Aspects of this disclosure related to methods, articles, kits, and/or systems for the preparation and/or study of one or more target molecules in a sample. In some embodiments, a target molecule is a peptide, a protein, or a fragment or derivative thereof. Through the use of methods, articles, kits, and/or systems of the instant disclosure, target molecules may, in some embodiment, be more readily sequenced or prepared for sequencing.
Methods and devices for ultrasensitive detection of target molecules (e.g., target nucleic acids or target proteins) from a biological sample are provided herein. In some embodiments, methods and devices enable ultrasensitive determination of the concentration of target molecules.
C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
G01N 27/414 - Ion-sensitive or chemical field-effect transistors, i.e. ISFETS or CHEMFETS
H01L 27/085 - Devices consisting of a plurality of semiconductor or other solid-state components formed in or on a common substrate including integrated passive circuit elements with at least one potential-jump barrier or surface barrier the substrate being a semiconductor body including only semiconductor components of a single kind including field-effect components only
3.
MOLECULAR BARCODE ANALYSIS BY SINGLE-MOLECULE KINETICS
Aspects of the disclosure provide methods of determining molecular barcode content based on binding interactions between a barcode recognition molecule and a molecular barcode. In some aspects, the disclosure relates to methods comprising contacting a molecular barcode with a barcode recognition molecule that binds to one or more sites on the molecular barcode, detecting a series of signal pulses, and determining the barcode content based on a barcode-specific pattern in the series of signal pulses.
C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
C12Q 1/6876 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
G06K 19/06 - Record carriers for use with machines and with at least a part designed to carry digital markings characterised by the kind of the digital marking, e.g. shape, nature, code
Aspects of the disclosure relate to methods and systems for regenerating a sensor chip surface, including techniques for reuse of a single sensor chip in multiple sampling cycles by regenerating a surface of the sensor chip between successive sampling cycles. A method is provided for reusing an integrated device to process a sample, the sample being divided into a plurality of aliquots, the method comprising: loading a first aliquot of the plurality of aliquots into at least some of a plurality of chambers of the integrated device; sampling analytes of the first aliquot while the analytes are present in the at least some of the plurality of chambers; removing the first aliquot from the at least some of the plurality of chambers of the integrated device; and loading a second aliquot of the plurality of aliquots into the at least some of the plurality of chambers of the integrated device.
The present disclosure provides techniques for improving the rate and efficiency of charge transfer within an integrated circuit configured to receive incident photons. Some aspects of the present disclosure relate to integrated circuits that are configured to induce one or more intrinsic electric fields that increase the rate and efficiency of charge transfer within the integrated circuits. Some aspects of the present disclosure relate to integrated circuits configured to induce a charge carrier depletion in the photodetection region(s) of the integrated circuits. In some embodiments, the charge carrier depletion in the photodetection region(s) may be intrinsic, in that the depletion is induced even in the absence of external electric fields applied to the integrated circuit. Some aspects of the present disclosure relate to processes for operating and/or manufacturing integrated devices as described herein.
G01N 21/00 - Investigating or analysing materials by the use of optical means, i.e. using sub-millimetre waves, infrared, visible or ultraviolet light
G01N 21/77 - Systems in which material is subjected to a chemical reaction, the progress or the result of the reaction being investigated by observing the effect on a chemical indicator
Aspects of the present disclosure relate to techniques for calibrating an integrated device. According to some embodiments, there is provided a method for calibrating an integrated device, the method comprising: exciting, with light from at least one excitation source, a reference dye molecule; obtaining a signal emitted by the reference dye molecule, the signal containing information representative of at least one characteristic of the reference dye molecule; and adjusting one or more subsequent measurements obtained from a sample based on the information obtained from the signal emitted by the reference dye molecule.
G01N 21/63 - Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light optically excited
Aspects of the present disclosure relate to techniques for calibrating a system comprising integrated device. According to some embodiments, there is provided a method for calibrating a system comprising an integrated device, the method comprising: exciting, with light from at least one excitation source, a reference dye molecule disposed in a chamber of the integrated device; obtaining a signal emitted by the reference dye molecule, the signal containing information representative of a bleaching time of the reference dye molecule; and adjusting one or more characteristics of the system based on the bleaching time of the reference dye molecule.
Aspects of the present disclosure relate to methods and systems for increasing the number of samples that can be processed in parallel by an integrated device. An integrated device is provided having at least two reaction chambers disposed above an active photodetection area of a single pixel, such that the pixel is sensitive to photons from each of the at least two reaction chambers. In some embodiments, an integrated device may have at least four or more reaction chambers per photodetector. Signals from multiple reaction chambers may be distinguished using any combination of multiplexing techniques including techniques for waveguide multiplexing, intensity multiplexing, and/or lifetime multiplexing. According to further aspects of the technology described herein, there is provided techniques for increasing the amount of sample that can be processed by a single device by reloading an integrated device repeated times to process an increased number of samples by a single device.
G01N 21/63 - Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light optically excited
G01N 21/62 - Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light
Described herein are techniques that improve the collection and readout of charge carriers in an integrated circuit. Some aspects of the present disclosure relate to integrated circuits having pixels with a plurality of charge storage regions. Some aspects of the present disclosure relate to integrated circuits configured to substantially simultaneously collect and read out charge carriers, at least in part. Some aspects of the present disclosure relate to integrated circuits having a plurality of pixels configured to transfer charge carriers between charge storage regions within each pixel substantially at the same time. Some aspects of the present disclosure relate to integrated circuits having three or more sequentially coupled charge storage regions. Some aspects of the present disclosure relate to integrated circuits capable of increased charge transfer rates. Some aspects of the present disclosure relate to techniques for manufacturing and operating integrated circuits according to the other techniques described herein.
