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Updated: May 24, 2025
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.
Abstract:
Chromosomal structural variants (SVs) are major contributors to cancer development. Although multiple methods exist for detecting SVs, they are limited in throughput, such as fluorescent in situ hybridization and targeted panels, and use RNA, which degrades in formalin-fixed, paraffin-embedded (FFPE) blocks and is unable to detect SVs that do not produce a fusion transcript. High-throughput chromosome conformation capture (Hi-C) is a DNA-based next-generation sequencing (NGS) method that preserves the spatial conformation of the genome, capturing long-range genetic interactions and SVs. Herein, a retrospective study analyzing 71 FFPE specimens from 10 different solid tumors was performed. Results showed high concordance (98%) with clinical fluorescent in situ hybridization and RNA NGS in detecting known SVs. Furthermore, Hi-C provided insight into the mechanism of SV formation, including chromothripsis and extrachromosomal DNA, and detected rearrangements between genes and regulatory regions, all of which are undetectable by RNA NGS. Lastly, SVs were detected in 71% of cases in which previous clinical methods failed to identify a driver. Of these, 14% were clinically actionable based on current medical guidelines, and an additional 14% were not in medical guidelines but involve targetable biomarkers. Current data suggest that Hi-C is a robust and accurate method for genome-wide SV analyses from FFPE tissue and can be incorporated into current clinical NGS workflows.
Insights
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.
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.
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