AU2008204338B2 - Circular chromosome conformation capture (4C) - Google Patents
Circular chromosome conformation capture (4C) Download PDFInfo
- Publication number
- AU2008204338B2 AU2008204338B2 AU2008204338A AU2008204338A AU2008204338B2 AU 2008204338 B2 AU2008204338 B2 AU 2008204338B2 AU 2008204338 A AU2008204338 A AU 2008204338A AU 2008204338 A AU2008204338 A AU 2008204338A AU 2008204338 B2 AU2008204338 B2 AU 2008204338B2
- Authority
- AU
- Australia
- Prior art keywords
- dna
- sequences
- target
- sequence
- restriction enzyme
- 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.)
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Classifications
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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)
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) |
Publications (3)
| Publication Number | Publication Date |
|---|---|
| AU2008204338A1 AU2008204338A1 (en) | 2008-07-17 |
| AU2008204338A8 AU2008204338A8 (en) | 2009-08-06 |
| AU2008204338B2 true AU2008204338B2 (en) | 2014-03-06 |
Family
ID=39609120
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| AU2008204338A Active AU2008204338B2 (en) | 2007-01-11 | 2008-01-10 | Circular chromosome conformation capture (4C) |
Country Status (10)
| Country | Link |
|---|---|
| US (1) | US8642295B2 (enExample) |
| EP (1) | EP2121977B1 (enExample) |
| JP (1) | JP5690068B2 (enExample) |
| CN (1) | CN101688237A (enExample) |
| AU (1) | AU2008204338B2 (enExample) |
| BR (1) | BRPI0806565A2 (enExample) |
| DK (1) | DK2121977T3 (enExample) |
| ES (1) | ES2634266T3 (enExample) |
| PT (1) | PT2121977T (enExample) |
| WO (1) | WO2008084405A2 (enExample) |
Families Citing this family (81)
| 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 |
| US11111544B2 (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 |
| CN102712954A (zh) * | 2009-11-06 | 2012-10-03 | 小利兰·斯坦福大学托管委员会 | 器官移植患者移植排斥的非侵入性诊断 |
| 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 |
| US11939634B2 (en) | 2010-05-18 | 2024-03-26 | 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 |
| US11332793B2 (en) | 2010-05-18 | 2022-05-17 | 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 |
| US12152275B2 (en) | 2010-05-18 | 2024-11-26 | Natera, Inc. | Methods for non-invasive prenatal ploidy calling |
| US12221653B2 (en) | 2010-05-18 | 2025-02-11 | 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 |
| 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 |
| CA2798758C (en) | 2010-05-18 | 2019-05-07 | 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 |
| PT2591125T (pt) * | 2010-07-09 | 2018-05-09 | Cergentis B V | Estratégias 3-d de sequenciação de regiões genómicas de interesse |
| AU2012211957B2 (en) | 2011-02-04 | 2017-02-23 | The Trustees Of The University Of Pennsylvania | A method for detecting chromosome structure and gene expression simultaneously in single cells |
| CA2824387C (en) | 2011-02-09 | 2019-09-24 | Natera, Inc. | Methods for non-invasive prenatal ploidy calling |
| HK1199745A1 (en) | 2011-09-09 | 2015-07-17 | The Board Of Trustees Of The Leland Stanford Junior University | 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 |
| US9411930B2 (en) | 2013-02-01 | 2016-08-09 | The Regents Of The University Of California | Methods for genome assembly and haplotype phasing |
| WO2014121091A1 (en) | 2013-02-01 | 2014-08-07 | The Regents Of The University Of California | Methods for genome assembly and haplotype phasing |
| EP2971278B1 (en) * | 2013-03-15 | 2022-08-10 | 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 |
| GB2517936B (en) * | 2013-09-05 | 2016-10-19 | Babraham Inst | Chromosome conformation capture method including selection and enrichment steps |
| EP3049557B1 (en) | 2013-09-27 | 2021-05-05 | University of Washington | Methods and systems for large scale scaffolding of genome assemblies |
| GB201320351D0 (en) * | 2013-11-18 | 2014-01-01 | Erasmus Universiteit Medisch Ct | Method |
| EP3561075A1 (en) | 2014-04-21 | 2019-10-30 | Natera, Inc. | Detecting mutations in tumour biopsies and cell-free samples |
| US20180173846A1 (en) | 2014-06-05 | 2018-06-21 | Natera, Inc. | Systems and Methods for Detection of Aneuploidy |
| WO2016019360A1 (en) | 2014-08-01 | 2016-02-04 | 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 |
