EP1461458A2 - Multiplex-methylierungsnachweisverfahren - Google Patents

Multiplex-methylierungsnachweisverfahren

Info

Publication number
EP1461458A2
EP1461458A2 EP02795731A EP02795731A EP1461458A2 EP 1461458 A2 EP1461458 A2 EP 1461458A2 EP 02795731 A EP02795731 A EP 02795731A EP 02795731 A EP02795731 A EP 02795731A EP 1461458 A2 EP1461458 A2 EP 1461458A2
Authority
EP
European Patent Office
Prior art keywords
target
probes
probe
nucleic acid
sequence
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.)
Withdrawn
Application number
EP02795731A
Other languages
English (en)
French (fr)
Other versions
EP1461458A4 (de
Inventor
Jian-Bing Fan
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Illumina Inc
Original Assignee
Illumina Inc
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 Illumina Inc filed Critical Illumina Inc
Priority to EP07115172A priority Critical patent/EP1860200A1/de
Publication of EP1461458A2 publication Critical patent/EP1461458A2/de
Publication of EP1461458A4 publication Critical patent/EP1461458A4/de
Withdrawn legal-status Critical Current

Links

Classifications

    • 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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6816—Hybridisation assays characterised by the detection means
    • 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

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Analytical Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • Physics & Mathematics (AREA)
  • Immunology (AREA)
  • Biotechnology (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Pathology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
EP02795731A 2001-12-03 2002-12-03 Multiplex-methylierungsnachweisverfahren Withdrawn EP1461458A4 (de)

Priority Applications (1)

Application Number Priority Date Filing Date Title
EP07115172A EP1860200A1 (de) 2001-12-03 2002-12-03 Multiplexverfahren zur Methylierungsdetektion

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US33695801P 2001-12-03 2001-12-03
US336958P 2001-12-03
PCT/US2002/038672 WO2003048732A2 (en) 2001-02-07 2002-12-03 Multiplexed methylation detection methods

Related Child Applications (1)

Application Number Title Priority Date Filing Date
EP07115172A Division EP1860200A1 (de) 2001-12-03 2002-12-03 Multiplexverfahren zur Methylierungsdetektion

Publications (2)

Publication Number Publication Date
EP1461458A2 true EP1461458A2 (de) 2004-09-29
EP1461458A4 EP1461458A4 (de) 2005-10-26

Family

ID=32823667

Family Applications (1)

Application Number Title Priority Date Filing Date
EP02795731A Withdrawn EP1461458A4 (de) 2001-12-03 2002-12-03 Multiplex-methylierungsnachweisverfahren

Country Status (4)

Country Link
EP (1) EP1461458A4 (de)
AU (1) AU2002360474A1 (de)
CA (1) CA2467814A1 (de)
WO (1) WO2003048732A2 (de)

Families Citing this family (15)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7582420B2 (en) 2001-07-12 2009-09-01 Illumina, Inc. Multiplex nucleic acid reactions
US20110151438A9 (en) 2001-11-19 2011-06-23 Affymetrix, Inc. Methods of Analysis of Methylation
EP1860200A1 (de) * 2001-12-03 2007-11-28 Illumina, Inc. Multiplexverfahren zur Methylierungsdetektion
US8150627B2 (en) 2003-05-15 2012-04-03 Illumina, Inc. Methods and compositions for diagnosing lung cancer with specific DNA methylation patterns
US8150626B2 (en) 2003-05-15 2012-04-03 Illumina, Inc. Methods and compositions for diagnosing lung cancer with specific DNA methylation patterns
DE602004028478D1 (de) 2003-06-17 2010-09-16 Human Genetic Signatures Pty Verfahren zur genomamplifikation
DE602004018801D1 (de) 2003-09-04 2009-02-12 Human Genetic Signatures Pty Nukleinsäurenachweistest
US8168777B2 (en) 2004-04-29 2012-05-01 Human Genetic Signatures Pty. Ltd. Bisulphite reagent treatment of nucleic acid
DE602005022740D1 (de) 2004-09-10 2010-09-16 Human Genetic Signatures Pty Amplifikationsblocker umfassend interkalierende nukleinsäuren (ina) enthaltend interkalierende pseudonukleotide (ipn)
CN101111606B (zh) 2004-12-03 2012-05-16 人类遗传标记控股有限公司 通过化学修饰胞嘧啶而简化微生物核酸的方法
JP2008541705A (ja) 2005-05-26 2008-11-27 ヒューマン ジェネティック シグネチャーズ ピーティーワイ リミテッド 非標準塩基を含むプライマーを使用する等温鎖置換増幅
US7901882B2 (en) 2006-03-31 2011-03-08 Affymetrix, Inc. Analysis of methylation using nucleic acid arrays
AU2009311769A1 (en) * 2008-11-05 2010-05-14 Stichting Sanquin Bloedvoorziening Means and methods for investigating nucleic acid sequences
CA2848144C (en) 2011-09-07 2018-03-06 Human Genetic Signatures Pty Ltd Molecular detection assay
CN102559661B (zh) * 2012-01-18 2014-06-04 厦门基科生物科技有限公司 一种新型连接酶反应介导的扩增方法及用途

