EP1461458A2 - Procedes multiplexes de detection de methylation - Google Patents

Procedes multiplexes de detection de methylation

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Withdrawn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
German (de)
English (en)
Other versions
EP1461458A4 (fr
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/fr
Publication of EP1461458A2 publication Critical patent/EP1461458A2/fr
Publication of EP1461458A4 publication Critical patent/EP1461458A4/fr
Withdrawn legal-status Critical Current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

Definitions

  • the present invention is directed to the multiplex preparation and detection of methylated target nucleic acids.
  • the invention involves the use of methylation selective modification of target nucleic acids and detection of the modified target nucleic acids.
  • the methylation selective modification involves cleaving target nucleic acids with methylation selective enzymes and detection of the cleaved or uncleaved nucleic acids with probes. That is, in a preferred embodiment the method involves providing a first population of target nucleic acids as described herein and cleaving or shearing the first population so as to reduce the size of each target.
  • the target nucleic acids can be any region including but not limited to non-polymorphic regions.
  • the method involves the use of bisulfite. That is, in an alternative method for detecting methylation, the fact that non-methylated cytosines are converted to uracils when treated with bisulfite is exploited.
  • the hybridization properties of uracil are similar to that of thymine.
  • the sample DNA is treated with bisulfite, non-methylated cytosine hybridizes like thymine, while methylated cytosine will hybridize like cytosine.
  • This difference in hybridization properties can be detected by using appropriate target probes. That is, the methylated or non-methylated cytosine site can be treated as a C/T polymorphic site and detected by any of the assays as described herein.
  • the resulting modified target probes are detected by any of the detection methods as described herein.
  • the "Universal" primer sequences are designed not to solely serve as PCR primers, but also as a promoter sequence for RNA Polymerase.
  • the annealed (and/or ligated) target probes can be amplified not only by general PCR, but can also be amplified by in vitro transcription (IVT).
  • IVT in vitro transcription
  • the linear amplification produced by IVT should be better at maintaining the relative amounts of the different sequences in the initial template population than the exponential amplification of PCR.
  • the use of competitive hybridization target probes is done to elucidate either the identity of the nucleotide(s) at the detection position or the presence of a mismatch.
  • mismatch is a relative term and meant to indicate a difference in the identity of a base at a particular position, termed the "detection position" herein, between two sequences.
  • sequences that differ from wild type sequences are referred to as mismatches.
  • wild type may be difficult to determine as multiple alleles can be relatively frequently observed in the population, and thus “mismatch” in this context requires the artificial adoption of one sequence as a standard.
  • the sequence of the target prior to any modification as set forth herein constitutes "wild type” while the sequence subsequent to any methylation selective modification constitutes a "mismatch".
  • a method of methylation detection assays includes digesting genomic DNA with a methylation-sensitive restriction enzyme followed by detection of the differentially cleaved DNA, e g by Southern blot analysis (Issa, J P , Ottaviano, Y L , Celano, P , Hamilton, S R , Davidson, N E and Baylin, S B (1994) Methylation of the oestrogen receptor CpG island links ageing and neoplasia in human colon Nat Genet, 7, 536-540 , Taylor, J M , Kay, P H and Spagnolo, D V (2001 ) The diagnositc significance of Myf-3 hypermethylation in malignant lymphopro ferative disorders Leukemia, 15, 583-589) or PCR (Singer-Sam, J , LeBon, J M , Tanguay, R L and Riggs, A D (1990) A quantitative Hpall-PCR assay to measure
  • the present invention provides first target probe sets that comprise at least a first universal priming site.
  • the systems of the invention can take on a wide variety of configurations, including systems that rely on the initial immobilization of the target analyte (solid phase assays) and solution based assays
  • a plurality of target probes are used to identify the base at the detection position
  • each different readout probe comprises a different base at the position that will hybridize to the detection position of the target sequence (herein referred to as the readout or interrogation position) and a different adapter sequence for each different readout position
  • the readout probes are contacted with the array again under conditions that allow discrimination between match and mismatch, and the unhybridized probes are removed, etc
  • each different readout probe comprises either a different detection label (which, as outlined below, can be either a primary label or a secondary label) or a different adapter, and a different base at the position that will hybridize to the detection position of the target sequence (herein referred to as the readout position) such that differential hybridization will occur
  • a detectable label is incorporated into the readout probe
  • a set of readout probes are used, each comprising a different base at the readout position
  • each readout probe comprises a different label, that is distinguishable from the others
  • a first label may be used for probes comprising adenosme at the readout position
  • a second label may be used for probes comprising guanine at the readout position
  • the length and sequence of each readout probe is identical except for the
  • the allele specific primer also includes an adapter sequence and priming sequences as described herein
  • the extended first probe is adjacent to the 5' end of the second probe
  • the two ends of the probes are respectively perfectly complementary to the target sequence at these positions, and the two probes can be ligated together with a suitable hgase to form amplification templates
  • the base at the interrogation position must be perfectly complementary to the detection position in the target sequence to allow ligation. In the absence of perfect complementarity, no significant ligation will occur between the extended first probe and the second probe.
  • the detection substrate used for any of the above assays is a random array substrate, as described in U.S. Patent No.6,023,540 which is incorporated by reference herein, where the hybridization of complementary nucleic acid sequences, or address sequences, are used as the particular detection means.
  • the arrays can be manufactured with a standard set of nucleic acid address sequences, one address sequence for each different nucleic acid to be detected.
  • the complementary nucleic acid sequences are provided as part of the linear nucleic acid sequences of the mutation-detection probes, inside of the working portion of the amplification primers. During amplification, the address sequences are amplified along with each respective mutation-detection probe.

