Fox Chase Unlocks DNA's 3D Secrets to Revolutionize Cancer Care

PHILADELPHIA, PA – January 08, 2026 – Fox Chase Cancer Center has embarked on a pioneering collaboration with Arima Genomics, aiming to integrate a revolutionary form of genetic analysis into routine patient care. The partnership will bring advanced diagnostics based on the three-dimensional (3D) structure of DNA out of the research lab and into the clinic, establishing a new front in the war on cancer, with an initial focus on lymphomas and sarcomas.

A New Dimension in Cancer Diagnostics

For decades, cancer diagnostics has focused on reading the genome like a book, analyzing the linear sequence of DNA's A, T, C, and G's. But this one-dimensional view often misses a critical part of the story: how that long string of DNA is folded and organized within the cell's nucleus. A new partnership between a leading cancer center and a diagnostics innovator aims to change that.

Unlike conventional sequencing that breaks DNA into millions of tiny, disconnected pieces, the Hi-C technology platform developed by Arima Genomics captures the genome's intricate 3D architecture. This approach provides a map of how different parts of the genome, even those far apart on the linear sequence, interact in three-dimensional space. These spatial relationships are crucial for regulating gene activity and can be profoundly disrupted in cancer cells.

This expanded view allows clinicians to detect complex genomic changes, such as gene fusions and rearrangements, with far greater sensitivity than traditional methods like FISH (fluorescent in situ hybridization) or standard DNA sequencing. In some cases, Arima's platform has demonstrated a signal that is 100 to 1,000 times higher, uncovering structural variations that are invisible to other tests.

“It allows us to see not just what genetic changes occur, but how the DNA itself is organized, information that may reveal new therapeutic targets or confirm findings with greater precision,” said Johnathan Whetstine, PhD, Director of the Cancer Epigenetics Institute at Fox Chase.

From the Bench to the Bedside at Fox Chase

The collaboration marks a significant milestone, making Fox Chase Cancer Center the first institution worldwide to implement this 3D-genomics technology as a standard clinical protocol across multiple tumor types. This move cements the Philadelphia-based center’s reputation as a pioneer in adopting cutting-edge technologies to advance patient care.

The partnership is not a sudden development but the culmination of a longstanding scientific relationship between Arima and Fox Chase’s Cancer Epigenetics Institute. “This partnership represents a true bench-to-bedside translation of discovery,” Whetstine noted. “Our longstanding relationship with Arima has evolved from basic research collaboration to clinical implementation. Together, we’re redefining how genome organization can guide diagnosis and treatment.”

Under the agreement, Fox Chase will integrate Arima’s Aventa™ Lymphoma and Aventa FusionPlus tests into its diagnostic workflows. Beyond immediate patient care, the initiative has a powerful research component. De-identified patient response data will be collected and analyzed, creating a rich dataset for researchers at the Cancer Epigenetics Institute. This feedback loop is designed to accelerate the discovery of new drug targets and deepen the fundamental understanding of cancer biology, potentially shortening the gap from basic science to clinical impact.

Targeting Hard-to-Treat Cancers with New Hope

The initial clinical rollout will focus on lymphomas and sarcomas, two cancer types where accurate diagnosis of genomic rearrangements is critical but often challenging. For patients with these diseases, the new technology offers a tangible source of hope.

“Although there have been many advances in the treatment of lymphoma, the disease often will relapse into a state of unresponsiveness to the therapy that induced a remission,” explained Peter Abdelmessieh, DO, MSC, an Assistant Professor in Fox Chase’s Blood Cancer and Cellular Therapy Institute who was instrumental in developing the partnership. “Having access to this advanced tool from Arima provides a great benefit in guiding the diagnosis and treatment of patients with lymphoma.”

The clinical utility of this 3D genomics approach is supported by a growing body of evidence. A study from Johns Hopkins University, for instance, demonstrated that Arima's Hi-C based test could resolve ambiguous FISH results in cases of diffuse large B-cell lymphoma (DLBCL), providing clear clinical answers where there were none. The test not only confirmed standard results but also identified additional, clinically consequential rearrangements that routine panels had missed, altering diagnoses and refining patient prognoses.

In one real-world case, the technology identified a critical IRF4 rearrangement in a patient with Large B-Cell Lymphoma that had been missed by both FISH and standard next-generation sequencing at other institutions. This discovery led directly to a successful, targeted treatment plan. For solid tumors like sarcomas, the Aventa FusionPlus test has been shown to detect actionable gene fusions in over 20% of patients who had previously tested negative with other methods, opening doors to new therapeutic options.

Charting a Path to a New Standard of Care

While other companies like Foundation Medicine and Guardant Health have made strides in genomic profiling and liquid biopsies, Arima has carved out a unique niche by focusing on the genome’s structural dimension. This approach is not necessarily a replacement for existing technologies but a powerful, complementary tool that provides a more complete picture of a tumor’s genetic landscape.

“Arima’s Aventa tests provide the most sensitive detection for gene fusions and rearrangements, which are particularly important for the diagnosis and treatment of lymphomas and sarcomas, so we are thrilled that Fox Chase is showing the leadership to bring these tests to their patients on such a broad scale,” said Tom Willis, PhD, CEO of Arima Genomics.

A significant hurdle for any advanced diagnostic is navigating the complex regulatory and reimbursement environment. Arima operates a CLIA-certified laboratory and has secured a specific billing code for its lymphoma test, but broad adoption hinges on demonstrating clear clinical utility to payers like Medicare and private insurers.

This is where the Fox Chase partnership becomes strategically vital. By implementing the technology at scale within a world-renowned NCI-designated Comprehensive Cancer Center, the collaboration will generate a wealth of real-world data. This evidence is crucial for proving that the test not only provides interesting information but directly leads to better patient outcomes, thereby justifying its cost and establishing it as a new standard of care.

The insights gained from this pioneering implementation could ripple across the oncology landscape, encouraging other leading cancer centers to look beyond the linear code of DNA and embrace the three-dimensional reality of the cancer genome.