A method comprising effecting a change in a shape of a droplet, wherein the droplet is disposed over a substrate in sensing proximity to a sensor and the droplet has a starting surface area exposed to the sensor; and producing an expanded surface area of the droplet in the sensing proximity exposed to the sensor, wherein the expanded surface area exposed to the sensor is greater than the starting surface area exposed to the sensor.
This disclosure describes systems, non-transitory computer readable media, and methods for implementation of SV calling pipelines that can generate high-confidence diploid assemblies and SV call sets based on trio read data. For instance, a system is provided for implementing an SV calling pipeline via a bioinformatics subsystem executed on one or more processors that can receive a trio dataset of diploid read data of sequenced child (CH) and parental (M, P) genomes, and generate, based on consensus regions of the trio read data, a validated diploid assembly of the CH genome. Validation can be determined based on composition vectors of corresponding child and transmitting parent sequences at a given interval for each consensus region. The bioinformatics subsystem can then detect structural variants (SV) within the CH diploid assembly and output a VCF file of detected SVs as an SV truthset.
Presented herein are methods and compositions for tagmentation of nucleic acids. The methods are useful for generating tagged DNA fragments that are qualitatively and quantitatively representative of the target nucleic acids in the sample from which they are generated.
Methods and systems for analysis of image data generated from various reference points. Particularly, the methods and systems provided are useful for real time analysis of image and sequence data generated during DNA sequencing methodologies.
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
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).
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.
Methods and systems for analysis of image data generated from various reference points. Particularly, the methods and systems provided are useful for real time analysis of image and sequence data generated during DNA sequencing methodologies.
Presented are methods and compositions for preparing samples for amplification and sequencing. Particular embodiments relate to methods of preparing nucleic acid-containing cellular samples for library amplification, wherein the methods include lysing cells of the sample to form a lysate, amplifying the nucleic acids from the lysed samples, exposing the amplified nucleic acids to a solid surface, and clonallyr amplifying the amplified nucleic acids to generate clusters.
Light detection devices and related methods are provided. The devices may comprise a reaction structure for containing a reaction solution with a relatively high or low pH and a plurality of reaction sites that generate light emissions. The devices may comprise a device base comprising a plurality of light sensors, device circuitry coupled to the light sensors, and a plurality of light guides that block excitation light but permit the light emissions to pass to a light sensor. The device base may also include a shield layer extending about each light guide between each light guide and the device circuitry, and a protection layer that is chemically inert with respect to the reaction solution extending about each light guide between each light guide and the shield layer. The protection layer prevents reaction solution that passes through the reaction structure and the light guide from interacting with the device circuitry.
G01N 33/58 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing involving labelled substances
G02B 6/42 - Coupling light guides with opto-electronic elements
H10F 39/00 - Integrated devices, or assemblies of multiple devices, comprising at least one element covered by group , e.g. radiation detectors comprising photodiode arrays
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.
An apparatus includes an illumination assembly. The illumination assembly includes a plurality of light sources arranged in a two-dimensional array. The light sources are positioned within the array to provide overlapping illumination fields. The plurality of light sources provide illumination within a UV-A spectrum of wavelengths to thereby provide photocleaving within a fluid containment assembly.
B01J 19/12 - Processes employing the direct application of electric or wave energy, or particle radiationApparatus therefor employing electromagnetic waves
B01J 19/00 - Chemical, physical or physico-chemical processes in generalTheir relevant apparatus
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
15.
4,5-SUBSTITUTED NAPHTHALIMIDE DYES AND USES IN NUCLEIC ACID SEQUENCING
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.
Polynucleotide sequencing using ionophores is provided herein. In some examples, a sequencing method includes inhibiting current flow across a barrier; contacting a polymerase with a first polynucleotide, a second polynucleotide, and a fluid comprising a first nucleotide coupled to a first ionophore; while the polymerase adds the first nucleotide to the second polynucleotide based on a sequence of the first polynucleotide, providing a first current flow across the barrier using the first ionophore; and identifying the first nucleotide using an electrical characteristic of the first ionophore.
