1 Oct 2020

Single-cell sequencing: Industry trends and developments

Single-cell sequencing: Industry trends and developments

Single-cell sequencing is the characterization of genetic material at the individual cell level and is used to reveal cellular differences and understand the cell’s state and function. This technology has been applied in many biomedical fields, including immunology. Earlier on our blog, we discussed single-cell sequencing workflows and analyses, and their added value to the field of immunomics. In this post, we take a closer look at the market, forecasts, and highlight expert insights from the single-cell immune profiling industry.

Market growth, drivers, and challenges

The overall single-cell sequencing market is projected to experience significant growth: according to BIS Research, 2020, the forecasted market growth is from $1,234.0 million in 2018 to $5,986 million in 2029 at a Compound Annual Growth Rate (CAGR) of 15.2% [1]. Specifically, for applications that study immune repertoires, the market is set to grow to $209.7 million by 2028 at a CAGR of 8.4% [2]. In academic research, we observe a similar trend.

We queried Pubmed, a database comprising over 30 million biomedical papers, for publications containing the keywords “single-cell” with or without the term “immune” over the last decade. The Y-axis shows the percentage of matches that was generated in the year depicted on the X-axis. This trend indicates that the increase in publications that involve single-cell analysis in the field of immunology is more substantial compared to single-cell analysis alone. Combined with the overall observed market growth, this increased interest in single-cell sequencing holds great promise for further developments in the industry.

Percentage of Pubmed publications per year for searches with “Single-cell” and “Single- cell” + “immune” between 2010 and 2019. The yearly number of matches is normalized by the total number of matches in the period (2010-2019). The total number of search results for the period were 873 and 119 respectively.

A significant growth driver of the single-cell sequencing market are the technologic advances in sequencing platforms: “The availability of enhanced sequencing platforms, such as platforms with long-read technologies, enabled the researchers to generate cost-efficient and robust sequence data.” [1]

Looking at the landscape of proprietary software solutions, we see some of the biggest single-cell sequencing providers like 10x Genomics acknowledge the importance of Rep-Seq. Within a year, the number of case studies that were published on their website using  single-cell Rep-Seq technologies  has increased from just 10 (July 17, 2019) to over 80 (August 18, 2020). Further quality improvements and increasing throughput (and decreasing cost) will facilitate even more widespread use of single-cell sequencing technologies.

Innovation bottlenecks

Academic literature can provide insight into state-of-the-art technologies and applications, challenges in the field, and innovation trends. The added value of single-cell sequencing in the field of immunology has been clearly tangible in the academic literature for already 15 years. Researchers predicted that single-cell sequencing technologies would revolutionize the genomics industry. They proposed that the potential of single-cell sequencing to capture extensive details at the cell level would allow researchers to answer fundamental questions in biology and medicine [3]. In addition, other researchers suggested that recent innovations in the single-cell sequencing industry have created a shift in research focus away from bulk tissue samples and towards more detailed and extensive research into single cells. Although the potential of single-cell sequencing is widely accepted, academics employing the technology acknowledge the challenge of analyzing the resulting data [4]: “While single-cell sequencing methods are generating torrents of large-scale genomic data sets, the computational methods for analyzing these data are severely lacking. Single-cell sequencing data are distinct from standard NGS data and their analysis tools […]” [4]

Researchers that have studied the integration of large single-cell datasets, indicate that challenges expressed earlier [4], have not yet been solved: “[…] a key analytical challenge is to integrate these datasets into a harmonized atlas that can be used to better understand cellular identity and function.” [5]

Furthermore, currently the main limitations of single-cell sequencing for exploring the immune repertoire are the relatively low number of cells per analysis compared to the size of the repertoire, and the short length of the sequencing reads which does not capture the full rearranged receptor. Although the cell number is sufficient for small compartments and computational tools can reconstruct the full receptor [6], these are still a constraint to open the technology widespread usage for large repertoires of full-length receptors.

Thus, despite the innovation and advancement in data analysis technologies for single-cell sequencing, scientists still face challenges with regard to the data complexity and size. Effective solutions for the interrogation of sequencing results could further facilitate biological understanding, drive the development of new therapeutic molecules and personalized medicine.

Facilitating further growth

Although the market is expected to grow in the coming years, and the recent technological advances expand the range of possible applications, current technologies are still limited in terms of total cell numbers output compared to repertoire size. Analysis and integration of single-cell sequencing Rep-Seq data with bulk high-throughput sequencing and public datasets from other studies is still essential to for empower conclusions in biomedical studies.

Would you like to know more? Watch our on-demand webinar to find out how you can use Rep-Seq to unlock the full potential of your single-cell sequencing data using the IGX Platform.


[1] BIS Research. (2020). Global Single Cell Sequencing Market. Retrieved from https://bisresearch.com/industry-report/single-cell-sequencing-market.html
[2] Insights, Q. M. (2020). Immune Repertoire Sequencing Market, By Component (Component (Instrument, Assay Kits, Software, and Services), Application (Biomarker Discovery, Autoimmune Diseases, Cancer Immunotherapy, Infectious Disease Research, Asthma & Allergy Research, Vaccine Dev. Retrieved from https://www.quincemarketinsights.com/industry-analysis/immune-repertoire-sequencing-market
[3] Shapiro, E., Biezuner, T., & Linnarsson, S. (2013). Single-cell sequencing-based technologies will revolutionize whole-organism science. Nature Reviews Genetics.
[4] Wang, Y., & Navin, N. E. (2015). Advances and Applications of Single-Cell Sequencing Technologies. Molecular Cell.
[5] Stuart, T., Butler, A., Hoffman, P., Hafemeister, C., Papalexi, E., Mauck, W. M., … Satija, R. (2019). Comprehensive Integration of Single-Cell Data. Cell.
[6] Singh, M., Al-Eryani, G., Carswell, S., Ferguson, J. M., Blackburn, J., Barton, K., … Swarbrick, A. (2019). High-throughput targeted long-read single-cell sequencing reveals the clonal and transcriptional landscape of lymphocytes. Nature Communications.

Josine oude Lohuis
Josine oude Lohuis
Product Manager

As a Product Manager at ENPICOM, Josine is leading the development of the new antibody discovery module (ADM). This includes conducting strategic field exploration studies, defining new specifications, and driving software development by leveraging her diverse bioinformatics background and deep knowledge of immune repertoire sequencing technologies.