| EP3985115A1 (en) | 2014-12-12 | 2022-04-20 | 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 |
| CA2970370A1 (en) | 2014-12-24 | 2016-06-30 | Massachusetts Institute Of Technology | Crispr having or associated with destabilization domains |
| CA2976902A1 (en) | 2015-02-17 | 2016-08-25 | Dovetail Genomics Llc | Nucleic acid sequence assembly |
| WO2016154540A1 (en) | 2015-03-26 | 2016-09-29 | Dovetail Genomics Llc | Physical linkage preservation in dna storage |
| 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 |
| EP4428863A3 (en) | 2015-05-11 | 2024-12-11 | Natera, Inc. | Methods and compositions for determining ploidy |
| EP3436575A1 (en) | 2015-06-18 | 2019-02-06 | The Broad Institute Inc. | Novel crispr enzymes and systems |
| CA3012631A1 (en) | 2015-06-18 | 2016-12-22 | 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 |
| MY194686A (en) | 2015-06-24 | 2022-12-15 | Oxford BioDynamics PLC | Detection of chromosome interactions |
| WO2017061861A1 (en) * | 2015-10-05 | 2017-04-13 | Koninklijke Nederlandse Akademie Van Wetenschappen | Targeted locus amplification using cloning strategies |
| KR20180096586A (ko) | 2015-10-19 | 2018-08-29 | 더브테일 제노믹스 엘엘씨 | 게놈 어셈블리, 하플로타입 페이징 및 표적 독립적 핵산 검출을 위한 방법 |
| WO2017074788A1 (en) | 2015-10-27 | 2017-05-04 | 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 |
| SG11201807117WA (en) | 2016-02-23 | 2018-09-27 | Dovetail Genomics Llc | Generation of phased read-sets for genome assembly and haplotype phasing |
| DK3443119T3 (da) | 2016-04-15 | 2022-05-23 | Natera Inc | Fremgangsmåde til bestemmelse af lunge cancer |
| KR102670601B1 (ko) | 2016-04-19 | 2024-05-29 | 더 브로드 인스티튜트, 인코퍼레이티드 | 신규한 crispr 효소 및 시스템 |
| US11286478B2 (en) | 2016-04-19 | 2022-03-29 | The Broad Institute, Inc. | Cpf1 complexes with reduced indel activity |
| DK3455356T3 (da) | 2016-05-13 | 2021-11-01 | Dovetail Genomics Llc | Genfinding af langtrækkende bindingsinformation fra konserverede prøver |
| US20210222164A1 (en) | 2016-06-29 | 2021-07-22 | The Broad Institute, Inc. | Crispr-cas systems having destabilization domain |
| WO2018067517A1 (en) | 2016-10-04 | 2018-04-12 | 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 |
| ES2971286T3 (es) * | 2016-12-01 | 2024-06-04 | Oxford BioDynamics PLC | Aplicación de interacciones cromosómicas epigenéticas en diagnóstico de cáncer |
| US10011870B2 (en) | 2016-12-07 | 2018-07-03 | Natera, Inc. | Compositions and methods for identifying nucleic acid molecules |
| CA3047888C (en) | 2016-12-23 | 2025-05-27 | Oxford Biodynamics Ltd | METHOD FOR TYPING EPIGENETIC CHROMOSOME INTERACTIONS |
| 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 |
| EP3612629A1 (en) | 2017-04-18 | 2020-02-26 | The Broad Institute, Inc. | Compositions for detecting secretion and methods of use |
| SG11202003233YA (en) * | 2017-11-03 | 2020-05-28 | Oxford BioDynamics PLC | Genetic regulation of immunoresponse by chromosome interactions |
| EP3714052A1 (en) | 2017-11-21 | 2020-09-30 | Arima Genomics, Inc. | Preserving spatial-proximal contiguity and molecular contiguity in nucleic acid templates |
| US12084720B2 (en) | 2017-12-14 | 2024-09-10 | Natera, Inc. | Assessing graft suitability for transplantation |
| US12378592B2 (en) | 2018-01-31 | 2025-08-05 | Dovetail Genomics, Llc. | Sample prep for DNA linkage recovery |
| JP7573443B2 (ja) | 2018-04-14 | 2024-10-25 | ナテラ, インコーポレイテッド | 循環腫瘍dnaの個別化された検出を用いる癌検出およびモニタリングの方法 |
| 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 |
| 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 |
| WO2020006370A1 (en) * | 2018-06-29 | 2020-01-02 | 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 |
| US12421507B2 (en) | 2018-08-20 | 2025-09-23 | 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 |
| EP3973073A1 (en) | 2019-05-20 | 2022-03-30 | Arima Genomics, Inc. | Methods and compositions for enhanced genome coverage and preservation of spatial proximal contiguity |
| US20220235340A1 (en) | 2019-05-20 | 2022-07-28 | The Broad Institute, Inc. | Novel crispr-cas systems and uses thereof |
| EP3980559A1 (en) | 2019-06-06 | 2022-04-13 | Natera, Inc. | Methods for detecting immune cell dna and monitoring immune system |
| JP2023523002A (ja) | 2020-04-23 | 2023-06-01 | コーニンクレッカ ネーデルラントセ アカデミー ファン ヴェッテンシャッペン | 染色体近接実験における構造的変異検出 |
| 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)
