Refined characterization of circulating tumor DNA through biological feature integration

Abstract

Circulating tumor DNA (ctDNA) in blood plasma is present at very low concentrations compared to cell-free DNA (cfDNA) of non-tumor origin. To enhance ctDNA detection, recent studies have been focused on understanding the non-random fragmentation pattern of cfDNA. These studies have investigated fragment sizes, genomic position of fragment end points, and fragment end motifs. Although these features have been described and shown to be aberrant in cancer patients, there is a lack of understanding of how the individual and integrated analysis of these features enrich ctDNA fraction and enhance ctDNA detection. Using whole genome sequencing and copy number analysis of plasma samples from 5 high grade serious ovarian cancer patients, we observed that 1) ctDNA is enriched not only in fragments shorter than mono-nucleosomes ([~]167bp), but also in those shorter than di-nucleosomes ([~]240-330bp) (28-159% enrichment). 2) fragments that start and end at the border or within the nucleosome core are enriched in ctDNA (5-46% enrichment). 3) certain DNA motifs conserved in regions 10bp up- and down-stream of fragment ends (i.e. cleavage sites) could be used to detect tumor-derived fragments (10-44% enrichment). We further show that the integrated analysis of these three features resulted in a higher enrichment of ctDNA when compared to using fragment size alone (additional 7-25% enrichment after fragment size selection). We believe these genome wide features, which are independent of genetic mutational changes, could allow new ways to analyze and interpret cfDNA data, as significant aberrations of these features from a healthy state could improve its utility as a diagnostic biomarker. SignificanceIn recent years circulating tumor DNA (ctDNA) has received much attention, and investment, as a biomarker that could transform the clinical care of cancer patients. Despite this, there is much that is not known about this biomarker. Recently, it has been demonstrated that the biological properties of ctDNA can be leveraged to improve ctDNA based assays. Here we build on this by carrying out an in-depth analysis of three genome wide fragmentation patterns of cell-free DNA; specifically fragment size, positioning of fragment end points with respect to nucleosome occupancy, and fragment end motifs. Whilst previous studies have described these features in an individual manner and used them as point statistics for comparison between healthy individuals and cancer patients, our study is the first to show that the individual and integrative analysis of these features can be used to enrich for ctDNA and enable enhanced ctDNA detection. The features described are independent of specific genomic alterations, with signal integrated across the breadth of the genome. This allows informative analysis that leverages a larger proportion of sequencing reads, further building the case for the use of cost-effective approaches like shallow whole genome sequencing for cancer diagnostics.