WO2001073134A3 - Gene profiling arrays - Google Patents

Gene profiling arrays Download PDF

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Publication number
WO2001073134A3
WO2001073134A3 PCT/US2001/009993 US0109993W WO0173134A3 WO 2001073134 A3 WO2001073134 A3 WO 2001073134A3 US 0109993 W US0109993 W US 0109993W WO 0173134 A3 WO0173134 A3 WO 0173134A3
Authority
WO
WIPO (PCT)
Prior art keywords
mixtures
specimens
nucleic acid
arrays
cells
Prior art date
Application number
PCT/US2001/009993
Other languages
French (fr)
Other versions
WO2001073134A2 (en
Inventor
Francesco M Marincola
Lance D Miller
Ena Wang
Original Assignee
Francesco M Marincola
Lance D Miller
Us Gov Health & Human Serv
Ena Wang
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
Priority to US19270000P priority Critical
Priority to US60/192,700 priority
Application filed by Francesco M Marincola, Lance D Miller, Us Gov Health & Human Serv, Ena Wang filed Critical Francesco M Marincola
Publication of WO2001073134A2 publication Critical patent/WO2001073134A2/en
Publication of WO2001073134A3 publication Critical patent/WO2001073134A3/en

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Classifications

    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813Hybridisation assays
    • C12Q1/6834Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • C12Q1/6837Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips

Abstract

Ordered arrays of mixtures of nucleic acid molecules are provided, which mixtures reflect the expression profile of one or more specimens, such as different cells or tissues. In particular embodiments, complete mRNA mixtures from specimens are separately arrayed on a substrate. Specimens from which such mixtures of nucleic acid molecules are produced can be taken from any source, including animal, plant and/or microbial cells, and can be assembled in any collection desired. The collections can, for instance, include different cell types, different phenotypes, cells grown under different conditions, cells of different ages or developmental stages, and so forth. The nucleic acid arrays are provided in both macro- and microarray formats, and are suitable for gene profiling in which relative quantitative expression from a single source or multiple sources may be determined. Techniques are also disclosed for producing high-fidelity, amplified mixtures of nucleic acid molecules using a combination of anti-sense RNA amplification and template-switching synthesis. Amplified mixtures produced using this method can, for instance, be applied to the disclosed arrays. The disclosed arrays allow high throughput analysis of differential gene expression in a specimen (such as a tumor) or a variety of specimens (such as a variety of tumors), and are suitable for automated preparation and analysis.
PCT/US2001/009993 2000-03-28 2001-03-28 Gene profiling arrays WO2001073134A2 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
US19270000P true 2000-03-28 2000-03-28
US60/192,700 2000-03-28

Applications Claiming Priority (1)

Application Number Priority Date Filing Date Title
AU5106901A AU5106901A (en) 2000-03-28 2001-03-28 Gene profiling arrays

Publications (2)

Publication Number Publication Date
WO2001073134A2 WO2001073134A2 (en) 2001-10-04
WO2001073134A3 true WO2001073134A3 (en) 2003-01-16

Family

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Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2001/009993 WO2001073134A2 (en) 2000-03-28 2001-03-28 Gene profiling arrays

Country Status (2)

Country Link
AU (1) AU5106901A (en)
WO (1) WO2001073134A2 (en)

Cited By (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7771934B2 (en) 2000-12-13 2010-08-10 Nugen Technologies, Inc. Methods and compositions for generation of multiple copies of nucleic acid sequences and methods of detection thereof
US7771946B2 (en) 2001-03-09 2010-08-10 Nugen Technologies, Inc. Methods, kits and compositions for single primer linear isothermal amplification of nucleic acid sequences
US7846666B2 (en) 2008-03-21 2010-12-07 Nugen Technologies, Inc. Methods of RNA amplification in the presence of DNA
US7846733B2 (en) 2000-06-26 2010-12-07 Nugen Technologies, Inc. Methods and compositions for transcription-based nucleic acid amplification
US7939258B2 (en) 2005-09-07 2011-05-10 Nugen Technologies, Inc. Nucleic acid amplification procedure using RNA and DNA composite primers
US8034568B2 (en) 2008-02-12 2011-10-11 Nugen Technologies, Inc. Isothermal nucleic acid amplification methods and compositions
US8465950B2 (en) 2003-04-14 2013-06-18 Nugen Technologies, Inc. Global amplification using a randomly primed composite primer

Families Citing this family (10)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
AT455186T (en) * 2000-06-26 2010-01-15 Nugen Technologies Inc Methods and compositions for on transcription-based amplification of nucleic acids
US6794141B2 (en) 2000-12-22 2004-09-21 Arcturus Bioscience, Inc. Nucleic acid amplification
TWI335938B (en) * 2001-08-15 2011-01-11 Rna replication and amplification
CA2477670A1 (en) * 2002-03-15 2003-09-25 Arcturus Bioscience, Inc. Improved nucleic acid amplification
EP1371726A1 (en) * 2002-06-14 2003-12-17 Rijksuniversiteit Groningen Method for amplifying RNA
DE10393431T5 (en) * 2002-10-01 2005-11-17 Nimblegen Systems, Inc., Madison Microarrays with several oligonucleotides into single array features
GB0319332D0 (en) * 2003-08-16 2003-09-17 Astrazeneca Ab Amplification
NL1026335C2 (en) * 2004-06-04 2005-12-06 Univ Delft Tech A method for making a double-stranded polyribonucleotide sequence with terminal overhang, as well as a method of forming a double-stranded polynucleotidenconstruct and an application.
EP2607496B1 (en) 2008-12-23 2014-07-16 Illumina, Inc. Methods useful in nucleic acid sequencing protocols
EP3141613A1 (en) 2015-09-11 2017-03-15 Nederlandse Organisatie voor toegepast- natuurwetenschappelijk onderzoek TNO Detection of quality of surface water

Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1997024455A2 (en) * 1996-01-03 1997-07-10 Clontech Laboratories, Inc. METHODS AND COMPOSITIONS FOR FULL-LENGTH cDNA CLONING
WO1998055502A1 (en) * 1997-06-04 1998-12-10 Smithkline Beecham Corporation METHODS FOR RAPID CLONING OF FULL LENGTH cDNAs
WO1999025873A1 (en) * 1997-11-19 1999-05-27 Incyte Pharmaceuticals, Inc. METHOD FOR UNBIASED mRNA AMPLIFICATION

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1997024455A2 (en) * 1996-01-03 1997-07-10 Clontech Laboratories, Inc. METHODS AND COMPOSITIONS FOR FULL-LENGTH cDNA CLONING
WO1998055502A1 (en) * 1997-06-04 1998-12-10 Smithkline Beecham Corporation METHODS FOR RAPID CLONING OF FULL LENGTH cDNAs
WO1999025873A1 (en) * 1997-11-19 1999-05-27 Incyte Pharmaceuticals, Inc. METHOD FOR UNBIASED mRNA AMPLIFICATION

Non-Patent Citations (4)

* Cited by examiner, † Cited by third party
Title
DUGGAN D J ET AL: "EXPRESSION PROFILING USING CDNA MICROARRAYS", NATURE GENETICS, NEW YORK, NY, US, vol. 21, no. SUPPL, January 1999 (1999-01-01), pages 10 - 14, XP000865980, ISSN: 1061-4036 *
SCHMIDT W.M. ET AL.,: "Capselect:a high sensitive method for 5'cap-dependent enrichment of full-length cDNA in PCR-mediate analysis of mRNAs", NUCLEIC ACID RESEARCH, vol. 27, no. 12, - 1999, pages e31, XP002211678 *
WANG ENA ET AL.,: "high-fidelity mRNA amplification for gene profiling", NATURE BIOTECHNOLOGY, vol. 18, - April 2000 (2000-04-01), pages 457 - 459, XP002211679 *
ZHAO N ET AL: "High-density cDNA filter analysis: a novel approach for large-scale, quantitative analysis of gene expression", GENE, ELSEVIER BIOMEDICAL PRESS. AMSTERDAM, NL, vol. 156, no. 2, 1995, pages 207 - 213, XP004042356, ISSN: 0378-1119 *

Cited By (12)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7846733B2 (en) 2000-06-26 2010-12-07 Nugen Technologies, Inc. Methods and compositions for transcription-based nucleic acid amplification
US7771934B2 (en) 2000-12-13 2010-08-10 Nugen Technologies, Inc. Methods and compositions for generation of multiple copies of nucleic acid sequences and methods of detection thereof
US8334116B2 (en) 2000-12-13 2012-12-18 Nugen Technologies, Inc. Methods and compositions for generation of multiple copies of nucleic acid sequences and methods of detection thereof
US9181582B2 (en) 2001-03-09 2015-11-10 Nugen Technologies, Inc. Compositions for amplification of RNA sequences using composite primers
US8071311B2 (en) 2001-03-09 2011-12-06 Nugen Technologies, Inc. Methods and compositions for amplification of RNA sequences
US7771946B2 (en) 2001-03-09 2010-08-10 Nugen Technologies, Inc. Methods, kits and compositions for single primer linear isothermal amplification of nucleic acid sequences
US8465950B2 (en) 2003-04-14 2013-06-18 Nugen Technologies, Inc. Global amplification using a randomly primed composite primer
US9175325B2 (en) 2003-04-14 2015-11-03 Nugen Technologies, Inc. Global amplification using a randomly primed composite primer
US8852867B2 (en) 2005-09-07 2014-10-07 Nugen Technologies, Inc. Nucleic acid amplification procedure using RNA and DNA composite primers
US7939258B2 (en) 2005-09-07 2011-05-10 Nugen Technologies, Inc. Nucleic acid amplification procedure using RNA and DNA composite primers
US8034568B2 (en) 2008-02-12 2011-10-11 Nugen Technologies, Inc. Isothermal nucleic acid amplification methods and compositions
US7846666B2 (en) 2008-03-21 2010-12-07 Nugen Technologies, Inc. Methods of RNA amplification in the presence of DNA

Also Published As

Publication number Publication date
AU5106901A (en) 2001-10-08
WO2001073134A2 (en) 2001-10-04

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