometry [MS] or from PCR

69.

CONCURRENT SEQUENCING OF FORWARD AND REVERSE COMPLEMENT STRANDS ON CONCATENATED POLYNUCLEOTIDES

      
Application Number EP2023056669
Publication Number 2023/175041
Status In Force
Filing Date 2023-03-15
Publication Date 2023-09-21
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
  • ILLUMINA SOFTWARE, INC. (USA)
Inventor
  • Boutell, Jonathan
  • Gormley, Niall
  • Vessere, Gery
  • Karunakaran, Aathavan
  • Sridharan, Shagesh
  • Saraf, Nileshi

Abstract

The invention relates to methods of detecting mismatched base pairs in nucleic acid sequences.

IPC Classes  ?

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

70.

PARALLEL SAMPLE AND INDEX SEQUENCING

      
Application Number EP2023056671
Publication Number 2023/175042
Status In Force
Filing Date 2023-03-15
Publication Date 2023-09-21
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
  • ILLUMINA SOFTWARE, INC. (USA)
Inventor
  • Hunter, Shaun E.
  • Sangiorgio, Paul
  • Karunakaran, Aathavan
  • Bracher, David

Abstract

Systems and methods of identifying nucleobases in a template polynucleotide are disclosed. In one embodiment, such a method may include providing a substrate comprising a plurality of the template polynucleotides in a cluster. The method may further include generating light to stimulate fluorescent emissions from the cluster. The method may further include receiving a first signal emitted at a first intensity from a first plurality of nucleotide analogs hybridized to the plurality of template polynucleotides at a first site. The method may further include receiving a second signal emitted at a second intensity from a second plurality of nucleotide analogs hybridized to the plurality of template polynucleotides at a second site. The method may further include identifying the nucleobases hybridized at the first and second sites of the template polynucleotide based on a combination of the first and second signals.

IPC Classes  ?

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

71.

FLOW CELLS AND METHODS

      
Application Number 18146320
Status Pending
Filing Date 2022-12-23
First Publication Date 2023-09-07
Owner
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Basuki, Johan Sebastian
  • Boutell, Jonathan Mark
  • Fisher, Jeffrey S.
  • Fraser, Louise Jane
  • George, Wayne N.
  • Gormley, Niall Anthony
  • Jones, David
  • Ma, Xiaoyu
  • Martins Vitoriano, Maria Ines
  • Mei, Zhong
  • Miller, Oliver Jon
  • Price, Andrew
  • Ricoult, Sebastien Georg Gabriel
  • Thomson, Vicki S.
  • Weir, Jacqueline C.
  • Ma, Xiaoy
  • Chang, Weihua
  • Han, Hui

Abstract

An example of a flow cell includes a substrate having depressions separated by interstitial regions. First and second primers are immobilized within the depressions. First transposome complexes are immobilized within the depressions, and the first transposome complexes include a first amplification domain. Second transposome complexes are also immobilized within the depressions, and the second transposome complexes include a second amplification domain. Some of the first transposome complexes, or some of the second transposome complexes, or some of both of the first and second transposome complexes include a modification to reduce tagmentation efficiency.

IPC Classes  ?

  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers

72.

Sequence-Specific Targeted Transposition and Selection and Sorting of Nucleic Acids

      
Application Number 18169970
Status Pending
Filing Date 2023-02-16
First Publication Date 2023-09-07
Owner
  • Illumina, Inc. (USA)
  • Illumina Cambridge Limited (United Kingdom)
Inventor
  • Steemers, Frank J.
  • Boutell, Jonathan Mark
  • Gatti Lafranconi, Pietro
  • Miller, Oliver Jon
  • Bell, Emma
  • Ricoult, Sebastien Georg Gabriel
  • Gormley, Niall Anthony
  • Schneider, Kim

Abstract

A variety of different types of targeted transposome complexes are described herein that may be used to mediate sequence-specific targeted transposition of nucleic acids. Also described herein is a method of characterizing desired samples in a mixed pool of samples comprising both desired samples and unwanted samples comprising, to produce sequencing data from double-stranded nucleic acid, initially sequencing a library comprising a plurality of nucleic acid samples from a mixed pool, wherein each nucleic acid library comprises nucleic acids from a single sample and a unique sample barcode to distinguish the nucleic acids from the single sample from the nucleic acids from other samples in the library; analyzing the sequencing data and identifying unique sample barcodes associated with sequencing data from desired samples; performing a selection step on the library comprising enriching nucleic acid samples from desired samples and/or depleting nucleic acid samples from unwanted samples; and resequencing the nucleic acid library.

