Patents by Inventor Zhoutao Chen
Zhoutao Chen 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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Publication number: 20240026442Abstract: The present disclosure provides methods and compositions for tracking nucleic acid fragment origin by target-specific barcode tagging when original nucleic acid targets break into small fragments. Nucleic acid targets are captured in vitro on a solid support with clonally localized nucleic acid barcode templates. Many nucleic acid targets can be processed simultaneously in a massively parallel fashion without partition. These nucleic acid target tracking methods can be used for a variety of applications in both whole genome sequencing and targeted sequencing in order to accurately identify genomic variants, haplotype phasing and assembly, for example.Type: ApplicationFiled: October 3, 2023Publication date: January 25, 2024Applicant: Universal Sequencing Technology CorporationInventors: Zhoutao CHEN, Tsai-Chin WU, Long Kim PHAM, Yong WANG
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Patent number: 11807903Abstract: The present disclosure provides methods and compositions for tracking nucleic acid fragment origin by target-specific barcode tagging when original nucleic acid targets break into small fragments. Nucleic acid targets are captured in vitro on a solid support with clonally localized nucleic acid barcode templates. Many nucleic acid targets canbe processed simultaneously in a massively parallel fashion without partition. These nucleic acid target tracking methods can be used for a variety of applications in both whole genome sequencing and targeted sequencing in order to accurately identify genomic variants, haplotype phasing and assembly, for example.Type: GrantFiled: February 8, 2019Date of Patent: November 7, 2023Assignee: Universal Sequencing Technology CorporationInventors: Zhoutao Chen, Tsai-Chin Wu, Long Kim Pham, Yong Wang
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Publication number: 20230340554Abstract: In some embodiments, the present teachings provide compositions, systems, methods and kits for generating a population of nucleic acid fragments. In some embodiments, nucleic acids can be fragmented enzymatically. For example, methods for generating a population of nucleic acid fragments can include a nucleic acid nicking reaction. In one embodiment, the methods can include a nick translation reaction. A nicking reaction can introduce nicks at random positions on either strand of a double-stranded nucleic acid. A nick translation reaction can move the position of nicks to a new position so that the new positions of two of the nicks are aligned to create a double-stranded break. In some embodiments, methods for generating a population of nucleic acid fragments can include joining at least one end of a fragmented nucleic acid to one or more oligonucleotide adaptors.Type: ApplicationFiled: December 14, 2022Publication date: October 26, 2023Inventors: Zhoutao CHEN, Xiaoping DUAN, Kyusung PARK
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Publication number: 20230220453Abstract: The present disclosure provides methods and kits for tracking nucleic acid target origin by barcode tagging of the targets when they break into smaller fragments. Nucleic acid targets are captured in vitro by clonally localized nucleic acid barcode templates on a solid support. Millions of nucleic acid targets can be processed simultaneously in a massively parallel fashion without additional partition. These captured targets are broken into small fragments, and a target specific barcode sequence is tagged on each fragment as an identification of their original target. These nucleic acid target tracking methods can be used for a variety of applications in both whole genome sequencing and targeted sequencing.Type: ApplicationFiled: January 3, 2023Publication date: July 13, 2023Applicant: Universal Sequencing Technology CorporationInventors: Zhoutao Chen, Long Kim Pham, Junchen Gu, Ming Lei
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Publication number: 20230151355Abstract: The present disclosure provides methods for high throughput barcoding nucleic acids and/or protein inside the cells. The in-cell single cell capture method uses an individual cell itself as a compartment and delivers a plurality of unique identifiers, e.g. barcodes into the cell and captures the nucleic acid and/or protein targets within the cell directly. It significantly simplifies single cell analysis experimental setup and eliminates the need of external compartment generation. It provides a high throughput single cell expression profiling and cellular protein quantitation method. Targeted sequencing with in-cell capture will be able to significantly increase sensitivity and specificity for low frequent mutation detection, such as, somatic mutation in very early stage of cancer and truly enables early cancer detection.Type: ApplicationFiled: March 12, 2020Publication date: May 18, 2023Inventors: Zhoutao Chen, Devin Porter
