Technical and biological constraints on ctDNA-based genotyping

Circulating tumor DNA (ctDNA) is an emerging source of relevant tumor information across a variety of clinical contexts. In prostate cancer, existing sensitive strategies for early cancer detection and disease monitoring place emphasis on the use of ctDNA to detect treatment-predictive genomic biomarkers in the advanced setting. Multiple technical and biological variables can confound ctDNA-based metastatic cancer genotyping, complicating the integration of ctDNA into routine clinical management strategies. ctDNA fraction (ctDNA%) strongly influences assay detection sensitivity–specificity for different genomic events and is an underappreciated but critical variable in the interpretation of patient results. Copy-number variants (CNVs) are challenging to detect in samples with low ctDNA%, regardless of sequencing approach. Orthogonal methods can modestly improve detection but only to a finite lower limit. Sequencing sample-matched white-blood-cell DNA can improve the characterization of CNVs, assist with estimating ctDNA%, and remove interference from clonal hematopoiesis. Circulating tumor DNA (ctDNA) enables real-time genomic profiling of cancer without the need for tissue biopsy. ctDNA-based technology is seeing rapid uptake in clinical practice due to the potential to inform patient management from diagnosis to advanced disease. In metastatic disease, ctDNA can identify somatic mutations, copy-number variants (CNVs), and structural rearrangements that are predictive of therapy response. However, the ctDNA fraction (ctDNA%) is unpredictable and confounds variant detection strategies, undermining confidence in liquid biopsy results. Assay design also influences which types of genomic alterations are identifiable. Here, we describe the relationships between ctDNA%, methodology, and sensitivity–specificity for major classes of genomic alterations in prostate cancer. We provide recommendations to navigate the technical complexities that constrain the detection of clinically relevant genomic alterations in ctDNA. Circulating tumor DNA (ctDNA) enables real-time genomic profiling of cancer without the need for tissue biopsy. ctDNA-based technology is seeing rapid uptake in clinical practice due to the potential to inform patient management from diagnosis to advanced disease. In metastatic disease, ctDNA can identify somatic mutations, copy-number variants (CNVs), and structural rearrangements that are predictive of therapy response. However, the ctDNA fraction (ctDNA%) is unpredictable and confounds variant detection strategies, undermining confidence in liquid biopsy results. Assay design also influences which types of genomic alterations are identifiable. Here, we describe the relationships between ctDNA%, methodology, and sensitivity–specificity for major classes of genomic alterations in prostate cancer. We provide recommendations to navigate the technical complexities that constrain the detection of clinically relevant genomic alterations in ctDNA.