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.
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.
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.
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.
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.
F16F 15/03 - Suppression of vibrations of non-rotating, e.g. reciprocating, systems; Suppression of vibrations of rotating systems by use of members not moving with the rotating system using electromagnetic means
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.
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.
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.
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.
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.
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.
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
12.
METHODS OF NUCLEIC ACID SEQUENCING USING SURFACE-BOUND PRIMERS
Polynucleotide sequencing methods for sequencing one or more polynucleotide templates use 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.
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.
The technology disclosed relates to a system for inter-model prediction score recalibration. The system includes a first model that generates, based on evolutionary conservation summary statistics of amino acids in a reference protein sequence, a first set of pathogenicity scores with rankings for variants that mutate the reference sequence to alternate protein sequences. The system further includes a second model that generates, based on epistasis expressed by amino acid patterns spanning a multiple sequence alignment aligning the reference sequence to non-target sequences, a second set of pathogenicity scores with rankings for the variants. The system further includes a rank loss determination logic that determines a rank loss parameter by comparing the two sets of rankings, a loss function reconfiguration logic that reconfigures a loss function based on the rank loss parameter, and a training logic that uses the reconfigured loss function to train the first model.
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 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
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.
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.
The technology disclosed relates to variant calling of sequenced reads of a sample of a target species against a reference genome of a pseudo-target species. Low-quality variants are identified as false positive variants that are present in the second set of variants but absent from the first set of variants.
A first reference genome is segmented into a plurality of bins and high-quality sequenced reads are mapped on a bin-by-bin basis to the plurality of bins in the first reference genome, and a second reference genome is segmented into a plurality of bins and high-quality sequenced reads are mapped on a bin-by-bin basis to the plurality of bins in the second reference genome. A best-mapped bin is identified in the second reference genome based on the greatest degree of match between the best-mapped bin in the second reference genome and a corresponding bin in the first reference genome.
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
G06K 9/62 - Methods or arrangements for recognition using electronic means
G06N 3/12 - Computing arrangements based on biological models using genetic models
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.
A system comprises chunking logic that chunks (or splits) a multiple sequence alignment (MSA) into chunks, first attention logic that attends to a representation of the chunks and produces a first attention output, first aggregation logic that produces a first aggregated output that contains those features in the first attention output that correspond to masked residues in the plurality of masked residues, mask revelation logic that produces an informed output based on the first aggregated output and a Boolean mask, second attention logic that attends to the informed output and produces a second attention output based on masked residues revealed by the Boolean mask, second aggregation logic that produces a second aggregated output that contains those features in the second attention output that correspond to masked residues concealed by the Boolean mask, and output logic that produces identifications of the masked residues based on the second aggregated output.
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.
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.
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.
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.
This application describes methods of preparing an immobilized library of tagged RNA fragments. Also described herein are a number of methods of preparing DNA and RNA sequencing libraries from a single sample. These methods can include library preparation from single cells.
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.
The present disclosure relates to new compounds and their use as fluorescent labels. The compounds may be used as fluorescent labels for nucleotides in nucleic acid sequencing applications.
C12Q 1/6816 - Hybridisation assays characterised by the detection means
C09B 23/06 - Methine or polymethine dyes, e.g. cyanine dyes characterised by the methine chain containing an odd number of CH groups three CH groups, e.g. carbocyanines
C07D 209/08 - Indoles; Hydrogenated indoles with only hydrogen atoms or radicals containing only hydrogen and carbon atoms, directly attached to carbon atoms of the hetero ring
C07D 403/06 - Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group containing two hetero rings linked by a carbon chain containing only aliphatic carbon atoms
C09B 23/08 - Methine or polymethine dyes, e.g. cyanine dyes characterised by the methine chain containing an odd number of CH groups more than three CH groups, e.g. polycarbocyanines
G01N 33/58 - Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving labelled substances
C09B 23/10 - Methine or polymethine dyes, e.g. cyanine dyes characterised by the methine chain containing an even number of CH groups
28.
SEQUENCING FROM MULTIPLE PRIMERS TO INCREASE DATA RATE AND DENSITY
The present invention relates to a sequencing method which allows for increased rates of sequencing and an increase in the density of sequencing data. The system may be based on next generation sequencing methods such as sequencing by synthesis (SBS) but uses multiple primers bound at different positions on the same nucleic acid strand.
The present disclosure is concerned with compositions and methods for the paired-end sequencing of target nucleic acids, and more particularly to obtaining nucleotide sequence information from two separate regions of target nucleic acids using amplification sites having a single type of surface primer.
