Single-Cell Multi-Omics Market

Market Overview

The global Single-Cell Multi-Omics Market was valued at approximately USD 2.1 billion in 2024 and is projected to reach USD 7.4 billion by 2033, growing at a CAGR of 14.9% during the forecast period (2025–2033).

Single-cell multi-omics is defining the integrated analysis of multiple molecule types (i.e., DNA, RNA, proteins, metabolites) within single cells, to better understand cell heterogeneity and function. This novel technology offers the opportunity to investigate biological systems in more sophisticated detail than ever before, and is poised to provide the next breakthrough in cancer, immunology, regenerative medicine, and more. Through techniques such as single-cell RNA sequencing, ATAC-seq, and mass cytometry, scientists can study genes expressions, chromatin accessibility, and protein expression from a single sample. The industry is growing rapidly, and the market demand is increasing due to the rise in cancer and neurological diseases, the advancement to precision medicine, advancements in the fields of microfluidics and sequencing technology, increased investments from pharmaceutical companies and grants from the government and institutions pushing for single-cell studies.

Market Dynamics

Market Drivers

Rising Demand for Precision Medicine and Targeted Therapies

Single-cell multi-omics is driven largely by the current movement towards precision medicine. Precision medicine adapts treatment to individual variation in genes, environment, and lifestyle. Single-cell multi-omics allows researchers to identify cellular, molecular signatures in topological networks. It is particularly useful for identifying rare cell populations, identifying mechanisms of disease, and ultimately guiding targeted therapies.

For example, in 2024, 10x Genomics launched the Xenium platform, which is a spatial multi-omic platform that can resolve gene and protein activity within tissues. This is particularly useful when understanding tumor microenvironments. Even large pharmaceutical companies are getting in on the action; for example, Roche and Pfizer are partnering with single-cell technology companies to facilitate biomarker discovery and drug development!

According to NIH, over 60% of new clinical trials are now including biomarker-driven stratification, supporting the usefulness of single-cell datasets. This is happening largely in the oncology space, where tumor heterogeneity creates paradigm shift in treatment.

A Nature Biotechnology article made clear in 2024 that multi-omics profiling is useful for defining drug resistant subtypes of cancer cell populations, which lead to more effective therapies targeting specific subtypes. As need for precision and personalized treatments becomes widespread, a more concrete industry and research pipeline for single-cell multi-omics is emerging with great investment, and consequently, growth of the market.

Technological Advancements in Single-Cell Analysis Platforms

Speedy technological developments are rapidly driving the growth of the single-cell multi-omics market. Technologies such as microfluidics, next-generation sequencing (NGS), and mass cytometry have improved our ability to isolate, process, and analyze thousands of individual cells in a single experience increasingly accurately. Platforms like the BD Rhapsody, the 10x Genomics Chromium platform, and Fluidigm’s C1 system have improved multi-omic analysis of cells in parallel, improving overall throughput and data quality.

In 2023, Mission Bio released the Tapestri Platform to allow for simultaneous analysis of DNA and protein of individual cells in support for mutation tracking and lineage tracing in oncology research. Furthermore, automation and AI-based bioinformatics have simplified and expedited complex data processing, making multi-omics accessible to researchers at all levels.

Automation and AI will continue to reduce costs, lower errors, and enhance reproducibility, which will be key factors in universities and industry adopting single-cell multi-omics more broadly. While these technologies improve accessibility, integrated multi-omics tools are advancing spatial resolution and temporal resolution of gene expression and protein activity in order to better comprehend how cell functions relate to disease progression.

As technological platforms become more advanced and easier to utilize, translational research will increase and precision diagnostics will be stimulated, thereby continuing to expand the single-cell multi-omics market.

Market Restraints

High Cost and Technical Complexity of Single-Cell Multi-Omics Technologies

The key barriers to the growth of the single-cell multi-omics market are the high costs associated with these technologies and the technical complexity of working with them. Single-cell multi-omics technologies are expensive because they involve procuring advanced instruments for detection, unique reagents to target every omics layer, and high-throughput sequencing platforms that require end-to-end workflows.