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Publication number: 20230081062Abstract: The present disclosure provides methods for high throughput barcoding nucleic acids and/or protein inside the cells. The in-cell single cell capture method uses an individual cell itself as a compartment and delivers a plurality of unique identifiers, e.g., barcodes into the cell and captures the nucleic acid and/or protein targets within the cell directly. It significantly simplifies single cell analysis experimental setup and eliminates the need of external compartment generation. It provides a high throughput single cell expression profiling and cellular protein quantitation method, and targeted sequencing with in-cell capture will be able to significantly increase sensitivity and specificity for low frequent mutation detection, such as, somatic mutation in very early stage of cancer and truly enables early cancer detection. A spatial expression and/or variation detection method for a tissue sample is developed with the combination of the in-cell barcoding method and positional barcode on a planar array.Type: ApplicationFiled: February 12, 2021Publication date: March 16, 2023Applicant: Universal Sequencing Technology CorporationInventors: Zhoutao Chen, Devin Porter
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Patent number: 11542535Abstract: In some embodiments, the present teachings provide compositions, systems, methods and kits for generating a population of nucleic acid fragments. In some embodiments, nucleic acids can be fragmented enzymatically. For example, methods for generating a population of nucleic acid fragments can include a nucleic acid nicking reaction. In one embodiment, the methods can include a nick translation reaction. A nicking reaction can introduce nicks at random positions on either strand of a double-stranded nucleic acid. A nick translation reaction can move the position of nicks to a new position so that the new positions of two of the nicks are aligned to create a double-stranded break. In some embodiments, methods for generating a population of nucleic acid fragments can include joining at least one end of a fragmented nucleic acid to one or more oligonucleotide adaptors.Type: GrantFiled: June 25, 2014Date of Patent: January 3, 2023Assignee: Life Technologies CorporationInventors: Zhoutao Chen, Xiaoping Duan, Kyusung Park
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Publication number: 20220325275Abstract: The present invention provides methods to barcode nucleic acid for detection and sequencing. It applies a barcode template in a compartment with various targets, including nucleic acid fragments, nuclei and/or cells. After clonal amplification within the compartment, barcode sequence will integrate into its targets before the compartment is broken so that it will effectively barcode nucleic acid fragments originated from a nucleic acid fragment, a nucleus or a cell clonally. The barcode information can be used for tracking the origin of the fragment, nucleus or cell and be used for haplotype phasing and a variety of single cell-based applications N including whole genome sequencing, targeted sequencing, RNA sequencing and immune repertoire sequencing.Type: ApplicationFiled: June 4, 2020Publication date: October 13, 2022Inventors: Zhoutao Chen, Devin Porter, Guoya Mo, Tsai-Chin Wu
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Publication number: 20220298545Abstract: The present disclosure provides methods and compositions for tracking nucleic acid fragment origin by target-specific barcode tagging when original nucleic acid targets break into small fragments. Nucleic acid targets are captured in vitro on a solid support with clonally localized nucleic acid barcode templates. Many nucleic acid targets can be processed simultaneously in a massively parallel fashion without partition. These nucleic acid target tracking methods can be used for a variety of applications in both whole genome sequencing and targeted sequencing in order to accurately identify genomic variants, haplotype phasing and assembly, for example.Type: ApplicationFiled: August 19, 2020Publication date: September 22, 2022Inventors: Zhoutao Chen, Tsai-Chin Wu, Long Kim Pham, Yong Wang, Ming Lei
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Publication number: 20210047683Abstract: The present disclosure provides methods and compositions for tracking nucleic acid fragment origin by target-specific barcode tagging when original nucleic acid targets break into small fragments. Nucleic acid targets are captured in vitro on a solid support with clonally localized nucleic acid barcode templates. Many nucleic acid targets canbe processed simultaneously in a massively parallel fashion without partition. These nucleic acid target tracking methods can be used for a variety of applications in both whole genome sequencing and targeted sequencing in order to accurately identify genomic variants, haplotype phasing and assembly, for example.Type: ApplicationFiled: February 8, 2019Publication date: February 18, 2021Inventors: Zhoutao CHEN, Tsai-Chin WU, Long Kim PHAM, Yong WANG