IPC Classes  ?

  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C12N 15/11 - DNA or RNA fragments; Modified forms thereof
  • C12N 9/22 - Ribonucleases
  • C12N 9/12 - Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)

73.

FUNCTIONALIZED NANOSTRUCTURES AND FLOW CELL DEPRESSIONS

      
Application Number EP2023055109
Publication Number 2023/166024
Status In Force
Filing Date 2023-03-01
Publication Date 2023-09-07
Owner ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Artioli, Gianluca Andrea
  • Redivo, Luca
  • Richez, Alexandre
  • Von Hatten, Xavier

Abstract

A functionalized nanostructure includes a metal nanostructure; an un-cleavable first primer and a cleavable second primer attached to a first region of the metal nanostructure through i) a first thiol linkage attached to a first polymer chain having a first polarity or ii) respective first thiol linkages attached to respective first polymer chains having the first polarity; and a cleavable first primer and an un-cleavable second primer attached to a second region of the metal nanostructure through i) a second thiol linkage attached to a second polymer chain having a second polarity different from the first polarity or ii) respective second thiol linkages attached to respective second polymer chains having the second polarity.

IPC Classes  ?

  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12Q 1/6869 - Methods for sequencing

74.

PROTECTIVE SURFACE COATINGS FOR FLOW CELLS

      
Application Number 18195321
Status Pending
Filing Date 2023-05-09
First Publication Date 2023-08-31
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
  • ILLUMINA SINGAPORE PTE. LTD. (Singapore)
Inventor
  • Ramirez, Sean M.
  • Mather, Brian D.
  • Li, Edwin
  • Moon, Sojeong
  • Kim, Innsu Daniel
  • Richez, Alexandre
  • Vincent, Ludovic
  • Von Hatten, Xavier
  • Tran, Hai Quang
  • Zimmerley, Maxwell
  • Morrison, Julia
  • Artioli, Gianluca Andrea
  • Sly, Krystal
  • Black, Hayden
  • Kraft, Lewis J.
  • Xie, Hong
  • Wei, Wei
  • Sanford, Ryan

Abstract

An example of a method includes providing a substrate with an exposed surface comprising a first chemical group, wherein the providing optionally comprises modifying the exposed surface of the substrate to incorporate the first chemical group; reacting the first chemical group with a first reactive group of a functionalized polymer molecule to form a functionalized polymer coating layer covalently bound to the exposed surface of the substrate; grafting a primer to the functionalized polymer coating layer by reacting the primer with a second reactive group of the functionalized polymer coating layer; and forming a water-soluble protective coating on the primer and the functionalized polymer coating layer. Examples of flow cells incorporating examples of the water-soluble protective coating are also disclosed herein.

IPC Classes  ?

  • C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers

75.

APPARATUS AND METHOD FOR CAPTURING VIBRATION IN SYSTEM

      
Application Number US2023013783
Publication Number 2023/164107
Status In Force
Filing Date 2023-02-24
Publication Date 2023-08-31
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Holst, Gregory
  • Blair, Dustin
  • Earney, John
  • Evans, Geraint
  • Hage, Matthew

Abstract

An apparatus includes a chassis, a frame, a sample support member, an imaging assembly, an actuation assembly, and a vibration capture assembly. The frame is coupled with the chassis. The sample support member is supported by the frame. The actuation assembly is supported by the frame and is operable to drive movement of the imaging assembly relative to the sample support member. The vibration capture assembly is operable to selectively transition between a plurality of modes, including a damping mode and an isolation mode. In the damping mode, the vibration capture assembly is configured to resist movement of the frame relative to the chassis in response to operation of the actuation assembly. In the isolation mode, the vibration capture assembly is configured to prevent transmission of vibrational movement in the chassis to the frame.

IPC Classes  ?

  • G01N 21/84 - Systems specially adapted for particular applications
  • G01N 21/01 - Arrangements or apparatus for facilitating the optical investigation
  • G01N 1/36 - Embedding or analogous mounting of samples
  • G01N 21/64 - Fluorescence; Phosphorescence

76.

