WO2002103042A3 - Method and nucleic acids for the differentiation of prostate tumors - Google Patents

Method and nucleic acids for the differentiation of prostate tumors Download PDF

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Publication number
WO2002103042A3
WO2002103042A3 PCT/EP2002/006605 EP0206605W WO02103042A3 WO 2002103042 A3 WO2002103042 A3 WO 2002103042A3 EP 0206605 W EP0206605 W EP 0206605W WO 02103042 A3 WO02103042 A3 WO 02103042A3
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WO
WIPO (PCT)
Prior art keywords
differentiation
nucleic acids
prostate tumors
characterisation
pna
Prior art date
Application number
PCT/EP2002/006605
Other languages
French (fr)
Other versions
WO2002103042A2 (en
Inventor
Juergen Distler
Fabian Model
Peter Adorjan
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Epigenomics Ag
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
Application filed by Epigenomics Ag filed Critical Epigenomics Ag
Priority to EP02780768A priority Critical patent/EP1395686A2/en
Priority to JP2003505363A priority patent/JP2004529661A/en
Priority to CA002445731A priority patent/CA2445731A1/en
Publication of WO2002103042A2 publication Critical patent/WO2002103042A2/en
Publication of WO2002103042A3 publication Critical patent/WO2002103042A3/en

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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
    • C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P13/00—Drugs for disorders of the urinary system
    • A61P13/08—Drugs for disorders of the urinary system of the prostate
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • 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
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277—Apparatus
    • B01J2219/00497—Features relating to the solid phase supports
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277—Apparatus
    • B01J2219/00497—Features relating to the solid phase supports
    • B01J2219/00527—Sheets
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00596—Solid-phase processes
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00603—Making arrays on substantially continuous surfaces
    • B01J2219/00605—Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00603—Making arrays on substantially continuous surfaces
    • B01J2219/00605—Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports
    • B01J2219/0061—The surface being organic
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00603—Making arrays on substantially continuous surfaces
    • B01J2219/00605—Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports
    • B01J2219/00612—Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports the surface being inorganic
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00603—Making arrays on substantially continuous surfaces
    • B01J2219/00659—Two-dimensional arrays
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/0068—Means for controlling the apparatus of the process
    • B01J2219/00702—Processes involving means for analysing and characterising the products
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00718—Type of compounds synthesised
    • B01J2219/0072—Organic compounds
    • B01J2219/00722—Nucleotides
    • 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
    • C12Q2600/154—Methylation markers
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B40/00—Libraries per se, e.g. arrays, mixtures
    • C40B40/04—Libraries containing only organic compounds
    • C40B40/06—Libraries containing nucleotides or polynucleotides, or derivatives thereof

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  • Chemical & Material Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Engineering & Computer Science (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Analytical Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • General Health & Medical Sciences (AREA)
  • Immunology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biophysics (AREA)
  • Physics & Mathematics (AREA)
  • General Engineering & Computer Science (AREA)
  • Biochemistry (AREA)
  • Molecular Biology (AREA)
  • Microbiology (AREA)
  • Pathology (AREA)
  • Biotechnology (AREA)
  • Medicinal Chemistry (AREA)
  • General Chemical & Material Sciences (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Veterinary Medicine (AREA)
  • Animal Behavior & Ethology (AREA)
  • Oncology (AREA)
  • Public Health (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Hospice & Palliative Care (AREA)
  • Urology & Nephrology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Pharmaceuticals Containing Other Organic And Inorganic Compounds (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)

Abstract

The present invention relates to chemically modified genomic sequences, to oligonucleotides and/or PNA-oligomers for detecting the cytosine methylation state of genomic DNA, as well as to a method for ascertaining genetic and/or epigenetic parameters of genes for use in characterisation, classification, differentiation, diagnosis and therapy of prostate lesions.
PCT/EP2002/006605 2001-06-14 2002-06-14 Method and nucleic acids for the differentiation of prostate tumors WO2002103042A2 (en)

Priority Applications (3)

Application Number Priority Date Filing Date Title
EP02780768A EP1395686A2 (en) 2001-06-14 2002-06-14 Method and nucleic acids for the differentiation of prostate tumors
JP2003505363A JP2004529661A (en) 2001-06-14 2002-06-14 Methods and nucleic acids for prostate tumor identification
CA002445731A CA2445731A1 (en) 2001-06-14 2002-06-14 Method and nucleic acids for the differentiation of prostate tumors

