Patents by Inventor Chiu Tai Andrew Wong
Chiu Tai Andrew Wong has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Patent number: 11959074Abstract: A method for sequencing a target polynucleotide includes detecting a first series of nucleotide incorporations complementary to at least a portion of the target polynucleotide. The first series of nucleotide incorporations forms a first complementary polynucleotide. The target nucleotide is secured to a substrate disposed in a sequencing zone of an assembly. The method further includes moving the substrate to which the target nucleotide is secured to a templating zone of the assembly; removing the first complementary polynucleotide when the substrate is disposed at the templating zone of the assembly, the target polynucleotide remaining secured to the substrate; following the removing, moving the substrate to which the target polynucleotide is secured to the sequencing zone; and detecting a second series of nucleotide incorporations complementary to at least a portion of the target polynucleotide, the second series of nucleotide incorporations forming a second complementary polynucleotide.Type: GrantFiled: November 12, 2021Date of Patent: April 16, 2024Inventors: Chiu Tai Andrew Wong, Kylan Szeto, Shanti Shankar, Mark Beauchemin
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Patent number: 11905558Abstract: A sequencing system includes an automated sequencing instrument adapted to determine variant calls for one or more extracted polynucleotide samples with a performance of at least 98.5% raw read accuracy and a run time in a range of 5 hours to 14 hours to determine variant calls for 4 extracted polynucleotide samples using a targeted assay with one DNA pool per sample and an average amplicon size in a range of 100 to 120 bases.Type: GrantFiled: August 14, 2020Date of Patent: February 20, 2024Assignee: Life Technologies CorporationInventors: Mark Reed, Chiu Tai Andrew Wong, David Marran
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Publication number: 20220170093Abstract: A sequencing system includes an automated sequencing instrument adapted to determine variant calls for one or more extracted polynucleotide samples with a performance of at least 98.5% raw read accuracy and a total instrument run time in a range of 16 hours to 22 hours to determine variant calls when sequencing 6 cfTNA extracted polynucleotide samples using a targeted assay with one nucleic acid pool per sample.Type: ApplicationFiled: November 16, 2021Publication date: June 2, 2022Inventors: Joseph PODHASKY, Mark REED, David MARRAN, Chiu Tai Andrew WONG, Angie CHENG, Ru CAO
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Publication number: 20220154176Abstract: A method for sequencing a target polynucleotide includes detecting a first series of nucleotide incorporations complementary to at least a portion of the target polynucleotide. The first series of nucleotide incorporations forms a first complementary polynucleotide. The target nucleotide is secured to a substrate disposed in a sequencing zone of an assembly. The method further includes moving the substrate to which the target nucleotide is secured to a templating zone of the assembly; removing the first complementary polynucleotide when the substrate is disposed at the templating zone of the assembly, the target polynucleotide remaining secured to the substrate; following the removing, moving the substrate to which the target polynucleotide is secured to the sequencing zone; and detecting a second series of nucleotide incorporations complementary to at least a portion of the target polynucleotide, the second series of nucleotide incorporations forming a second complementary polynucleotide.Type: ApplicationFiled: November 12, 2021Publication date: May 19, 2022Inventors: Chiu Tai Andrew WONG, Kylan SZETO, Shanti SHANKAR, Mark BEAUCHEMIN
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Publication number: 20220146450Abstract: A method for correcting nucleotide incorporation signals for fluid potential effects or disturbances arising in nucleic acid sequencing-by-synthesis includes: disposing a plurality of template polynucleotide strands in a plurality of defined spaces disposed on a sensor array, the template polynucleotide strands having a sequencing primer and a polymerase bound therewith; exposing the template polynucleotide strands to a series of flows of nucleotide species flowed through a fluid manifold, the fluid manifold comprising passages for flowing nucleotide species and a branch passage for flowing a solution, the branch passage comprising a reference electrode and a sensing electrode; obtaining a plurality of nucleotide incorporation signals corresponding to the plurality of defined spaces, the nucleotide incorporation signals having a signal intensity related to a number of nucleotide incorporations; and correcting at least some of the plurality of nucleotide incorporation signals for fluid potential effects or disType: ApplicationFiled: October 12, 2021Publication date: May 12, 2022Inventors: Chiu Tai Andrew WONG, Todd REARICK, John DONOHUE
