WO2002000940A3 - Image analysis for phenotyping sets of mutant cells - Google Patents

Image analysis for phenotyping sets of mutant cells Download PDF

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Publication number
WO2002000940A3
WO2002000940A3 PCT/US2001/020136 US0120136W WO0200940A3 WO 2002000940 A3 WO2002000940 A3 WO 2002000940A3 US 0120136 W US0120136 W US 0120136W WO 0200940 A3 WO0200940 A3 WO 0200940A3
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WO
WIPO (PCT)
Prior art keywords
features
quantitative
phenotype
phenotyping
sets
Prior art date
Application number
PCT/US2001/020136
Other languages
French (fr)
Other versions
WO2002000940A2 (en
WO2002000940A9 (en
Inventor
Corey E Nislow
Nolan H Sigal
David G Drubin
Cynthia L Adams
Original Assignee
Cytokinetics Inc
Corey E Nislow
Nolan H Sigal
David G Drubin
Cynthia L Adams
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 Cytokinetics Inc, Corey E Nislow, Nolan H Sigal, David G Drubin, Cynthia L Adams filed Critical Cytokinetics Inc
Priority to EP01948675A priority Critical patent/EP1322788A2/en
Priority to AU2001270126A priority patent/AU2001270126A1/en
Publication of WO2002000940A2 publication Critical patent/WO2002000940A2/en
Publication of WO2002000940A3 publication Critical patent/WO2002000940A3/en
Publication of WO2002000940A9 publication Critical patent/WO2002000940A9/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1079—Screening libraries by altering the phenotype or phenotypic trait of the host
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries

Abstract

A method described herein phenotypes a set of mutant strains in a quantitative manner. Specifically, the method characterizes a cellular and subcellular architecture of mutant alleles grown in a variety of conditions using various morphological and molecular markers, combined with automated image acquisition and analysis. Phenotypic features may include the cytoskeleton, organelles, cell morphology, DNA replication state, the relationship of these features to each other, etc. From these features a quantitative 'fingerprint' can be generated for each phenotype. This quantitative phenotypic information is made available in a database that links geneotype to phenotype. Genes characterized in this manner may be clustered into functional categories, pathways, higher order protein assemblies, and the like.
PCT/US2001/020136 2000-06-23 2001-06-22 Image analysis for phenotyping sets of mutant cells WO2002000940A2 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
EP01948675A EP1322788A2 (en) 2000-06-23 2001-06-22 Image analysis for phenotyping sets of mutant cells
AU2001270126A AU2001270126A1 (en) 2000-06-23 2001-06-22 Image analysis for phenotyping sets of mutant cells

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US21385000P 2000-06-23 2000-06-23
US60/213,850 2000-06-23

Publications (3)

Publication Number Publication Date
WO2002000940A2 WO2002000940A2 (en) 2002-01-03
WO2002000940A3 true WO2002000940A3 (en) 2003-04-24
WO2002000940A9 WO2002000940A9 (en) 2003-07-03

Family

ID=22796742

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2001/020136 WO2002000940A2 (en) 2000-06-23 2001-06-22 Image analysis for phenotyping sets of mutant cells

Country Status (4)

Country Link
US (1) US20020049544A1 (en)
EP (1) EP1322788A2 (en)
AU (1) AU2001270126A1 (en)
WO (1) WO2002000940A2 (en)

Families Citing this family (11)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US8032346B1 (en) 2002-08-28 2011-10-04 Rigel Pharmaceuticals, Inc. System and method for high-content oncology assay
US7970549B1 (en) 2002-08-28 2011-06-28 Rigel Pharmaceuticals Inc. System and method for high-content oncology assay
WO2005010677A2 (en) * 2003-07-18 2005-02-03 Cytokinetics, Inc. Characterizing biological stimuli by response curves
US20050246105A1 (en) * 2004-01-28 2005-11-03 Vance Faber Interpolated image response
US8009889B2 (en) 2006-06-27 2011-08-30 Affymetrix, Inc. Feature intensity reconstruction of biological probe array
US8165663B2 (en) 2007-10-03 2012-04-24 The Invention Science Fund I, Llc Vasculature and lymphatic system imaging and ablation
US8285367B2 (en) 2007-10-05 2012-10-09 The Invention Science Fund I, Llc Vasculature and lymphatic system imaging and ablation associated with a reservoir
US8285366B2 (en) 2007-10-04 2012-10-09 The Invention Science Fund I, Llc Vasculature and lymphatic system imaging and ablation associated with a local bypass
JP5695639B2 (en) * 2009-06-01 2015-04-08 アミリス， インコーポレイテッド Method for producing genetically modified microorganism
US11074433B2 (en) * 2016-12-12 2021-07-27 Nec Corporation Information processing apparatus, genetic information generation method and program
CN113486849A (en) * 2021-07-27 2021-10-08 哈尔滨工业大学 Method for identifying spatial mutation rice phenotype change

