Patents Assigned to Roche Sequencing Solutions, Inc.
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Patent number: 11859240Abstract: The invention provides methods, compositions, kits and devices for the detection of target molecules. In some embodiments, the invention allows for multiplexed target molecule detection.Type: GrantFiled: January 26, 2023Date of Patent: January 2, 2024Assignee: ROCHE SEQUENCING SOLUTIONS, INC.Inventor: Garry P. Nolan
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Publication number: 20230416813Abstract: This disclosure provides a biochip comprising a plurality of wells. The biochip includes a membrane that is disposed in or adjacent to an individual well of the plurality of wells. The membrane comprises a nanopore, and the individual well comprises an electrode that detects a signal upon ionic flow through the pore in response to a species passing through or adjacent to the nanopore. The electrode can be a non-sacrificial electrode. A lipid bilayer can be formed over the plurality of wells using a bubble.Type: ApplicationFiled: June 19, 2023Publication date: December 28, 2023Applicant: Roche Sequencing Solutions, Inc.Inventors: Randall W. Davis, Edward Shian Liu, Eric Takeshi Harada, Anne Aguirre, Andrew Trans, James Pollard, Cynthia Cech
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Patent number: 11846281Abstract: A delivery system for a sensor chip includes a plurality of selectable ports and a two-way pump port selectively connectable to each of the selectable ports. The two-way pump port is configured to allow material to be drawn or delivered from or to the two-way pump port. The delivery system also includes a chamber and a bypass waste channel that is selectively connectable to the two-way pump port. The plurality of selectable ports includes a selectable chamber port connected to the chamber and the chamber has a chamber waste exit. Material may selectively flow through the chamber to a waste collection via the chamber waste exit or flow to the waste collection via the bypass waste channel that bypasses the chamber waste exit.Type: GrantFiled: November 12, 2020Date of Patent: December 19, 2023Assignee: Roche Sequencing Solutions, Inc.Inventor: Robert A Yuan
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Patent number: 11821034Abstract: Provided are methods of nucleic acid sample preparation for analysis, including analysis using nanopore sequencing applications. In particular provided are methods that allow for the creation of circular and linear DNA samples that contain asymmetric ends to ligate different and desired adaptors to the end of the sample, methods to create single nucleic acid molecules that automatically form concatemers for higher sequencing throughput; methods to create multiple copies (temperature dependent, multi-primed, open-fold replication) of one original nucleic acid sample, or to create single nucleic acid molecules containing multiple copies of more than one original nucleic acid sample (concatemerized samples) for improved accuracy and throughput are described; and methods for improved modified base calling.Type: GrantFiled: July 28, 2021Date of Patent: November 21, 2023Assignee: Roche Sequencing Solutions, Inc.Inventors: Randall Davis, Michael Dorwart, Janine Mok
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Patent number: 11821041Abstract: The invention is a method of predicting recurrence of colorectal cancer in a patient following surgery, the method comprising analysis of circulating tumor DNA from a patient's sample.Type: GrantFiled: August 7, 2019Date of Patent: November 21, 2023Assignee: Roche Sequencing Solutions, Inc.Inventors: Hans-Peter Adams, Aarthi Balasubramanyam, Bernd Hinzmann, John Lee, John Palma, Andre Rosenthal, Urich-Peter Rohr
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Patent number: 11814676Abstract: A method of forming a plurality of lipid bilayers over an array of cells in a nanopore based sequencing chip is disclosed. Each of the cells comprises a well. A salt buffer solution is flowed over the array of cells in the nanopore based sequencing chip to substantially fill the wells in the cells with the salt buffer solution. A lipid and solvent mixture is flowed over the array of cells to deposit the lipid and solvent mixture over at least some of the wells in the cells. A first portion of the cells, each having a lipid bilayer over its well, is detected. A second portion of the cells, each having a lipid membrane but not a lipid bilayer over its well, is detected. An electrical lipid-thinning stimulus is selectively applied to the second portion of the cells but not to the first portion of the cells.Type: GrantFiled: June 21, 2021Date of Patent: November 14, 2023Assignee: Roche Sequencing Solutions, Inc.Inventors: Kevin Aliado, Roger J. A. Chen, Jing Luo, J. William Maney, Jr., William Nielsen, Kyle Umeda, Ashraf Wahba
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Patent number: 11802276Abstract: Disclosed are methods for isolating polymerase complexes from a mixture of polymerase complex components. The polymerase complexes can comprise a nanopore to provide isolated nanopore sequencing complexes. The methods relate to the positive and negative isolation of the polymerase complexes and/or nanopore sequencing complexes. Also disclosed is a nucleic acid adaptor for isolating active polymerase complexes, polymerase complexes comprising the nucleic acid adaptor, and methods for isolating active polymerase complexes using the nucleic acid adaptor.Type: GrantFiled: May 24, 2018Date of Patent: October 31, 2023Assignee: Roche Sequencing Solutions, Inc.Inventors: Helen Franklin, Cynthia Cech, Timothy Kellogg Craig, Aruna Ayer, Kirti Dhiman, Natalie B. Chechelski Johnston, Joshua N. Mabry, Arkadiusz Bibillo, Peter Crisalli, Randall W. Davis
