Concordance of Targeted Sequencing from Circulating Tumor DNA and Paired Tumor Tissue for Early Breast Cancer

Chi Cheng Huang, Yi Fang Tsai, Chun Yu Liu, Pei Ju Lien, Yen Shu Lin, Ta Chung Chao, Chin Jung Feng, Yen Jen Chen, Jiun I. Lai, Han Fang Cheng, Bo Fang Chen, Chih Yi Hsu, Jen Hwey Chiu, Ling Ming Tseng*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


In this study, we evaluated the concordance of targeted sequencing between paired ctDNA and matched tumor samples from early breast cancers treated with curative intention. Molecular profiling was performed using the Oncomine Comprehensive Assay v3 and the Oncomine Breast cfDNA Assay v2. The liquid biopsy detection rate was 39% (all-stage breast cancers, n = 612). Among 246 early-stage patients assayed for both ctDNA and matched tumor, the cfDNA assay detected 73 (29.6%) and the comprehensive assay detected 201 (81.7%) breast cancers with at least one alteration (χ2 test, p = 0.001). In total, 67 (25.6%) cases tested positive on both platforms, while the cfDNA and comprehensive assays detected an additional 10 (4%) and 138 (56%) cases, respectively. The most prevalent mutant genes were TP53 (68.3%) and KRAS (53.5%), while the PIK3CA (39.4%), AKT1 (45.9%), and ERBB2 (17.1%) mutations constituted biomarkers for FDA-approved therapeutics. Our study showed that tumor tissue should be the source of actionable mutation detection for early breast cancers, considering that the concordance rate between tumor and liquid biopsy was only one-quarter.

Original languageEnglish
Article number4475
Issue number18
StatePublished - Sep 2023


  • concordance
  • ctDNA
  • early-stage breast cancer
  • liquid biopsy
  • targeted sequencing
  • tumor sequencing


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