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Patent number: 11169111Abstract: A method for correcting nucleotide incorporation signals for fluid potential effects or disturbances arising in nucleic acid sequencing-by-synthesis includes: disposing a plurality of template polynucleotide strands in a plurality of defined spaces disposed on a sensor array, the template polynucleotide strands having a sequencing primer and a polymerase bound therewith; exposing the template polynucleotide strands to a series of flows of nucleotide species flowed through a fluid manifold, the fluid manifold comprising passages for flowing nucleotide species and a branch passage for flowing a solution, the branch passage comprising a reference electrode and a sensing electrode; obtaining a plurality of nucleotide incorporation signals corresponding to the plurality of defined spaces, the nucleotide incorporation signals having a signal intensity related to a number of nucleotide incorporations; and correcting at least some of the plurality of nucleotide incorporation signals for fluid potential effects or disType: GrantFiled: March 22, 2019Date of Patent: November 9, 2021Assignee: Life Technologies CorporationInventors: Chiu Tai Andrew Wong, Todd Rearick, John Donohue
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Publication number: 20210054450Abstract: A sequencing system includes an automated sequencing instrument adapted to determine variant calls for one or more extracted polynucleotide samples with a performance of at least 98.5% raw read accuracy and a run time in a range of 5 hours to 14 hours to determine variant calls for 4 extracted polynucleotide samples using a targeted assay with one DNA pool per sample and an average amplicon size in a range of 100 to 120 bases.Type: ApplicationFiled: August 14, 2020Publication date: February 25, 2021Inventors: Mark REED, Chiu Tai Andrew WONG, David MARRAN
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Publication number: 20200072826Abstract: The disclosure generally relates to systems, methods, and apparatuses for magnetic bead loading. An example embodiment of the disclosure relates to mixing magnetic beads with sequencing beads to form a solution. The solution containing both beads is injected onto a microchip having a plurality of microwells. The magnetic beads may have larger diameter than the microwell while the sequencing beads may have a smaller diameter, allowing them to enter and reside in the microwell. One or more magnets positioned under the microchip move back and forth across the microchip surface. The magnetic beads form a line and follow the movement of the magnets. During rounds of sweeping, the sequencing beads load into the respective wells. The magnets may be disengaged and the magnetic beads may be washed away after the sequencing beads are loaded.Type: ApplicationFiled: August 16, 2019Publication date: March 5, 2020Inventors: Hua YU, Xiaoling YANG, Rui ZHENG, Chiu Tai Andrew WONG, Jeremy GRAY
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Publication number: 20200041444Abstract: A method for correcting nucleotide incorporation signals for fluid potential effects or disturbances arising in nucleic acid sequencing-by-synthesis includes: disposing a plurality of template polynucleotide strands in a plurality of defined spaces disposed on a sensor array, the template polynucleotide strands having a sequencing primer and a polymerase bound therewith; exposing the template polynucleotide strands to a series of flows of nucleotide species flowed through a fluid manifold, the fluid manifold comprising passages for flowing nucleotide species and a branch passage for flowing a solution, the branch passage comprising a reference electrode and a sensing electrode; obtaining a plurality of nucleotide incorporation signals corresponding to the plurality of defined spaces, the nucleotide incorporation signals having a signal intensity related to a number of nucleotide incorporations; and correcting at least some of the plurality of nucleotide incorporation signals for fluid potential effects or disType: ApplicationFiled: March 22, 2019Publication date: February 6, 2020Inventors: Chiu Tai Andrew WONG, Todd REARICK, John DONOHUE
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Patent number: 10416112Abstract: A method for correcting nucleotide incorporation signals for fluid potential effects or disturbances arising in nucleic acid sequencing-by-synthesis includes: disposing a plurality of template polynucleotide strands in a plurality of defined spaces disposed on a sensor array, the template polynucleotide strands having a sequencing primer and a polymerase bound therewith; exposing the template polynucleotide strands to a series of flows of nucleotide species flowed through a fluid manifold, the fluid manifold comprising passages for flowing nucleotide species and a branch passage for flowing a solution, the branch passage comprising a reference electrode and a sensing electrode; obtaining a plurality of nucleotide incorporation signals corresponding to the plurality of defined spaces, the nucleotide incorporation signals having a signal intensity related to a number of nucleotide incorporations; and correcting at least some of the plurality of nucleotide incorporation signals for fluid potential effects or disType: GrantFiled: September 14, 2015Date of Patent: September 17, 2019Assignee: LIFE TECHNOLOGIES CORPORATIONInventors: Chiu Tai Andrew Wong, Todd Rearick, John Donohue
