Cancer Genomics Research
Cancer Genomics Research Clinical Cancer Research Cancer Companion Diagnostics NGS in Oncology

Cancer single-cell analysis

Study individual cancer cells for variations in DNA, RNA, the epigenome, and protein

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Analyzing cancer at the cellular level

Single-cell sequencing powered by next-generation sequencing (NGS) can examine the genomes or transcriptomes of individual cancer cells, providing a high-resolution view of cell-to-cell variation. Although it can be helpful in some cases to average samples, interrogating individual cells can reveal insights for heterogeneous samples such as tumor microenvironments. Cancer single-cell analysis can reveal drivers of cancer at the DNA, RNA, epigenetic, and protein levels (individually or as multiomic experiments) that may otherwise be missed when aggregating samples in bulk.1

Bulk-cell analysis vs single-cell analysis

Choosing between bulk-cell and single-cell analysis depends on the overall research goals. Profiling single cells can help you understand how unique populations impact cancer and how they might be exploited therapeutically.


Some key benefits of single-cell sequencing over bulk-cell sequencing include:

  • Detecting functional cell populations in the tumor microenvironment
  • Uncovering the impact of noncancerous cell populations such as immune cells (eg, B-cells and T-cells) and fibroblasts on tumor biology
  • Understanding the effects of epigenetic heterogeneity in cancer progression
  • Constructing the evolution of somatic variants from tumor samples
  • Identifying and characterizing cancer stem cell populations
Explore more cancer sequencing methods

Approaches to cancer single-cell analysis

Single-cell transcriptomics

Single-cell transcriptomics enables unprecedented insights into cellular function and individual cell interactions within their environment. Illumina NGS technology maximizes the discovery power of single-cell gene expression studies, enabling researchers to assay millions of individual cells in a single assay with high accuracy and sensitivity.

Learn more about single-cell RNA-Seq

Assay for transposase-accessible chromatin using sequencing (ATAC-Seq)

ATAC-Seq profiles chromatin accessibility across diverse cell types in complex tissues, revealing how chromatin structure influences gene expression. Single-cell ATAC-Seq provides high resolution by combining cell barcoding with Tn5 tagmentation, which tags open chromatin regions with sequencing adapters. Tagged fragments are then purified, amplified, and sequenced to generate detailed accessibility maps.

Learn more about ATAC-Seq

Single-cell immune repertoire

The single-cell immune repertoire refers to the diverse collection of individual immune cells within an organism, each equipped with unique receptor molecules on their surface. These receptors enable immune cells to recognize and respond to threats, such as pathogens or abnormal cells.

Analyzing the single-cell immune repertoire involves studying the genetic sequences that encode these receptors, providing insights into the immune system's diversity, functionality, and specificity at the individual cell level. This analysis holds promise in understanding immune responses in diseases, facilitating personalized medicine approaches, and developing targeted therapies.

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How Creighton University is advancing cancer research with single-cell sequencing

Hear from Jun Xia, PhD and Yusi Fu, PhD, codirectors of the Innovative Genomics & Bioinformatics Core (IGBC) at Creighton University, about their cancer research and the people who inspire their work. With the help of the NextSeq 2000 System, they have developed highly accurate single-cell sequencing methods to detect cancer biomarkers and fast-tracked their research, opening doors with collaborators to better understand the fundamental processes that drive cancer.

Illumina single-cell workflows

This eBook from Illumina is your guide to understanding single-cell workflows from sample prep to data analysis. Learn best practices, explore platform options, and gain insights to design robust experiments.

Featured single-cell products

Illumina Single Cell 3' RNA Prep

Accessible and highly scalable single-cell RNA-Seq solution for mRNA capture, barcoding, and library prep without complex workflows or microfluidics

NovaSeq X Series ordering

Advanced chemistry, optics, and informatics combine to deliver exceptional sequencing speed and data quality, outstanding throughput, and scalability.

DRAGEN secondary analysis ordering

Maximize genomic insights with Illumina DRAGEN secondary analysis, learn about the latest updates, read FAQs, and find product support.

Resources

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Illumina Connected Analytics single-cell RNA workflow

In this demonstration, we will show you how an Illumina Connected Analytics (ICA) user can perform a single-cell RNA analysis workflow consisting of a DRAGEN secondary analysis pipeline and interpret those results using an interactive R Shiny application in the ICA Bench environment.

Speak to a specialist

Interested in learning more about single-cell cancer research?

References
  1. Aldridge S, Teichmann SA. Single cell transcriptomics comes of age. Nat Commun. 2020;11(1):4307. doi:10.1038/s41467-02018158-5