G01N 21/27 - Colour; Spectral properties, i.e. comparison of effect of material on the light at two or more different wavelengths or wavelength bands using photo-electric detection
G01N 21/31 - Investigating relative effect of material at wavelengths characteristic of specific elements or molecules, e.g. atomic absorption spectrometry
G01N 21/62 - Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light
G01N 21/63 - Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light optically excited
Provided herein are methods and integrated devices for improved sequencing of nucleic acid and peptide biomolecules. The present disclosure relates to improved mechanisms for protecting a luminescent label from photo-induced damage through the use of quenching moieties. Further provided herein are methods for improved immobilization of quenching moieties and other molecules of interest through functionalization with chemical moieties, such as click chemistry handles, capable of participating in cross-linking reactions. Quenching moieties may be immobilized to the surface of a sample well in a sequencing substrate or apparatus in a manner that minimizes or eliminates photobleaching of the labeled molecule. The disclosed methods provide for minimized photodamage, increased sensitivity, accuracy and length of reads during nucleic acid and polypeptide sequencing.
Aspects of the application provide methods of identifying and sequencing proteins, polypeptides, and amino acids, and compositions useful for the same. In some aspects, the application provides amino acid recognition molecules, such as amino acid binding proteins and fusion polypeptides thereof. In some aspects, the application provides amino acid recognition molecules comprising a shielding element that enhances photo stability in polypeptide sequencing reactions.
Methods and devices for preparing target molecules (e.g., target nucleic acids or target proteins) from a biological sample are provided herein. In some embodiments, methods and devices involve sample lysis, sample fragmentation, enrichment of target molecule(s), and/or functionalization of target molecule(s).
The present disclosure relates to compounds and methods for selective C-terminal functionalization of peptides. In certain embodiments, the compounds have improved water-solubility, and are suitable for use in connection with peptide sequencing methodologies.
Systems and methods are described for producing an amplitude-modulated laser pulse train. The laser pulse train can be used to cause fluorescence in materials at which the pulse trains are directed. The parameters of the laser pulse train are selected to increase fluorescence relative to a constant-amplitude laser pulse train. The amplitude-modulated laser pulse trains produced using the teachings of this invention can be used to enable detection of specific molecules in applications such as gene or protein sequencing.
H01S 3/00 - Lasers, i.e. devices using stimulated emission of electromagnetic radiation in the infrared, visible or ultraviolet wave range
H01S 3/081 - Construction or shape of optical resonators or components thereof comprising three or more reflectors
H01S 3/102 - Controlling the intensity, frequency, phase, polarisation or direction of the emitted radiation, e.g. switching, gating, modulating or demodulating by controlling the active medium, e.g. by controlling the processes or apparatus for excitation
H01S 3/11 - Mode locking; Q-switching; Other giant-pulse techniques, e.g. cavity dumping
Disclosed herein are aspects of a pulsed laser light source (106) for producing excitation light (104) in an integrated bioanalytical system (101). The light source (106) comprises one or more laser diodes (102) that produces pulsed light signals (104) synchronized with a common clock source (130) for excitation of samples within reaction chambers (108) on at least one chip (101). The light source (106) may be used to provide excitation for a system with a large sensor array with reduced cost, size and electrical power requirements.
Some aspects relate to integrated devices for obtaining timing and/or spectral information from incident light. In some embodiments, a pixel may include one or more charge storage regions configured to receive charge carriers generated responsive to incident photons from a light source, with charge carriers stored in the charge storage region(s) indicative of spectral and timing information. In some embodiments, a pixel may include regions having different depths, each configured to generate charge carriers responsive to incident photons. In some embodiments, a pixel may include multiple charge storage regions having different depths, and one or more of the charge storage regions may be configured to receive the incident photons and generate charge carriers therein. In some embodiments, a pixel may include an optical sorting element configured to direct at least some incident photons to one charge storage region and other incident photons to another charge storage region.
Systems and methods for optical power distribution within an integrated device, in a substantially uniform manner, to a large number of sample wells and/or other photonic elements. The integrated device and related instruments and systems may be used to analyze samples in parallel. The integrated device may include a grating coupler configured to receive light from an excitation source and optically couple with multiple waveguides (2-104) configured to couple with sample wells (2-102). Vertical extents of optical modes of individual waveguides may be modulated to adjust confinement of light within the waveguides (2-104). This modulation may enable more uniform distribution of excitation light to the sample wells (2-102), improve excitation efficiency, and prevent overpower on regions of the integrated device.
Aspects of the technology described herein relate to improved semiconductor-based image sensor designs. In some embodiments, an integrated circuit may comprise a photodetection region and a drain region electrically coupled to the photodetection region, and the photodetection region may be configured to induce an intrinsic electric field in a direction from the photodetection region to the drain region(s). In some embodiments, a charge storage region and the drain region may be positioned on a same side of the photodetection region. In some embodiments, at least one drain layer may be configured to receive incident photons and/or charge carriers via the photodetection region. In some embodiments, an integrated circuit may comprise a plurality of pixels and a control circuit configured to control a transfer of charge carriers in the plurality of pixels.