MACHINE-LEARNING MODELS FOR DETECTING AND ADJUSTING VALUES FOR NUCLEOTIDE METHYLATION LEVELS

      
Application Number US2023063048
Publication Number 2023/164492
Status In Force
Filing Date 2023-02-22
Publication Date 2023-08-31
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Norberg, Steven
  • Guerrero, Luis Fernando Camarillo
  • Brown, Colin
  • Manzo, Andrea
  • Shultzaberger, Sarah E.
  • Eberle, Michael
  • Almasi, Sepideh
  • Rohrback, Suzanne
  • Mathonet, Pascale
  • Dolzhenko, Egor

Abstract

This disclosure describes methods, non-transitory computer readable media, and systems that can use a machine-learning to determine factors or scores indicating an error level with which a given methylation assay detects methylation of cytosine bases. For instance, the disclosed systems use a machine-learning model to generate a bias score indicating a degree to which a given methylation assay errs in detecting cytosine methylation when specific sequence contexts surround such cytosines compared to other sequence contexts. The machine-learning model may take various forms of models, including a decision-tree model, a neural network, or a combination of a decision-tree model and a neural network. In some cases, the disclosed system combines or uses bias scores from multiple machine-learning models to generate a consensus bias score.

IPC Classes  ?

  • G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
  • G16B 40/00 - ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding

77.

CYCLOOCTATETRAENE CONTAINING DYES AND COMPOSITIONS

      
Application Number 18168856
Status Pending
Filing Date 2023-02-14
First Publication Date 2023-08-24
Owner Illumina Cambridge Limited (United Kingdom)
Inventor
  • Wu, Xiaolin
  • Liu, Xiaohai
  • Romanov, Nikolai Nikolaevich
  • Francais, Antoine
  • Mccauley, Patrick
  • Callingham, Michael
  • Anastasi, Carole

Abstract

Embodiments of the present disclosure relate to cyclooctatetraene containing dyes and their uses as fluorescent labels. Also provided are composition containing cyclooctatetraene. The dyes and compositions may be used in various biological applications, such as nucleic acid sequencing.

IPC Classes  ?

78.

CYCLOOCTATETRAENE CONTAINING DYES AND COMPOSITIONS

      
Application Number 18310727
Status Pending
Filing Date 2023-05-02
First Publication Date 2023-08-24
Owner Illumina Cambridge Limited (United Kingdom)
Inventor
  • Wu, Xiaolin
  • Liu, Xiaohai
  • Romanov, Nikolai Nikolaevich
  • Francais, Antoine
  • Mccauley, Patrick
  • Callingham, Michael
  • Anastasi, Carole

Abstract

Embodiments of the present disclosure relate to cyclooctatetraene containing dyes and their uses as fluorescent labels. Also provided are composition containing cyclooctatetraene. The dyes and compositions may be used in various biological applications, such as nucleic acid sequencing.

IPC Classes  ?

79.

COMPOSITIONS FOR USE IN POLYUNUCLEOTIDE SEQUENCING

      
Application Number 18106198
Status Pending
Filing Date 2023-02-06
First Publication Date 2023-08-03
Owner ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Gatti-Lafranconi, Pietro
  • Sansom, Helen
  • Hancock, Matthew

Abstract

A polynucleotide sequencing method comprises (i) removing a label and a blocking moiety from a blocked, labeled nucleotide incorporated into a copy polynucleotide strand that is complementary to at least a portion of a template polynucleotide strand; and (ii) washing the removed label and blocking moiety away from the copy strand with a wash solution comprising a first buffer comprising a scavenger compound. Removing the label and blocking moieties may comprise chemically removing the moieties. The first buffer may also comprise an antioxidant and may be used in a scanning buffer used during a nucleotide detection step.

IPC Classes  ?

  • C12Q 1/6869 - Methods for sequencing
  • B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers

80.

IMAGE-BASED VARIANT PATHOGENICITY DETERMINATION

      
Application Number US2023061479
Publication Number 2023/147490
Status In Force
Filing Date 2023-01-27
Publication Date 2023-08-03
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Hamp, Tobias
  • Gao, Hong
  • Farh, Kai-How

Abstract

Described herein are technologies for classifying a protein structure (such as technologies for classifying the pathogenicity of a protein structure related to a nucleotide variant). Such a classification is based on two-dimensional images taken from a three-dimensional image of the protein structure. With respect to some implementations, described herein are multi-view convolutional neural networks (CNNs) for classifying a protein structure based on inputs of two-dimensional images taken from a three-dimensional image of the protein structure. In some implementations, a computer-implemented method of determining pathogenicity of variants includes accessing a structural rendition of amino acids, capturing images of those parts of the structural rendition that contain a target amino acid from the amino acids, and, based on the images, determining pathogenicity of a nucleotide variant that mutates the target amino acid into an alternate amino acid.

