An apparatus includes a channel, a plurality of reaction sites, and a sensor assembly. The sensor assembly includes at least one gate electrode, one or more source electrodes, one or more drain electrodes, and a plurality of sensing channels. Each source electrode is positioned adjacent to a corresponding reaction site of the plurality of reaction sites. Each drain electrode is positioned adjacent to a corresponding reaction site of the plurality of reaction sites. Each sensing channel of the plurality of sensing channels extends from a corresponding source electrode of the one or more source electrodes to a corresponding drain electrode of the one or more drain electrodes. Each sensing channel is positioned to receive an ion emitted from a corresponding reaction site of the plurality of reaction sites as a voltage is applied to the at least one gate electrode during a sequencing by synthesis process.
A genotyping array includes first and second sample probes. Each first sample probe a) is a single probe having a 3' terminus that complements a base directly adjacent to a query site of a respective sample fragment or b) includes two probes, each having a 3' terminus that complements a base at the query site of the respective sample fragment, or c) a combination of a) and b). The second sample probe includes a target probe selected from: i) a first target probe including a degenerate base within a predetermined number of bases of its 3' terminus; ii) a second target probe including predetermined mismatched bases with a first off-target fragment; iii) a third target probe including a complement of a known mismatch region of a second off-target fragment in place of a known complementary region of the second off-target fragment; and iv) any combination of i) through iii).
This disclosure describes methods, non-transitory computer-readable media, and systems that can determine a haplotype diversity metric and generate a variant call format (VCF) file with the haplotype diversity metric. For example, the disclosed systems can identify a first set of nucleotide sequences with a preliminary indication of the presence of a target variant. The disclosed systems can further determine a first haplotype diversity value for the first set of nucleotide sequences with the target variant and a second diversity value for a second set of nucleotides that do not include the target variant. Based on the first and second haplotype diversity values, the disclosed systems can further determine a haplotype diversity metric for the first set of nucleotide sequences with the target variant. The disclosed systems can further generate a VCF file with the haplotype diversity metric.
The present application relates to dyes containing a 4,5-substituted naphthalimide core and their uses as fluorescent labels. These dyes may be used as fluorescent labels for nucleotides in nucleic acid sequencing applications.
In some examples, a method of amplifying a polynucleotide includes capturing the polynucleotide at a recess of a sacrificial material disposed on a substrate; removing at least a portion of the sacrificial material to expand the recess having the polynucleotide captured therein; and amplifying the polynucleotide at the expanded recess. A hydrogel may be disposed within the recess and may include a capture primer to which the polynucleotide hybridizes when capturing the polynucleotide; and amplification primers to which amplicons of the polynucleotide hybridize when amplifying the polynucleotide. The hydrogel may expand from the recess into the expanded recess.
The present disclosure provides engineered deaminases that bind to single-stranded DNA (ssDNA) and deaminate ssDNA at a temperature that destabilizes ssDNA secondary structure. Compositions comprising the engineered deaminases, polynucleotides encoding the engineered deaminases, and methods of using the engineered deaminases to detect the locations of modified cytosines in nucleic acids are also provided.
The disclosed embodiments concern methods for designing probes for improving environmental sample (including wastewater samples and other samples) surveillance and surveillance of other samples for various viruses. In certain embodiments described herein, methods and systems are provided for designing a pool of probes for enriching a sample for one or more target viral nucleic acids.
In an example, a deoxyribonucleic acid (DNA) sample is introduced to a flow cell including depressions and first and second transposome complexes immobilized within the depressions, whereby tagmentation generates respective DNA sample fragments in at least some depressions. The first and second transposome complexes respectively include first and second amplification domains. A pre-grafted particle suspension is introduced into the flow cell, whereby at least some pre-grafted particles respectively attach within a plurality of the at least some depressions. The suspension includes a liquid carrier and pre-grafted particles, which include first and second primers attached to a core. The first and second primers have a same sequence, respectively, as the first and second amplification domains. Amplification is initiated such that, within each of the plurality of the at least some depressions, the respective DNA sample fragments are amplified on a respective one of the at least some pre-grafted particles.
Hardware acceleration may be leveraged for performing secondary analysis. The hardware acceleration may be implemented by utilizing a plurality of field programmable gate arrays (FPGAs) installed on a device. Requests may be made from client processes for performing secondary analysis of sequencing data at a computing device. Each FPGA may be configured with an engine, or set of engines, configured to perform the secondary analysis to service the requests from client process. An FPGA may be configured with a plurality of engines configured for performing secondary analysis. The FPGA may be configured with a single instance comprising different types of engines for performing different types of secondary analysis. The FPGA may be configured with multiple instances of an engine, or set of engines, configured to perform the same or similar type of secondary analysis. The FPGA may share its resources with multiple client processes using one or more shared engines.
G16B 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
13.
DETERMINING SPLICE SITES IN NUCLEOTIDE SEQUENCES USING CONDITIONAL PROBABILITIES GENERATED VIA A NEURAL NETWORK
This disclosure describes methods, non-transitory computer-readable media, and systems that generate quantitative predictions of splice sites for nucleotide sequences. For example, in some cases, the disclosed systems use a neural network to analyze a nucleotide sequence that includes a conditioned nucleobase and flanking nucleobases. Based on the analysis, the neural network generates conditional probabilities for the flanking nucleobases, where each conditional probability indicates a likelihood that a corresponding flanking nucleobase is part of a matching splice site (e.g., a matching donor or acceptor) for the conditioned nucleobase. By generating such conditional probabilities, the disclosed system quantitatively identifies potential splice sites within the nucleotide sequence.
Some examples herein provide a sequencing flowcell that includes an imaging sensor; a hydrogel disposed on the imaging sensor and comprising a moiety; and a first complex non-covalently coupled to the moiety, the first complex comprising a first oligonucleotide. A method of using the sequencing flowcell may include decoupling the first complex from the moiety; and coupling a second complex to the moiety, the second complex comprising a second oligonucleotide. Methods of forming the flowcell are also provided.
There is set forth herein, in one example, an apparatus (100). The apparatus can comprise, for example: a biosensor (200) comprising pixel(s) (201), a first reaction site (206, 206a-206f) to emit light responsive to a cluster (C1, C2) at the site being exposed to excitation light (101); the emitted light is a first optical signal propagated through the biosensor on a first signal path to a pixel. The apparatus includes a second reaction site (206, 206a-206f) to emit light responsive to a cluster (C1, C2) at this site being exposed to the excitation light; the emitted light is a second optical signal propagated through the biosensor on a second signal path to the pixel. The apparatus includes a first layer (252) and a second layer (252) both situated in the signal paths and associated to the pixel, the first, to selectively open the signal path when a first voltage is applied, and the second, to selectively open the signal path when a second voltage is applied.
