Study

single-stranded DNA study

Study ID Alternative Stable ID Type
EGAS00001005093 Other

Study Description

A ssDNA library protocol was applied to cfDNA from plasma samples obtained from different DNA extraction methods and revealed significant differences in DNA fragmentation patterns in comparison to dsDNA-based protocols. In particular, a specific combination of methods revealed a population of ultrashort fragments, organized at ~50 bp. We observed significant differences in the relative abundance of these ultrashort DNA fragments in plasma from healthy individuals and cancer patients. Through shallow whole genome sequencing (sWGS, <0.5-fold coverage) and the analysis of somatic copy number aberrations (SCNA), we determined the landscape of genetic alterations in this newly identified population of cfDNA fragments. In addition, we studied their potential link with regulatory regions by investigating the genome-wide coverage patterns at transcription start sites (TSS). Furthermore, we demonstrated that the ultrashort cfDNA fragments map to regions associated with secondary DNA structures, G-quadruplexes (G4s).

Study Datasets 1 dataset.

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Dataset ID Description Technology Samples
EGAD00001007019 This dataset includes fastq files from sWGS and exome sequencing data derived from dsDNA and ssDNA libraries of plasma cfDNA samples extracted by a column- or bead-based DNA extraction method Illumina HiSeq 2500 Illumina HiSeq 4000 Illumina NovaSeq 6000 NextSeq 550 198

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