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
DE10128508A DE10128508A1 (en) 2001-06-14 2001-06-14 Methods and nucleic acids for the differentiation of prostate tumors
DE10128508.6 2001-06-14

Publications (2)

Publication Number Publication Date
WO2002103042A2 WO2002103042A2 (en) 2002-12-27
WO2002103042A3 true WO2002103042A3 (en) 2003-10-30

Family

ID=7688047

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/EP2002/006605 WO2002103042A2 (en) 2001-06-14 2002-06-14 Method and nucleic acids for the differentiation of prostate tumors

Country Status (6)

Country Link
US (1) US7381808B2 (en)
EP (1) EP1395686A2 (en)
JP (1) JP2004529661A (en)
CA (1) CA2445731A1 (en)
DE (1) DE10128508A1 (en)
WO (1) WO2002103042A2 (en)

Families Citing this family (16)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
AU2001248352A1 (en) * 2000-03-15 2001-09-24 Epigenomics Ag Diagnosis of diseases associated with the cell cycle
JP2003531589A (en) * 2000-04-06 2003-10-28 エピゲノミクス アーゲー Diagnosis of diseases associated with apoptosis
EP1297182A2 (en) * 2000-06-30 2003-04-02 Epigenomics AG Diagnosis of diseases associated with cell signalling
DE10054974A1 (en) * 2000-11-06 2002-06-06 Epigenomics Ag Diagnosis of diseases associated with Cdk4
DE10054972A1 (en) * 2000-11-06 2002-06-06 Epigenomics Ag Diagnosis of diseases associated with humus
WO2003004696A2 (en) * 2001-07-02 2003-01-16 Epigenomics Ag A distributed system for epigenetic based prediction of complex phenotypes
US7901880B2 (en) 2003-10-21 2011-03-08 Orion Genomics Llc Differential enzymatic fragmentation
JP4824575B2 (en) * 2003-12-01 2011-11-30 エピゲノミクス アクチェンゲゼルシャフト Methods and nucleic acids for analysis of gene expression associated with the development of prostate cell proliferative disorders
JP2005229957A (en) * 2004-02-23 2005-09-02 Japan Science & Technology Agency Telomere protein trf2 dna-binding domain mutant protein, telomere dna mutant and use of complex structure between trf2 dna binding domain and duplex dna
EP1693468A1 (en) 2005-02-16 2006-08-23 Epigenomics AG Method for determining the methylation pattern of a polynucleic acid
EP1871912B1 (en) 2005-04-15 2012-02-29 Epigenomics AG Method for determining DNA methylation in blood or urine samples
US8084734B2 (en) * 2006-05-26 2011-12-27 The George Washington University Laser desorption ionization and peptide sequencing on laser induced silicon microcolumn arrays
JP5415963B2 (en) * 2007-02-21 2014-02-12 オスロ ユニベルシテートシケヒュース ホーエフ New cancer marker
US8110796B2 (en) 2009-01-17 2012-02-07 The George Washington University Nanophotonic production, modulation and switching of ions by silicon microcolumn arrays
US9490113B2 (en) * 2009-04-07 2016-11-08 The George Washington University Tailored nanopost arrays (NAPA) for laser desorption ionization in mass spectrometry
US20140274757A1 (en) 2013-03-14 2014-09-18 Marie K. Kirby Differential Methylation Level of CpG Loci That Are Determinative of a Biochemical Reoccurrence of Prostate Cancer

Citations (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1998056952A1 (en) * 1997-06-09 1998-12-17 University Of Southern California A cancer diagnostic method based upon dna methylation differences
WO1999028498A2 (en) * 1997-11-27 1999-06-10 Epigenomics Gmbh Method for producing complex dna methylation fingerprints
WO1999055905A1 (en) * 1998-04-23 1999-11-04 Commonwealth Scientific And Industrial Research Organisation ASSAY FOR METHYLATION IN THE GST-Pi GENE
WO2000070090A1 (en) * 1999-05-14 2000-11-23 University Of Southern California Process for high throughput dna methylation analysis
DE19935772A1 (en) * 1999-07-26 2001-02-08 Epigenomics Gmbh Method for the relative quantification of the methylation of cytosine bases in amplified nucleic acid fragments
WO2001068911A2 (en) * 2000-03-15 2001-09-20 Epigenomics Ag Diagnosis of diseases associated with the cell cycle
WO2002034942A2 (en) * 2000-10-23 2002-05-02 Cancer Research Technology Limited Nucleic acid amplification-based methods for the determination of a methylation profile and reagents therefor
WO2002040710A2 (en) * 2000-11-14 2002-05-23 Epigenomics Ag Method for detecting methylation states for a toxicological diagnostic