Pre-grafted particles include a core, and both a primer set and a transposome dimer attached to the core. In one example method, the transposome dimer is uniquely indexed. In this method, different sets of pre-grafted particles are introduced into respective wells of a well plate. A first sample is introduced into a first well, where it is tagmented to generate first sample fragments that are attached to the pre-grafted particles of a first set present in the first well. A second sample is introduced into a second well, where it is tagmented to generate second sample fragments that are attached to the pre-grafted particles of a second set present in the second well. The first and second sample fragments respectively include first and second index sequences. The different sets are pooled to form a particle mixture, and the particle mixture is introduced into a flow cell.
The present disclosure is concerned with modified proteins, methods, compositions, and kits for mapping of methylation status of nucleic acids, including 5-methylcytosine. In some embodiments, the proteins are altered cytidine deaminases, such as altered APOBEC3A proteins. In some embodiments, the proteins selectively act on cytosines and have significantly reduced activity on modified cytosines, such as 5-methylcytosine.
C12N 15/62 - DNA sequences coding for fusion proteins
C12Q 1/34 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving hydrolase
This disclosure describes embodiments of methods, non-transitory computer readable media, and systems that can utilize one or more machine learning models to predict insert lengths of a sample genomic sequence from which nucleotide read pairs are sequenced. For example, the disclosed systems can generate predictions for insert lengths based on cluster metrics from primary analysis on a sequencing device, such as signal intensity. By applying a machine-learning-based insert length prediction model to process the cluster metrics, the disclosed systems generate a predicted insert length (e.g., a distribution or a mean). To determine cluster metrics, the disclosed systems can analyze data from oligonucleotide clusters and/or from a sample genomic sequence used to sequence nucleotide read pairs during primary analysis. Based on predicted insert lengths from cluster metrics, the disclosed systems can determine improved genotype calls for genomic samples, such as calls in genomic regions comprising tandem repeats or structural variants.
A polymer is disposed through a nanopore that encodes a polynucleotide's sequence and includes monomer units that encode nucleotides and include first and second reporter moieties and first and second arresting constructs. The first reporter moiety is translocated into the nanopore's aperture, where a first value of an electrical property of the first reporter moiety is measured while the first arresting construct pauses translocation. The second reporter moiety is translocated into the aperture, where a second value of an electrical property of the second reporter moiety is measured while the second arresting construct pauses translocation. The first value and the second value for each monomer unit is used to identify the nucleotide encoded by that monomer unit; and distinguish the nucleotide encoded by that monomer unit from the nucleotides encoded by adjacent monomer units, including by those that encode the same type of nucleotide as that monomer unit.
In some examples, a dendritic molecule may include a dendritic core; a seeding primer coupled to the dendritic core; and a plurality of dendrons, each of the dendrons comprising an inert, elongated polymer comprising a first end coupled to the dendritic core and a second end coupled to a first functional group, wherein the first functional group is to react with a second functional group to form a covalent bond. In other examples, a dendritic molecule may include a dendritic core; a single-stranded polynucleotide covalently bonded to the dendritic core; and a plurality of dendrons, each of the dendrons comprising an inert, elongated polymer comprising a first end coupled to the dendritic core and a second end.
A kit for biological sequencing operations includes a flow cell including a plurality of depressions having a first diameter. The kit further includes a suspension including: a liquid carrier; and a plurality of functionalized nanostructures dispersed throughout the liquid carrier. Each of the plurality of functionalized nanostructures has a second diameter that is equal to or less than the first diameter. Each of the plurality of functionalized nanostructures includes: a nanostructure core; and a plurality of primers attached to the nanostructure core. The kit further includes a plurality of mechanical loading beads having a third diameter that is greater than the first diameter.
A biological material complex is described herein. In some embodiments, the biological material complex includes a solid surface having a terminal hydrazine that is available to bind to a functional group of a biological material. Applications, uses, and variations of the disclosed complex include, but are not limited to, separating, purifying, and labeling biological materials.
This disclosure related to solid supports and methods for cluster amplification. In some embodiments, methods use a capture polynucleotide for seeding library fragments and lawn primers comprising clustering primer sequences.
In some examples, a hybrid particle for use in capturing a polynucleotide may include a scaffold molecule including a seeding primer and a plurality of first moieties, and a nanoparticle including a plurality of second moieties. The scaffold molecule is coupled to the nanoparticle via interactions between the plurality of first moieties and the plurality of second moieties.
The present disclosure is concerned with modified proteins, methods, compositions, and kits for mapping of methylation status of nucleic acids, including 5-methylcytosine and 5-hydroxymethyl cytosine (5hmC). The proteins selectively act on certain modified cytosines of target nucleic acids and include one or more substitution mutations that enhance the selectivity of the proteins for certain modified cytosines, enhance the stability of the proteins, or enhance both selectivity and stability. Also provided are compositions and kits that include one or more of the proteins and methods for using one or more of the proteins.
C12N 9/78 - Hydrolases (3.) acting on carbon to nitrogen bonds other than peptide bonds (3.5)
C12N 15/52 - Genes encoding for enzymes or proenzymes
C12Q 1/34 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving hydrolase
C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
The present disclosure is concerned with modified proteins, methods, compositions, and kits for mapping of methylation status of nucleic acids, including 5-methylcytosine and 5-hydroxymethyl cytosine. In some embodiments, the modified proteins have been altered to increase protein stability. In some embodiment, the proteins selectively act on certain modified cytosines of target nucleic acids and include one or more substitution mutations that enhance the selectivity of the proteins for certain modified cytosines, optionally enhance the stability of the proteins, or optionally enhance both selectivity and stability. Also provided are compositions and kits that include one or more of the proteins and methods for using one or more of the proteins.
28.
TRACKING AND MODIFYING CLUSTER LOCATION ON NUCLEOTIDE-SAMPLE SLIDES IN REAL TIME
This disclosure describes embodiments of methods, systems, and non-transitory computer readable media that can (i) estimate a location error for a predicted location of a cluster of oligonucleotides based on the cluster's signal and (ii) modify the predicted location of the cluster to improve signal detection and base calling on a sequencing device. For example, the disclosed systems can receive a signal from a cluster of oligonucleotides at a predicted location. The disclosed systems can further determine an intensity -value error between an intensity value and an expected intensity value for the signal at the predicted location. Based on the intensity -value error and intensity values from other locations (e.g., other clusters of oligonucleotides) within the region, the disclosed system can determine an estimated location error for the predicted location. The disclosed systems can modify the predicted location of the cluster of oligonucleotides based on the estimated location error.