Researchers in academia and clinical labs are constrained by technology acquisition costs. To illustrate the costs associated with technologies such as the 10x Genomics Chromium or BD Rhapsody, the capital equipment are generally above USD 100,000, as well as having the associated recurring costs of consumables and/or reagents.

In addition, multi-omics analysis requires complex workflows that may take years for laboratories to build upon, owing to the required expertise in cell isolation, library preparation and computing with complex bioinformatic and statistical analysis. In areas with restricted research infrastructure, this limits the adoption of these technologies.

Data interpretation and analysis presents a challenge, not just because of the vast and deeply layered datasets, but the analytical complexity of these rich datasets requires sophisticated computing and computational expertise. Organizations often have neither access nor funding in these emerging economies for the type of infrastructures that allow for implementing these technologies.

Nevertheless, the promise of personalized medicine and disease advances have propelled technological development into new frontiers; nonetheless, financing and technical complexities will severely limit the access and implementation of single-cell multi-omics platforms from becoming standard practice in biomedical research.

Segmental Analysis

The Single-Cell Multi-Omics Market is segmented by type, technique, application, and end-user. Each segment plays a pivotal role in advancing personalized medicine, drug discovery, and disease research through deep cellular analysis.

By Type

The segment of Single-cell Transcriptomics has the biggest market share in 2024 largely due to its wide use to investigate patterns of gene expression at single-cell resolution. The increasing use of single-cell, RNA sequencing (scRNA-seq) modalities to investigate cell differentiation, tumor heterogeneity, and immune cell profiling is contributing to the overall predominance of this category.

The segment of Single-cell Genomics continues to gain traction as well, especially in cancer genomics, where rarer mutations cannot be easily studied unless evaluated at a cell-level. Single-cell Proteomics is also growing at a rapid pace thanks to an increased emphasis on protein-level insights, particularly in immuno-oncology and immunological-related disorders.

The Single-cell Epigenomics category is also gaining momentum as these techniques are useful for investigating chromatin accessibility and DNA methylation, two important aspects of development biology and neuroscience investigation. Lastly, Single-cell Metabolomics is a lesser-known segment, but as technologies surrounding these approaches improve, greater understanding of cellular metabolism in disease should lead to increasing growth in this segment.

By End-User

Academic and Research Institutions are a key player in the market as they have the largest expected revenue share in 2024, owing to ongoing basic research in genomics, developmental biology, and disease modeling. Many of the leading universities and research hospitals adopt single-cell multi-omics for exploratory studies.

Pharmaceutical and Biotechnology Companies make up the largest segment with rapid growth as they use multi-omics to inform and address all aspects of biology such as target discovery, drug response profiling, and biomarker discovery. Moreover, there is a growing trend for collaboration between pharma and omics platform providers, leading to greater growth.

The value of single-cell tools in diagnostics is beginning to be realized by Clinical Laboratories for cancer and immunological conditions although, adoption is still in its earliest phases, primarily as the costs and complexities of tasks for purposes of diagnostics, poses challenges. The growth of single-cell has also increased the capabilities of Contract Research Organizations (CROs), a segment with slow but steady growth as many of their pharmaceutical clients are requesting more multi-omics research for outsourcing needs.

By Technique

In 2024, in the techniques category, Single-cell RNA Sequencing (scRNA-seq) is winning out due to the fact that researchers in wide sectors of transcriptomic profiling in cancer, neurology, and immunology are getting into scRNA-seq without a problem. The reason that this technique dominates is because it allows researchers to decode the cellular heterogeneity in every tissue and to discover new cell sub-types, which enables them to perform an incredibly unique single-cell study.

Single-cell RNA Sequencing is a widely available and affordable technology that allows researchers to do scRNA-seq without limitation and as scRNA-seq becomes more ubiquitous, it is steadily supported by such robust analytical pipelines. Because of these advantages, the developing area of single-cell ATAC Sequencing is also gaining traction especially in epigenetic studies because it provides state-of-the-art mapping of chromatin accessibility and other regulatory elements in single-cells.

It cannot be overlooked that Mass Cytometry has entered into a high-growth segment as well because this technique can eventually be used to quantify dozens of proteins at the same time at the single-cell level and has demonstrated important uses in the areas of immune profiling and clinical oncology.