H01L 31/08 - SEMICONDUCTOR DEVICES NOT COVERED BY CLASS - Details thereof in which radiation controls flow of current through the device, e.g. photoresistors
C12M 1/34 - Measuring or testing with condition measuring or sensing means, e.g. colony counters
Methods of single-polypeptide sequencing. The methods comprise providing an enriched sample comprising a population of polypeptides; splitting the enriched sample into two or more subsamples; contacting each of at least two of the subsamples with a different modifying agent, wherein the modifying agent comprises a cleaving agent, e.g. an exopeptidase, thereby generating polypeptide fragments having a combination of cleavage patterns; and sequencing, in parallel, the polypeptide fragments, thereby determining the amino acid sequences of the polypeptide fragments. The fragments may be aligned in order to reconstruct the polypeptide sequence. Also provided herein is a kit comprising a plurality of enrichment molecules, e.g. antibodies, aptamers or enzymes and a sample preparation device comprising barcodes and capture probes.
C12Q 1/00 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
C40B 50/00 - Methods of creating libraries, e.g. combinatorial synthesis
C40B 70/00 - Tags or labels specially adapted for combinatorial chemistry or libraries, e.g. fluorescent tags or barcodes
Some embodiments relate to an integrated circuit, comprising: a pixel, comprising: a photodetection region; and a drain configured to discard charge carriers from within a semiconductor region of the pixel outside of the photodetection region. Some embodiments relate to an integrated circuit, comprising: a pixel, comprising: a photodetection region; and a drain configured to discard charge carriers from the photodetection region, wherein the drain comprises a semiconductor region and the semiconductor region is contacted by a metal contact. Some embodiments relate to an integrated circuit, comprising: a pixel, comprising: a photodetection region; and a drain configured to discard charge carriers from the photodetection region, wherein the drain comprises a semiconductor region that to which electrical contact is made through a conductive path that does not include a polysilicon electrode.
Methods of preparing a multiplexed sample for polypeptide sequencing using barcodes. Methods for multiplexed samples for polypeptide sequencing in which the polypeptide populations are physically separated. Kit comprising a population of barcodes and device for preparing a sample comprising a sample preparation module comprising barcodes and immobilised capture probes configured to interact with a cartridge comprising a reservoir.
C07K 1/22 - Affinity chromatography or related techniques based upon selective absorption processes
C40B 40/10 - Libraries containing peptides or polypeptides, or derivatives thereof
C40B 50/00 - Methods of creating libraries, e.g. combinatorial synthesis
C40B 50/14 - Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creation; Particular methods of cleavage from the solid support
C40B 70/00 - Tags or labels specially adapted for combinatorial chemistry or libraries, e.g. fluorescent tags or barcodes
C12Q 1/37 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving hydrolase involving peptidase or proteinase
22.
PERISTALTIC PUMPING OF FLUIDS AND ASSOCIATED METHODS, SYSTEMS, AND DEVICES
Embodiments described herein generally relate to apparatuses, cartridges, and pumps for peristaltic pumping of fluids and associated methods, systems, and devices. The pumping of fluids is, in certain cases, an important aspect of a variety of applications, such as bioanalytical applications (e.g., biological sample analysis, sequencing, identification). The inventive features described herein may, in some embodiments, provide an ability to pump fluids in ways that combine certain advantages of robotic fluid handling systems (e.g., automation, programmability, configurability, flexibility) with certain advantages of microfluidics (e.g., small fluid volumes with high fluid resolution, precision, monolithic consumables, limiting of the wetting of components to consumables).
Aspects of the application provide methods of preparing an enriched sample for polypeptide sequencing, and compositions, kits and devices useful for the same.
Methods and devices for isolating or enriching target molecules from a sample using lysis, fragmentation and affinity purification, e.g., using scodaphoresis, are provided herein. In particular embodiments, a device for enriching a target molecule from a biological sample is characterized in that the device comprises an automated sample preparation module comprising a cartridge housing that is configured to receive a removable cartridge. In some embodiments, methods and devices further involve detection, analysis and/or sequencing of a target molecule.
Methods of polypeptide sequencing and/or nucleic acid sequencing which may be carried out on single cell samples and may use barcode components and which facilitate the direct sequencing without amplification. All proteins in the sample may be first labelled with one barcode, secondly the nucleic acids or metabolites are labelled with a second barcode. Also provided herein are compositions, kits and devices useful for the same.
Methods and devices for enriching and analyzing target molecules from a sample are provided herein. In some embodiments, methods and devices using cartridges involve enrichment of target molecules (e.g., using SCODA) and detection and analysis using sequencing. The method may employ lysing of cells, fragmentation of target in the sample preparation module and enriching the target in the module and moving the target to the sequencing module.
Embodiments described herein generally relate to apparatuses, cartridges, and pumps for peristaltic pumping of fluids and associated methods, systems, and devices. The pumping of fluids is, in certain cases, an important aspect of a variety of applications, such as bioanalytical applications (e.g., biological sample analysis, sequencing, identification). The inventive features described herein may, in some embodiments, provide an ability to pump fluids in ways that combine certain advantages of robotic fluid handling systems (e.g., automation, programmability, configurability, flexibility) with certain advantages of microfluidics (e.g., small fluid volumes with high fluid resolution, precision, monolithic consumables, limiting of the wetting of components to consumables).
Aspects of the application provide methods of producing substrates having modified surfaces. In some aspects, methods of surface modification involve treating a surface of a substrate with an organic reagent in vapor phase to form an organic layer over the surface. In some aspects, methods of forming a stable surface coating on an oxidized surface are provided. Organic phosphoryl halide is used.