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Publication number: 20200115752Abstract: Provided herein are compositions, systems, methods, and kits for joining together the ends of one or more polynucleotides using at least one pair of blocking oligonucleotide adaptors. Blocking oligonucleotide adaptors can be used to reduce the formation of adaptor dimers or trimers (or higher-order concatemers) which can improve the yield of desirable polynucleotide-adaptor products in any recombinant nucleic acid workflow. Blocking oligonucleotide adaptors can comprise a double-stranded oligonucleotide adaptor (duplex) having an overhang cohesive portion that anneals with a blocking oligonucleotide which can be a separate single-stranded oligonucleotide. A blocking oligonucleotide, when annealed to an overhang portion, can prevent undesirable hybridization of the overhang portion to another nucleic acid, such as the overhang portion from another blocking oligonucleotide adaptor or a polynucleotide of interest.Type: ApplicationFiled: October 21, 2019Publication date: April 16, 2020Inventors: Bin LI, Zhoutao CHEN, Tanya BIORAC, Melvin WEI
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Patent number: 10508306Abstract: In some embodiments, methods for obtaining sequence information from a nucleic acid template linked to a support include hybridizing a first primer to a template strand linked to a support, sequencing a portion of the nucleic acid template, thereby forming an extended first primer product that is complementary to a portion of the nucleic acid template, In some embodiments, the method further includes introducing a nick into a portion of the template strand that is hybridized to the extended first primer product, degrading a portion of the template strand from the nick using a degrading agent, where a portion of the extended first primer remains hybridized to an undegraded portion of the template strand, and sequencing at least some of the single-stranded portion of the extended first primer by synthesis.Type: GrantFiled: September 6, 2018Date of Patent: December 17, 2019Assignee: LIFE TECHNOLOGIES CORPORATIONInventors: Jason Myers, Zhoutao Chen, Devin Dressman, Theo Nikiforov
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Patent number: 10450608Abstract: Provided herein are compositions, systems, methods, and kits for joining together the ends of one or more polynucleotides using at least one pair of blocking oligonucleotide adaptors. Blocking oligonucleotide adaptors can comprise a double-stranded oligonucleotide adaptor (duplex) having an overhang cohesive portion that anneals with a blocking oligonucleotide which can be a separate single-stranded oligonucleotide. Also provided herein are compositions generated using the blocking oligonucleotide adapters, including circularized polynucleotides, that may be manipulated, for example, through nick translation, to yield a linear mate pair construct.Type: GrantFiled: December 8, 2016Date of Patent: October 22, 2019Assignee: LIFE TECHNOLOGIES CORPORATIONInventors: Bin Li, Zhoutao Chen, Tanya Biorac, Melvin Wei
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Publication number: 20190078150Abstract: The present disclosure provides methods and kits for tracking nucleic acid target origin by barcode tagging of the targets when they break into smaller fragments. Nucleic acid targets are captured in vitro by clonally localized nucleic acid barcode templates on a solid support. Millions of nucleic acid targets can be processed simultaneously in a massively parallel fashion without additional partition. These captured targets are broken into small fragments, and a target specific barcode sequence is tagged on each fragment as an identification of their original target. These nucleic acid target tracking methods can be used for a variety of applications in both whole genome sequencing and targeted sequencing.Type: ApplicationFiled: March 1, 2017Publication date: March 14, 2019Inventors: Zhoutao Chen, Long Kim Pham, Junchen Gu, Ming Lei
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Publication number: 20180371541Abstract: In some embodiments, methods for obtaining sequence information from a nucleic acid template linked to a support include hybridizing a first primer to a template strand linked to a support, sequencing a portion of the nucleic acid template, thereby forming an extended first primer product that is complementary to a portion of the nucleic acid template, In some embodiments, the method further includes introducing a nick into a portion of the template strand that is hybridized to the extended first primer product, degrading a portion of the template strand from the nick using a degrading agent, where a portion of the extended first primer remains hybridized to an undegraded portion of the template strand, and sequencing at least some of the single-stranded portion of the extended first primer by synthesis.Type: ApplicationFiled: September 6, 2018Publication date: December 27, 2018Inventors: Jason Myers, Zhoutao Chen, Devin Dressman, Theo Nikiforov
