WO1999011823A3 - Selection of pcr primer pairs to amplify a group of nucleotide sequences - Google Patents

Selection of pcr primer pairs to amplify a group of nucleotide sequences Download PDF

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Publication number
WO1999011823A3
WO1999011823A3 PCT/US1998/018392 US9818392W WO9911823A3 WO 1999011823 A3 WO1999011823 A3 WO 1999011823A3 US 9818392 W US9818392 W US 9818392W WO 9911823 A3 WO9911823 A3 WO 9911823A3
Authority
WO
WIPO (PCT)
Prior art keywords
nucleotide sequences
group
primer pairs
amplify
provides
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.)
Ceased
Application number
PCT/US1998/018392
Other languages
French (fr)
Other versions
WO1999011823A2 (en
Inventor
Michael Mcclelland
Graziano Pesole
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.)
Sidney Kimmel Cancer Center
Original Assignee
Sidney Kimmel Cancer Center
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 Sidney Kimmel Cancer Center filed Critical Sidney Kimmel Cancer Center
Priority to AU93027/98A priority Critical patent/AU9302798A/en
Priority to EP98945882A priority patent/EP1007739A2/en
Publication of WO1999011823A2 publication Critical patent/WO1999011823A2/en
Publication of WO1999011823A3 publication Critical patent/WO1999011823A3/en
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

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    • 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
    • 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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/686—Polymerase chain reaction [PCR]

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

Abstract

The present invention provides a method of determining a set of primer pairs for amplifying a group of related nucleotide sequences. A method of the invention is performed by identifying a group of related nucleotide sequences; generating the set of primers that matches each of the related nucleotide sequences; determining for each systematic pairing of each primer which of the related nucleotide sequences are amplified; and selecting from the systematic pairings a subset which amplifies all of the related nucleotide sequences. The invention also provides a method of using a set of primer pairs, which amplify a group of related nucleotide sequences, to identify nucleotide sequences related to the original group of nucleotide sequences. The invention also provides a computer apparatus for carrying out the computer-executed steps of the method. The invention further provides a computer program product comprising a signal bearing media for carrying out the method.
PCT/US1998/018392 1997-09-05 1998-09-04 Selection of pcr primer pairs to amplify a group of nucleotide sequences Ceased WO1999011823A2 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
AU93027/98A AU9302798A (en) 1997-09-05 1998-09-04 Selection of pcr primer pairs to amplify a group of nucleotide sequences
EP98945882A EP1007739A2 (en) 1997-09-05 1998-09-04 Selection of pcr primer pairs to amplify a group of nucleotide sequences

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US92581697A 1997-09-05 1997-09-05
US08/925,816 1997-09-05

Publications (2)

Publication Number Publication Date
WO1999011823A2 WO1999011823A2 (en) 1999-03-11
WO1999011823A3 true WO1999011823A3 (en) 1999-06-10

Family

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Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US1998/018392 Ceased WO1999011823A2 (en) 1997-09-05 1998-09-04 Selection of pcr primer pairs to amplify a group of nucleotide sequences

Country Status (3)

Country Link
EP (1) EP1007739A2 (en)
AU (1) AU9302798A (en)
WO (1) WO1999011823A2 (en)

Families Citing this family (9)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
AU785425B2 (en) 2001-03-30 2007-05-17 Genetic Technologies Limited Methods of genomic analysis
US6740510B2 (en) 2001-09-05 2004-05-25 Perlegen Sciences, Inc. Methods for amplification of nucleic acids
US6898531B2 (en) 2001-09-05 2005-05-24 Perlegen Sciences, Inc. Algorithms for selection of primer pairs
WO2003021259A1 (en) * 2001-09-05 2003-03-13 Perlegen Sciences, Inc. Selection of primer pairs
JP5409005B2 (en) * 2005-10-27 2014-02-05 ロゼッタ インファーマティックス エルエルシー Nucleic acid amplification using non-random primers
ATE488587T1 (en) 2005-12-06 2010-12-15 Ambion Inc RETRANSMISSION PRIMERS AND METHOD OF DESIGN THEREOF
EP2209912A1 (en) * 2007-10-26 2010-07-28 Rosetta Inpharmatics LLC Cdna synthesis using non-random primers
US20100159533A1 (en) * 2008-11-24 2010-06-24 Helicos Biosciences Corporation Simplified sample preparation for rna analysis
WO2012032510A1 (en) 2010-09-07 2012-03-15 Yeda Research And Development Co. Ltd. Primers for amplifying dna and methods of selecting same

Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1992014844A1 (en) * 1991-02-25 1992-09-03 California Institute Of Biological Research Consensus sequence primed polymerase chain reaction method for fingerprinting genomes
WO1993018176A1 (en) * 1992-03-11 1993-09-16 Dana-Farber Cancer Institute METHODS TO CLONE mRNA
WO1993024655A1 (en) * 1992-05-27 1993-12-09 Amersham International Plc Rna analysis

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1992014844A1 (en) * 1991-02-25 1992-09-03 California Institute Of Biological Research Consensus sequence primed polymerase chain reaction method for fingerprinting genomes
WO1993018176A1 (en) * 1992-03-11 1993-09-16 Dana-Farber Cancer Institute METHODS TO CLONE mRNA
WO1993024655A1 (en) * 1992-05-27 1993-12-09 Amersham International Plc Rna analysis

Non-Patent Citations (8)

* Cited by examiner, † Cited by third party
Title
JOHNSTON S L ET AL: "A NOVEL METHOD FOR SEQUENCING MEMBERS OF MULTI-GENE FAMILIES", NUCLEIC ACIDS RESEARCH, vol. 23, no. 15, August 1995 (1995-08-01), pages 3074/3075, XP002911090 *
LIANG P ET AL: "DIFFERENTIAL DISPLAY OF EUKARYOTIC MESSENGER RNA BY MEANS OF THE POLYMERASE CHAIN REACTION", SCIENCE, vol. 257, no. 5072, 14 August 1992 (1992-08-14), pages 967 - 971, XP000508268 *
LIBERT F ET AL.: "Selective amplification and cloning of four new members of the G protein-coupled receptor family", SCIENCE, vol. 244, 1989, pages 569 - 572, XP002090068 *
LOPEZ-NIETO C E AND NIGAM S K: "Selective amplificationof protein-coding regions of large sets of genes using statistically designed primer sets", NATURE BIOTECHNOLOGY, vol. 14, 1996, XP002090066 *
LOWE T ET AL.: "A computer program for selection of oligonucleotide primers for polymerase chain reaction", NUCLEIC ACIDS RESEARCH, vol. 18, no. 7, 1990, pages 1757 - 1761, XP002090070 *
PESOLE G ET AL.: "GeneUp: a program to select short PCR primer pairs that occur in multiple members of sequence lists", BIOTECHNIQUES, vol. 25, no. 1, 1998, pages 112 - 117, XP002090071 *
PESOLE G ET AL.: "WORDUP: an efficient algorithm for discovering statistically significant patterns in DNA sequences", NUCLEIC ACIDS RESEARCH, vol. 20, no. 11, 1992, pages 2871 - 2875, XP002090067 *
STONE B AND WHARTON W: "Targeted RNA fingerprinting: The cloning of differentially-expressed cDNA fragments enriched for members of the zinc finger gene family", NUCLEIC ACIDS RESEARCH, vol. 22, no. 13, 1994, pages 2612 - 2618, XP002090069 *

Also Published As

Publication number Publication date
AU9302798A (en) 1999-03-22
EP1007739A2 (en) 2000-06-14
WO1999011823A2 (en) 1999-03-11

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