C23C 16/44 - Chemical coating by decomposition of gaseous compounds, without leaving reaction products of surface material in the coating, i.e. chemical vapour deposition (CVD) processes characterised by the method of coating
C23C 16/04 - Coating on selected surface areas, e.g. using masks
29.
INCREASED EMISSION COLLECTION EFFICIENCY IN INTEGRATED OPTICAL DEVICES
Apparatus and methods for improving optical signal collection in an integrated device are described. A microdisk (1-605) can be formed in an integrated device and increase collection and/or concentration of radiation incident on the microdisk (1-605) and re-radiated by the microdisk (1-605). An example integrated device that can include a microdisk (1-605) may be used for analyte detection and/or analysis. Such an integrated device may include a plurality of pixels, each having a reaction chamber (1-130) for receiving a sample to be analyzed, an optical microdisk (1-605), and an optical sensor (1-122) configured to detect optical emission from the reaction chamber (1-130). The microdisk (1-605) can comprise a dielectric material having a first index of refraction that is embedded in one or more surrounding materials (1-610) having one or more different refractive index values.
G01N 21/63 - Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light optically excited
C12M 1/34 - Measuring or testing with condition measuring or sensing means, e.g. colony counters
Described herein are techniques to reduce or remove the impact of secondary path photons and/or charge carriers on storage bins of an integrated device to improve noise performance, and thus, sample analysis. Some embodiments relate to optical rejection techniques such as including an optical barrier positioned to block at least some photons from reaching the storage bins. Some embodiments relate to electrical rejection techniques such as including an electrical barrier configured to block at least some charge carriers from reaching the storage bins along at least one secondary path. Some embodiments relate to an integrated device in which at least one storage bin is shaped and/or positioned relative to the photodetector to facilitate receipt of some charge carriers (e.g., fluorescent emission charge carriers) and/or photons and to impede receipt of other charge carriers (e.g., noise charge carriers) and/or photons.
G01N 21/63 - Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light optically excited
Compositions comprising modified recombinant polymerizing enzymes are provided, along with nucleic acid molecules encoding the modified polymerizing enzymes. In some aspects, methods of using such polymerizing enzymes to synthesize a nucleic acid molecule or to sequence a nucleic acid template are provided.
Apparatus and methods relating to photonic bandgap optical nanostructures are described. Such optical nanostructures may exhibit prohibited photonic bandgaps or allowed photonic bands, and may be used to reject (e.g., block or attenuate) radiation at a first wavelength while allowing transmission of radiation at a second wavelength. Examples of photonic bandgap optical nanostructures includes periodic and quasi-periodic structures, with periodicity or quasi-periodicity in one, two, or three dimensions and structural variations in at least two dimensions. Such photonic bandgap optical nanostructures may be formed in integrated devices that include photodiodes and CMOS circuitry arranged to analyze radiation received by the photodiodes.
Described herein are systems and techniques for identifying polypeptides using data collected by a protein sequencing device. The protein sequencing device may collect data obtained from detected light emissions by luminescent labels during binding interactions of reagents with amino acids of the polypeptide. The light emissions may result from application of excitation energy to the luminescent labels. The device may provide the data as input to a trained machine learning model to obtain output that may be used to identify the polypeptide. The output may indicate, for each of a plurality of locations in the polypeptide, one or more likelihoods that one or more respective amino acids is present at the location. The output may be matched to an amino acid sequence that specifies a protein.
G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
G16B 40/00 - ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
Apparatus and methods relating to coupling radiation from an incident beam (1-122) into a plurality of waveguides (1-, 2-, 3-212a...e) with a grating coupler (1-, 2-, 3-210) are described. A grating coupler (1-, 2-, 3-210) can have offset receiving regions and grating portions with offset periodicity to improve sensitivity of the grating coupler (1-, 2-, 3-210) to misalignment of the incident beam (1-122).
Apparatus and methods relating to attenuating excitation radiation incident on a sensor (1-122) in an integrated device that is used for sample analysis are described. At least one semiconductor film (1-336) of a selected material and crystal morphology is located between a waveguide (1-115) and a sensor (1-122) in an integrated device that is formed on a substrate (1-105). Rejection ratios greater than 100 or more can be obtained for excitation and emission wavelengths that are 40 nm apart for a single layer of semiconductor material (1-135).
Compositions useful for the detection of single molecules in a sample are provided. In some aspects, the disclosure provides a nucleotide connected to a nucleic acid comprising a FRET label comprising at least three luminescent molecules. In some embodiments, the nucleic acids described herein comprise one or more structural features that provide enhanced fluorescence intensity. In some aspects, methods of sequencing using the labeled nucleotides of the disclosure are provided.
C07H 19/00 - Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro derivatives thereof
C12Q 1/6818 - Hybridisation assays characterised by the detection means involving interaction of two or more labels, e.g. resonant energy transfer
Optical waveguides and couplers for delivering light to an array of photonic elements in a photonic integrated device. The photonic integrated device and related instruments and systems may be used to analyze samples in parallel. The photonic integrated device may include a grating coupler configured to receive light from an external light source and optically couple with multiple waveguides configured to optically couple with sample wells of the photonic integrated device.
G01N 21/77 - Systems in which material is subjected to a chemical reaction, the progress or the result of the reaction being investigated by observing the effect on a chemical indicator
38.
