WO2013078470A3 - Multiplex isolation of protein-associated nucleic acids - Google Patents

Multiplex isolation of protein-associated nucleic acids Download PDF

Info

Publication number
WO2013078470A3
WO2013078470A3 PCT/US2012/066472 US2012066472W WO2013078470A3 WO 2013078470 A3 WO2013078470 A3 WO 2013078470A3 US 2012066472 W US2012066472 W US 2012066472W WO 2013078470 A3 WO2013078470 A3 WO 2013078470A3
Authority
WO
WIPO (PCT)
Prior art keywords
nucleic acids
protein
associated nucleic
multiplex isolation
oligonudeotide
Prior art date
Application number
PCT/US2012/066472
Other languages
French (fr)
Other versions
WO2013078470A2 (en
Inventor
Joseph Fernandez
Mary Anne Jelinek
Brian Stanley EGAN
Original Assignee
MOTIF, Active
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by MOTIF, Active filed Critical MOTIF, Active
Priority to US14/359,877 priority Critical patent/US9938524B2/en
Priority to EP12852118.4A priority patent/EP2783001B1/en
Publication of WO2013078470A2 publication Critical patent/WO2013078470A2/en
Priority to US14/892,911 priority patent/US10689643B2/en
Publication of WO2013078470A3 publication Critical patent/WO2013078470A3/en
Priority to US16/946,073 priority patent/US11306307B2/en
Priority to US17/705,005 priority patent/US20220356465A1/en

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1093—General methods of preparing gene libraries, not provided for in other subgroups
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6804—Nucleic acid analysis using immunogens

Abstract

The invention provides novel methods and materials for genetic and genomic analysis using single or multiplex isolation of protein-associated nucleic acids, including transposase-assisted chromatin immunoprecipitation (TAM-ChIP) and antibody-oligonudeotide proximity ligation. These methods comprise tagging and isolating chromatin or other protein-associated nucleic acids and using antibody-oligonudeotide complexes that recognize the proteins associated with such nucleic acids.
PCT/US2012/066472 2011-11-22 2012-11-23 Multiplex isolation of protein-associated nucleic acids WO2013078470A2 (en)

Priority Applications (5)

Application Number Priority Date Filing Date Title
US14/359,877 US9938524B2 (en) 2011-11-22 2012-11-23 Multiplex isolation of protein-associated nucleic acids
EP12852118.4A EP2783001B1 (en) 2011-11-22 2012-11-23 Multiplex isolation of protein-associated nucleic acids
US14/892,911 US10689643B2 (en) 2011-11-22 2014-05-22 Targeted transposition for use in epigenetic studies
US16/946,073 US11306307B2 (en) 2011-11-22 2020-06-04 Targeted transposition for use in epigenetic studies
US17/705,005 US20220356465A1 (en) 2011-11-22 2022-03-25 Targeted transposition for use in epigenetic studies

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201113000061A 2011-11-22 2011-11-22
US61 2011-11-22

Related Child Applications (5)

Application Number Title Priority Date Filing Date
US14/359,877 A-371-Of-International US9938524B2 (en) 2011-11-22 2012-11-23 Multiplex isolation of protein-associated nucleic acids
PCT/US2014/039250 Continuation WO2014190214A1 (en) 2011-11-22 2014-05-22 Targeted transposition for use in epigenetic studies
US14/892,911 Continuation US10689643B2 (en) 2011-11-22 2014-05-22 Targeted transposition for use in epigenetic studies
US14/892,911 Continuation-In-Part US10689643B2 (en) 2011-11-22 2014-05-22 Targeted transposition for use in epigenetic studies
USPCT/US2014/003925 Continuation 2014-05-22

Publications (2)

Publication Number Publication Date
WO2013078470A2 WO2013078470A2 (en) 2013-05-30
WO2013078470A3 true WO2013078470A3 (en) 2015-05-14

Family

ID=48470429

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2012/066472 WO2013078470A2 (en) 2011-11-22 2012-11-23 Multiplex isolation of protein-associated nucleic acids

Country Status (1)

Country Link
WO (1) WO2013078470A2 (en)

