WO2005024068A3 - Allele-specific sequence variation analysis - Google Patents

Allele-specific sequence variation analysis Download PDF

Info

Publication number
WO2005024068A3
WO2005024068A3 PCT/US2004/028997 US2004028997W WO2005024068A3 WO 2005024068 A3 WO2005024068 A3 WO 2005024068A3 US 2004028997 W US2004028997 W US 2004028997W WO 2005024068 A3 WO2005024068 A3 WO 2005024068A3
Authority
WO
WIPO (PCT)
Prior art keywords
allele
specific sequence
sequence variation
variation analysis
systems
Prior art date
Application number
PCT/US2004/028997
Other languages
French (fr)
Other versions
WO2005024068A2 (en
Inventor
Martin Beaulieu
Den Boom Dirk Van
Original Assignee
Sequenom Inc
Martin Beaulieu
Den Boom Dirk Van
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 Sequenom Inc, Martin Beaulieu, Den Boom Dirk Van filed Critical Sequenom Inc
Publication of WO2005024068A2 publication Critical patent/WO2005024068A2/en
Publication of WO2005024068A3 publication Critical patent/WO2005024068A3/en

Links

Classifications

    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813Hybridisation assays
    • C12Q1/6827Hybridisation assays for detection of mutation or polymorphism

Abstract

Fragmentation-based methods and systems, particularly mass spectrometry based methods and systems, for the analysis of sequence variations including haplotypes are provided. Also provided are methods for obtaining a specific allele from a nucleic acid mixture, such as genomic DNA.
PCT/US2004/028997 2003-09-05 2004-09-02 Allele-specific sequence variation analysis WO2005024068A2 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US50048903P 2003-09-05 2003-09-05
US60/500,489 2003-09-05

Publications (2)

Publication Number Publication Date
WO2005024068A2 WO2005024068A2 (en) 2005-03-17
WO2005024068A3 true WO2005024068A3 (en) 2005-09-22

Family

ID=34272962

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2004/028997 WO2005024068A2 (en) 2003-09-05 2004-09-02 Allele-specific sequence variation analysis

Country Status (2)

Country Link
US (1) US9394565B2 (en)
WO (1) WO2005024068A2 (en)

Families Citing this family (13)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6994969B1 (en) * 1999-04-30 2006-02-07 Methexis Genomics, N.V. Diagnostic sequencing by a combination of specific cleavage and mass spectrometry
US7332275B2 (en) * 1999-10-13 2008-02-19 Sequenom, Inc. Methods for detecting methylated nucleotides
CA2507189C (en) * 2002-11-27 2018-06-12 Sequenom, Inc. Fragmentation-based methods and systems for sequence variation detection and discovery
US20050009053A1 (en) * 2003-04-25 2005-01-13 Sebastian Boecker Fragmentation-based methods and systems for de novo sequencing
US9394565B2 (en) 2003-09-05 2016-07-19 Agena Bioscience, Inc. Allele-specific sequence variation analysis
WO2005098050A2 (en) * 2004-03-26 2005-10-20 Sequenom, Inc. Base specific cleavage of methylation-specific amplification products in combination with mass analysis
WO2006065732A2 (en) * 2004-12-13 2006-06-22 Autogenomics, Inc. Compositions and methods for nucleic acid analysis of sequences with insertions or deletions
JP5017269B2 (en) * 2005-07-26 2012-09-05 ユニヴァーシティ オブ メディシン アンド デンティストリ オブ ニュージャーシィ Antibody profile specific to tuberculosis
WO2008064687A1 (en) * 2006-11-27 2008-06-05 Fluimedix Fidelity enhanced allele specific amplification method
US20090006002A1 (en) * 2007-04-13 2009-01-01 Sequenom, Inc. Comparative sequence analysis processes and systems
EP2943579B1 (en) * 2013-01-10 2018-09-12 Dharmacon, Inc. Libraries and methods for generating molecules
KR101815529B1 (en) * 2016-07-29 2018-01-30 (주)신테카바이오 Human Haplotyping System And Method
AU2021227928A1 (en) * 2020-02-27 2022-09-15 Monsanto Technology Llc Methods for selecting inheritable edits

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20030027169A1 (en) * 2000-10-27 2003-02-06 Sheng Zhang One-well assay for high throughput detection of single nucleotide polymorphisms
WO2004050839A2 (en) * 2002-11-27 2004-06-17 Sequenom, Inc. Fragmentation-based methods and systems for sequence variation detection and discovery

