Methods for making nucleotide probes for sequencing and synthesis

Church, George M.; Zhang, Kun; Chou, Joseph

Title: Methods for making nucleotide probes for sequencing and synthesis

Abstract

Compositions and methods for making a plurality of probes for analyzing a plurality of nucleic acid samples are provided. Compositions and methods for analyzing a plurality of nucleic acid samples to obtain sequence information in each nucleic acid sample are also provided.

Inventors:: Church, George M.; Zhang, Kun; Chou, Joseph

Issue Date:: 2020-12-08

Research Org.:: Harvard Univ., Cambridge, MA (United States)

Sponsoring Org.:: USDOE

OSTI Identifier:: 1771707

Patent Number(s):: 10858692

Application Number:: 15/945,192

Assignee:: President and Fellows of Harvard College (Cambridge, MA)

Patent Classifications (CPCs):: C - CHEMISTRY C12 - BIOCHEMISTRY C12Q - MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS

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C - CHEMISTRY C12 - BIOCHEMISTRY C12Q - MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS
C12Q2537/143 - Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
C12Q2535/113 - Cycle sequencing
C12Q2565/543 - characterised by the use of two or more capture oligonucleotide primers in concert, e.g. bridge amplification
C12Q1/6813 - Hybridisation assays
C12Q1/6837 - using probe arrays or probe chips

Show less

DOE Contract Number:: FG02-02ER63445

Resource Type:: Patent

Resource Relation:: Patent File Date: 04/04/2018

Country of Publication:: United States

Language:: English

Citation Formats


                    Church, George M., Zhang, Kun, and Chou, Joseph. Methods for making nucleotide probes for sequencing and synthesis.  United States: N. p., 2020. 
        Web.

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                    Church, George M., Zhang, Kun, & Chou, Joseph. Methods for making nucleotide probes for sequencing and synthesis.  United States.

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                    Church, George M., Zhang, Kun, and Chou, Joseph. Tue .  
        "Methods for making nucleotide probes for sequencing and synthesis".  United States.  https://www.osti.gov/servlets/purl/1771707.

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@article{osti_1771707,

  title        = {Methods for making nucleotide probes for sequencing and synthesis},

  author       = {Church, George M. and Zhang, Kun and Chou, Joseph},

  abstractNote = {Compositions and methods for making a plurality of probes for analyzing a plurality of nucleic acid samples are provided. Compositions and methods for analyzing a plurality of nucleic acid samples to obtain sequence information in each nucleic acid sample are also provided.},

  doi          = {},

  journal      = {},
number       = ,

  volume       = ,

  place        = {United States},

  year         = {2020},

  month        = {12}

}

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Title: Methods for making nucleotide probes for sequencing and synthesis

Abstract

Citation Formats

Circle-to-circle amplification for precise and sensitive DNA analysis journal, March 2004

Padlock probes: circularizing oligonucleotides for localized DNA detection journal, September 1994

Allele detection using primer extension with sequence-coded identity tags patent, September 2001

Detection of nucleic acid sequence differences using the ligase detection reaction with addressable arrays patent, January 2003

Allelic Variation in Human Gene Expression journal, August 2002

Direct multiplex characterization of genomic DNA patent, February 2005

Detection of specific sequences in nucleic acids patent, November 1989

Analysis of Polynucleotide Sequence patent-application, November 2002

Cell-free cloning using φ29 DNA polymerase journal, November 2005

Allele quantification using molecular inversion probes (MIP) journal, November 2005

Monitoring for and detecting microbes used in bioterrorism patent-application, December 2004

Nucleic acid amplification method: ramification-extension amplification method (RAM) patent, August 1999

Multiplexed genotyping with sequence-tagged molecular inversion probes journal, May 2003

Direct Multiplex Characterization of Genomic DNA patent-application, May 2004

Mutation detection and single-molecule counting using isothermal rolling-circleamplification journal, July 1998

Homogeneous assay system using the nuclease activity of a nucleic acid polymerase patent, May 1993

Circularizing nucleic acid probe able to interlock with a target sequence through catenation patent, February 1999

Universal DNA microarray method for multiplex detection of low abundance point mutations journal, September 1999

Process for amplifying nucleic acid sequences patent, July 1987

Process for amplifying, detecting, and/or cloning nucleic acid sequences patent, January 1989

Sequencing Using Tag Array patent-application, January 2007

Multiplex PCR patent-application, June 2003

Method to detect mutations in a nucleic acid using a hybridization-ligation procedure patent, February 1999

Replica amplification of nucleic acid arrays patent, August 2002

Replica amplification of nucleic acid arrays patent, January 2003

Method for producing a tobacco filter material patent, February 2002

Molecular beacon probes combined with amplification by NASBA enable homogeneous, real-time detection of RNA journal, May 1998

DNA polymerase blends and uses thereof patent-application, October 2004

Sequencing genomes from single cells by polymerase cloning journal, May 2006

Toward genome-wide SNP genotyping journal, June 2005

Methods and compositions for whole genome amplification and genotyping patent-application, February 2005

Use of Mass Labelled Probes to Detect Target Nucleic Acids Using Mass Spectrometry patent-application, December 2007

Nucleic acid sequence amplification methods patent, March 1995

Highly multiplexed molecular inversion probe genotyping: Over 10,000 targeted SNPs genotyped in a single tube assay journal, January 2005

