Hi-C Technology Reveals Actionable Gene Fusions and Rearrangements in Diffuse Large B-Cell Lymphoma Unidentified by...

Area of Science:

• Genomics
• Molecular Diagnostics
• Oncology

Background:

• Fluorescence in situ hybridization (FISH) is a standard lymphoma diagnostic tool but has limitations in genomic coverage and identifying atypical fusion partners.
• These FISH limitations can lead to inconclusive diagnoses in complex lymphoma cases.
• Formalin-fixed paraffin-embedded (FFPE) samples present challenges for comprehensive genomic analysis.

Purpose of the Study:

• To evaluate a novel Hi-C-based sequencing assay for detecting gene fusions and rearrangements in FFPE lymphoma samples.
• To assess the utility of Hi-C in cases where conventional FISH was inconclusive or failed to detect expected biomarkers.
• To compare the diagnostic capabilities of Hi-C assay against standard FISH.

Main Methods:

• Analysis of five diffuse large B-cell lymphoma cases using both standard FISH and a Hi-C-based lymphoma assay.
• Standard FISH employed break-apart and dual-fusion probes for key lymphoma genes (MYC, BCL2, BCL6).
• Hi-C assay utilized high-resolution sequencing of FFPE tissue to map chromatin interactions and identify structural variations.

Main Results:

• The Hi-C assay detected additional structural variants beyond those identified by FISH in all five cases.
• Hi-C identified typical and atypical translocation partners, cryptic breakpoints, and novel genomic events (e.g., TP53 loss, KMT2A amplification).
• Whole-genome coverage by Hi-C enabled comprehensive profiling of complex rearrangements undetectable by FISH.

Conclusions:

• The Hi-C-based assay is a transformative diagnostic tool for lymphomas, overcoming FISH limitations.
• It provides unbiased, high-resolution detection of structural variations, enhancing diagnostic accuracy.
• This approach supports personalized therapeutic strategies and warrants further clinical validation.