The technology disclosed relates to training a pathogenicity predictor. In particular, the technology disclosed relates to accessing a gapped training set that includes respective gapped protein samples for respective positions in a proteome, accessing a non-gapped training set that includes non-gapped benign protein samples and non-gapped pathogenic protein samples, generating respective gapped spatial representations for the gapped protein samples, and generating respective non-gapped spatial representations for the non-gapped benign protein samples and the non-gapped pathogenic protein samples, training a pathogenicity predictor over one or more training cycles and generating a trained pathogenicity predictor, wherein each of the training cycles uses as training examples gapped spatial representations from the respective gapped spatial representations and non-gapped spatial representations from the respective non-gapped spatial representations, and using the trained pathogenicity classifier to determine pathogenicity of variants.
An apparatus and method for imaging includes an imaging system formed of a movable objective stage proximal to a sample and positioned for providing an excitation beam onto and for capturing an emission from the sample. The movable objective stage includes an optical lens apparatus and a turn reflector optically coupled to the imaging optics, where at least one of the optical lens apparatus and the turn reflector are movable relative to one another for scanning the sample, and wherein the movement is achieved while maintaining a substantially fixed optical path length between the optical lens apparatus and a fixed plane in a fixed imaging optics stage.
The technology disclosed relates to determining pathogenicity of nucleotide variants. In particular, the technology disclosed relates to specifying a particular amino acid at a particular position in a protein as a gap amino acid, and specifying remaining amino acids at remaining positions in the protein as non-gap amino acids, generating a gapped spatial representation of the protein that includes spatial configurations of the non-gap amino acids, and excludes a spatial configuration of the gap amino acid, determining an evolutionary conservation at the particular position of respective amino acids of respective amino acid classes based at least in part on the gapped spatial representation, and based at least in part on the evolutionary conservation of the respective amino acids, determining a pathogenicity of respective nucleotide variants that respectively substitute the particular amino acid with the respective amino acids in alternate representations of the protein.
G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
G16B 15/00 - ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
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. Another example of an array includes a support, a modified epoxy POSS resin film on a surface of the support, and a patterned hydrophobic polymer layer on the modified epoxy POSS resin film. The modified epoxy POSS resin film includes a polymer growth initiation site, and the patterned hydrophobic polymer layer defines exposed discrete areas of the modified epoxy POSS resin film. A polymer brush is attached to the polymer growth initiation site in the exposed discrete areas.
A polynucleotide sequencing method includes a wash step that employs a composition including a polymerase. The composition may also include a plurality of nucleotides. The composition may be configured to prevent the polymerase from incorporating one of the plurality of nucleotides into a copy polynucleotide strand. The composition may be substantially free of Mg2+.
Provided herein are various examples of a method of coupling oligonucleotides to a polymer. The method may include selectively irradiating first inactive moieties in a one or more first region of a polymer with light, while not irradiating second inactive moieties in a one or more second region of the polymer, to generate first active moieties in the one or more first region of the polymer. The method may also include coupling the first active moieties to first oligonucleotides. The method may further include irradiating the second inactive moieties in the one or more second region of the polymer with light to generate second active moieties in the one or more second region of the polymer. The method may also include coupling the second active moieties to second oligonucleotides.
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.
Some of the resin compositions are ultraviolet light or thermally curable, while others are ultraviolet light curable. One example of the ultraviolet light or thermally curable resin composition consists of a predetermined mass ratio of a (meth)acrylate cyclosiloxane monomer and a non-siloxane (meth)acrylate based monomer ranging from about >0:<100 to about 80:20; from 0 mass % to about 10 mass %, based on a total solids content of the resin composition, of an initiator selected from the group consisting of an azo-initiator, an acetophenone, a phosphine oxide, a brominated aromatic acrylate, and a dithiocarbamate; a surface additive; and a solvent.
An example of an ultraviolet light curable resin composition includes a predetermined mass ratio of a first epoxy substituted polyhedral oligomeric silsesquioxane monomer and a second substituted polyhedral oligomeric silsesquioxane monomer, wherein the first and second epoxy substituted polyhedral oligomeric silsesquioxane monomers are different, and wherein the predetermined mass ratio ranges from about 3:7 to about 7:3; bis-(4-methylphenyl)iodonium hexafluorophosphate as a first initiator; a second initiator selected from the group consisting of a free radical initiator and a cationic initiator other than bis-(4-methylphenyl)iodonium hexafluorophosphate; a surface additive; and a solvent.
An example flow cell includes a substrate having a surface. The flow cell also includes a polymeric hydrogel attached to at least a portion of the substrate surface, where the polymeric hydrogel includes a dark quencher. The flow cell further includes at least one primer set attached to the polymeric hydrogel.
