Diagnosing lymphoma and sarcoma can be extraordinarily complex, with more than 70 recognized subtypes of lymphoma and more than 100 distinct types of sarcoma. Many subtypes share similar features yet behave in dramatically different ways in standard testing, leaving oncologists with diagnostic quandaries and delays to treatment.

Over the last few decades, cancer diagnosis has relied on traditional pathology and two-dimensional genomics testing, which does not always capture the full complexity of the way cancer behaves because these modalities “read” DNA like a flat two-dimensional map instead of a three-dimensional structure.

“For years, we’ve known that the way DNA folds inside the cell matters,” said Johnathan Whetstine, PhD, Director of the Fox Chase Cancer Center Institute for Cancer Epigenetics and Co-Leader of the Nuclear Dynamics and Cancer Program. Fox Chase Cancer Center is the first NCI-designated Comprehensive Cancer Center in the country to bring 3D genomics testing into routine clinical care for lymphoma and sarcoma, providing a deeper, more detailed view of not just which genes are mutated, but how those genes are organized and interacting inside the cell.

Through our unique Cancer Epigenetics Institute and Fox Chase Cancer Center collaboration with Arima Genomics, Inc., we can leverage Arima’s HiC-based technology—an approach that captures the way DNA folds and interacts inside the cell—into its diagnostic workflows for lymphoma and sarcoma through Arima’s Aventa™ Lymphoma and Aventa FusionPlus tests,respectively. “Most exciting is that we can now translate this knowledge into something clinically actionable for patients,” said Whetstine.

“These are complicated diseases,” said Peter Abdelmessieh, DO, MSC, Assistant Professor in the Blood Cancer and Cellular Therapy Institute at Fox Chase Cancer Center and in the Cancer Epigenetics Institute and Nuclear Dynamics and Cancer Program, “and these pioneering tests will allow physicians to better identify genomic changes, improve diagnosis, and inform individualized cancer treatment.”

Guiding Diagnosis and Treatment

“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. Having access to this advanced tool from Arima provides a great benefit in guiding the diagnosis and treatment of patients with lymphoma,” added Abdelmessieh, who was instrumental in working with Whetstine to develop the partnership.

A Streamlined, More Precise Diagnosis

3D genomics testing provides another layer of clarity. By examining how DNA is structurally arranged inside the cell, pathologists and oncologists can identify structural changes actively driving cancer behavior and distinguish between closely related subtypes that may otherwise appear nearly identical, reducing the uncertainty that can delay important treatment decisions.

In some cases, the technology has even helped reclassify cancers previously labeled “not otherwise specified,” giving physicians clearer direction for care.

This vastly improved view of cancer provides insight into what is happening inside the cancer cell. “We’re not just identifying mutations. We’re understanding how structural changes in the genome are potential altering gene regulation and behavior,” said Whetstine.

“We can perform this testing on existing slides, so we don’t even need new biopsies, making this highly accessible, and reduce the need for trial-and-error approaches,” said Abdelmessieh.

“With a more streamlined diagnosis, patients with complex cancers can begin their targeted treatment plans that much sooner.”

Proactive, 3D Cancer Care

In combination with standard-of-care genomic and biologic testing, Fox Chase physicians can get ahead of the disease rather than reacting only after it progresses. “For our treatment planning, this is vital,” said Abdelmessieh. “If we understand the pathways driving the disease, we can select therapies much more aligned with the biology of that specific tumor and more likely to produce a lasting result.”

In peer-reviewed studies and through clinical use at multiple institutions, Arima Aventa tests have demonstrated their ability to identify gene fusions and rearrangements crucial to accurate cancer diagnosis and treatment.

“This partnership represents a true bench-to-bedside translation of discovery,” said Whetstine. “Our long-standing relationship with Arima has evolved from basic research collaboration to clinical implementation. Together, we’re redefining how genome organization can guide diagnosis and treatment and setting the stage to further understand fundamental cancer biology and determine new drug targets that truly impact patient care.”