Citations (14)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP0139489A2 (de) * 1983-09-26 1985-05-02 Ortho Diagnostic Systems Inc. Sandwichhybridisierungsverfahren zum Nachweis von Nukleinsäuren
EP0238332A2 (de) * 1986-03-19 1987-09-23 Cetus Corporation Flüssiges Hybridisationsverfahren und Satz zum Nachweis der Anwesenheit von Nukleinsäuresequenzen in Proben
US5232829A (en) * 1989-09-29 1993-08-03 Hoffmann-La Roche Inc. Detection of chlamydia trachomatis by polymerase chain reaction using biotin labelled lina primers and capture probes
EP0614987A1 (de) * 1993-02-26 1994-09-14 Becton, Dickinson and Company Nukleinsäure-Hybridisierungstest unter Verwendung einer Durchflusses durch eine Membran
US5387505A (en) * 1990-05-04 1995-02-07 Eastman Kodak Company Preparation and isolation of single-stranded biotinylated nucleic acids by heat avidin-biotin cleavage
WO1995025538A1 (en) * 1994-03-18 1995-09-28 The General Hospital Corporation Cleaved amplified rflp detection methods
WO1998004746A1 (en) * 1996-07-31 1998-02-05 Mount Sinai School Of Medicine Of The City University Of New York Nucleic acid amplification method: ramification-extension amplification method (ram)
US5786146A (en) * 1996-06-03 1998-07-28 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
US5849544A (en) * 1992-07-24 1998-12-15 University Of Australia Amplification and detection process
WO1998056952A1 (en) * 1997-06-09 1998-12-17 University Of Southern California A cancer diagnostic method based upon dna methylation differences
WO1998059243A1 (en) * 1997-06-24 1998-12-30 The Trustees Of Boston University High density streptavidin supports
WO1999001580A1 (en) * 1997-07-03 1999-01-14 Case Western Reserve University Compositions and methods for detection of genomic imprinting disorders
WO2000026401A1 (en) * 1998-11-03 2000-05-11 The Johns Hopkins University School Of Medicine METHYLATED CpG ISLAND AMPLIFICATION (MCA)
WO2000070090A1 (en) * 1999-05-14 2000-11-23 University Of Southern California Process for high throughput dna methylation analysis