The present disclosure relates to compositions including a shell surrounding an interior compartment, wherein said interior compartment comprises one or more reagent and wherein said shell releases said interior compartment when said shell is exposed to a first release condition, wherein said interior compartment releases said one or more reagent when said interior compartment is exposed to a second release condition, and wherein said first release condition is different from said second release condition. Also disclosed are compositions including a dissolvable first shell, and a dissolvable second shell, the second shell comprising one or more reagent. Also disclosed are methods for controlling release of one or more reagent using the compositions described herein. The present disclosure further relates to cartridges that include 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.
Embodiments of the present disclosure relate to nucleotides labeled with photoswitchable compounds. Also provided herein are methods and kits of using these labeled nucleotides for sequencing applications.
Presented herein are altered polymerase enzymes for improved incorporation of nucleotides and nucleotide analogues, in particular altered polymerases that maintain low pre-phasing rates when using ambiently stored polymerases, as well as methods and kits using the same.
The technology disclosed describes determination of which elements of a sequence are nearest to uniformly spaced cells in a grid, where the elements have element coordinates, and the cells have dimension-wise cell indices and cell coordinates. The determination includes generating an element-to-cells mapping that maps, to each of the elements, a subset of the cells. The subset of the cells mapped to a particular element in the sequence includes a nearest cell in the grid and one or more neighborhood cells in the grid, and the nearest cell is selected based on matching element coordinates of the particular element to the cell coordinates. The determination further includes generating a cell-to-elements mapping that maps, to each of the cells, a subset of the elements, and using the cell-to-elements mapping to determine, for each of the cells, a nearest element in the sequence.
An example of a kit includes a flow cell, a primer fluid, and a cleaving fluid. The flow cell includes at least one surface functionalized with a polymeric hydrogel including azide functional groups or amine functional groups. The primer fluid includes a plurality of alkyne-containing primers, each alkyne-containing primer having an amino cleavable group attaching a primer sequence of the alkyne-containing primer to an alkyne-containing moiety of the alkyne-containing primer. The cleaving fluid includes a substance that is reactive with the amino cleavable group.
Method includes positioning a first carrier assembly on a system stage. The carrier assembly includes a support frame having an inner frame edge that defines a window of the support frame. The first carrier assembly includes a first substrate that is positioned within the window and surrounded by the inner frame edge. The first substrate has a sample thereon. The method includes detecting optical signals from the sample of the first substrate. The method also includes replacing the first carrier assembly on the system stage with a second carrier assembly on the system stage. The second carrier assembly includes the support frame and an adapter plate held by the support frame. The second carrier assembly has a second substrate held by the adapter plate that has a sample thereon. The method also includes detecting optical signals from the sample of the second substrate.
The present application relates to secondary amine-substituted coumarin compounds and their uses as fluorescent labels. The compounds may be used as fluorescent labels for nucleotides in nucleic acid sequencing applications.
C07D 417/04 - Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group containing two hetero rings directly linked by a ring-member-to-ring- member bond
C07D 405/04 - Heterocyclic compounds containing both one or more hetero rings having oxygen atoms as the only ring hetero atoms, and one or more rings having nitrogen as the only ring hetero atom containing two hetero rings directly linked by a ring-member-to-ring- member bond
C07D 413/04 - Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and oxygen atoms as the only ring hetero atoms containing two hetero rings directly linked by a ring-member-to-ring- member bond
C07H 19/10 - Pyrimidine radicals with the saccharide radical being esterified by phosphoric or polyphosphoric acids
The present application relates to exocyclic amine-substituted coumarin derivatives and their uses as fluorescent labels. These compounds may be used as fluorescent labels for nucleotides in nucleic acid sequencing applications.
Embodiments of the present application relate to substrate comprising a surface-bound azido functionalized organosilane wherein the substrate is free or substantially free of a hydrogel or a hydrophilic polymer. Methods of preparing such substrate surface for sequencing applications are also disclosed.
Novel rhodamine dye compounds, labelled conjugates comprising the dyes are described, together with methods for their use. The dyes and labelled conjugates are useful as molecular probes in a variety of applications, such as in assays involving staining of cells, protein binding, and analysis of nucleic acids, such as hybridization assays and nucleic acid sequencing.
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.
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
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.
The present disclosure relates to a composition including one or more modified nucleotide, wherein the modified nucleotide comprises a purine or pyrimidine base and a sugar moiety having a 3′-hydroxy blocking group, and a radical scavenger, wherein the composition is lyophilised. The present disclosure further relates to a composition including one or more functional protein; one or more functional protein activator; and one or more non-reducing sugar, wherein the composition is lyophilised. Also disclosed are methods of rehydration of one or more compositions described herein and kits including one or more compositions described herein. Further disclosed are cartridges including a flow cell comprising one or more reagent reservoirs, where the one or more reagent reservoirs include one or more compositions described herein.
