Embodiments of the present disclosure present systems, devices and methods for fragmenting high-molecular weight (HMW) genomic DNA (HMW DNA). In some embodiments, a HMW DNA sample is provided, then, one or more reagents are added to the HMW DNA sample to produce a HMW DNA sample mixture. Thereafter, a Cas9 preparation is added to the HMW DNA sample mixture establishing a HMW DNA – Cas9 mixture where it is then incubated, the Cas9 enzyme is inactivated, and the fragmented DNA purified.
Embodiments described herein relate to systems, devices, and methods for performing preparative electrophoresis. In some embodiments, a housing defines a plurality of cavities each configured to receive a vertical channel. Each vertical channel may include a hydrogel defining a sample well configured to receive a sample of DNA fragments. The vertical channel may be placed in fluidic communication with at least a first reservoir and a second reservoir. In some embodiments, preparative electrophoresis may be completed for the plurality of vertical channels simultaneously. The embodiments described herein may be integrated into automatic workflows for high-throughput applications. The embodiments described herein may be used for both long-read and short-read sequencing applications.
G01N 27/30 - Électrodes, p. ex. électrodes pour testsDemi-cellules
G01N 11/10 - Recherche des propriétés d'écoulement des matériaux, p. ex. la viscosité, la plasticitéAnalyse des matériaux en déterminant les propriétés d'écoulement en déplaçant un corps à l'intérieur du matériau
G01N 35/02 - Analyse automatique non limitée à des procédés ou à des matériaux spécifiés dans un seul des groupes Manipulation de matériaux à cet effet en utilisant une série de récipients à échantillons déplacés par un transporteur passant devant un ou plusieurs postes de traitement ou d'analyse
G01N 33/543 - Tests immunologiquesTests faisant intervenir la formation de liaisons biospécifiquesMatériaux à cet effet avec un support insoluble pour l'immobilisation de composés immunochimiques
C12N 15/11 - Fragments d'ADN ou d'ARNLeurs formes modifiées
3.
SYSTEMS, DEVICES, AND METHODS FOR ELECTROPHORETIC EXTRACTING AND ENRICHING EXTRACHROMOSOMAL DNA
Embodiments of the present disclosure present methods, systems, and devices for extrachromosomal DNA extraction, and in some embodiments, isolation of DNA therefrom, and/or analysis of the extracted and/or isolated DNA, including, in some embodiments, ecDNA.
The invention relates to cassettes for culturing cells. The invention also relates to analytical and preparative incubators for housing the cassettes. The invention also relates to methods of using the cassettes, for example, to culture cells wherein the processes of feeding and passaging cells are automated.
C12M 3/00 - Appareillage pour la culture de tissus, de cellules humaines, animales ou végétales, ou de virus
A61K 35/12 - Substances provenant de mammifèresCompositions comprenant des tissus ou des cellules non spécifiésCompositions comprenant des cellules souches non embryonnairesCellules génétiquement modifiées
C12M 1/34 - Mesure ou test par des moyens de mesure ou de détection des conditions du milieu, p. ex. par des compteurs de colonies
C12M 1/00 - Appareillage pour l'enzymologie ou la microbiologie
C12M 1/12 - Appareillage pour l'enzymologie ou la microbiologie avec des moyens de stérilisation, filtration ou dialyse
5.
SYSTEMS, DEVICES, AND METHODS FOR ELECTROPHORETIC EXTRACTING AND ENRICHING EXTRACHROMOSOMAL DNA
Embodiments of the present disclosure present methods, systems, and devices for extrachromosomal DNA extraction, and in some embodiments, isolation of DNA therefrom, and/or analysis of the extracted and/or isolated DNA, including, in some embodiments, ecDNA.
C12Q 1/68 - Procédés de mesure ou de test faisant intervenir des enzymes, des acides nucléiques ou des micro-organismesCompositions à cet effetProcédés pour préparer ces compositions faisant intervenir des acides nucléiques
6.
