With a $22 million financing, how does Arima Genomics promote the implementation of the 3D genomics industry?

In June 2025, Arima Genomics, a US-based enterprise in the 3D genomics platform field, announced the completion of a $22 million Series C financing round led by Illumina Ventures. This financing round involved genomics pioneers John Stuelpnagel and Dr. Mostafa Ronaghi, as well as existing investors Co-Win Ventures and Berkeley Catalyst Fund. The funds from this round will mainly be used to launch the "Focused Pipeline Of Clinical Assays," which uses its sequencing-based methods to determine 3D genome structures, such as gene fusions and rearrangements.

As a venture capital firm focusing on genomics and precision medicine, Illumina Ventures relies on the existing strategic partnerships of Illumina (NASDAQ: ILMN), a global gene sequencing giant, to develop breakthrough science and technology into market-leading companies. By leading this financing round, Illumina Ventures may aim to increase its investment in the cutting-edge applications of 3D genomics, spatial omics, and structural variation detection. Moreover, Aventa appointed Dr. Tom Willis, a former Illumina executive, as CEO, further clarifying and strengthening its strategic focus on tumor structural variation detection.

This financing sends a clear trend signal: Following spatial transcriptomics and single-cell sequencing, 3D genomics is gradually becoming a new focus at the intersection of basic scientific research and precision medicine.

As one of the representative enterprises in this field, Arima is promoting the commercialization of complex technologies such as Hi-C (High-throughput Chromosome Conformation Capture) through the path of "standardized kits + modular analysis processes," attempting to break the limitations of laboratory scenarios and truly bring 3D genomics into scientific research and clinical practice that can be applied on a large scale and commercialized.

One sample changes a company, moving from scientific research to the front line of clinical practice

Arima Genomics was founded in 2015 and initially focused on developing standardized tools to help researchers analyze the 3D folding structure of DNA, opening a new window for chromatin interaction research.

The turning point occurred in 2022. A biopsy sample from a patient with glioblastoma (GBM) was sent to Arima. This patient had previously undergone multiple rounds of DNA and RNA testing, but the pathogenic mechanism had never been identified. The Arima team used its 3D genomics platform to identify structural rearrangements missed by traditional methods, developed a new targeted treatment plan for the patient, and achieved positive results.

This experience made Arima realize that it is difficult to capture the pathogenic variants hidden in the 3D structure with only linear sequences, and this is the key to precision treatment. Since then, Arima has not been limited to providing scientific research services but has started to engage in clinical testing scenarios, restoring a more "complete" genomic map for each patient.

In Arima's view, the significance of technology is not a research paper but a report that can change a patient's fate. This culture that combines scientific rigor and clinical empathy has also promoted Arima's transformation from a single tool developer and kit supplier to a spatial omics platform enterprise. Meanwhile, its financing rhythm not only supports the continuous expansion of its product line but also indicates its ambition to enter the clinical scenario.

In 2022, Arima completed a $7 million Series B financing round. The funds were mainly used for product matrix expansion and bioinformatics platform construction, laying the foundation for approaching the clinical field. In 2023, the company joined the US BRAIN Initiative, engaged in spatial omics research on the nervous system, and co-established the Aventa Genomics laboratory with Protean, a precision oncology diagnostic company, entering the clinical testing track. In October of the same year, Aventa launched the FusionPlus product, supporting the detection of fusion genes in FFPE tumor samples.

Table 1: Key financing and industrialization timeline of Arima Genomics

Multi-product matrix: Creating a diverse tool library for spatial omics with a single kit

DNA is not spread flat in the nucleus but is coiled and folded like a ball of wool. This 3D structure affects which genes can be turned on or off, thereby determining the functional performance of cells. 3D genomics is the science that studies this way of chromatin folding, and the Hi-C technique is the most commonly used method, which can map the spatial contact map of the entire genome.

In the cutting-edge technology track of spatial omics, Arima Genomics' product system is not just a combination of several kits but a complete tool platform built around 3D genomics (Hi-C) technology. The product system includes three major modules: research products, clinical services, and bioinformatics services, covering diverse applications from chromatin interactions, structural variations, and viral integrations to protein regulation and epigenetic modifications.

Putting experiments into a "box": The standardized starting point for Hi-C library construction

Arima's initial star product is an experimental kit called Arima-HiC+. It modularizes and pre-prepares multiple time-consuming and error-prone steps in traditional Hi-C experiments, allowing researchers to obtain reproducible results through a fast 6-hour automation-friendly protocol, just like performing an RNA-seq. This also makes the 3D genome map, which was once "only available to top laboratories," have the possibility of being "reproducible and batch-produced" for the first time.

With the expansion of sample types, Arima also launched a version suitable for clinically paraffin-embedded tissues (FFPE) - Arima-HiC+ FFPE. While maintaining the integrity of the map, it improves the signal recovery efficiency of degraded tissue samples and is suitable for detecting and discovering structural variations in archived or clinical samples.

If HiC+ is a general version, for in-depth interaction analysis of specific regions, Arima also provides Promoter Capture Hi-C and Custom Capture Hi-C solutions, which can directionally capture promoters, enhancers, or specific pathogenic gene regions, helping scientists conduct in-depth research on gene regulation logic and potential target identification.

For scenarios with high-resolution requirements, such as studying complex cancer models or organ development, Arima's High Coverage Hi-C provides a higher data acquisition ability, making the spatial structure map more detailed and hierarchical.