This disclosure describes methods, non-transitory computer readable media, and systems that can train a genome-location-classification model to classify or score genomic coordinates or regions by the degree to which nucleobases can be accurately identified at such genomic coordinates or regions. For instance, the disclosed systems can determine sequencing metrics for sample nucleic-acid sequences or contextual nucleic-acid subsequences surrounding particular nucleobase calls. By leveraging ground-truth classifications for genomic coordinates, the disclosed systems can train a genome-location-classification model to relate data from one or both of the sequencing metrics and contextual nucleic-acid subsequences to confidence classifications for such genomic coordinates or regions. After training, the disclosed systems can also apply the genome-location-classification model to sequencing metrics or contextual nucleic-acid subsequences to determine individual confidence classifications for individual genomic coordinates or regions and then generate at least one digital file comprising such confidence classifications for display on a computing device.
The present approach relates generally to image-based approaches for detecting deviations from a linear movement when scanning a surface. More particularly, the approach relates to the use of linear fiducials to detect, in real-time, deviations from a linear scan path during operation of a scanning imaging system. Such linear fiducials may include both sample sites and blank regions or sites or, in certain embodiments, may utilize elongated sample sites (e.g., linear features) within the linear fiducial.
The technology disclosed relates to determining pathogenicity of nucleotide variants. In particular, the technology disclosed relates to specifying a particular amino acid at a particular position in a protein as a gap amino acid, and specifying remaining amino acids at remaining positions in the protein as non-gap amino acids. The technology disclosed further relates to generating a gapped spatial representation of the protein that includes spatial configurations of the non-gap amino acids, and excludes a spatial configuration of the gap amino acid, and determining a pathogenicity of a nucleotide variant based at least in part on the gapped spatial representation, and a representation of an alternate amino acid created by the nucleotide variant at the particular position.
G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
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
56.
SYSTEMS AND METHODS FOR SEQUENCING NUCLEOTIDES USING TWO OPTICAL CHANNELS
The disclosed technology relates to the field of nucleic acid sequencing, and more particularly, to systems and methods for DNA sequencing utilizing a single optical excitation and at least three fluorescent labels. In some embodiments, the disclosed technology uses a first nucleotide coupled to a first fluorescent label which can emit light to be detectable by a first detector, a second nucleotide coupled to a second fluorescent label which can emit light to be detectable by a second detector, a third nucleotide coupled to a third fluorescent label which can emit light to be detectable by both the first and second detectors, and a fourth nucleotide coupled to no fluorescent label. The disclosed technology may identify a nucleotide in the nucleic acid sequence based on whether the emission is received by the first detector, the second detector, both the first and second detectors, or neither the first nor second detector.
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. In particular embodiments, the solid surface comprises immobilized transposomes in a dried format, suitable for reconstitution upon contact with liquid, such as a liquid sample.
C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
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
58.
COMPOSITIONS AND METHODS FOR SEQUENCING BY SYNTHESIS
The present application relates to compositions and methods for sequencing by synthesis, where one or more palladium scavengers were used to improve sequencing metrics such phasing and prephasing values.
A method for purifying nucleotides is provided, that includes preparing a solution comprising (a) 3′-blocked nucleotides, (b) 3′-OH nucleotides, (c) a polishing polymerase, and (d) a template. The polishing polymerase and the template are used to selectively polymerize the 3′-OH nucleotides and thus reduce a concentration in the solution of the 3′-OH nucleotides relative to the 3′-blocked nucleotides.
In one example, a method of preparing a fluidic channel includes covalently coupling a first region of a substrate to a first region of a cover using first moieties covalently coupled to the first region of the substrate and second moieties covalently coupled to the first region of the cover. The covalent coupling between the first region of the substrate and the first region of the cover suspends a second region of the cover over a second region of the substrate to form a fluidic channel.
In an example of a method for making a flow cell, a light sensitive material is deposited over a resin layer including depressions separated by interstitial regions, wherein the depressions overlie a first resin portion having a first thickness and the interstitial regions overlie a second resin portion having a second thickness that is greater than the first thickness. A predetermined ultraviolet light dosage that is based on the first and second thicknesses is directed through the resin layer, whereby the light sensitive material overlying the depressions is exposed to ultraviolet light and the second resin portion absorbs the ultraviolet light, thereby defining an altered light sensitive material at a first predetermined region over the resin layer. The altered light sensitive material is utilized to generate a functionalized layer at the first predetermined region or at a second predetermined region over the resin layer.
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
B01J 19/00 - Chemical, physical or physico-chemical processes in general; Their relevant apparatus
G03F 7/038 - Macromolecular compounds which are rendered insoluble or differentially wettable
The present application relates to substituted dyes containing bis-boron fused heterocycles and their uses as fluorescent labels. These compounds may be used as fluorescent labels for nucleotides in nucleic acid sequencing applications.