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)

Abstract

Cette invention a trait à des dosages multiplexés, sensibles et précis, servant à la détection d'un analysat cible ainsi qu'à la détection d'une méthylation dans des échantillons d'acide nucléique.
EP02795731A 2001-12-03 2002-12-03 Procedes multiplexes de detection de methylation Withdrawn EP1461458A4 (fr)

Priority Applications (1)

Application Number Priority Date Filing Date Title
EP07115172A EP1860200A1 (fr) 2001-12-03 2002-12-03 Procédés multiplexes de détection de methylation

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 (fr) 2001-02-07 2002-12-03 Procedes multiplexes de detection de methylation

Related Child Applications (1)

Application Number Title Priority Date Filing Date
EP07115172A Division EP1860200A1 (fr) 2001-12-03 2002-12-03 Procédés multiplexes de détection de methylation

Publications (2)

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

Family

ID=32823667

Family Applications (1)

Application Number Title Priority Date Filing Date
EP02795731A Withdrawn EP1461458A4 (fr) 2001-12-03 2002-12-03 Procedes multiplexes de detection de methylation

Country Status (4)

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

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 (fr) * 2001-12-03 2007-11-28 Illumina, Inc. Procédés multiplexes de détection de methylation
US8150626B2 (en) 2003-05-15 2012-04-03 Illumina, Inc. Methods and compositions for diagnosing lung cancer with specific DNA methylation patterns
US8150627B2 (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
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
CN101056883B (zh) 2004-09-10 2012-10-10 人类遗传标记控股有限公司 包括含有嵌入性假核苷酸(ipn)的嵌入性核酸(ina)的扩增阻断剂
NZ555620A (en) 2004-12-03 2008-08-29 Human Genetic Signatures Pty Methods for simplifying microbial nucleic acids by chemical modification of cytosines
EP1883707B1 (fr) 2005-05-26 2014-04-09 Human Genetic Signatures PTY Ltd Amplification par deplacement de brin isotherme utilisant des amorces contenant une base non reguliere
US7901882B2 (en) 2006-03-31 2011-03-08 Affymetrix, Inc. Analysis of methylation using nucleic acid arrays
US9017971B2 (en) 2008-11-05 2015-04-28 Stichting Sanquin Bloedvoorziening Means and methods for investigating nucleic acid sequences
US9732375B2 (en) 2011-09-07 2017-08-15 Human Genetic Signatures Pty. Ltd. Molecular detection assay using direct treatment with a bisulphite reagent
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

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EP0238332A2 (fr) * 1986-03-19 1987-09-23 Cetus Corporation Méthode d'hybridation en phase liquide et trousse de réactifs pour détecter la présence de séquences d'acides nucléiques dans des échantillons
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WO1998004746A1 (fr) * 1996-07-31 1998-02-05 Mount Sinai School Of Medicine Of The City University Of New York Une methode d'amplification d'acide nucleique par ramification-extension: la 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 (fr) * 1997-06-09 1998-12-17 University Of Southern California Methode de diagnostic du cancer basee sur des differences de methylation d'adn
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EP0139489A2 (fr) * 1983-09-26 1985-05-02 Ortho Diagnostic Systems Inc. Méthode d'hybridation en sandwich pour la détection d'acides nucléiques
EP0238332A2 (fr) * 1986-03-19 1987-09-23 Cetus Corporation Méthode d'hybridation en phase liquide et trousse de réactifs pour détecter la présence de séquences d'acides nucléiques dans des échantillons
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WO1995025538A1 (fr) * 1994-03-18 1995-09-28 The General Hospital Corporation Methodes de detection de polymorphismes amplifies et clives des sites de restriction
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WO1998059243A1 (fr) * 1997-06-24 1998-12-30 The Trustees Of Boston University Support pour streptavidine haute densite
WO1999001580A1 (fr) * 1997-07-03 1999-01-14 Case Western Reserve University Compositions et procedes de detection de dysfonctionnements d'empreinte genomique
WO2000026401A1 (fr) * 1998-11-03 2000-05-11 The Johns Hopkins University School Of Medicine AMPLIFICATION D'ILOTS CpG METHYLES (MCA)
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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
WO2003048732A2 (fr) 2003-06-12
EP1461458A4 (fr) 2005-10-26
WO2003048732A3 (fr) 2003-09-25
CA2467814A1 (fr) 2003-06-12
AU2002360474A1 (en) 2003-06-17

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