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Publication number: 20230340589Abstract: Disclosed herein are apparatuses for nucleic acid sequencing using magnetic labels (e.g., magnetic particles) and magnetic sensors. Also disclosed are methods of making and using such apparatuses. An apparatus for nucleic acid sequencing comprises a plurality of magnetic sensors, a plurality of binding areas disposed above the plurality of magnetic sensors, each of the binding areas for holding fluid, and at least one line for detecting a characteristic of at least a first magnetic sensor of the plurality of magnetic sensors, the characteristic indicating presence or absence of one or more magnetic nanoparticles coupled to a first binding area associated with the first magnetic sensor.Type: ApplicationFiled: March 7, 2021Publication date: October 26, 2023Applicants: Western Digital Technologies, Inc., Roche Sequencing Solutions, Inc.Inventors: Patrick BRAGANCA, Neil Charles SMITH, Juraj TOPOLANCIK, Yann ASTIER
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Patent number: 11795508Abstract: The present invention provides methods for non-invasive determination of sex in a fetus or of Y chromosomal frequency abnormalities—indicative of aneuploidy or sex mosaicisms in a fetus—by detecting and determining the relative contribution genetic sequences from the Y chromosome in view of the percent fetal contribution in a maternal mixed sample.Type: GrantFiled: May 18, 2018Date of Patent: October 24, 2023Assignee: Roche Sequencing Solutions, Inc.Inventors: Craig Struble, Arnold Oliphant, Eric Wang
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Publication number: 20230332222Abstract: Described herein are variants of alpha-hemolysin having at least one amino acid substitution at H35G, E111N, M113A, and/or K147N in the mature, wild-type alpha-hemolysin amino acid sequence. In certain examples, the variant may have a substitution at E111S, M113S, T145S, K147S, or L135I in the mature alpha-hemolysin amino acid sequence. The ?-hemolysin variants may also include a substitution at H144A and/or a series of glycine residues spanning residues 127 to 131 of the mature, wild-type alpha hemolysin. Also provided are nanopore assemblies including the alpha-hemolysin variants, the assembly having an increased nanopore lifetime. Further, provided are variants that, in addition to providing increased lifetime, provide a decreased time-to-thread. Hence, the variants provided herein both increase nanopore lifetime and improve efficiency and accuracy of DNA sequencing reactions using nanopores comprising the variants.Type: ApplicationFiled: February 21, 2023Publication date: October 19, 2023Applicant: Roche Sequencing Solutions, Inc.Inventors: Mark Ambroso, Timothy Craig, Matthew DiPietro, Corissa Harris, Marshall Porter
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Patent number: 11788132Abstract: Techniques for measuring sequences of nucleic acids are provided. Time-based measurements (e.g., forming a histogram) particular to a given sequencing cell can be used to generate a tailored model. The model can include probability functions, each corresponding to different states (e.g., different states of a nanopore). Such probability functions can be fit to a histogram of measurements obtained for that cell. The probability functions can be updated over a sequencing run of the nucleic acid so that drifts in physical properties of the sequencing cell can be compensated. A hidden Markov model can use such probability functions as emission probabilities for determining the most likely nucleotide states over time. For sequencing cells involving a polymerase, a 2-state classification between bound and unbound states of the polymerase can be performed. The bound regions can be further analyzed by a second classifier to distinguish between states corresponding to different bound nucleotides.Type: GrantFiled: March 1, 2022Date of Patent: October 17, 2023Assignee: Roche Sequencing Solutions, Inc.Inventors: John Mannion, Morgan Mager
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Patent number: 11788073Abstract: Described herein is a variant pol6 polymerase having at least one mutation selected from H223, N224, Y225, H227, I295, Y342, T343, I357, S360, L361, I363, S365, S366, Y367, P368, D417, E475, Y476, F478, K518, H527, T529, M531, N535, G539, P542, N545, Q546, A547, L549, 1550, N552, G553, F558, A596, G603, A610, V615, Y622, C623, D624, I628, Y629, R632, N635, M641, A643, I644, T647, I648, T651, I652, K655, W656, D657, V658, H660, F662, L690 and combinations thereof.Type: GrantFiled: March 5, 2021Date of Patent: October 17, 2023Assignee: Roche Sequencing Solutions, Inc.Inventors: Aruna Ayer, Cleoma Arnold, Charles Wayan Schwab, Eileen Thai, Ilya Lederman, Colin Alexander McGaw, Tyler O'Brien Shultz
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Patent number: 11781171Abstract: The invention provides methods, compositions, kits and devices for the detection of target molecules. In some embodiments, the invention allows for multiplexed target molecule detection.Type: GrantFiled: April 12, 2023Date of Patent: October 10, 2023Assignee: ROCHE SEQUENCING SOLUTIONS, INC.Inventor: Garry P. Nolan