Preparative electrophoretic method for targeted purification of genomic DNA fragments
A sample containing particles having high-molecular-weight (HMW) DNA is entrapped in a gel matrix, and the gel matrix is exposed to a lysis reagent configured to release the HMW DNA from the particles. The HMW DNA may be purified by subjecting the gel matrix to an electrophoretic field that removes the HMW DNA from the particles, lysis reagents, and/or other sample constituents, from the gel matrix such that the HMW DNA remains. The gel matrix may be subjected with DNA cleavase reagents configured to cleave at specific DNA sequences within the HMW DNA to liberate defined segments of the DNA as fragments of reduced size. The gel matrix may also be subjected to an electrophoretic field, which moves and separates the DNA fragments from uncleaved DNA of the HMW DNA, which remains substantially immobile. The electrophoretically separated DNA fragments may be isolated from the gel matrix.
An electrophoresis cassette may include sample well(s), gel column(s) containing a separation gel, and elution modules arranged adjacent the gel column(s). A sample may be provided to the electrophoresis cassette and high-molecular weight (HMW) DNA may be isolated from the sample. Single-copy DNA sequences may be cleaved on both sides of a repeat region of the DNA sequences to produce a cleaved sample, which then may be fractionated using gel electrophoresis. DNA fractions may be isolated from consecutive sections of the separation gel and subjected to PCR assays to detect single-copy sequences within the DNA fraction, said single-copy sequence containing repeat expansion sequences. The subjected DNA fractions may be electroeluted into the plurality of elution modules. A size of DNA fractions having the repeat expansion sequences may be determined. It is also determined if that size is above a normal repeat size range.
A cassette for retaining molecules during electrophoresis has a housing with a lane configured therein. The lane has a first elongate edge and a second elongate edge, and an elution module is configured to be received in the late to divide the lane into a first chamber and a second chamber. A first buffer reservoir is positioned adjacent the first elongate edge, and a second buffer reservoir is positioned adjacent the second elongate edge. The first side of the elution module facing the first chamber comprises a porous sterile filtration membrane. The second side of the elution module facing the second chamber comprises an ultrafiltration membrane that has a pore size to retain molecules during electrophoresis.
Methods, systems and apparatus for automated extraction, purification, and processing of nucleic acids from biological samples are presented. In some embodiments, hydrogel supports are used to immobilize particulate biological input samples and extract nucleic acids during operations. The use of hydrogel facilitates automated sample processing on robotic liquid handling systems. Devices, methods, and systems are also provided for electrophoretic sample preparation.
An electrophoresis cassette may include sample well(s), gel column(s) containing a separation gel, and elution modules arranged adjacent the gel column(s). A sample may be provided to the electrophoresis cassette and high-molecular weight DNA may be isolated from the sample. Single-copy DNA sequences may be cleaved on both sides of a repeat region of the DNA sequences to produce a cleaved sample, which then may be fractionated using gel electrophoresis. DNA fractions may be isolated from consecutive sections of the separation gel and subjected to PCR assays to detect single-copy sequences within the DNA fraction, said single-copy sequence containing repeat expansion sequences. The subjected DNA fractions may be electroeluted into the plurality of elution modules. A size of DNA fractions having the repeat expansion sequences may be determined. It is also determined if that size is above a normal repeat size range.
G01N 27/26 - Recherche ou analyse des matériaux par l'emploi de moyens électriques, électrochimiques ou magnétiques en recherchant des variables électrochimiquesRecherche ou analyse des matériaux par l'emploi de moyens électriques, électrochimiques ou magnétiques en utilisant l'électrolyse ou l'électrophorèse
G01N 27/28 - Composants de cellules électrolytiques
11.
