WO2016193846A3 - Degenerate primer sets - Google Patents
Degenerate primer sets Download PDFInfo
- 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
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
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.
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)
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)
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 | Process for testing bacteria gene chip 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 | Method for analyzing structure composition of microorganism community by employing single-chain conformation polymorphism technique |
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 |
-
2016
- 2016-05-17 WO PCT/IB2016/052852 patent/WO2016193846A2/en active Application Filing
Patent Citations (15)
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 | Process for testing bacteria gene chip 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 | Method for analyzing structure composition of microorganism community by employing single-chain conformation polymorphism technique |
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)
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 * |
Also Published As
Publication number | Publication date |
---|---|
WO2016193846A2 (en) | 2016-12-08 |
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