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Illumina Inc patents


Recent patent applications related to Illumina Inc. Illumina Inc is listed as an Agent/Assignee. Note: Illumina Inc may have other listings under different names/spellings. We're not affiliated with Illumina Inc, we're just tracking patents.

ARCHIVE: New 2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 | Company Directory "I" | Illumina Inc-related inventors


 new patent  Solid inspection apparatus and method of use

An inspection apparatus is provided that comprises an optical target including a solid host material and a fluorescing material embedded in the solid host material. The solid host material has a predetermined phonon energy hostpe. ... Illumina Inc

 new patent  Phasing correction

Memory efficient methods determine corrected color values from image data acquired by a nucleic acid sequencer during a base calling cycle. Such methods may: (a) obtain an image of a substrate (e.g., a portion of a flow cell) including a plurality of sites where nucleic acid bases are read; (b) measure color values of the plurality of sites from the image of the substrate; (c) store the color values in a processor buffer of the sequencer's one or more processors; (d) retrieve partially phase-corrected color values of the plurality of sites, where the partially phase-corrected color values were stored in the sequencer's memory during an immediately preceding base calling cycle; (e) determine a prephasing correction; and (f) determine the corrected color values. ... Illumina Inc

 new patent  Flow cell package and method for making the same

A flow cell package includes first and second surface-modified patterned wafers and a spacer layer. The first surface-modified patterned wafer includes first depressions separated by first interstitial regions, a first functionalized molecule bound to a first silane or silane derivative in at least some of the first depressions, and a first primer grafted to the first functionalized molecule in the at least some of the first depressions. ... Illumina Inc

 new patent  Arrays with quality control tracers

An array includes a support including a plurality of discrete wells, a gel material positioned in each of the plurality of discrete wells, and a quality control tracer grafted to the gel material in each of the plurality of discrete wells. The quality control tracer comprises (a) a cleavable nucleotide sequence comprising a cleavage site and (b) a detectable label; and in some aspects, is a cleavable nucleotide sequence with a detectable label and a non-reactive nucleotide sequence or a primer nucleotide sequence.. ... Illumina Inc

 new patent  Systems and methods of improving droplet operations in fluidic systems

Embodiments of present application are directed to micro fluidic devices and particularly digital micro fluidic devices with improved droplet operations, and methods of improving droplet operations in micro fluidic devices.. . ... Illumina Inc

Predictive focus tracking apparatus and methods

An imaging system may include a sample stage comprising a surface to support a sample container, the sample container having a plurality of sample locations; an optical stage having an objective lens, the optical stage being positionable relative to the sample stage to image samples at the sample locations; an actuator physically coupled to at least one of the sample stage and the optical stage to move the sample stage relative to the optical stage to focus the optical stage onto a current sample location; and a drive circuit to determine a focus setting for a next sample location and to provide a drive signal to the actuator before the optical stage is positioned to image a sample at the next sample location, wherein at least one parameter of the drive signal is determined using a difference between a focus setting for the current sample location and the determined focus setting for the next sample location.. . ... Illumina Inc

Flow cell liquid degassing system and method

A system utilizes a flow cell for holding an analyte of interest for examination, such as a genetic material to be imaged for sequencing. Liquids, such as reagents and washing fluids are introduced into the flow cell during operations. ... Illumina Inc

Reagent mixing system and methods

A method includes, under control of control circuitry implementing a mixing protocol, aspirating reagents from multiple different reagent reservoirs into a cache channel. Designated amounts of the reagents are automatically aspirated from the corresponding reagent reservoirs by corresponding sippers based on the mixing protocol implemented by the control circuitry. ... Illumina Inc

Automated volumetric reagent delivery testing

A system includes a reagent selector valve controllable to select a reagent flow path from a plurality of reagent flow paths, and a pump coupled to the reagent flow path to draw a liquid through the reagent flow path in accordance with a prescribed test protocol. The system includes a discharge flow path to expel the drawn liquid, and a flow meter to measure liquid displaced by the pump and that outputs data representative of the measured flow. ... Illumina Inc

Modular optical analytic systems and methods

A system for biological sample analysis includes a plurality of modular subassemblies and a precision mounting plate, wherein each modular subassembly includes an enclosure and a plurality of optical components pre-aligned to the enclosure, and the enclosure includes a plurality of precision mounting structures, and each modular subassembly is mechanically coupled to the precision mounting plate, such that each precision mounting structure from a modular subassembly attaches directly to a corresponding precision mounting structure located on the precision mounting plate or an adjacent modular subassembly to optimize optomechanical tolerance.. . ... Illumina Inc

Reagent nozzle sipper mixing system and method

An analysis instrument may perform analytical operations on an analyte that is combined with multiple reagents prior to being introduced into a flow cell. The instrument may include a nozzle sipper that aspirates reagents from a recipient, along with an analyte. ... Illumina Inc

Pressure and leak testing methods

An analysis system includes a fluidic system includes a number of components that are interconnected to form a fluidic system having a plurality of flow paths. An example method of pressure testing the fluidic system includes (a) selecting a flow path from the plurality of flow paths through a flow cell in accordance with a prescribed test protocol; (b) actuating a pump to pressurize a fluid in the selected flow path; (c) generating pressure data representative of the pressure in the selected flow path; and (d) processing the pressure data to determine whether the selected flow path maintains pressure in a desired manner.. ... Illumina Inc

