Cancer identification research

How does cancer identification work?

Two common methods used in the research field to identify cancer include the standard tissue biopsy as well as blood testing known as liquid biopsy. Liquid biopsy is a testing method that looks for cell-free DNA (cfDNA), cell-free RNA (cfRNA) or other tumor-derived markers in biofluid samples (e.g., blood, saliva). Small tumors shed nucleic acids, also called cell-free DNA (cfDNA), into the bloodstream, and genetic signatures from the tumor can be identified through next generation sequencing (NGS) of the DNA extracted from blood. Research focuses on liquid biopsy sampling methods because it provides a non-invasive approach for tumor profiling, measuring minimal residual disease, and the discovery of cancer biomarkers.

Challenges of circulating tumor DNA (ctDNA)

The amount of cfDNA in blood is very small, so sequencing technologies must be extremely efficient. Next generation sequencing has 3 main steps: library prep, sequencing, and analysis. During the library preparation step, DNA is converted into libraries, which allow the sample to be sequenced. A high conversion rate of DNA to library during the library preparation step will increase the identification of low ­frequency variants.

Error correction and accuracy can be further enhanced through the use of unique molecular identifiers (UMls). UMls are short sequences, often with degenerate bases, that incorporate a unique barcode onto each molecule within a given sample library. UMls have been shown to reduce the rate of false-positives and improve variant identification. By incorporating individual barcodes on each original DNA fragment, variant alleles present in the original sample (true variants) can be distinguished from errors introduced during library preparation, target enrichment, or sequencing. Any identified errors can be removed by bioinformatics methods before final data analysis.

Cancer research and the benefits of using liquid biopsy

Liquid biopsies offer several benefits over traditional tissue biopsy for studying cancer. Tissue biopsy relies on localized sampling of cancerous tissue to study the disease, usually through a time consuming, invasive, and technically difficult sampling process. Since liquid biopsy uses bodily fluids like blood or salvia, samples can be collected in a technically low-risk, non-invasive, and affordable manner.

Further, because liquid biopsy allows researchers to monitor and track cfDNA that has been released by tumor cells (ctDNA) [2], they can gain a more comprehensive understanding of the genetic makeup of a tumor. This is beneficial because the high level of heterogeneity of tumors makes it challenging for researchers to thoroughly identify cancer-related mutations from localized tissue biopsy samples alone. The genetic picture provided by liquid biopsy samples can allow researchers to take a broader approach towards cancer-related biomarkers, not just those obtained from a single sampled area.

While liquid biopsy has a number of important benefits over tissue biopsy, researchers use these two approaches in tandem to better assess the evolution of cancer overtime, monitor MRD, and quantify mutational loads.