WO2001011082A3 - Methods of gene expression monitoring - Google Patents

Methods of gene expression monitoring Download PDF

Info

Publication number
WO2001011082A3
WO2001011082A3 PCT/US2000/021734 US0021734W WO0111082A3 WO 2001011082 A3 WO2001011082 A3 WO 2001011082A3 US 0021734 W US0021734 W US 0021734W WO 0111082 A3 WO0111082 A3 WO 0111082A3
Authority
WO
WIPO (PCT)
Prior art keywords
cells
expression profile
population
similarity
genes
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/US2000/021734
Other languages
French (fr)
Other versions
WO2001011082A2 (en
Inventor
Yanxiang Cao
Lubert Stryer
David Lockhart
Catherine G Dulac
Ian Tietjen
Jason Rihel
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.)
Affymetrix Inc
Harvard University
Original Assignee
Affymetrix Inc
Harvard University
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 Affymetrix Inc, Harvard University filed Critical Affymetrix Inc
Priority to EP00952685A priority Critical patent/EP1330539A2/en
Priority to AU65337/00A priority patent/AU6533700A/en
Priority to JP2001526844A priority patent/JP2003524412A/en
Publication of WO2001011082A2 publication Critical patent/WO2001011082A2/en
Anticipated expiration legal-status Critical
Publication of WO2001011082A3 publication Critical patent/WO2001011082A3/en
Ceased legal-status Critical Current

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
    • C12Q1/6809—Methods for determination or identification of nucleic acids involving differential detection

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Analytical Chemistry (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Microbiology (AREA)
  • Immunology (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)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

The invention provides methods of monitoring expression of a plurality of genes in a cell or small population of cells. Preferred methods entail contacting an array of probes with a population of nucleic acids derived from a population of fewer than 1000 cells then determining the relative hybridization of the probes to the population of nucleic acid as a measure of the relative representation of genes from the cells. The invention further provides methods of classifying cells. These preferred methods entail determining an expression profile of each of the plurality of cells then classifying the cells in clusters determined by similarity of expression profile. The invention further provides methods of monitoring differentiation of a cell lineage. These preferred methods entail determining an expression profile of each of a plurality of cells at different differentiation stages within the lineage. These cells can then be classified into clusters determined by similarity of expression profile. The clusters can then be ordered by similarity of expression profile. A time course of expression levels for each of the plurality of genes at different stages of differentiation in the cell lineage can then be determined.
PCT/US2000/021734 1999-08-09 2000-08-09 Methods of gene expression monitoring Ceased WO2001011082A2 (en)

Priority Applications (3)

Application Number Priority Date Filing Date Title
EP00952685A EP1330539A2 (en) 1999-08-09 2000-08-09 Methods of gene expression monitoring
AU65337/00A AU6533700A (en) 1999-08-09 2000-08-09 Methods of gene expression monitoring
JP2001526844A JP2003524412A (en) 1999-08-09 2000-08-09 Gene expression monitoring method

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US14808199P 1999-08-09 1999-08-09
US60/148,081 1999-08-09
US16092599P 1999-10-22 1999-10-22
US60/160,925 1999-10-22

Publications (2)

Publication Number Publication Date
WO2001011082A2 WO2001011082A2 (en) 2001-02-15
WO2001011082A3 true WO2001011082A3 (en) 2003-04-17

Family

ID=26845499

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2000/021734 Ceased WO2001011082A2 (en) 1999-08-09 2000-08-09 Methods of gene expression monitoring

Country Status (5)

Country Link
US (1) US20060292614A1 (en)
EP (1) EP1330539A2 (en)
JP (1) JP2003524412A (en)
AU (1) AU6533700A (en)
WO (1) WO2001011082A2 (en)

Families Citing this family (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6960439B2 (en) 1999-06-28 2005-11-01 Source Precision Medicine, Inc. Identification, monitoring and treatment of disease and characterization of biological condition using gene expression profiles
US6964850B2 (en) 2001-11-09 2005-11-15 Source Precision Medicine, Inc. Identification, monitoring and treatment of disease and characterization of biological condition using gene expression profiles
US20050048463A1 (en) * 2003-05-07 2005-03-03 Deng David Xing-Fei Systems and methods for determining cell type composition of mixed cell populations using gene expression signatures
KR100813263B1 (en) 2006-08-17 2008-03-13 삼성전자주식회사 Probe design method for target sequence detection and target sequence detection method using the probe
RU2709815C1 (en) * 2019-05-14 2019-12-23 Федеральное бюджетное учреждение науки "Нижегородский научно-исследовательский институт эпидемиологии и микробиологии им. академика И.Н. Блохиной" Федеральной службы по надзору в сфере защиты прав потребителей и благополучия человека Method of searching for molecular markers of a pathological process for differential diagnosis, monitoring and targeted therapy

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1999029877A1 (en) * 1997-12-12 1999-06-17 The Regents Of The University Of California Methods for defining cell types