Method and apparatus for illumination of drilling rigs and surrounding locations

A lighting assembly can be quickly and efficiently mounted to a crown of a drilling rig derrick in order to provide wide-area illumination of the derrick and surrounding work location. An adjustable support frame member can be operationally attached to a hand rail of a derrick crown using fixed-length bracket members, adjustable-length bracket members and/or a combination(s) thereof. ... Illumina Inc

System and methods for selective effluent collection

A system may include a flow cell through which a plurality of reagents may be pumped during a genetic sequencing operation, an effluent line that, in operation, is to conduct a used reagent, a used reagent valve to receive the used reagent from the effluent line and controllable to select one of a plurality of disposal paths for the used reagent, and control circuitry coupled to the used reagent valve that, in operation, is to control the used reagent valve to select a desired one of the disposal paths depending upon which reagent is being pumped though the flow cell.. . ... Illumina Inc

07/05/18 / #20180187255

Common line selector valve for a system

A system may include a flow cell to support analytes of interest; a selector valve coupled to the flow cell to select a flow path through the flow cell from a plurality of flow paths; a pump coupled to the flow cell to displace fluids through the selected flow path during an analysis operation; and control circuitry coupled to the selector valve to command the selector valve to select the selected flow path.. . ... Illumina Inc

07/05/18 / #20180187252

Kinetic exclusion amplification of nucleic acid libraries

An example method includes reacting a first solution and a different, second solution on a flow cell by flowing the first solution over amplification sites on the flow cell and subsequently flowing the second solution over the amplification sites. The first solution includes target nucleic acids and a first reagent mixture that comprises nucleoside triphosphates and replication enzymes. ... Illumina Inc

07/05/18 / #20180187251

Methods of reducing density-dependent gc bias in amplification

The invention provides methods for amplifying nucleic acids, particularly methods for reducing density-dependent gc bias and for reducing nucleic acid damage in a bridge amplification of a nucleic acid template. The invention also provides methods for evaluating the effect of reagents and/or additives on nucleic acid damage during bridge amplification of nucleic acid template strands. ... Illumina Inc

07/05/18 / #20180185849

Flowcell cartridge with floating seal bracket

A cartridge for use with chemical or biological analysis systems is provided. The cartridge may include a floating microfluidic plate that is held in the cartridge using one or more floating support brackets that incorporate gaskets that may seal against fluidic ports on the microfluidic plate. ... Illumina Inc

07/05/18 / #20180185848

Balanced ac modulation for driving droplet operations electrodes

A droplet actuator device for conducting droplet operations is provided that comprises a substrate defines a device channel to conduct droplet operations. Electrodes are arranged proximate to the substrate. ... Illumina Inc

07/05/18 / #20180185842

Reagent channel mixing system and method

An analysis system may perform operations on an analyte that may be combined with multiple regents prior to being introduced into a flow cell. The instrument may include a volume into which the reagents to be combined with the analyte are aspirated one-by-one. ... Illumina Inc

07/05/18 / #20180185840

Sample tube with integrated mixing plunger head

Disclosed herein are devices and techniques for providing for enhanced fluid mixing in a sample vial. A plunger head may be removably housed inside of a cap that is attached to a container; the cap may have an opening allowing a shaft, e.g., a probe or sipper shaft, to be inserted into the cap and into the plunger head. ... Illumina Inc

06/28/18 / #20180179575

Arrays including a resin film and a patterned polymer layer

An example of an array includes a support, a cross-linked epoxy polyhedral oligomeric silsesquioxane (poss) resin film on a surface of the support, and a patterned hydrophobic polymer layer on the cross-linked epoxy poss resin film. The patterned hydrophobic polymer layer defines exposed discrete areas of the cross-linked epoxy poss resin film, and a polymer coating is attached to the exposed discrete areas. ... Illumina Inc

06/28/18 / #20180178416

Imprinting apparatus

An imprinting apparatus includes a silicon master having a plurality of nanofeatures defined therein. An anti-stick layer coats the silicon master, the anti-stick layer including a molecule having a cyclosiloxane with at least one silane functional group. ... Illumina Inc

06/28/18 / #20180178215

Multilayer fluidic devices and methods for their fabrication

A fluidic device including an inorganic solid support attached to an organic solid support by a bonding layer, wherein the inorganic solid support has a rigid structure and wherein the bonding layer includes a material that absorbs radiation at a wavelength that is transmitted by the inorganic solid support or the organic solid support; and a channel formed by the inorganic solid support and the organic solid support, wherein the bonding layer that attaches the inorganic solid support to the organic solid support provides a seal against liquid flow. Methods for making fluidic devices, such as this, are also provided.. ... Illumina Inc

06/21/18 / #20180171311

Modified transposases for improved insertion sequence bias and increased dna input tolerance

Presented herein are transposase enzymes and reaction conditions for improved fragmentation and tagging of nucleic acid samples, in particular altered transposases and reaction conditions which exhibit improved insertion sequence bias, as well as methods and kits using the same.. . ... Illumina Inc

06/14/18 / #20180163946

Light emitting panel assemblies with bottom-mounted light source and light guides therefor

A light emitting panel assembly is provided. The light emitting panel assembly includes: a housing; a light guide within the housing, the light guide having a first major surface with a plurality of extraction elements, a second major surface, a lower surface, an upper surface, a light source adjacent to the lower surface of the light guide; and an upper guide reflector having a diffuse reflective surface adjacent to and facing the upper surface of the light guide, whereby light from the light source traveling through the light guide toward the upper guide reflector spreads within the light guide, and whereby the upper guide reflector homogenizes the light before the light is redirected to the light guide. ... Illumina Inc

