WO2004024949A3 - Method of rapid detection of mutations and nucleotide polymorphisms using chemometrics - Google Patents

Method of rapid detection of mutations and nucleotide polymorphisms using chemometrics Download PDF

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Publication number
WO2004024949A3
WO2004024949A3 PCT/DK2003/000594 DK0300594W WO2004024949A3 WO 2004024949 A3 WO2004024949 A3 WO 2004024949A3 DK 0300594 W DK0300594 W DK 0300594W WO 2004024949 A3 WO2004024949 A3 WO 2004024949A3
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WO
WIPO (PCT)
Prior art keywords
mutations
analysis
chemometrics
probe
nucleotide polymorphisms
Prior art date
Application number
PCT/DK2003/000594
Other languages
French (fr)
Other versions
WO2004024949A2 (en
Inventor
Mogens Fenger
Original Assignee
Hvidovre Hospital
Mogens Fenger
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 Hvidovre Hospital, Mogens Fenger filed Critical Hvidovre Hospital
Priority to AU2003260294A priority Critical patent/AU2003260294A1/en
Priority to EP03794827A priority patent/EP1567673A2/en
Publication of WO2004024949A2 publication Critical patent/WO2004024949A2/en
Publication of WO2004024949A3 publication Critical patent/WO2004024949A3/en

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    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/10—Signal processing, e.g. from mass spectrometry [MS] or from PCR
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
    • 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
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • 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
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/689—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria
    • 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
    • C12Q2600/156—Polymorphic or mutational markers
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N20/00—Machine learning
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00—Computing arrangements based on biological models
    • G06N3/02—Neural networks
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Organic Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Engineering & Computer Science (AREA)
  • Analytical Chemistry (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Physics & Mathematics (AREA)
  • Genetics & Genomics (AREA)
  • General Health & Medical Sciences (AREA)
  • Immunology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Molecular Biology (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Pathology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Medical Informatics (AREA)
  • Epidemiology (AREA)
  • Databases & Information Systems (AREA)
  • Artificial Intelligence (AREA)
  • Bioethics (AREA)
  • Evolutionary Computation (AREA)
  • Data Mining & Analysis (AREA)
  • Hospice & Palliative Care (AREA)
  • Oncology (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Signal Processing (AREA)
  • Public Health (AREA)
  • Software Systems (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Theoretical Computer Science (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

The present invention relates to methods, kits and systems for determining the presence or absence of target polynucleotides through hybridisation with polynucleotide probes comprising a detectable label and subsequent spectral analysis, preferably using multivariate analysis. The analysis of the spectral data allows to determine whether or not the probe is part of a hybrid polynucleotide and thus whether or not the target polynucleotide is present. Furthermore, the analysis of the spectral data allows to determine, when the probe is part of a hybrid polynucleotide, whether or not there is one or more mismatch between the probe and the target. The methods, kits and systems may be used for the determination of mutations and polymorphisms.
PCT/DK2003/000594 2002-09-13 2003-09-12 Method of rapid detection of mutations and nucleotide polymorphisms using chemometrics WO2004024949A2 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
AU2003260294A AU2003260294A1 (en) 2002-09-13 2003-09-12 Method of rapid detection of mutations and nucleotide polymorphisms using chemometrics
EP03794827A EP1567673A2 (en) 2002-09-13 2003-09-12 Method of rapid detection of mutations and nucleotide polymorphisms using chemometrics

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
DKPA200201351 2002-09-13
DKPA200201351 2002-09-13

Publications (2)

Publication Number Publication Date
WO2004024949A2 WO2004024949A2 (en) 2004-03-25
WO2004024949A3 true WO2004024949A3 (en) 2004-05-27

Family

ID=31984970

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/DK2003/000594 WO2004024949A2 (en) 2002-09-13 2003-09-12 Method of rapid detection of mutations and nucleotide polymorphisms using chemometrics

Country Status (3)

Country Link
EP (1) EP1567673A2 (en)
AU (1) AU2003260294A1 (en)
WO (1) WO2004024949A2 (en)