A method of base calling nucleobases of first and second polynucleotide sequence portions. The method comprises accessing intensity data for a current sequencing cycle of a sequencing run, wherein the intensity data is a combined intensity of a first signal obtained based upon a respective first nucleobase of at least one first polynucleotide sequence portion and a second signal obtained based upon a respective second nucleobase of at least one second polynucleotide sequence portion; base calling the first nucleobase based on the intensity data; accessing a plurality of mappings representing adjustments to signal intensity obtained based upon a current nucleobase of at least one polynucleotide sequence portion, wherein said adjustments are dependent on at least one preceding and/or succeeding nucleobase in said polynucleotide sequence portion; base calling the second nucleobase based on the intensity data, the base call of the first nucleobase and the plurality of mappings.
In one aspect, the disclosed technology relates to nanopore sequencing with a polynucleotide comprising a plurality of nucleotides, wherein each nucleotide comprises a macromolecular block. In some embodiments, the macromolecular blocks are configured for slowing or halting the polynucleotide translocation through a nanopore. In some embodiments the macromolecular blocks have linear and branched structures.
C07H 19/00 - Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radicalNucleosidesMononucleotidesAnhydro derivatives thereof
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
C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
A method of determining one or more bases in sequencing data comprises: receiving sequencing data comprising a first sequence read and a second sequence read, wherein the first and second sequence reads are generated by determining, for each of a plurality of sequencing cycles, a base of the first sequence read and a base of the second sequence read, based on a combined intensity of signals detected from respective bases of first and second polynucleotide sequence portions during the sequencing cycle; determining one or more bases in the first sequence read, based on information obtained from the second sequence read; and/or determining one or more bases in the second sequence read, based on information obtained from the first sequence read.
Aspects relate to solid supports and methods for use in nucleic acid sequencing, in particular solid supports and methods for use in concurrent sequencing. The invention also relates to methods and kits for use in nucleic acid sequencing, in particular methods for use in optimising the signal-to-noise ratio in simultaneous sequencing, in particular by using a calculated amount of terminated primer(s).
The invention relates to methods and kits for use in nucleic acid sequencing, in particular methods for use in double-stranded sequencing, and in particular for use in double-stranded sequence by synthesis (SBS). In a further embodiment, the methods of the invention can be used in concurrent sequencing.
Described are DNA sequencing systems and methods. Systems and methods may calculate a genomic null distribution of read pairs on a flow cell having approximately zero probability of being linked with one another and calculate a spatial null distribution of read pairs having approximately zero probability of being spatially linked. The system may generate a link quality score representing a probability of incorrectly assigning a link between the two polynucleotide reads based on the calculated genomic null distribution and the calculated spatial null distribution.
G16B 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
35.
METHODS AND SYSTEMS FOR IDENTIFYING FUNCTIONAL NON-CODING VARIANTS
The presently disclosed techniques are generally directed to facilitating the identification of functional rare variants (236), such as variants within promoter regions. In certain embodiments, promoter regions to be assessed for functional variants may be identified or localized using a TSS predictor model (530) integrating multiple data sources to accurately identify transcription start site (TSS) positions, which are used to localize promoter regions for a gene. In further aspects as discussed herein, allele specific expression is evaluated for genes of interest, as opposed to total gene expression at the gene of interest. This may be done by selecting a suitable allele-expression single nucleotide polymorphism (aeSNP) for the gene. In certain embodiments discussed herein, the aeSNP closest to the TSS determined for the gene is selected as the best or most suitable SNP for assessing allele-specific expression.
A method for detecting 5 '-methylcytosine and/or 5'-hydroxymethylcytosine in a target DNA is disclosed. Such methods comprise converting 5 '-methylcytosine and/or 5 '-hydroxymethylcytosine to 5 '-formylcytosine and/or 5 '-carboxylcytosine to produce converted DNA. Treating the converted DNA with a coupling reagent to attach a functional group at the 5 '-formyl and/or 5 '-carboxyl group to produce a coupled DNA. Amplifying the coupled DNA so as to introduce a discrepant region at the site of the functional group to produce discrepant DNA. Sequencing the discrepant DNA to identify the discrepant region that deviates from a reference sequence, thereby detecting 5 '-methylcytosine and/or 5 '-hydroxymethylcytosine in a target DNA. In particular embodiments, the DNA is amplified with at least two distinct polymerases. At least one of the polymerases is a processive polymerase. At least one of these polymerases is a lesion polymerase. The lesion polymerase introduces the discrepant region. The attached functional group causes the processive polymerase to release from the DNA.
Aptamer detection techniques are provided that facilitate sequencing library preparation. In embodiments, reporter probes complementary to aptamers may be used to generate amplification products to form a sequencing library. In embodiments, the aptamer may be used as part of a library preparation.
A methylation detection array includes a substrate with depressions, a bead in each depression, and a sample probe attached to each bead. The sample probes include probe sets (i.e., unmethylated probe and corresponding methylated probe). Unmethylated and methylated probes are each based on: i) a bisulfite or enzymatically converted top strand sequence of a corresponding top strand sequence that contains a high minor allele frequency single nucleotide polymorphism (SNP) where a reference is [G] followed by [CG]; or ii) a bisulfite or enzymatically converted bottom strand sequence of a corresponding bottom strand sequence that contains a high minor allele frequency SNP where a reference is [G] followed by [N] and preceded by [CG]; or iii) a bisulfite or enzymatically converted bottom strand sequence of a corresponding bottom strand sequence that contains a high minor allele frequency SNP where a reference is [C] followed by [G] and preceded by [CG].
Aptamer detection techniques with dynamic range compression are described that permit removal of a portion of more abundant aptamers in an aptamer-based assay. In an embodiment, high abundance oligonucleotides, when in double-stranded form, may tend to reanneal to one another under certain hybridization conditions relative to low abundance oligonucleotides. These reannealed fragments may be digested or may be unavailable for amplification. In an embodiment, different-length complementary regions may be used to differentially capture high abundance oligonucleotides relative to low abundance oligonucleotides. Low abundance oligonucleotides may be captured with longer complementary regions, which may provide more robust hybridization at annealing temperatures relative to shorter complementary regions.