APPARATUSES, METHODS AND SYSTEMS FOR AUTOMATED PROCESSING OF NUCLEIC ACIDS AND ELECTROPHORETIC SAMPLE PREPARATION
Various implementations disclosed herein relate to automated processing of nucleic acids and electrophoretic sample preparation. An exemplary disposable cassette for automated molecular processing may include a base housing, a central channel arranged in the housing, and an elution module configured to be received in central channel and to divide the central channel into a first chamber and a second chamber. The elution module comprises a housing having a proximal side, a distal side and an elution module channel passing from the proximal side to the distal side. The elution module also comprises a first membrane attached to a proximal side of the elution module, a second membrane attached to a distal side of the elution module, and a porthole in fluid communication with the elution module channel and configured for receiving a sample.
The disclosure provides cassettes, electrophoresis systems, methods for making the device, and methods of fractionating a sample using the cassettes and electrophoresis systems described herein.
Methods, systems and apparatus for automated extraction, purification, and processing of nucleic acids from biological samples are presented. In some embodiments, hydrogel supports are used to immobilize particulate biological input samples and extract nucleic acids during operations. The use of hydrogel facilitates automated sample processing on robotic liquid handling systems. Devices, methods, and systems are also provided for electrophoretic sample preparation.
A nucleic acid sample may be provided, and the sample may be treated by applying a first enzymatic nucleic acid modifying reagent to produce a first nucleic acid solution. A first protease reagent may be applied to the first nucleic acid solution to produce a second nucleic acid solution. The application of the first protease reagent may completely or substantially inactivate the first enzymatic nucleic acid modifying reagent. A first inhibitor reagent may be applied in order to produce a third nucleic acid solution, and the first inhibitor reagent may completely or substantially inactivate the first protease reagent.
C12Q 1/68 - Procédés de mesure ou de test faisant intervenir des enzymes, des acides nucléiques ou des micro-organismesCompositions à cet effetProcédés pour préparer ces compositions faisant intervenir des acides nucléiques
C12N 9/00 - Enzymes, p. ex. ligases (6.)ProenzymesCompositions les contenantProcédés pour préparer, activer, inhiber, séparer ou purifier des enzymes
C12Q 1/37 - Procédés de mesure ou de test faisant intervenir des enzymes, des acides nucléiques ou des micro-organismesCompositions à cet effetProcédés pour préparer ces compositions faisant intervenir une hydrolase faisant intervenir une peptidase ou une protéinase
A sample containing particles having high-molecular-weight (HMW) DNA is entrapped in a gel matrix, and the gel matrix is exposed to a lysis reagent configured to release the HMW DNA from the particles. The HMW DNA may be purified by subjecting the gel matrix to an electrophoretic field that removes the HMW DNA from the particles, lysis reagents, and/or other sample constituents, from the gel matrix such that the HMW DNA remains. The gel matrix may be subjected with DNA cleavase reagents configured to cleave at specific DNA sequences within the HMW DNA to liberate defined segments of the DNA as fragments of reduced size. The gel matrix may also be subjected to an electrophoretic field, which moves and separates the DNA fragments from uncleaved DNA of the HMW DNA, which remains substantially immobile. The electrophoretically separated DNA fragments may be isolated from the gel matrix.
C07H 21/02 - Composés contenant au moins deux unités mononucléotide comportant chacune des groupes phosphate ou polyphosphate distincts liés aux radicaux saccharide des groupes nucléoside, p. ex. acides nucléiques avec le ribosyle comme radical saccharide
A sample containing particles having high-molecular-weight (HMW) DNA is entrapped in a gel matrix, and the gel matrix is exposed to a lysis reagent configured to release the HMW DNA from the particles. The HMW DNA may be purified by subjecting the gel matrix to an electrophoretic field that removes the HMW DNA from the particles, lysis reagents, and/or other sample constituents, from the gel matrix such that the HMW DNA remains. The gel matrix may be subjected with DNA cleavase reagents configured to cleave at specific DNA sequences within the HMW DNA to liberate defined segments of the DNA as fragments of reduced size. The gel matrix may also be subjected to an electrophoretic field, which moves and separates the DNA fragments from uncleaved DNA of the HMW DNA, which remains substantially immobile. The electrophoretically separated DNA fragments may be isolated from the gel matrix.
