What’s Next for Single-Cell Genomics?

April 14, 2022

By MedGenome Scientific Affairs

Single-cell genomic analysis has emerged as a powerful method for studying complex disease. By providing comprehensive analyses of individual cells, single-cell sequencing allows researchers to examine cellular heterogeneity, which especially useful in oncology, neurology, immunology, and developmental research.

Because it can analyze individual cells in depth, scientists can obtain unbiased cell analyses. According to Lei et al., “Single-cell sequencing significantly outperforms previous sequencing technologies in terms of our understanding of the human biology of embryonic cells, intracranial neurons, malignant tumor cells and immune cells because it can probe cellular and microenvironmental heterogeneity at single-cell resolution.”1

A relatively new technique, single-cell genomic sequencing technologies continue to improve; in turn, scientists are developing new approaches and discovering novel uses. While technological limitations remain, single-cell genomic analysis promises to advance understanding of cell types to inform novel therapies.

The next milestone in this field is single-nucleus RNA sequencing (snRNA-seq), which allowed the extension of single-cell transcriptomics analyses to human diseases for which live tissue is difficult to obtain. One of the first studies was conducted by Lake et al., which involved single-cell analysis of molecular pathology in the brain of patients with autism spectrum disorder (ASD).

What is Single-Cell Genomic Sequencing?

Scientists use single-cell genomics to study the functionality and properties of a cell.2 Whereas conventional genetic sequencing uses tissue samples to produce the average diversity of cells, single-cell genomics drills down to the single-cell level.3 This level of specificity allows scientists to study cell-to-cell variations and identify rare cells that play a role in disease progression.

Single-cell genomic techniques accomplish the following:4

  • Characterize and identify heterogeneous cell populations
  • Discover new cell markers and regulatory pathways
  • Uncover novel cell types, cell states and rare cell types
  • Reconstruct developmental hierarchies and reveal lineage relationships

Single-Cell Genomic Analysis Techniques

In its early days (a little over ten years ago), single-cell sequencing caused a stir in the scientific community, but its high cost made it impractical to use in most situations. Technology has advanced, however, enabling high-throughput single-cell sequencing via multiple profiling strategies.

In addition to single-cell RNA sequencing (RNA-seq), other sequencing platforms and methods allow scientists to capture information on cell-surface proteins, chromatin state, genetic perturbations, and genome data.5 Each method expands on RNA data to provide a unique perspective on cell state and identity.

The Single-Cell Sequencing Protocol
Preparing samples for processing and capturing individual cells is a complex process that involves four primary steps:6

  • Isolation of single cells from a cell population
  • Extraction, processing, and amplification of the genetic material of each isolated cell
  • Preparation of a “sequencing library” including the genetic material of an isolated cell
  • Sequencing of the library using a next-generation sequencer

To successfully generate single-cell libraries from the diverse starting material including tissue types and cells. MedGenome has integrated several validated single-cell isolation and library preparation platforms such as Miltenyi tissue dissociation.

Single Cell Sequencing Protocol

Single-Cell Genomics Applications
Because immune cells have several distinct functions, single-cell sequencing is a valuable tool for understanding the immune system and identifying new targets for treatment.4 Researchers have used the technique to identify subpopulations of spleen and blood natural killer (NK) cells in humans and mice, contributing to translational research. Researchers have also used single-cell RNA-seq to study highly heterogeneous immune cells, helping them better understand why the immune system weakens with age.

Researchers out of Duke University recently used single-cell sequencing to study cerebral cavernous malformations (CCMs), a blood vessel abnormality that can lead to brain hemorrhage.7 Using the technique helped them answer questions about CCM pathogenesis.

Single-cell genomic techniques are becoming especially valuable to oncology researchers, allowing them to better understand treatment response and resistance, as well as inform diagnosis and monitoring.8 As a study published in Biomolecules concludes, “the molecular characteristics of each cellular component and its interconnections—either promoting or inhibiting tumor growth—are all points that can be leveraged during therapeutic development. Therefore, single-cell genomics and the related multi-omics technologies are exploratory tools that far exceed the scope and effectiveness of preceding bulk genomic analyses.” 8

Partner with a Single-Cell Genomics Solutions Expert
Whether you’re studying tumor cell response or immune cell functions, single-cell genomics is a complex but powerful method for understanding the cellular structure, behavior, and heterogeneity. Get in touch with MedGenome to explore various single-cell sequencing solutions and our abilities to design and support your experiment.


  1. 1 Lei, Y., Tang, R., Xu, J. et al. Applications of single-cell sequencing in cancer research: progress and perspectives. J Hematol Oncol 14, 91 (2021). https://doi.org/10.1186/s13045-021-01105-2
  2. 2 Kaur, Raman et al. Chapter 9 – Single-Cell Genomics: Technology and Applications. Single-Cell Omics, Academic Press (2019) https://doi.org/10.1016/B978-0-12-814919-5.00009-9
  3. 3 Wang Q, Yang KL, Zhang Z, et al. Characterization of Global Research Trends and Prospects on Single-Cell Sequencing Technology: Bibliometric Analysis. J Med Internet Res. 2021;23(8):e25789. doi:10.2196/25789
  4. 4 Tang X, Huang Y, Lei J, Luo H, Zhu X. The single-cell sequencing: new developments and medical applications. Cell Biosci. (2019);9:53. doi:10.1186/s13578-019-0314-y
  5. 5 Vargas, Derek. Advancing Single-Cell Multi-Omic Approaches to Biomedical Research. MedGenome blog, (2021) https://research.medgenome.com/advancing-single-cell-multi-omic-approaches-biomedical-research
  6. 6 Vaga, Stephanie Ph.D. Understanding Single-Cell Sequencing, How It Works, and Its Applications. Technology Networks, (2022) https://www.nature.com/articles/s41431-019-0508-0https://www.technologynetworks.com/genomics/articles/understanding-single-cell-sequencing-how-it-works-and-its-applications-357578#D5
  7. 7 Snellings DA, Girard R, Lightle R, et al. Developmental venous anomalies are a genetic primer for cerebral cavernous malformations. Nat Cardiovasc Res. (2022);1:246-252. doi:10.1038/s44161-022-00035-7
  8. 8 Kim N, Eum HH, Lee HO. Clinical Perspectives of Single-Cell RNA Sequencing. Biomolecules. 2021;11(8):1161. doi:10.3390/biom11081161
  9. 9 Lake BB, Ai R, Kaeser GE, Salathia NS, et al. Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain. SCIENCE 2016; 6293: 1586-1590. doi: 10.1126/science.aaf1204

#single cell genomic sequencing, #single cell sequencing, #single cell genomics, #single cell genomic analysis

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