SAMPLE WELL FABRICATION TECHNIQUES AND STRUCTURES FOR INTEGRATED SENSOR DEVICES
A method of forming an integrated device includes forming a sample well within a cladding layer of a substrate; forming a sacrificial spacer layer over the substrate and into the sample well; performing a directional etch of the sacrificial spacer layer so as to form a sacrificial sidewall spacer on sidewalls of the sample well; forming, over the substrate and into the sample well, a functional layer that provides a location for attachment of a biomolecule; and removing the sacrificial spacer material.
Aspects of the application provide methods of identifying and sequencing proteins, polypeptides, and amino acids, and compositions useful for the same. In some aspects, the application provides methods of obtaining data during a degradation process of a polypeptide, and outputting a sequence representative of the polypeptide. In some aspects, the application provides amino acid recognition molecules comprising a shielding element that enhances photostability in polypeptide sequencing reactions.
Systems and methods for detecting lifetime of luminescent molecules using photodetectors configured to perform photon counting are described. The systems and methods may involve an array of photodetectors for detecting photons emitted from a sample, which may include the luminescent molecules, and detection circuitry associated with the array of photodetectors. The detection circuitry may be configured to count, during at least a first time period and a second time period, a quantity of incident photons at a photodetector in the array of photodetectors.
Methods of forming an integrated device, and in particular forming one or more sample wells in an integrated device, are described. The methods may involve forming a metal stack over a cladding layer, forming an aperture in the metal stack, forming first spacer material within the aperture, and forming a sample well by removing some of the cladding layer to extend a depth of the aperture into the cladding layer. In the resulting sample well, at least one portion of the first spacer material is in contact with at least one layer of the metal stack.
Provided herein is a biomolecule comprising a fluorescent marker. The label is a Cy3B having formula (I) wherein, Q1 and Q2 are independently monomeric or oligomeric biomolecules.
C09B 57/00 - Other synthetic dyes of known constitution
C07D 413/14 - Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and oxygen atoms as the only ring hetero atoms containing three or more hetero rings
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
An integrated circuit includes a photodetection region configured to receive incident photons. The photodetection region is configured to produce a plurality of charge carriers in response to the incident photons. The integrated circuit includes a charge carrier storage region. The integrated circuit also includes a charge carrier segregation structure configured to selectively direct charge carriers of the plurality of charge carriers directly into the at least one charge carrier storage region based upon times at which the charge carriers are produced.
Instrument control and data acquisition in advanced analytic systems that utilize optical pulses for sample analysis are described. Clocking signals for data acquisition, data processing, communication, and/or other data handling functionalities can be derived from an on-board pulsed optical source, such as a passively mode-locked laser. The derived clocking signals can operate in combination with one or more clocking signals from a stable oscillator, so that instrument operation and data handling can tolerate interruptions in operation of the pulsed optical source.
Methods and apparatus for predicting an association between input data in a first modality and data in a second modality using a statistical model trained to represent interactions between data having a plurality of modalities including the first modality and the second modality, the statistical model comprising a plurality of encoders and decoders, each of which is trained to process data for one of the plurality of modalities, and a joint-modality representation coupling the plurality of encoders and decoders. The method comprises selecting, based on the first modality and the second modality, an encoder/decoder pair or a pair of encoders, from among the plurality of encoders and decoders, and processing the input data with the joint-modality representation and the selected encoder/decoder pair or pair of encoders to predict the association between the input data and the data in the second modality.
G16C 20/70 - Machine learning, data mining or chemometrics
G16B 5/00 - ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
46.
SYSTEMS AND METHODS FOR UNIFYING STATISTICAL MODELS FOR DIFFERENT DATA MODALITIES
Techniques for performing a prediction task using a multi-modal statistical model configured to receive input data from multiple modalities including input data from a first modality and input data from a second modality different from the first modality. The techniques include: obtaining information specifying the multi-modal statistical model including values of parameters of each of multiple components of the multi-modal statistical model, the multiple components including first and second encoders for processing input data for the first and second modalities, respectively, first and second modality embeddings, a joint-modality representation, and a predictor; obtaining first input data for the first data modality; providing the first input data to the first encoder to generate a first feature vector; identifying a second feature vector using the joint-modality representation, the first modality embedding and the first feature vector; and generating a prediction for the prediction task using the predictor and the second feature vector.
Described herein are machine learning techniques for generating biological polymer assemblies of macromolecules. For example, the system may use machine learning techniques to generate a genome assembly of an organism's DNA, a gene sequence of a portion of an organism's DNA, or an amino acid sequence of a protein. The system may access biological polymer sequences generated by a sequencing device and an assembly generated from the sequences. The system may generate input to a machine learning model using the sequences and the assembly. The system may provide the input to the machine learning model to obtain a corresponding output. The system may use the corresponding output to identify biological polymers at locations in the assembly, and then update the assembly to indicate the identified biological polymers at the locations in the assembly to obtain an updated assembly.
A method and apparatus for characterizing an optical element. The optical element is part of a laser and is mounted on a translation stage to scan the optical element transverse to an intracavity laser beam. A performance characteristic of the laser is recorded as a function of position of the optical element.