Families Citing this family (52)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US10083273B2 (en) 2005-07-29 2018-09-25 Natera, Inc. System and method for cleaning noisy genetic data and determining chromosome copy number
US11111543B2 (en) 2005-07-29 2021-09-07 Natera, Inc. System and method for cleaning noisy genetic data and determining chromosome copy number
US10081839B2 (en) 2005-07-29 2018-09-25 Natera, Inc System and method for cleaning noisy genetic data and determining chromosome copy number
US9424392B2 (en) 2005-11-26 2016-08-23 Natera, Inc. System and method for cleaning noisy genetic data from target individuals using genetic data from genetically related individuals
US11111544B2 (en) 2005-07-29 2021-09-07 Natera, Inc. System and method for cleaning noisy genetic data and determining chromosome copy number
EP2473638B1 (en) 2009-09-30 2017-08-09 Natera, Inc. Methods for non-invasive prenatal ploidy calling
US9677118B2 (en) 2014-04-21 2017-06-13 Natera, Inc. Methods for simultaneous amplification of target loci
US11326208B2 (en) 2010-05-18 2022-05-10 Natera, Inc. Methods for nested PCR amplification of cell-free DNA
US11332785B2 (en) 2010-05-18 2022-05-17 Natera, Inc. Methods for non-invasive prenatal ploidy calling
US11408031B2 (en) 2010-05-18 2022-08-09 Natera, Inc. Methods for non-invasive prenatal paternity testing
WO2011146632A1 (en) 2010-05-18 2011-11-24 Gene Security Network Inc. Methods for non-invasive prenatal ploidy calling
US11939634B2 (en) 2010-05-18 2024-03-26 Natera, Inc. Methods for simultaneous amplification of target loci
US20190010543A1 (en) 2010-05-18 2019-01-10 Natera, Inc. Methods for simultaneous amplification of target loci
US11332793B2 (en) 2010-05-18 2022-05-17 Natera, Inc. Methods for simultaneous amplification of target loci
US11339429B2 (en) 2010-05-18 2022-05-24 Natera, Inc. Methods for non-invasive prenatal ploidy calling
US11322224B2 (en) 2010-05-18 2022-05-03 Natera, Inc. Methods for non-invasive prenatal ploidy calling
US10316362B2 (en) 2010-05-18 2019-06-11 Natera, Inc. Methods for simultaneous amplification of target loci
JP6328934B2 (en) 2010-12-22 2018-05-23 ナテラ， インコーポレイテッド Noninvasive prenatal testing
AU2011358564B9 (en) 2011-02-09 2017-07-13 Natera, Inc Methods for non-invasive prenatal ploidy calling
US10689643B2 (en) 2011-11-22 2020-06-23 Active Motif, Inc. Targeted transposition for use in epigenetic studies
US9938524B2 (en) 2011-11-22 2018-04-10 Active Motif, Inc. Multiplex isolation of protein-associated nucleic acids
EP2999784B2 (en) * 2013-05-22 2022-11-23 Active Motif, Inc. Targeted transposition for use in epigenetic studies
US20160208323A1 (en) * 2013-06-21 2016-07-21 The Broad Institute, Inc. Methods for Shearing and Tagging DNA for Chromatin Immunoprecipitation and Sequencing
US10577655B2 (en) 2013-09-27 2020-03-03 Natera, Inc. Cell free DNA diagnostic testing standards
US10262755B2 (en) 2014-04-21 2019-04-16 Natera, Inc. Detecting cancer mutations and aneuploidy in chromosomal segments
CN113774132A (en) 2014-04-21 2021-12-10 纳特拉公司 Detection of mutations and ploidy in chromosomal segments
JP6784601B2 (en) * 2014-06-23 2020-11-11 ザ ジェネラル ホスピタル コーポレイション Genome-wide and unbiased DSB identification evaluated by sequencing (GUIDE-Seq)
US10526641B2 (en) 2014-08-01 2020-01-07 Dovetail Genomics, Llc Tagging nucleic acids for sequence assembly
RU2761432C2 (en) * 2015-02-10 2021-12-08 Иллюмина, Инк. Method and composition for analysis of cellular components
NZ734854A (en) 2015-02-17 2022-11-25 Dovetail Genomics Llc Nucleic acid sequence assembly
WO2016154540A1 (en) 2015-03-26 2016-09-29 Dovetail Genomics Llc Physical linkage preservation in dna storage
US11479812B2 (en) 2015-05-11 2022-10-25 Natera, Inc. Methods and compositions for determining ploidy
RS59838B1 (en) 2015-08-12 2020-02-28 Cemm Forschungszentrum Fuer Molekulare Medizin Gmbh Methods for studying nucleic acids
US11479805B2 (en) 2015-08-21 2022-10-25 The General Hospital Corporation Combinatorial single molecule analysis of chromatin
WO2017044843A1 (en) 2015-09-11 2017-03-16 The General Hospital Corporation Full interrogation of nuclease dsbs and sequencing (find-seq)
AU2016331185A1 (en) 2015-09-30 2018-04-26 The General Hospital Corporation Comprehensive in vitro reporting of cleavage events by sequencing (CIRCLE-seq)
SG11201803289VA (en) 2015-10-19 2018-05-30 Dovetail Genomics Llc Methods for genome assembly, haplotype phasing, and target independent nucleic acid detection
CN105463089A (en) * 2015-12-21 2016-04-06 同济大学 Assay for transposase accessible chromatin using sequencing (ATAC-seq) method applied to zebrafish embryos
US10975417B2 (en) 2016-02-23 2021-04-13 Dovetail Genomics, Llc Generation of phased read-sets for genome assembly and haplotype phasing
DK3455356T3 (en) 2016-05-13 2021-11-01 Dovetail Genomics Llc RECOVERY OF LONG-TERM BINDING INFORMATION FROM PRESERVED SAMPLES
EP3508574A4 (en) 2016-08-30 2020-04-01 Kyushu University, National University Corporation Method for inserting desired dna fragment into site located adjacent to binding domain of dna-binding protein
WO2018067517A1 (en) * 2016-10-04 2018-04-12 Natera, Inc. Methods for characterizing copy number variation using proximity-litigation sequencing
US10011870B2 (en) 2016-12-07 2018-07-03 Natera, Inc. Compositions and methods for identifying nucleic acid molecules
CA3049139A1 (en) 2017-02-21 2018-08-30 Natera, Inc. Compositions, methods, and kits for isolating nucleic acids
US10914729B2 (en) 2017-05-22 2021-02-09 The Trustees Of Princeton University Methods for detecting protein binding sequences and tagging nucleic acids
CA3073448A1 (en) 2017-08-23 2019-02-28 The General Hospital Corporation Engineered crispr-cas9 nucleases with altered pam specificity
EP4339298A3 (en) * 2017-09-25 2024-04-17 Fred Hutchinson Cancer Center High efficiency targeted in situ genome-wide profiling
EP3694993A4 (en) 2017-10-11 2021-10-13 The General Hospital Corporation Methods for detecting site-specific and spurious genomic deamination induced by base editing technologies
WO2019076768A1 (en) * 2017-10-16 2019-04-25 Tervisetehnoloogiate Arenduskeskus As Method and kit for dna library preparation
AU2019256287A1 (en) 2018-04-17 2020-11-12 The General Hospital Corporation Sensitive in vitro assays for substrate preferences and sites of nucleic acid binding, modifying, and cleaving agents
US11525159B2 (en) 2018-07-03 2022-12-13 Natera, Inc. Methods for detection of donor-derived cell-free DNA
CN113718017B (en) * 2021-09-10 2024-01-09 上海交通大学 Preparation method of single-cell ChIP-seq library

