Cancer Res Treat.  2023 Apr;55(2):351-366. 10.4143/crt.2022.1026.

Clinical Circulating Tumor DNA Testing for Precision Oncology

• Kim H
• Park KU

• KMID: 2541224
• DOI: http://doi.org/10.4143/crt.2022.1026

Abstract

Circulating tumor DNA (ctDNA) is the portion of the cell-free DNA in the blood of cancer patients released from tumor cells via apoptosis, necrosis, or active release. From 10 mL of blood, the 4-5 mL of plasma obtained from a cancer patient contains 5-10 ng/mL of ctDNA. The plasma contains not only ctDNA of tumor origin, but also DNA from normal cells or clonal hematopoiesis. Another characteristic of ctDNA is its rapid clearance from circulation; it has a half-life of 16 minutes to 2.5 hours. Obtaining reliable results from ctDNA requires the application and approval of standardized clinical validation guidelines; however, the status of numerous ctDNA tests currently varies. The clinical use of ctDNA testing should be carefully considered based on the test’s specific needs and characteristics. Here we provide the different characteristics of ctDNA tests and information regarding their validation and approval status.

Keyword

Circulating tumor DNA; Clinical validation; Clinical utility; Precision oncology

Figure

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  Fig. 1 The number of publications searched on the PubMed database (https://pubmed.ncbi.nlm.nih.gov/) from 1974 to 2021 using the following keywords: cell-free DNA, cfDNA; circulating tumor DNA, ctDNA; and liquid biopsy. Search was limited to exact match for each term, and the species limited to human. The liquid biopsy was first reported in 1974, and cell-free DNA was first reported in 1986. Since 2014, the number of publications for all search terms, including circulating tumor DNA has increased exponentially. The rapid increase in publications resulted in fragmented use of similar nomenclatures, and the number of search results using terms with the same meaning are displayed differently.

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  Fig. 2 Defining a systematic nomenclature for confounding terms regarding circulating tumor DNA (ctDNA). The ctDNA is a concept that belongs to cell-free nucleic acid in a broad sense and cell-free DNA in a narrow sense. The cell-free nucleic acids are biologically and structurally diverse. Depending on the origin of the nucleic acids, the nucleic acids are mixed, such as nucleic acids derived from various cells or microorganisms. For systematic nomenclature, a top-down approach from cell-free nucleic acid into subclasses are necessary. First, nucleic acids can be classified according to its presence in circulation such as blood and lymphatics, or in non-circulatory fluids, such as urine, saliva, and cerebrospinal fluid. As the use of term cell-free nucleic acids is not limited to cancer, but also applied in prenatal testing and post-transplant surveillance, the terms should be organized by their classifications. Figures were created with BioRender [23].

• 

  Fig. 3 Different features of circulating tumor DNA (ctDNA) in the plasma. Different tumor-related clinical information can be obtained depending on the structural features of the ctDNA detected during the examination. In ctDNA, DNA abnormalities related to cancer are identified as somatic mutations, copy number aberrations, and structural abnormalities of chromosomes such as inversions, translocations, insertions, and deletions. In addition, useful information can be obtained through epigenetic aberrations such as methylation patterns and DNA fragment size distributions. Figures were created with BioRender [23].

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  Fig. 4 A brief summary of the FDA-approved assays in chronological order. Assays are presented in the order of FDA approval date (circle) placed within the timeline (red line). The assays listed above are categorized as in vitro diagnostic devices and assays provided as laboratory services are listed under the timeline. ALK, anaplastic lymphoma kinase; AS-PCR, allele-specific PCR; BCT, blood collection tube; EGFR, epidermal growth factor receptor; cfDNA, cell-free DNA; FDA, Food and Drug Administration; FFPE, formalin-fixed paraffin-embedded; N/A, not applicable; NGS, next-generation sequencing; RT-PCR, real time-polymerase chain reaction.

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  Fig. 5 Current variances present among circulating tumor DNA (ctDNA) testing used in clinical trials. The following critical testing conditions were identified from the clinical trials using ctDNA provided from ClinicalTrials.gov when available; blood collection tube (A), whole blood volume (B), time to sample processing (C), 1st centrifugations (D), 2nd centrifugations (E), DNA extraction method (F), input DNA volume (G), and use of Food and Drug Administration (FDA)–approved test (H). The degree of agreement in factors of whole blood volume, sample processing methods used for ctDNA acquisition, and utilization of FDA-approved assay was low.

Reference

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