Patent Citations (15)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP0139489A2 (de) * 1983-09-26 1985-05-02 Ortho Diagnostic Systems Inc. Sandwichhybridisierungsverfahren zum Nachweis von Nukleinsäuren
EP0238332A2 (de) * 1986-03-19 1987-09-23 Cetus Corporation Flüssiges Hybridisationsverfahren und Satz zum Nachweis der Anwesenheit von Nukleinsäuresequenzen in Proben
US5232829A (en) * 1989-09-29 1993-08-03 Hoffmann-La Roche Inc. Detection of chlamydia trachomatis by polymerase chain reaction using biotin labelled lina primers and capture probes
US5387505A (en) * 1990-05-04 1995-02-07 Eastman Kodak Company Preparation and isolation of single-stranded biotinylated nucleic acids by heat avidin-biotin cleavage
US5849544A (en) * 1992-07-24 1998-12-15 University Of Australia Amplification and detection process
EP0614987A1 (de) * 1993-02-26 1994-09-14 Becton, Dickinson and Company Nukleinsäure-Hybridisierungstest unter Verwendung einer Durchflusses durch eine Membran
WO1995025538A1 (en) * 1994-03-18 1995-09-28 The General Hospital Corporation Cleaved amplified rflp detection methods
US6200756B1 (en) * 1996-06-03 2001-03-13 The Johns Hopkins University School Of Medicine Methods for identifying methylation patterns in a CpG-containing nucleic acid
US5786146A (en) * 1996-06-03 1998-07-28 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
WO1998004746A1 (en) * 1996-07-31 1998-02-05 Mount Sinai School Of Medicine Of The City University Of New York Nucleic acid amplification method: ramification-extension amplification method (ram)
WO1998056952A1 (en) * 1997-06-09 1998-12-17 University Of Southern California A cancer diagnostic method based upon dna methylation differences
WO1998059243A1 (en) * 1997-06-24 1998-12-30 The Trustees Of Boston University High density streptavidin supports
WO1999001580A1 (en) * 1997-07-03 1999-01-14 Case Western Reserve University Compositions and methods for detection of genomic imprinting disorders
WO2000026401A1 (en) * 1998-11-03 2000-05-11 The Johns Hopkins University School Of Medicine METHYLATED CpG ISLAND AMPLIFICATION (MCA)
WO2000070090A1 (en) * 1999-05-14 2000-11-23 University Of Southern California Process for high throughput dna methylation analysis

Non-Patent Citations (19)

