CN101688237A - 环状染色体构象捕获（4c） - Google Patents

环状染色体构象捕获（4c） Download PDF

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Publication number
CN101688237A
CN101688237A CN200880008027A CN200880008027A CN101688237A CN 101688237 A CN101688237 A CN 101688237A CN 200880008027 A CN200880008027 A CN 200880008027A CN 200880008027 A CN200880008027 A CN 200880008027A CN 101688237 A CN101688237 A CN 101688237A
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dna
sequence
restriction enzyme
target
sequences
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Chinese (zh)
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沃特·德拉特
弗兰克·格罗斯维尔德
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Erasmus University Medical Center
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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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6816—Hybridisation assays characterised by the detection means
    • C12Q1/6823—Release of bound markers

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  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Microbiology (AREA)
  • Immunology (AREA)
  • Physics & Mathematics (AREA)
  • Molecular Biology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Analytical Chemistry (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
CN200880008027A 2007-01-11 2008-01-10 环状染色体构象捕获（4c） Pending CN101688237A (zh)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US99975007P 2007-01-11 2007-01-11
US60/999,750 2007-01-11
US97790007P 2007-10-05 2007-10-05
US60/977,900 2007-10-05
PCT/IB2008/000625 WO2008084405A2 (en) 2007-01-11 2008-01-10 Circular chromosome conformation capture (4c)

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CN101688237A true CN101688237A (zh) 2010-03-31

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CN200880008027A Pending CN101688237A (zh) 2007-01-11 2008-01-10 环状染色体构象捕获（4c）

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US (1) US8642295B2 (https=)
EP (1) EP2121977B1 (https=)
JP (1) JP5690068B2 (https=)
CN (1) CN101688237A (https=)
AU (1) AU2008204338B2 (https=)
BR (1) BRPI0806565A2 (https=)
DK (1) DK2121977T3 (https=)
ES (1) ES2634266T3 (https=)
PT (1) PT2121977T (https=)
WO (1) WO2008084405A2 (https=)

Cited By (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN103180459A (zh) * 2010-07-09 2013-06-26 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
CN104169433A (zh) * 2011-02-04 2014-11-26 宾夕法尼亚大学董事会 在单细胞中同时检测染色体结构和基因表达的方法
CN105658813A (zh) * 2013-09-05 2016-06-08 巴布拉哈姆研究院 包括选择和富集步骤的染色体构象捕获方法
CN105992825A (zh) * 2013-11-18 2016-10-05 鹿特丹伊拉斯谟大学医疗中心 用于分析三维dna结构中的核苷酸序列相互作用的方法

Families Citing this family (80)