Family Cites Families (197)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
DE3312929A1 (en) 1982-06-02 1983-12-08 Gesellschaft für Biotechnologische Forschung mbH (GBF), 3300 Braunschweig METHOD FOR SEQUENCE ANALYZING AN OPTIONALLY MODIFIED OLIGORIBONUCLEOTIDS OR OLIGODESOXYRIBONUKLETIDS
US4683202A (en) * 1985-03-28 1987-07-28 Cetus Corporation Process for amplifying nucleic acid sequences
US4683195A (en) * 1986-01-30 1987-07-28 Cetus Corporation Process for amplifying, detecting, and/or-cloning nucleic acid sequences
US5173418A (en) 1985-05-10 1992-12-22 Benzon Pharma, A/S Production in Escherichia coli of extracellular Serratia spp. hydrolases
US4762823A (en) 1985-10-16 1988-08-09 Sloan-Kettering Institute For Cancer Research Nucleosides of 5-monofluoromethyluracil and 5-difluoromethyluracil
US5079342A (en) * 1986-01-22 1992-01-07 Institut Pasteur Cloned DNA sequences related to the entire genomic RNA of human immunodeficiency virus II (HIV-2), polypeptides encoded by these DNA sequences and use of these DNA clones and polypeptides in diagnostic kits
US4826360A (en) * 1986-03-10 1989-05-02 Shimizu Construction Co., Ltd. Transfer system in a clean room
EP0269520A3 (en) 1986-11-21 1988-08-24 Institut Pasteur Retrovirus of the type hiv-2, susceptible to provoke aids, and its antigenic and nucleic-acid constituents
FR2620049B2 (en) * 1986-11-28 1989-11-24 Commissariat Energie Atomique PROCESS FOR PROCESSING, STORING AND / OR TRANSFERRING AN OBJECT INTO A HIGHLY CLEAN ATMOSPHERE, AND CONTAINER FOR CARRYING OUT SAID METHOD
US4837726A (en) 1987-06-19 1989-06-06 Applied Biosystems, Inc. Quantitation of chromatographic information
US4802102A (en) 1987-07-15 1989-01-31 Hewlett-Packard Company Baseline correction for chromatography
IE61148B1 (en) 1988-03-10 1994-10-05 Ici Plc Method of detecting nucleotide sequences
EP0655501B2 (en) 1988-06-14 2016-07-27 QIAGEN GmbH HIV-2 virus variants
US5003059A (en) * 1988-06-20 1991-03-26 Genomyx, Inc. Determining DNA sequences by mass spectrometry
EP0395481A3 (en) 1989-04-25 1991-03-20 Spectra-Physics, Inc. Method and apparatus for estimation of parameters describing chromatographic peaks
US5256775A (en) * 1989-06-05 1993-10-26 Gilead Sciences, Inc. Exonuclease-resistant oligonucleotides
GB2236186B (en) * 1989-08-22 1994-01-05 Finnigan Mat Gmbh Process and device for laser desorption of analyte molecular ions, especially of biomolecules
US5122457A (en) * 1989-10-19 1992-06-16 Schering Corporation Expression systems utilizing bacteriophage t7 promoters, gene sequences, and t7 rna polymerase
EP0594584A1 (en) * 1990-01-12 1994-05-04 The Scripps Research Institute Nucleic acid enzymes for cleaving dna
NZ236819A (en) * 1990-02-03 1993-07-27 Max Planck Gesellschaft Enzymatic cleavage of fusion proteins; fusion proteins; recombinant dna and pharmaceutical compositions
IT1239733B (en) 1990-02-23 1993-11-15 Eniricerche Spa NEUTRAL THERMO-STABLE MUTANTS AND MEANS AND METHODS FOR THEIR PREPARATION
US5288644A (en) 1990-04-04 1994-02-22 The Rockefeller University Instrument and method for the sequencing of genome
DE69109109T2 (en) * 1990-05-09 1995-09-14 Massachusetts Inst Technology UBIQUIT-SPECIFIC PROTEASE.
US5264563A (en) 1990-08-24 1993-11-23 Ixsys Inc. Process for synthesizing oligonucleotides with random codons
WO1992013629A1 (en) 1991-01-31 1992-08-20 Wayne State University A method for analyzing an organic sample
US5364759B2 (en) 1991-01-31 1999-07-20 Baylor College Medicine Dna typing with short tandem repeat polymorphisms and identification of polymorphic short tandem repeats
US5210412A (en) * 1991-01-31 1993-05-11 Wayne State University Method for analyzing an organic sample
US5578443A (en) 1991-03-06 1996-11-26 Regents Of The University Of Minnesota DNA sequence-based HLA typing method
CA2066556A1 (en) * 1991-04-26 1992-10-27 Toyoji Sawayanagi Alkaline protease, method for producing the same, use thereof and microorganism producing the same
US5846717A (en) 1996-01-24 1998-12-08 Third Wave Technologies, Inc. Detection of nucleic acid sequences by invader-directed cleavage
WO1993006239A1 (en) 1991-09-24 1993-04-01 Keygene N.V. Selective restriction fragment amplification: a general method for dna fingerprinting
IT1260447B (en) 1992-01-27 1996-04-09 PROCEDURE AND EQUIPMENT FOR THE INTEGRAL AUTOMATION OF AN ANALYSIS LABORATORY
US5436150A (en) * 1992-04-03 1995-07-25 The Johns Hopkins University Functional domains in flavobacterium okeanokoities (foki) restriction endonuclease
WO1993021592A1 (en) 1992-04-16 1993-10-28 The Dow Chemical Company Improved method for interpreting complex data and detecting abnormal instrument or process behavior
US5646020A (en) * 1992-05-14 1997-07-08 Ribozyme Pharmaceuticals, Inc. Hammerhead ribozymes for preferred targets
US5792664A (en) 1992-05-29 1998-08-11 The Rockefeller University Methods for producing and analyzing biopolymer ladders