* Cited by examiner, † Cited by third party
Title
BERG E S ET AL: "HYBRID PCR SEQUENCING: SEQUENCING OF PCR PRODUCTS USING A UNIVERSAL PRIMER" BIOTECHNIQUES, EATON PUBLISHING, NATICK, US, vol. 17, no. 5, 1 November 1994 (1994-11-01), pages 896,898,900-901, XP000474854 ISSN: 0736-6205 *
COSTELLO J F ET AL: "Abberant CpG-island methylation has non-random and tumour-type-specific patterns" NATURE GENETICS, NATURE AMERICA, NEW YORK, US, vol. 25, 1 February 2000 (2000-02-01), pages 132-138, XP002242654 ISSN: 1061-4036 *
COSTELLO J F ET AL: "METHYLATION MATTERS" JOURNAL OF MEDICAL GENETICS, LONDON, GB, vol. 38, no. 5, May 2001 (2001-05), pages 285-303, XP008018005 *
EADS C A ET AL: "MethyLight: a high-throughput assay to measure DNA methylation." NUCLEIC ACIDS RESEARCH. 15 APR 2000, vol. 28, no. 8, 15 April 2000 (2000-04-15), page E32, XP002249149 ISSN: 1362-4962 *
GONZALGO M L AND JONES P A: "Rapid quantification of methylation differences at specific sites using methylation-sensitive single nucleotide primer extension (Ms-SNuPE)" NUCLEIC ACIDS RESEARCH, OXFORD UNIVERSITY PRESS, SURREY, GB, vol. 25, no. 12, 1997, pages 2529-2531, XP002106409 ISSN: 0305-1048 *
GONZALGO MARK L ET AL: "Quantitative methylation analysis using methylation-sensitive single-nucleotide primer extension (Ms-SNuPE)" METHODS (ORLANDO), vol. 27, no. 2, June 2002 (2002-06), pages 128-133, XP009052711 ISSN: 1046-2023 *
HAMMONS GEORGE J ET AL: "Specific site methylation in the 5'-flanking region of CYP1A2: Interindividual differences in human livers" LIFE SCIENCES, vol. 69, no. 7, 6 July 2001 (2001-07-06), pages 839-845, XP002326913 ISSN: 0024-3205 *
HAYASHIZAKI Y ET AL: "RESTRICTION LANDMARK GENOMIC SCANNING METHOD AND ITS VARIOUS APPLICATIONS" ELECTROPHORESIS, WEINHEIM, DE, vol. 14, no. 4, April 1993 (1993-04), pages 251-258, XP009035246 ISSN: 0173-0835 *
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 *
HUANG TIM HUI-MING ET AL: "Methylation profiling of CpG islands in human breast cancer cells" HUMAN MOLECULAR GENETICS, OXFORD UNIVERSITY PRESS, SURREY, GB, vol. 8, no. 3, March 1999 (1999-03), pages 459-470, XP002175857 ISSN: 0964-6906 *
KUPPUSWAMY M N ET AL: "SINGLE NUCLEOTIDE PRIMER EXTENSION TO DETECT GENETIC DISEASES: EXPERIMENTAL APPLICATION TO HEMOPHILIA B (FACTOR IX) AND CYSTIC FIBROSIS GENES" PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF USA, NATIONAL ACADEMY OF SCIENCE. WASHINGTON, US, vol. 88, no. 4, 15 February 1991 (1991-02-15), pages 1143-1147, XP000371662 ISSN: 0027-8424 *
LADNER D P ET AL: "Multiplex detection of hotspot mutations by rolling circle-enabled universal microarrays." LABORATORY INVESTIGATION; A JOURNAL OF TECHNICAL METHODS AND PATHOLOGY. AUG 2001, vol. 81, no. 8, August 2001 (2001-08), pages 1079-1086, XP002326914 ISSN: 0023-6837 *
LIZARDI P M ET AL: "MUTATION DETECTION AND SINGLE-MOLECULE COUNTING USING ISOTHERMAL ROLLING-CIRCLE AMPLIFICATION" NATURE GENETICS, NEW YORK, NY, US, vol. 19, no. 3, July 1998 (1998-07), pages 225-232, XP000856939 ISSN: 1061-4036 *
OAKELEY E J: "DNA METHYLATION ANALYSIS: A REVIEW OF CURRENT METHODOLOGIES" PHARMACOLOGY AND THERAPEUTICS, ELSEVIER, GB, vol. 84, no. 3, 1999, pages 389-400, XP001029527 ISSN: 0163-7258 *
PROMMER M ET AL: "A GENOMIC SEQUENCING PROTOCOL THAT YIELDS A POSITIVE DISPLAY OF 5-METHYLCYTOSINE RESIDUES IN INDIVIDUAL DNA STRANDS" PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF USA, NATIONAL ACADEMY OF SCIENCE. WASHINGTON, US, vol. 89, March 1992 (1992-03), pages 1827-1831, XP009016394 ISSN: 0027-8424 *
See also references of WO03048732A2 *
TOYOTA MINORU ET AL: "Identification of differentially methylated sequences in colorectal cancer by methylated CpG island amplification" CANCER RESEARCH, AMERICAN ASSOCIATION FOR CANCER RESEARCH, BALTIMORE, MD, US, vol. 59, no. 10, 15 May 1999 (1999-05-15), pages 2307-2312, XP002211911 ISSN: 0008-5472 *
TRINH BINH N ET AL: "DNA methylation analysis by MethyLight technology" METHODS : A COMPANION TO METHODS IN ENZYMOLOGY, ACADEMIC PRESS INC., NEW YORK, NY, US, vol. 25, no. 4, December 2001 (2001-12), pages 456-462, XP002318911 ISSN: 1046-2023 *
YAN P S ET AL: "CpG island arrays: an application toward deciphering epigenetic signatures of breast cancer" CLINICAL CANCER RESEARCH, THE AMERICAN ASSOCIATION FOR CANCER RESEARCH, US, vol. 6, no. 4, April 2000 (2000-04), pages 1432-1438, XP002245955 ISSN: 1078-0432 *

Also Published As

Publication number Publication date
CA2467814A1 (en) 2003-06-12
WO2003048732A2 (en) 2003-06-12
AU2002360474A1 (en) 2003-06-17
EP1461458A4 (de) 2005-10-26
WO2003048732A3 (en) 2003-09-25

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