06/07/18 / #20180158126

Methods and systems for using a cloud computing environment to share biological related data

The present disclosure provides a novel approach for shifting or distributing various information (e.g., protocols, analysis methods, sample preparation data, sequencing data, etc.) to a cloud-based network. For example, the techniques relate to a cloud computing environment configured to receive this information from one or more individual sample preparation devices, sequencing devices, and/or computing systems. ... Illumina Inc

06/07/18 / #20180155783

Conformational probes and methods for sequencing nucleic acids

This disclosure provides a method of determining a sequence of nucleotides for a nucleic acid template. The method can include the steps of contacting the nucleic acid template with a conformationally labeled polymerase and at least four different nucleotide species under conditions wherein the conformationally labeled polymerase catalyzes sequential addition of the nucleotide species to form a nucleic acid complement of the nucleic acid template, wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase and wherein the rate or time duration for the conformational signal change is distinguishable for each different nucleotide species; detecting a series of changes in the signal from the conformationally labeled polymerase under the conditions; and determining the rates or time durations for the changes in the signal, thereby determining the sequence of nucleotides for the nucleic acid template.. ... Illumina Inc

06/07/18 / #20180155774

Compositions, systems, and methods for sequencing polynucleotides using tethers anchored to polymerases adjacent to nanopores

A composition includes a nanopore including first and second sides and an aperture, nucleotides each including an elongated tag, and a first polynucleotide that is complementary to a second polynucleotide. A polymerase can be disposed adjacent to the first side of the nanopore and configured to add nucleotides to the first polynucleotide based on a sequence of the second polynucleotide. ... Illumina Inc

06/07/18 / #20180155709

Surface-based tagmentation

Presented herein are methods and compositions surface-based tagmentation. In particular embodiments, methods of preparing an immobilized library of fragmented and tagged dna molecules on a solid surface are presented. ... Illumina Inc

06/07/18 / #20180155469

Novel polymers and dna copolymer coatings

Some embodiments described herein relate to new polymer coatings for surface functionalization and new processes for grafting pre-grafted dna-copolymers to surface(s) of substrates for use in dna sequencing and other diagnostic applications.. . ... Illumina Inc

05/24/18 / #20180142378

Platform for discovery and analysis of therapeutic agents

A method of characterizing candidate agents including steps of (a) providing a library of candidate agents attached to nucleic acid tags; (b) contacting the library with a solid support to attach the candidate agents to the solid support, whereby an array of candidate agents is formed; (c) contacting the array with a screening agent, wherein one or more candidate agents in the array react with the screening agent; (d) detecting the array to determine that at least one candidate agent in the array reacts with the screening agent; (e) sequencing the nucleic acid tag to determine the tag sequences attached to candidate agents in the array; and (f) identifying the at least one candidate agent in the array that reacts with the screening agent based on the tag sequence that is attached to the at least one candidate agent.. . ... Illumina Inc

05/24/18 / #20180142281

Enhanced utilization of surface primers in clusters

Presented herein are methods and compositions for enhancing utilization of surface primers during the surface amplification process. The methods are useful for surface amplification at improved densities. ... Illumina Inc

05/24/18 / #20180141020

Compositions and methods for single molecular placement on a substrate

Provided herein are methods and compositions for placing single target molecules on a patterned substrate.. . ... Illumina Inc

05/10/18 / #20180127816

Methods for chemical ligation of nucleic acids

Provided herein are methods for preparing nucleic acid libraries, capturing dna obtained from a limited number of cells, and selectively cleaving ssdna or dsdna using various chemical ligation and click chemistry reactions described herein.. . ... Illumina Inc

05/03/18 / #20180119139

Structured substrates for improving detection of light emissions and methods relating to the same

A structured substrate (100) including a substrate body (102) having an active side (104). The substrate body (102) includes reaction cavities or sites (106) that open along the active side (104) and interstitial regions (118) that separate the reaction cavities (106). ... Illumina Inc

05/03/18 / #20180117587

Cartridge assembly

A cartridge assembly that comprises a housing, including a flow cell chamber to receive a flow cell, and a well plate having liquid wells to receive desired amounts of liquids. The well plate includes a valve station, a pump station and a fluidics analysis station, and channels associated therewith. ... Illumina Inc

04/19/18 / #20180105874

Pyrophosphorolytic sequencing

A method for determining the sequence of a target nucleic acid, including steps of contacting a target nucleic acid with a polymerase to sequentially remove nucleotide triphosphates from the target nucleic acid, wherein the nucleotide triphosphates that are removed have a variety of different base moieties; and distinguishing the different base moieties for the nucleotide triphosphates that are removed. Also provided is a apparatus including a nanopore positioned in a fluid impermeable barrier to form a passage through which a nucleotide triphosphate can pass from a first fluid reservoir to a second fluid reservoir, and a reaction mix in the first fluid reservoir that includes a polymerase, target nucleic acid having two strands, and pyrophosphorolytic concentration of pyrophosphate.. ... Illumina Inc

04/12/18 / #20180100193

Method for nucleotide detection

A method of inhibiting light-induced degradation of nucleic acids includes irradiating a portion of the nucleic acids in the presence of a detection solution comprising a polyphenolic compound. A method of detecting a nucleic acid having a fluorescent tag includes irradiating at least a portion of the nucleic acid with light of a suitable wavelength to induce a fluorescence emission and detecting the fluorescence emission. ... Illumina Inc