* 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
US11111544B2 (en) 2005-07-29 2021-09-07 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
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
US9074244B2 (en) * 2008-03-11 2015-07-07 Affymetrix, Inc. Array-based translocation and rearrangement assays
HUE052213T2 (hu) 2009-11-06 2021-04-28 Univ Leland Stanford Junior Grafitkilökõdés nem invazív diagnosztizálása szervátültetett betegekben
US12221653B2 (en) 2010-05-18 2025-02-11 Natera, Inc. Methods for simultaneous amplification of target loci
US9677118B2 (en) 2014-04-21 2017-06-13 Natera, Inc. Methods for simultaneous amplification of target loci
US10316362B2 (en) 2010-05-18 2019-06-11 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
US11332785B2 (en) 2010-05-18 2022-05-17 Natera, Inc. Methods for non-invasive prenatal ploidy calling
US20190010543A1 (en) 2010-05-18 2019-01-10 Natera, Inc. Methods for simultaneous amplification of target loci
US11939634B2 (en) 2010-05-18 2024-03-26 Natera, Inc. Methods for simultaneous amplification of target loci
US12152275B2 (en) 2010-05-18 2024-11-26 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
US11326208B2 (en) 2010-05-18 2022-05-10 Natera, Inc. Methods for nested PCR amplification of cell-free DNA
US11339429B2 (en) 2010-05-18 2022-05-24 Natera, Inc. Methods for non-invasive prenatal ploidy calling
EP2572003A4 (en) 2010-05-18 2016-01-13 Natera Inc METHOD FOR NONINVASIVE PRANATAL PLOIDIE ASSIGNMENT
US11322224B2 (en) 2010-05-18 2022-05-03 Natera, Inc. Methods for non-invasive prenatal ploidy calling
WO2012088456A2 (en) 2010-12-22 2012-06-28 Natera, Inc. Methods for non-invasive prenatal paternity testing
AU2011358564B9 (en) 2011-02-09 2017-07-13 Natera, Inc Methods for non-invasive prenatal ploidy calling
GB2496016B (en) 2011-09-09 2016-03-16 Univ Leland Stanford Junior Methods for obtaining a sequence
US20140100126A1 (en) 2012-08-17 2014-04-10 Natera, Inc. Method for Non-Invasive Prenatal Testing Using Parental Mosaicism Data
EP3885446A1 (en) 2013-02-01 2021-09-29 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
WO2014144491A1 (en) * 2013-03-15 2014-09-18 The Broad Institute, Inc Methods for determining multiple interactions between nucleic acids in a cell
KR101672531B1 (ko) * 2013-04-18 2016-11-17 주식회사 젠큐릭스 조기 유방암 예후 예측 진단용 유전자 마커 및 이의 용도
EP3049557B1 (en) 2013-09-27 2021-05-05 University of Washington Methods and systems for large scale scaffolding of genome assemblies
EP3957749A1 (en) 2014-04-21 2022-02-23 Natera, Inc. Detecting tumour specific mutations in biopsies with whole exome sequencing and in cell-free samples
US20180173845A1 (en) 2014-06-05 2018-06-21 Natera, Inc. Systems and Methods for Detection of Aneuploidy
CA2956925C (en) 2014-08-01 2024-02-13 Dovetail Genomics, Llc Tagging nucleic acids for sequence assembly
EP3201350B1 (en) * 2014-09-30 2020-12-02 Global Life Sciences Solutions USA LLC Method for nucleic acid analysis directly from an unpurified biological sample
WO2016094872A1 (en) 2014-12-12 2016-06-16 The Broad Institute Inc. Dead guides for crispr transcription factors
EP3889260A1 (en) 2014-12-12 2021-10-06 The Broad Institute, Inc. Protected guide rnas (pgrnas)
WO2016094874A1 (en) 2014-12-12 2016-06-16 The Broad Institute Inc. Escorted and functionalized guides for crispr-cas systems
WO2016106244A1 (en) 2014-12-24 2016-06-30 The Broad Institute Inc. Crispr having or associated with destabilization domains
NZ734854A (en) 2015-02-17 2022-11-25 Dovetail Genomics Llc Nucleic acid sequence assembly
US11807896B2 (en) 2015-03-26 2023-11-07 Dovetail Genomics, Llc Physical linkage preservation in DNA storage
WO2016182893A1 (en) 2015-05-08 2016-11-17 Teh Broad Institute Inc. Functional genomics using crispr-cas systems for saturating mutagenesis of non-coding elements, compositions, methods, libraries and applications thereof
WO2016183106A1 (en) 2015-05-11 2016-11-17 Natera, Inc. Methods and compositions for determining ploidy
CA3012607A1 (en) 2015-06-18 2016-12-22 The Broad Institute Inc. Crispr enzymes and systems
EP4159856A1 (en) 2015-06-18 2023-04-05 The Broad Institute, Inc. Novel crispr enzymes and systems
US9790490B2 (en) 2015-06-18 2017-10-17 The Broad Institute Inc. CRISPR enzymes and systems
