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Cancer liquid biopsy


Liquid biopsy is a non-invasive testing method that looks for cell-free, circulating tumor DNA (cfDNA, ctDNA) or other tumor-derived markers in biofluid samples.

What is 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). Researchers have started to focus on liquid biopsy sampling methods because it provides a non-invasive approach for tumor profiling, measuring minimal residual disease (MRD), and the discovery of cancer biomarkers [1].

Liquid biopsy vs tissue biopsy 

As mentioned above, liquid biopsies offer a number of 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 saliva, 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.

Challenges of using liquid biopsy for cancer research

Samples obtained through liquid biopsy can be studied using targeted next generation sequencing (NGS) approaches such as amplicon sequencing, custom hybridization capture, whole exome sequencing, methylation sequencing (methyl-seq), and targeted RNA sequencing (targeted RNA-seq). These high-throughput approaches make it possible to track mutations in cfDNA and identify new cancer-related biomarkers.

However, profiling cfDNA can be challenging as these genetic targets are present at very low concentrations. Therefore, NGS library preparation should be done with care in order to obtain sufficient material to generate enough sequencing data for analysis, especially when the goal is the identification of rare mutations or new biomarkers.

IDT offers the xGen™ cfDNA & FFPE DNA Library Prep Kit, which helps to enable users to generate high-quality, NGS sequencing libraries from cfDNA and FFPE samples. This kit includes adapters that contain unique molecular identifiers (UMIs) which aid in bioinformatic error correction after sequencing, helping to enable the identification of low frequency variants in research samples. The xGen cfDNA &FFPE DNA Library Prep Kit was also designed to work seamlessly with xGen Hybridization Capture Probes and Reagents. This is an important feature of this kit as target enrichment via amplicon sequencing or hybridization capture is a key step of targeted NGS library preparation.

Hybridization capture uses biotinylated oligonucleotide probes to capture regions of interest, while amplification uses PCR for target enrichment. Both approaches target specific sequences to allow for deeper sequencing of genetic regions of interest. The type of enrichment approach you choose largely depends on the aim of your research study. Both amplicon sequencing and hybridization capture are powerful approaches for the identification of rare mutations and disease associated variants and genotyping. However, for approaches like whole exome sequencing, custom hybridization capture could be necessary.

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Cancer molecular profiling

Research in the discovery and identification of new, targetable biomarkers is driven by comprehensive tumor profiling using NGS. However, converting tissue samples into NGS libraries is often challenging due to the low quantity and quality of DNA in such samples. Download this application note to explore how low-frequency variants have been identified in this application.


Applicable technologies

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1. Lone SN, Nisar S, Masoodi T, et al. Liquid biopsy: a step closer to transform diagnosis, prognosis and future of cancer treatments. Mol Cancer. 2022;21(1):79. 

2. Neumann MHD, Bender S, Krahn T, Schlange T. ctDNA and CTCs in Liquid Biopsy - Current Status and Where We Need to Progress. Comput Struct Biotechnol J. 2018;16:190-195.