JPH07507394A (en) 1992-05-29 1995-08-10 ザ ロックフェラー ユニバーシティ Methods and materials for peptide sequencing using a mass spectrometer
US5440119A (en) 1992-06-02 1995-08-08 Labowsky; Michael J. Method for eliminating noise and artifact peaks in the deconvolution of multiply charged mass spectra
WO1994000562A1 (en) 1992-06-24 1994-01-06 The Mt. Sinai School Of Medicine Of The City University Of New York A novel human immunodeficiency virus
US5700672A (en) 1992-07-23 1997-12-23 Stratagene Purified thermostable pyrococcus furiousus DNA ligase
EP0596205A3 (en) 1992-11-03 1996-02-21 Hewlett Packard Co Bench supervisor system.
US5795714A (en) 1992-11-06 1998-08-18 Trustees Of Boston University Method for replicating an array of nucleic acid probes
US5503980A (en) * 1992-11-06 1996-04-02 Trustees Of Boston University Positional sequencing by hybridization
US6436635B1 (en) 1992-11-06 2002-08-20 Boston University Solid phase sequencing of double-stranded nucleic acids
US5422253A (en) 1992-12-07 1995-06-06 Wisconsin Alumni Research Foundation Method of site specific nucleic acid cleavage
CA2152353C (en) 1992-12-23 2005-05-03 Rodney S. Markin Method for automatic testing of laboratory specimens
US6194144B1 (en) * 1993-01-07 2001-02-27 Sequenom, Inc. DNA sequencing by mass spectrometry
US5605798A (en) 1993-01-07 1997-02-25 Sequenom, Inc. DNA diagnostic based on mass spectrometry
EP1262564A3 (en) 1993-01-07 2004-03-31 Sequenom, Inc. Dna sequencing by mass spectrometry
US6074823A (en) * 1993-03-19 2000-06-13 Sequenom, Inc. DNA sequencing by mass spectrometry via exonuclease degradation
CA2158642A1 (en) * 1993-03-19 1994-09-29 Hubert Koster Dna sequencing by mass spectrometry via exonuclease degradation
US5604098A (en) * 1993-03-24 1997-02-18 Molecular Biology Resources, Inc. Methods and materials for restriction endonuclease applications
EP0690870A4 (en) 1993-03-24 1998-05-20 Molecular Biology Resources Dinucleotide restriction endonuclease preparations and methods of use
CA2122203C (en) * 1993-05-11 2001-12-18 Melinda S. Fraiser Decontamination of nucleic acid amplification reactions
US5837832A (en) 1993-06-25 1998-11-17 Affymetrix, Inc. Arrays of nucleic acid probes on biological chips
US5861242A (en) * 1993-06-25 1999-01-19 Affymetrix, Inc. Array of nucleic acid probes on biological chips for diagnosis of HIV and methods of using the same
JPH09505397A (en) 1993-11-17 1997-05-27 アマーシャム・インターナショナル・ピーエルシー Nucleic acid sequencing by primer extension mass spectrometry
US5908779A (en) * 1993-12-01 1999-06-01 University Of Connecticut Targeted RNA degradation using nuclear antisense RNA
US5538897A (en) 1994-03-14 1996-07-23 University Of Washington Use of mass spectrometry fragmentation patterns of peptides to identify amino acid sequences in databases
US5714330A (en) * 1994-04-04 1998-02-03 Lynx Therapeutics, Inc. DNA sequencing by stepwise ligation and cleavage
US5807522A (en) 1994-06-17 1998-09-15 The Board Of Trustees Of The Leland Stanford Junior University Methods for fabricating microarrays of biological samples
US5853979A (en) 1995-06-30 1998-12-29 Visible Genetics Inc. Method and system for DNA sequence determination and mutation detection with reference to a standard
US5498545A (en) * 1994-07-21 1996-03-12 Vestal; Marvin L. Mass spectrometer system and method for matrix-assisted laser desorption measurements
US5453613A (en) 1994-10-21 1995-09-26 Hewlett Packard Company Mass spectra interpretation system including spectra extraction
US5807718A (en) 1994-12-02 1998-09-15 The Scripps Research Institute Enzymatic DNA molecules
US6270962B1 (en) 1995-01-30 2001-08-07 The Regents Of The University Of California Methods for the elimination of DNA sequencing artifacts
US6428955B1 (en) 1995-03-17 2002-08-06 Sequenom, Inc. DNA diagnostics based on mass spectrometry
US5858705A (en) * 1995-06-05 1999-01-12 Human Genome Sciences, Inc. Polynucleotides encoding human DNA ligase III and methods of using these polynucleotides
AU758454B2 (en) 1995-04-11 2003-03-20 Sequenom, Inc. Solid phase sequencing of biopolymers
JPH11503611A (en) 1995-04-11 1999-03-30 トラスティーズ・オブ・ボストン・ユニバーシティ Solid-phase sequencing of biopolymers
JP2001500606A (en) 1995-05-19 2001-01-16 パーセプティブ バイオシステムズ,インコーポレーテッド Method and apparatus for statistically certain polymer sequencing using mass spectrometry
US5753439A (en) * 1995-05-19 1998-05-19 Trustees Of Boston University Nucleic acid detection methods
US5869240A (en) * 1995-05-19 1999-02-09 Perseptive Biosystems, Inc. Methods and apparatus for sequencing polymers with a statistical certainty using mass spectrometry
US5874283A (en) * 1995-05-30 1999-02-23 John Joseph Harrington Mammalian flap-specific endonuclease
DK0843735T4 (en) 1995-07-11 2007-01-22 Univ College Cork Nat Univ Ie Glycol-mediated detection of known nucleotide sequences
AU6960396A (en) 1995-08-31 1997-03-19 General Hospital Corporation, The Batten disease gene
US6146854A (en) 1995-08-31 2000-11-14 Sequenom, Inc. Filtration processes, kits and devices for isolating plasmids