G01N 27/12 - Investigating or analysing materials by the use of electric, electrochemical, or magnetic means by investigating impedance by investigating resistance of a solid body in dependence upon absorption of a fluidInvestigating or analysing materials by the use of electric, electrochemical, or magnetic means by investigating impedance by investigating resistance of a solid body in dependence upon reaction with a fluid
18.
METHODS FOR APPENDING ADAPTORS ONTO POLYNUCLEOTIDES
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.
A method comprises: directing, using an objective and a first reflective surface, first autofocus light toward a sensor, the first autofocus light reflected from a first surface of a substrate; preventing second autofocus light from reaching the sensor, the second autofocus light reflected from a second surface of the substrate; and directing, using the objective and a second reflective surface, emission light toward the sensor, the emission light originating from a sample at the substrate.
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.
An example of a biotin-streptavidin cleavage composition includes a formamide reagent and a salt buffer. The formamide reagent is present in the biotin-streptavidin cleavage composition in an amount ranging from about 10% to about 50%, based on a total volume of the biotin-streptavidin cleavage composition. The salt buffer makes up the balance of the biotin-streptavidin cleavage composition. In some examples, the biotin-streptavidin cleavage composition is used to cleave library fragments from a solid support. In other examples, other mechanisms are used to cleave library fragments from a solid support.
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.
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.
An imprinting apparatus includes a silicon master having a plurality of nanofeatures defined therein. An anti-stick layer coats the silicon master, the anti-stick layer including a molecule having a cyclosiloxane with at least one silane functional group. A method includes forming a master template by: depositing a formulation on a silicon master including a plurality of nanofeatures defined therein, the formulation including a solvent and a molecule having a cyclosiloxane with at least one silane functional group; and curing the formulation, thereby forming an anti-stick layer on the silicon master, the anti-stick layer including the molecule. The method further includes depositing a silicon-based working stamp material on the anti-stick layer of the master template; curing the silicon-based working stamp material to form a working stamp including a negative replica of the plurality of nanofeatures; and releasing the working stamp from the master template.
B81C 1/00 - Manufacture or treatment of devices or systems in or on a substrate
C09D 4/00 - Coating compositions, e.g. paints, varnishes or lacquers, based on organic non-macromolecular compounds having at least one polymerisable carbon-to-carbon unsaturated bond
C09D 133/26 - Homopolymers or copolymers of acrylamide or methacrylamide
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
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.
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 21/02 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with ribosyl as saccharide radical
C07H 21/04 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical
C12Q 1/6853 - Nucleic acid amplification reactions using modified primers or templates
30.
KITS AND METHODS FOR BIOLOGICAL SEQUENCING OPERATIONS
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.
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.
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.
The invention provides compositions and methods for determining the fraction of fetal nucleic acids in a maternal sample comprising a mixture of fetal and maternal nucleic acids. The fraction of fetal nucleic acids can be used in determining the presence or absence of fetal aneuploidy.
C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
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
G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
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
36.
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.
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.
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.
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.
A method for reducing sequencing by synthesis cycle time using a microfluidic device is provided. The microfluidic device comprises a flow cell having an inlet port, an outlet port, and a flow channel extending between the inlet port and the outlet port, wherein the flow channel receives an analyte of interest and one or more reagents for analyzing and detecting molecules. To aid in the acceleration of the reactions, the microfluidic device comprises a mixing device to increase the rates of diffusion of the reagents from the fluid bulk to an active surface of the flow cell. The mixing device comprises at least one of an electrothermal mixing device, an active mechanical mixing device, and a vibrational mixing device.
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
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.
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.
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
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.
The disclosure provides compositions, methods, and kits that facilitate the characterization of omic variation in tissues while preserving spatial information related to the origin of target analytes in the tissue.