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Publication number: 20180298436Abstract: The present disclosure provides, in one aspect, a device and a method for unit sequencing and/or analysis of a molecular sequence comprising attaching the molecular sequence to a plate and controlling the progression of the molecular sequence through a pore of a nanopore chip, wherein the separation distance between the nanopore chip and the scan plate is controlled by a precision mechanical drive, and the molecular sequence is sensed as it progresses through the nanopore.Type: ApplicationFiled: October 31, 2016Publication date: October 18, 2018Inventors: Ming Lei, Robert Roorda, Zhoutao Chen, Nga Ho, Yong Wang
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Patent number: 10081837Abstract: In some embodiments, methods for obtaining sequence information from a nucleic acid template linked to a support include hybridizing a first primer to a template strand linked to a support, sequencing a portion of the nucleic acid template, thereby forming an extended first primer product that is complementary to a portion of the nucleic acid template, In some embodiments, the method further includes introducing a nick into a portion of the template strand that is hybridized to the extended first primer product, degrading a portion of the template strand from the nick using a degrading agent, where a portion of the extended first primer remains hybridized to an undegraded portion of the template strand, and sequencing at least some of the single-stranded portion of the extended first primer by synthesis.Type: GrantFiled: October 11, 2017Date of Patent: September 25, 2018Assignee: Life Technologies CorporationInventors: Jason Myers, Zhoutao Chen, Devin Dressman, Theo Nikiforov
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Publication number: 20180030534Abstract: In some embodiments, methods for obtaining sequence information from a nucleic acid template linked to a support include hybridizing a first primer to a template strand linked to a support, sequencing a portion of the nucleic acid template, thereby forming an extended first primer product that is complementary to a portion of the nucleic acid template, In some embodiments, the method further includes introducing a nick into a portion of the template strand that is hybridized to the extended first primer product, degrading a portion of the template strand from the nick using a degrading agent, where a portion of the extended first primer remains hybridized to an undegraded portion of the template strand, and sequencing at least some of the single-stranded portion of the extended first primer by synthesis.Type: ApplicationFiled: October 11, 2017Publication date: February 1, 2018Inventors: Jason MYERS, Zhoutao CHEN, Devin DRESSMAN, Theo NIKIFOROV
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Patent number: 9822411Abstract: In some embodiments, methods for obtaining sequence information from a nucleic acid template linked to a support include hybridizing a first primer to a template strand linked to a support, sequencing a portion of the nucleic acid template, thereby forming an extended first primer product that is complementary to a portion of the nucleic acid template, In some embodiments, the method further includes introducing a nick into a portion of the template strand that is hybridized to the extended first primer product, degrading a portion of the template strand from the nick using a degrading agent, where a portion of the extended first primer remains hybridized to an undegraded portion of the template strand, and sequencing at least some of the single-stranded portion of the extended first primer by synthesis.Type: GrantFiled: February 3, 2017Date of Patent: November 21, 2017Assignee: LIFE TECHNOLOGIES CORPORATIONInventors: Jason Myers, Zhoutao Chen, Devin Dressman, Theo Nikiforov
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Publication number: 20170145500Abstract: In some embodiments, methods for obtaining sequence information from a nucleic acid template linked to a support include hybridizing a first primer to a template strand linked to a support, sequencing a portion of the nucleic acid template, thereby forming an extended first primer product that is complementary to a portion of the nucleic acid template, In some embodiments, the method further includes introducing a nick into a portion of the template strand that is hybridized to the extended first primer product, degrading a portion of the template strand from the nick using a degrading agent, where a portion of the extended first primer remains hybridized to an undegraded portion of the template strand, and sequencing at least some of the single-stranded portion of the extended first primer by synthesis.Type: ApplicationFiled: February 3, 2017Publication date: May 25, 2017Inventors: Jason MYERS, Zhoutao CHEN, Devin DRESSMAN, Theo NIKIFOROV