Untargeted profiling of cell-free circulating DNA

Qing Zhou, Tina Moser, Samantha Perakis, Ellen Heitzer


The potential of cell-free circulating tumor DNA (ctDNA) as a diagnostic, predictive and prognostic biomarker, has clearly been recognized and numerous studies have already proven clinical utility of ctDNA analyses. As ctDNA reflects the full spectrum of tumor-specific alterations, a wide range of methodological approaches have been developed for the analysis of ctDNA. While targeted approaches have the potential of capturing major known driver mutations at a high resolution, these methods mostly interrogate only single or small set of genes and are therefore unable to assess the genetic heterogeneity of ctDNA in an unbiased manner. However, given that tumor genomes are constantly changing as a consequence of progression or under the selective pressures of targeted therapies, a comprehensive genome-wide analysis is advantageous at least in late-stage cancer patients. Despite the advantages of ensuring a comprehensive view on the genetic landscape, untargeted and genome-wide methods such was whole exome sequencing (WES) or whole genome sequencing (WGS) are currently limited to samples with the elevated levels of total ctDNA since deep sequencing at an exome- or genome-wide level is still prohibitively expensive. Here, we review studies which applied untargeted approaches for ctDNA analyses including WES, WGS and epigenetic profiling, highlight the advantages over targeted approaches and discuss related limitations. Moreover, we present novel approaches of ctDNA, which move beyond somatic copy number alterations (SCNA) and single nucleotide variants (SNV).