Family Cites Families (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5861248A (en) * 1996-03-29 1999-01-19 Urocor, Inc. Biomarkers for detection of prostate cancer

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1999029877A1 (en) * 1997-12-12 1999-06-17 The Regents Of The University Of California Methods for defining cell types

Non-Patent Citations (6)

* Cited by examiner, † Cited by third party
Title
BOWTELL ET AL.: "Options available-from start to finish-for obtaining expression data by microarray", NATURE GENETICS, vol. 21, no. supplemental, January 1999 (1999-01-01), pages 25 - 32, XP000865983 *
BRADY ET AL.: "Analysis of gene expression in a complex differentiation hierarchy by global amplification of cDNA from single cells", CURRENT BIOLOGY, vol. 5, 1995, pages 909 - 922, XP001053242 *
BRAIL ET AL.: "Gene expression in individual cells: analysis using global single cell reverse transcription polymerase chain reaction (GSC RT-PCR)", MUTATION RESEARCH GENOMICS, vol. 406, no. 2-4, 1 August 1999 (1999-08-01), pages 45 - 54, XP001042375 *
DUGGAN ET AL.: "Expression profiling using cDNA microarrays", NATURE GENETICS, vol. 21, no. supplemental, January 1999 (1999-01-01), pages 10 - 14, XP000865980 *
LUO ET AL.: "Gene expression profiles of laser-captured adjacent neuronal subtypes", NATURE MEDICINE, vol. 5, no. 1, January 1999 (1999-01-01), pages 117 - 122, XP002187082 *
TOELLNER ET AL.: "The use of reverse transcription polymerase chain reaction to analyse large numbers of mRNA species from a single cell", JOURNAL OF IMMUNOLOGICAL METHODS, vol. 191, no. 1, 1996, pages 71 - 75, XP004020856 *

Also Published As

Publication number Publication date
AU6533700A (en) 2001-03-05
JP2003524412A (en) 2003-08-19
WO2001011082A2 (en) 2001-02-15
EP1330539A2 (en) 2003-07-30
US20060292614A1 (en) 2006-12-28

Similar Documents

Publication Publication Date Title
Granek et al. Environmental and genetic determinants of colony morphology in yeast
Vyas et al. Fission yeast Schizosaccharomyces pombe: a unicellular “micromammal” model organism
Heichinger et al. Genome-wide characterization of fission yeast DNA replication origins
Gerke et al. Natural isolates of Saccharomyces cerevisiae display complex genetic variation in sporulation efficiency
Klosinska et al. Yeast cells can access distinct quiescent states
Hughes et al. Mapping yeast transcriptional networks
Lugowski et al. DRUID: a pipeline for transcriptome-wide measurements of mRNA stability
DE69625920D1 (en) EXPRESSION DETECTION THROUGH HYBRIDIZATION ON OLIGONUCLEOTID ARRAYS HIGH CAPACITY
US20090138203A1 (en) Systems and methods for using molecular networks in genetic linkage analysis of complex traits
WO2001012851A3 (en) Identification of genetic markers of biological age and metabolism
MacAlpine et al. Replication and preferential inheritance of hypersuppressive petite mitochondrial DNA
CA2283261A1 (en) Methods for identifying nucleic acid sequences encoding agents that affect cellular phenotypes
DE69632716D1 (en) METHOD FOR DRUG EXAMINATION
Gawronski et al. Single cell transcriptomics of noncoding RNAs and their cell‐specificity
CN104899474A (en) Method and system for rectifying MB-seq methylation level based on ridge regression
Barsi et al. General approach for in vivo recovery of cell type-specific effector gene sets
WO2002016650A3 (en) Compositions and methods for exon profiling
WO2003004640A1 (en) Dna arrays for measuring sensitivity to anticancer agent
WO2001011082A3 (en) Methods of gene expression monitoring
EP1277842A3 (en) Method for quantifying nucleic acid by cell counting
Kawaguchi et al. Expression profiling of tetraploid mouse embryos in the developmental stages using a cDNA microarray analysis
Miller 13 Are Pleiotropic Mutations and Holocene Selective Sweeps the Only Evolutionary-genetic Processes Left for Explaining Heritable Variation in Human Psychological Traits?
Wang et al. Genetic evidence for ongoing balanced selection at human DNA repair genes ERCC8, FANCC, and RAD51C
WO2000058521A3 (en) Methods for the identification of reporter and target molecules using comprehensive gene expression profiles
Barnes et al. Genetical variation for enzyme activity in a population of Drosophila melanogaster

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 MZ 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)
WWE Wipo information: entry into national phase

Ref document number: 2000952685

Country of ref document: EP

REG Reference to national code

Ref country code: DE

Ref legal event code: 8642

WWP Wipo information: published in national office

Ref document number: 2000952685

Country of ref document: EP

WWW Wipo information: withdrawn in national office

Ref document number: 2000952685

Country of ref document: EP