Commentary
Commentary on Liquid Biopsy Detection of a TP53 Variant in a “Disease-Free” Pediatric Patient with a History of TP53-mutant Adrenocortical Carcinoma
Sasha Witts,ª Nicholas J. Clemons [D,a,b and David S. Liua,c,d,e,*
Plasma cell-free DNA (cfDNA) may assist in cancer diagno- sis, prognosis, surveillance, and assessing treatment re- sponse. In the analysis of cfDNA, matched tumor and normal tissue/cells are commonly used to differentiate germline variants vs tumor-derived somatic variants in the cfDNA. Without access to tumor tissue for comparison, variant allele frequency (VAF) may be used to infer whether a variant in cfDNA is hereditary. While a VAF of approxi- mately 50% may indicate a germline mutation, preferential amplification or normal homologue capture may result in <50% VAF for certain germline variants. However, as de- scribed in a recent case report by Blackburn et al. (1), post- zygotic genetic mosaicism can complicate the analysis and interpretation of cfDNA, particularly in the context of mon- itoring for minimal residual disease (MRD).
Blackburn et al. (1) describe plasma cfDNA analysis in a patient with metastatic adrenocortical carcinoma and mosaic Li-Fraumeni syndrome (LFS). The incidence of post-zygotic TP53 mutational mosaicism in patients with LFS-associated cancers can be as high as 11% (2). This decreases the specificity of cfDNA for MRD, par- ticularly if the TP53 variant is the only abnormality de- tected, as this cfDNA may be derived from non-tumor origins. The VAF for a post-zygotic mosaic mutation will thus vary depending on the extent of mosaicism and is uninformative for monitoring MRD if there is truly a tumor-free reference point or “baseline”. Therefore, sequencing and comparing several non-tumor tissues (e.g., blood, skin, and buccal mucosa) with the tu- mor should be undertaken early, especially when (a) there are no other variants detected in plasma, (b) the TP53
variant is non-oncogenic, (c) the VAF is low, and (d) there is a family history of LFS-associated cancers.
In our experience (3), the factors that increase the reliability of plasma cfDNA for MRD are (a) VAF that changes appropriately with treatment (e.g., surgical resection), (b) known pathological variant detected, (c) variant(s) found only in tumor but not in normal tissue at sufficient read depth, (d) VAF >5%, and (e) concur- rent variants detected in both tumor and plasma.
Currently, the lack of standardized protocols, se- quencing platforms, and VAF thresholds preclude the clinical translation of cfDNA. Cases like these further challenge the interpretation of cfDNA.
Author Contributions: The corresponding author takes full responsibility that all authors on this publication have met the following required criteria of eligibility for authorship: (a) significant contributions to the conception and design, acquisition of data, or analysis and interpretation of data; (b) drafting or revising the article for intellectual content; (c) final approval of the published article; and (d) agreement to be accountable for all aspects of the article thus ensuring that questions related to the accuracy or integrity of any part of the article are appropriately investigated and re- solved. Nobody who qualifies for authorship has been omitted from the list.
Sasha Witts (Conceptualization-Equal, Formal analysis-Equal, Methodology-Equal, Writing-original draft-Equal, Writing-review & editing-Equal), Nicholas Clemons (Conceptualization-Equal, Formal analysis-Equal, Supervision-Equal, Writing-review & editing-Equal), and David Liu (Conceptualization-Equal, Formal analysis-Equal, Supervision-Equal, Writing-original draft-Equal, Writing-review & editing-Equal).
Authors’ Disclosures or Potential Conflicts of Interest: No authors declared any potential conflicts of interest.
References
1. Blackburn PR, Lei S, Jia S, Tatevossian RG, Koo SC. Liquid biopsy de- tection of a TP53 variant in a “disease-free” pediatric patient with a history of TP53-mutant adrenocortical carcinoma. Clin Chem 2025; 71:24-30.
2. Ceyhan-Birsoy O, Selenica P, Chui MH, Jayakumaran G, Ptashkin R, Misyura M, et al. Paired tumor-normal sequencing provides insights into the TP53-related cancer spectrum in patients with Li-Fraumeni syndrome. J Natl Cancer Inst 2021;113:1751-60.
3. Allan Z, Liu DS, Lee MM, Tie J, Clemons NJ. A practical approach to interpreting circulating tumor DNA in the man- agement of gastrointestinal cancers. Clin Chem 2024;70: 49-59.
ªDivision of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Australia; bSir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia; “Upper Gastrointestinal Surgery Unit, Division of Surgery, Anaesthesia and Procedural Medicine, Austin Health, Heidelberg, Victoria, Australia; dGeneral and Gastrointestinal Surgery Research and Trials Unit, Department of Surgery, University of Melbourne, Austin Precinct, Heidelberg, Victoria, Australia; ªDivision of Cancer Surgery, Peter MacCallum Cancer Centre, Melbourne, Australia.
*Address correspondence to this author at: Division of Cancer Surgery, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, Victoria 3000, Australia. Tel +61-3-8559-5000; e-mail David.Liu@ petermac.org.
Received July 15, 2024; accepted August 5, 2024.
https://doi.org/10.1093/clinchem/hvae132
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