H01S 3/00 - Lasers, i.e. devices using stimulated emission of electromagnetic radiation in the infrared, visible or ultraviolet wave range
H01S 3/105 - Controlling the intensity, frequency, phase, polarisation or direction of the emitted radiation, e.g. switching, gating, modulating or demodulating by controlling the mutual position or the reflecting properties of the reflectors of the cavity
H01S 3/11 - Mode locking; Q-switching; Other giant-pulse techniques, e.g. cavity dumping
H01S 3/042 - Arrangements for thermal management for solid state lasers
H01S 3/081 - Construction or shape of optical resonators or components thereof comprising three or more reflectors
H01S 3/086 - One or more reflectors having variable properties or positions for initial adjustment of the resonator
H01S 3/0941 - Processes or apparatus for excitation, e.g. pumping using optical pumping by coherent light of a semiconductor laser, e.g. of a laser diode
H01S 3/131 - Stabilisation of laser output parameters, e.g. frequency or amplitude by controlling the active medium, e.g. by controlling the processes or apparatus for excitation
A method includes obtaining, from one or more sequencing devices, raw data detected from luminescent labels associated with nucleotides during nucleotide incorporation events; and processing the raw data to perform a comparison of base calls produced by a learning enabled, automatic base calling module of the one or more sequencing devices with actual values associated with the raw data, wherein the base calls identify one or more individual nucleotides from the raw data. Based on the comparison, an update to the learning enabled, automatic base calling module is created using at least some of the obtained raw data, and the update is made available to the one or more sequencing devices.
CA 03086769 2020-06-23 (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property 111111 1 11111111 111111 1 11 11111 1 111 11111 1 111 1 111 1111 1111 1 11 11111 1 11 11111111111 1111111 Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2019/136202 A3 11 July 2019 (11.07.2019) WIPO I PCT (51) International Patent Classification: remy; 636 Nortontown Road, Guilford, CT 0643'7 (11S). BOIL 3/00 (2006.01) GORYAYNOV, Alexander; 155 Bradley Street, Apt. 2, New Haven, CT 06511 (US). SCHMID, Gerard; 140 Wi1- (21) International Application Number: drose Avenue, Guilford, CT 0643'7 (US). KABIRI, Ali; 58 PCT/US2019/012271 Green Hill Road, Madison, CT 06443 (US). REARICK, (22) International Filing Date: Todd; 5 Wyndemere Court, Cheshire, CT 06410 (US). 04 January 2019 (04.01.2019) SCHULTZ, Jonathan, C.; 121 Landon's Way, Guilford, CT 0643'7 (US). GHASEMI, Farshid; 1120 Village Walk, (25) Filing Language: English Guilford, CT 0643'7 (11S). FIFE, Keith, G.; 635 Matadero (26) Publication Language: English Avenue, Palo Alto, CA 94306 (US). (30) Priority Data: (74) Agent: PRITZKER, Randy, J. et al.; Wolf, Greenfield & 62/614,912 08 January 2018 (08.01.2018) US Sacks, P.C., 600 Atlantic Avenue, Boston, MA 02210-2206 (US). (71) Applicant: QUANTUM-SI INCORPORATED [US/US]; 530 Old Whitfield Street, Guilford, CT 06437 (11S). (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AIVI, (72) Inventors: ROTHBERG, Jonathan, M.; 215 Uncas Point AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, By BZ, Road, Guilford, CT 06437 (US). CHEN, Guojun; 115 CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, Maple Street, Sherborn, MA 01770 (US). LACKEY, Je- DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, (54) Title: SYSTEM AND METHODS FOR ELECTROKINETIC LOADING OF SUB-MICRON-SCALE REACTION CHAMBERS ___________________ Z 2-110 = 2-112 .. .... .. 2-116 .. 1-114 - = , ' ... ..0 = . . .. ... : =: ......... 1_108 . ..... . -A 1 2-120A .. % 1-106a .. ... 1-106b 1-220 MISIMISIMINERCEMISHI . monmEmelmssmarmg 2-117 d 1-118 FIG. 2-1 cr) C...1 (57) Abstract: Apparatus and techniques for electrokinetic loading of samples of interest into sub- micron-scale reaction chambers are .1119 described. Embodiments include an integrated device and related apparatus for analyzing samples in parallel. The integrated device may include at least one reaction chamber formed through a surface of the integrated device and configured to receive a sample of interest, NI such as a molecule of nucleic acid. The integrated device may further include electrodes patterned adjacent to the reaction chamber that -...., produce one or more electric fields that assist loading the sample into the reaction chamber. The apparatus may further include a sample reservoir having a fluid seal with the surface of the integrated device and configured to hold a suspension containing the samples. [Continued on next page] CA 03086769 2020-06-23 WO 2019/136202 A3 1 11111 1 011111 II 111111 11111 11111 11111 1111 1 1111111111 11111 II 11111 11111 III 11111111111 1111 1111 HR, HU, ID, EL, IN, ER, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (84) Designated States (unless otherwise indicated, for every kind of regional protection available): AREPO (BW, GH, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, KM, ML, MR, NE, SN, TD, TG). Published: ¨ with international search report (Art. 21(3)) ¨ before the expiration of the time limit for amending the claims and to be republished in the event of receipt of amendments (Rule 48.2(h)) (88) Date of publication of the international search report: 0'7November 2019 (0'7.11.2019) (15) Information about Correction: see Notice of 29 August 2019 (29.08.2019)
A hand-held bioanalytic instrument is described that can perform massively parallel sample analysis including single-molecule gene sequencing. The instrument includes a pulsed optical source that produces ultrashort excitation pulses and a compact beam-steering assembly. The beam-steering assembly provides automated alignment of excitation pulses to an interchangeable bio-optoelectronic chip that contains tens of thousands of reaction chambers or more. The optical source, beam-steering assembly, bio-optoelectronic chip, and coupling optics register to an alignment structure in the instrument that can form at least one wall of an enclosure and dissipate heat.