Embodiments of the present disclosure relate to methods and kits for sequencing by synthesis utilizing biorthogonal chemical reactions between unlabeled nucleotides and post incorporation labeling reagents.
This disclosure provides methods and compositions relating to the characterization of the chikungunya virus genome, including specific sets of oligonucleotide primers for the amplification of the chikungunya virus genome for downstream sequencing, alignment, and identification of variants in the chikungunya virus genome.
C12Q 1/70 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving virus or bacteriophage
Provided herein are methods and compositions relating to the characterization of the dengue virus genome. The disclosure provides oligonucleotides primers for the amplification of the dengue virus genome for downstream sequencing, alignment, and identification of variants in the dengue virus genome.
C12Q 1/70 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving virus or bacteriophage
An example optical alignment target includes a translucent or transparent substrate having a bottom surface; an opaque material formed over the bottom surface in a pattern; an enclosed channel disposed below the bottom surface; and a fluid suspension contained in the enclosed channel. The pattern has an opaque portion of an opaque material and has a gap portion devoid of the opaque material. The fluid suspension includes a carrier liquid and a light emitting material suspended in the carrier liquid. The light emitting material is selected from the group consisting of quantum dots and cerium powder.
Methods, systems, and apparatus, including computer programs encoded on computer-storage media, for compressing genomic data. One of the methods includes obtaining a genomic data read; mapping the read to a plurality of different candidate reference genomes; selecting one of the candidate reference genomes based on the mapping; performing reference-based compression of the read using the selected reference genome; and storing the compressed genomic data read.
A microreactor array is provided that includes a plurality of microreactors in a substrate. The plurality of microreactors is in fluid communication with a common fluid delivery channel. Each of the microreactors includes an electrode configured to generate one or more gaseous bubbles that can block reagent access to selected microreactors. A method for selective reactions in a microreactor array is also provided. The method includes flooding the array of microreactors with a first fluid selected to release a gas during electrolysis, applying a bias to the electrode associated with one or more selected microreactors in the array, thereby forming one or more gaseous bubbles at or near the electrode. The next step involves flushing the array with a second fluid, and carrying out a reaction in the microreactors that are not blocked by the bubble.
This application relates to methods and compositions for protecting fully functional nucleotides (ffNs) against degradation. In some examples, micelles or surfactants are used to protect ffNs. In some examples, bulky cation compounds are used to protect ffNs. In some examples, the compositions that protect ffNs are included in lyophilized material.
An example of a flow cell includes a substrate including a surface and a dendron architecture. The dendron architecture includes a functionalized focal point of attachment that is attached to the substrate surface and a plurality of peripheral functional groups that are orthogonal to the functionalized focal point of attachment. The flow cell further includes a primer set attached to the dendron architecture via the plurality of peripheral functional groups.
Embodiments of the present disclosure relate to patterned substrates with functionalized surface such as flow cells, as well as methods of fabricating the patterned substrate. In particular, patterned substrates of the present disclosure may be prepared using two or more imprint resin layers, one of which acts as a photomask for the photoresist during substate patterning, without the need of any metallic photomask. Embodiments of the patterned substrate may be used for simultaneous paired-end sequencing methods.
G03F 7/00 - Photomechanical, e.g. photolithographic, production of textured or patterned surfaces, e.g. printed surfacesMaterials therefor, e.g. comprising photoresistsApparatus specially adapted therefor
B01J 19/00 - Chemical, physical or physico-chemical processes in generalTheir relevant apparatus
49.
SYSTEMS AND METHODS OF SEQUENCING POLYNUCLEOTIDES WITH ALTERNATIVE SCATTERPLOTS
The application relates to DNA sequencing systems and methods. Systems and methods for determining the nucleotide sequence of a polynucleotide may include introducing a fourth labelled nucleotide in a two-channel sequencing by synthesis system to create alternative X-Y scatterplot shapes where the x-axis represents the intensity of fluorescence at one wavelength (channel 1), and the y-axis represents intensity of fluorescence at another wavelength (channel 2 The alternative scatterplot shapes may allow for additional encoding space for empty well detection.
The application relates to DNA sequencing systems and methods. Systems and methods for determining the nucleotide sequence of a polynucleotide may include introducing a fourth labeled nucleotide in a two-channel sequencing by synthesis system that allows for encoding space for a detecting a fifth labeled nucleotide or empty well detection.
Methods are provided for assigning nucleic acid sequence reads to target polynucleotides, including providing a substrate having transposome complexes immobilized thereon, wherein the transposome complexes comprise a transposase and a first polynucleotide comprising an end sequence and a first tag; contacting the transposome complexes with target polynucleotides under conditions to fragment the target polynucleotides; amplifying the fragmented target polynucleotides to form a plurality of nucleic acid clusters on the substrate; obtaining location information for the plurality of nucleic acid clusters on the substrate; determining the nucleic acid sequence reads of the fragmented nucleic acids in each of the nucleic acid clusters; and assigning the nucleic acid sequence reads to the target polynucleotides using the obtained location information.
This disclosure describes methods, non-transitory-computer readable media, and systems that can modify sequencing runs to ensure all genomic samples meet a target read-coverage level. The disclosed system can estimate read coverage for each genomic sample in a genomic pool based on (i) clusters belonging to each sample derived from indexing sequences and/or (ii) filter metrics corresponding to each sample within a flow-cell pool. The disclosed systems can modify a sequencing run based on the estimated read coverage and a target read coverage. For example, the disclosed systems can adjust a number of sequencing cycles within a sequencing run to ensure that all genomic samples meet the target read coverage. Additionally, or alternatively, the disclosed systems can determine a set of flow cell tiles to be imaged to ensure that all genomic samples meet the target read coverage.
53.
MACHINE-LEARNING MODEL FOR RECALIBRATING GENOTYPE CALLS CORRESPONDING TO GERMLINE VARIANTS AND SOMATIC MOSAIC VARIANTS
This disclosure describes methods, non-transitory computer readable media, and systems that can utilize a machine-learning model to recalibrate genotype calls (e.g., variant calls) corresponding to germline variants and somatic mosaic variants. For instance, based on sequencing metrics for nucleotide reads of a genomic sample, the disclosed systems can utilize a variant-call-recalibration machine-learning model to generate genotype probabilities for variants within genomic regions corresponding to candidate germline variants and candidate somatic mosaic variants. Further, the disclosed systems can generate genotype calls, such as variant calls corresponding to somatic mosaic variants, based on the generated genotype probabilities.