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
The present application discloses a novel DNA origami structure and a nanopore construct associated with the DNA origami structure. The DNA origami structure includes a first hydrophilic section at a first end of the DNA origami structure, a stopper section adjacent the first hydrophilic section, a second hydrophilic section at a second end of the DNA origami structure, a hydrophobic section between the stopper section and the second hydrophilic section, and an open cavity running through the DNA origami structure from the first end to the second end. The stopper section is configured to lay against the membrane when the DNA origami structure is inserted through the membrane.
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.
The technology disclosed relates to determining tag signals from measured intensities for purposes of base calling in next-generation sequencing. In particular, the measured intensities are collected by light sensors in a sensor array directed to a sample surface including pixel areas and holding a plurality of clusters during a sequence of sampling events. Each light sensor is directed to and measuring intensity from one of the pixel areas during each sampling event. The method includes adjusting the measured intensities from a pixel in the pixel areas for background intensity based on variations in background levels of the light sensors in the sensor array and determining an intensity of a tag signal originating from the pixel based on the adjusted measured intensities of the pixel.
G06V 10/50 - Extraction of image or video features by performing operations within image blocksExtraction of image or video features by using histograms, e.g. histogram of oriented gradients [HoG]Extraction of image or video features by summing image-intensity valuesProjection analysis
66.
APPARATUS AND METHOD FOR REMOVING CAP WITH SWAB FROM CONTAINER
An apparatus includes a vial engagement assembly, a cap engagement assembly, and a processor. The processor activates relative movement along a first dimension between the cap engagement assembly and a vial positioned in a stage of the vial engagement assembly to engage a cap engagement head with a cap secured to the vial. A rotary shaft is rotated about a first rotation axis to remove the cap from the vial via the cap engagement head. The processor then activates relative movement along a second dimension between the cap engagement assembly and the vial to provide deformation of a swab head of a swab shaft extending from the cap. The swab head deforms against an inner sidewall of the vial. The rotary shaft further rotates to rotate the cap, swab shaft, and swab head via the cap engagement head while the swab head deforms against the inner sidewall of the vial.
Embodiments herein relate to combinations for use in light energy excitation. Light energy, according to one example, can be directed toward a detector surface that can support biological or chemical samples.
An example of a flow cell includes a substrate, a plurality of chambers defined on or in the substrate, and a plurality of depressions defined in the substrate and within a perimeter of each of the plurality of chambers. The depressions are separated by interstitial regions. Primers are attached within each of the plurality of depressions, and a capture site is located within each of the plurality of chambers.
B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glasswareDroppers
B01J 19/00 - Chemical, physical or physico-chemical processes in generalTheir relevant apparatus
C08L 37/00 - Compositions of homopolymers or copolymers of compounds having one or more unsaturated aliphatic radicals, each having only one carbon-to-carbon double bond, and at least one being terminated by a heterocyclic ring containing oxygenCompositions of derivatives of such polymers
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
C40B 40/08 - Libraries containing RNA or DNA which encodes proteins, e.g. gene libraries
C40B 50/18 - Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creationParticular methods of cleavage from the solid support using a particular method of attachment to the solid support
Presented are methods and compositions for obtaining sequence information from one or more individual cells. The methods are useful for obtaining sequence information for a single nucleotide sequence, and for multiplex generation of sequence information from one or more individual cells.
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
71.
ARTIFICIAL INTELLIGENCE-BASED MANY-TO-MANY BASE CALLING
The technology disclosed relates to artificial intelligence-based base calling. The technology disclosed relates to accessing a progression of per-cycle analyte channel sets generated for sequencing cycles of a sequencing run, processing, through a neural network-based base caller (NNBC), windows of per-cycle analyte channel sets in the progression for the windows of sequencing cycles of the sequencing run such that the NNBC processes a subject window of per-cycle analyte channel sets in the progression for the subject window of sequencing cycles of the sequencing run and generates provisional base call predictions for three or more sequencing cycles in the subject window of sequencing cycles, from multiple windows in which a particular sequencing cycle appeared at different positions, using the NNBC to generate provisional base call predictions for the particular sequencing cycle, and determining a base call for the particular sequencing cycle based on the plurality of base call predictions.