US11802305B2 (en) 2015-06-24 2023-10-31 Oxford BioDynamics PLC Detection processes using sites of chromosome interaction
WO2017061861A1 (en) * 2015-10-05 2017-04-13 Koninklijke Nederlandse Akademie Van Wetenschappen Targeted locus amplification using cloning strategies
CA3002740A1 (en) 2015-10-19 2017-04-27 Dovetail Genomics, Llc Methods for genome assembly, haplotype phasing, and target independent nucleic acid detection
EP3368687B1 (en) 2015-10-27 2021-09-29 The Broad Institute, Inc. Compositions and methods for targeting cancer-specific sequence variations
WO2017106657A1 (en) 2015-12-18 2017-06-22 The Broad Institute Inc. Novel crispr enzymes and systems
JP7441003B2 (ja) 2016-02-23 2024-02-29 ダブテイル ゲノミクス エルエルシー ゲノムアセンブリのためのフェージングされたリードセットの生成とハプロタイプフェージング
WO2017181202A2 (en) 2016-04-15 2017-10-19 Natera, Inc. Methods for lung cancer detection
CN110382692A (zh) 2016-04-19 2019-10-25 博德研究所 新型crispr酶以及系统
EP3445853A1 (en) 2016-04-19 2019-02-27 The Broad Institute, Inc. Cpf1 complexes with reduced indel activity
WO2017197300A1 (en) 2016-05-13 2017-11-16 Dovetail Genomics Llc Recovering long-range linkage information from preserved samples
US12595478B2 (en) 2016-06-29 2026-04-07 The Broad Institute, Inc. Crispr-Cas systems having destabilization domain
WO2018064208A1 (en) 2016-09-28 2018-04-05 The Broad Institute, Inc. Systematic screening and mapping of regulatory elements in non-coding genomic regions, methods, compositions, and applications thereof
US11485996B2 (en) 2016-10-04 2022-11-01 Natera, Inc. Methods for characterizing copy number variation using proximity-litigation sequencing
GB201618485D0 (en) 2016-11-02 2016-12-14 Ucl Business Plc Method of detecting tumour recurrence
MY190153A (en) * 2016-12-01 2022-03-31 Oxford BioDynamics PLC Application of epigenetic chromosomal interactions in cancer diagnostics
US10011870B2 (en) 2016-12-07 2018-07-03 Natera, Inc. Compositions and methods for identifying nucleic acid molecules
CN110225981B (zh) 2016-12-23 2024-03-15 牛津生物动力有限责任公司 分型方法
CN107058484B (zh) * 2016-12-26 2020-06-16 孙涛 一种应用于高通量测序同时检测t细胞和b细胞免疫组库的引物组合及试剂盒
US20210293783A1 (en) 2017-04-18 2021-09-23 The General Hospital Corporation Compositions for detecting secretion and methods of use
ES2987603T3 (es) * 2017-11-03 2024-11-15 Oxford BioDynamics PLC Regulación genética de la respuesta inmunitaria por interacciones cromosómicas
US11873481B2 (en) 2017-11-21 2024-01-16 Arima Genomics, Inc. Preserving spatial-proximal contiguity and molecular contiguity in nucleic acid templates
JP2021506342A (ja) 2017-12-14 2021-02-22 ティーエーアイ ダイアグノスティックス インコーポレイテッドＴａｉ Ｄｉａｇｎｏｓｔｉｃｓ，Ｉｎｃ． 移植のための移植片適合性の評価
WO2019152543A1 (en) 2018-01-31 2019-08-08 Dovetail Genomics, Llc Sample prep for dna linkage recovery
CA3090426A1 (en) 2018-04-14 2019-10-17 Natera, Inc. Methods for cancer detection and monitoring by means of personalized detection of circulating tumor dna
CN108804872A (zh) * 2018-06-08 2018-11-13 中国农业科学院农业基因组研究所 利用外切酶组合消除三维基因组学技术噪音的方法及应用
CN109033745A (zh) * 2018-06-08 2018-12-18 中国农业科学院农业基因组研究所 一种消除三维基因组学技术噪音的方法及应用
AU2019291907A1 (en) * 2018-06-29 2021-02-18 Grail, Inc. Nucleic acid rearrangement and integration analysis
US12234509B2 (en) 2018-07-03 2025-02-25 Natera, Inc. Methods for detection of donor-derived cell-free DNA
WO2020041380A1 (en) 2018-08-20 2020-02-27 The Broad Institute, Inc. Methods and compositions for optochemical control of crispr-cas9
CN113272441A (zh) 2018-11-20 2021-08-17 阿瑞玛基因组学公司 保留空间邻近连续性信息的制备核酸的方法和组合物
CN109609611A (zh) * 2018-12-26 2019-04-12 上海优甲医疗科技有限公司 一种基于高通量测序技术的基因定量测序方法
US20220235340A1 (en) 2019-05-20 2022-07-28 The Broad Institute, Inc. Novel crispr-cas systems and uses thereof
EP3973073A1 (en) 2019-05-20 2022-03-30 Arima Genomics, Inc. Methods and compositions for enhanced genome coverage and preservation of spatial proximal contiguity
EP3980559A1 (en) 2019-06-06 2022-04-13 Natera, Inc. Methods for detecting immune cell dna and monitoring immune system
CN115803447A (zh) 2020-04-23 2023-03-14 荷兰皇家科学院 染色体邻近实验中的结构变异检测
GB202111194D0 (en) * 2021-08-03 2021-09-15 Cergentis B V Method
WO2025117544A1 (en) 2023-11-29 2025-06-05 The Broad Institute, Inc. Engineered omega guide molecule and iscb compositions, systems, and methods of use thereof