An imaging system includes a focus tracking module including: a light source to project a first pair of spots on a sample; and a first image sensor to obtain one or more first images of the first pair of spots; a second image sensor to obtain one or more second images of the sample; one or more mirrors optically coupled to the second image sensor, the one or more mirrors positioned in an optical path from the sample to the second image sensor; and a controller to: determine, using at least a first separation distance measurement of the first pair of spots from the one or more first images, a first sample tilt of the sample about a first axis of the imaging system; and actuate, based at least on the first sample tilt, the one or more mirrors to offset the first sample tilt about the first axis.
Disclosed herein are formulations and methods for denaturing DNA that utilize betaine as the denaturant. In some examples, the formulations include additives other than betaine, such as, for example, dimethyl sulfoxide (DMSO) and/or diethylene glycol (DEG).
Systems and related reagent cartridge queuing methods are disclosed. In accordance with an implementation, an apparatus includes a first reagent cartridge, a second reagent cartridge, and a system. The system includes a sipper manifold assembly having a sipper, a queue to carry the first reagent cartridge and the second reagent cartridge, a cartridge moving assembly, and a cartridge receptacle assembly. The cartridge moving assembly includes a gantry, a carriage actuator, and a carriage. The carriage is coupled to the gantry and the carriage actuator is to move the carriage relative to the gantry. The cartridge receptacle assembly has a cartridge receptacle to receive the first reagent cartridge or the second reagent cartridge. The carriage is to move the first reagent cartridge from the queue and position the first reagent cartridge into the cartridge receptacle.
G01N 35/02 - Automatic analysis not limited to methods or materials provided for in any single one of groups Handling materials therefor using a plurality of sample containers moved by a conveyor system past one or more treatment or analysis stations
G01N 35/00 - Automatic analysis not limited to methods or materials provided for in any single one of groups Handling materials therefor
G01N 35/10 - Devices for transferring samples to, in, or from, the analysis apparatus, e.g. suction devices, injection devices
In some examples, a method for capturing and amplifying a polynucleotide includes capturing the polynucleotide at a particle comprising a first region and a second region. The first region may include a first moiety that captures the polynucleotide. The second region may include a plurality of amplification primers and have a surface area which is substantially larger than the surface area of the first portion. The method includes using the plurality of amplification primers to amplify the captured polynucleotide.
Described are DNA sequencing systems and methods. Systems and methods for determining the nucleotide sequence of a polynucleotide may include determining the sequence of a polynucleotide with more than four types of bases by increasing the number of encoding states in sequencing by synthesis (SBS) systems. The systems and methods may expand the encoding space of current systems by discretizing the amplitude space in a channel into more than two states, and/or by adding additional channels.
This application relates to functionalized magnetic particles and methods of using magnetic particles to generate amplicons. In some examples, a method of modifying a magnetic particle comprising a first functional group includes contacting the magnetic article with a first molecule comprising a polymer coupled to second and third functional groups, wherein the first functional group reacts with the second functional group to form a bond via which the polymer is coupled to the magnetic particle. The method may include contacting the magnetic particle with a second molecule, the second molecule comprising an oligonucleotide coupled to a fourth functional group, wherein the third functional group reacts with the fourth functional group to form a bond via which the ligonucleotide is coupled to the magnetic particle.
This disclosure describes methods, non-transitory-computer readable media, and systems that can simultaneously determine estimated methylation-level values for cytosine bases and genotype calls for a target genomic sample. The disclosed system can utilize a Bayesian method on a target genomic sample's nucleotide-read data to generate estimated methylation-level values that indicate genomic coordinates at which the target genomic sample comprises a reference cytosine base or a nucleobase that could be called as a cytosine. The disclosed system can estimate methylation-level values based on prior genotype probabilities and observed nucleobases at a genomic coordinate from a read pileup of a target genomic sample. Based on the estimated methylation-level values and base-call-quality metrics, the disclosed system may generate posterior genotype probabilities for the genomic sample at the genomic coordinate. Based on the posterior genotype probabilities, the disclosed system can generate a genotype call for the target genomic sample.
Methods, systems, and apparatus, including computer programs encoded on computer-storage media, for classification of a single cell from a biological sample of an entity. In one aspect, the method can include obtaining data indicating a plurality of reference positions where a known variant sequence exists for the entity in respective reference positions of the plurality of reference positions, obtaining a plurality of reads for the single cell from the biological sample of the entity, determining, for respective reads of the obtained plurality of reads, a score indicating whether a variant sequence in the respective reads of the biological sample of the entity matches the plurality of reference positions where the known variant sequence exists, and classifying the single cell as a tumor cell or normal cell based on an aggregation of the score determined for the respective reads of the obtained plurality of reads.
G16H 50/20 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems
G16H 50/30 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for calculating health indicesICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for individual health risk assessment
62.
INTERLOCKING NUCLEIC ACIDS FOR TARGET HYBRIDIZATION
Interlocking nucleic acids for target hybridization are described. The interlocking nucleic acids include individual nucleic acids having respective capture regions that hybridize to the target nucleic acid and interlocking regions that bind to each other. In an embodiment, the interlocking nucleic acids are part of a probe set that specifically binds to a target nucleic acid to permit capture of the target nucleic acid. In an embodiment, the interlocking nucleic acids may be part of a primer used for amplification of the target nucleic acid.
In some examples, a method of capturing a polynucleotide on a particle that includes a capture primer includes transporting the particle to a first aperture between a first fluidic compartment and a second fluidic compartment. The particle may be located in the first fluidic compartment, and the polynucleotide may be at least partially located in the second fluidic compartment. The method may include transporting the polynucleotide from the second fluidic compartment to the first fluidic compartment through the first aperture. The method may include hybridizing the polynucleotide to the capture primer.
A methylation detection array includes a substrate having a plurality of depressions defined therein; a plurality of beads, each of the plurality of beads positioned within one of the plurality of depressions; a plurality of sample probes respectively attached to some of the plurality of beads; and a plurality of lambda phage control probes respectively attached to some other of the plurality of beads. The plurality of lambda phage control probes includes a probe set including an unmethylated probe and a corresponding methylated probe; and a single probe. Each of the plurality of lambda phage control probes targets a cytosine in a CH site of a lambda phage target sequence and is free of additional CpG sites. The plurality of lambda phage control probes make up from greater than 0% to less than 5% of a total of the sample probes and the control probes.
