Mapping and chromosome analysis: the potential of fluorescence in situ hybridization

Joos, Stefan; Fink, Thomas; Rätsch, Andreas; Lichter, Peter

doi:10.1016/0168-1656(94)90032-9

Cited by 45 publications

(33 citation statements)

References 97 publications

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“…D uring the past decade, fluorescence in situ hybridization (FISH) techniques have been shown to be important tools in a variety of molecular genetic and cell biological approaches (for reviews see Trask 1991;McNeil et al 1991;Tkachuk et al 1991;Joos et al 1994;Dirks 1996). Both direct and indirect FISH techniques are available to detect the nucleic acid target of choice (Speel et al 1995).…”

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confidence: 99%

Sensitive Multicolor Fluorescence In Situ Hybridization Using Catalyzed Reporter Deposition (CARD) Amplification

Speel

Ramaekers

Hopman

1997

J Histochem Cytochem.

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SUMMARYWe describe the simultaneous localization of DNA sequences in cell and chromosome preparations by means of differently fluorochrome-labeled (AMCA, FITC, TRITC) tyramides using the catalyzed reporter deposition (CARD) procedure. For this purpose, repeated as well as single-copy DNA probes were labeled with biotin, digoxigenin, and FITC, hybridized, and visualized with three different cytochemical detection systems based on horseradish peroxidase conjugates. These were sequentially applied to interphase nuclei and metaphase chromosomes at low concentrations to prevent crossreaction and nonspecific background. In situ localized peroxidase activity was visualized by the deposition of fluorochrome-labeled tyramide molecules. To allow specific deposition of a second and a third tyramide conjugate for multiple-target fluorescence in situ hybridization (FISH), remaining peroxidase activity was always completely inactivated by a mild acid treatment before application of the next peroxidase conjugate. The CARD reactions were optimized for maximal signal-to-noise ratio and discrete localization by tuning reaction time, H 2 O 2 , and tyramide concentrations. For both repeated and single-copy DNA targets, high FISH signal intensities were obtained, providing improvement of sensitivity over conventional indirect detection systems. In addition, the fluorescence CARD detection system proved to be highly efficient and easy to implement in multiple-labeling studies, such as reported here for FISH.

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confidence: 99%

Sensitive Multicolor Fluorescence In Situ Hybridization Using Catalyzed Reporter Deposition (CARD) Amplification

Speel

Ramaekers

Hopman

1997

J Histochem Cytochem.

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“…Other fields of application will be important in the future for the control of the quality of the bioproducts: different systems are already proposed on a commercial basis for the quantification of electrophoresis gels, but developments are under way also for automatic DNA fingerprinting and Fluorescence In-Situ Hybridization (FISH) [216][217][218][219].…”

Section: Discussionmentioning

confidence: 99%

Biomass Quantification by Image Analysis

Pons

Vivier

1999

Bioanalysis and Biosensors for Bioprocess Monitoring

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Microbiologists have always rely on microscopy to examine microorganisms. When microscopy, either optical or electron-based, is coupled to quantitative image analysis, the spectrum of potential applications is widened: counting, sizing, shape characterization, physiology assessment, analysis of visual texture, motility studies are now easily available for obtaining information on biomass. In this chapter the main tools used for cell visualization as well as the basic steps of image treatment are presented. General shape descriptors can be used to characterize the cell morphology, but special descriptors have been defined for filamentous microorganisms. Physiology assessment is often based on the use of fluorescent dyes. The quantitative analysis of visual texture is still limited in bioengineering but the characterization of the surface of microbial colonies may open new prospects, especially for cultures on solid substrates. In many occasions, the number of parameters extracted from images is so large that data-mining tools, such as Principal Components Analysis, are useful for summarizing the key pieces of information.

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“…Clone-based laboratory methods maintain importance in the study of large genomes through applications such as fluorescent in situ hybridization (FISH; du Manoir et al 1993;Joos et al 1994;Levsky and Singer 2003) and comparative genomic hybridization (CGH; Kallioniemi et al 1992;Houldsworth and Chaganti 1994;Lapierre et al 1998;Pinkel et al 1998;Snijders et al 2001;Fiegler et al 2003). The generation of high-depth fingerprint maps will therefore continue to be a desired component of the generation of integrated genomic resources.…”

Section: Discussionmentioning

confidence: 99%

Integrated and Sequence-Ordered BAC- and YAC-Based Physical Maps for the Rat Genome

Krzywinski¹,

Wallis²,

Gösele³

et al. 2004

Genome Res.

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As part of the effort to sequence the genome of Rattus norvegicus, we constructed a physical map comprised of fingerprinted bacterial artificial chromosome (BAC) clones from the CHORI-230 BAC library. These BAC clones provide ∼13-fold redundant coverage of the genome and have been assembled into 376 fingerprint contigs. A yeast artificial chromosome (YAC) map was also constructed and aligned with the BAC map via fingerprinted BAC and P1 artificial chromosome clones (PACs) sharing interspersed repetitive sequence markers with the YAC-based physical map. We have annotated 95% of the fingerprint map clones in contigs with coordinates on the version 3.1 rat genome sequence assembly, using BAC-end sequences and in silico mapping methods. These coordinates have allowed anchoring 358 of the 376 fingerprint map contigs onto the sequence assembly. Of these, 324 contigs are anchored to rat genome sequences localized to chromosomes, and 34 contigs are anchored to unlocalized portions of the rat sequence assembly. The remaining 18 contigs, containing 54 clones, still require placement. The fingerprint map is a high-resolution integrative data resource that provides genome-ordered associations among BAC, YAC, and PAC clones and the assembled sequence of the rat genome.

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Mapping and chromosome analysis: the potential of fluorescence in situ hybridization

Cited by 45 publications

References 97 publications

Sensitive Multicolor Fluorescence In Situ Hybridization Using Catalyzed Reporter Deposition (CARD) Amplification

Sensitive Multicolor Fluorescence In Situ Hybridization Using Catalyzed Reporter Deposition (CARD) Amplification

Biomass Quantification by Image Analysis

Integrated and Sequence-Ordered BAC- and YAC-Based Physical Maps for the Rat Genome

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