Arima’s technology used to identify key gene fusions and rearrangements missed by FISH, RNA, and DNA sequencing

Arima Genomics, Inc. (Arima), a company leveraging 3D genomics to reveal actionable insights that will empower researchers and clinicians to improve human health, today announced the publication of a study in The Journal of Molecular Diagnostics showing its proprietary technology detected clinical structural variants missed by conventional clinical tests. Conducted in collaboration with researchers from NYU Langone Health, Weill Cornell School of Medicine, Scripps Cancer Center, Moores Cancer Center at the University of California, San Diego, and the University of Colorado School of Medicine, the retrospective study found that Arima’s technology identified gene fusions or rearrangements in 71% of cases where standard molecular techniques failed. Importantly, in 14% of these cases where no driver had been found by other techniques, a clinically actionable variant was identified.

“Structural variants like gene fusions are central to cancer diagnostics, but current clinical tests miss many events that are crucial to diagnostic and therapeutic decision-making,” said Matija Snuderl, MD, Professor of Pathology and Director of Molecular Pathology and Diagnostics at NYU Langone Health and corresponding author of the study. “Arima’s technology allowed us to detect hidden variants — many of them clinically actionable — in cases where standard tests came up empty. This provided important information to our understanding of the cancers and directly impacted patient care in some cases, confirming diagnoses and improving treatment options.”

In the current study, researchers analyzed 71 formalin-fixed, paraffin-embedded (FFPE) specimens across ten solid tumor types, comparing results using Arima’s technology to results from prior clinical testing via fluorescence in situ hybridization (FISH), RNA sequencing, and DNA sequencing. Arima’s technology demonstrated 98% concordance with positive cases detected by conventional methods. Among the 14 samples negative by standard techniques, structural variants in 71% (10/14) were uncovered. Among these:

• 14% (2/14) harbored gene fusions or rearrangements listed in current clinical guidelines, directly impacting patient care.
• 14% (2/14) involved rearrangements affecting therapeutically targetable genes, potentially expanding treatment options even though they are not currently classified as actionable in guidelines.

Several cases described in the paper highlight the utility of Arima’s technology in achieving proper diagnosis and enabling appropriate therapeutic intervention.

For example, one young patient experiencing seizures was initially believed to have a non-tumorous brain abnormality called focal cortical dysplasia. DNA methylation results hinted at a possible low-grade glioma but remained inconclusive following two commercial RNA sequencing panels, which did not identify a diagnostic fusion for low-grade glioma. Only when the patient’s sample was analyzed with Arima’s technology did doctors detect a MYBL1::MAML2 fusion, confirming a low-grade glioma diagnosis and allowing the patient to receive the proper treatment.

In another case involving a pediatric glioblastoma patient, Arima��s technology detected a complex rearrangement involving PD-L1 that standard RNA and DNA tests missed. Later confirmatory testing using immunohistochemistry showed that PD-L1 was overexpressed on the tumor cells and provided an opportunity for immunotherapy treatment based on PD-L1 expression—an option that would have been overlooked without the enhanced sensitivity of Arima’s technology.

Arima’s technology uses high-throughput chromosome conformation capture (Hi-C) sequencing to map the spatial architecture of the genome within FFPE tumor samples. By revealing how DNA is organized in 3D space, it detects gene fusions, rearrangements, and translocations with 100-1000 times higher signal compared to standard methods like RNA or DNA sequencing or FISH, resulting in superior sensitivity.

Beyond actionable findings, the study also described how Arima’s technology offers deep insights into tumor biology by detecting complex genomic rearrangements such chromothripsis and extrachromosomal DNA (ecDNA). Recent literature has suggested ecDNA may be involved in treatment resistance, but may also be targetable with on-market therapies.

“Our technology provides a unique method to amplify the signal of rearrangements,” said Anthony Schmitt, PhD, Senior Vice President of Science at Arima Genomics. “This allows us to capture structural rearrangements with far greater sensitivity and detail in FFPE samples—bringing both immediate clinical benefit and new avenues for research.”

This new publication adds to a growing body of clinical evidence supporting Arima’s technology, building on recent studies conducted in collaboration with institutions such as Yale School of Medicine, Harvard Medical School, and Seattle Children’s Hospital.^1-3

About Arima Genomics

Arima Genomics, Inc. is leveraging 3D genomics to reveal actionable insights that will empower researchers and clinicians to improve human health. The company offers the most advanced technologies for preserving the structural organization of the genome to drive discovery in genome biology and improve the clinical diagnosis of complex cancers. Arima’s technology is available to clinicians through its CLIA-certified laboratory, Aventa. To learn more, connect with us on X, LinkedIn, and YouTube.

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“Structural variants like gene fusions are central to cancer diagnostics, but current clinical tests miss many events that are crucial to diagnostic and therapeutic decision-making,” said study author Matija Snuderl, MD, of NYU Langone Health.