04/05/18 / #20180097544

Controlling power to a load with signals along a power line

A circuit, system and method for controlling electrical power to a load, the circuit has a controller with power supply input nodes and a controller data input node. Two power supply input terminals supply electrical power to the circuit. ... Illumina Inc

04/05/18 / #20180095969

Phenotype/disease specific gene ranking using curated, gene library and network based data structures

The present invention relates to methods, systems and apparatus for capturing, integrating, organizing, navigating and querying large-scale data from high-throughput biological and chemical assay platforms. It provides a highly efficient meta-analysis infrastructure for performing research queries across a large number of studies and experiments from different biological and chemical assays, data types and organisms, as well as systems to build and add to such an infrastructure. ... Illumina Inc

04/05/18 / #20180094316

Multiplex nucleic acid reactions

A method for detecting nucleic acids by (a) providing a sample having target nucleic acids, each nucleic acid having contiguous first, second, and third domains; (b) contacting the sample with probe sets to form hybridization complexes, wherein each probe set includes (i) a first probe having a sequence that is complementary to the first domain; and (ii) a second probe having a sequence substantially complementary to the third domain; (c) extending the first probes along the second domains of the complexes while the complexes are immobilized on a solid support; (d) ligating the extended first probes to the second probes to form templates; (e) amplifying the templates with primers that are complementary to the first and second priming sequences to produce amplicons; and (f) detecting the amplicons on the surface of a nucleic acid array.. . ... Illumina Inc

04/05/18 / #20180094140

Fluorescent dyes and their uses as biomarkers

The present application relates to new fluorescent dyes and their uses as fluorescent labels. The compounds may be used as fluorescent labels for nucleotides in nucleic acid sequencing applications.. ... Illumina Inc

03/29/18 / #20180085752

Imprinted substrates

Imprinted substrates are often used to produce miniaturized devices for use in electrical, optic and biochemical applications. Imprinting techniques, such as nanoimprinting lithography, may leave residues in the surface of substrates that affect bonding and decrease the quality of the produced devices. ... Illumina Inc

03/15/18 / #20180075186

Systems and methods for off-target sequence detection

A computer-implemented method, computer system and computer-readable medium for identifying off-target matches from a set of candidate primer sequences on a genome reference sequence can include: receiving onto a data storage unit a plurality of candidate primer sequences; for each candidate primer sequence, calculating, using a processor, a plurality of candidate matches on the genome reference sequence for the candidate primer sequences; calculating, using the processor, verified matches on the genome reference sequence based on the candidate matching locations satisfying a plurality of matching verification rules; performing matching calculations of the verified matches to determine whether the verified matches form a match condition on the genome reference sequence; and generating a location profile on the genome reference sequence based on the match condition from the verified matches that meet a predetermined threshold.. . ... Illumina Inc

03/15/18 / #20180073065

Structured substrates for improving detection of light emissions and methods relating to the same

Structured substrate including (a) a plurality of nanoparticles distributed on a solid support, (b) a gel material forming a layer in association with the plurality of nanoparticles, and (c) a library of target nucleic acids in the gel material.. . ... Illumina Inc

03/15/18 / #20180073016

Compositions and methods for representational selection of nucleic acids from complex mixture

The invention provides a method of selecting a representational sample of nucleic acid sequences from a complex mixture. The method includes: (a) contacting a complex mixture of nucleic acids under conditions sufficient for hybridization with a population of capture probes complementary to one or more nucleic acids comprising a predetermined portion of the sequence collectively present in the complex mixture to form hybridization complexes of the one or more nucleic acids with the population of probes, the population of capture probes being attached to a solid support, and (b) removing unhybridized nucleic acids to select a representational sample of nucleic acids having a complexity of less than 10% but more than 0.001% of the complex mixture, wherein the representational sample comprises a nucleic acid copy having a proportion of each sequence in the copy relative to all other sequences in the copy substantially the same as the proportions of the sequences in the predetermined portion of one or more nucleic acids within the complex mixture. ... Illumina Inc

03/01/18 / #20180060523

Federated systems and methods for medical data sharing

Systems, computer-implemented methods, and non-transitory computer readable media are provided for sharing medical data. The disclosed systems may be configured to create a first workgroup having a first knowledgebase. ... Illumina Inc

03/01/18 / #20180060401

Semantic distance systems and methods for determining related ontological data

Systems, computer-implemented methods, and non-transitory computer readable media are provided for determining related ontological data. The disclosed systems may be configured to receive a first ontology and a second ontology, the first ontology and the second ontology comprising hierarchically organized ontological data. ... Illumina Inc

02/22/18 / #20180051323

Reducing dna damage during sample preparation and sequencing using siderophore chelators

Embodiments disclosed herein provide reagents and kits for nucleic acid preparation comprising a siderophore. Embodiments disclosed herein provide methods for preparing a nucleic acid library, which comprise: providing a plurality of nucleic acid molecules from a sample; and manipulating the plurality of nucleic acid molecules in a reagent for nucleic acid preparation comprising a siderophore. ... Illumina Inc

02/15/18 / #20180044732

Multibase delivery for long reads in sequencing by synthesis protocols

The present technology relates to molecular sciences, such as genomics. More particularly, the present technology relates to methods for obtaining long lengths of sequencing data.. ... Illumina Inc

02/08/18 / #20180037950

Methods and arrays for producing and sequencing monoclonal clusters of nucleic acid

