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 (~ 167 bp), but also in those shorter than di-nucleosomes (~ 240–330 bp) (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 10 bp 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.
Highlights
The utility of circulating tumor DNA in plasma is well d ocumented[1]
In order to determine what molecular features are differentially enriched in plasma cell-free DNA (cfDNA) originating from healthy cells and Circulating tumor DNA (ctDNA) originating from tumor cells, paired-end whole genome sequencing was carried out on plasma samples from 5 high grade serious ovarian cancer (HGSOC) patients with 22.75–35.61X genomic coverage
For ichorCNA analysis, we built a panel of normals using the 10 random bootstrap sets (RBS) from the pool of controls, and measured the tumor fraction of all RBS using it as a reference
Summary
It is a specific biomarker that enables early detection of cancer[2], allows treatment monitoring[3] and provides prognostic information about tumor burden post treatment or s urgery[3]. CfDNA is released into the bloodstream from various cellular o rigins[15] and by different biological processes such as apoptosis or n ecrosis[16]. This is supported by the fragment size distribution of cfDNA, which shows a modal size of 167 bp corresponding to DNA wrapped around histone (~ 147 bp) plus linker region (~ 10 bp). The different ancestries can mark cfDNA with specific nonrandom fragmentation features that could be used to trace the molecules back to their origin or classify plasma samples as healthy or c ancer[17,18]
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