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Publication number: 20190204293Abstract: A chemical sensor for analyte solutions utilizes AC excitation of a sample distributed in one or more micro-wells of a measurement device. The sensors utilize narrowband filtering of the measured signal(s), resulting in a large reduction in noise. Synchronous detection is utilized to provide high discrimination of the desired signal from noise or interfering sources. Conductance and by extension impedance is measured by applying a constant alternating current (AC) voltage across the electrodes of each micro-well and measuring the resulting current.Type: ApplicationFiled: December 21, 2018Publication date: July 4, 2019Inventors: John DONOHUE, Phil WAGGONER, Scott PARKER, Wolfgang HINZ, Chiu Tai Andrew WONG
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Patent number: 10192024Abstract: An embodiment of a method for generating a flow order that minimizes the accumulation of phasic synchrony error in sequence data is described that comprises the steps of: (a) generating a plurality of sequential orderings of nucleotides species comprising a k-base length, wherein the sequential orderings define a sequence of introduction of nucleotide species into a sequencing by synthesis reaction environment; (b) simulating acquisition of sequence data from one or more reference genomes using the sequential orderings, wherein the sequence data comprises an accumulation of phasic synchrony error; and (c) selecting one or more of the sequential orderings using a read length parameter and an extension rate parameter.Type: GrantFiled: March 13, 2013Date of Patent: January 29, 2019Assignee: 454 Life Sciences CorporationInventors: Yi-Ju Chen, Chiu Tai Andrew Wong
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Publication number: 20170030854Abstract: Provided herein is a sensor comprising a substrate having a first reaction region and a second reaction region, a first electrode associated with the first reaction region, a second electrode associated with the second reaction region and a third electrode wherein the third electrode is common to both the first reaction region and the second reaction region.Type: ApplicationFiled: July 28, 2016Publication date: February 2, 2017Inventors: Creighton BUIE, John DONOHUE, Chiu Tai Andrew WONG, James A. BALL, Wolfgang HINZ, James BUSTILLO, Jordan OWENS, Shifeng LI
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Patent number: 9317654Abstract: Provided herein are methods for correcting an error associated with phasic synchrony of sequence data generated from a population of template molecules by detecting signals generated in response to nucleotide species introduced during a sequencing reaction; generating an observed value for the signal detected from each of the nucleotide species; defining positive incorporation values and negative incorporation values from the observed values using a carry forward value and an incomplete extension value; revising the carry forward value and the incomplete extension value using a noise value derived from observed values associated with the negative incorporation values; re-defining the positive incorporation values and the negative incorporation values using the revised carry forward value and the revised incomplete extension value; and repeating the steps of revising and re-defining until convergence of the positive incorporation values and the negative incorporation values.Type: GrantFiled: December 18, 2012Date of Patent: April 19, 2016Assignee: 454 Life Sciences CorporationInventors: Yi-Ju Chen, Chiu Tai Andrew Wong
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Publication number: 20160103093Abstract: A method for correcting nucleotide incorporation signals for fluid potential effects or disturbances arising in nucleic acid sequencing-by-synthesis includes: disposing a plurality of template polynucleotide strands in a plurality of defined spaces disposed on a sensor array, the template polynucleotide strands having a sequencing primer and a polymerase bound therewith; exposing the template polynucleotide strands to a series of flows of nucleotide species flowed through a fluid manifold, the fluid manifold comprising passages for flowing nucleotide species and a branch passage for flowing a solution, the branch passage comprising a reference electrode and a sensing electrode; obtaining a plurality of nucleotide incorporation signals corresponding to the plurality of defined spaces, the nucleotide incorporation signals having a signal intensity related to a number of nucleotide incorporations; and correcting at least some of the plurality of nucleotide incorporation signals for fluid potential effects or disType: ApplicationFiled: September 14, 2015Publication date: April 14, 2016Inventors: Chiu Tai Andrew WONG, Todd REARICK, John DONOHUE