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20100240101A1 (en) * 2009-03-19 2010-09-23 Massachusetts Institute Of Technology Parallel Proximity Ligation Event Analysis

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20100240101A1 (en) * 2009-03-19 2010-09-23 Massachusetts Institute Of Technology Parallel Proximity Ligation Event Analysis

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
DEMATTEI M.-V. ET AL.: "Site-directed integration of transgenes: transposons revisited using DNA-binding-domain technologies.", GENETICA, vol. 138, 2010, pages 531 - 540, XP019789321 *
KIDDER B.L. ET AL.: "ChIP-Seq: technical considerations for obtaining high-quality data.", NATURE IMMUNOLOGY, vol. 12, no. 10, 2011, pages 918 - 922, XP055240604 *

Also Published As

Publication number Publication date
WO2013078470A2 (en) 2013-05-30

Similar Documents

Publication Publication Date Title
WO2013078470A3 (en) Multiplex isolation of protein-associated nucleic acids
EP4034564A4 (en) Variant nucleic acid libraries for single domain antibodies
EP3294448A4 (en) Rapid methods for the extraction of nucleic acids from biological samples
EP3429752A4 (en) Systems and methods for performing biological assays
WO2016130704A3 (en) Methods and compositions for analyzing cellular components
WO2015160895A3 (en) Modified transposases for improved insertion sequence bias and increased dna input tolerance
WO2014145820A3 (en) Multiple tagging of long dna fragments
WO2013170170A3 (en) Compositions and methods for gene therapy
EP3559231A4 (en) Methods for processing nucleic acid samples
WO2012048340A3 (en) High-throughput immune sequencing
WO2015013465A3 (en) Methods and compositions for detecting bacterial contamination
EP3201350A4 (en) Method for nucleic acid analysis directly from an unpurified biological sample
EP4007818A4 (en) Methods and reagents for nucleic acid sequencing and associated applications
EP3794113A4 (en) Methods for processing nucleic acid samples
WO2016109799A3 (en) Method of rna isolation from clinical samples
WO2014018601A3 (en) New modular base-specific nucleic acid binding domains from burkholderia rhizoxinica proteins
EP3739063A4 (en) Fluorescent nucleic acid nanostructure-graphene biosensor for nucleic acid detection
EP3942066A4 (en) Nucleic acid hybridization methods
EP3487998A4 (en) Compositions and methods for identifying rna binding polypeptide targets
EP3740604A4 (en) Compositions and methods for preparing nucleic acid libraries
EP4306544A3 (en) Production of heteromultimeric proteins using mammalian cells
EP3749765A4 (en) Methods and compositions for tracking nucleic acid fragment origin for nucleic acid sequencing
EP3765017A4 (en) Methods using nucleic acid signals for revealing biological attributes
JO3729B1 (en) Uti fusion proteins
WO2011100752A3 (en) Methods and materials for assessing rna expression

Legal Events

Date Code Title Description
WWE Wipo information: entry into national phase

Ref document number: 14359877

Country of ref document: US

NENP Non-entry into the national phase

Ref country code: DE

WWE Wipo information: entry into national phase

Ref document number: 2012852118

Country of ref document: EP