IPC Classes  ?

  • G16B 15/20 - Protein or domain folding
  • G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
  • G16B 40/20 - Supervised data analysis
  • G16H 50/20 - ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems
  • G16H 50/30 - ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for individual health risk assessment

81.

METHODS OF DETECTING METHYLCYTOSINE AND HYDROXYMETHYLCYTOSINE BY SEQUENCING

      
Application Number US2023011047
Publication Number 2023/141154
Status In Force
Filing Date 2023-01-18
Publication Date 2023-07-27
Owner
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
  • DAI, Jane Qian (USA)
Inventor
  • Wu, Xiaolin
  • Francais, Antoine
  • Liu, Xiaohai

Abstract

Embodiments of the present disclosure relates to various bisulfite-free chemical methods for detecting methylation of cytosine in the DNA sample. These methods convert methylated and hydroxymethylated cytosine in the nucleic acid sequence to a modified or pseudo thymine or a uracil moiety which then can be detected in sequencing.

IPC Classes  ?

  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay

82.

METHODS OF NUCLEIC ACID SEQUENCING USING SURFACE-BOUND PRIMERS

      
Application Number EP2022087978
Publication Number 2023/126457
Status In Force
Filing Date 2022-12-28
Publication Date 2023-07-06
Owner
  • ILLUMINA CAMBRIDGE LTD. (United Kingdom)
  • ILLUMINA, INC. (USA)
Inventor
  • Boutell, Jonathan Mark
  • Carrami, Eli
  • Gatti Lafranconi, Pietro
  • Balding, Philip
  • Miller, Oliver Jon
  • Klausing, Kay
  • Robbins, Justin
  • Wu, Xiaolin

Abstract

Polynucleotide sequencing methods for sequencing one or more polynucleotide templates that uses primers bound to a surface as sequencing primers. The surface primers may include at least a portion of a surface oligonucleotide used during cluster formation. The sequencing methods may be used for single stranded sequencing or double stranded sequencing. Double stranded sequencing methods may employ an enzyme that has nick-translation activity. A kit includes all the reagents needed for sequencing does not include sequencing primers. The kit may be used to accomplish the sequencing methods of the present disclosure.

IPC Classes  ?

83.

IMAGING SYSTEMS AND RELATED METHODS

      
Application Number US2022054084
Publication Number 2023/129548
Status In Force
Filing Date 2022-12-27
Publication Date 2023-07-06
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Boege, Steven
  • Condello, Danilo
  • Prince, Simon
  • Bryant, Jason
  • Siu, Merek

Abstract

Imaging systems and related methods are disclosed. In accordance with an implementation, a system includes a flow cell receptacle to receive a flow cell that receives a sample and an imaging system having a light source assembly, and an imaging device. The light source assembly to form a substantially collimated beam. The optical assembly including an asymmetric beam expander group that includes one or more asymmetric elements or anamorphic elements disposed along an optical axis. The optical assembly to receive the substantially collimated beam from the light source assembly, and transform the substantially collimated beam into a shaped sampling beam having an elongated cross section in a far field at or near a focal plane of the optical assembly to optically probe the sample. The imaging device to obtain image data associated with the sample in response to the optical probing of the sample with the sampling beam.

IPC Classes  ?

84.

MASK PATTERNS FOR PROTEIN LANGUAGE MODELS FOR PREDICTING PATHOGENICITY

      
Application Number US2022082368
Publication Number 2023/129897
Status In Force
Filing Date 2022-12-23
Publication Date 2023-07-06
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Hamp, Tobias
  • Dietrich, Anastasia Susanna Dagmar
  • Ede, Jeffrey Mark
  • Wu, Yibing
  • Farh, Kai-How

Abstract

The technology disclosed relates to accessing a multiple sequence alignment that aligns a query residue sequence to a plurality of non-query residue sequences, applying a set of periodically-spaced masks to a first set of residues at a first set of positions in the multiple sequence alignment, and cropping a portion of the multiple sequence alignment that includes the set of periodically-spaced masks at the first set of positions, and a second set of residues at a second set of positions in the multiple sequence alignment to which the set of periodically-spaced masks is not applied. The first set of residues includes a residue-of-interest at a position-of-interest in the query residue sequence.