It is worth noting that all kits support mainstream sequencing platforms such as Illumina, PacBio, and Oxford Nanopore, with good technical compatibility and process portability. This not only enhances its application scope in different experimental scenarios but also makes its products easier to integrate into existing sequencing workflows.

Serving the clinic, constructing a spatial molecular perspective for pathological samples

Through its Aventa clinical testing laboratory certified by CLIA (Clinical Laboratory Improvement Amendments), Arima launched Aventa, a structural variation detection service dedicated to clinical samples. This type of service is currently widely used in early clinical research of pharmaceutical companies and precision medication decision-making assistance, becoming the first step for the Hi-C technology to enter translational medicine.

Among them, Aventa FusionPlus focuses on fusion genes and chromosomal rearrangements in FFPE samples of solid tumors, providing auxiliary evidence for cancer typing and targeted drug screening; Aventa Lymphoma is designed specifically for lymphoma, identifying complex but biologically significant chromatin rearrangement events.

Outsourcing and integration services: Making spatial omics a tool accessible to everyone

For institutional users who do not have experimental conditions or want to quickly start 3D genomics research, Arima also provides a complete "turnkey" outsourcing service. Users only need to submit samples, and Arima will be responsible for the rest of the process - from library construction to sequencing, from data processing to map analysis - and finally directly deliver the structural interaction map and downstream analysis results.

For higher-level research needs, Arima also launched the Single Cell Methyl-3C service, which integrates methylation and 3D interaction information, to analyze the epigenetic regulatory network at the single-cell level, moving towards a new direction of spatial multi-omics integration.

Table 2: An overview of Arima's products

From boxed products to clinical testing solutions and then to one-stop outsourcing, Arima has completed a closed-loop path from basic scientific research to clinical verification in a "modular" way.

When 3D genomics enters the clinic

The value of a technology lies not only in explaining the unknown but also in influencing reality. With the continuous optimization of product performance, the 3D genomics technology represented by Arima Genomics is gradually moving from the "ivory tower" of scientific research to the real world - entering highly application-oriented scenarios such as tumor diagnosis, gene editing safety assessment, and viral integration detection, becoming a "linking bridge" between gene regulation mechanism research and disease variation research.

The 3D genomics platform constructed by Arima Genomics has gradually gone beyond the scope of basic scientific research and expanded to multiple high-value scenarios.

In epigenetics, this platform helps researchers depict the 3D distribution of key transcription factors in chromatin through tools such as HiC+ and HiChIP, revealing long-range regulatory mechanisms such as DNA methylation and histone modifications, and is widely used in stem cell differentiation, developmental biology, and tumor transformation research.

In tumor genomics, the Arima-SV module compensates for the insufficiency of traditional whole-genome sequencing (WGS) in analyzing complex structural variations (SV), especially in the research of virus-related tumors - for example, the NIH and Harvard teams used its platform to reveal the spatial association mechanism between HPV virus integration and oncogene activation.

In addition, in gene editing safety assessment, Hi-C provides a new means for monitoring "off-target effects" at the structural level and is increasingly becoming one of the quality control links in projects such as CRISPR therapy and cell therapy.

Arima also launched a viral integration detection tool to identify the insertion sites of viruses such as HPV and HBV and analyze their carcinogenic mechanisms in the 3D structure, which has been extended to vaccine evaluation and viral latency research.

In genome assembly, Hi-C, as an auxiliary jigsaw tool, is used in combination with long-read platforms such as PacBio and ONT to construct chromosome-level reference genomes and is widely used in agricultural breeding, species evolution, and rare disease gene mapping. These applications spanning basic and translational research are turning "spatial information" from a laboratory variable into a key variable in precision medicine.

The Hi-C standardized platform constructed by Arima Genomics is quietly changing the way of using spatial omics: In the future landscape of precision medicine, the dimension of "space" will no longer be just a modifier of technology but will become an important infrastructure linking mechanism understanding and diagnosis and treatment practices. In this sense, Arima is not just making products but reshaping the usage logic and implementation path of an emerging field.

China's 3D genomics project ushers in a development window period

In recent years, with the iterative breakthroughs in multi-omics technologies, Chinese enterprises' exploration in the field of 3D genomics has been steadily advancing. For example, Novogene provides genome assembly and spatial interaction analysis by combining Hi-C and long-read sequencing, which is widely used in human sample research and crop breeding. Annoroad has incorporated Hi-C into its scientific research service system and explored the integrated analysis of Hi-C with spatial transcriptomics and other multi-omics technologies. These practices are promoting the transformation of Chinese spatial omics from scientific research services to precision medicine application research.

Arima's development path provides three lessons for Chinese enterprises:

First, it uses product engineering thinking to smooth the implementation of 3D omics technology - By modular encapsulation, it makes complex experimental processes standard and reproducible, reducing the usage threshold. Second, Arima focuses on high-clinical-value scenarios such as structural variations and viral integrations, successfully promoting spatial omics into real applications such as tumor diagnosis and gene editing quality control. Finally, it expands its business boundaries through the "platform + cooperation" model, serving not only scientific research institutions but also integrating into the R & D processes of pharmaceutical companies and CDMOs, forming extensive industrial linkages.

In the future, with the continuous accumulation of China's capabilities in spatial multi-omics and bioinformatics analysis platforms, 3D genomics is expected to follow a development path of "independent innovation + engineering implementation." In this process, Arima is not the "only answer" but is undoubtedly an engineering model worthy of reference.

This article is from the WeChat official account "Arterial Network" (ID: vcbeat), written by Huang Yurou and published by 36Kr with authorization.