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

01/18/18 / #20180016571

Transposase compositions for reduction of insertion bias

Presented herein are methods and compositions for tagmentation of nucleic acids. The methods are useful for generating tagged dna fragments that are qualitatively and quantitatively representative of the target nucleic acids in the sample from which they are generated.. ... Illumina Inc

01/11/18 / #20180010123

Compositions and methods for preparing oligonucleotide solutions

The present invention is directed to methods and compositions for generating a pool of oligonucleotides. The invention finds use in preparing a population or subpopulations of oligonucleotides in solution. ... Illumina Inc

12/28/17 / #20170369942

Compositions, systems, and methods for detecting events using tethers anchored to or adjacent to nanopores

Compositions, systems, and methods for detecting events are provided. A composition can include a nanopore including a first side, a second side, and an aperture extending through the first and second sides; and a permanent tether including head and tail regions and an elongated body disposed therebetween. ... Illumina Inc

12/14/17 / #20170356030

Compositions, systems, and methods for detecting the presence of polymer subunits using chemiluminescence

Under one aspect, a composition includes a substrate; a first polynucleotide coupled to the substrate; a second polynucleotide hybridized to the first polynucleotide; and a catalyst coupled to a first nucleotide of the second polynucleotide, the catalyst being operable to cause a chemiluminogenic molecule to emit a photon. Under another aspect, a method includes providing a catalyst operable to cause a first chemiluminogenic molecule to emit a photon; providing a substrate; providing a first polynucleotide coupled to the substrate; hybridizing a second polynucleotide to the first polynucleotide; coupling a first quencher to a first nucleotide of the second polynucleotide; and inhibiting, by the first quencher, photon emission by the first chemiluminogenic molecule.. ... Illumina Inc

12/14/17 / #20170355970

Modified polymerases for improved incorporation of nucleotide analogues

Presented herein are polymerase enzymes for improved incorporation of nucleotide analogues, in particular nucleotides which are modified at the 3′ sugar hydroxyl, as well as methods and kits using the same.. . ... Illumina Inc

12/07/17 / #20170353444

Tenant-aware distributed application authentication

Flexible authentication technologies customized to particular tenants of a data center network can be implemented. For example, an administrator can specify a primary authentication server and specify at which data centers different applications are to be hosted for a given tenant. ... Illumina Inc

11/30/17 / #20170342487

Polymer coatings

The present disclosure relates to polymer coatings covalently attached to the surface of a substrate and the preparation of the polymer coatings, such as poly(n-(5-azidoacetamidylpentyl)acrylamide-co-acrylamide) (pazam), in the formation and manipulation of substrates, such as molecular arrays and flow cells. The present disclosure also relates to methods of preparing a substrate surface by using beads coated with a covalently attached polymer, such as pazam, and the method of determining a nucleotide sequence of a polynucleotide attached to a substrate surface described herein.. ... Illumina Inc

11/30/17 / #20170342482

Methods for sequencing a polynucleotide template

The invention relates to methods for pairwise sequencing of a polynucleotide template which result in the sequential determination of nucleotide sequence in two distinct and separate regions of the polynucleotide template.. . ... Illumina Inc

11/30/17 / #20170342474

Polynucleotide amplification using crispr-cas systems

A method for amplifying a target nucleic acid including providing a system having a crrna or a derivative thereof, and a cas protein or a variant thereof. The crrna or the derivative thereof contains a target-specific nucleotide region substantially complementary to a region of the target nucleic acid, and contacting the target nucleic acid with the system to form a complex.. ... Illumina Inc

11/30/17 / #20170342406

Nucleic acid arrays

The present invention provides methods for creating an array of features on a surface based on content transferred from a plurality of beads to the surface. Nucleic acid content can be transferred using a method including the steps of (a) providing a surface having one or more primer oligonucleotides attached to the surface; (b) providing a pool of beads, wherein beads in the pool have a plurality of templates attached thereto, the plurality comprising multiple copies of a single nucleic acid template sequence; (c) arraying the beads onto the surface by hybridizing the templates to the primer oligonucleotides; and (d) extending the primers to produce copies of the templates attached to the surface.. ... Illumina Inc

11/23/17 / #20170335380

Kinetic exclusion amplification of nucleic acid libraries

A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. ... Illumina Inc

11/16/17 / #20170327885

Method for sequencing a polynucleotide template

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.. ... Illumina Inc

11/16/17 / #20170325438

Illuminating outrigger tip

An outrigger tip attachable to an outrigger pole comprises a translucent elongate main body including a proximal end portion having an opening for accessing an inner cavity, and the proximal end portion of the translucent elongate main body being sized and configured for engaging an open end of the outrigger pole. A light emitting diode assembly is sized and configured for engaging the inner cavity through the opening on the proximal end portion of the translucent elongate main body. ... Illumina Inc

11/09/17 / #20170321195

Polymerases

Presented herein are methods and compositions for thermostable dna polymerases that may be used to improve the pcr process and to improve the results obtained when using a thermostable dna polymerase in other recombinant techniques such as dna sequencing, nick-translation, and reverse transcription.. . ... Illumina Inc

10/26/17 / #20170308569

Methods and apparatus for performing real-time analytics based on multiple types of streamed data

Streaming data from a plurality of streaming data sources can be received. The streaming data may not be stored in persistent storage. ... Illumina Inc