IPC Classes  ?

  • G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
  • G16B 30/10 - Sequence alignment; Homology search
  • G16B 40/20 - Supervised data analysis

85.

SPECIES PROXIMITY-AWARE EVOLUTIONARY CONSERVATION PROFILES

      
Application Number US2022082423
Publication Number 2023/129923
Status In Force
Filing Date 2022-12-27
Publication Date 2023-07-06
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Hamp, Tobias
  • Farh, Kai-How

Abstract

The technology disclosed relates to generating species-differentiable evolutionary profiles using a weighting logic. In particular, the technology disclosed relates to determining a weighted summary statistic for a given residue category at a given position in a multiple sequence alignment based on one or more weights of one or more sequences in the multiple sequence alignment that have a residue of the given residue category at the given position.

IPC Classes  ?

  • G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
  • G16B 30/10 - Sequence alignment; Homology search
  • G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
  • G16B 10/00 - ICT specially adapted for evolutionary bioinformatics, e.g. phylogenetic tree construction or analysis

86.

VARIANT CALLING WITHOUT A TARGET REFERENCE GENOME

      
Application Number US2022082462
Publication Number 2023/129953
Status In Force
Filing Date 2022-12-28
Publication Date 2023-07-06
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Gao, Hong
  • Hamp, Tobias
  • Mcmaster-Schraiber, Joshua Goodwin Jon
  • Sundaram, Laksshman
  • Farh, Kai-How

Abstract

The technology disclosed relates to determining feasibility of using a reference genome of a non-target species for variant calling a sample of a target species. In particular, the technology disclosed relates to mapping sequenced reads of a sample of a target species to a reference genome of a non-target species to detect a first set of variants in the sequenced reads of the sample of the target species, and mapping the sequenced reads of the sample of the target species to a reference genome of a pseudo-target species to detect a second set of variants in the sequenced reads of the sample of the target species.

IPC Classes  ?

  • G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
  • G16B 30/10 - Sequence alignment; Homology search

87.

INTER-MODEL PREDICTION SCORE RECALIBRATION

      
Application Number US2022082464
Publication Number 2023/129955
Status In Force
Filing Date 2022-12-28
Publication Date 2023-07-06
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Hamp, Tobias
  • Farh, Kai-How

Abstract

The technology disclosed relates to inter-model prediction score recalibration. In one implementation, the technology disclosed relates to a system including a first model that generates, based on evolutionary conservation summary statistics of amino acids in a target protein sequence, a first pathogenicity score-to-rank mapping for a set of variants in the target protein sequence; and a second model that generates, based on epistasis expressed by amino acid patterns spanning the target protein sequence and a plurality of non-target protein sequences aligned in multiple sequence alignment, a second pathogenicity score-to-rank mapping for the set of variants. The system also includes a reassignment logic that reassigns pathogenicity scores from the first set of pathogenicity scores to the set of variants based on the first and second score-to-rank mappings, and an output logic to generate a ranking of the set of variants based on the reassigned scores.

IPC Classes  ?

  • G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
  • G16B 40/20 - Supervised data analysis
  • G16B 40/30 - Unsupervised data analysis
  • G16B 15/30 - Drug targeting using structural data; Docking or binding prediction
  • G16B 30/10 - Sequence alignment; Homology search

88.

WAX-MICROSPHERE MATRIX COMPOSITIONS AND METHODS OF MAKING AND USING THE SAME

      
Application Number IB2022062557
Publication Number 2023/119164
Status In Force
Filing Date 2022-12-20
Publication Date 2023-06-29
Owner ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor Ricoult, Sébastien

Abstract

The present disclosure relates to a method including exposing a composition comprising a wax-microsphere matrix to a first melt-condition, wherein said wax-microsphere matrix comprises a wax component and a plurality of lyophilised microspheres, wherein said plurality of lyophilised microspheres comprise one or more reagent, whereby exposing said composition comprising said wax-microsphere matrix to said first melt-condition melts the wax component; exposing said composition to a first release-condition to rehydrate at least one lyophilised microsphere; and exposing said at least one rehydrated lyophilised microsphere to a separation-condition to separate said wax component from said at least one rehydrated lyophilised microsphere. Also disclosed are methods of preparing a wax-microsphere matrix and releasing one or more reagent from a wax-microsphere matrix as well as compositions. Also disclosed are cartridges with a reagent reservoir including the compositions described herein. Also disclosed are systems for controlling release of one or more reagent including the compositions described herein.

