RT Journal
A1 Hudecova, Irena
A1 Smith, Christopher G.
A1 Hänsel-Hertsch, Robert
A1 Chilamakuri, Chandra S.
A1 Morris, James A.
A1 Vijayaraghavan, Aadhitthya
A1 Heider, Katrin
A1 Chandrananda, Dineika
A1 Cooper, Wendy N.
A1 Gale, Davina
A1 Garcia-Corbacho, Javier
A1 Pacey, Simon
A1 Baird, Richard D.
A1 Rosenfeld, Nitzan
A1 Mouliere, Florent
T1 Characteristics, origin, and potential for cancer diagnostics of ultrashort plasma cell-free DNA
JF Genome Research 
JO Genome Research 
YR 2022 
FD February 01 
VO 32 
IS 2 
SP 215 
OP 227 
DO 10.1101/gr.275691.121 
UL http://genome.cshlp.org/content/32/2/215.abstract 
AB Current evidence suggests that plasma cell-free DNA (cfDNA) is fragmented around a mode of 166 bp. Data supporting this view has been mainly acquired through the analysis of double-stranded cfDNA. The characteristics and diagnostic potential of single-stranded and damaged double-stranded cfDNA in healthy individuals and cancer patients remain unclear. Here, through a combination of high-affinity magnetic bead–based DNA extraction and single-stranded DNA sequencing library preparation (MB-ssDNA), we report the discovery of a large proportion of cfDNA fragments centered at ∼50 bp. We show that these “ultrashort” cfDNA fragments have a greater relative abundance in plasma of healthy individuals (median = 19.1% of all sequenced cfDNA fragments, n = 28) than in plasma of patients with cancer (median = 14.2%, n = 21, P < 0.0001). The ultrashort cfDNA fragments map to accessible chromatin regions of blood cells, particularly in promoter regions with the potential to adopt G-quadruplex (G4) DNA secondary structures. G4-positive promoter chromatin accessibility is significantly enriched in ultrashort plasma cfDNA fragments from healthy individuals relative to patients with cancers (P < 0.0001), in whom G4-cfDNA enrichment is inversely associated with copy number aberration-inferred tumor fractions. Our findings redraw the landscape of cfDNA fragmentation by identifying and characterizing a novel population of ultrashort plasma cfDNA fragments. Sequencing of MB-ssDNA libraries could facilitate the characterization of gene regulatory regions and DNA secondary structures via liquid biopsy. Our data underline the diagnostic potential of ultrashort cfDNA through classification for cancer patients.