C12Q 1/6809 - Methods for determination or identification of nucleic acids involving differential detection
C12Q 1/6837 - Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
65.
REAGENT RESERVOIRS AND RELATED SYSTEMS AND METHODS
Reagent reservoirs and related systems and methods are disclosed. An apparatus includes a flexible container and a coupling. The flexible container includes an end and a tapered bottom. The flexible container includes an interior containing dried reagent. The coupling has a portion coupled to the end of the flexible container. The coupling has a port fluidly coupled to the interior of the flexible container. Rehydrating fluid is to flow through the port and into the interior of the flexible container. An interaction between the rehydrating fluid and the tapered bottom is to cause a vortex within the interior of the flexible container to rehydrate a substantial portion of the dried reagent.
B65D 75/58 - Opening or contents-removing devices added or incorporated during package manufacture
B65D 75/30 - Articles or materials enclosed between two opposed sheets or blanks having their margins united, e.g. by pressure-sensitive adhesive, crimping, heat-sealing, or welding
66.
METHOD AND SYSTEM FOR ESTIMATING IMPACT OF MUTATIONS ON FITNESS, LIFESPAN, AND FECUNDITY
Techniques are described for estimating selection coefficients (700) for missense mutations (500) and PTVs (504). In certain embodiments, such estimates may be based on forward-time population modeling and/or deep learning to facilitate estimation of individual-level selection burdens (704) and/or to identify individuals with increased (or decreased) genetic risk of reduced fitness (712) (including lifespan (812) and/or fecundity (912) metrics) relative to a threshold (720), such as a statistically mean or median fitness, lifespan, or fecundity based on a subject's demographic data.
G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
G16B 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
G16H 50/30 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for calculating health indicesICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for individual health risk assessment
An example flow cell includes a first substrate; a second substrate attached to the first substrate; a flow channel defined between the first substrate and the second substrate; a first primer set attached to the first substrate, the first primer set including an un-cleavable first primer and a cleavable second primer; a second primer set attached to the second substrate, the second primer set including a cleavable first primer and an un-cleavable second primer; and a removable blocking mechanism passivating i) the first primer set or the second primer set or ii) the cleavable first primer and the cleavable second primer.
Provided herein include various examples of a method for manufacturing aspects of a flow cell. The method may include bonding a die to a first carrier with a first bonding material, encapsulating the die with a molding material, bonding a second carrier to a surface of the molding material with a second bonding material, releasing the first carrier from the die encapsulated with the molding material to expose a surface that includes fanout regions, applying chemistry to the exposed surface of the die such that the given surface of the die becomes an active detection area for the flow cell, and placing a lidding layer over the exposed surface to form a space over the active detection area; the space defines a fluidic channel.
The invention relates to solid supports and methods for use in nucleic acid sequencing, in particular solid supports and methods for use in concurrent sequencing.
The invention provides methods for measuring quantities of mRNA transcripts present in a sample, where sequence information for each molecule is read from what is essentially a random start site within that molecule and in which a short binning index (e.g., about 3 bases) is added to the sequence information. The binning index is useful to resolve any bias arising with the use of the intrinsic sequences to uniquely identify and count the molecules.
In some examples, a method of sequencing a polynucleotide includes hybridizing the polynucleotide to a first oligonucleotide coupled to a particle. The hybridized polynucleotide may be amplified using additional oligonucleotides coupled to the particle, to generate amplicons coupled to the particle. After the amplifying, the particle, having the amplicons coupled thereto, may be disposed within a flowcell. After disposing the particle within the flowcell, the particle may be dissolved, leaving the amplicons within the flowcell. The flowcell may be used to sequence the amplicons.
The present disclosure relates to methods, systems and compositions directed to unspooling a substrate from a source coil and polishing a surface of the substrate, wherein before the polishing, the substrate includes depressions separated by interstices and a coating including a hydrogel disposed on the depressions and the interstices, and the polishing includes applying a slurry to the surface of the substrate and removing the hydrogel from the interstices but not the depressions by contacting the surface of the substrate with one or more polisher and introducing relative movement between the one or more polisher and the surface.
B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glasswareDroppers
G03F 7/00 - Photomechanical, e.g. photolithographic, production of textured or patterned surfaces, e.g. printed surfacesMaterials therefor, e.g. comprising photoresistsApparatus specially adapted therefor
Disclosed herein are flow cells and methods of sequencing using flow cells. In some examples, the flow cells include a first surface that includes a first set of capture primers and a second set of capture primers, and a second surface that includes a first set of capture primers and a second set of capture primers.
This disclosure relates to methods of identifying and mapping methylation sites. In some embodiments, these methods incorporate cytosine deamination and base excision repair. In some embodiments, these methods incorporate use of hairpin adapters. Methods of sequence analysis are also described herein.
Compounds of the disclosure include modified dideoxynucleotide triphosphates (ddNPT) including multiple binding unit containing arms to provide multivalent binding unit molecules.
Examples provided herein are related to detecting a methylated nucleotide using a quencher coupled to the methylated nucleotide. In some examples, a methylated nucleotide in a polynucleotide may be detected using a method that includes coupling a quencher to the methylated nucleotide. The method may include adding fluorescently labeled nucleotides to a primer hybridized to the polynucleotide. The method may include using the quencher to reduce fluorescence from at least one of the added, fluorescently labeled nucleotides. The method may include using the reduced fluorescence caused by the first quencher to detect the methylated nucleotide.
The technology relates in part to methods for determining copy number variations (CNVs) known or suspected to be associated with a variety of medical conditions. In some aspects, the technology relates to determining CNVs of fetuses using maternal samples comprising maternal and fetal cell free DNA. In some aspects, the technology relates to determining CNVs known or suspected to be associated with a variety of medical conditions. In some aspects, methods to improve the sensitivity and/or specificity of sequence data analysis by deriving a fragment size parameter are provided. In some aspects, information from fragments of different sizes is used to evaluate copy number variations. In some aspects, information from fragments of different sizes is used to discriminate between fetal and maternal CNVs. In some aspects, the technology relates to systems and computer program products for evaluation of CNVs of sequences of interest.