IPC Classes  ?

  • C12Q 1/6848 - Nucleic acid amplification reactions characterised by the means for preventing contamination or increasing the specificity or sensitivity of an amplification reaction

89.

DYNAMIC GRAPHICAL STATUS SUMMARIES FOR NUCELOTIDE SEQUENCING

      
Application Number US2022077422
Publication Number 2023/122363
Status In Force
Filing Date 2022-09-30
Publication Date 2023-06-29
Owner
  • ILLUMINA SOFTWARE, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Ward, Jeremy
  • Constandse, Rodger
  • Smoot, Michael
  • Beoris, Michelle
  • French, Adam

Abstract

This disclosure describes methods, non-transitory computer readable media, and systems that can query the status of various stages in an end-to-end sequencing process and generate a graphical status summary for the sequencing process that depicts icons indicating statuses of the various stages. For instance, the disclosed systems can generate a graphical status summary for a nucleotide sequencing taskset that includes icons depicting statuses of a sequencing run, a data transfer of base-call data to a device for variant analysis, and the variant analysis—each part of the same nucleotide sequencing taskset. By exchanging data with a sequencing device for read data and one or more servers for variant analysis, the disclosed system can quickly provide a graphical status summary of an end-to-end sequencing process marked by various tasks within a nucleotide sequencing taskset.

IPC Classes  ?

  • G16B 45/00 - ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
  • G16B 50/30 - Data warehousing; Computing architectures
  • G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
  • G16B 30/10 - Sequence alignment; Homology search

90.

PERIODATE COMPOSITIONS AND METHODS FOR CHEMICAL CLEAVAGE OF SURFACE-BOUND POLYNUCLEOTIDES

      
Application Number US2022081798
Publication Number 2023/122499
Status In Force
Filing Date 2022-12-16
Publication Date 2023-06-29
Owner ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Miller, Oliver
  • Marafini, Pietro

Abstract

Embodiments of the present disclosure relates to periodate salt compositions for use in the chemical linearization of double-stranded polynucleotides in preparation for sequencing application, for example, sequencing-by-synthesis (SBS). Kits containing the periodate salt composition and methods of sequencing polynucleotides are also described.

IPC Classes  ?

91.

FLOW CELLS AND METHODS

      
Application Number US2022082280
Publication Number 2023/122755
Status In Force
Filing Date 2022-12-22
Publication Date 2023-06-29
Owner
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
  • ILLUMINA, INC. (USA)
  • ILLUMINA SINGAPORE PTE. LTD. (Singapore)
Inventor
  • Basuki, Johan Sebastian
  • Boutell, Jonathan Mark
  • Fisher, Jeffrey S.
  • Fraser, Louise Jane
  • George, Wayne N.
  • Gormley, Niall Anthony
  • Jones, David
  • Ma, Xiaoyu
  • Martins Vitoriano, Maria Ines
  • Mei, Zhong
  • Miller, Oliver Jon
  • Price, Andrew
  • Ricoult, Sebastien Georg Gabriel
  • Thomson, Vicki S.
  • Weir, Jacqueline C.
  • Chang, Weihua
  • Han, Hui

Abstract

An example of a flow cell includes a substrate having depressions separated by interstitial regions. First and second primers are immobilized within the depressions. First transposome complexes are immobilized within the depressions, and the first transposome complexes include a first amplification domain. Second transposome complexes are also immobilized within the depressions, and the second transposome complexes include a second amplification domain. Some of the first transposome complexes, or some of the second transposome complexes, or some of both of the first and second transposome complexes include a modification to reduce tagmentation efficiency.

IPC Classes  ?

  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA

92.