An integrated device and related instruments and systems for analyzing samples in parallel are described. The integrated device may include sample wells arranged on a surface of where individual sample wells are configured to receive a sample labeled with at least one fluorescent marker configured to emit emission light in response to excitation light. The integrated device may further include photodetectors positioned in a layer of the integrated device, where one or more photodetectors are positioned to receive a photon of emission light emitted from a sample well. The integrated device further includes one or more photonic structures positioned between the sample wells and the photodetectors, where the one or more photonic structures are configured to attenuate the excitation light relative to the emission light such that a signal generated by the one or more photodetectors indicates detection of photons of emission light.
Compositions useful for the detection of single molecules in a sample are provided. In some aspects, the disclosure provides a nucleic acid connected to a nucleotide and two or more luminescent labels. In some embodiments, the nucleic acids described herein comprise one or more structural features that provide enhanced fluorescence intensity. In some aspects, methods of sequencing using the labeled nucleotides of the disclosure are provided.
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 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
G01N 21/62 - Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light
54.
SUBSTRATES HAVING MODIFIED SURFACE REACTIVITY AND ANTIFOULING PROPERTIES IN BIOLOGICAL REACTIONS
Methods of preparing surfaces of sample wells are provided. In some aspects, methods of preparing a sample well surface involve contacting the sample well with a block copolymer to form an antifouling overlay over a metal oxide surface of the sample well. In some aspects, methods of passivating and/or selectively functionalizing a sample well surface are provided.
Methods of loading a molecule of interest into a sample well are provided. In some aspects, methods of loading a molecule of interest into a sample well involve loading a molecule of interest into a sample well in the presence of a crowding agent and/or a condensing agent. In some aspects, methods of loading a sequencing template into a sample well are provided.
Compositions comprising modified recombinant polymerizing enzymes are provided, along with nucleic acid molecules encoding the modified polymerizing enzymes. In some aspects, methods of using such polymerizing enzymes to synthesize a nucleic acid molecule or to sequence a nucleic acid template are provided.
An integrated circuit includes a photodetection region configured to receive incident photons. The photodetection region is configured to produce a plurality of charge carriers in response to the incident photons. The integrated circuit includes at least one charge carrier storage region. The integrated circuit also includes a charge carrier segregation structure configured to selectively direct charge carriers of the plurality of charge carriers directly into the at least one charge carrier storage region based upon times at which the charge carriers are produced.
Apparatus and methods for coupling an optical beam from an optical source to a hitech system are described. A compact, low-cost beam-shaping and steering assembly may be located between the optical source and hi-tech system and provide automated adjustments to beam parameters such as beam position, beam rotation, and beam incident angles. The beam shaping and steering assembly may be used to couple an elongated beam to a plurality of optical waveguides.
G02B 26/08 - Optical devices or arrangements for the control of light using movable or deformable optical elements for controlling the direction of light
System and methods for optical power distribution to a large numbers of sample wells within an integrated device that can analyze single molecules and perform nucleic acid sequencing are described. The integrated device may include a grating coupler configured to receive an optical beam from an optical source and optical splitters configured to divide optical power of the grating coupler to waveguides of the integrated device positioned to couple with the sample wells. Outputs of the grating coupler may vary in one or more dimensions to account for an optical intensity profile of the optical source.
G01N 21/77 - Systems in which material is subjected to a chemical reaction, the progress or the result of the reaction being investigated by observing the effect on a chemical indicator
Apparatus and methods for producing ultrashort optical pulses are described. A high- power, solid-state, passively mode-locked laser can be manufactured in a compact module that can be incorporated into a portable instrument. The mode-locked laser can produce sub- 50-ps optical pulses at a repetition rates between 200 MHz and 50 MHz, rates suitable for massively parallel data-acquisition. The optical pulses can be used to generate a reference clock signal for synchronizing data-acquisition and signal-processing electronics of the portable instrument.
H01S 3/10 - Controlling the intensity, frequency, phase, polarisation or direction of the emitted radiation, e.g. switching, gating, modulating or demodulating
61.
INTEGRATED DEVICE FOR DETECTING AND ANALYZING MOLECULES
System and methods for analyzing single molecules and performing nucleic acid sequencing. An integrated device may include multiple pixels with sample wells configured to receive a sample, which when excited, emits radiation. The integrated device includes a surface having a trench region recessed from a portion of the surface and an array of sample wells, disposed in the trench region. The integrated device also includes a waveguide configured to couple excitation energy to at least one sample well in the array and positioned at a first distance from a surface of the trench region and at a second distance from the surface in a region separate from the trench region. The first distance is smaller than the second distance. The system also includes an instrument that interfaces with the integrated device. The instrument may include an excitation energy source for providing excitation energy to the integrated device by coupling to an excitation energy coupling region of the integrated device.
System and methods for identifying nucleotides based on data acquired from a sensor during sequencing of nucleic acids. The method may include obtaining characteristics of light detected from luminescent labels associated with the nucleotides during nucleotide incorporation events. The characteristics may include, for each nucleotide incorporation event, a temporal characteristic of the light and an intensity characteristic of the light. The temporal characteristic representing a speed of decay of a probability of photon emission by a luminescent label after excitation. The method may further include grouping points representing the characteristics of the nucleotide incorporation events into groups of points. The individual points may represent at least the temporal characteristic and the intensity characteristic for a corresponding nucleotide incorporation event. The method may further include assigning the groups of points to individual nucleotides.
