WO2000065088A3 - Primers for identifying typing or classifying nucleic acids - Google Patents

Primers for identifying typing or classifying nucleic acids Download PDF

Info

Publication number
WO2000065088A3
WO2000065088A3 PCT/EP2000/003636 EP0003636W WO0065088A3 WO 2000065088 A3 WO2000065088 A3 WO 2000065088A3 EP 0003636 W EP0003636 W EP 0003636W WO 0065088 A3 WO0065088 A3 WO 0065088A3
Authority
WO
WIPO (PCT)
Prior art keywords
primers
typing
nucleic acids
identifying
hla
Prior art date
Application number
PCT/EP2000/003636
Other languages
French (fr)
Other versions
WO2000065088A2 (en
Inventor
Per-Johan Ulfendahl
Kin-Chun Wong
Original Assignee
Amersham Pharm Biotech Ab
Ulfendahl Per Johan
Wong Kin Chun
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 Amersham Pharm Biotech Ab, Ulfendahl Per Johan, Wong Kin Chun filed Critical Amersham Pharm Biotech Ab
Priority to AU50625/00A priority Critical patent/AU5062500A/en
Publication of WO2000065088A2 publication Critical patent/WO2000065088A2/en
Publication of WO2000065088A3 publication Critical patent/WO2000065088A3/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
    • C12Q1/6869—Methods for sequencing
    • C12Q1/6874—Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation
    • 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
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • C12Q1/6837—Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
    • 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
    • C12Q1/6881—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] 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
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/172—Haplotypes
    • 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)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Organic Chemistry (AREA)
  • Health & Medical Sciences (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Engineering & Computer Science (AREA)
  • Analytical Chemistry (AREA)
  • Immunology (AREA)
  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Physics & Mathematics (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Cell Biology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

A method is described for identifying a rather small set of extendible primers for use in the identification, typing or classification of a nucleic acid of known sequence having known polymorphisms. A matrix of primers and pairs of primer extensions is prepared and subjected to analysis by a set covering problem algorithm, e.g. a greedy algorithm or one which invloves a Lagrangian relaxation heuristic. Sets of primers are described for use in the identification, classification or typing of an organism, allele or gene selected from class 1 HLA, class 2 HLA and 16S rRNA.
PCT/EP2000/003636 1999-04-26 2000-04-20 Primers for identifying typing or classifying nucleic acids WO2000065088A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU50625/00A AU5062500A (en) 1999-04-26 2000-04-20 Primers for identifying typing or classifying nucleic acids

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
EP99303215 1999-04-26
EP99303215.0 1999-04-26

Publications (2)

Publication Number Publication Date
WO2000065088A2 WO2000065088A2 (en) 2000-11-02
WO2000065088A3 true WO2000065088A3 (en) 2001-08-09

Family

ID=8241346

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/EP2000/003636 WO2000065088A2 (en) 1999-04-26 2000-04-20 Primers for identifying typing or classifying nucleic acids

Country Status (2)

Country Link
AU (1) AU5062500A (en)
WO (1) WO2000065088A2 (en)

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9284285B2 (en) 2006-06-27 2016-03-15 Aerpio Therapeutics, Inc. Human protein tyrosine phosphatase inhibitors and methods of use

Families Citing this family (19)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
AU1601701A (en) * 1999-11-15 2001-05-30 John G. Hartwell Methods for generating single stranded cdna fragments
EP1291440A1 (en) * 2000-06-01 2003-03-12 Nisshinbo Industries, Inc. Kit and method for determining hla type
US7807447B1 (en) 2000-08-25 2010-10-05 Merck Sharp & Dohme Corp. Compositions and methods for exon profiling
US6713257B2 (en) 2000-08-25 2004-03-30 Rosetta Inpharmatics Llc Gene discovery using microarrays
WO2002029659A1 (en) * 2000-10-04 2002-04-11 International Reagents Corporation Medical system with the use of dna chips
AU2012200697B2 (en) * 2001-05-07 2015-02-19 Agriculture Victoria Services Pty Ltd Modification of plant and seed development and plant responses to stresses and stimuli (4)
WO2003034029A2 (en) 2001-10-15 2003-04-24 Bioarray Solutions, Ltd. Multiplexed analysis of polymorphic loci by concurrent interrogation and enzyme-mediated detection
AU2003206830A1 (en) * 2002-02-04 2003-09-02 Vermicon Ag Methods for specific rapid detection of pathogenic food-relevant bacteria
US7507568B2 (en) 2002-09-25 2009-03-24 The Proctor & Gamble Company Three dimensional coordinates of HPTPbeta
US7226755B1 (en) 2002-09-25 2007-06-05 The Procter & Gamble Company HPTPbeta as a target in treatment of angiogenesis mediated disorders
WO2004029289A2 (en) * 2002-09-26 2004-04-08 Roche Diagnostics Gmbh Analysis of the hla class i genes and susceptibility to type i diabetes
EP1536021A1 (en) 2003-11-27 2005-06-01 Consortium National de Recherche en Genomique (CNRG) Method for HLA typing
DK2371865T3 (en) 2006-04-07 2017-10-23 Aerpio Therapeutics Inc Antibodies that bind human protein tyrosine phosphatase beta (HPTP-β) and uses thereof
US7795444B2 (en) 2006-06-27 2010-09-14 Warner Chilcott Company Human protein tyrosine phosphatase inhibitors and methods of use
US8846685B2 (en) 2006-06-27 2014-09-30 Aerpio Therapeutics Inc. Human protein tyrosine phosphatase inhibitors and methods of use
US7589212B2 (en) 2006-06-27 2009-09-15 Procter & Gamble Company Human protein tyrosine phosphatase inhibitors and methods of use
US9096555B2 (en) 2009-01-12 2015-08-04 Aerpio Therapeutics, Inc. Methods for treating vascular leak syndrome
US8883832B2 (en) 2009-07-06 2014-11-11 Aerpio Therapeutics Inc. Compounds, compositions, and methods for preventing metastasis of cancer cells
MY160399A (en) 2009-07-06 2017-03-15 Aerpio Therapeutics Inc Compounds, compositions, and methods for preventing metastasis of cancer cells

Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1995013396A2 (en) * 1993-11-11 1995-05-18 U-Gene Research B.V. A method for identifying microorganisms, and aids useful thereof
WO1995015400A1 (en) * 1993-12-03 1995-06-08 The Johns Hopkins University Genotyping by simultaneous analysis of multiple microsatellite loci
JPH08308596A (en) * 1995-03-10 1996-11-26 Wakunaga Pharmaceut Co Ltd Detection of hla
US5883238A (en) * 1993-03-18 1999-03-16 N.V. Innogenetics S.A. Process for typing HLA-B using specific primers and probes sets
WO1999019509A2 (en) * 1997-10-10 1999-04-22 Visible Genetics Inc. Method and kit for amplification, sequencing and typing of classical hla class i genes

Patent Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5883238A (en) * 1993-03-18 1999-03-16 N.V. Innogenetics S.A. Process for typing HLA-B using specific primers and probes sets
WO1995013396A2 (en) * 1993-11-11 1995-05-18 U-Gene Research B.V. A method for identifying microorganisms, and aids useful thereof
WO1995015400A1 (en) * 1993-12-03 1995-06-08 The Johns Hopkins University Genotyping by simultaneous analysis of multiple microsatellite loci
JPH08308596A (en) * 1995-03-10 1996-11-26 Wakunaga Pharmaceut Co Ltd Detection of hla
WO1999019509A2 (en) * 1997-10-10 1999-04-22 Visible Genetics Inc. Method and kit for amplification, sequencing and typing of classical hla class i genes

Non-Patent Citations (11)

* Cited by examiner, † Cited by third party
Title
BEIN G ET AL.: "Rapid HLA-DRB1 genotyping by nested PCR amplification", TISSUE ANTIGENS, vol. 39, 1992, pages 68 - 73, XP000949259 *
BUNCE M ET AL.: "The PCR-SSP manager computer program: A tool for maintaining sequence alignments and automatically updating the specificities of PCR-SSP primers and primer mixes", TISSUE ANTIGENS, vol. 52, 1998, pages 158 - 174, XP000972134 *
CEREB N ET AL: "LOCUS-SPECIFIC AMPLIFICATION OF HLA CLASS I GENES FROM GENOMIC DNA: LOCUS-SPECIFIC SEQUENCES IN THE FIRST AND THIRD INTRONS OF HLA-A, -B, AND -C ALLELES", TISSUE ANTIGENS,DK,MUNKSGAARD, COPENHAGEN, vol. 45, 1995, pages 1 - 11, XP000197333, ISSN: 0001-2815 *
DATABASE WPI 1997 Derwent World Patents Index; AN 059711, XP002133096, "Detection and typing of class I MHC HLA-DR antigens - can check multiple specimens easily and type all HLA-DR (D-related) antigens known to be present in the Japanese population" *
DOI K AND IMAI H: "Greedy algorithms for finding a small set of primers satisfying cover and length resolution conditions in PCR experiments", GENOME INF. SER., vol. 8, 1997, pages 43 - 52, XP000900076 *
LEVINE J E ET AL.: "SSOP typing of the tenth international histocompatibility workshop reference cell lines for HLA genes", TISSUE ANTIGENS, vol. 44, 1994, pages 174 - 183, XP000972173 *
LO V M: "HEURISTIC ALGORITHMS FOR TASK ASSIGNMENT IN DISTRIBUTED SYSTEMS", IEEE TRANSACTIONS ON COMPUTERS,US,IEEE INC. NEW YORK, vol. 37, no. 11, 1 November 1988 (1988-11-01), pages 1384 - 1397, XP000005083, ISSN: 0018-9340 *
METSPALU A ET AL.: "Arrared primer extension (APEX) for mutation detection using gene specific DNA chips", AMERICAN JOURNAL OF HUMAN GENETICS, vol. 61, no. 4Sup, 1997, pages A224, XP000900002 *
OLERUP O ET AL.: "HLA-DQB1 and -DQA1 typing by PCR ampification with sequence-specific primers (PCR-SSP) in 2 hours", TISSUE ANTIGENS, vol. 41, 1993, pages 119 - 134, XP000972084 *
PIRRUNG M C ET AL.: "Design and use of a solid phase DNA-based computational device to solve satisfiability (SAT) problems", FASEB JOURNAL, vol. 11, no. 9, 1997, pages A1214, XP002133095 *
VASKO F J: "An efficient heuristic for large set covering problems", NAVAL RESEARCH LOGISTICS QUARTERLY, vol. 31, 1984, pages 163 - 171, XP000890158 *