US5869242A (en) * 1995-09-18 1999-02-09 Myriad Genetics, Inc. Mass spectrometry to assess DNA sequence polymorphisms
US6190865B1 (en) * 1995-09-27 2001-02-20 Epicentre Technologies Corporation Method for characterizing nucleic acid molecules
US6090549A (en) * 1996-01-16 2000-07-18 University Of Chicago Use of continuous/contiguous stacking hybridization as a diagnostic tool
US20010018514A1 (en) 1998-07-31 2001-08-30 Mcgall Glenn H. Nucleic acid labeling compounds
US6090606A (en) * 1996-01-24 2000-07-18 Third Wave Technologies, Inc. Cleavage agents
US5830712A (en) * 1996-02-06 1998-11-03 Allelix Biopharmaceuticals Inc. Selective template deletion method
US5686656A (en) 1996-02-27 1997-11-11 Aviv Amirav Method and device for the introduction of a sample into a gas chromatograph
US6051378A (en) * 1996-03-04 2000-04-18 Genetrace Systems Inc. Methods of screening nucleic acids using mass spectrometry
WO1997037041A2 (en) 1996-03-18 1997-10-09 Sequenom, Inc. Dna sequencing by mass spectrometry
DE19613082C2 (en) 1996-04-02 1999-10-21 Koenig & Bauer Ag Method and device for the qualitative assessment of processed material
WO1997037953A1 (en) 1996-04-08 1997-10-16 Glaxo Group Ltd. Mass-based encoding and qualitative analysis of combinatorial libraries
WO1997040462A2 (en) 1996-04-19 1997-10-30 Spectra Biomedical, Inc. Correlating polymorphic forms with multiple phenotypes
US5928906A (en) 1996-05-09 1999-07-27 Sequenom, Inc. Process for direct sequencing during template amplification
US6022688A (en) * 1996-05-13 2000-02-08 Sequenom, Inc. Method for dissociating biotin complexes
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
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
WO1997047766A1 (en) 1996-06-10 1997-12-18 University Of Utah Research Foundation Rapid, accurate identification of dna sequence variants by electrospray mass spectrometry
DE69734828T2 (en) * 1996-06-10 2006-10-26 Novozymes, Inc., Davis 5-AMINOLEVULINSEAU SYNTHASE FROM ASPERGILLUS ORYZAE AND DAFUER CODING NUCLEIC ACID
FR2749662B1 (en) 1996-06-11 1998-08-28 Elf Aquitaine ROBOTIZED LABORATORY OF SAMPLES ANALYSIS
AU4042597A (en) 1996-07-19 1998-02-10 Hybridon, Inc. Method for sequencing nucleic acids using matrix-assisted laser desorption ionization time-of-flight mass spectrometry
US6008334A (en) 1996-07-24 1999-12-28 The Board Of Regents Of The University Of Oklahoma Base-protected nucleotide analogs with protected thiol groups
US5928870A (en) * 1997-06-16 1999-07-27 Exact Laboratories, Inc. Methods for the detection of loss of heterozygosity
GB9618960D0 (en) * 1996-09-11 1996-10-23 Medical Science Sys Inc Proteases
US5885841A (en) * 1996-09-11 1999-03-23 Eli Lilly And Company System and methods for qualitatively and quantitatively comparing complex admixtures using single ion chromatograms derived from spectroscopic analysis of such admixtures
US5777324A (en) * 1996-09-19 1998-07-07 Sequenom, Inc. Method and apparatus for maldi analysis
US5965363A (en) 1996-09-19 1999-10-12 Genetrace Systems Inc. Methods of preparing nucleic acids for mass spectrometric analysis
WO1998012355A1 (en) 1996-09-19 1998-03-26 Genetrace Systems Methods of preparing nucleic acids for mass spectrometric analysis
US5864137A (en) * 1996-10-01 1999-01-26 Genetrace Systems, Inc. Mass spectrometer
US6091424A (en) 1996-11-01 2000-07-18 Tom Sawyer Software Labeling graphical features of drawings
US5900481A (en) * 1996-11-06 1999-05-04 Sequenom, Inc. Bead linkers for immobilizing nucleic acids to solid supports
CA2270132A1 (en) 1996-11-06 1998-05-14 Sequenom, Inc. Dna diagnostics based on mass spectrometry
US6140053A (en) 1996-11-06 2000-10-31 Sequenom, Inc. DNA sequencing by mass spectrometry via exonuclease degradation
US6024925A (en) * 1997-01-23 2000-02-15 Sequenom, Inc. Systems and methods for preparing low volume analyte array elements
ATE259056T1 (en) 1996-11-06 2004-02-15 Sequenom Inc METHOD FOR MASS SPECTROMETRY
US6133436A (en) 1996-11-06 2000-10-17 Sequenom, Inc. Beads bound to a solid support and to nucleic acids
WO1998020019A1 (en) 1996-11-06 1998-05-14 Sequenom, Inc. Compositions and methods for immobilizing nucleic acids to solid supports
EP0960214A4 (en) 1996-12-06 2004-08-04 Urocor Inc Diagnosis of disease state using mrna profiles
US6297006B1 (en) 1997-01-16 2001-10-02 Hyseq, Inc. Methods for sequencing repetitive sequences and for determining the order of sequence subfragments
WO1998033808A2 (en) 1997-02-04 1998-08-06 Hubert Koster A reversible stoichiometric process for conjugating biomolecules
US6059724A (en) * 1997-02-14 2000-05-09 Biosignal, Inc. System for predicting future health
WO1998040520A1 (en) 1997-03-14 1998-09-17 Hybridon, Inc. Method for sequencing of modified nucleic acids using electrospray ionization-fourier transform mass spectrometry
EP0985148A4 (en) * 1997-05-28 2004-03-10 Inst Medical W & E Hall Nucleic acid diagnostics based on mass spectrometry or mass separation and base specific cleavage
