Tumor-naïve multimodal profiling of circulating tumor DNA to detect minimal residual disease in solid tumors.

[BACKGROUND] Circulating tumor DNA (ctDNA) analysis that is tumor-informed and personalized requires high-quality tissue specimens, which are unavailable in certain clinical contexts and pathology practice in Southeast Asia.

[OBJECTIVES] We aimed to develop and clinically validate an alternative tumor-naïve ctDNA assay.

[DESIGN] A retrospective observational study.

[METHODS] Our tumor-naïve multimodal profiling integrated mutation detection, using both amplicon and hybridization sequencing, with analysis of copy number alteration (CNA) and fragmentomics of cfDNA. We analyzed blood samples of 948 cancer patients and 566 non-cancer donors enrolled in previous studies to evaluate the analytical performance of ctDNA detection. Clinical performance was assessed using post-surgical samples of 97 breast cancer and 51 colorectal cancer patients to compare tumor-naïve ctDNA status with clinical recurrence. The performance was directly compared with the tumor-informed method using identical samples.

[RESULTS] For mutations, a combination of amplicon and hybridization sequencing provided higher sensitivity and broader coverage of mutation detection than single methods. Variants of clonal hematopoiesis of intermediate potential were common, mainly in the gene, and must be excluded. Besides mutations, the addition of CNA and fragment length profiles significantly improved the sensitivity of ctDNA detection in the metastatic stage, but modestly in the early stage. In breast cancer, surveillance tumor-naïve ctDNA achieved 54.5% sensitivity and 98.8% specificity for predicting recurrence (hazard ratio (HR) = 23.3,  < 0.0001). In colorectal cancer, the sensitivity and specificity of surveillance ctDNA for predicting recurrence were 80.0% and 100%, respectively (HR = 35.6,  < 0.0001). The overall accuracy of the tumor-naïve method was lower than the tumor-informed method, but the performance gap varied by cancer stage and cancer type.

[CONCLUSION] The tumor-naïve method could be a reliable alternative to monitor ctDNA when obtaining high-quality tissue samples is challenging. The performance of this method was better in high ctDNA-shedding cancer or at the metastatic stage.