CA2922244C - 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
CA2922244C
CA2922244C CA2922244A CA2922244A CA2922244C CA 2922244 C CA2922244 C CA 2922244C CA 2922244 A CA2922244 A CA 2922244A CA 2922244 A CA2922244 A CA 2922244A CA 2922244 C CA2922244 C CA 2922244C
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nucleic acid
dna
pcr
day
beads
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French (fr)
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CA2922244A1 (en
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Peter Fraser
Cameron OSBORNE
Stefan SCHOENFELDER
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Babraham Institute
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Babraham Institute
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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
    • C12Q1/6869—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
    • C12Q1/6876—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
    • C12Q1/6806—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)
CA2922244A 2013-09-05 2014-09-04 Chromosome conformation capture method including selection and enrichment steps Active CA2922244C (en)

Applications Claiming Priority (3)

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

Publications (2)

Publication Number Publication Date
CA2922244A1 CA2922244A1 (en) 2015-03-12
CA2922244C true CA2922244C (en) 2023-01-24

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Family Applications (1)

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CA2922244A Active CA2922244C (en) 2013-09-05 2014-09-04 Chromosome conformation capture method including selection and enrichment steps

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
JP7549582B2 (ja) 2018-10-01 2024-09-11 ロンザ リミテッド 予測可能かつ安定な導入遺伝子発現を有するｓｓｉ細胞および形成の方法
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
WO2021097284A1 (en) * 2019-11-15 2021-05-20 Phase Genomics Inc. Chomosome conformation capture from tissue samples
US20230140574A1 (en) * 2020-03-31 2023-05-04 Qiagen Gmbh Nucleic acid purification from fixed biological samples
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
EP1899488B1 (en) * 2005-07-04 2015-09-16 Erasmus University Medical Center Chromosome conformation capture-on-chip (4c) assay
EP2121977B1 (en) * 2007-01-11 2017-06-21 Erasmus University Medical Center Circular chromosome conformation capture (4c)
WO2009099602A1 (en) * 2008-02-04 2009-08-13 Massachusetts Institute Of Technology Selection of nucleic acids by solution hybridization to oligonucleotide baits
US9434985B2 (en) * 2008-09-25 2016-09-06 University Of Massachusetts Methods of identifying interactions between genomic loci
JP5413924B2 (ja) * 2009-08-21 2014-02-12 国立大学法人大阪大学 特定ゲノム領域の単離方法
PT2591125T (pt) * 2010-07-09 2018-05-09 Cergentis B V Estratégias 3-d de sequenciação de regiões genómicas de interesse
US20130230857A1 (en) * 2010-11-05 2013-09-05 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
WO2012159025A2 (en) * 2011-05-18 2012-11-22 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
GB2517936A (en) 2015-03-11
JP6514210B2 (ja) 2019-05-22
CA2922244A1 (en) 2015-03-12
WO2015033134A1 (en) 2015-03-12
EP3041951B1 (en) 2018-11-28
JP2016533758A (ja) 2016-11-04
CN105658813A (zh) 2016-06-08
US20160194713A1 (en) 2016-07-07
CN105658813B (zh) 2021-01-05
EP3041951A1 (en) 2016-07-13
AU2014316880A1 (en) 2016-03-10
AU2020280999A1 (en) 2021-01-07
GB201315777D0 (en) 2013-10-23
AU2020280999B2 (en) 2023-02-02
GB2517936B (en) 2016-10-19

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