10/12/17 / #20170292147

Haplotype resolved genome sequencing

Methods of determining a haplotype or partial haplotype of a dna sample containing high molecular weight segments of genomic dna are disclosed. Such methods may include sequencing dna in an enriched dna sample to produce a plurality of sequence reads, where some of the sequence reads contain a first allele of the first haplotype and other of the sequence reads contain a second allele of the first haplotype. ... Illumina Inc

10/12/17 / #20170292124

Methods and systems for construction of normalized nucleic acid libraries

The present disclosure generally relates to nucleic acid amplification systems and methods suitable for construction of nucleic acid samples, including construction of normalized nucleic acid libraries. In some embodiments, the method includes providing one or more input nucleic acid samples, contacting each of the input nucleic acid samples (e.g., input library) with a reaction mixture including first amplification or normalization primers and second amplification or normalization primers, wherein the first amplification or normalization primers are immobilized on a solid support and the second amplification or normalization primers are in solution phase, and amplifying the input nucleic acid samples under conditions such that substantially all of the first amplification or normalization primers are incorporated into amplification products. ... Illumina Inc

10/05/17 / #20170283794

Methods for selecting and amplifying polynucleotides

The invention provides methods for generating a nucleic acid library. Target-specific primer-probes are hybridized to a target nucleic acid fragment to create a hybridization product. ... Illumina Inc

10/05/17 / #20170281967

System and associated methods for dynamically adjusting circadian rhythm responsive to calendared future events

A method is for dynamically adjusting a circadian rhythm of an observer via a user device that includes control circuitry and an associated memory. The method includes accessing a calendar, identifying future events to precondition for and determining a preconditioning schedule for at least one of the identified future events. ... Illumina Inc

09/28/17 / #20170275690

Photonic superlattice-based devices and compositions for use in luminescent imaging, and methods of using the same

Under one aspect, a device is provided for use in luminescent imaging. The device can include a photonic superlattice including a first material, the first material having a first refractive index. ... Illumina Inc

09/28/17 / #20170275602

Polymerases

Modified dna polymerases have an affinity for dna such that the polymerase has an ability to incorporate one or more nucleotides into a plurality of separate dna templates in each reaction cycle. The polymerases are capable of forming an increased number of productive polymerase-dna complexes in each reaction cycle. ... Illumina Inc

09/28/17 / #20170275601

Recombinase mutants

Presented herein are recombinases for improved recombinase-mediated amplification of nucleic acids, such as a pcr-library having single-stranded adapter regions, on a patterned flow cell surface for improved cluster amplifications, as well as methods and kits using the same.. . ... Illumina Inc

09/21/17 / #20170268055

Compositions and methods for polynucleotide sequencing

Methods and compositions for characterizing a target polynucleotide, including, characterizing the sequence of the target polynucleotide, using the fractional translocation steps of the target polynucleotide's translocation through a pore.. . ... Illumina Inc

09/14/17 / #20170260582

Hybrid nanopore sensors

The disclosure provides detection apparatus having one or more nanopores, methods for making apparatus having one or more nanopore and methods for using apparatus having one or more nanopores. Uses include, but are not limited to detection and sequencing of nucleic acids.. ... Illumina Inc

09/14/17 / #20170260581

Preservation of information related to genomic dna methylation

The present invention relates to compositions, methods and systems for analyzing the methylation state of nucleic acids. Some embodiments relate to a compositions, methods and systems for analyzing the methylation state of dna with a gene array.. ... Illumina Inc

09/07/17 / #20170253626

Functionalization and purification of molecules by reversible group exchange

Embodiments of the present disclosure include methods and compositions for functionalizing molecules, such as oligonucleotides, with functional groups, including polyhistidine tags useful in affinity methods. Some embodiments include methods for modifying and purifying complex mixtures of molecules by exchange of functional tags.. ... Illumina Inc

08/31/17 / #20170249421

Detecting repeat expansions with short read sequencing data

The disclosed embodiments concern methods, apparatus, systems and computer program products for determining the presence or absence of repeat expansions of interest, including repeat expansions of repeat sequences that are medically significant. Some embodiments provide methods for identifying and calling medically relevant repeat expansions using anchored reads. ... Illumina Inc

08/31/17 / #20170246635

Integrated optoelectronic read head and fluidic cartridge useful for nucleic acid sequencing

A detection apparatus having a read head including a plurality of microfluorometers positioned to simultaneously acquire a plurality of the wide-field images in a common plane; and (b) a translation stage configured to move the read head along a substrate that is in the common plane. The substrate can be a flow cell that is included in a cartridge, the cartridge also including a housing for (i) a sample reservoir; (ii) a fluidic line between the sample reservoir and the flow cell; (iii) several reagent reservoirs in fluid communication with the flow cell, (iv) at least one valve configured to mediate fluid communication between the reservoirs and the flow cell; and (v) at least one pressure source configured to move liquids from the reservoirs to the flow cell. ... Illumina Inc

08/17/17 / #20170237445

Methods and systems for data analysis and compression

The present disclosure provides computer implemented methods and systems for analysing datasets, such as large data sets output from nucleic acid sequencing technologies. In particular, the present disclosure provides for data analysis comprising computing the bwt of a collection of strings in an incremental, character by character, manner. ... Illumina Inc

07/27/17 / #20170212123

Methods of nucleic acid sequencing

Provided herein is a method of using transposition to improve methods of sequencing rna molecules. Provided herein is a method of tagging nucleic acid duplexes, such as dna:rna duplexes or dna:dna duplexes. ... Illumina Inc