In an example of a method for making a flow cell, a metal material is sputtered over a transparent substrate including depressions separated by interstitial regions to form a metal film having a first thickness over the interstitial regions and having a second thickness over the depressions, the second thickness being about 30 nm or less and being at least ⅓ times smaller than the first thickness. A light sensitive material is deposited over the metal film; and the metal film is used to develop the light sensitive material through the transparent substrate to define an altered light sensitive material at a first predetermined region over the transparent substrate. The altered light sensitive material is utilized to generate a functionalized layer at the first predetermined region or at a second predetermined region over the transparent substrate.
B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
G03F 7/039 - Macromolecular compounds which are photodegradable, e.g. positive electron resists
G03F 7/11 - Photosensitive materials - characterised by structural details, e.g. supports, auxiliary layers having cover layers or intermediate layers, e.g. subbing layers
G03F 7/038 - Macromolecular compounds which are rendered insoluble or differentially wettable
An example of a flow cell includes a substrate and a pattern of two different silanes on at least a portion of a surface of the substrate. A first polymer is attached to a first of the two different silanes and a second polymer is attached to a second of the two different silanes. The first and second polymers respectively include a first functional group and a second functional group of a functional group pair, the functional group pair being selected from the group consisting of an activated ester functional group and an azide functional group, a tetrazine functional group and an activated ester functional group, and a tetrazine functional group and an azide functional group. A first primer set is grafted to the first polymer and a second primer set is grafted to the second polymer. The first and second primer sets are different.
An example method includes introducing a first fluid to a flow channel of a flow cell including a working electrode having a surface that is at least partially exposed to the flow channel, the surface being unmodified or modified with a first member of a transition metal complex binding pair, whereby a linking moiety of a complex present in the first fluid chemically attaches the complex to the surface to form a temporarily modified surface of the working electrode; performing a sensing operation involving the complex of the temporarily modified surface; and applying a desorption voltage of the linking moiety to the working electrode, thereby detaching the linking moiety and regenerating the surface.
A method for detecting different analytes includes mixing different analytes with sensing probes, wherein at least some of the sensing probes are specific to respective ones of the analytes. The analytes respectively are captured by the sensing probes that are specific to those analytes. Fluorophores respectively are coupled to sensing probes that captured respective analytes. The sensing probes are mixed with beads, wherein the beads are specific to respective ones of the sensing probes, and wherein the beads include different codes identifying the analytes to which those sensing probes are specific. The sensing probes respectively are coupled to beads that are specific to those sensing probes. The beads are identified that are coupled to the sensing probes that captured analytes using at least fluorescence from the fluorophores coupled to those sensing probes. The analytes that are captured are identified.
The technology disclosed relates to determining pathogenicity of variants. In particular, the technology disclosed relates to generating amino acid-wise distance channels for a plurality of amino acids in a protein. Each of the amino acid-wise distance channels has voxel-wise distance values for voxels in a plurality of voxels. A tensor includes the amino acid-wise distance channels and at least an alternative allele of the protein expressed by a variant. A deep convolutional neural network determines a pathogenicity of the variant based at least in part on processing the tensor. The technology disclosed further augments the tensor with supplemental information like a reference allele of the protein, evolutionary conservation data about the protein, annotation data about the protein, and structure confidence data about the protein.
The present disclosure relates to a composition comprising a shell surrounding a core, wherein the core comprises one or more lyophilised microspheres. Also described herein is a method comprising providing one or more lyophilised microspheres; and coating the one or more lyophilised microspheres with a shell under conditions effective to encapsulate the one or more lyophilised microspheres. The present disclosure further relates to a system comprising one or more composition as described herein, and one or more lyophilised cake, wherein the one or more composition and the one or more lyophilised cake are combined under conditions effective to form a rehydration system. Also described herein is a method of controlling release of one or more encapsulated microspheres comprising providing a composition as described herein and mixing the composition with a rehydration solution under a first condition effective to control release of one or more lyophilised microspheres from the composition.
A method for seeding and amplifying target nucleic acids derived from a sample in a cluster at a site on a surface of a substrate includes retaining at least a portion of the target nucleic acids in an inactive form that cannot seed to provide a relatively low concentration of active form target nucleic acids available for seeding. As the active form target nucleic acids seed on the surface of the substrate, they may be amplified. Because the concentration of active form target nucleic acids is low, the likelihood is low that a second active form target nucleic acid will seed at the same site within the same cluster before the first active form target nucleic acid is sufficiently amplified to dominate. Accordingly, the likelihood that the cluster will pass filters is increased relative to traditional seeding and amplification methods employing a higher concentration of active form target nucleic acids.
C12Q 1/6848 - Nucleic acid amplification reactions characterised by the means for preventing contamination or increasing the specificity or sensitivity of an amplification reaction
C12Q 1/70 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
70.