Families Citing this family (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP1740723A2 (en) * 2004-04-29 2007-01-10 Nederlandse Organisatie voor Toegepast-Natuuurwetenschappelijk Onderzoek TNO Staphylococcus aureus specific diagnostics
EP1591535A1 (en) * 2004-04-29 2005-11-02 Nederlandse Organisatie voor toegepast-natuurwetenschappelijk onderzoek TNO Classification of organisms based on genome representing arrays
DE102008059985B3 (en) * 2008-12-02 2010-04-01 Ip Bewertungs Ag Real-time PCR using gigahertz or terahertz spectrometry
WO2011103467A2 (en) 2010-02-19 2011-08-25 Life Technologies Corporation Methods and systems for nucleic acid sequencing validation, calibration and normalization
KR101184566B1 (en) * 2012-05-11 2012-09-20 케이맥(주) Method for integrated analysis of real-time pcr and dna chip
US20140272946A1 (en) * 2013-03-15 2014-09-18 Src, Inc. Methods and Systems For DNA-Based Detection And Reporting
CN113580099B (en) * 2021-06-21 2022-10-14 东南大学 Coding type nanometer machine and control and preparation method thereof

Citations (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5633134A (en) * 1992-10-06 1997-05-27 Ig Laboratories, Inc. Method for simultaneously detecting multiple mutations in a DNA sample
US5635352A (en) * 1993-12-08 1997-06-03 Chiron Corporation Solution phase nucleic acid sandwich assays having reduced background noise
US5849486A (en) * 1993-11-01 1998-12-15 Nanogen, Inc. Methods for hybridization analysis utilizing electrically controlled hybridization
US6048690A (en) * 1991-11-07 2000-04-11 Nanogen, Inc. Methods for electronic fluorescent perturbation for analysis and electronic perturbation catalysis for synthesis
US6261782B1 (en) * 1999-04-06 2001-07-17 Yale University Fixed address analysis of sequence tags
US6341257B1 (en) * 1999-03-04 2002-01-22 Sandia Corporation Hybrid least squares multivariate spectral analysis methods
US6584413B1 (en) * 2001-06-01 2003-06-24 Sandia Corporation Apparatus and system for multivariate spectral analysis
US6675106B1 (en) * 2001-06-01 2004-01-06 Sandia Corporation Method of multivariate spectral analysis

Patent Citations (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6048690A (en) * 1991-11-07 2000-04-11 Nanogen, Inc. Methods for electronic fluorescent perturbation for analysis and electronic perturbation catalysis for synthesis
US5633134A (en) * 1992-10-06 1997-05-27 Ig Laboratories, Inc. Method for simultaneously detecting multiple mutations in a DNA sample
US5849486A (en) * 1993-11-01 1998-12-15 Nanogen, Inc. Methods for hybridization analysis utilizing electrically controlled hybridization
US5635352A (en) * 1993-12-08 1997-06-03 Chiron Corporation Solution phase nucleic acid sandwich assays having reduced background noise
US6341257B1 (en) * 1999-03-04 2002-01-22 Sandia Corporation Hybrid least squares multivariate spectral analysis methods
US6261782B1 (en) * 1999-04-06 2001-07-17 Yale University Fixed address analysis of sequence tags
US6584413B1 (en) * 2001-06-01 2003-06-24 Sandia Corporation Apparatus and system for multivariate spectral analysis
US6675106B1 (en) * 2001-06-01 2004-01-06 Sandia Corporation Method of multivariate spectral analysis

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
KURT VARMUZA: "Chemometrics: Statistics and Multivariate Data Analysis in Chemistry - Application Examples", INT. CONF. ON STATISTICS AND RELATED FIELDS, 5 June 2003 (2003-06-05) - 9 June 2003 (2003-06-09), Honolulu, Hawaii 2003, pages 1 - 29, XP002267859 *
LEE K R ET AL: "Chemometrics approach to the determination of polymorphism of a drug compound by infrared spectroscopy.", DRUG DEVELOPMENT AND INDUSTRIAL PHARMACY. UNITED STATES FEB 2000, vol. 26, no. 2, February 2000 (2000-02-01), pages 135 - 147, XP002267858, ISSN: 0363-9045 *

Also Published As

Publication number Publication date
AU2003260294A1 (en) 2004-04-30
AU2003260294A8 (en) 2004-04-30
EP1567673A2 (en) 2005-08-31
WO2004024949A2 (en) 2004-03-25

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