FACILITATING SECURE EXECUTION OF EXTERNAL WORKFLOWS FOR GENOMIC SEQUENCING DIAGNOSTICS

      
Application Number US2022077405
Publication Number 2023/122362
Status In Force
Filing Date 2022-09-30
Publication Date 2023-06-29
Owner
  • ILLUMINA SOFTWARE, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Smoot, Michael
  • Ward, Jeremy
  • French, Adam
  • Taylor, Russell

Abstract

This disclosure describes methods, non-transitory computer readable media, and systems that can facilitate execution of external workflows for diagnostic analysis of nucleotide sequencing data utilizing a container orchestration engine. For example, the disclosed systems can utilize a container orchestration engine to allow external systems (e.g., third-party systems) to generate and implement workflows for analyzing sequencing data. In executing individual workflow containers of a sequencing diagnostic workflow, the disclosed systems can isolate the workflow containers to prevent access to, or corruption of, other data while also orchestrating allocation of computing resources available at a genomic sequence processing device to execute the workflow containers.

IPC Classes  ?

  • G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
  • G06F 9/28 - Enhancement of operational speed, e.g. by using several microcontrol devices operating in parallel
  • G06F 9/46 - Multiprogramming arrangements
  • G06F 9/48 - Program initiating; Program switching, e.g. by interrupt
  • G06F 9/50 - Allocation of resources, e.g. of the central processing unit [CPU]
  • G06F 9/54 - Interprogram communication
  • G16B 50/30 - Data warehousing; Computing architectures
  • H04L 67/1008 - Server selection for load balancing based on parameters of servers, e.g. available memory or workload

93.

PERIODATE COMPOSITIONS AND METHODS FOR CHEMICAL CLEAVAGE OF SURFACE-BOUND POLYNUCLEOTIDES

      
Application Number US2022081764
Publication Number 2023/122491
Status In Force
Filing Date 2022-12-16
Publication Date 2023-06-29
Owner ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Miller, Oliver
  • Marafini, Pietro

Abstract

Embodiments of the present disclosure relates to periodate salt compositions for use in the chemical linearization of double-stranded polynucleotides in preparation for sequencing application, for example, sequencing-by-synthesis (SBS). Kits containing the periodate salt composition and methods of sequencing polynucleotides are also described.

IPC Classes  ?

  • 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]

94.

Reduced dimensionality structured illumination microscopy with patterned arrays of nanowells

      
Application Number 18154405
Grant Number 11933728
Status In Force
Filing Date 2023-01-13
First Publication Date 2023-06-22
Grant Date 2024-03-19
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Skinner, Gary
  • Evans, Geraint
  • Hong, Stanley

Abstract

Techniques are described for reducing the number of angles needed in structured illumination imaging of biological samples through the use of patterned flowcells, where nanowells of the patterned flowcells are arranged in, e.g., a square array, or an asymmetrical array. Accordingly, the number of images needed to resolve details of the biological samples is reduced. Techniques are also described for combining structured illumination imaging with line scanning using the patterned flowcells.

IPC Classes  ?

  • G06V 10/10 - Image acquisition
  • B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
  • G01N 21/05 - Flow-through cuvettes
  • G01N 21/64 - Fluorescence; Phosphorescence
  • G02B 21/06 - Means for illuminating specimen
  • G02B 21/16 - Microscopes adapted for ultraviolet illumination
  • G02B 21/36 - Microscopes arranged for photographic purposes or projection purposes
  • G02B 27/42 - Diffraction optics

95.

HYBRID CLUSTERING

      
Application Number US2022053005
Publication Number 2023/114397
Status In Force
Filing Date 2022-12-15
Publication Date 2023-06-22
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Ma, Xiaoyu
  • Lessard-Viger, Mathieu
  • Fisher, Jeffrey
  • Boutell, Jonathan

Abstract

The present disclosure is generally directed to strategies for template capture and amplification during sequencing.

IPC Classes  ?

  • C12Q 1/6844 - Nucleic acid amplification reactions
  • C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]

96.

METHOD FOR SEQUENCING A POLYNUCLEOTIDE TEMPLATE

      
Application Number 18113216
Status Pending
Filing Date 2023-02-23
First Publication Date 2023-06-22
Owner Illumina Cambridge Limited (United Kingdom)
Inventor Smith, Geoffrey Paul

Abstract

The invention relates to methods for pairwise sequencing of a double-stranded polynucleotide template, which permit the sequential determination of nucleotide sequences in two distinct and separate regions on complementary strands of the double-stranded polynucleotide template. The two regions for sequence determination may or may not be complementary to each other.

IPC Classes  ?

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

97.

