EP1461458A4 - Multiplexed methylation detection methods - Google Patents

Multiplexed methylation detection methods

Info

Publication number
EP1461458A4
EP1461458A4 EP02795731A EP02795731A EP1461458A4 EP 1461458 A4 EP1461458 A4 EP 1461458A4 EP 02795731 A EP02795731 A EP 02795731A EP 02795731 A EP02795731 A EP 02795731A EP 1461458 A4 EP1461458 A4 EP 1461458A4
Authority
EP
European Patent Office
Prior art keywords
detection methods
methylation detection
multiplexed
multiplexed methylation
methods
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Withdrawn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
German (de)
French (fr)
Other versions
EP1461458A2 (en
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/en
Publication of EP1461458A2 publication Critical patent/EP1461458A2/en
Publication of EP1461458A4 publication Critical patent/EP1461458A4/en
Withdrawn legal-status Critical Current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 Multiplexed methylation detection methods Withdrawn EP1461458A4 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
EP07115172A EP1860200A1 (en) 2001-12-03 2002-12-03 Multiplexed methylation detection methods

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 (en) 2001-12-03 2002-12-03 Multiplexed methylation detection methods

Publications (2)

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

Family

ID=32823667

Family Applications (1)

Application Number Title Priority Date Filing Date
EP02795731A Withdrawn EP1461458A4 (en) 2001-12-03 2002-12-03 Multiplexed methylation detection methods

Country Status (4)

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

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 (en) * 2001-12-03 2007-11-28 Illumina, Inc. Multiplexed methylation detection methods
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
US7799525B2 (en) 2003-06-17 2010-09-21 Human Genetic Signatures Pty Ltd. Methods for genome amplification
WO2005024053A1 (en) 2003-09-04 2005-03-17 Human Genetic Signatures Pty Ltd Nucleic acid detection assay
US8168777B2 (en) 2004-04-29 2012-05-01 Human Genetic Signatures Pty. Ltd. Bisulphite reagent treatment of nucleic acid
WO2006026828A1 (en) 2004-09-10 2006-03-16 Human Genetic Signatures Pty Ltd Amplification blocker comprising intercalating nucleic acids (tna) containing intercalating pseudonucleotides (ipn)
NZ555620A (en) 2004-12-03 2008-08-29 Human Genetic Signatures Pty Methods for simplifying microbial nucleic acids by chemical modification of cytosines
AU2006251866B2 (en) 2005-05-26 2007-11-29 Human Genetic Signatures Pty Ltd Isothermal strand displacement amplification using primers containing a non-regular base
US7901882B2 (en) 2006-03-31 2011-03-08 Affymetrix, Inc. Analysis of methylation using nucleic acid arrays
EP2356253A1 (en) * 2008-11-05 2011-08-17 Stichting Sanquin Bloedvoorziening Means and methods for investigating nucleic acid sequences
CN103874766B (en) 2011-09-07 2017-07-18 人类遗传标记控股有限公司 Molecular Detection is determined
CN102559661B (en) * 2012-01-18 2014-06-04 厦门基科生物科技有限公司 Novel amplification method and application of ligase reaction mediate

Citations (14)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP0139489A2 (en) * 1983-09-26 1985-05-02 Ortho Diagnostic Systems Inc. Sandwich hybridization method for nucleic acid detection
EP0238332A2 (en) * 1986-03-19 1987-09-23 Cetus Corporation Liquid hybridization method and kit for detecting the presence of nucleic acid sequences in samples
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 (en) * 1993-02-26 1994-09-14 Becton, Dickinson and Company Flow-through membrane nucleic acid hybridization assay
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 (en) * 1983-09-26 1985-05-02 Ortho Diagnostic Systems Inc. Sandwich hybridization method for nucleic acid detection
EP0238332A2 (en) * 1986-03-19 1987-09-23 Cetus Corporation Liquid hybridization method and kit for detecting the presence of nucleic acid sequences in samples
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 (en) * 1993-02-26 1994-09-14 Becton, Dickinson and Company Flow-through membrane nucleic acid hybridization assay
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 (18)

* 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 (2001-05-01), 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), pages 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 (2002-06-01), 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 (1993-04-01), 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 (1999-03-01), 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 (2001-08-01), 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 (1998-07-01), 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 (1992-03-01), pages 1827 - 1831, XP009016394, ISSN: 0027-8424 *
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 (2001-12-01), 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 (2000-04-01), pages 1432 - 1438, XP002245955, ISSN: 1078-0432 *

Also Published As

Publication number Publication date
WO2003048732A3 (en) 2003-09-25
CA2467814A1 (en) 2003-06-12
AU2002360474A1 (en) 2003-06-17
WO2003048732A2 (en) 2003-06-12
EP1461458A2 (en) 2004-09-29

Similar Documents

Publication Publication Date Title
AU2003297654A8 (en) Multiplexed methylation detection methods
GB2369428B (en) Detection system
AU2002363907A8 (en) Captioning system
HK1051400A1 (en) Force detector
GB0102355D0 (en) Security system
EP1461458A4 (en) Multiplexed methylation detection methods
GB0126267D0 (en) Repeater detection
GB0129596D0 (en) Risk detection
GB0104843D0 (en) Detection system
GB2377313B (en) Security system
GB0018002D0 (en) Novel detection technique
GB0125010D0 (en) Security system
GB0126048D0 (en) Security system
GB0117374D0 (en) Security System
GB0114339D0 (en) Security system
GB0130825D0 (en) Detector system
PL357663A1 (en) Door protection system
GB0125316D0 (en) Security system
GB0005632D0 (en) Door system
GB0007634D0 (en) Improved detector
GB2378833B (en) Object detection system
GB0117468D0 (en) Detection system
GB0116256D0 (en) Security system
GB0100919D0 (en) Detection methods
GB0101858D0 (en) Multiplexed sensors

Legal Events

Date Code Title Description
PUAI Public reference made under article 153(3) epc to a published international application that has entered the european phase

Free format text: ORIGINAL CODE: 0009012

17P Request for examination filed

Effective date: 20040702

AK Designated contracting states

Kind code of ref document: A2

Designated state(s): AT BE BG CH CY CZ DE DK EE ES FI FR GB GR IE IT LI LU MC NL PT SE SI SK TR

AX Request for extension of the european patent

Extension state: AL LT LV MK RO

A4 Supplementary search report drawn up and despatched

Effective date: 20050909

17Q First examination report despatched

Effective date: 20051208

STAA Information on the status of an ep patent application or granted ep patent

Free format text: STATUS: THE APPLICATION IS DEEMED TO BE WITHDRAWN

18D Application deemed to be withdrawn

Effective date: 20100309