In one aspect, the disclosed technology relates to systems and methods for estimating a copy number of repeat units in a target genomic region in a nucleic acid sample from a subject. In some embodiments, a machine learning model is trained to learn the relationship between the known copy numbers of repeat units in predetermined invariant tandem repeat loci and specific features of the predetermined loci and specific features of training genomic regions in the nucleic acid sample from the subject that correspond to the predetermined loci. The copy number of repeat units in the target genomic region can be estimated by applying the trained machine learning model to specific features of a tandem repeat locus corresponding to the target genomic region and specific features of the target genomic region. In another aspect, the disclosed technology relates to computer-readable media including instructions for performing the disclosed methods.
Methods, systems, and apparatus, including computer programs encoded on computer-storage media, for multi-region joint detection. In some implementations, a method for identifying variants using multi-region joint detection in genetic sample sequences includes generating a set of candidate diplotypes mapped to at least two different regions in a reference sequence; generating a set of joint diplotype candidates comprising two or more candidate diplotypes of the set of candidate diplotypes; querying, for diplotypes at one or more locations of the at least two different regions in the reference sequence, a population database comprising genetic sequences of previously sequenced organisms; determining one or more values representing the frequency of specific diplotypes occurring within the genetic sequences of previously sequenced organisms; and generating, using the one or more values, an indication that the variant of the first joint diplotype candidate is an actual variant.
Methods, systems, and apparatus, including computer programs encoded on computer-storage media, for region-ambiguous joint detection. In some implementations, identifying variants using region-ambiguous variant detection in a genetic sample includes generating a plurality of joint diplotype candidates comprising four or more haplotypes of the plurality of haplotypes, determining a posterior probability for each of the plurality of joint diplotype candidates, determining a preferred copy number configuration of the multiple different copy number configurations, wherein the preferred copy number configuration is a copy number configuration that occurs more frequently than any other copy number configuration in the plurality of joint diplotype candidates; determining a region-ambiguous quality score for the plurality of joint diplotype candidates in a given position in a given region, and determining whether a variant exists in at least one of the first or second region of the reference genome based on the determined region-ambiguous quality score.
Described herein are methods, compositions, and kits for removing false positive uracils due to the deamination of unmethylated cytosines in assays using engineered cytosine deaminases to deaminate methylated cytosines. The methods, compositions, and kits utilize a dual enzymatic process. After cytidine deaminase treatment, the DNA is first incubated with Uracil DNA Glycosylase (UDG), which generates abasic sites where dC to dU conversions have occurred. The DNA is then incubated with a high-fidelity polymerase supplemented with a deoxycytidyl transferase, such as Rev1, to repair the lesion with the installation of a cytidine.
This disclosure describes methods, non-transitory computer-readable media, and systems that can (i) identify reads that align with at least some portion of alternative contiguous sequences representing structural variant haplotypes within a structural variant reference genome and (ii) generate a structural-variant-alignment tag within an alignment file for such read alignments to guide identifying candidate structural-variant locations. In addition to employing structural-variant-alignment tags, the disclosed systems identify read fragments that align or overlap with portions of alternate contiguous sequences representing an insertion (or other structural variant) and further masks such insertion-overlapping read fragments as part of an alignment file. When a read aligns completely within an insertion-representing alternate contiguous sequence, the disclosed system can mark the genomic coordinate corresponding to a primary contiguous sequence at which the insertion alternate contiguous sequence is lifted over and generates an unaligned read base indicator indicating that such an insertion-aligned nucleotide read is masked.
An apparatus includes a sample stage region, an optical assembly, and a camera assembly. The optica! assembly includes an objective element, a tube lens, a first dichroic element, and a compensating element. The objective dement provides a field of view including the object plane. The tube lens is configured to receive light transmitted through the objective element. The optical assembly is configured to transmit light in at least a first color channel, a second color channel, a third color channel, and a fourth color channel from the tube lens toward the first dichroic element. The first dichroic element is configured to transmit light of the first and third color channels while reflecting light of the second and fourth color channels. The compensating element is configured to induce an astigmatism in the first and third color channels offsetting an astigmatism induced by the dichroic element.
The present disclosure is concerned with compositions, articles, kits, and methods for producing an array that includes clonal clusters. In one embodiment, methods include producing clonal clusters on an array that preserves methylation status, such as the methylation state of methylated CpG dinucleotides of the seed DNA molecules.
Actuation systems and methods are disclosed. An apparatus includes a housing, a printed circuit board, and a plurality of shape memory alloy actuators. The printed circuit board is coupled to the housing. Each shape memory alloy actuator has a pair of wire mounts, an actuator rod, a shape memory alloy wire, and a latch assembly. The pair of wire mounts are coupled to opposing sides of the printed circuit board and the actuator rod has a wire guide. The shape memory alloy wire is coupled to the wire mounts and positioned around the wire guide. The latch assembly is coupled to the printed circuit board. Applying a voltage to the shape memory alloy wire retracts the shape memory alloy wire and causes the corresponding actuator rod to move between a first position and a second position. The latch assembly is to hold the actuator rods in the second position.
F15B 13/02 - Fluid distribution or supply devices characterised by their adaptation to the control of servomotors
F15B 15/14 - Fluid-actuated devices for displacing a member from one position to anotherGearing associated therewith characterised by the construction of the motor unit of the straight-cylinder type
F15B 15/22 - Other details for accelerating or decelerating the stroke
H05K 7/14 - Mounting supporting structure in casing or on frame or rack
87.
METHODS FOR DOUBLE-STRANDED SEQUENCING BY SYNTHESIS
Nucleotide sequencing methods for sequencing an oligonucleotide strand while the oligonucleotide strand is a part of a double-stranded complex. At least one strand of the double-stranded complex is immobilized on a surface. Sequencing primers may not be immobilized on a surface. Double stranded sequencing methods may employ an enzyme that has nick-translation activity.
Methods, system, and computer programs for reducing a resource metric of a multireference genome. The method includes obtaining a set of augmentations of the multireference genome, performing one or more optimization operations on the set of augmentations to create a candidate augmentation optimization, determining (i) whether the candidate augmentation optimization deviates from a preferred variant tuple set and (ii) whether the candidate augmentation optimization reduces a resource metric of the multireference genome by a threshold amount, and based on a determination (i) that the candidate augmentation optimization does not deviate from the preferred variant tuple set and (ii) that the candidate augmentation optimization reduces a resource metric of the multireference genome by a threshold amount: committing the candidate augmentation optimization to the multireference genome to reduce the resource metric of the multireference genome.