07/20/17 / #20170204458

Labelled nucleotides

Nucleosides and nucleotides are disclosed that are linked to detectable labels via a cleavable linker group.. . ... Illumina Inc

07/13/17 / #20170199210

Detection apparatus having a microfluorometer, a fluidic system, and a flow cell latch clamp module

Detection apparatus includes a microfluorometer having an objective, an excitation radiation source, and a detector. The detection apparatus also includes a fluidic system for delivering reagents from a reagent cartridge to a flow cell. ... Illumina Inc

07/13/17 / #20170197193

Microarray fabrication system and method

A microarray is designed capture one or more molecules of interest at each of a plurality of sites on a substrate. The sites comprise base pads, such as polymer base pads, that promote the attachment of the molecules at the sites. ... Illumina Inc

07/06/17 / #20170191126

Nucleic acid synthesis techniques

A method for synthesizing a nucleic acid includes synthesizing one or more nucleic acid fragments on a substrate. The synthesized one or more nucleic acid fragments may be amplified on the substrate. ... Illumina Inc

06/22/17 / #20170175205

Distinguishing methylation levels in complex biological samples

Provided herein is a method for distinguishing an aberrant methylation level for dna from a first cell type, including steps of (a) providing a test data set that includes (i) methylation states for a plurality of sites from test genomic dna from at least one test organism, and (ii) coverage at each of the sites for detection of the methylation states; (b) providing methylation states for the plurality of sites in reference genomic dna from one or more reference individual organisms, (c) determining, for each of the sites, the methylation difference between the test genomic dna and the reference genomic dna, thereby providing a normalized methylation difference for each site; and (d) weighting the normalized methylation difference for each site by the coverage at each of the sites, thereby determining an aggregate coverage-weighted normalized methylation difference score. Also provided herein are sensitive methods for using genomic dna methylation levels to distinguish cancer cells from normal cells and to classify different cancer types according to their tissues of origin.. ... Illumina Inc

06/22/17 / #20170175109

Compositions and methods for representational selection of nucleic acids from complex mixture

The invention provides a method of selecting a representational sample of nucleic acid sequences from a complex mixture. The method includes: (a) contacting a complex mixture of nucleic acids under conditions sufficient for hybridization with a population of capture probes complementary to one or more nucleic acids comprising a predetermined portion of the sequence collectively present in the complex mixture to form hybridization complexes of the one or more nucleic acids with the population of probes, the population of capture probes being attached to a solid support, and (b) removing unhybridized nucleic acids to select a representational sample of nucleic acids having a complexity of less than 10% but more than 0.001% of the complex mixture, wherein the representational sample comprises a nucleic acid copy having a proportion of each sequence in the copy relative to all other sequences in the copy substantially the same as the proportions of the sequences in the predetermined portion of one or more nucleic acids within the complex mixture. ... Illumina Inc

06/15/17 / #20170167698

Led lamp beads with multiple light-emitting points

Led lamp beads with multiple light-emitting points comprising a certain number of luminous bodies and package resins; in which after at least two luminous bodies are connected in parallel, they are wrapped in a package resin and connected to an anode pin and a cathode pin inserted into the package resin. The present invention structure is simple and has a rational design. ... Illumina Inc

06/15/17 / #20170166961

Modified nucleosides or nucleotides

Some embodiments described herein relate to modified nucleotide and nucleoside molecules with novel 3′-hydroxy protecting groups. Also provided herein are methods to prepare such modified nucleotide and nucleoside molecules and sequencing by synthesis processes using such modified nucleotide and nucleoside molecules.. ... Illumina Inc

06/08/17 / #20170161900

Data processing system and methods

Methods and systems for analysis of image data generated from various reference points. Particularly, the methods and systems provided are useful for real time analysis of image and sequence data generated during dna sequencing methodologies.. ... Illumina Inc

06/08/17 / #20170159118

Sequencing by orthogonal synthesis

A method for sequencing includes steps of (a) providing first and second nucleic acid templates, wherein the two templates have different sequences; (b) extending a first primer bound to the first template using a first polymerase species and a first set of nucleotide analogs; (c) extending a second primer bound to the second template using a second polymerase species and a second set of nucleotide analogs, wherein the first polymerase species is different from the second polymerase species and wherein the first set of nucleotide analog is different from the second set of nucleotide analog, (d) detecting the first and second primer extension products; and (e) repeating steps (b) through (d), thereby determining the different sequences of the first and second templates.. . ... Illumina Inc

06/01/17 / #20170152081

Liquid storage and delivery mechanisms and methods

A liquid storage and delivery mechanism and method of use are provided. The mechanism comprises shells that include corresponding reservoirs to hold individual quantities of liquid. ... Illumina Inc

06/01/17 / #20170151565

Optical alignment tool

Provided is an inspection apparatus including: (a) a translucent or transparent plate having a bottom surface, at least a portion of the bottom surface having an opaque material printed thereon in a pattern having at least one transparent or translucent portion; and (h) a chamber disposed below the bottom surface, whereby light emitted from the chamber or through the chamber can pass through the at least one transparent or translucent portion.. . ... Illumina Inc

05/18/17 / #20170137876

Methods of increasing sequencing accuracy

The present invention provides methods of increasing sequencing accuracy. For example, the methods of the invention use linear amplification to generate a relatively small population of template molecules that may be subsequently amplified into a larger clonal population of dna molecules for sequencing.. ... Illumina Inc