Methods of sequencing molecules based on luminescence lifetimes and/or intensities are provided. In some aspects, methods of sequencing nucleic acids involve determining the luminescence lifetimes, and optionally luminescence intensities, of a series of Iuminescently labeled nucleotides incorporated during a nucleic acid sequencing reaction. In some aspects, the disclosure provides compositions comprising luminescently labeled nucleotides.
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 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
Apparatus and methods for producing ultrashort optical pulses (1-110) are described. A high-power, solid-state, passively mode- locked laser (1-110) can be manufactured in a compact module that can be incorporated into a portable instrument for biological or chemical analyses. The pulsed laser may produce sub-100-ps optical pulses at a repetition rate commensurate with electronic data- acquisition rates. The optical pulses may excite samples in reaction chambers of the instrument, and be used to generate a reference clock for operating signal-acquisition and signal-processing electronics of the instrument.
C12Q 1/00 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
H01S 5/06 - Arrangements for controlling the laser output parameters, e.g. by operating on the active medium
65.
METHOD OF DETERMINING THE SEQUENCE OF A NUCLEIC ACID USING TIME RESOLVED LUMINESCENCE
Methods of sequencing molecules based on luminescence lifetimes and/or intensities are provided. In some aspects, methods of sequencing nucleic acids involve determining the luminescence lifetimes, and optionally luminescence intensities, of a series of luminescently labeled nucleotides incorporated during a nucleic acid sequencing reaction.
Apparatus and methods for analyzing single molecule and performing nucleic acid sequencing. An apparatus can include an assay chip that includes multiple pixels with sample wells configured to receive a sample, which, when excited, emits emission energy; at least one element for directing the emission energy in a particular direction; and a light path along which the emission energy travels from the sample well toward a sensor. The apparatus also includes an instrument that interfaces with the assay chip. The instrument includes an excitation light source for exciting the sample in each sample well; a plurality of sensors corresponding the sample wells. Each sensor may detect emission energy from a sample in a respective sample well. The instrument includes at least one optical element that directs the emission energy from each sample well towards a respective sensor of the plurality of sensors.
G01N 21/63 - Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light optically excited
An integrated circuit includes a photodetection region configured to receive incident photons. The photodetection region is configured to produce a plurality of charge carriers in response to the incident photons. The integrated circuit also includes at least one charge carrier storage region. The integrated circuit also includes a charge carrier segregation structure configured to selectively direct charge carriers of the plurality of charge carriers into the at least one charge carrier storage region based upon times at which the charge carriers are produced.
G01N 21/63 - Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light optically excited
System and methods for analyzing single molecules and performing nucleic acid sequencing. An integrated device includes multiple pixels with sample wells configured to receive a sample, which when excited, emits radiation. The integrated device includes at least one waveguide configured to propagate excitation energy to the sample wells from a region of the integrated device configured to couple with an excitation energy source. A pixel may also include at least one element for directing the emission energy towards a sensor within the pixel. The system also includes an instrument that interfaces with the integrated device. The instrument may include an excitation energy source for providing excitation energy to the integrated device by coupling to an excitation energy coupling region of the integrated device. One of multiple markers distinguishable by temporal parameters of the emission energy may label the sample and configuration of the sensor within a pixel may allow for detection of a temporal parameter associated with the marker labeling the sample.
C12M 1/34 - Measuring or testing with condition measuring or sensing means, e.g. colony counters
G01N 21/63 - Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light optically excited
Apparatus and methods for analyzing single molecule and performing nucleic acid sequencing. An apparatus can include an assay chip that includes multiple pixels with sample wells configured to receive a sample, which, when excited, emits emission energy; at least one element for directing the emission energy in a particular direction; and a light path along which the emission energy travels from the sample well toward a sensor. The apparatus also includes an instrument that interfaces with the assay chip. The instrument includes an excitation light source for exciting the sample in each sample well; a plurality of sensors corresponding the sample wells. Each sensor may detect emission energy from a sample in a respective sample well. The instrument includes at least one optical element that directs the emission energy from each sample well towards a respective sensor of the plurality of sensors.
G01N 21/62 - Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light
G01N 21/63 - Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light optically excited
Apparatus and methods for analyzing single molecule and performing nucleic acid sequencing. An integrated device includes multiple pixels with sample wells configured to receive a sample, which, when excited, emits radiation; at least one element for directing the emission radiation in a particular direction; and a light path along which the emission radiation travels from the sample well toward a sensor. The apparatus also includes an instrument that interfaces with the integrated device. Each sensor may detect emission radiation from a sample in a respective sample well. The instrument includes an excitation light source for exciting the sample in each sample well.
An active- source -pixel, integrated device capable of performing biomolecule detection and/or analysis, such as single-molecule nucleic acid sequencing, is described. An active pixel of the integrated device includes a sample well into which a sample to be analyzed may diffuse, an excitation source for providing excitation energy to the sample well, and a sensor configured to detect emission from the sample. The sensor may comprise two or more segments that produce a set of signals that are analyzed to differentiate between and identify tags that are attached to, or associated with, the sample. Tag differentiation may be spectral and/or temporal based. Identification of the tags may be used to detect, analyze, and/or sequence the biomolecule.
G01N 21/63 - Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light optically excited
G01N 35/00 - Automatic analysis not limited to methods or materials provided for in any single one of groups ; Handling materials therefor
patents