Substrates comprising a functionalizable layer, a polymer layer comprising a plurality of micro-scale or nano-scale patterns, or combinations thereof, and a backing layer and the preparation thereof by using room temperature UV nano-embossing processes are disclosed. The substrates can be prepared by a roll-to-roll continuous process. The substrates can be used as flow cells, nanofluidic or microfluidic devices for biological molecules analysis.
B32B 3/26 - Layered products comprising a layer with external or internal discontinuities or unevennesses, or a layer of non-planar shapeLayered products comprising a layer having particular features of form characterised by a particular shape of the outline of the cross-section of a continuous layerLayered products comprising a layer with external or internal discontinuities or unevennesses, or a layer of non-planar shapeLayered products comprising a layer having particular features of form characterised by a layer with cavities or internal voids
B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glasswareDroppers
B29C 59/00 - Surface shaping, e.g. embossingApparatus therefor
B29C 59/02 - Surface shaping, e.g. embossingApparatus therefor by mechanical means, e.g. pressing
B29K 77/00 - Use of polyamides, e.g. polyesteramides, as moulding material
B29K 105/00 - Condition, form or state of moulded material
B32B 3/30 - Layered products comprising a layer with external or internal discontinuities or unevennesses, or a layer of non-planar shapeLayered products comprising a layer having particular features of form characterised by a particular shape of the outline of the cross-section of a continuous layerLayered products comprising a layer with external or internal discontinuities or unevennesses, or a layer of non-planar shapeLayered products comprising a layer having particular features of form characterised by a layer with cavities or internal voids characterised by a layer formed with recesses or projections, e.g. grooved, ribbed
C08G 69/00 - Macromolecular compounds obtained by reactions forming a carboxylic amide link in the main chain of the macromolecule
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
Provided herein include various examples of an apparatus, a sensor system and examples of a method for manufacturing aspects of an apparatus, a sensor system. The apparatus may include a die. The apparatus may also include a substrate comprising a cavity. The die may be oriented in a portion of the cavity in the substrate, where the orientation defines a first space in the cavity adjacent to a first edge of the upper surface of the die and a second space in the cavity adjacent to the second edge of the upper surface of the die. The apparatus may further include fluidics fan-out regions comprising a first cured material deposited in the first space and the second space, a surface of the fluidics fan-out regions being contiguous with the upper surface of the die.
H01L 23/053 - ContainersSeals characterised by the shape the container being a hollow construction and having an insulating base as a mounting for the semiconductor body
B81B 1/00 - Devices without movable or flexible elements, e.g. microcapillary devices
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.
The invention relates to methods and kits for use in nucleic acid sequencing, in particular methods for use in concurrent sequencing, including concurrent sequencing of tandem insert libraries. Further, the invention relates to methods of detecting mismatched base pairs in nucleic acid sequences. In another embodiment, the disclosed technology relates to using next generation sequencing to determine the nucleotide sequences of two or more polynucleotide sequence portions in a single sequencing run.
Provided herein are compositions that include nucleic acid fragments produced from double-stranded template nucleic acids, such as cell free DNA. The compositions can be used as positive or negative controls for quality of library preparation methods, calibration of an instrument such as a sequencing instrument, and/or a validation for a nucleic acid sequencing test. Also provided are methods for making the nucleic acid fragments.
An example primer set includes first and second nuclease resistant primers. The first nuclease resistant primer includes a first sequence; a first cleavage site attached at a 3′ end of the first sequence; and a first nuclease resistant modification incorporated between the first sequence and the first cleavage site. The second nuclease resistant primer includes a second sequence that is different from the first sequence; a second nuclease resistant modification incorporated at a 3′ end of the second sequence; and a second cleavage site attached between the second sequence and the second nuclease resistant modification. The second cleavage site is different from the first cleavage site.