C07H 21/02 - Composés contenant au moins deux unités mononucléotide comportant chacune des groupes phosphate ou polyphosphate distincts liés aux radicaux saccharide des groupes nucléoside, p. ex. acides nucléiques avec le ribosyle comme radical saccharide
The invention relates to cassettes for culturing cells. The invention also relates to analytical and preparative incubators for housing the cassettes. The invention also relates to methods of using the cassettes, for example, to culture cells wherein the processes of feeding and passaging cells are automated.
C12M 3/00 - Appareillage pour la culture de tissus, de cellules humaines, animales ou végétales, ou de virus
C12M 1/00 - Appareillage pour l'enzymologie ou la microbiologie
C12M 1/12 - Appareillage pour l'enzymologie ou la microbiologie avec des moyens de stérilisation, filtration ou dialyse
C12M 1/34 - Mesure ou test par des moyens de mesure ou de détection des conditions du milieu, p. ex. par des compteurs de colonies
A61K 35/12 - Substances provenant de mammifèresCompositions comprenant des tissus ou des cellules non spécifiésCompositions comprenant des cellules souches non embryonnairesCellules génétiquement modifiées
The invention provides an electrophoresis cassette, methods for making the electrophoresis cassette, and method of fractionating analytes from a sample based upon electrophoretic mobility in a single application of the sample to an electrophoretic system.
G01F 11/00 - Appareils qu'il faut actionner de l'extérieur, adaptés à chaque opération répétée et identique, pour mesurer et séparer le volume prédéterminé d'un fluide ou d'un matériau solide fluent à partir d'une alimentation ou d'un récipient sans tenir compte du poids, et pour fournir ce volume
19.
APPARATUSES, METHODS AND SYSTEMS FOR AUTOMATED PROCESSING OF NUCLEIC ACIDS AND ELECTROPHORETIC SAMPLE PREPARATION
Methods, systems and apparatus for automated extraction, purification, and processing of nucleic acids from biological samples are presented. In some embodiments, hydrogel supports are used to immobilize particulate biological input samples and extract nucleic acids during operations. The use of hydrogel facilitates automated sample processing on robotic liquid handling systems. Devices, methods, and systems are also provided for electrophoretic sample preparation.
C12P 19/34 - Polynucléotides, p. ex. acides nucléiques, oligoribonucléotides
C12Q 1/68 - Procédés de mesure ou de test faisant intervenir des enzymes, des acides nucléiques ou des micro-organismesCompositions à cet effetProcédés pour préparer ces compositions faisant intervenir des acides nucléiques
20.
METHODS AND SYSTEMS FOR CONTROLLING THE SHEAR MODULUS OF GENOMIC LENGTH DSDNA MOLECULES
In some embodiments, a method for manipulating DNA molecules for use in a microfluidic device is provided, where the method may comprise providing a solution of a plurality of DNA molecules having a first radius of gyration under under a zero flow velocity, and maintaining the DNA molecules in a spherical shape under a flow velocity.
G01N 15/02 - Recherche de la dimension ou de la distribution des dimensions des particules
C07H 21/04 - Composés contenant au moins deux unités mononucléotide comportant chacune des groupes phosphate ou polyphosphate distincts liés aux radicaux saccharide des groupes nucléoside, p. ex. acides nucléiques avec le désoxyribosyle comme radical saccharide
21.
APPARATUSES, METHODS AND SYSTEMS FOR AUTOMATED PROCESSING OF NUCLEIC ACIDS AND ELECTROPHORETIC SAMPLE PREPARATION
Methods, systems and apparatus for automated extraction, purification, and processing of nucleic acids from biological samples are presented. In some embodiments, hydrogel supports are used to immobilize particulate biological input samples and extract nucleic acids during operations. The use of hydrogel facilitates automated sample processing on robotic liquid handling systems. Devices, methods, and systems are also provided for electrophoretic sample preparation.