| 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 |
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| 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 |
| US4277437A (en) * | 1978-04-05 | 1981-07-07 | Syva Company | Kit for carrying out chemically induced fluorescence immunoassay |
| US4275149A (en) * | 1978-11-24 | 1981-06-23 | Syva Company | Macromolecular environment control in specific receptor assays |
| US4366241A (en) * | 1980-08-07 | 1982-12-28 | Syva Company | Concentrating zone method in heterogeneous immunoassays |
| US4965188A (en) * | 1986-08-22 | 1990-10-23 | Cetus Corporation | Process for amplifying, detecting, and/or cloning nucleic acid sequences using a thermostable enzyme |
| 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 |
| 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 |
| ES2155822T3 (es) | 1990-12-06 | 2001-06-01 | Affymetrix Inc | Compuestos y su utilizacion en una estrategia de sintesis binaria. |
| DE69233087T2 (de) | 1991-11-22 | 2003-12-24 | Affymetrix, Inc. (N.D.Ges.D.Staates Delaware) | Verfahren zur Herstellung von Polymerarrays |
| WO1995011995A1 (en) | 1993-10-26 | 1995-05-04 | Affymax Technologies N.V. | Arrays of nucleic acid probes on biological chips |
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| JP2000504575A (ja) | 1996-02-08 | 2000-04-18 | アフィメトリックス,インコーポレイテッド | 微生物のチップベースの種分化および表現型特徴付け |
| US6126939A (en) | 1996-09-03 | 2000-10-03 | Yeda Research And Development Co. Ltd. | Anti-inflammatory dipeptide and pharmaceutical composition thereof |
| EP1483587A2 (en) * | 2002-03-08 | 2004-12-08 | The Babraham Institute | Tagging and recovery of elements associated with target molecules |
-
2008
- 2008-01-10 EP EP08719319.9A patent/EP2121977B1/en active Active
- 2008-01-10 DK DK08719319.9T patent/DK2121977T3/en active
- 2008-01-10 ES ES08719319.9T patent/ES2634266T3/es active Active
- 2008-01-10 AU AU2008204338A patent/AU2008204338B2/en active Active
- 2008-01-10 BR BRPI0806565-9A patent/BRPI0806565A2/pt not_active Application Discontinuation
- 2008-01-10 CN CN200880008027A patent/CN101688237A/zh active Pending
- 2008-01-10 US US12/522,555 patent/US8642295B2/en active Active
- 2008-01-10 WO PCT/IB2008/000625 patent/WO2008084405A2/en not_active Ceased
- 2008-01-10 PT PT87193199T patent/PT2121977T/pt unknown
- 2008-01-10 JP JP2009545253A patent/JP5690068B2/ja active Active
Patent Citations (1)
| 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 (3)
| Title |
|---|
| SIMONIS, M. et al., Nature Genetics, 2006, vol. 38, no. 11, pages 1348-1354 * |
| WURTELE, H. et al., Chromosome Research, 2006, vol. 14, pages 477-495 * |
| ZHAO, Z. et al., Nature Genetics, 2006, vol. 38, no. 11, pages 1341-1347 * |
Also Published As
| Publication number | Publication date |
|---|---|
| WO2008084405A3 (en) | 2009-01-29 |
| WO2008084405A2 (en) | 2008-07-17 |
| AU2008204338A8 (en) | 2009-08-06 |
| BRPI0806565A2 (pt) | 2014-05-06 |
| PT2121977T (pt) | 2017-08-18 |
| EP2121977A2 (en) | 2009-11-25 |
| ES2634266T3 (es) | 2017-09-27 |
| AU2008204338A1 (en) | 2008-07-17 |
| DK2121977T3 (en) | 2017-09-18 |
| US8642295B2 (en) | 2014-02-04 |
| CN101688237A (zh) | 2010-03-31 |
| JP2010515449A (ja) | 2010-05-13 |
| JP5690068B2 (ja) | 2015-03-25 |
| EP2121977B1 (en) | 2017-06-21 |
| US20100062947A1 (en) | 2010-03-11 |
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Legal Events
| Date | Code | Title | Description |
|---|---|---|---|
| TH | Corrigenda |
Free format text: IN VOL 23, NO 29, PAGE(S) 9329 UNDER THE HEADING PCT APPLICATIONS THAT HAVE ENTERED THE NATIONAL PHASE - NAME INDEX UNDER THE NAME ERASMUS UNIVERSITY MEDICAL CENTER, APPLICATION NO. 2008204338, UNDER INID (54) CORRECT THE TITLE TO READ CIRCULAR CHROMOSOME CONFORMATION CAPTURE (4C). |
|
| FGA | Letters patent sealed or granted (standard patent) | ||
| MK14 | Patent ceased section 143(a) (annual fees not paid) or expired | ||
| NA | Applications received for extensions of time, section 223 |
Free format text: AN APPLICATION TO EXTEND THE TIME FROM 10 JAN 2015 TO 10 SEP 2015 IN WHICH TO PAY A RENEWAL FEE HASBEEN FILED . |
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| NB | Applications allowed - extensions of time section 223(2) |
Free format text: THE TIME IN WHICH TO PAY A RENEWAL FEE HAS BEEN EXTENDED TO 10 SEP 2015 . |