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5235522A (en) * 1990-10-10 1993-08-10 Cell Analysis Systems, Inc. Method and apparatus for automated analysis of biological specimens
WO1998045704A2 (en) * 1997-04-07 1998-10-15 Bioimage A/S A method for extracting quantitative information relating to an influence on a cellular response

Family Cites Families (41)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US577888A (en) * 1897-03-02 thomas
SE455736B (en) * 1984-03-15 1988-08-01 Sarastro Ab PROCEDURE KIT AND MICROPHOTOMETRATION AND ADDITIONAL IMAGE COMPOSITION
EP0184600B1 (en) * 1984-12-10 1990-03-14 Prutec Limited Method for optically ascertaining parameters of species in a liquid analyte
US4922092A (en) * 1986-11-26 1990-05-01 Image Research Limited High sensitivity optical imaging apparatus
US4965725B1 (en) * 1988-04-08 1996-05-07 Neuromedical Systems Inc Neural network based automated cytological specimen classification system and method
US4959301A (en) * 1988-04-22 1990-09-25 Massachusetts Institute Of Technology Process for rapidly enumerating viable entities
US5162990A (en) * 1990-06-15 1992-11-10 The United States Of America As Represented By The United States Navy System and method for quantifying macrophage phagocytosis by computer image analysis
US5784162A (en) * 1993-08-18 1998-07-21 Applied Spectral Imaging Ltd. Spectral bio-imaging methods for biological research, medical diagnostics and therapy
US5991028A (en) * 1991-02-22 1999-11-23 Applied Spectral Imaging Ltd. Spectral bio-imaging methods for cell classification
US5548661A (en) * 1991-07-12 1996-08-20 Price; Jeffrey H. Operator independent image cytometer
US5790710A (en) * 1991-07-12 1998-08-04 Jeffrey H. Price Autofocus system for scanning microscopy
US5655028A (en) * 1991-12-30 1997-08-05 University Of Iowa Research Foundation Dynamic image analysis system
US5355215A (en) * 1992-09-30 1994-10-11 Environmental Research Institute Of Michigan Method and apparatus for quantitative fluorescence measurements
US5733721A (en) * 1992-11-20 1998-03-31 The Board Of Regents Of The University Of Oklahoma Cell analysis method using quantitative fluorescence image analysis
US5776748A (en) * 1993-10-04 1998-07-07 President And Fellows Of Harvard College Method of formation of microstamped patterns on plates for adhesion of cells and other biological materials, devices and uses therefor
US5932872A (en) * 1994-07-01 1999-08-03 Jeffrey H. Price Autofocus system for scanning microscopy having a volume image formation
US5790692A (en) * 1994-09-07 1998-08-04 Jeffrey H. Price Method and means of least squares designed filters for image segmentation in scanning cytometry
US5768412A (en) * 1994-09-19 1998-06-16 Hitachi, Ltd. Region segmentation method for particle images and apparatus thereof
US5902732A (en) * 1995-10-04 1999-05-11 Cytoscan Sciences Llc Drug screening process measuring changes in cell volume
US5893095A (en) * 1996-03-29 1999-04-06 Virage, Inc. Similarity engine for content-based retrieval of images
US6103479A (en) * 1996-05-30 2000-08-15 Cellomics, Inc. Miniaturized cell array methods and apparatus for cell-based screening
US5989835A (en) * 1997-02-27 1999-11-23 Cellomics, Inc. System for cell-based screening
US5804436A (en) * 1996-08-02 1998-09-08 Axiom Biotechnologies, Inc. Apparatus and method for real-time measurement of cellular response
US6008010A (en) * 1996-11-01 1999-12-28 University Of Pittsburgh Method and apparatus for holding cells
WO1998029736A1 (en) * 1996-12-31 1998-07-09 Genometrix Incorporated Multiplexed molecular analysis apparatus and method
US5995143A (en) * 1997-02-07 1999-11-30 Q3Dm, Llc Analog circuit for an autofocus microscope system
US6416959B1 (en) * 1997-02-27 2002-07-09 Kenneth Giuliano System for cell-based screening
US6169816B1 (en) * 1997-05-14 2001-01-02 Applied Imaging, Inc. Identification of objects of interest using multiple illumination schemes and finding overlap of features in corresponding multiple images
AU8846498A (en) * 1997-08-07 1999-03-01 Imaging Research, Inc. A digital imaging system for assays in well plates, gels and blots
US5962250A (en) * 1997-10-28 1999-10-05 Glaxo Group Limited Split multi-well plate and methods
US5962520A (en) * 1998-04-02 1999-10-05 The University Of Akron Hydrolytically unstable, biocompatible polymer
US6518035B1 (en) * 1998-06-02 2003-02-11 Rosetta Inpharmatics, Inc. Targeted methods of drug screening using co-culture methods
US6146830A (en) * 1998-09-23 2000-11-14 Rosetta Inpharmatics, Inc. Method for determining the presence of a number of primary targets of a drug
US6222093B1 (en) * 1998-12-28 2001-04-24 Rosetta Inpharmatics, Inc. Methods for determining therapeutic index from gene expression profiles
US7151847B2 (en) * 2001-02-20 2006-12-19 Cytokinetics, Inc. Image analysis of the golgi complex
US20030228565A1 (en) * 2000-04-26 2003-12-11 Cytokinetics, Inc. Method and apparatus for predictive cellular bioinformatics
US6743576B1 (en) * 1999-05-14 2004-06-01 Cytokinetics, Inc. Database system for predictive cellular bioinformatics
US6651008B1 (en) * 1999-05-14 2003-11-18 Cytokinetics, Inc. Database system including computer code for predictive cellular bioinformatics
US6599694B2 (en) * 2000-12-18 2003-07-29 Cytokinetics, Inc. Method of characterizing potential therapeutics by determining cell-cell interactions
US6956961B2 (en) * 2001-02-20 2005-10-18 Cytokinetics, Inc. Extracting shape information contained in cell images
US6658143B2 (en) * 2002-04-29 2003-12-02 Amersham Biosciences Corp. Ray-based image analysis for biological specimens

