US20070231817A1 - 4c - Google Patents

4c Download PDF

Info

Publication number
US20070231817A1
US20070231817A1 US11/622,328 US62232807A US2007231817A1 US 20070231817 A1 US20070231817 A1 US 20070231817A1 US 62232807 A US62232807 A US 62232807A US 2007231817 A1 US2007231817 A1 US 2007231817A1
Authority
US
United States
Prior art keywords
dna
probes
restriction enzyme
sequences
array
Prior art date
Legal status (The legal status 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 status listed.)
Pending
Application number
US11/622,328
Other languages
English (en)
Inventor
Wouter De Laat
Frank Grosveld
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Individual
Original Assignee
Individual
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
Priority claimed from GBGB0513676.7A external-priority patent/GB0513676D0/en
Priority claimed from GBGB0605449.8A external-priority patent/GB0605449D0/en
Application filed by Individual filed Critical Individual
Publication of US20070231817A1 publication Critical patent/US20070231817A1/en
Pending legal-status Critical Current

Links

Images

Classifications

    • 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
    • C12Q1/6809—Methods for determination or identification of nucleic acids involving differential detection
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
    • 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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • C12Q1/6837—Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
    • 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
    • C12Q2521/00—Reaction characterised by the enzymatic activity
    • C12Q2521/50—Other enzymatic activities
    • C12Q2521/501—Ligase
    • 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
    • C12Q2523/00—Reactions characterised by treatment of reaction samples
    • C12Q2523/10—Characterised by chemical treatment
    • C12Q2523/101—Crosslinking agents, e.g. psoralen
    • 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
    • C12Q2565/00—Nucleic acid analysis characterised by mode or means of detection
    • C12Q2565/50—Detection characterised by immobilisation to a surface
    • C12Q2565/501—Detection characterised by immobilisation to a surface being an array of oligonucleotides
US11/622,328 2005-07-04 2007-01-11 4c Pending US20070231817A1 (en)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
GBGB0513676.7A GB0513676D0 (en) 2005-07-04 2005-07-04 4c
GB0513676.7 2005-07-04
GBGB0605449.8A GB0605449D0 (en) 2006-03-17 2006-03-17 4c
GB0605449.8 2006-03-17
PCT/IB2006/002268 WO2007004057A2 (en) 2005-07-04 2006-07-03 Chromosome conformation capture-on-chip (4c) assay

Related Parent Applications (1)

Application Number Title Priority Date Filing Date
PCT/IB2006/002268 Continuation-In-Part WO2007004057A2 (en) 2005-07-04 2006-07-03 Chromosome conformation capture-on-chip (4c) assay

Publications (1)

Publication Number Publication Date
US20070231817A1 true US20070231817A1 (en) 2007-10-04

Family

ID=37604842

Family Applications (2)

Application Number Title Priority Date Filing Date
US11/622,328 Pending US20070231817A1 (en) 2005-07-04 2007-01-11 4c
US12/006,747 Active 2027-09-17 US8153373B2 (en) 2005-07-04 2008-01-04 Capture and characterized co-localized chromatin (4C) technology

Family Applications After (1)

Application Number Title Priority Date Filing Date
US12/006,747 Active 2027-09-17 US8153373B2 (en) 2005-07-04 2008-01-04 Capture and characterized co-localized chromatin (4C) technology

Country Status (18)

Country Link
US (2) US20070231817A1 (de)
EP (1) EP1899488B1 (de)
JP (1) JP5416405B2 (de)
KR (1) KR101383593B1 (de)
AU (1) AU2006264564B2 (de)
BR (1) BRPI0611702B1 (de)
CA (1) CA2614118C (de)
CY (1) CY1117260T1 (de)
DK (1) DK1899488T3 (de)
ES (1) ES2556113T3 (de)
HU (1) HUE026922T2 (de)
IL (1) IL187919A (de)
NO (1) NO20076430L (de)
NZ (1) NZ564262A (de)
PL (1) PL1899488T3 (de)
RU (1) RU2478716C2 (de)
SI (1) SI1899488T1 (de)
WO (1) WO2007004057A2 (de)