MULTI-CHANNEL PROTEIN VOXELIZATION TO PREDICT VARIANT PATHOGENICITY USING DEEP CONVOLUTIONAL NEURAL NETWORKS
A system includes at least a voxelizer, an alternative allele encoder, an evolutionary conservation encoder, and a convolutional neural network. The voxelizer accesses a three-dimensional structure of a reference amino acid sequence of a protein and fits a three-dimensional grid of voxels on atoms in the three-dimensional structure on an amino acid-basis to generate amino acid-wise distance channels. The alternative allele encoder encodes an alternative allele sequence to each voxel in the three-dimensional grid of voxels. The evolutionary conservation encoder encodes an evolutionary conservation sequence to each voxel in the three-dimensional grid of voxels. The convolutional neural network applies three-dimensional convolutions to a tensor that includes the amino acid-wise distance channels encoded with the alternative allele sequence and respective evolutionary conservation sequences and determines a pathogenicity of a variant nucleotide based at least in part on the tensor.
The technology disclosed relates to efficiently determining which atoms in a protein are nearest to voxels in a grid. The atoms have three-dimensional (3D) atom coordinates, and the voxels have 3D voxel coordinates. The technology disclosed generates an atom-to-voxels mapping that maps, to each of the atoms, a containing voxel selected based on matching 3D atom coordinates of a particular atom of the protein to the 3D voxel coordinates in the grid. The technology disclosed generates a voxel-to-atoms mapping that maps, to each of the voxels, a subset of the atoms. The subset of the atoms mapped to a particular voxel in the grid includes those atoms in the protein that are mapped to the particular voxel by the atom-to-voxels mapping. The technology disclosed includes using the voxel-to-atoms mapping to determine, for each of the voxels, a nearest atom in the protein.
For example, a flowcell includes: a nanowell layer having a first set of nanowells and a second set of nanowells to receive a sample; a first linear waveguide associated with the first set of nanowells, and a second linear waveguide associated with the second set of nanowells; and a first grating for the first linear waveguide, and a second grating for the second linear waveguide, the first and second gratings providing differential coupling of first light and second light.
The technology disclosed relates to determining pathogenicity of variants. In particular, the technology disclosed relates to generating amino acid-wise distance channels for a plurality of amino acids in a protein. Each of the amino acid-wise distance channels has voxel-wise distance values for voxels in a plurality of voxels. A tensor includes the amino acid-wise distance channels and at least an alternative allele of the protein expressed by a variant. A deep convolutional neural network determines a pathogenicity of the variant based at least in part on processing the tensor. The technology disclosed further augments the tensor with supplemental information like a reference allele of the protein, evolutionary conservation data about the protein, annotation data about the protein, and structure confidence data about the protein.
Examples provided herein are related to detecting methylcytosine and its derivatives using S-adenosyl-L-methionine analogs (xSAMs). Compositions and methods for performing such detection are disclosed. A target polynucleotide may include cytosine (C) and methylcytosine (mC). The method may include (a) protecting the C in the target polynucleotide from deamination; and (b) after step (a), deaminating the mC in the target polynucleotide to form thymine (T). Protecting the C from deamination may include adding a protective group to the 5 position of the C, e.g., using a methyltransferase enzyme that adds the first protective group from an xSAM.
Embodiments provided herein relate to methods and compositions for preparing an immobilized library of barcoded DNA fragments of a target nucleic acid, identifying genomic variants, determining the contiguity information, phasing information, and methylation status of the target nucleic acid.
Provided herein is a method for sequencing a polynucleotide molecules. The method includes the steps of providing a plurality of polynucleotide molecules attached to a surface, wherein a first portion of each polynucleotide molecule is attached to a first location of the surface and a second portion of each polynucleotide molecule is attached to a second location of the surface, the relative proximity of the first and second locations being correlated with the probability that the first and second portions are paired, separating the first and second portions of the polynucleotide molecules on the surface, determining the sequences of the first and second portions of the polynucleotide molecules and comparing the relative proximities and the sequences to determine which first and second portions are paired and to determine the sequence of the target polynucleotide molecules.
A method of generating an asymmetric closed-ended double stranded nucleic acid template from a double stranded nucleic acid template having free 5′ and 3′ ends by use of hairpin or dumbbell adaptors, and sequencing therefrom.
In one example, an unsaturated cyclic dione is coupled to the substrate, and is reacted with an indole or indazole including a first functional group to form a first adduct coupling the first functional group to the substrate. In another example, an unsaturated cyclic dione is coupled to a substrate and reacted with a diene including a functional group to form an adduct coupling the functional group to the substrate. In another example, an indole or indazole is coupled to a substrate, and is reacted with an unsaturated cyclic dione including an oligonucleotide to form an adduct coupling the oligonucleotide to the substrate. In another example, a diene is coupled to a substrate, and is reacted with an unsaturated cyclic dione including an oligonucleotide to form an adduct coupling the oligonucleotide to the substrate.
