Patents by Inventor Jianbiao Zheng
Jianbiao Zheng 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: 11821030Abstract: Methods for multiplex amplification of a plurality of targets of distinct sequence from a complex mixture are disclosed. In one aspect targets are circularized using a single circularization probe that is complementary to two regions in the target that flank a region to be amplified. The targets may hybridize to the circularization probe so that 5? or 3? flaps are generated and methods for removing flaps and circularizing the resulting product are disclosed. In another aspect targets are hybridized to dU probes so that 5? and 3? flaps are generated. The flaps are cleaved using 5? or 3? flap endonucleases or 3? to 5? exonucleases. The target sequences are then ligated to common primers, the dU probes digested and the ligated targets amplified.Type: GrantFiled: October 26, 2020Date of Patent: November 21, 2023Assignee: AFFYMETRIX, INC.Inventors: Jianbiao Zheng, Li Weng, Malek Faham
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Publication number: 20210123091Abstract: Methods for multiplex amplification of a plurality of targets of distinct sequence from a complex mixture are disclosed. In one aspect targets are circularized using a single circularization probe that is complementary to two regions in the target that flank a region to be amplified. The targets may hybridize to the circularization probe so that 5? or 3? flaps are generated and methods for removing flaps and circularizing the resulting product are disclosed. In another aspect targets are hybridized to dU probes so that 5? and 3? flaps are generated. The flaps are cleaved using 5? or 3? flap endonucleases or 3? to 5? exonucleases. The target sequences are then ligated to common primers, the dU probes digested and the ligated targets amplified.Type: ApplicationFiled: October 26, 2020Publication date: April 29, 2021Inventors: Jianbiao Zheng, Li Weng, Malek Faham
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Patent number: 10822649Abstract: Methods for multiplex amplification of a plurality of targets of distinct sequence from a complex mixture are disclosed. In one aspect targets are circularized using a single circularization probe that is complementary to two regions in the target that flank a region to be amplified. The targets may hybridize to the circularization probe so that 5? or 3? flaps are generated and methods for removing flaps and circularizing the resulting product are disclosed. In another aspect targets are hybridized to dU probes so that 5? and 3? flaps are generated. The flaps are cleaved using 5? or 3? flap endonucleases or 3? to 5? exonucleases. The target sequences are then ligated to common primers, the dU probes digested and the ligated targets amplified.Type: GrantFiled: October 2, 2018Date of Patent: November 3, 2020Assignee: AFFYMETRIX, INC.Inventors: Jianbiao Zheng, Li Weng, Malek Faham
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Patent number: 10526650Abstract: The invention is directed to sequence-based profiling of populations of nucleic acids by multiplex amplification and attachment of one or more sequence tags to target nucleic acids and/or copies thereof followed by high-throughput sequencing of the amplification product. In some embodiments, the invention includes successive steps of primer extension, removal of unextended primers and addition of new primers either for amplification (for example by PCR) or for additional primer extensions. Some embodiments of the invention are directed to minimal residual disease (MRD) analysis of patients being treated for cancer. Sequence tags incorporated into sequence reads provide an efficient means for determining clonotypes and at the same time provide a convenient means for detecting carry-over contamination from other samples of the same patient or from samples of a different patient which were tested in the same laboratory.Type: GrantFiled: August 2, 2018Date of Patent: January 7, 2020Assignee: Adaptive Biotechnologies CorporationInventors: Thomas Asbury, Kieran Hervold, Chitra Kotwaliwale, Malek Faham, Martin Moorhead, Li Weng, Tobias Wittkop, Jianbiao Zheng
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Patent number: 10385475Abstract: The invention is directed to a method of sequencing low-complexity amplicons randomly arrayed at high density on a surface. Methods of the invention include preparing amplicons for sequencing by a sets of primers that ensure initial signals front different amplicons on the surface will be evenly distributed among the different nucleotides being added in a sequencing by synthesis operation.Type: GrantFiled: August 28, 2012Date of Patent: August 20, 2019Assignee: ADAPTIVE BIOTECHNOLOGIES CORP.Inventors: Jianbiao Zheng, Thomas Willis, Malek Faham