US5976806A (en) 1997-06-25 1999-11-02 Pioneer Hi-Bred International, Inc. DNA ligase assay
US5975492A (en) 1997-07-14 1999-11-02 Brenes; Arthur Bellows driver slot valve
DE69823206T2 (en) 1997-07-25 2004-08-19 Affymetrix, Inc. (a Delaware Corp.), Santa Clara METHOD FOR PRODUCING A BIO-INFORMATICS DATABASE
US6207370B1 (en) 1997-09-02 2001-03-27 Sequenom, Inc. Diagnostics based on mass spectrometric detection of translated target polypeptides
US5888795A (en) * 1997-09-09 1999-03-30 Becton, Dickinson And Company Thermostable uracil DNA glycosylase and methods of use
US6112161A (en) 1997-09-17 2000-08-29 Hewlett-Packard Method, apparatus, and article of manufacture for enhanced intergration of signals
US6090558A (en) * 1997-09-19 2000-07-18 Genetrace Systems, Inc. DNA typing by mass spectrometry with polymorphic DNA repeat markers
US6485944B1 (en) 1997-10-10 2002-11-26 President And Fellows Of Harvard College Replica amplification of nucleic acid arrays
US5932451A (en) 1997-11-19 1999-08-03 Incyte Pharmaceuticals, Inc. Method for unbiased mRNA amplification
US5948902A (en) 1997-11-20 1999-09-07 South Alabama Medical Science Foundation Antisense oligonucleotides to human serine/threonine protein phosphatase genes
DE19754482A1 (en) * 1997-11-27 1999-07-01 Epigenomics Gmbh Process for making complex DNA methylation fingerprints
DK1036198T3 (en) * 1997-12-08 2013-01-02 California Inst Of Techn Method for Preparation of Polynucleotide and Polypeptide Sequences
US6268131B1 (en) * 1997-12-15 2001-07-31 Sequenom, Inc. Mass spectrometric methods for sequencing nucleic acids
DE19803309C1 (en) * 1998-01-29 1999-10-07 Bruker Daltonik Gmbh Position coordinate determination method for ion peak of mass spectrum
US6054276A (en) * 1998-02-23 2000-04-25 Macevicz; Stephen C. DNA restriction site mapping
JP3575295B2 (en) 1998-04-15 2004-10-13 住友電装株式会社 Electrical connector plug
US6723564B2 (en) * 1998-05-07 2004-04-20 Sequenom, Inc. IR MALDI mass spectrometry of nucleic acids using liquid matrices
US20030017483A1 (en) * 1998-05-12 2003-01-23 Ecker David J. Modulation of molecular interaction sites on RNA and other biomolecules
US6099553A (en) 1998-05-21 2000-08-08 Applied Medical Resources Corporation Suture clinch
US6104028A (en) 1998-05-29 2000-08-15 Genetrace Systems Inc. Volatile matrices for matrix-assisted laser desorption/ionization mass spectrometry
GB9827152D0 (en) 1998-07-03 1999-02-03 Devgen Nv Characterisation of gene function using double stranded rna inhibition
JP2000067805A (en) * 1998-08-24 2000-03-03 Hitachi Ltd Mass spectro meter
US6440705B1 (en) * 1998-10-01 2002-08-27 Vincent P. Stanton, Jr. Method for analyzing polynucleotides
WO2000018967A1 (en) 1998-10-01 2000-04-06 Variagenics, Inc. A method for analyzing polynucleotides
WO2000022130A2 (en) 1998-10-15 2000-04-20 Chiron Corporation Metastatic breast and colon cancer regulated genes
US6270835B1 (en) 1999-10-07 2001-08-07 Microcoating Technologies, Inc. Formation of this film capacitors
EP1133573A2 (en) 1998-11-24 2001-09-19 The Johns Hopkins University Genotyping by mass spectrometric analysis of short dna fragments
GB9904585D0 (en) 1999-02-26 1999-04-21 Gemini Research Limited Clinical and diagnostic database
US6225061B1 (en) 1999-03-10 2001-05-01 Sequenom, Inc. Systems and methods for performing reactions in an unsealed environment
US6331427B1 (en) 1999-03-26 2001-12-18 Millennium Pharmaceuticals, Inc. Protease homologs
US20020009394A1 (en) 1999-04-02 2002-01-24 Hubert Koster Automated process line
US6309833B1 (en) * 1999-04-12 2001-10-30 Nanogen/Becton Dickinson Partnership Multiplex amplification and separation of nucleic acid sequences on a bioelectronic microchip using asymmetric structures
EP1173622B1 (en) * 1999-04-30 2005-06-15 Methexis Genomics N.V. Diagnostic sequencing by a combination of specific cleavage and mass spectrometry
US6994969B1 (en) 1999-04-30 2006-02-07 Methexis Genomics, N.V. Diagnostic sequencing by a combination of specific cleavage and mass spectrometry
EP2088209B1 (en) 1999-10-13 2017-05-31 Sequenom, Inc. Methods for generating databases for identifying polymorphic genetic markers
US7917301B1 (en) 2000-09-19 2011-03-29 Sequenom, Inc. Method and device for identifying a biological sample
US7332275B2 (en) * 1999-10-13 2008-02-19 Sequenom, Inc. Methods for detecting methylated nucleotides
WO2001055455A2 (en) 2000-01-31 2001-08-02 Millennium Pharmaceuticals, Inc. Resistance sequences and uses thereof
US6475736B1 (en) 2000-05-23 2002-11-05 Variagenics, Inc. Methods for genetic analysis of DNA using biased amplification of polymorphic sites
EP1179589A1 (en) 2000-08-08 2002-02-13 F. Hoffmann-La Roche Ag MMX-1, a member of the family of human cancer/testis antigens, a protein encoded thereby and a process for determining whether a tumor sample has metastatic potential
GB0019499D0 (en) 2000-08-08 2000-09-27 Diamond Optical Tech Ltd system and method