C08F 283/12 - Macromolecular compounds obtained by polymerising monomers on to polymers provided for in subclass on to polysiloxanes
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
Embodiments of the present disclosure relate to nucleotide molecules with a 3′ AOM blocking group. Also provided herein are methods to prepare such nucleotide molecules, and the uses of fully functionalized nucleotides containing the 3′-OH blocking group for sequencing applications.
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
80.
LONG STOKES SHIFT CHROMENOQUINOLINE DYES AND USES IN SEQUENCING APPLICATIONS
The present application relates to long Stokes shift chromenoquinoline dyes and their uses as fluorescent labels. For example, these dyes may be used to label nucleotides for nucleic acid sequencing applications.
C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
C07D 491/147 - Ortho-condensed systems the condensed system containing one ring with oxygen as ring hetero atom and two rings with nitrogen as ring hetero atom
C07D 491/22 - Heterocyclic compounds containing in the condensed ring system both one or more rings having oxygen atoms as the only ring hetero atoms and one or more rings having nitrogen atoms as the only ring hetero atoms, not provided for by groups , , or in which the condensed system contains four or more hetero rings
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.
The present disclosure relates to methods, systems, kits and compositions for nucleic acid sequencing applications. In particular, the method utilizes two imaging events with different excitation wavelengths and a single emission channel to collect the fluorescent signal patterns of different types of nucleotide conjugates to determine the identity of the incorporated nucleotide conjugates. The method described herein does not require a chemical treatment of the nucleotide conjugates in the incorporation mixture between the two imaging events.
The present application relates to alkylpyridinium substituted coumarin dyes and their uses as fluorescent labels. For example, these dyes may be used to label nucleotides for nucleic acid sequencing applications.
Embodiments of the present disclosure relate to methods, kits and compositions for two-channel nuclei acid sequencing using blue and violet light excitation (e.g., lasers at 450-460 nm and 400-405 nm respectively). In particular, the nucleotides may be directly labeled with a blue dye, a violet dye, or both a blue dye and a violet dye. Alternatively, one or more nucleotides for incorporation may be unlabeled and affinity reagents containing a blue dye, a violet dye, or both a blue dye and a violet dye may be used to bind specifically to each type of nucleotides incorporated.
A hydrogel includes a dendritic core with 2 to 30 arms, and first and second acrylamide monomers incorporated into each arm. The first acrylamide monomer is: (I), wherein R1 and R2 are independently selected from an alkyl, an alkylamino, an alkylamido, an alkylthio, an aryl, a glycol, and optionally substituted variants thereof; and the second acrylamide monomer is: (II), wherein R3 and R4 are independently hydrogen or an alkyl; L is a linker including a linear chain of 2 to 20 atoms selected from carbon, oxygen, and nitrogen and optional substituents on the carbon and any nitrogen atoms; A is an N substituted amide: (III), where R5 is hydrogen or an alkyl; E is a linear chain of 1 to 4 atom(s) selected from carbon, oxygen and nitrogen, and optional substituents on the carbon and any nitrogen atoms; and Z is an optional nitrogen containing heterocycle.
A hydrogel includes a dendritic core with 2 to 30 arms, and first and second acrylamide monomers incorporated into each arm. The first acrylamide monomer is: (I), wherein R1 and R2 are independently selected from an alkyl, an alkylamino, an alkylamido, an alkylthio, an aryl, a glycol, and optionally substituted variants thereof; and the second acrylamide monomer is: (II), wherein R3 and R4 are independently hydrogen or an alkyl; L is a linker including a linear chain of 2 to 20 atoms selected from carbon, oxygen, and nitrogen and optional substituents on the carbon and any nitrogen atoms; A is an N substituted amide: (III), where R5 is hydrogen or an alkyl; E is a linear chain of 1 to 4 atom(s) selected from carbon, oxygen and nitrogen, and optional substituents on the carbon and any nitrogen atoms; and Z is an optional nitrogen containing heterocycle.
Some embodiments of the present application relate to novel modified nucleotide linkers for increasing the efficiency of nucleotide incorporation in Sequencing by Synthesis applications. Methods of preparing these modified nucleotide linkers are also provided herewith.
An image sensor structure includes an image layer having an array of light detectors disposed therein. A device stack is disposed over the image layer. An array of light guides is disposed in the device stack. Each light guide is associated with a light detector. An array of nanowells is disposed over the device stack. Each nanowell is associated with a first light guide of the array of light guides. A first primer set is disposed throughout a first well region of each nanowell. A second primer set is disposed throughout a second well region of each nanowell. The second well region is adjacent the first well region. The first and second primer sets are operable to attach a forward strand cluster of forward polynucleotide strands in the first well region and a reverse strand cluster of reverse polynucleotide strands in the second well region.
