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Multi-region sequencing reveals genetic correlation between esophageal squamous cell carcinoma and matched cell-free DNA

  • Zuyang Yuan
    Affiliations
    Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
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  • Xinfeng Wang
    Affiliations
    Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
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  • Xiao Geng
    Affiliations
    Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
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  • Yin Li
    Affiliations
    Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
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  • Fengwei Tan
    Affiliations
    Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
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  • Qi Xue
    Affiliations
    Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
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  • Shugeng Gao
    Affiliations
    Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
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  • Jie He
    Correspondence
    Corresponding author.
    Affiliations
    Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
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      Highlights

      • First study to compare the correlation between multiregional solid tumor and matched cell-free DNA in esophageal squamous cell carcinoma (ESCC).
      • Some frequent ESCC-associated mutations could be detected in cfDNA.
      • The next generation sequencing approaches revealed the highly intratumoral heterogeneity in ESCC and enabled the detection of both ubiquitous and heterogeneous mutations in cfDNA.
      • cfDNA has the potential to be a biomarker for the presence of tumor cells in ESCC patients and aid in monitoring and accurate prediction of therapeutic response during ESCC treatments and management.

      Abstract

      Purpose

      This study aimed to determine if both ubiquitous and heterogeneous somatic mutations could be detected in circulating cell-free DNA (cfDNA) in patients with esophageal squamous cell carcinoma (ESCC).

      Methods

      Paired multi-regional tumor tissues, cfDNA, and white blood cells (WBCs) were collected from five ESCC patients before treatment, as part of an ongoing prospective study (NCT02395705). Samples from Cohort 1 were sequenced by whole-exome sequencing and samples from Cohort 2 were sequenced by targeted capture sequencing. Somatic single-nucleotide variations (SNVs) were detected by comparing solid tumor or cfDNA with matched WBCs, with a minimum variant allele frequency (VAF) of 0.1% and P value <0.05.

      Results

      Genomic DNA (gDNA) and plasma-derived cfDNA from 26 samples were sequenced successfully. In Cohort 1, a significant linear relationship between the tumor and cfDNA VAFs (R2= 0.78, P < 0.0001) was found. In Cohort 2, cfDNA could recover an average of 60.7% (31/51; range, 35.7–76.2%) of somatic mutations present in matched solid tumors. There was a significant positive correlation in VAFs between cfDNA and matched solid tumor tissues (R2= 0.92, P < 0.0001).

      Conclusions

      Both sequencing approaches revealed high intratumoral heterogeneity in ESCC, and enabled the detection of both ubiquitous and heterogeneous mutations in cfDNA.

      Keywords

      Abbreviations:

      cfDNA (circulating cell-free DNA), ESCC (esophageal squamous cell carcinoma), WBC (white blood cell), SNV (single-nucleotide variation), VAF (variant allele frequency), gDNA (genomic DNA), EAC (esophageal adenocarcinoma), ctDNA (cell-free tumor DNA), NGS (next-generation sequencing), WES (whole-exome sequencing), InDels (insertions and deletions), VAFmin (minimum variant allele frequency), Mb (megabases)
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