EP1358616A2 (en) 2000-11-02 2003-11-05 Epigenomics AG Systems, methods and computer program products for guiding selection of a therapeutic treatment regimen based on the methylation status of the dna
DE10061348C2 (en) * 2000-12-06 2002-10-24 Epigenomics Ag Method for the quantification of cytosine methylations in complex amplified genomic DNA
DE10112515B4 (en) * 2001-03-09 2004-02-12 Epigenomics Ag Method for the detection of cytosine methylation patterns with high sensitivity
US20030013099A1 (en) * 2001-03-19 2003-01-16 Lasek Amy K. W. Genes regulated by DNA methylation in colon tumors
US7056663B2 (en) * 2001-03-23 2006-06-06 California Pacific Medical Center Prognostic methods for breast cancer
US20040102905A1 (en) * 2001-03-26 2004-05-27 Epigenomics Ag Method for epigenetic feature selection
US6522477B2 (en) * 2001-04-17 2003-02-18 Karl Storz Imaging, Inc. Endoscopic video camera with magnetic drive focusing
US20020155587A1 (en) 2001-04-20 2002-10-24 Sequenom, Inc. System and method for testing a biological sample
WO2002086163A1 (en) 2001-04-20 2002-10-31 Karolinska Innovations Ab Methods for high throughput genome analysis using restriction site tagged microarrays
WO2002101353A2 (en) 2001-06-08 2002-12-19 U.S. Genomics, Inc. Methods and products for analyzing nucleic acids based on methylation status
DE10130800B4 (en) * 2001-06-22 2005-06-23 Epigenomics Ag Method for the detection of cytosine methylation with high sensitivity
DE10132212B4 (en) 2001-06-27 2005-11-24 Epigenomics Ag Method for the detection of cytosine methylation by comparative analysis of the single strands of amplicons
MXPA04000432A (en) * 2001-07-15 2004-10-27 Keck Graduate Inst Amplification of nucleic acid fragments using nicking agents.
DE10151055B4 (en) 2001-10-05 2005-05-25 Epigenomics Ag Method for detecting cytosine methylation in CpG islands
DE10154317B4 (en) 2001-10-26 2005-06-09 Epigenomics Ag Method for the detection of cytosine methylations in immobilized DNA samples
EP1440407A2 (en) 2001-10-31 2004-07-28 Epigenomics AG A method for epigenetic knowledge generation
EP1456413B1 (en) 2001-11-16 2008-04-23 The Johns Hopkins University School Of Medicine Method of detection of prostate cancer
JP2003245087A (en) * 2001-11-22 2003-09-02 Sankyo Co Ltd Method for diagnosing gene
DE10201138B4 (en) 2002-01-08 2005-03-10 Epigenomics Ag Method for the detection of cytosine methylation patterns by exponential ligation of hybridized probe oligonucleotides (MLA)
EP1344832A1 (en) 2002-03-15 2003-09-17 Epigenomics AG Methods and nucleic acids for the analysis of methylation within the gene melastatin
ATE349555T1 (en) 2002-03-15 2007-01-15 Epigenomics Ag DISCOVERY AND DIAGNOSTIC METHODS USING 5-METHYLCYTOSINE DNA GLYCOSYLASE
US20050164193A1 (en) 2002-03-25 2005-07-28 Epigenomics Ag Method for the analysis of methylation patterns within nucleic acids by means of mass spectrometry
EP1492887A1 (en) * 2002-04-11 2005-01-05 Sequenom, Inc. Methods and devices for performing chemical reactions on a solid support
US20040014101A1 (en) * 2002-05-03 2004-01-22 Pel-Freez Clinical Systems, Inc. Separating and/or identifying polymorphic nucleic acids using universal bases
WO2004013284A2 (en) 2002-08-02 2004-02-12 Tufts University A method to assess genomic dna methylation using high-performance liquid chromatography-electospray ionization mass spectrometry
US20050009053A1 (en) * 2003-04-25 2005-01-13 Sebastian Boecker Fragmentation-based methods and systems for de novo sequencing
US20050009059A1 (en) 2003-05-07 2005-01-13 Affymetrix, Inc. Analysis of methylation status using oligonucleotide arrays
US8150626B2 (en) 2003-05-15 2012-04-03 Illumina, Inc. Methods and compositions for diagnosing lung cancer with specific DNA methylation patterns
US20050026183A1 (en) * 2003-05-15 2005-02-03 Jian-Bing Fan Methods and compositions for diagnosing conditions associated with specific DNA methylation patterns
US20040253141A1 (en) 2003-06-16 2004-12-16 Schembri Carol T. Apparatus and method for nucleic acid spatial ordering
US9394565B2 (en) 2003-09-05 2016-07-19 Agena Bioscience, Inc. Allele-specific sequence variation analysis
ES2382780T3 (en) 2003-10-21 2012-06-13 Orion Genomics, Llc Procedures for quantitative determination of methylation density in a DNA locus
WO2005093095A1 (en) 2004-03-24 2005-10-06 Epigenomics Ag Method for analysis of cytosine methylation
WO2005098050A2 (en) 2004-03-26 2005-10-20 Sequenom, Inc. Base specific cleavage of methylation-specific amplification products in combination with mass analysis
US7608394B2 (en) 2004-03-26 2009-10-27 Sequenom, Inc. Methods and compositions for phenotype identification based on nucleic acid methylation
US20060073501A1 (en) * 2004-09-10 2006-04-06 Van Den Boom Dirk J Methods for long-range sequence analysis of nucleic acids
WO2007016668A2 (en) 2005-08-02 2007-02-08 Sequenom, Inc. Methods and compositions for disease prognosis based on nucleic acid methylation