05/11/17 / #20170130260

Methods and compositions for preparing sequencing libraries

Embodiments provided herein relate to methods and compositions for next generation sequencing. Some embodiments include the preparation of a template library from a target nucleic acid in contact with a surface, and sequencing the library on the surface. ... Illumina Inc

05/11/17 / #20170128940

Inertial droplet generation and particle encapsulation

Described are microfluidic devices and methods for providing a predetermined number of microspheres or beads, together with a cell, within a fluid droplet being processed. The system may provide each droplet with a single bead and a single cell, and the bead may contain dna or other reagents for later identifying the specific cell associated with that bead.. ... Illumina Inc

04/13/17 / #20170101676

Off-target capture reduction in sequencing techniques

Presented herein are methods and compositions for enhancing specific enrichment of target sequences in a nucleic acid library. Off-target hybridization probes may be used to reduce binding and/or capture of off-target regions of a nucleic acid library in a targeted sequencing workflow. ... Illumina Inc

03/09/17 / #20170067104

Labelled nucleotides

Nucleosides and nucleotides are disclosed that are linked to detectable labels via a cleavable linker group.. . ... Illumina Inc

02/23/17 / #20170051340

Detection of nucleic acid reactions on bead arrays

The present invention is directed to methods and compositions for the use of microsphere arrays to detect and quantify a number of nucleic acid reactions. The invention finds use in genotyping, i.e. ... Illumina Inc

02/16/17 / #20170044525

Multiplexed single cell gene expression analysis using template switch and tagmentation

Presented herein are methods and compositions for multiplexed single cell gene expression analysis. Some methods and compositions include the use of droplets and/or beads bearing unique barcodes such as unique molecular barcodes (umi).. ... Illumina Inc

02/02/17 / #20170029883

Compositions and methods for nucleotide sequencing

The invention provides nucleoside and nucleotide molecules containing cleavable linkers linking a label such as a dye. The invention also provides nucleosides and nucleotide molecules containing a blocking group, either immovable or non-removable. ... Illumina Inc

02/02/17 / #20170029857

Amplification methods to minimise sequence specific bias

Methods for amplifying nucleic acids are provided. The methods can be used to minimise sequence specific bias caused by the preferential amplification of certain nucleic acid sequences. ... Illumina Inc

01/26/17 / #20170023210

Device for shaping light beams emitted by lighting fixtures

A device adapted to perform the shaping of light beams emitted by lighting fixtures, in particular by lighting fixtures comprising punctiform light sources such as, for example, leds. The device according to the present invention, in particular, allows shaping the light flow produced by lighting devices comprising punctiform light sources, so as to filter any parasitic reflection phenomena of the light flow emitted.. ... Illumina Inc

01/26/17 / #20170022559

Methods and compositions for nucleic acid sequencing

The present disclosure provides methods and systems for detecting multiple different nucleotides in a sample. In particular, the disclosure provides for detection of multiple different nucleotides in a sample utilizing fewer detection moieties than the number of nucleotides being detected and/or fewer imaging events than the number of nucleotides being detected.. ... Illumina Inc

01/26/17 / #20170021325

Preparation of templates for nucleic acid sequencing

The invention relates to methods of generating templates for a nucleic acid sequencing reaction which comprise: providing at least one double-stranded nucleic acid molecule, wherein both strands of the double-stranded nucleic acid molecule are attached to a solid support at the 5′ end, cleaving one or both strands of the double-stranded nucleic acid molecule, and subjecting the cleaved strand(s) to denaturing conditions to remove the portion of the cleaved strand(s) not attached to the solid support, thereby generating a partially or substantially single-stranded template for a nucleic acid sequencing reaction.. . ... Illumina Inc

01/19/17 / #20170016060

Disposable, integrated microfluidic cartridge and methods of making and using same

The disclosed embodiments concern microfluidic cartridges for detecting biological reactions. In some embodiments, the microfluidic cartridges are configured to perform sequencing operations on a nucleic acid sample. ... Illumina Inc

01/12/17 / #20170009227

Reducing adapter dimer formation

Provided herein is a method of reducing adapter dimer formation comprising contacting a sample comprising target nucleic acid sequences with 5′ and 3′ adapters in the presence of one or more hairpin oligonucleotides. Also provided is a method of preparing a library of nucleic acid sequences comprising contacting first adapter oligonucleotides with a sample comprising target nucleic acid sequences under conditions to form first ligation products, contacting the sample with one or more hairpin oligonucleotides that binds to the first adapter oligonucleotides, and contacting the sample with second adapter oligonucleotides under conditions to bind to the first ligation products and form second ligation products, wherein the second ligation products form the library of nucleic acid sequences.. ... Illumina Inc

01/05/17 / #20170002408

Labelled nucleotides

The invention provides a nucleotide or nucleoside having a base attached to a detectable label via a cleavable linker, characterised in that the cleavable linker contains a moiety selected from the group comprising: formula (i) (wherein x is selected from the group comprising o, s, nh and nq wherein q is a c1-10 substituted or unsubstituted alkyl group, y is selected from the group comprising o, s, nh and n(allyl), t is hydrogen or a c1-10 substituted or unsubstituted alkyl group and * indicates where the moiety is connected to the remainder of the nucleotide or nucleoside).. . ... Illumina Inc

01/05/17 / #20170002407

Labelled nucleotides

Nucleosides and nucleotides are disclosed that are linked to detectable labels via a cleavable linker group.. . ... Illumina Inc








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