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Publication number: 20140073511Abstract: An embodiment of a method for sequencing a species of nucleic acid template using pH inert reference sensors is described that comprises the steps of: introducing a nucleotide species to an array of wells where a plurality of the wells comprise a species of nucleic acid template and a plurality of the wells comprise a plurality of functional groups with a high pH buffering characteristic, and in at least a first well a polymerase species incorporates the nucleotide species into a plurality of strands complementary to the species of nucleic acid template disposed in the first well and results in a release of a plurality of hydrogen ions; detecting a signal in the first well that is responsive to the hydrogen ions and one or more noise sources; detecting a signal in a second well comprising the functional groups with the high pH buffering characteristic that is responsive to the one or more noise sources; and subtracting the second well signal from the first well signal to generate a corrected signal associatedType: ApplicationFiled: August 19, 2013Publication date: March 13, 2014Inventors: Chiu Tai Andrew Wong, Gianni Calogero Ferreri, Sagnik Basuray, Arthika Bappal, Suresh Gopalkrishna Shenoy, Xavier Victor Gomes
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Publication number: 20130311105Abstract: An embodiment of a method for generating a flow order that minimizes the accumulation of phasic synchrony error in sequence data is described that comprises the steps of: (a) generating a plurality of sequential orderings of nucleotides species comprising a k-base length, wherein the sequential orderings define a sequence of introduction of nucleotide species into a sequencing by synthesis reaction environment; (b) simulating acquisition of sequence data from one or more reference genomes using the sequential orderings, wherein the sequence data comprises an accumulation of phasic synchrony error; and (c) selecting one or more of the sequential orderings using a read length parameter and an extension rate parameter.Type: ApplicationFiled: March 13, 2013Publication date: November 21, 2013Inventors: Yi-Ju Chen, Chiu Tai Andrew Wong
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Patent number: 8364417Abstract: An embodiment of a method for correcting an error associated with phasic synchrony of sequence data generated from a population of template molecules is described that comprises the steps of detecting signals generated in response to nucleotide species introduced during a sequencing reaction; generating an observed value for the signal detected from each of the nucleotide species; defining positive incorporation values and negative incorporation values from the observed values using a carry forward value and an incomplete extension value; and revising the carry forward value and the incomplete extension value using a noise value that is derived from observed values associated with the negative incorporation values.Type: GrantFiled: March 8, 2011Date of Patent: January 29, 2013Assignee: 454 Life Sciences CorporationInventors: Yi-Ju Chen, Chiu Tai Andrew Wong
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Publication number: 20110287432Abstract: An embodiment of a method for optimizing sequencing performance is described that comprises the steps of calculating a nucleotide species specific degradation rate of an apyrase enzyme for a plurality of nucleotide species; determining a concentration for each of the nucleotide species using the nucleotide species specific degradation rate; iteratively providing the concentration of each of the nucleotide species in a reaction environment comprising a polymerase enzyme and a species of template nucleic acid molecule, wherein one or more molecules of the nucleotide species are incorporated into a nascent molecule in a sequencing reaction and the apyrase enzyme is introduced to the reaction environment to degrade unincorporated nucleotide species molecules; and detecting a signal in response to the incorporation of the nucleotide species.Type: ApplicationFiled: May 18, 2011Publication date: November 24, 2011Inventors: Chiu Tai Andrew Wong, Yi-Ju Chen, Vinod Bhagwan Makhijani
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Publication number: 20110213563Abstract: An embodiment of a method for correcting an error associated with phasic synchrony of sequence data generated from a population of template molecules is described that comprises the steps of detecting signals generated in response to nucleotide species introduced during a sequencing reaction; generating an observed value for the signal detected from each of the nucleotide species; defining positive incorporation values and negative incorporation values from the observed values using a carry forward value and an incomplete extension value; revising the carry forward value and the incomplete extension value using a noise value that is derived from observed values associated with the negative incorporation values; re-defining the positive incorporation values and the negative incorporation values using the revised carry forward value and the revised incomplete extension value; and repeating the steps of revising and re-defining until convergence of the positive incorporation values and the negative incorporationType: ApplicationFiled: March 8, 2011Publication date: September 1, 2011Applicant: 454 LIFE SCIENCES CORPORATIONInventors: Yi-Ju Chen, Chiu Tai Andrew Wong