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

Julanee LeenanitikulPrangwalai ChanchaemSuwanan MankhongSikrit DenariyakoonValla FongchaiyaAreeya ArayataweegoolPattama AngspattPloytuangporn WongchanapaiVerayuth PrapanpojKris ChatamraTrairak PisitkunSira SriswasdiPiriya Wongkongkathep
Published in: PloS one (2023)
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.
Keyphrases
  • circulating tumor
  • cell free
  • circulating tumor cells
  • squamous cell carcinoma
  • small cell lung cancer
  • copy number
  • papillary thyroid
  • gene expression
  • dna methylation
  • young adults
  • single molecule
  • data analysis