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9284285B2 (en) 2006-06-27 2016-03-15 Aerpio Therapeutics, Inc. Human protein tyrosine phosphatase inhibitors and methods of use

Also Published As

Publication number Publication date
AU5062500A (en) 2000-11-10
WO2000065088A2 (en) 2000-11-02

Similar Documents

Publication Publication Date Title
WO2000065088A3 (en) Primers for identifying typing or classifying nucleic acids
WO1999014375A3 (en) Dna typing by mass spectrometry with polymorphic dna repeat markers
EP1961826A3 (en) A method for direct nucleic acid sequencing
WO2001013086A3 (en) Detection of nucleic acids
WO2004023092A3 (en) Genetic analysis and authentication
EP1591541A3 (en) Method of nucleic acid sequencing
CA2310077A1 (en) De novo or "universal" sequencing array
CA2254111A1 (en) Artificial mismatch hybridization
EP2474631A3 (en) Genetic polymorphisms associated with myocardial infarction, methods of detection and uses thereof
Lareu et al. Sequence variation of a hypervariable short tandem repeat at the D1S1656 locus
WO2000052208A3 (en) Customized oligonucleotide microchips that convert multiple genetic information to simple patterns
WO2001071042A8 (en) Detection kits, such as nucleic acid arrays, for detecting the expression of 10,000 or more drosophila genes and uses thereof
AU6846798A (en) Method of nucleic acid sequencing
WO2003040395A3 (en) Universal nucleotides for nucleic acid analysis
BR0308134A (en) quick analysis of variations in a genome
WO2004013346A3 (en) Methods and compositions for genotyping
WO2004010101A3 (en) Detection of chemical ligation using fluorescence quenching leaving groups
WO2004044163A3 (en) Methods for identifying risk of melanoma and treatments thereof
Galan et al. Cross‐amplification tests of ungulate primers in roe deer (Capreolus capreolus) to develop a multiplex panel of 12 microsatellite loci
WO2000009693A3 (en) Identification of the gene causing the mouse scurfy phenotype and its human ortholog
WO2005027710A3 (en) Methods for identifying subjects at risk of melanoma and treatments thereof
WO2003029435A3 (en) Detection of polynucleotide hybridization
CA2142156A1 (en) Nucleic Acid Sequences Specific for Mycobacterium Kansasii
TW329476B (en) Method for detecting contaminant DNA in a protein product and kits used for the same purpose
AU2003234932A1 (en) Nucleic acid amplification primers for detecting cytokeratins and examination method with the use of the primers

Legal Events

Date Code Title Description
AK Designated states

Kind code of ref document: A2

Designated state(s): AE AL AM AT AU AZ BA BB BG BR BY CA CH CN CR CU CZ DE DK DM EE 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 NO NZ PL PT RO RU SD SE SG SI SK SL TJ TM TR TT TZ UA UG US UZ VN YU ZA ZW

AL Designated countries for regional patents

Kind code of ref document: A2

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

121 Ep: the epo has been informed by wipo that ep was designated in this application
DFPE Request for preliminary examination filed prior to expiration of 19th month from priority date (pct application filed before 20040101)
AK Designated states

Kind code of ref document: A3

Designated state(s): AE AL AM AT AU AZ BA BB BG BR BY CA CH CN CR CU CZ DE DK DM EE 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 NO NZ PL PT RO RU SD SE SG SI SK SL TJ TM TR TT TZ UA UG US UZ VN YU ZA ZW

AL Designated countries for regional patents

Kind code of ref document: A3

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

REG Reference to national code

Ref country code: DE

Ref legal event code: 8642

122 Ep: pct application non-entry in european phase
NENP Non-entry into the national phase

Ref country code: JP