This disclosure describes methods, non-transitory computer readable media, and systems that can utilize one or more machine learning models to predict relationships between human genes and phenotypes. For example, the disclosed systems can generate for human genes in relation to various clinical phenotypes. As a basis for generating such predictions, the disclosed systems can train a gene embedding neural network to determine relationships between genes and phenotypes using a two-stage training process that includes a supervised training stage and an unsupervised fine-tuning stage. In addition, the disclosed systems can utilize the gene embedding neural network to generate gene-to-phenotype scores indicating relationships between genes and phenotypes based on similarities among genes (as represented by gene embeddings). Further, the disclosed systems can utilize a diagnostic variant model to determine whether genomic samples exhibit diagnostic variants based on gene-to-phenotype scores as well as other variant-level features of the genomic samples.
Methods of making barriers including nanopores and crosslinked amphiphilic molecules, and barriers made using the same, are provided herein. In some examples, a method of forming a barrier between first and second fluids includes forming at least one layer comprising a plurality of amphiphilic molecules, wherein the amphiphilic molecules comprise reactive moieties. The method may include using first crosslinking reactions of the reactive moieties to only partially crosslink amphiphilic molecules of the plurality to one another. The method may include, after using the first crosslinking reactions, inserting the nanopore into the at least one layer. The method may include, after inserting the nanopore, using second crosslinking reactions of the reactive moieties to further crosslink amphiphilic molecules of the plurality to one another.
Methods and systems that include training a machine learning model for detecting biological constituents in a sample are provided. A computer-implemented method, and systems executing the method, may include collecting metagenomic data that includes biological constituents obtained from a sample; generating a first molecular data set of covariates; generating a second molecular data set of covariates; generating a training set comprising the first and second covariates as well as combined covariates; and training the machine learning model using aggregate molecular covariates to predict biological constituents from metagenomics data.
Methods and compositions for mapping the effects of gene variants using high throughput sequencing and machine learning to determine the pathogenicity of each variant.
In an example of a method of making a flow cell, a functional material is deposited over a resin layer including depressions separated by interstitial regions. The resin layer includes an ultraviolet (UV) light blocking additive. The depressions overlie a first portion of the resin layer having a first thickness, and the interstitial regions overlie a second portion of the resin layer having a second thickness that is greater than the first thickness. The functional material is susceptible to interaction with the resin layer when exposed to UV light. A predetermined UV light dosage is directed through the resin layer, whereby the functional material within the depressions is exposed to the UV light and attaches to the resin layer within the depressions. The functional material overlying the interstitial regions is blocked from being exposed to the UV light by the second resin portion.
An apparatus and method to compensate for under-corrected aberrations computationally is disclosed. The system includes an excitation radiation source that emits an excitation beam that is focused on a flow cell surface. More specifically, the excitation beam is focused on either an upper surface, a lower surface, or in a channel between the upper and lower surfaces of the flow cell. As imaging both the upper and lower surfaces simultaneously will result in aberration in at least one of the upper and lower surfaces, aberration correction is useful for dual surface imaging. A processor is configured to determine base calls of irradiated sites that fluoresce within the flow cell. An aberration compensation model is trained to compensate for aberrations in at least one image or image data corresponding to the upper surface, the lower surface, or the channel between the upper and lower surfaces.
An apparatus includes a sample stage region, an optical assembly, and a camera assembly. The optica! assembly includes an objective element, a tube lens, and a compensating element. The objective element provides a field of view, at least a portion of the sample stage region is within the field of view. The objective element has a variable astigmatism. The tube lens is configured to receive light transmitted through the objective element and further transmit the light through an image space. The compensating element is in the image space. The compensating element is configured to induce a second astigmatism. The second astigmatism is configured to offset the variable astigmatism. The camera assembly is configured to receive light transmitted from the compensating assembly.
This disclosure describes methods, non-transitory computer readable media, and systems that can utilize a machine learning model to recalibrate genotype calls (e.g., variant calls) of existing sequencing data files. For instance, the disclosed systems the disclosed systems can access one or more existing sequencing data files for a genomic sample, where the files include nucleotide-read data and genotype calls at particular genomic coordinate. From the one or more existing sequencing data files, the disclosed system extracts sequencing metrics for nucleotide reads or a particular genotype call at a particular genomic coordinate. By processing the extracted sequencing metrics, the systems further utilize a call-recalibration-machine-learning model to generate variant-call classifications indicating an accuracy of the particular genotype call. In some cases, the systems update or recalibrate the genotype call or quality-measuring sequencing metrics for the genotype call based on the variant-call classifications.
Provided herein are methods for modification-based controlled polynucleotide translocation in nanopores for sequencing, modified nucleotides, and kits and systems for performing the disclosed methods. In some embodiments, modifications can be used to control polynucleotide translocation by modifying nucleotides on a strand of polynucleotide to carry a modification, where the modifications can arrest or slow translocation when encountering the nanopore. In some embodiments, application of a voltage can move one nucleotide and its attached modification through the nanopore at a time.
In some examples, a structure is contacted with polynucleotides having a variety of lengths and each including first and second adapters. The structure includes a substrate including first and second regions spaced apart from one another by a gap of at least 100 nm, a first set of capture primers coupled to the first region of the substrate, and a second set of capture primers coupled to the second region of the substrate. The first adapter of the polynucleotide is hybridized to a capture primer of the first set of capture primers. Based on that polynucleotide being sufficiently long to bridge the gap, it is amplified using the first and second sets of capture primers. Based upon that polynucleotide being insufficiently long to bridge the gap, it is not amplified. Optionally, a wall may be disposed in the gap.
In some examples, a method includes disposing a first hydrogel within a first recess of a substrate and over a pillar. The substrate may include a second recess in which the pillar is disposed, and a wall separating the first recess from the second recess. While the first hydrogel is disposed within the first recess, the pillar may be removed. After removing the pillar, a second hydrogel may be disposed within the second recess. Also provided herein are nonlimiting examples of manners in which recesses, walls, and patterned hydrogels may be formed.
G03F 7/00 - Photomechanical, e.g. photolithographic, production of textured or patterned surfaces, e.g. printed surfacesMaterials therefor, e.g. comprising photoresistsApparatus specially adapted therefor
Encoded aptamer candidate libraries with nucleotide modification are described. The aptamer candidates include a first conserved primer region and a second conserved primer region. aptamer candidates also include a variable region disposed between the first conserved primer region and the second conserved primer region and that includes at least one modified nucleotide. A code region includes a nucleotide sequence that is unique for a modification type of the at least one modified nucleotide such that a sequence of each aptamer candidate can be used to identify the associated modification type.
patents