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5235522A (en) * 1990-10-10 1993-08-10 Cell Analysis Systems, Inc. Method and apparatus for automated analysis of biological specimens
WO1998045704A2 (en) * 1997-04-07 1998-10-15 Bioimage A/S A method for extracting quantitative information relating to an influence on a cellular response

Non-Patent Citations (4)

* Cited by examiner, † Cited by third party
Title
BRACHAT A ET AL: "Analysis of deletion phenotypes and GFP fusions of 21 novel Saccharomyces cerevisiae open reading frames", YEAST - YEAST FUNCTIONAL ANALYSIS REPORT, vol. 16, no. 3, 24 February 2000 (2000-02-24), XP002226049, Retrieved from the Internet <URL:http://www3.interscience.wiley.com/cgi-bin/issuetoc?ID=70001680> [retrieved on 20021220] *
RONCERO C ET AL: "Isolation and Characterization of Saccharomyces cerevisiae Mutants Resistant to Calcofuor White", JOURNAL OF BACTERIOLOGY, vol. 170, no. 4, April 1988 (1988-04-01), pages 1950 - 1954, XP008011949 *
ROSS-MACDONALD P ET AL: "Large-scale analysis of the yeast genome by transposon tagging and gene disruption", NATURE, vol. 402, 25 November 1999 (1999-11-25), pages 413 - 418, XP002226050, Retrieved from the Internet <URL:http://bioinfo.mbb.yale.edu/e-print/genome-transposon-nature/text.pdf> [retrieved on 20021217] *
WINZELER E A ET AL: "FUNCTIONAL CHARACTERIZATION OF THE S. CEREVISIAE GENOME BY GENE DELETION AND PARALLEL ANALYSIS", SCIENCE, AMERICAN ASSOCIATION FOR THE ADVANCEMENT OF SCIENCE, NEW YORK, US, vol. 285, no. 5429, 6 August 1999 (1999-08-06), pages 901 - 906, XP001025980, ISSN: 0036-8075 *

Also Published As

Publication number Publication date
WO2002000940A2 (en) 2002-01-03
WO2002000940A9 (en) 2003-07-03
US20020049544A1 (en) 2002-04-25
EP1322788A2 (en) 2003-07-02
AU2001270126A1 (en) 2002-01-08

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