Performance of the hybrid tumor-informed and tumor-agnostic ctDNA testing to predict breast cancer recurrence and progression: A real-world study in Southeast Asia.

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Background: ctDNA is a novel biomarker to monitor treatment response and predict cancer recurrence. Tumor-informed ctDNA assays require high-quality tumor tissues which are unobtainable in many contexts. We developed a hybrid tumor-informed and tumor-agnostic approach to overcome this constraint and evaluate its performance in real-world samples. Methods: We retrospectively analyzed 262 real-world blood samples of 180 patients diagnosed with stage I-IV breast cancer (BC). ctDNA was detected by tumor-informed personalized mutations, combined with a tumor-agnostic BC-specific hotspot panel (K-TRACK, Gene Solutions). The longitudinal ctDNA status was then compared with clinical outcomes documented for 69 early-stage and 17 metastatic-stage patients. Results: The overall pre-treatment ctDNA detection rates were 56.1% and 70.9% for early- and metastatic- stages respectively, and highest in HER2+ and triple negative BC. Compared to the tumor-informed approach, the hybrid approach improved ctDNA detection rate by 20.4% for cases with suboptimal FFPE quality. In the early stage, post-operative ctDNA was detected in 80.0% (8/10) of the patients having recurrence, with lead time up to 11.0 months; while 98.3% (58/59) of those with no recurrence had negative results. ctDNA positivity was an independent prognostic factor (p<0.001) that increased risk of recurrence (HR=147.8, 95% CI: 26.3-831.3). In the metastatic stage, at 12 weeks after therapy initiation, 85.7% (6/7) of the molecular responders, who had ctDNA cleared or reduced by >50% of baseline VAF level, achieved clinical partial response or stable disease; while 70.0% (7/10) of the molecular non-responders had confirmed progressive disease. In a subgroup of metastatic ER+ patients, tumor-agnostic hotspot panel identified new resistance mutations including ESR1 Y537N (7.1%), ESR1 Y538G (3.6%), ESR1 P535H (1.8%). Conclusions: Our hybrid tumor-informed and tumor-agnostic ctDNA assay improved ctDNA detection rate, and predicted cancer recurrence and progression with high accuracy in real-world samples.