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FISH - Fluorescent In-situ Hybridization

FISH - Fluorescent In-situ Hybridization

Fluorescence in situ hybridization, or FISH, was developed in the early 1980s and has quickly become one of the most widely used techniques in cytogenetics. Labeled probes are used to bind complementary DNA or RNA sequences on a chromosome or in a region within a cell. Earlier, the probes could only be obtained by cloning or reverse transcription of a DNA template. Currently, the probe oligonucleotides can be synthesized synthetically. Additionally, with the advancement of optical techniques,...

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Updated: Jun 21, 2025

Robust 3D DNA FISH Using Directly Labeled Probes

Robust 3D DNA FISH Using Directly Labeled Probes

Published on: August 15, 2013

SnapFISH-IMPUTE: an imputation method for multiplexed DNA FISH data.

Hongyu Yu^1,2, Daiqing Wu³, Shreya Mishra⁴

¹Department of Statistics, University of Wisconsin-Madison, Madison, WI, USA.

Communications Biology

|July 9, 2024

Summary

This summary is machine-generated.

SnapFISH-IMPUTE addresses missing data in multiplexed DNA FISH, improving chromatin conformation analysis. This method accurately imputes missing values, enhancing downstream applications like enhancer-promoter loop identification.

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Last Updated: Jun 21, 2025

Robust 3D DNA FISH Using Directly Labeled Probes

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Genotyping and Quantification of In Situ Hybridization Staining in Zebrafish

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Published on: January 28, 2020

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Chromatin spatial organization is vital for gene regulation.
Multiplexed DNA FISH allows visualization of nuclear chromatin conformation.
Limited detection efficiency in FISH leads to incomplete data, hindering analysis.

Purpose of the Study:

To introduce SnapFISH-IMPUTE, a computational method for imputing missing values in multiplexed DNA FISH data.
To assess the accuracy and utility of SnapFISH-IMPUTE in analyzing chromatin conformation.

Main Methods:

Development of the SnapFISH-IMPUTE algorithm for data imputation.
Application and validation of SnapFISH-IMPUTE on multiple published multiplexed DNA FISH datasets.
Evaluation of the method's impact on downstream analyses.

Main Results:

SnapFISH-IMPUTE preserves the distribution of pairwise distances between imaging loci.
Imputed chromatin conformations are statistically indistinguishable from observed conformations.
Imputation significantly enhances the accuracy of identifying enhancer-promoter loops and cell type clustering.

Conclusions:

SnapFISH-IMPUTE effectively resolves data incompleteness in multiplexed DNA FISH.
The method improves the reliability and power of chromatin conformation studies.
SnapFISH-IMPUTE facilitates more robust downstream biological interpretations.