WO2001020044A3 - Signal counting for in situ hybridization - Google Patents

Signal counting for in situ hybridization Download PDF

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Publication number
WO2001020044A3
WO2001020044A3 PCT/US2000/025465 US0025465W WO0120044A3 WO 2001020044 A3 WO2001020044 A3 WO 2001020044A3 US 0025465 W US0025465 W US 0025465W WO 0120044 A3 WO0120044 A3 WO 0120044A3
Authority
WO
WIPO (PCT)
Prior art keywords
signals
probe
spots
counted
various features
Prior art date
Application number
PCT/US2000/025465
Other languages
French (fr)
Other versions
WO2001020044A2 (en
Inventor
Olli P Kallioniemi
Juha Kononen
Lukas Budendorf
Edward R Dougherty
Artyom M Grigoryan
Original Assignee
Us Health
Olli P Kallioniemi
Juha Kononen
Lukas Budendorf
Edward R Dougherty
Artyom M Grigoryan
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 Us Health, Olli P Kallioniemi, Juha Kononen, Lukas Budendorf, Edward R Dougherty, Artyom M Grigoryan filed Critical Us Health
Priority to AU74949/00A priority Critical patent/AU7494900A/en
Publication of WO2001020044A2 publication Critical patent/WO2001020044A2/en
Publication of WO2001020044A3 publication Critical patent/WO2001020044A3/en

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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
    • 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
    • C12Q1/6816—Hybridisation assays characterised by the detection means
    • 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
    • C12Q1/6841—In situ hybridisation
    • G01N15/1433—
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06V—IMAGE OR VIDEO RECOGNITION OR UNDERSTANDING
    • G06V20/00—Scenes; Scene-specific elements
    • G06V20/60—Type of objects
    • G06V20/69—Microscopic objects, e.g. biological cells or cellular parts
    • G06V20/695—Preprocessing, e.g. image segmentation

Abstract

Fluorescently tagged nucleic acid probe signals are counted in biological specimens by determining a ratio of signals from a test probe to signals of a reference probe. Probe signals need not be counted with reference to cells, nuclei, or nuclear contours. Gene amplification or deletion can thus be detected by analyzing the ratio. Successive image slices are obtained by confocal microscopy, and the images are digitized. The digital images are transformed and analyzed to combine contiguous fluorescent signal segments in successive optical sections to identify discrete probe signals, or spots. Spots overlapping in the axial and transverse dimensions of a three-dimensional representation of the biological specimens can be distinguisghed. A graphical user interface presents various features for consideration by a user, who can provide guidance to a computer system counting the spots. Various features directed to identifying spot clusters and autofluorescent material can increase accuracy of spot counting.
PCT/US2000/025465 1999-09-17 2000-09-15 Signal counting for in situ hybridization WO2001020044A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU74949/00A AU7494900A (en) 1999-09-17 2000-09-15 Signal counting for in situ hybridization

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US15460199P 1999-09-17 1999-09-17
US60/154,601 1999-09-17

Publications (2)

Publication Number Publication Date
WO2001020044A2 WO2001020044A2 (en) 2001-03-22
WO2001020044A3 true WO2001020044A3 (en) 2002-05-10

Family

ID=22551987

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2000/025465 WO2001020044A2 (en) 1999-09-17 2000-09-15 Signal counting for in situ hybridization

Country Status (2)

Country Link
AU (1) AU7494900A (en)
WO (1) WO2001020044A2 (en)

