Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

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,...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Phase 2 dose-expansion trial of OBI-3424, a DNA-alkylating prodrug, in patients with advanced solid tumors expressing AKR1C3.

The oncologist·2026

Same author

Genomic Characterization of Classic Adamantinoma, Osteofibrous Dysplasia, and Osteofibrous Dysplasia-like Adamantinoma.

Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc·2026

Same author

Dose-Expansion Study of OBI-999, a Globo H-Targeting Antibody-Drug Conjugate, in Patients with Advanced Solid Tumors.

The oncologist·2026

Same author

Influence of climate variability and seasonal trends on malaria incidence in Dar es Salaam, Tanzania using generalized additive models.

Epidemiology and infection·2026

Same author

Application of Hi-C sequencing to detect oncogene rearrangements for diagnosis and treatment of large B-cell lymphoma.

Blood advances·2026

Same author

Low-Dose Vemurafenib Plus Rituximab in Front-Line and Relapsed or Refractory Hairy Cell Leukemia: The Scripps Regimen.

Blood advances·2026

Search research articles

Related Experiment Video

Updated: May 24, 2025

Author Spotlight: FISH as a Tool for Precise Gene Amplification Assessment in Cancer Specimens

Author Spotlight: FISH as a Tool for Precise Gene Amplification Assessment in Cancer Specimens

Published on: July 12, 2024

Detection of Gene Fusions and Rearrangements in Formalin-Fixed, Paraffin-Embedded Solid Tumor Specimens Using

Kristyn Galbraith¹, Jamin Wu¹, Kristin Sikkink²

¹Department of Pathology, NYU Langone Health, and NYU Grossman School of Medicine, New York, New York.

The Journal of Molecular Diagnostics : JMD

|March 1, 2025

Summary

High-throughput chromosome conformation capture (Hi-C) accurately detects cancer-driving chromosomal structural variants (SVs) in FFPE tissues. This DNA-based method surpasses RNA-based approaches, revealing novel SVs and actionable biomarkers.

More Related Videos

Oncogenic Gene Fusion Detection Using Anchored Multiplex Polymerase Chain Reaction Followed by Next Generation Sequencing

Oncogenic Gene Fusion Detection Using Anchored Multiplex Polymerase Chain Reaction Followed by Next Generation Sequencing

Published on: July 5, 2019

Chromosomics: Detection of Numerical and Structural Alterations in All 24 Human Chromosomes Simultaneously Using a Novel OctoChrome FISH Assay

Chromosomics: Detection of Numerical and Structural Alterations in All 24 Human Chromosomes Simultaneously Using a Novel OctoChrome FISH Assay

Published on: February 6, 2012

Related Experiment Videos

Last Updated: May 24, 2025

Author Spotlight: FISH as a Tool for Precise Gene Amplification Assessment in Cancer Specimens

Author Spotlight: FISH as a Tool for Precise Gene Amplification Assessment in Cancer Specimens

Published on: July 12, 2024

Oncogenic Gene Fusion Detection Using Anchored Multiplex Polymerase Chain Reaction Followed by Next Generation Sequencing

Oncogenic Gene Fusion Detection Using Anchored Multiplex Polymerase Chain Reaction Followed by Next Generation Sequencing

Published on: July 5, 2019

Chromosomics: Detection of Numerical and Structural Alterations in All 24 Human Chromosomes Simultaneously Using a Novel OctoChrome FISH Assay

Chromosomics: Detection of Numerical and Structural Alterations in All 24 Human Chromosomes Simultaneously Using a Novel OctoChrome FISH Assay

Published on: February 6, 2012

Area of Science:

Genomics
Cancer Biology
Molecular Diagnostics

Background:

Chromosomal structural variants (SVs) are key drivers of cancer development.
Existing SV detection methods have limitations, including low throughput and reliance on RNA, which is degraded in FFPE samples and cannot detect non-fusion SVs.

Purpose of the Study:

To evaluate the efficacy of high-throughput chromosome conformation capture (Hi-C) for genome-wide SV analysis in formalin-fixed, paraffin-embedded (FFPE) tumor tissues.
To compare Hi-C performance against established clinical methods like FISH and RNA NGS.
To identify novel SVs and potential therapeutic targets in FFPE samples.

Main Methods:

Retrospective analysis of 71 FFPE specimens from 10 solid tumor types using Hi-C, a DNA-based next-generation sequencing (NGS) method.
Comparison of Hi-C results with clinical FISH and RNA NGS data.
Analysis of SV formation mechanisms and clinical actionability.

Main Results:

Hi-C demonstrated high concordance (98%) with clinical FISH and RNA NGS for known SV detection.
Hi-C identified SV formation mechanisms (e.g., chromothripsis, extrachromosomal DNA) and intergenic rearrangements missed by RNA NGS.
SV drivers were detected in 71% of cases where prior clinical methods failed, with 14% being clinically actionable and another 14% involving targetable biomarkers.

Conclusions:

Hi-C is a robust and accurate method for comprehensive SV analysis in FFPE tissues.
Hi-C can uncover previously undetected SVs and mechanisms of cancer development.
Hi-C has the potential to be integrated into clinical NGS workflows for improved cancer diagnostics and treatment strategies.