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Publication number: 20190161788Abstract: Methods for multiplex amplification of a plurality of targets of distinct sequence from a complex mixture are disclosed. In one aspect targets are circularized using a single circularization probe that is complementary to two regions in the target that flank a region to be amplified. The targets may hybridize to the circularization probe so that 5? or 3? flaps are generated and methods for removing flaps and circularizing the resulting product are disclosed. In another aspect targets are hybridized to dU probes so that 5? and 3? flaps are generated. The flaps are cleaved using 5? or 3? flap endonucleases or 3? to 5? exonucleases. The target sequences are then ligated to common primers, the dU probes digested and the ligated targets amplified.Type: ApplicationFiled: October 2, 2018Publication date: May 30, 2019Inventors: Jianbiao Zheng, Li Weng, Malek Faham
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Publication number: 20190040462Abstract: The invention is directed to sequence-based profiling of populations of nucleic acids by multiplex amplification and attachment of one or more sequence tags to target nucleic acids and/or copies thereof followed by high-throughput sequencing of the amplification product. In some embodiments, the invention includes successive steps of primer extension, removal of unextended primers and addition of new primers either for amplification (for example by PCR) or for additional primer extensions. Some embodiments of the invention are directed to minimal residual disease (MRD) analysis of patients being treated for cancer. Sequence tags incorporated into sequence reads provide an efficient means for determining clonotypes and at the same time provide a convenient means for detecting carry-over contamination from other samples of the same patient or from samples of a different patient which were tested in the same laboratory.Type: ApplicationFiled: August 2, 2018Publication date: February 7, 2019Inventors: Thomas Asbury, Kieran Hervold, Chitra Kotwaliwale, Malek Faham, Martin Moorhead, Li Weng, Tobias Wittkop, Jianbiao Zheng
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Patent number: 10119162Abstract: Methods for multiplex amplification of a plurality of targets of distinct sequence from a complex mixture are disclosed. In one aspect targets are circularized using a single circularization probe that is complementary to two regions in the target that flank a region to be amplified. The targets may hybridize to the circularization probe so that 5? or 3? flaps are generated and methods for removing flaps and circularizing the resulting product are disclosed. In another aspect targets are hybridized to dU probes so that 5? and 3? flaps are generated. The flaps are cleaved using 5? or 3? flap endonucleases or 3? to 5? exonucleases. The target sequences are then ligated to common primers, the dU probes digested and the ligated targets amplified.Type: GrantFiled: November 16, 2016Date of Patent: November 6, 2018Assignee: AFFYMETRIX, INC.Inventors: Jianbiao Zheng, Li Weng, Malek Faham
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Patent number: 10077473Abstract: The invention is directed to sequence-based profiling of populations of nucleic acids by multiplex amplification and attachment of one or more sequence tags to target nucleic acids and/or copies thereof followed by high-throughput sequencing of the amplification product. In some embodiments, the invention includes successive steps of primer extension, removal of unextended primers and addition of new primers either for amplification (for example by PCR) or for additional primer extensions. Some embodiments of the invention are directed to minimal residual disease (MRD) analysis of patients being treated for cancer. Sequence tags incorporated into sequence reads provide an efficient means for determining clonotypes and at the same time provide a convenient means for detecting carry-over contamination from other samples of the same patient or from samples of a different patient which were tested in the same laboratory.Type: GrantFiled: June 1, 2017Date of Patent: September 18, 2018Assignee: Adaptive Biotechnologies Corp.Inventors: Thomas Asbury, Kieran Hervold, Chitra Kotwaliwale, Malek Faham, Martin Moorhead, Li Weng, Tobias Wittkop, Jianbiao Zheng
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Publication number: 20180087050Abstract: The present invention provides compositions, methods, and kits for inserting a plurality of synthetic transposons each comprising a different nucleic acid sequence (i.e., molecular barcode) in a target nucleic acid of interest to allow extraction of contiguity information in the target nucleic acid. The molecular barcodes are also useful for reducing amplification or sequencing bias and errors, and for guiding accurate sequence assembly of the target nucleic acid from sequencing reads. The compositions, methods, and kits described herein have many applications, including haplotyping, genome assembly, sequencing of repetitive regions, detection of structural variations and copy number variations, chromosomal conformation analysis, and methylation analysis.Type: ApplicationFiled: May 26, 2016Publication date: March 29, 2018Inventors: Jianbiao ZHENG, Changping SHI