Families Citing this family (19)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7219016B2 (en) 2001-04-20 2007-05-15 Yale University Systems and methods for automated analysis of cells and tissues
FR2826977B1 (en) * 2001-07-03 2004-07-16 Imstar S A METHOD AND SYSTEM FOR DETECTING INTER-CHROMOSOMAL IMBALANCE BY IN SITU HYBRIDIZATION OF FLUORESCENT PROBES (FISH) ON INTERPHASE CELL CORES
WO2004113922A2 (en) 2003-06-19 2004-12-29 Applied Precision, Llc System and method employing photokinetic techniques in cell biology imaging applications
US8068988B2 (en) 2003-09-08 2011-11-29 Ventana Medical Systems, Inc. Method for automated processing of digital images of tissue micro-arrays (TMA)
WO2005027015A2 (en) 2003-09-10 2005-03-24 Bioimagene, Inc. Method and system for quantitatively analyzing biological samples
WO2005076216A2 (en) * 2004-02-03 2005-08-18 Bioimagene, Inc. Method and system for automaticed digital image based flourescent in situ hybridization (fish) analysis
US8367351B2 (en) 2006-05-05 2013-02-05 Historx, Inc. Methods for determining signal transduction activity in tumors
EP2047262A4 (en) 2006-07-13 2011-03-16 Univ Yale Methods for making cancer prognoses based on the subcellular localization of biomarkers
GB0807466D0 (en) * 2008-04-24 2008-05-28 Univ Nottingham Trent Improvements relating to assays including a labelled reagent
JP5916991B2 (en) * 2010-11-09 2016-05-11 オリンパス株式会社 Methods for analyzing genetically abnormal cells
US8755580B2 (en) 2012-03-17 2014-06-17 Sony Corporation Flourescent dot counting in digital pathology images
WO2014043253A1 (en) * 2012-09-11 2014-03-20 Neogenomics Laboratories Automated fish reader using learning machines
US9042631B2 (en) 2013-01-24 2015-05-26 General Electric Company Method and systems for cell-level fish dot counting
US9488639B2 (en) * 2013-02-25 2016-11-08 Flagship Biosciences, Inc. Cell-based tissue analysis
JP7214756B2 (en) * 2018-05-15 2023-01-30 ベンタナ メディカル システムズ， インコーポレイテッド Quantification of signal in stain aggregates
CN111175267A (en) * 2020-01-18 2020-05-19 珠海圣美生物诊断技术有限公司 Cell interpretation method and system based on FISH technology
CN114463609B (en) * 2022-04-13 2022-07-05 珠海横琴圣澳云智科技有限公司 Method and device for determining fluorescent mixed points in cell microscopic image
CN114739970B (en) * 2022-06-09 2022-09-16 珠海横琴圣澳云智科技有限公司 Method and device for judging fluorescent signal point fracture
CN116144739A (en) * 2023-03-06 2023-05-23 中国医学科学院北京协和医院 Gene rearrangement signal recording method based on fluorescence in situ hybridization of separation probe

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5817462A (en) * 1995-02-21 1998-10-06 Applied Spectral Imaging Method for simultaneous detection of multiple fluorophores for in situ hybridization and multicolor chromosome painting and banding
WO1999044063A2 (en) * 1998-02-25 1999-09-02 The United States Of America, Represented By The Secretary, Department Of Health And Human Services Tumor tissue microarrays for rapid molecular profiling

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5817462A (en) * 1995-02-21 1998-10-06 Applied Spectral Imaging Method for simultaneous detection of multiple fluorophores for in situ hybridization and multicolor chromosome painting and banding
WO1999044063A2 (en) * 1998-02-25 1999-09-02 The United States Of America, Represented By The Secretary, Department Of Health And Human Services Tumor tissue microarrays for rapid molecular profiling

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
AUBELE ET AL.: "Comparative FISH analysis of numerical chromosome 7 abnormalities in 5-um and 15-um paraffin-embedded tissue sections from prostatic carcinoma", HISTOCHEMISTRY AND CELL BIOLOGY, vol. 107, no. 2, 1997, pages 121 - 126, XP001024090 *
RODENACKER ET AL.: "Groping for quantitative digital 3-D image analysis: an approach to quantitative fluorescence in situ hybridization in thick tissue sections of prostate carcinoma", ANALYTICAL CELLULAR PATHOLOGY, vol. 15, no. 1, 1997, pages 19 - 29, XP001024113 *

Also Published As

Publication number Publication date
WO2001020044A2 (en) 2001-03-22
AU7494900A (en) 2001-04-17

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