Cited By (11)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20090186352A1 (en) * 2006-02-17 2009-07-23 Isis Innovation Limited DNA Conformation
WO2010036323A1 (en) * 2008-09-25 2010-04-01 University Of Massachusetts Medical School Method of identifing interactions between genomic loci
WO2015089243A1 (en) 2013-12-11 2015-06-18 The Regents For Of The University Of California Methods for labeling dna fragments to recontruct physical linkage and phase
US9715573B2 (en) 2015-02-17 2017-07-25 Dovetail Genomics, Llc Nucleic acid sequence assembly
CN110225981A (zh) * 2016-12-23 2019-09-10 牛津生物动力有限公司 分型方法
CN110234769A (zh) * 2016-12-01 2019-09-13 牛津生物动力有限公司 表观遗传染色体相互作用在癌症诊断中的应用
US10457934B2 (en) 2015-10-19 2019-10-29 Dovetail Genomics, Llc Methods for genome assembly, haplotype phasing, and target independent nucleic acid detection
US10526641B2 (en) 2014-08-01 2020-01-07 Dovetail Genomics, Llc Tagging nucleic acids for sequence assembly
US10947579B2 (en) 2016-05-13 2021-03-16 Dovetail Genomics, Llc Recovering long-range linkage information from preserved samples
US10975417B2 (en) 2016-02-23 2021-04-13 Dovetail Genomics, Llc Generation of phased read-sets for genome assembly and haplotype phasing
US11807896B2 (en) 2015-03-26 2023-11-07 Dovetail Genomics, Llc Physical linkage preservation in DNA storage

Families Citing this family (18)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US8071296B2 (en) 2006-03-13 2011-12-06 Agency For Science, Technology And Research Nucleic acid interaction analysis
US8642295B2 (en) 2007-01-11 2014-02-04 Erasmus University Medical Center Circular chromosome conformation capture (4C)
US8263367B2 (en) * 2008-01-25 2012-09-11 Agency For Science, Technology And Research Nucleic acid interaction analysis
PT2591125T (pt) 2010-07-09 2018-05-09 Cergentis B V Estratégias 3-d de sequenciação de regiões genómicas de interesse
WO2014121091A1 (en) 2013-02-01 2014-08-07 The Regents Of The University Of California Methods for genome assembly and haplotype phasing
US9411930B2 (en) 2013-02-01 2016-08-09 The Regents Of The University Of California Methods for genome assembly and haplotype phasing
GB2517936B (en) * 2013-09-05 2016-10-19 Babraham Inst Chromosome conformation capture method including selection and enrichment steps
GB201320351D0 (en) 2013-11-18 2014-01-01 Erasmus Universiteit Medisch Ct Method
GB2520765A (en) 2013-12-02 2015-06-03 Vanadis Diagnostics Ab Multiplex detection of nucleic acids
GB2520763A (en) 2013-12-02 2015-06-03 Vanadis Diagnostics Ab Nucleic acid probe and method of detecting genomic fragments
EP3031929A1 (de) 2014-12-11 2016-06-15 Mdc Max-Delbrück-Centrum Für Molekulare Medizin Berlin - Buch Genom-Architekturabbildung
JP2018518992A (ja) * 2015-06-24 2018-07-19 オックスフォード バイオダイナミックス リミテッド 染色体相互作用の部位を用いた検出法
WO2017066907A1 (zh) * 2015-10-19 2017-04-27 安诺优达基因科技(北京)有限公司 一种构建高可利用数据率的Hi-C文库的方法
GB201608000D0 (en) 2016-05-06 2016-06-22 Oxford Biodynamics Ltd Chromosome detection
CA3076450A1 (en) * 2017-10-02 2019-04-11 Oxford Biodynamics Limited Biomarker
USD877547S1 (en) 2018-07-09 2020-03-10 Apple Inc. Retail fixture
GB202111195D0 (en) 2021-08-03 2021-09-15 Cergentis B V Method for targeted sequencing
GB202111194D0 (en) 2021-08-03 2021-09-15 Cergentis B V Method

Family Cites Families (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2003076949A2 (en) * 2002-03-08 2003-09-18 The Babraham Institute Tagging and recovery of elements associated with target molecules
US8642295B2 (en) * 2007-01-11 2014-02-04 Erasmus University Medical Center Circular chromosome conformation capture (4C)