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Publication number: 20170335390Abstract: The invention is directed to sequence-based profiling of populations of nucleic acids by multiplex amplification and attachment of one or more sequence tags to target nucleic acids and/or copies thereof followed by high-throughput sequencing of the amplification product. In some embodiments, the invention includes successive steps of primer extension, removal of unextended primers and addition of new primers either for amplification (for example by PCR) or for additional primer extensions. Some embodiments of the invention are directed to minimal residual disease (MRD) analysis of patients being treated for cancer. Sequence tags incorporated into sequence reads provide an efficient means for determining clonotypes and at the same time provide a convenient means for detecting carry-over contamination from other samples of the same patient or from samples of a different patient which were tested in the same laboratory.Type: ApplicationFiled: June 1, 2017Publication date: November 23, 2017Inventors: Thomas Asbury, Kieran Hervold, Chitra Kotwaliwale, Malek Faham, Martin Moorhead, Li Weng, Tobias Wittkop, Jianbiao Zheng
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Patent number: 9708657Abstract: The invention is directed to sequence-based profiling of populations of nucleic acids by multiplex amplification and attachment of one or more sequence tags to target nucleic acids anchor copies thereof followed by high-throughput sequencing of the amplification product. In some embodiments, the invention includes successive steps of primer extension, removal of unextended primers and addition of new primers either for amplification (for example by PCR) or for additional primer extension. Some embodiments of the invention are directed to minimal residual disease (MRD) analysis of patients being treated for cancer. Sequence tags incorporated into sequence reads provide an efficient means for determining clonotypes and at the same time provide a convenient means for detecting carry-over contamination from other samples of the same patient or from samples of a different patient which were tested in the same laboratory.Type: GrantFiled: June 27, 2014Date of Patent: July 18, 2017Assignee: Adaptive Biotechnologies Corp.Inventors: Thomas Asbury, Kieran Hervold, Chitra Kotwaliwale, Malek Faham, Martin Moorhead, Li Weng, Tobias Wittkop, Jianbiao Zheng
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Publication number: 20170191132Abstract: The invention includes a method for determining the disease status of an individual suffering from ankylosing spondylitis by monitoring the individual's T-cell repertoire for the presence and/or level of clonotypes encoding T-cell receptor chains with segments identical to ant or related to the peptide LCASSLEASGSSYNEQFFGPGTRLTV (SEQ ID NO: 1) or the peptide VYFCASSDSSGSTDTQYFGPGTRLTV (SEQ ID NO: 2). The invention also includes therapeutic antibodies specific for these peptides for ameliorating the effects ankylosing spondylitis.Type: ApplicationFiled: February 3, 2017Publication date: July 6, 2017Inventors: Malek Faham, Victoria Carlton, Martin Moorhead, Jianbiao Zheng, Thomas Asbury
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Publication number: 20170073731Abstract: Methods for multiplex amplification of a plurality of targets of distinct sequence from a complex mixture are disclosed. In one aspect targets are circularized using a single circularization probe that is complementary to two regions in the target that flank a region to be amplified. The targets may hybridize to the circularization probe so that 5? or 3? flaps are generated and methods for removing flaps and circularizing the resulting product are disclosed. In another aspect targets are hybridized to dU probes so that 5? and 3? flaps are generated. The flaps are cleaved using 5? or 3? flap endonucleases or 3? to 5? exonucleases. The target sequences are then ligated to common primers, the dU probes digested and the ligated targets amplified.Type: ApplicationFiled: November 16, 2016Publication date: March 16, 2017Inventors: Jianbiao Zheng, Li Weng, Malek Faham
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Publication number: 20170067099Abstract: Methods for multiplex amplification of a plurality of targets of distinct sequence from a complex mixture are disclosed. In one aspect targets are circularized using a single circularization probe that is complementary to two regions in the target that flank a region to be amplified. The targets may hybridize to the circularization probe so that 5? or 3? flaps are generated and methods for removing flaps and circularizing the resulting product are disclosed. In another aspect targets are hybridized to dU probes so that 5? and 3? flaps are generated. The flaps are cleaved using 5? or 3? flap endonucleases or 3? to 5? exonucleases. The target sequences are then ligated to common primers, the dU probes digested and the ligated targets amplified.Type: ApplicationFiled: November 16, 2016Publication date: March 9, 2017Inventors: Jianbiao Zheng, Li Weng, Malek Faham
