Plasma contains ultrashort single-stranded DNA in addition to nucleosomal cell-free DNA

Jordan Cheng, Marco Morselli, Wei Lun Huang, You Jeong Heo, Thalyta Pinheiro-Ferreira, Feng Li, Fang Wei, David Chia, Yong Kim, Hua Jun He, Kenneth D. Cole, Wu Chou Su, Matteo Pellegrini, David T.W. Wong

Research output: Contribution to journalArticlepeer-review

8 Citations (Scopus)


Plasma cell-free DNA is being widely explored as a biomarker for clinical screening. Currently, methods are optimized for the extraction and detection of double-stranded mononucleosomal cell-free DNA of ∼160bp in length. We introduce uscfDNA-seq, a single-stranded cell-free DNA next-generation sequencing pipeline, which bypasses previous limitations to reveal a population of ultrashort single-stranded cell-free DNA in human plasma. This species has a modal size of 50nt and is distinctly separate from mononucleosomal cell-free DNA. Treatment with single-stranded and double-stranded specific nucleases suggests that ultrashort cell-free DNA is primarily single-stranded. It is distributed evenly across chromosomes and has a similar distribution profile over functional elements as the genome, albeit with an enrichment over promoters, exons, and introns, which may be suggestive of a terminal state of genome degradation. The examination of this cfDNA species could reveal new features of cell death pathways or it can be used for cell-free DNA biomarker discovery.

Original languageEnglish
Article number104554
Issue number7
Publication statusPublished - 2022 Jul 15

All Science Journal Classification (ASJC) codes

  • General


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