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20030027169A1 (en) * 2000-10-27 2003-02-06 Sheng Zhang One-well assay for high throughput detection of single nucleotide polymorphisms
WO2004050839A2 (en) * 2002-11-27 2004-06-17 Sequenom, Inc. Fragmentation-based methods and systems for sequence variation detection and discovery

Non-Patent Citations (17)

* Cited by examiner, † Cited by third party
Title
BEAULIEU M. ET AL.: "A novel method for molecular haplotyping combining an improved AS-PCR technique with base specific cleavage of nucleic acid analyzed by mass spectrometry.", AMERICAN JOURNAL OF HUMAN GENETICS, vol. 73, no. 5, November 2003 (2003-11-01), & 53RD ANNUAL MEETING OF THE AMERICAN SOCIETY OF HUMAN GENETICS; LOS ANGELES, CA, USA; NOVEMBER 04-08, 2003, pages 441, XP001206988, ISSN: 0002-9297 *
BÖCKER S.: "SNP and mutation discovery using base-specific cleavage and MALDI-TOF mass spectrometry.", BIOINFORMATICS (OXFORD, ENGLAND) 2003, vol. 19 Suppl 1, 2003, pages i44 - i53, XP002338050, ISSN: 1367-4803 *
EITAN Y. ET AL.: "Direct micro-haplotyping by multiple double PCR amplifications of specific alleles (MD-PASA).", NUCLEIC ACIDS RESEARCH, vol. 30, no. 12, 15 June 2002 (2002-06-15), pages E62.1 - E62.8, XP002338095, ISSN: 1362-4962 *
ELSO C. ET AL.: "Mutation detection using mass spectrometric separation of tiny oligonucleotide fragments", GENOME RESEARCH, vol. 12, no. 9, September 2002 (2002-09-01), pages 1428 - 1433, XP002338049, ISSN: 1088-9051 *
FEI Z. ET AL.: "ANALYSIS OF SINGLE NUCLEOTIDE POLYMORPHISMS BY PRIMER EXTENSION AND MATRIX-ASSISTED LASER DESORPTION/IONIZATION TIME-OF-FLIGHT MASS SPECTROMETRY", RAPID COMMUNICATIONS IN MASS SPECTROMETRY, HEYDEN, LONDON, GB, vol. 14, no. 11, 2000, pages 950 - 959, XP009000471, ISSN: 0951-4198 *
HARTMER R. ET AL.: "RNase T1 mediated base-specific cleavage and MALDI-TOF MS for high-throughput comparative sequence analysis.", NUCLEIC ACIDS RESEARCH. 1 MAY 2003, vol. 31, no. 9, 1 May 2003 (2003-05-01), pages E47.1 - E47.10, XP002338048, ISSN: 1362-4962 *
JU L.-Y. ET AL.: "APPLICATION OF SILVER STAINING TO THE RAPID TYPING OF THE POLYMORPHISM OF HLA-DQ ALLELES BY ENZYMATIC AMPLIFICATION AND ALLELE-SPECIFIC RESTRICTION FRAGMENT LENGTH POLYMORPHISM", ELECTROPHORESIS, WEINHEIM, DE, vol. 12, no. 4, January 1991 (1991-01-01), pages 270 - 273, XP008009406, ISSN: 0173-0835 *
KREBS S. ET AL.: "RNaseCut: a MALDI mass spectrometry-based method for SNP discovery.", NUCLEIC ACIDS RESEARCH. 1 APR 2003, vol. 31, no. 7, 1 April 2003 (2003-04-01), pages E37.1 - E37.8, XP002338047, ISSN: 1362-4962 *
MCKINZIE P.B. ET AL.: "Detection of rare K-ras codon 12 mutations using allele-specific competitive blocker PCR", MUTATION RESEARCH, AMSTERDAM, NL, vol. 517, no. 1-2, 27 May 2002 (2002-05-27), pages 209 - 220, XP002332580, ISSN: 0027-5107 *
RODI C.P. ET AL.: "A STRATEGY FOR THE RAPID DISCOVERY OF DISEASE MARKERS USING THE MASSARRAY SYSTEM", BIOTECHNIQUES, EATON PUBLISHING, NATICK, US, vol. 32, no. SUPPL, June 2002 (2002-06-01), pages S62 - S69, XP008049561, ISSN: 0736-6205 *
ROSS P. ET AL.: "HIGH LEVEL MULTIPLEX GENOTYPING BY MALDI-TOF MASS SPECTROMETRY", NATURE BIOTECHNOLOGY, US, vol. 16, 16 December 1998 (1998-12-16), pages 1347 - 1351, XP000939003, ISSN: 1087-0156 *
SARKAR G. ET AL.: "HAPLOTYPING BY DOUBLE PCR AMPLIFICATION OF SPECIFIC ALLELES", BIOTECHNIQUES, EATON PUBLISHING, US, vol. 10, no. 4, 1991, pages 436,438,440, XP001068404, ISSN: 0736-6205 *
SARKAR G. ET AL: "CHARACTERIZATION OF POLYMERASE CHAIN REACTION AMPLIFICATION OF SPECIFIC ALLELES", ANALYTICAL BIOCHEMISTRY, ACADEMIC PRESS, SAN DIEGO, CA, US, vol. 186, January 1990 (1990-01-01), pages 64 - 68, XP000386280, ISSN: 0003-2697 *
SOMMER S.S. ET AL.: "PCR AMPLIFICATION OF SPECIFIC ALLELES PASA IS A GENERAL METHOD FOR RAPIDLY DETECTING KNOWN SINGLE-BASE CHANGES", BIOTECHNIQUES, EATON PUBLISHING, US, vol. 12, no. 1, 1992, pages 82 - 87, XP002201653, ISSN: 0736-6205 *
TANG K. ET AL.: "Chip-based genotyping by mass spectrometry", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF USA, NATIONAL ACADEMY OF SCIENCE. WASHINGTON, US, vol. 96, no. 18, 31 August 1999 (1999-08-31), pages 10016 - 10020, XP002208514, ISSN: 0027-8424 *
TANG K. ET AL.: "Single nucleotide polymorphism analyses by MALDI-TOF MS", INTERNATIONAL JOURNAL OF MASS SPECTROMETRY, ELSEVIER SCIENCE PUBLISHERS, AMSTERDAM, NL, vol. 226, no. 1, 15 March 2003 (2003-03-15), pages 37 - 54, XP004413198, ISSN: 1387-3806 *
VAN DEN BOOM D. ET AL.: "MALDI-TOF MS: a platform technology for genetic discovery", INTERNATIONAL JOURNAL OF MASS SPECTROMETRY, ELSEVIER, AMSTERDAM, NL, vol. 238, no. 2, 1 November 2004 (2004-11-01), pages 173 - 188, XP004639199, ISSN: 1387-3806 *