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Patent number: 9528148Abstract: Methods for multiplex amplification of a plurality of targets of distinct sequence from a complex mixture are disclosed. In one aspect targets are circularized using a single circularization probe that is complementary to two regions in the target that flank a region to be amplified. The targets may hybridize to the circularization probe so that 5? or 3? flaps are generated and methods for removing flaps and circularizing the resulting product are disclosed. In another aspect targets are hybridized to dU probes so that 5? and 3? flaps are generated. The flaps are cleaved using 5? or 3? flap endonucleases or 3? to 5? exonucleases. The target sequences are then ligated to common primers, the dU probes digested and the ligated targets amplified.Type: GrantFiled: March 23, 2015Date of Patent: December 27, 2016Assignee: Affymetrix, Inc.Inventors: Jianbiao Zheng, Li Weng, Malek Faham
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Patent number: 9523122Abstract: Methods for multiplex amplification of a plurality of targets of distinct sequence from a complex mixture are disclosed. In one aspect targets are circularized using a single circularization probe that is complementary to two regions in the target that flank a region to be amplified. The targets may hybridize to the circularization probe so that 5? or 3? flaps are generated and methods for removing flaps and circularizing the resulting product are disclosed. In another aspect targets are hybridized to dU probes so that 5? and 3? flaps are generated. The flaps are cleaved using 5? or 3? flap endonucleases or 3? to 5? exonucleases. The target sequences are then ligated to common primers, the dU probes digested and the ligated targets amplified.Type: GrantFiled: February 16, 2015Date of Patent: December 20, 2016Assignee: Affymetrix, Inc.Inventors: Jianbiao Zheng, Li Weng, Malek Faham
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Publication number: 20160355893Abstract: The invention is directed to the use of sequence tags to improve sequence determination of amplicons of related sequences, particularly large and complex amplicons, such as those comprising recombined nucleic acids encoding immune receptor molecules. In one aspect, sequence reads having the same sequence tags are aligned after which final base calls are determined from a (possibly weighted) average base call from sequence read base calls at each position. Similarly, in another aspect, sequence reads comprising series of incorporation signals are aligned by common sequence tags and base calls in homopolymer regions are made as a function incorporation signal values at each “flow” position.Type: ApplicationFiled: March 15, 2013Publication date: December 8, 2016Inventors: Malek Faham, Martin Moorhead, Thomas Willis, Jianbiao Zheng
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Patent number: 9506119Abstract: The invention is directed to the use of sequence tags to improve sequence determination of amplicons of related sequences, particularly large and complex amplicons, such as those comprising recombined nucleic acids encoding immune receptor molecules. In one aspect, sequence reads having the same sequence tags are aligned after which final base calls are determined from a (possibly weighted) average base call from sequence read base calls at each position. Similarly, in another aspect, sequence reads comprising series of incorporation signals are aligned by common sequence tags and base calls in homopolymer regions are made as a function incorporation signal values at each “flow” position.Type: GrantFiled: March 15, 2013Date of Patent: November 29, 2016Assignee: Adaptive Biotechnologies Corp.Inventors: Malek Faham, Martin Moorhead, Thomas Willis, Jianbiao Zheng
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Patent number: 9394567Abstract: The invention is directed to methods for detecting and quantifying nucleic acid contamination in a tissue sample of an individual containing T cells and/or B cells, which is used for generating a sequence-based clonotype profile. In one aspect, the invention is implemented by measuring the presence and/or level of an endogenous or exogenous nucleic acid tag by which nucleic acid from an intended individual can be distinguished from that of unintended individuals. Endogenous tags include genetic identity markers, such as short tandem repeats, rare clonotypes or the like, and exogenous tags include sequence tags employed to determine clonotype sequences from sequence reads.Type: GrantFiled: April 9, 2013Date of Patent: July 19, 2016Assignee: ADAPTIVE BIOTECHNOLOGIES CORPORATIONInventors: Thomas Asbury, Victoria Carlton, Malek Faham, Stephen C. Macevicz, Martin Moorhead, Thomas Willis, Jianbiao Zheng