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.
Provided in one example is a method of manufacturing a flowcell that includes: forming a core layer, the core layer disposed between a substrate and a nanowell layer, the nanowell layer having nanowells to receive a sample, the core layer having a higher refractive index than the substrate and the nanowell layer; and forming a grating to couple light to the core layer.
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
B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glasswareDroppers
Systems and methods for conducting designated reactions utilizing a base instrument and a removable cartridge. The removable cartridge includes a fluidic network that receives and fluidically directs a biological sample to conduct the designated reactions. The removable cartridge also includes a flow-control valve that is operably coupled to the fluidic network and is movable relative to the fluidic network to control flow of the biological sample therethrough. The removable cartridge is configured to separably engage a base instrument. The base instrument includes a valve actuator that engages the flow-control valve of the removable cartridge. A detection assembly held by at least one of the removable cartridge or the base instrument may be used to detect the designated reactions.
The invention provides a method of karyotyping (for example for the detection of trisomy) a target cell to detect chromosomal imbalance therein, the method comprising: (a) interrogating closely adjacent biallelic SNPs across the chromosome of the target cell (b) comparing the result at (a) with the SNP haplotype of paternal and maternal chromosomes to assemble a notional haplotype of target cell chromosomes of paternal origin and of maternal origin (c) assessing the notional SNP haplotype of target cell chromosomes of paternal origin and of maternal origin to detect aneuploidy of the chromosome in the target cell. Also provided are related computer-implemented embodiments and systems.
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.
Versions of a sequencing system may be monitored to enable changing of a version of a server subsystem operating the sequencing system to service requests from client subsystems for performing analysis of sequencing data. A monitor subsystem may be utilized for receiving and authorizing requests from client subsystems. The monitor subsystem may identify a version associated with a server subsystem operating the sequencing system to be implemented for servicing the request. The monitor subsystem may allow the server subsystem to be accessed for servicing the request from the client subsystem when the version associated with the client subsystem is compatible with the version associated with the server subsystem. The monitor subsystem may prevent the server subsystem from being accessed when the version associated with the client subsystem is incompatible with the version associated with the server subsystem.
H04L 67/00 - Network arrangements or protocols for supporting network services or applications
G06F 8/71 - Version control Configuration management
H04L 41/082 - Configuration setting characterised by the conditions triggering a change of settings the condition being updates or upgrades of network functionality
87.
COMPOSITIONS AND METHODS FOR NUCLEIC ACID SEQUENCING
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
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.
A flow cell assembly is provided that includes a support layer of low-background material, a film of anodized metal oxide (AMO) material adhered to the support layer, and a substrate formed, in part, by one or more patterns imparted in the AMO material. A flow cell assembly herein may include a support layer of low-background material, a film of AMO material adhered to the support layer, and a substrate surface comprising one or more patterns imparted in the AMO material. Each pattern may comprise an array of nanowell features surrounded by interstitial regions of featureless AMO film.
A system, a method and a non-transitory computer readable storage medium for base calling are described. The base calling method includes processing through a neural network first image data comprising images of clusters and their surrounding background captured by a sequencing system for one or more sequencing cycles of a sequencing run. The base calling method further includes producing a base call for one or more of the clusters of the one or more sequencing cycles of the sequencing run.
