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 similar to 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.

Plasma contains ultrashort single-stranded DNA in addition to nucleosomal cell-free DNA / Cheng, Jordan; Morselli, Marco; Huang, Wei-Lun; Heo, You Jeong; Pinheiro-Ferreira, Thalyta; Li, Feng; Wei, Fang; Chia, David; Kim, Yong; He, Hua-Jun; Cole, Kenneth D; Su, Wu-Chou; Pellegrini, Matteo; Wong, David T W. - In: ISCIENCE. - ISSN 2589-0042. - 25:7(2022), p. 104554. [10.1016/j.isci.2022.104554]

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

Morselli, Marco;
2022

Abstract

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 similar to 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.
Plasma contains ultrashort single-stranded DNA in addition to nucleosomal cell-free DNA / Cheng, Jordan; Morselli, Marco; Huang, Wei-Lun; Heo, You Jeong; Pinheiro-Ferreira, Thalyta; Li, Feng; Wei, Fang; Chia, David; Kim, Yong; He, Hua-Jun; Cole, Kenneth D; Su, Wu-Chou; Pellegrini, Matteo; Wong, David T W. - In: ISCIENCE. - ISSN 2589-0042. - 25:7(2022), p. 104554. [10.1016/j.isci.2022.104554]
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/11381/2927351
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