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WO2016193846A3 - Degenerate primer sets - Google Patents

Degenerate primer sets Download PDF

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Publication number
WO2016193846A3
WO2016193846A3 PCT/IB2016/052852 IB2016052852W WO2016193846A3 WO 2016193846 A3 WO2016193846 A3 WO 2016193846A3 IB 2016052852 W IB2016052852 W IB 2016052852W WO 2016193846 A3 WO2016193846 A3 WO 2016193846A3
Authority
WO
WIPO (PCT)
Prior art keywords
primers
primer sets
degenerate primer
design
enough
Prior art date
Application number
PCT/IB2016/052852
Other languages
French (fr)
Other versions
WO2016193846A2 (en
Inventor
Sonia CHOTHANI
Sitharthan Kamalakaran
Original Assignee
Koninklijke Philips N.V.
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 Koninklijke Philips N.V. filed Critical Koninklijke Philips N.V.
Publication of WO2016193846A2 publication Critical patent/WO2016193846A2/en
Publication of WO2016193846A3 publication Critical patent/WO2016193846A3/en

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
    • C12Q1/6888—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
    • 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
    • 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
    • C12Q2600/16—Primer sets for multiplex assays
    • 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Physics & Mathematics (AREA)
  • Biotechnology (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Organic Chemistry (AREA)
  • Biophysics (AREA)
  • Molecular Biology (AREA)
  • Theoretical Computer Science (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Immunology (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

A set of broad ranging primers to allow rapid amplification of any pathogenic bacteria as well as a methodology for the design of these primers. One approach to providing such a set in accord with the present invention is to design primers for regions/genes that are conserved enough for universal primer binding and at the same time have enough variability to give distinguishing capacity. The set may be selected based on optimizing for degeneracy and coverage.
PCT/IB2016/052852 2015-05-29 2016-05-17 Degenerate primer sets WO2016193846A2 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201562167996P 2015-05-29 2015-05-29
US62/167,996 2015-05-29

Publications (2)

Publication Number Publication Date
WO2016193846A2 WO2016193846A2 (en) 2016-12-08
WO2016193846A3 true WO2016193846A3 (en) 2017-02-02

Family

ID=56119712

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/IB2016/052852 WO2016193846A2 (en) 2015-05-29 2016-05-17 Degenerate primer sets

Country Status (1)

Country Link
WO (1) WO2016193846A2 (en)

Families Citing this family (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
KR101889146B1 (en) * 2016-06-28 2018-08-17 재단법인대구경북과학기술원 Method for rapid design of valid high-quality primers and probes for multiple target genes in qPCR experiments
KR101912555B1 (en) * 2018-01-30 2018-10-26 재단법인대구경북과학기술원 Method for rapid design of valid high-quality primers and probes for multiple target genes in qPCR experiments

Citations (15)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6054278A (en) * 1997-05-05 2000-04-25 The Perkin-Elmer Corporation Ribosomal RNA gene polymorphism based microorganism identification
US20060115873A1 (en) * 2004-12-01 2006-06-01 Peak Sang-Hyun Novel exothermic material, method and device for lysing cells using the exothermic material
CN1824805A (en) * 2005-12-09 2006-08-30 上海大学 Gene Chip Detection Method of Bacteria in Sewage
US20060211002A1 (en) * 2005-03-18 2006-09-21 Jan Weile Antibiotic susceptibility and virulence factor detection in Pseudomonas aeruginosa
US20060246473A1 (en) * 2004-12-23 2006-11-02 Oh Ji-Young Primer set capable of specifically amplifying a target sequence found in 10 bacterial species and probe oligonucleotide specifically hybridizable with each target sequence of the 10 bacterial species
EP1801238A1 (en) * 2005-12-20 2007-06-27 Samsung Electronics Co., Ltd. Microarray substrate, method of manufacturing the same, microarray using the microarray substrate, and method of analyzing target biomolecule using the microarray
US20080076127A1 (en) * 2006-09-26 2008-03-27 Samsung Electronics Co., Ltd. Method and compositions for detecting helicobacter pylori
CN101210262A (en) * 2007-12-24 2008-07-02 哈尔滨工业大学 A Method for Analyzing the Structural Composition of Microbial Communities Using Single-Strand Conformational Polymorphism
WO2009049007A2 (en) * 2007-10-10 2009-04-16 Magellan Biosciences, Inc. Compositions, methods and systems for rapid identification of pathogenic nucleic acids
WO2009124085A1 (en) * 2008-04-01 2009-10-08 University Of Washington Improvement of sequence data by reduction of noise due to carry-over primer
US20090263809A1 (en) * 2008-03-20 2009-10-22 Zygem Corporation Limited Methods for Identification of Bioagents
WO2012116289A2 (en) * 2011-02-25 2012-08-30 Tricorder Diagnostics, Llc Microbial signatures as indicators of radiation exposure
US20120231459A1 (en) * 2011-03-09 2012-09-13 Gen-Probe Incorporated Chemiluminescent probes for multiplex molecular quantification and uses thereof
US20130052172A1 (en) * 2011-08-26 2013-02-28 John Edward Baker Methods for diagnosing and treating cardiac defects
US20130315922A1 (en) * 2009-04-27 2013-11-28 Gerard Eberl Method for inducing lymphoid tissue and modulating intestinal homeostasis

