Cytogenetic Advances in NHL Diagnosis by Leveraging Hi-C Sequencing
Reference:
Sikkink, et al.
AMP 2025 - Boston, MA
Abstract:
Introduction: Non-Hodgkin lymphoma (NHL) is a diverse group of more than 50 distinct neoplasms that originate from lymphocytes, including B cells, T cells, and natural killer cells. This heterogeneity is reflected in its wide range of morphological, clinical, and genetic features. NHL subtypes differ in their cellular origin, clinical presentation, prognosis, and response to treatment, making accurate classification essential for effective disease management. Clinical genetic testing often involves cytogenetic analysis of rearrangements by fluorescence in-situ hybridization (FISH); however, FISH testing is often performed using a panel of probes and analyzed through microscopy and manual image analysis for multiple target biomarkers. FISH probe selection is also often limited by a priori suspicion about the diagnosis and the availability of probes provided by the reference laboratory. Methods: Formalin-fixed, paraffin-embedded(FFPE) Hi-C sequencing from Arima Genomics represents a new, whole-genome sequencing-based clinical assay that enables whole-genome detection of chromosome rearrangements from routine FFPE clinical specimens. This study demonstrates the ability of FFPE-compatible Hi-C to detect clinically relevant rearrangements in samples to clarify diagnosis. Analysis of 15 lymphoma specimens was performed including high-grade B cell lymphoma (5), Burkitt lymphoma (2), follicular lymphoma (3), mantle cell lymphoma (3), and anaplastic large cell lymphoma (2). Results: Rearrangements that were detected by FISH were also detected by Hi-C(13/15 cases, 87%). In cases with variants not called during initial Hi-C, sequence read support was present but below threshold; deeper sequencing identified the rearrangements, suggesting that the specimen sequenced had alleles at very low variant allele frequency. Rearrangements not detected or tested for by FISH were also observed(targeted but missed by FISH [1/15, 7%], targeted but partner not resolved[7/15, 47%], not targeted but clinically relevant [4/15, 27%]). Hi-C detected rearrangements missed by FISH that were clinically significant, including those involving MYC, confirming a diagnosis of Burkitt lymphoma;DUSP22, confirming a diagnosis of ALK-negative anaplastic large cell lymphoma; and MYC and BCL2 rearrangements found in a diffuse large B cell lymphoma, prompting reconsideration of diagnosis to double-hit lymphoma. In a case suspected of mantle cell lymphoma, a CCND2rearrangement was detected, confirming that diagnosis. Conclusions: FFPE Hi-C sequencing provides an all-in-one tool for cytogenomic variants that are diagnostic across lymphoma subtypes. It is especially useful in clinically ambiguous cases and when appropriate FISH testing is not readily available.