AU2014316880A1 - Chromosome conformation capture method including selection and enrichment steps - Google Patents

Chromosome conformation capture method including selection and enrichment steps Download PDF

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Publication number
AU2014316880A1
AU2014316880A1 AU2014316880A AU2014316880A AU2014316880A1 AU 2014316880 A1 AU2014316880 A1 AU 2014316880A1 AU 2014316880 A AU2014316880 A AU 2014316880A AU 2014316880 A AU2014316880 A AU 2014316880A AU 2014316880 A1 AU2014316880 A1 AU 2014316880A1
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Prior art keywords
nucleic acid
dna
pcr
day
beads
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Abandoned
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AU2014316880A
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English (en)
Inventor
Peter Fraser
Cameron OSBORNE
Stefan SCHOENFELDER
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Babraham Institute
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Babraham Institute
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Publication of AU2014316880A1 publication Critical patent/AU2014316880A1/en
Priority to AU2020280999A priority Critical patent/AU2020280999B2/en
Abandoned legal-status Critical Current

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    • 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
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • 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
    • C12Q1/6869—Methods for sequencing
    • 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
    • C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
    • 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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6853—Nucleic acid amplification reactions using modified primers or templates
    • C12Q1/6855—Ligating adaptors
    • 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
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • 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
    • C12Q2537/00—Reactions characterised by the reaction format or use of a specific feature
    • C12Q2537/10—Reactions characterised by the reaction format or use of a specific feature the purpose or use of
    • C12Q2537/159—Reduction of complexity, e.g. amplification of subsets, removing duplicated genomic regions
    • 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
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/16—Primer sets for multiplex assays

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Engineering & Computer Science (AREA)
  • Analytical Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • Molecular Biology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Immunology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Physics & Mathematics (AREA)
  • Biochemistry (AREA)
  • Microbiology (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Pathology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
AU2014316880A 2013-09-05 2014-09-04 Chromosome conformation capture method including selection and enrichment steps Abandoned AU2014316880A1 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU2020280999A AU2020280999B2 (en) 2013-09-05 2020-11-30 Chromosome conformation capture method including selection and enrichment steps

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
GB1315777.1 2013-09-05
GB1315777.1A GB2517936B (en) 2013-09-05 2013-09-05 Chromosome conformation capture method including selection and enrichment steps
PCT/GB2014/052664 WO2015033134A1 (en) 2013-09-05 2014-09-04 Chromosome conformation capture method including selection and enrichment steps

Related Child Applications (1)

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AU2020280999A Division AU2020280999B2 (en) 2013-09-05 2020-11-30 Chromosome conformation capture method including selection and enrichment steps

Publications (1)

Publication Number Publication Date
AU2014316880A1 true AU2014316880A1 (en) 2016-03-10

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AU2014316880A Abandoned AU2014316880A1 (en) 2013-09-05 2014-09-04 Chromosome conformation capture method including selection and enrichment steps
AU2020280999A Active AU2020280999B2 (en) 2013-09-05 2020-11-30 Chromosome conformation capture method including selection and enrichment steps

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Country Status (8)

Country Link
US (1) US20160194713A1 (enExample)
EP (1) EP3041951B1 (enExample)
JP (1) JP6514210B2 (enExample)
CN (1) CN105658813B (enExample)
AU (2) AU2014316880A1 (enExample)
CA (1) CA2922244C (enExample)
GB (1) GB2517936B (enExample)
WO (1) WO2015033134A1 (enExample)

Families Citing this family (12)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
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
GB201518843D0 (en) * 2015-10-23 2015-12-09 Isis Innovation Method of analysing DNA sequences
CN107119120A (zh) * 2017-05-04 2017-09-01 河海大学常州校区 一种基于染色质3d构象技术的关键作用分子检测方法
CN108300767B (zh) * 2017-10-27 2021-08-20 清华大学 一种核酸复合体中核酸区段相互作用的分析方法
CN108220394B (zh) * 2018-01-05 2021-03-23 清华大学 基因调控性染色质相互作用的鉴定方法、系统及其应用
CN109448783B (zh) * 2018-08-07 2022-05-13 清华大学 一种染色质拓扑结构域边界的分析方法
CN113227388A (zh) 2018-10-01 2021-08-06 龙沙有限公司 具有可预测和稳定的转基因表达的ssi细胞及形成方法
US20220213546A1 (en) * 2019-05-22 2022-07-07 Oxford Nanopore Technologies Plc Protocol for detecting interactions within one or more dna molecules within a cell
GB201914325D0 (en) * 2019-10-04 2019-11-20 Babraham Inst Novel meethod
CA3160441A1 (en) * 2019-11-15 2021-05-20 Phase Genomics Inc. Chromosome conformation capture from tissue samples
CN115335519A (zh) * 2020-03-31 2022-11-11 凯杰有限公司 从固定的生物样品纯化核酸
GB202319199D0 (en) 2023-12-14 2024-01-31 Enhanc3D Genomics Ltd Conformation capture methods

Family Cites Families (10)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CA2614118C (en) * 2005-07-04 2013-11-26 Erasmus University Medical Center 4c
EP2121977B1 (en) * 2007-01-11 2017-06-21 Erasmus University Medical Center Circular chromosome conformation capture (4c)
US20100029498A1 (en) * 2008-02-04 2010-02-04 Andreas Gnirke Selection of nucleic acids by solution hybridization to oligonucleotide baits
WO2010036323A1 (en) * 2008-09-25 2010-04-01 University Of Massachusetts Medical School Method of identifing interactions between genomic loci
US8415098B2 (en) * 2009-08-21 2013-04-09 Osaka University Method for isolating specific genomic regions
CN103180459B (zh) * 2010-07-09 2016-10-19 赛尔冉迪思股份有限公司 3-d目的基因组区域的测序策略
WO2012061600A1 (en) * 2010-11-05 2012-05-10 The Broad Institute, Inc. Hybrid selection using genome-wide baits for selective genome enrichment in mixed samples
US9365897B2 (en) * 2011-02-08 2016-06-14 Illumina, Inc. Selective enrichment of nucleic acids
EP2710146A2 (en) * 2011-05-18 2014-03-26 Life Technologies Corporation Chromosome conformation analysis
US8663924B2 (en) * 2011-11-30 2014-03-04 Agilent Technologies, Inc. Quantitative PCR-based method to predict the efficiency of target enrichment for next-generation sequencing using repetitive DNA elements (lines/sines) as negative controls

Also Published As

Publication number Publication date
JP6514210B2 (ja) 2019-05-22
CN105658813B (zh) 2021-01-05
JP2016533758A (ja) 2016-11-04
GB2517936A (en) 2015-03-11
US20160194713A1 (en) 2016-07-07
GB201315777D0 (en) 2013-10-23
CA2922244A1 (en) 2015-03-12
AU2020280999A1 (en) 2021-01-07
CA2922244C (en) 2023-01-24
GB2517936B (en) 2016-10-19
CN105658813A (zh) 2016-06-08
EP3041951B1 (en) 2018-11-28
EP3041951A1 (en) 2016-07-13
WO2015033134A1 (en) 2015-03-12
AU2020280999B2 (en) 2023-02-02

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