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.
The present disclosure provides methods and systems for determining and/or characterizing one or more haplotypes and/or phasing of haplotypes in a nucleic acid sample. In particular, the disclosure provides methods for determining a haplotype and/or phasing of haplotypes in a nucleic acid sample by incorporating synthetic polymorphisms into fragments of a nucleic acid sample and utilizing the synthetic polymorphisms in determining one or more haplotypes and/or phasing of haplotypes.
The present disclosure provides methods and systems for determining and/or characterizing one or more haplotypes and/or phasing of haplotypes in a nucleic acid sample. In particular, the disclosure provides methods for determining a haplotype and/or phasing of haplotypes in a nucleic acid sample by incorporating synthetic polymorphisms into fragments of a nucleic acid sample and utilizing the synthetic polymorphisms in determining one or more haplotypes and/or phasing of haplotypes.
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.
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
In an example method, a hydrogel is applied to a surface of a substrate and primers are grafted to the applied hydrogel. Before or after the primers are grafted, plasmonic nanostructures are introduced to the applied hydrogel. This substrate can make up one surface of a flow cell. When the flow cell is used in a sequencing operation, the plasmonic nanostructures can enhance fluorescent signals that are generated.
An example of an incorporation mix includes a liquid carrier, a complex, and a labeled nucleotide. The complex includes a polymerase and a plasmonic nanostructure linked to the polymerase. The labeled nucleotide includes a nucleotide, a 3′ OH blocking group attached to a sugar of the nucleotide, and a dye label attached to a base of the nucleotide.
An example of a functionalized plasmonic nanostructure includes a plasmonic nanostructure core; a polymeric hydrogel attached to the plasmonic nanostructure core, the polymeric hydrogel having a thickness ranging from about 10 nm to about 200 nm; and a plurality of primers attached to side chains or arms of the polymeric hydrogel, wherein at least some of the plurality of primers are attached to the polymeric hydrogel at different distances from the plasmonic nanostructure core.
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
C08F 265/10 - Macromolecular compounds obtained by polymerising monomers on to polymers of unsaturated monocarboxylic acids or derivatives thereof as defined in group on to polymers of amides or imides
An example of a kit includes a flow cell and a cleavage mix. An example flow cell includes a substrate; a catalytic polymeric hydrogel on the substrate, the catalytic polymeric hydrogel including a deblocking catalyst; and an amplification primer attached to the catalytic polymeric hydrogel. The deblocking catalyst accelerates cleavage of a blocking group of a 3′ OH blocked nucleotide introduced to the flow cell and incorporated into a template strand attached to the amplification primer. An example of the cleavage mix includes a component to initiate cleavage of the blocking group.
C12Q 1/6848 - Nucleic acid amplification reactions characterised by the means for preventing contamination or increasing the specificity or sensitivity of an amplification reaction
A method is used to generate an analysis image of a moving sample based on one or more exposures. An illumination source illuminates a field of view of a camera for one or more pulses while the sample moves through the field of view. The distance moved by the sample during each of these one or more pulses may be less than the size of one pixel in an image captured by the camera.
An analysis substrate comprises: a localization layer to be provided with a sample comprising a nucleotide provided with a fluorescent dye; and a sensor layer comprising an array of sensor pixels, the localization layer being on-chip relative to the sensor layer, one or more of the array of sensor pixels to receive a propagation of fluorescence from the fluorescent dye.
Described herein are methods and systems for performing chemical or enzymatic reactions using electrophoresis. Devices, systems, and methods for preparing a library of tagged nucleic acid fragments from a target double-stranded nucleic acid using electrophoresis are also provided. Application of one or more electric fields causes molecules to migrate through the electrophoresis gel matrix.
For example, a flowcell includes: a nanowell layer having a first set of nanowells and a second set of nanowells to receive a sample; a first linear waveguide associated with the first set of nanowells, and a second linear waveguide associated with the second set of nanowells; and a first grating for the first linear waveguide, and a second grating for the second linear waveguide, the first and second gratings providing differential coupling of first light and second light.
A composition for amplifying a polynucleotide is provided that includes a substrate comprising a first region and a second region. A first plurality of capture primers is coupled to the first region of the substrate. A second plurality of capture primers is coupled to the second region of the substrate. The capture primers of the second plurality of capture primers are longer than the capture primers of the first plurality of capture primers. A first plurality of orthogonal capture primers are coupled to the first region of the substrate. A second plurality of orthogonal capture primers are coupled to the second region of the substrate. The orthogonal capture primers of the second plurality of orthogonal capture primers are shorter than the orthogonal capture primers of the first plurality of orthogonal capture primers.
patents