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2007004057A2 (en) * 2005-07-04 2007-01-11 Erasmus University Medical Center Chromosome conformation capture-on-chip (4c) assay

Family Cites Families (22)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
NL154598B (nl) 1970-11-10 1977-09-15 Organon Nv Werkwijze voor het aantonen en bepalen van laagmoleculire verbindingen en van eiwitten die deze verbindingen specifiek kunnen binden, alsmede testverpakking.
US3817837A (en) 1971-05-14 1974-06-18 Syva Corp Enzyme amplification assay
US3939350A (en) 1974-04-29 1976-02-17 Board Of Trustees Of The Leland Stanford Junior University Fluorescent immunoassay employing total reflection for activation
US3996345A (en) 1974-08-12 1976-12-07 Syva Company Fluorescence quenching with immunological pairs in immunoassays
US4275149A (en) 1978-11-24 1981-06-23 Syva Company Macromolecular environment control in specific receptor assays
US4277437A (en) 1978-04-05 1981-07-07 Syva Company Kit for carrying out chemically induced fluorescence immunoassay
US4366241A (en) 1980-08-07 1982-12-28 Syva Company Concentrating zone method in heterogeneous immunoassays
US4683195A (en) 1986-01-30 1987-07-28 Cetus Corporation Process for amplifying, detecting, and/or-cloning nucleic acid sequences
US4683202A (en) 1985-03-28 1987-07-28 Cetus Corporation Process for amplifying nucleic acid sequences
US4965188A (en) 1986-08-22 1990-10-23 Cetus Corporation Process for amplifying, detecting, and/or cloning nucleic acid sequences using a thermostable enzyme
GB8607679D0 (en) 1986-03-27 1986-04-30 Winter G P Recombinant dna product
US5143854A (en) 1989-06-07 1992-09-01 Affymax Technologies N.V. Large scale photolithographic solid phase synthesis of polypeptides and receptor binding screening thereof
DE69132531T2 (de) 1990-12-06 2001-09-13 Affymetrix, Inc. (N.D.Ges.D.Staates Delaware) Verbindungen und ihre Verwendung in einer binären Synthesestrategie
DE69233501T2 (de) 1991-11-22 2006-02-23 Affymetrix, Inc. (n.d.Ges.d.Staates Delaware), Santa Clara Kombinatorische Strategien für die Polymersynthese
US5837832A (en) 1993-06-25 1998-11-17 Affymetrix, Inc. Arrays of nucleic acid probes on biological chips
JPH09507121A (ja) 1993-10-26 1997-07-22 アフィマックス テクノロジーズ ナームロゼ ベノートスハップ 生物学的チップ上の核酸プローブアレー
US5571639A (en) 1994-05-24 1996-11-05 Affymax Technologies N.V. Computer-aided engineering system for design of sequence arrays and lithographic masks
US5795716A (en) 1994-10-21 1998-08-18 Chee; Mark S. Computer-aided visualization and analysis system for sequence evaluation
US5599695A (en) 1995-02-27 1997-02-04 Affymetrix, Inc. Printing molecular library arrays using deprotection agents solely in the vapor phase
EP0937159A4 (en) 1996-02-08 2004-10-20 Affymetrix Inc SPECIATION OF MICROORGANISMS FROM MICROPLATES AND CHARACTERIZATION OF THE PHENOTYPES THEREOF
US6126939A (en) 1996-09-03 2000-10-03 Yeda Research And Development Co. Ltd. Anti-inflammatory dipeptide and pharmaceutical composition thereof
CA2481312A1 (en) 2002-03-08 2003-09-18 The Babraham Institute Tagging and recovery of elements associated with target molecules

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2007004057A2 (en) * 2005-07-04 2007-01-11 Erasmus University Medical Center Chromosome conformation capture-on-chip (4c) assay

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
孙立军等: "基因差异表达的高通量分析及其在肿瘤研究中的应用", 《癌症》 *
陈文炳等: "应用多重PCR同时检测多种转基因成分", 《检验检疫科学》 *

Cited By (7)

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Publication number Priority date Publication date Assignee Title
CN103180459A (zh) * 2010-07-09 2013-06-26 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
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
US12006538B2 (en) 2010-07-09 2024-06-11 Cergentis Bv 3-D genomic region of interest sequencing strategies
CN104169433A (zh) * 2011-02-04 2014-11-26 宾夕法尼亚大学董事会 在单细胞中同时检测染色体结构和基因表达的方法
CN105658813A (zh) * 2013-09-05 2016-06-08 巴布拉哈姆研究院 包括选择和富集步骤的染色体构象捕获方法
CN105658813B (zh) * 2013-09-05 2021-01-05 巴布拉哈姆研究院 包括选择和富集步骤的染色体构象捕获方法
CN105992825A (zh) * 2013-11-18 2016-10-05 鹿特丹伊拉斯谟大学医疗中心 用于分析三维dna结构中的核苷酸序列相互作用的方法

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EP2121977A2 (en) 2009-11-25
JP5690068B2 (ja) 2015-03-25
WO2008084405A3 (en) 2009-01-29
US20100062947A1 (en) 2010-03-11
PT2121977T (pt) 2017-08-18
AU2008204338B2 (en) 2014-03-06
ES2634266T3 (es) 2017-09-27
WO2008084405A2 (en) 2008-07-17
DK2121977T3 (en) 2017-09-18
JP2010515449A (ja) 2010-05-13
AU2008204338A1 (en) 2008-07-17
AU2008204338A8 (en) 2009-08-06
BRPI0806565A2 (pt) 2014-05-06
US8642295B2 (en) 2014-02-04
EP2121977B1 (en) 2017-06-21

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Application publication date: 20100331