Patent Citations (15)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6054278A (en) * 1997-05-05 2000-04-25 The Perkin-Elmer Corporation Ribosomal RNA gene polymorphism based microorganism identification
US20060115873A1 (en) * 2004-12-01 2006-06-01 Peak Sang-Hyun Novel exothermic material, method and device for lysing cells using the exothermic material
US20060246473A1 (en) * 2004-12-23 2006-11-02 Oh Ji-Young Primer set capable of specifically amplifying a target sequence found in 10 bacterial species and probe oligonucleotide specifically hybridizable with each target sequence of the 10 bacterial species
US20060211002A1 (en) * 2005-03-18 2006-09-21 Jan Weile Antibiotic susceptibility and virulence factor detection in Pseudomonas aeruginosa
CN1824805A (en) * 2005-12-09 2006-08-30 上海大学 Gene Chip Detection Method of Bacteria in Sewage
EP1801238A1 (en) * 2005-12-20 2007-06-27 Samsung Electronics Co., Ltd. Microarray substrate, method of manufacturing the same, microarray using the microarray substrate, and method of analyzing target biomolecule using the microarray
US20080076127A1 (en) * 2006-09-26 2008-03-27 Samsung Electronics Co., Ltd. Method and compositions for detecting helicobacter pylori
WO2009049007A2 (en) * 2007-10-10 2009-04-16 Magellan Biosciences, Inc. Compositions, methods and systems for rapid identification of pathogenic nucleic acids
CN101210262A (en) * 2007-12-24 2008-07-02 哈尔滨工业大学 A Method for Analyzing the Structural Composition of Microbial Communities Using Single-Strand Conformational Polymorphism
US20090263809A1 (en) * 2008-03-20 2009-10-22 Zygem Corporation Limited Methods for Identification of Bioagents
WO2009124085A1 (en) * 2008-04-01 2009-10-08 University Of Washington Improvement of sequence data by reduction of noise due to carry-over primer
US20130315922A1 (en) * 2009-04-27 2013-11-28 Gerard Eberl Method for inducing lymphoid tissue and modulating intestinal homeostasis
WO2012116289A2 (en) * 2011-02-25 2012-08-30 Tricorder Diagnostics, Llc Microbial signatures as indicators of radiation exposure
US20120231459A1 (en) * 2011-03-09 2012-09-13 Gen-Probe Incorporated Chemiluminescent probes for multiplex molecular quantification and uses thereof
US20130052172A1 (en) * 2011-08-26 2013-02-28 John Edward Baker Methods for diagnosing and treating cardiac defects

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
DATABASE Geneseq [online] 24 January 2008 (2008-01-24), "Bacterial gene detecting probe #2.", XP002761972, retrieved from EBI accession no. GSN:AOD61978 Database accession no. AOD61978 *

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Publication number Publication date
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