Nucleic acid detecting reagent patent, May 2001

Rolling Circle Amplification of RNA patent-application, July 2004

Identification of alleles patent, March 2004

Simultaneous analysis of multiple genomes patent-application, January 2006

Process for amplifying, detecting, and/or-cloning nucleic acid sequences patent, July 1987

Process for amplifying, detecting, and/or cloning nucleic acid sequences using a thermostable enzyme patent, October 1990

Nucleic acid memory device patent-application, December 2003

Monitoring amplification of DNA during PCR patent, January 2001

Methods for reducing the complexity of DNA sequences patent, September 2001

Universal tag assay patent-application, May 2004

Method of oligonucleotide synthesis patent-application, July 2005

Parallel gene analysis with allele-specific padlock probes and tag microarrays journal, September 2003

Parallel Genotyping of Human SNPs Using Generic High-density Oligonucleotide Tag Arrays journal, June 2000

Rolling circle replication reporter systems patent, February 2001

Replica amplification of nucleic acid arrays patent, November 2002

Nucleic acid detection methods using universal priming patent-application, January 2003

Nucleic acid amplification methods patent-application, December 2002

Signal amplification of padlock probes by rolling circle replication journal, November 1998

Nucleic acid ligand inhibitors to DNA polymerases patent, February 2001

Accurate multiplex gene synthesis from programmable DNA microchips journal, December 2004

Nucleic acid hybridization methods patent-application, August 2005

Circle-to-circle amplification for precise and sensitive DNA analysis
journal, March 2004

Padlock probes: circularizing oligonucleotides for localized DNA detection
journal, September 1994

Allele detection using primer extension with sequence-coded identity tags
patent, September 2001

Detection of nucleic acid sequence differences using the ligase detection reaction with addressable arrays
patent, January 2003

Allelic Variation in Human Gene Expression
journal, August 2002

Direct multiplex characterization of genomic DNA
patent, February 2005

Detection of specific sequences in nucleic acids
patent, November 1989

Analysis of Polynucleotide Sequence
patent-application, November 2002

Cell-free cloning using φ29 DNA polymerase
journal, November 2005

Allele quantification using molecular inversion probes (MIP)
journal, November 2005

Monitoring for and detecting microbes used in bioterrorism
patent-application, December 2004

Nucleic acid amplification method: ramification-extension amplification method (RAM)
patent, August 1999

Multiplexed genotyping with sequence-tagged molecular inversion probes
journal, May 2003

Direct Multiplex Characterization of Genomic DNA
patent-application, May 2004

Mutation detection and single-molecule counting using isothermal rolling-circleamplification
journal, July 1998

Homogeneous assay system using the nuclease activity of a nucleic acid polymerase
patent, May 1993

Circularizing nucleic acid probe able to interlock with a target sequence through catenation
patent, February 1999

Universal DNA microarray method for multiplex detection of low abundance point mutations
journal, September 1999

Process for amplifying nucleic acid sequences
patent, July 1987

Process for amplifying, detecting, and/or cloning nucleic acid sequences
patent, January 1989

Sequencing Using Tag Array
patent-application, January 2007

Multiplex PCR
patent-application, June 2003

Method to detect mutations in a nucleic acid using a hybridization-ligation procedure
patent, February 1999

Replica amplification of nucleic acid arrays
patent, August 2002

Replica amplification of nucleic acid arrays
patent, January 2003

Method for producing a tobacco filter material
patent, February 2002

Molecular beacon probes combined with amplification by NASBA enable homogeneous, real-time detection of RNA
journal, May 1998

DNA polymerase blends and uses thereof
patent-application, October 2004

Sequencing genomes from single cells by polymerase cloning
journal, May 2006

Toward genome-wide SNP genotyping
journal, June 2005

Methods and compositions for whole genome amplification and genotyping
patent-application, February 2005

Use of Mass Labelled Probes to Detect Target Nucleic Acids Using Mass Spectrometry
patent-application, December 2007

Nucleic acid sequence amplification methods
patent, March 1995

Highly multiplexed molecular inversion probe genotyping: Over 10,000 targeted SNPs genotyped in a single tube assay
journal, January 2005

Nucleic acid detecting reagent
patent, May 2001

Rolling Circle Amplification of RNA
patent-application, July 2004

Identification of alleles
patent, March 2004

Simultaneous analysis of multiple genomes
patent-application, January 2006

Process for amplifying, detecting, and/or-cloning nucleic acid sequences
patent, July 1987

Process for amplifying, detecting, and/or cloning nucleic acid sequences using a thermostable enzyme
patent, October 1990

Nucleic acid memory device
patent-application, December 2003

Monitoring amplification of DNA during PCR
patent, January 2001

Methods for reducing the complexity of DNA sequences
patent, September 2001

Universal tag assay
patent-application, May 2004

Method of oligonucleotide synthesis
patent-application, July 2005

Parallel gene analysis with allele-specific padlock probes and tag microarrays
journal, September 2003

Parallel Genotyping of Human SNPs Using Generic High-density Oligonucleotide Tag Arrays
journal, June 2000

Rolling circle replication reporter systems
patent, February 2001

Replica amplification of nucleic acid arrays
patent, November 2002

Nucleic acid detection methods using universal priming
patent-application, January 2003

Nucleic acid amplification methods
patent-application, December 2002

Signal amplification of padlock probes by rolling circle replication
journal, November 1998

Nucleic acid ligand inhibitors to DNA polymerases
patent, February 2001

Accurate multiplex gene synthesis from programmable DNA microchips
journal, December 2004

Nucleic acid hybridization methods
patent-application, August 2005