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Patent number: 11773511Abstract: Methods and compositions are described herein for primer extension target enrichment of immune receptor (BCR or TCR) sequences.Type: GrantFiled: August 18, 2020Date of Patent: October 3, 2023Assignee: Roche Sequencing Solutions, Inc.Inventors: Jan Berka, Carolina Dallett, Richard Dannebaum, Brian Godwin, Seoyoung Kim, Jainee Lewis, Khai Luong, Sedide Ozturk, Joseph Platzer, Florian Rubelt, Dilduz Telman
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Patent number: 11773388Abstract: The present disclosure provides a method for enrichment of at least one target nucleic acid in a library of nucleic acids. A first oligonucleotide is hybridized to a target nucleic acid in library of nucleic acids having first and second adapters. The hybridized first oligonucleotide is extended with a first polymerase, thereby producing a first primer extension complex including the target nucleic acid and the extended first oligonucleotide. The first primer extension complex is captured, enriched relative to the library of nucleic acids, and a second oligonucleotide is hybridized to the target nucleic acid. The hybridized second oligonucleotide is extended with a second polymerase, thereby producing a second primer extension complex including the target nucleic acid and the extended second oligonucleotide, and further liberating the extended first oligonucleotide from the first primer extension complex.Type: GrantFiled: June 22, 2020Date of Patent: October 3, 2023Assignees: Roche Sequencing Solutions, Inc., Kapa Biosystems, Inc.Inventors: Daniel Burgess, Brian Christopher Godwin, Alexander Lovejoy, Bronwen Miller, Jo-Anne Elizabeth Penkler, Joseph Platzer
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Patent number: 11773130Abstract: The present disclosure provides 3? protected nucleotides, including those 3? protected nucleotides having a detectable tag. Systems and methods of sequencing nucleic acids using the 3? protected nucleotides are also disclosed, such as the sequencing of a nucleic acid using a nanopore or the sequencing of a nucleic acid via sequencing-by-synthesis.Type: GrantFiled: July 6, 2022Date of Patent: October 3, 2023Assignee: Roche Sequencing Solutions, Inc.Inventors: Frank Bergmann, Peter Crisalli, Dieter Heindl, Omid Khakshoor, Meng Taing
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Patent number: 11767348Abstract: The present disclosure provides variant OmpG polypeptides, compositions comprising the OmpG variant polypeptides, and methods for using the variant OmpG polypeptides as nanopores for determining the sequence of single stranded nucleic acids. The variant OmpG nanopores reduce the ionic current noise versus the parental OmpG polypeptide from which they are derived and thereby enable sequencing of polynucleotides with single nucleotide resolution. The reduced ionic current noise also provides for the use of these OmpG nanopore variants in other single molecule sensing applications, e.g., protein sequencing.Type: GrantFiled: July 10, 2020Date of Patent: September 26, 2023Assignee: Roche Sequencing Solutions, Inc.Inventors: Cynthia Cech, Tim Craig, Christos Tzitzilonis, Alexander Yang, Liv Jensen, Charlotte Yang, Corissa Harris, Matthew Dipietro, Dhruti Dalal
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Patent number: 11768195Abstract: A method of forming a nanopore in a lipid bilayer is disclosed. A nanopore forming solution is deposited over a lipid bilayer. The nanopore forming solution has a concentration level and a corresponding activity level of pore molecules such that nanopores are substantially not formed un-stimulated in the lipid bilayer. Formation of a nanopore in the lipid bilayer is initiated by applying an agitation stimulus level to the lipid bilayer. In some embodiments, the concentration level and the corresponding activity level of pore molecules are at levels such that less than 30 percent of a plurality of available lipid bilayers have nanopores formed un-stimulated therein.Type: GrantFiled: August 16, 2021Date of Patent: September 26, 2023Assignee: Roche Sequencing Solutions, Inc.Inventors: Roger J. A. Chen, Randall Davis
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Patent number: 11761033Abstract: The present invention relates to a kit and a method of linear amplification of a least one nucleic acid target in a sample, said method comprising: (a) contacting each target in the sample with a nucleic acid polymerase and a primer comprising a component preventing copying of the primer by the nucleic acid polymerase; and at least one nuclease blocking nucleotide; (b) generating a primer extension product; (c) preventing priming by the 3?-end of the primer extension product, and (d) repeating steps b) and c) at least once.Type: GrantFiled: April 16, 2020Date of Patent: September 19, 2023Assignee: Roche Sequencing Solutions, Inc.Inventor: Brian Christopher Godwin
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Patent number: 11753738Abstract: The invention relates to a method for making nanopores in thin layers or monolayers of transition metal dichalcogenides that enables accurate and controllable formation of pore within those thin layer(s) with sub-nanometer precision.Type: GrantFiled: July 28, 2022Date of Patent: September 12, 2023Assignees: Ecole Polytechnique Federale De Lausanne (EPFL), Roche Sequencing Solutions, Inc.Inventors: Jiandong Feng, Ke Liu, Aleksandra Radenovic, Yann Astier