PLoS ONE (Jan 2023)

Concordance between whole exome sequencing of circulating tumor DNA and tumor tissue.

  • Julanee Leenanitikul,
  • Prangwalai Chanchaem,
  • Suwanan Mankhong,
  • Sikrit Denariyakoon,
  • Valla Fongchaiya,
  • Areeya Arayataweegool,
  • Pattama Angspatt,
  • Ploytuangporn Wongchanapai,
  • Verayuth Prapanpoj,
  • Kris Chatamra,
  • Trairak Pisitkun,
  • Sira Sriswasdi,
  • Piriya Wongkongkathep

DOI
https://doi.org/10.1371/journal.pone.0292879
Journal volume & issue
Vol. 18, no. 10
p. e0292879

Abstract

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Next generation sequencing of circulating tumor DNA (ctDNA) has been used as a noninvasive alternative for cancer diagnosis and characterization of tumor mutational landscape. However, low ctDNA fraction and other factors can limit the ability of ctDNA analysis to capture tumor-specific and actionable variants. In this study, whole-exome sequencings (WES) were performed on paired ctDNA and tumor biopsy in 15 cancer patients to assess the extent of concordance between mutational profiles derived from the two source materials. We found that up to 16.4% ctDNA fraction can still be insufficient for detecting tumor-specific variants and that good concordance with tumor biopsy is consistently achieved at higher ctDNA fractions. Most importantly, ctDNA analysis can consistently capture tumor heterogeneity and detect key cancer-related genes even in a patient with both primary and metastatic tumors.