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DE1990508U (en) 1968-08-01 Siemens-Electrogeräte Gesellschaft mit beschränkter Haftung, 1000 Berlin und 8000 München Device for pressing a tubular heat sensor against the protective tube wall in electric water heaters
US6582908B2 (en) * 1990-12-06 2003-06-24 Affymetrix, Inc. Oligonucleotides
US5474796A (en) * 1991-09-04 1995-12-12 Protogene Laboratories, Inc. Method and apparatus for conducting an array of chemical reactions on a support surface
US6017704A (en) * 1996-06-03 2000-01-25 The Johns Hopkins University School Of Medicine Method of detection of methylated nucleic acid using agents which modify unmethylated cytosine and distinguishing modified methylated and non-methylated nucleic acids
DE19905082C1 (en) 1999-01-29 2000-05-18 Epigenomics Gmbh Identification of methylation patterns of cytosine in genome DNA comprises chemical treatment to produce different base pairing behavior between cytosine and 5-methylcytosine
JP2003531589A (en) 2000-04-06 2003-10-28 エピゲノミクス アーゲー Diagnosis of diseases associated with apoptosis
EP1297182A2 (en) 2000-06-30 2003-04-02 Epigenomics AG Diagnosis of diseases associated with cell signalling
DE10037769A1 (en) 2000-08-03 2002-02-21 Epigenomics Gmbh Diagnosis of diseases associated with CD24
ES2249464T3 (en) 2000-09-09 2006-04-01 Degussa Ag NUCLEOTIDE SEQUENCES CODING FOR THE SAHH GEN.
DE10054972A1 (en) 2000-11-06 2002-06-06 Epigenomics Ag Diagnosis of diseases associated with humus
DE10054974A1 (en) 2000-11-06 2002-06-06 Epigenomics Ag Diagnosis of diseases associated with Cdk4
WO2003004696A2 (en) 2001-07-02 2003-01-16 Epigenomics Ag A distributed system for epigenetic based prediction of complex phenotypes

Patent Citations (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1998056952A1 (en) * 1997-06-09 1998-12-17 University Of Southern California A cancer diagnostic method based upon dna methylation differences
WO1999028498A2 (en) * 1997-11-27 1999-06-10 Epigenomics Gmbh Method for producing complex dna methylation fingerprints
WO1999055905A1 (en) * 1998-04-23 1999-11-04 Commonwealth Scientific And Industrial Research Organisation ASSAY FOR METHYLATION IN THE GST-Pi GENE
WO2000070090A1 (en) * 1999-05-14 2000-11-23 University Of Southern California Process for high throughput dna methylation analysis
DE19935772A1 (en) * 1999-07-26 2001-02-08 Epigenomics Gmbh Method for the relative quantification of the methylation of cytosine bases in amplified nucleic acid fragments
WO2001068911A2 (en) * 2000-03-15 2001-09-20 Epigenomics Ag Diagnosis of diseases associated with the cell cycle
WO2002034942A2 (en) * 2000-10-23 2002-05-02 Cancer Research Technology Limited Nucleic acid amplification-based methods for the determination of a methylation profile and reagents therefor
WO2002040710A2 (en) * 2000-11-14 2002-05-23 Epigenomics Ag Method for detecting methylation states for a toxicological diagnostic

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
HERMAN J G ET AL: "METHYLATION-SPECIFIC PCR: A NOVEL PCR ASSAY FOR METHYLATION STATUS OF CPG ISLANDS", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF USA, NATIONAL ACADEMY OF SCIENCE. WASHINGTON, US, vol. 93, 1 September 1996 (1996-09-01), pages 9821 - 9826, XP002910406, ISSN: 0027-8424 *

Also Published As

Publication number Publication date
EP1395686A2 (en) 2004-03-10
US7381808B2 (en) 2008-06-03
US20030113750A1 (en) 2003-06-19
WO2002103042A2 (en) 2002-12-27
DE10128508A1 (en) 2003-02-06
CA2445731A1 (en) 2002-12-27
JP2004529661A (en) 2004-09-30

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