Assessment of ctDNA tumor fraction and confidence in driver-negative liquid biopsy findings.

Abstract

e15126 Background: Circulating tumor DNA (ctDNA) analysis enables non-invasive detection of tumor-specific genomic alterations, supporting the clinical utility of liquid biopsy in cancer diagnosis, prognosis, and treatment selection. However, negative results can be difficult to interpret when circulating tumor DNA (ctDNA) levels (viz. Tumor fraction) are low. ctDNA tumor fraction is a key determinant of assay sensitivity and may distinguish true negative findings from cases with insufficient tumor shedding. ctDNA tumor fraction varies by cancer type, disease stage, and tumor burden, and low tumor fraction can limit mutation detection. Understanding the impact of ctDNA tumor fraction is critical for interpreting liquid biopsy results, optimizing assay performance, and guiding clinical decision-making. This study evaluates ctDNA tumor fraction as a clinically actionable metric to guide treatment decisions and advise reflex tissue testing upon negative liquid biopsy results using the OncoIndx next-generation sequencing (NGS) assay. Methods: A retrospective concordance analysis was performed on paired tissue biopsy (TBx) and liquid biopsy (LBx) samples from 279 patients with diverse solid tumors tested using the OncoIndx next-generation sequencing assay. Positive percent agreement between tissue and liquid biopsy for detection of oncogenic driver alterations was calculated. Patients were stratified by ctDNA tumor fraction ( > 20% vs < 20%) to evaluate positive and negative concordance between TBx and LBx findings. Results: From the analysis, we found that 176 patients were ctDNA-negative and 103 were ctDNA-positive. From the ctDNA positive cohort, 99 patients showed concordance with tumor fraction ( > 20%) with a positive predictive agreement of 96.1% while 4 patients were found to have tumor fraction < 20%. From the ctDNA negative cohort of 176 patients, 161 patients were found to have ctDNA tumor fraction above 20% ( > 20%) and only 15 patients were found with tumor fraction < 20%. This clearly indicates that 91.5% (n = 161) of patients in the ctDNA negative cohort with high tumor fraction fall under the category of true NMD which was also found to be negative in paired tissue biopsy sample. Whereas, the 8.5% (n = 15) of patients in ctDNA negative cohort who might require reflex testing since their tumor fraction was below the 20% cut-off. Conclusions: ctDNA tumor fraction is a critical interpretive biomarker that can guide reflex tissue testing after negative liquid biopsy results. Incorporation of tumor fraction thresholds into clinical reporting with OncoIndx may reduce unnecessary invasive procedures while minimizing the risk of missed actionable mutations, thereby improving confidence in precision oncology decision-making.