CITE-seq (Cellular Indexing of Transcriptomes and Epitopes) is a developing methodology that encompasses transcriptomics and proteomics together in one workflow, allowing researchers to integrate data on genes expression levels and protein abundance in single-cells.

scChIP-seq and other technical methods such as spatial transcriptomics and DNA methylation which are also not as frequently used, are becoming more attractive for unique methodological applications in developmental biology and neuroscience.

By Application

As a application segment, cancer research is the dominant segment, and will have the largest market share in 2024. Single-cell multi-omics provides deep profiling of tumor heterogeneity, drug resistance mechanisms, and aspects of the tumor microenvironment – information that is critical for patients in a personalized oncology approach.

As multi-omics becomes more mainstream, the increase in single-cell data will be used research-wise and pharma-wise to ultimately identify biomarkers of cancer, and stratify patients for selected targeted therapies. Immunology is a rapidly growing segment within single cell profiling, using multi-omics to decode immune cell differentiation, examine vaccine responses, and better understand complex autoimmune disease processes.

Techniques such as mass cytometry and CITE-seq facilitate immune profiling at single-cell resolution. Neurology is also a rapidly emerging area where researchers are starting to use single-cell epigenomics and transcriptomics to study complex human brain disorders like Alzheimer’s, Parkinson’s, and multiple sclerosis. Single-cell multi-omics has been also advantageous to stem cell research to better understand differentiation pathways and regenerative potential.

Infectious diseases applications witnessed accelerated adoption during the COVID-19 pandemic, particularly examining immune responses and viral-host interactions. Other application segments like cardiovascular disease and developmental biology are just starting emerge as more multi-omics tools become accessible and affordable.

Regional Analysis

North America

North America is projected to retain the largest share of 41.2% in 2024, supported by strong research infrastructure, significant levels of government and private funding, and an early adoption of next-generation omics technologies. The U.S. leads the way, with funding from U.S. government agencies, primarily the National Institutes of Health (NIH), which have placed a high level of investment into single-cell projects.

Furthermore, a number of key companies in the single-cell research market, including 10x Genomics, Berkeley Lights, and BD Biosciences, are based in the U.S., which is a significant generator of regional market growth. The U.S. also boasts a concentration of wealth through its top academic centers and a robust pharmaceutical sector that continues to drive greater single-cell product development and usage.

Europe

Europe illustrates a mature market that has established bases in a number of countries, including Germany, the UK, France, Sweden, and the Netherlands. Europe also possesses highly regarded genomics research programs— most notably the Human Cell Atlas and EU Horizon 2020 initiatives that are under development to support single-cell studies and projects.

The aging population of Europe coupled with increasing levels of government funding specifically allocated to addressing kidney cancer and research into neurological diseases will serve as additional value drivers for market growth. Finally, Germany appears to be in an advantageous position as it is the European leader in integrating technology into clinical research institutions.

Asia-Pacific

Asia-Pacific is estimated to accelerate at the highest CAGR of 16.7% during the forecast period due to increasing biomedical research, growing healthcare investments, and increasing knowledge of precision medicine. Countries in the region such as China, Japan, South Korea, and India are aggressively investing in developing omics infrastructure. China’s National Genomics Data Center and Japan’s focus on aging-related studies are driving growth in the regional market.

Latin America and Middle East & Africa

Latin America and Middle East & Africa are experiencing moderate growth. Countries such as Brazil, Mexico, South Africa, and Saudi Arabia are slowly building capacity in single-cell technologies. With an increase in global research collaborations, there is an increasing emphasis on single-cell techniques. There is an increase in investments in healthcare. However, challenges remain due to limited access to high-quality equipment, lack of technical skills, and disparities in healthcare infrastructure.

Recent Development

1. June 2025: Illumina announced the acquisition of SomaLogic to integrate proteomics with its sequencing platforms, expanding its single-cell multi-omics capabilities.
2. May 2025: 10x Genomics launched the Visium HD 3′ Gene Expression assay, enhancing spatial transcriptomics resolution across fresh and fixed tissue samples.
3. February 2024: 10x Genomics introduced the GEM‑X workflow on the Chromium X Series, enabling improved single-cell gene expression profiling compatible with diverse sample types.