G06F 18/23211 - Non-hierarchical techniques using statistics or function optimisation, e.g. modelling of probability density functions with adaptive number of clusters
G06F 18/2415 - Classification techniques relating to the classification model, e.g. parametric or non-parametric approaches based on parametric or probabilistic models, e.g. based on likelihood ratio or false acceptance rate versus a false rejection rate
G06N 3/084 - Backpropagation, e.g. using gradient descent
G06N 5/046 - Forward inferencingProduction systems
G06N 7/01 - Probabilistic graphical models, e.g. probabilistic networks
G06V 10/26 - Segmentation of patterns in the image fieldCutting or merging of image elements to establish the pattern region, e.g. clustering-based techniquesDetection of occlusion
G06V 10/44 - Local feature extraction by analysis of parts of the pattern, e.g. by detecting edges, contours, loops, corners, strokes or intersectionsConnectivity analysis, e.g. of connected components
G06V 10/75 - Organisation of the matching processes, e.g. simultaneous or sequential comparisons of image or video featuresCoarse-fine approaches, e.g. multi-scale approachesImage or video pattern matchingProximity measures in feature spaces using context analysisSelection of dictionaries
G06V 10/762 - Arrangements for image or video recognition or understanding using pattern recognition or machine learning using clustering, e.g. of similar faces in social networks
G06V 10/764 - Arrangements for image or video recognition or understanding using pattern recognition or machine learning using classification, e.g. of video objects
G06V 10/77 - Processing image or video features in feature spacesArrangements for image or video recognition or understanding using pattern recognition or machine learning using data integration or data reduction, e.g. principal component analysis [PCA] or independent component analysis [ICA] or self-organising maps [SOM]Blind source separation
G06V 10/778 - Active pattern-learning, e.g. online learning of image or video features
G06V 10/82 - Arrangements for image or video recognition or understanding using pattern recognition or machine learning using neural networks
G06V 10/98 - Detection or correction of errors, e.g. by rescanning the pattern or by human interventionEvaluation of the quality of the acquired patterns
G06V 20/40 - ScenesScene-specific elements in video content
G06V 20/69 - Microscopic objects, e.g. biological cells or cellular parts
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
94.
SYSTEMS AND METHODS FOR DETERMINING MICROSATELLITE INSTABILITY
Presented herein are techniques for determining microsatellite instability. The techniques include generating a reference sample dataset representative of or mimicing a hypothetical matched sample for an individual sample of interest. The reference sample dataset may be generated from a set of reference normal samples that are not matched to the sample of interest. For samples of interest lacking a matched sample, the reference sample dataset may be used to determine microsatellite instability and to provide an indication of a presence, absence, or degree of microsatellite instability of the sample of interest. The reference sample dataset may be generated such that individual microsatelliate regions associated with a high degree of variability between ethnic groups are filtered out, masked, or otherwise not considered.
G16H 10/60 - ICT specially adapted for the handling or processing of patient-related medical or healthcare data for patient-specific data, e.g. for electronic patient records
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
G01N 33/50 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing
G06F 9/30 - Arrangements for executing machine instructions, e.g. instruction decode
G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
A computer-implemented method of performing an optimized burden test for a particular gene, in which an optimal combination (862) of a maximum allele count and a minimum pathogenicity score threshold that maximize significance of burden testing for rare deleterious variants are determined using a grid search (822) protocol. Each combination of maximum allele count and minimum pathogenicity score threshold is tested with a t-test (824) to obtain effect size and p-value (842). The combination of allele count and pathogenicity score threshold with the most significant p-value (842) is selected as the optimal parameters for the rare deleterious variant burden test for a particular gene.
A closure for an apparatus comprises: a plurality of light sources; a lightguide to distribute light from the plurality of light sources, the lightguide having a first primary surface opposite a second primary surface, wherein the first primary surface has a first surface treatment, and wherein light emitted from the lightguide indicates a status of the apparatus; and a frame supporting the plurality of light sources and the lightguide for selective movement of the closure vertically or horizontally relative to the apparatus.
Presented herein are altered polymerase enzymes for improved incorporation of nucleotides and nucleotide analogues, in particular altered polymerases that maintain high fidelity under reduced incorporation times, as well as methods and kits using the same.
Presented herein are methods and compositions for targeted amplification of DNA and sample identification. The methods are particularly useful in validation and quality control of samples and to confirm that WGS sequence data is properly paired with a patient sample prior to delivering sequence data to a physician or to a patient.
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.