WAX-MICROSPHERE MATRIX COMPOSITIONS AND METHODS OF MAKING AND USING THE SAME

      
Application Number 18068868
Status Pending
Filing Date 2022-12-20
First Publication Date 2023-06-22
Owner ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor Ricoult, Sébastien

Abstract

The present disclosure relates to a method including exposing a composition comprising a wax-microsphere matrix to a first melt-condition, wherein said wax-microsphere matrix comprises a wax component and a plurality of lyophilised microspheres, wherein said plurality of lyophilised microspheres comprise one or more reagent, whereby exposing said composition comprising said wax-microsphere matrix to said first melt-condition melts the wax component; exposing said composition to a first release-condition to rehydrate at least one lyophilised microsphere; and exposing said at least one rehydrated lyophilised microsphere to a separation-condition to separate said wax component from said at least one rehydrated lyophilised microsphere. Also disclosed are methods of preparing a wax-microsphere matrix and releasing one or more reagent from a wax-microsphere matrix as well as compositions. Also disclosed are cartridges with a reagent reservoir including the compositions described herein. Also disclosed are systems for controlling release of one or more reagent including the compositions described herein.

IPC Classes  ?

  • C10G 73/40 - Physical treatment of waxes or modified waxes, e.g. granulation, dispersion, emulsion, irradiation
  • C08L 91/06 - Waxes

98.

ORTHOGONAL HYBRIDIZATION

      
Application Number US2022053002
Publication Number 2023/114394
Status In Force
Filing Date 2022-12-15
Publication Date 2023-06-22
Owner
  • ILLUMINA, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Shen, Fei
  • Lessard-Viger, Mathieu
  • Brustad, Eric
  • Meade, Allison
  • Armijo, Esteban
  • Howard, Michael
  • Fisher, Jeffrey
  • Boutell, Jonathan
  • Saracho, Ramon
  • Benice, Olivia
  • Mcdonald, Seth
  • Storms, Lena
  • Brodin, Jeffrey

Abstract

The present disclosure is directed to decoupling library capture (template seeding) from cluster generation to optimise both processes. This is achieved by introducing orthogonality between the seeding and clustering primer.

IPC Classes  ?

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

99.

SYSTEMS AND METHODS FOR ITERATIVE AND SCALABLE POPULATION-SCALE VARIANT ANALYSIS

      
Application Number US2022053036
Publication Number 2023/114415
Status In Force
Filing Date 2022-12-15
Publication Date 2023-06-22
Owner
  • ILLUMINA SOFTWARE, INC. (USA)
  • ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor
  • Huang, Zhuoyi
  • De Beer, Jacobus
  • Schulz-Trieglaff, Ole Benjamin
  • Birnbaum, Adam
  • Montaño, Bernardo Ochoa

Abstract

An iterative process may be implemented for incrementally aggregating available batches of sample data with previously available batches to perform sequencing analysis. Genomic variant call files associated with one or more samples may be received in batches from sequencing devices and aggregated for performing sequencing analysis. The aggregated genomic variant call files may be used to generate cohort files and census files that comprise summary information related to the genomic variant call files in each batch. The census data in census files may be aggregated into a global census file that includes summary genome variant data. Multi-sample variant call files may be generated based on the global census file, cohort files, and census files. The genomic variant call files may be processed using parallel processing at multiple compute nodes. The files may be further compressed and overlapping data may be efficiently stored in buffer positions.

IPC Classes  ?

  • G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
  • G16B 30/10 - Sequence alignment; Homology search
  • G16B 50/30 - Data warehousing; Computing architectures
  • G16B 50/50 - Compression of genetic data

100.

METHODS FOR METAL DIRECTED CLEAVAGE OF SURFACE-BOUND POLYNUCLEOTIDES

      
Application Number US2022081633
Publication Number 2023/114896
Status In Force
Filing Date 2022-12-15
Publication Date 2023-06-22
Owner ILLUMINA CAMBRIDGE LIMITED (United Kingdom)
Inventor Canzi, Gabriele

Abstract

Embodiments of the present disclosure relate to method of chemical linearization of double stranded polynucleotides for sequencing by synthesis. In particular, a heterogenous cobalt catalyst is used to cleave one or more diol moieties at a predetermined cleavage site of one strand of the double stranded polynucleotides.

IPC Classes  ?

  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12Q 1/6837 - Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
  1     2     3     ...     7        Next Page