Also Published As

Publication number Publication date
US20050089904A1 (en) 2005-04-28
US9394565B2 (en) 2016-07-19
WO2005024068A2 (en) 2005-03-17

Similar Documents

Publication Publication Date Title
WO2004065617A3 (en) Haplotype analysis
WO2004023092A3 (en) Genetic analysis and authentication
WO2003010328A3 (en) Complexity management of genomic dna
WO2003040395A3 (en) Universal nucleotides for nucleic acid analysis
WO1999014375A3 (en) Dna typing by mass spectrometry with polymorphic dna repeat markers
WO2004097369A3 (en) Fragmentation-based methods and systems for de novo sequencing
EP1350851A4 (en) Method of detecting polymorphism in dna by using mass spectroscopy
WO2005024068A3 (en) Allele-specific sequence variation analysis
WO2004058990A3 (en) Genetic polymorphisms associated with stenosis, methods of detection and uses thereof
WO2004072230A3 (en) Real-time polymerase chain reaction using large target amplicons
WO2004067779A3 (en) Genetic polymorphisms associated with rheumatoid arthritis, methods of detection and uses thereof
WO2008104002A8 (en) Methods for rapid forensic dna analysis
EP1362929A3 (en) Methods for genotyping
WO2010039991A3 (en) Method of generating informative dna templates for high-throughput sequencing applications
WO2002034883A3 (en) A one-well assay for high throughput detection of single nucleotide polymorphisms
WO2004003220A3 (en) Methods and composition for analyzing compromised samples using snps
EP1573037A3 (en) Methods and compositions for analyzing compromised samples using single nucleotide polymorphism panels
AU2002952797A0 (en) Centrifugal device and method using same
WO2001088189A3 (en) Microsatellite-aflp®
WO2004083403A3 (en) Genetic polymorphisms associated with rheumatoid arthritis, methods of detection and uses thereof
WO2007089542A3 (en) Systems and methods of analyzing nucleic acid polymers by using particle beams
WO2005033328A3 (en) Compositions and processes for genotyping single nucleotide polymorphisms
WO2001029262A3 (en) Genotyping reagents, kits and methods of use thereof
WO2005045059A3 (en) Allele assignment and probe selection in multiplexed assays of polymorphic targets
EP1405923A3 (en) Gene mapping method using microsatellite genetic polymorphism markers

Legal Events

Date Code Title Description
AK Designated states

Kind code of ref document: A2

Designated state(s): AE AG AL AM AT AU AZ BA BB BG BR BW BY BZ CA CH CN CO CR CU CZ DE DK DM DZ EC EE EG ES FI GB GD GE GH GM HR HU ID IL IN IS JP KE KG KP KR KZ LC LK LR LS LT LU LV MA MD MG MK MN MW MX MZ NA NI NO NZ OM PG PH PL PT RO RU SC SD SE SG SK SL SY TJ TM TN TR TT TZ UA UG UZ VC VN YU ZA ZM ZW

AL Designated countries for regional patents

Kind code of ref document: A2

Designated state(s): BW GH GM KE LS MW MZ NA SD SL SZ TZ UG ZM ZW AM AZ BY KG KZ MD RU TJ TM AT BE BG CH CY CZ DE DK EE ES FI FR GB GR HU IE IT LU MC NL PL PT RO SE SI SK TR BF BJ CF CG CI CM GA GN GQ GW ML MR NE SN TD TG

121 Ep: the epo has been informed by wipo that ep was designated in this application
122 Ep: pct application non-entry in european phase