C12Q 1/68 - Procédés de mesure ou de test faisant intervenir des enzymes, des acides nucléiques ou des micro-organismesCompositions à cet effetProcédés pour préparer ces compositions faisant intervenir des acides nucléiques
C12P 19/34 - Polynucléotides, p. ex. acides nucléiques, oligoribonucléotides
The disclosure provides cassettes, electrophoresis systems, methods for making the device, and methods of fractionating a sample using the cassettes and electrophoresis systems described herein.
The invention relates to cassettes for culturing cells. The invention also relates to analytical and preparative incubators for housing the cassettes. The invention also relates to methods of using the cassettes, for example, to culture cells wherein the processes of feeding and passaging cells are automated.
C12M 3/00 - Appareillage pour la culture de tissus, de cellules humaines, animales ou végétales, ou de virus
C12N 5/02 - Propagation de cellules individuelles ou de cellules en suspensionLeur conservationMilieux de culture à cet effet
A61K 35/12 - Substances provenant de mammifèresCompositions comprenant des tissus ou des cellules non spécifiésCompositions comprenant des cellules souches non embryonnairesCellules génétiquement modifiées
C12Q 1/02 - Procédés de mesure ou de test faisant intervenir des enzymes, des acides nucléiques ou des micro-organismesCompositions à cet effetProcédés pour préparer ces compositions faisant intervenir des micro-organismes viables
The invention relates to cassettes for culturing cells. The invention also relates to analytical and preparative incubators for housing the cassettes. The invention also relates to methods of using the cassettes, for example, to culture cells wherein the processes of feeding and passaging cells are automated.
A61K 35/12 - Substances provenant de mammifèresCompositions comprenant des tissus ou des cellules non spécifiésCompositions comprenant des cellules souches non embryonnairesCellules génétiquement modifiées
The disclosure provides an electrophoresis cassette (502) comprising a macrofluidic separation channel (525) for separating a sample, elution channels (522,523) for extracting the separated fractions from the separation channel and elution modules (524) for collecting the extracted separated fractions. Methods for making the device, and and methods of fractionating a sample using the cassettes and electrophoresis systems described herein.
The disclosure provides an electrophoresis cassette (502) comprising a macrofluidic separation channel (525) for separating a sample, elution channels (522,523) for extracting the separated fractions from the separation channel and elution modules (524) for collecting the extracted separated fractions. Methods for making the device, and and methods of fractionating a sample using the cassettes and electrophoresis systems described herein.
Systems and methods for processing fluid samples are disclosed. Fluid sample processing is accomplished using a series of microfluidic bump arrays include an automated and integrated system for sorting particles from a biological sample, lysing those particles to expose total RNA or DNA, purifying the RNA or DNA, processing the RNA or DNA by chemical or enzymatic modification, to select RNA or DNA molecules by size, or to generate, optionally, a sequencing library. The sequencing library is suitable for use in next generation sequencing ("NGS").
The invention provides an electrophoresis cassette, methods for making the electrophoresis cassette, and method of fractionating analytes from a sample based upon electrophoretic mobility in a single application of the sample to an electrophoretic system.
The invention provides an electrophoresis cassette, methods for making the electrophoresis cassette, and method of fractionating analytes from a sample based upon electrophoretic mobility in a single application of the sample to an electrophoretic system.
The invention provides an electrophoresis cassette, wherein a macrofluidic separation channel (9) splits into separate portions (5, 6), one of which having an elution chamber (28) being formed by an analyte-permeable barrier (32) and an analyte-impermeable barrier (33).
The invention provides an electrophoresis cassette, wherein a macrofluidic separation channel (9) splits into separate portions (5, 6), one of which having an elution chamber (28) being formed by an analyte-permeable barrier (32) and an analyte-impermeable barrier (33).
brevets