Cited By (21)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20090186352A1 (en) * 2006-02-17 2009-07-23 Isis Innovation Limited DNA Conformation
US9777327B2 (en) 2006-02-17 2017-10-03 Oxford University Innovation Limited DNA conformation (loop structures) in normal and abnormal gene expression
US11384396B2 (en) 2006-02-17 2022-07-12 Oxford University Innovation Limited DNA conformation (loop structures) in normal and abnormal gene expression
WO2010036323A1 (en) * 2008-09-25 2010-04-01 University Of Massachusetts Medical School Method of identifing interactions between genomic loci
US9434985B2 (en) 2008-09-25 2016-09-06 University Of Massachusetts Methods of identifying interactions between genomic loci
US9708648B2 (en) 2008-09-25 2017-07-18 University Of Massachusetts HiC: method of identifying interactions between genomic loci
US10745744B2 (en) 2008-09-25 2020-08-18 University Of Massachusetts HiC: method of identifying interactions between genomic loci
WO2015089243A1 (en) 2013-12-11 2015-06-18 The Regents For Of The University Of California Methods for labeling dna fragments to recontruct physical linkage and phase
US11091758B2 (en) 2013-12-11 2021-08-17 The Regents Of The University Of California Methods for labeling DNAa fragments to reconstruct physical linkage and phase
AU2014362322B2 (en) * 2013-12-11 2021-05-27 The Regents For Of The University Of California Methods for labeling DNA fragments to recontruct physical linkage and phase
EP3540074A1 (de) * 2013-12-11 2019-09-18 The Regents of the University of California Verfahren zur markierung innerer regionen von nukleinsäuremolekülen
US10526641B2 (en) 2014-08-01 2020-01-07 Dovetail Genomics, Llc Tagging nucleic acids for sequence assembly
US9715573B2 (en) 2015-02-17 2017-07-25 Dovetail Genomics, Llc Nucleic acid sequence assembly
US10318706B2 (en) 2015-02-17 2019-06-11 Dovetail Genomics, Llc Nucleic acid sequence assembly
US11600361B2 (en) 2015-02-17 2023-03-07 Dovetail Genomics, Llc Nucleic acid sequence assembly
US11807896B2 (en) 2015-03-26 2023-11-07 Dovetail Genomics, Llc Physical linkage preservation in DNA storage
US10457934B2 (en) 2015-10-19 2019-10-29 Dovetail Genomics, Llc Methods for genome assembly, haplotype phasing, and target independent nucleic acid detection
US10975417B2 (en) 2016-02-23 2021-04-13 Dovetail Genomics, Llc Generation of phased read-sets for genome assembly and haplotype phasing
US10947579B2 (en) 2016-05-13 2021-03-16 Dovetail Genomics, Llc Recovering long-range linkage information from preserved samples
CN110234769A (zh) * 2016-12-01 2019-09-13 牛津生物动力有限公司 表观遗传染色体相互作用在癌症诊断中的应用
CN110225981A (zh) * 2016-12-23 2019-09-10 牛津生物动力有限公司 分型方法

Also Published As

Publication number Publication date
AU2006264564A1 (en) 2007-01-11
PL1899488T3 (pl) 2016-03-31
EP1899488A2 (de) 2008-03-19
CY1117260T1 (el) 2017-04-26
DK1899488T3 (en) 2015-12-21
CA2614118C (en) 2013-11-26
HUE026922T2 (en) 2016-07-28
JP5416405B2 (ja) 2014-02-12
ES2556113T3 (es) 2016-01-13
US20100075861A1 (en) 2010-03-25
BRPI0611702A2 (pt) 2010-09-28
US8153373B2 (en) 2012-04-10
JP2009500031A (ja) 2009-01-08
IL187919A (en) 2012-10-31
KR101383593B1 (ko) 2014-04-09
SI1899488T1 (sl) 2016-05-31
BRPI0611702B1 (pt) 2015-05-19
CA2614118A1 (en) 2007-01-11
NZ564262A (en) 2010-02-26
WO2007004057A2 (en) 2007-01-11
IL187919A0 (en) 2008-03-20
RU2008104024A (ru) 2009-08-10
AU2006264564B2 (en) 2012-04-19
WO2007004057A3 (en) 2007-05-18
EP1899488B1 (de) 2015-09-16
RU2478716C2 (ru) 2013-04-10
NO20076430L (no) 2008-04-03
KR20080016953A (ko) 2008-02-22

Similar Documents

Publication Publication Date Title
US8153373B2 (en) Capture and characterized co-localized chromatin (4C) technology
US8642295B2 (en) Circular chromosome conformation capture (4C)
US11932848B2 (en) Mapping of genomic interactions
US20180282796A1 (en) Typing and Assembling Discontinuous Genomic Elements
US20120179384A1 (en) Method for analyzing nucleic acid mutation using array comparative genomic hybridization technique
Gilson et al. Comprehensive DNA methylation profiling of human repetitive DNA elements using an MeDIP-on-RepArray assay
Class et al. Patent application title: CIRCULAR CHROMOSOME CONFORMATION CAPTURE (4C) Inventors: Wouter De Laat (Rotterdam, NL) Frank Grosveld (Rotterdam, NL) Assignees: Erasmus University Medical Center
CN101238225A (zh) 染色体构象芯片捕获（4c）测定