Liquid Biopsy Research

liquid biopsy diagram

Study biomarkers in liquid biopsies with NGS

Scientists can use liquid biopsy samples to detect and characterize various cancer-derived biomarkers present in the blood. These biomarkers are absent in healthy individuals and those who are cancer-free. Illumina offers innovative next-generation sequencing (NGS) liquid biopsy solutions for cancer biomarker research to analyze:

  • Circulating tumor cells (CTCs)
  • Cell-free DNA (cfDNA) and circulating tumor DNA (ctDNA)
  • Cell-free RNA (cfRNA) and circulating tumor RNA (ctRNA)
  • Circulating proteins for detection and profiling

Limitations of tissue biopsy

Several challenges limit the utility of tissue biopsy for use in translational and clinical cancer research, including:

  • Inaccessibility of the tissue of interest
  • Requirement for specialized skills from qualified medical personnel
  • Invasiveness of repeat biopsies over time
  • Limited representation of intra- and inter-tumor heterogeneity
  • Patient ineligibility for physical biopsy due to significant procedural risk, insufficient quality or quantity of tissue, and other factors
Doctor listening to patient's lungs.

What are circulating tumor cells (CTCs)?

CTCs are cells shed from tumors into the bloodstream. Multiple studies have demonstrated that CTCs have metastatic potential and are associated with aggressive or advanced disease and poor prognosis in various cancer types. While CTCs can serve as biomarkers for liquid biopsy-based cancer characterization, their rarity in the bloodstream (< 1 to < 50 CTCs in 7.5ml of blood on average) remains a significant challenge for detection and characterization. NGS-based technologies, which can detect low levels of CTCs with high throughput capabilities, are opening an exciting frontier for cancer screening and early detection.

liquid biopsy tube

Popular methods of CTC isolation involve:

  • Enrichment of CTCs based on antigen expression, eg, epithelial cell adhesion molecule (EpCAM)
  • Depletion of non-CTCs, such as blood cells and immune cells
  • Leukapheresis

Technological advances in single-cell isolation and single-cell sequencing methodologies have enabled detailed analysis of single CTCs at the genomic, transcriptomic, and epigenomic levels. Combining liquid biopsy with single-cell sequencing of CTCs can elucidate the cellular heterogeneity that contributes to tumor biology.

Understanding cancer biology female scientist

Understanding cancer biology with methylation microarrays

Methylation patterns in cfDNA

Abnormal methylation patterns are a hallmark of many cancers. Changes in DNA methylation occur early during tumorigenesis and result in a state where most of the genome becomes hypomethylated and CpG islands become hypermethylated.

This switch in global methylation patterns leads to genomic instability and silencing of tumor suppressor genes, driving tumor progression and metastasis. Importantly, multiple studies have demonstrated that the methylation pattern of ctDNA recapitulates the pattern present in the cell/tissue of origin. This indicates that liquid biopsy analysis of ctDNA methylation can be used for early detection of cancer, analysis of tissue of origin, surveillance of minimal residual disease (MRD), monitoring therapy response, and more.

Cell-free RNA (cfRNA) and circulating tumor RNA (ctRNA)

cfRNAs can be released from multiple cell types present in the bloodstream as well as from cancer cells. These ctRNAs are potential biomarkers that can be assayed by liquid biopsy to identify specific cancers, detect cancer initiation, reveal tissue-of-origin, elucidate molecular mechanisms of disease, monitor therapeutic response, and more.

Unlike DNA, which is identical in every cell/tissue (except for genetic variants), RNA is dynamically and differentially expressed between cell types and tissues. This enables ctRNAs to be used to detect cancer and potentially localize it in the body. The diverse nature of RNA expression may also enable use of ctRNAs to determine and classify cancer subtypes early in disease, which is important given the wide range in progression, treatment options, and prognosis between cancers, even those associated with the same organ or tissue.

Short and long RNAs in liquid biopsy: How to sequence them and what they tell us about cancer

In this on-demand Illumina webinar, speakers discuss methodologies for sequencing long or short RNAs from liquid biopsy samples, along with implications for cancer research.

app note Illumina genomics architecture

2023 Liquid Biopsy eBook: Circulating tumor cells, ctDNA, and cfRNA sequencing methods for liquid biopsy research

This 20+ page eBook provides published, comprehensive workflows for thorough characterization of liquid biopsy samples using NGS and microarrays.

  • Overviews of liquid biopsy analytes
  • Research examples, diagrams, and tables outlining every step of circulating tumor cell (CTC) sequencing, circulating tumor DNA (ctDNA) methylation profiling, ctDNA sequencing and cell-free RNA (cfRNA) sequencing
  • Links to application notes, downloadable methods guides, and more resources

Download eBook

Recommended liquid biopsy research solutions

As a genomics technology leader, Illumina offers integrated workflows and innovative solutions that are validated for liquid biopsy analyte sequencing for cancer research.