title: Genomewide bisulfite sequencing reveals the origin and time-dependent fragmentation of urinary cfDNA.
abstract: Urinary cell-free (cf) DNA holds great potential as a completely noninvasive form of liquid biopsy. Knowledge of the composition of cfDNA by tissue of origin is useful for guiding its clinical uses. We conducted a global survey of urinary cfDNA composition using genomewide bisulfite sequencing. While previous studies focused on detecting cfDNA from a single source at a time, genomewide tissue specific methylation signatures allow us to simultaneously deduce the proportional contribution from each contributing tissue. The proportional contributions derived from methylation deconvolution are highly correlated with those calculated using allograft-derived donor-specific genetic markers in the urine of hematopoetic stem cell and renal transplant recipients. We found a large variation of proportional contributions from different tissues. We then assessed if cfDNA undergoes time-dependent fragmentation in urine by conducting in vitro incubation experiments. In vitro incubation at 37°C showed that urinary cfDNA concentration decreased under first order kinetics with a half-life of 2.6 to 5.1h. This is reflected in parallel by a decrease in the proportion of long fragments and increase in amplitude of 10bp periodicity seen in the cfDNA size profile. This global survey of urinary cfDNA has deepened our understanding of the composition, degradation and variation of cfDNA in the urinary tract and has laid a foundation for the use of genomewide urinary cfDNA sequencing as a molecular diagnostics tool.
authors.affiliation: Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China; Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong, China.
authors.forename: Timothy H T
authors.initials: THT
authors.lastname: Cheng
authors.affiliation: Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China; Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong, China.
authors.forename: Peiyong
authors.initials: P
authors.lastname: Jiang
authors.affiliation: Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China; Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong, China.
authors.forename: Jacqueline C W
authors.initials: JCW
authors.lastname: Tam
authors.affiliation: Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China; Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong, China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Sun
authors.affiliation: Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China; Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong, China.
authors.forename: Wing-Shan
authors.initials: WS
authors.lastname: Lee
authors.affiliation: Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China; Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong, China.
authors.forename: Stephanie C Y
authors.initials: SCY
authors.lastname: Yu
authors.affiliation: SH Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong, China.
authors.forename: Jeremy Y C
authors.initials: JYC
authors.lastname: Teoh
authors.affiliation: SH Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong, China.
authors.forename: Peter K F
authors.initials: PKF
authors.lastname: Chiu
authors.affiliation: SH Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong, China.
authors.forename: Chi-Fai
authors.initials: CF
authors.lastname: Ng
authors.affiliation: Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong, China.
authors.forename: Kai-Ming
authors.initials: KM
authors.lastname: Chow
authors.affiliation: Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong, China.
authors.forename: Cheuk-Chun
authors.initials: CC
authors.lastname: Szeto
authors.affiliation: Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China; Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong, China.
authors.forename: K C Allen
authors.initials: KCA
authors.lastname: Chan
authors.affiliation: Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China; Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong, China.
authors.forename: Rossa W K
authors.initials: RWK
authors.lastname: Chiu
authors.affiliation: Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China; Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong, China. Electronic address: loym@cuhk.edu.hk.
authors.forename: Y M Dennis
authors.initials: YMD
authors.lastname: Lo
mesh_terms: D064591:Allografts; D004247:DNA / Q000235:genetics / Q000652:urine; D053938:DNA Fragmentation; D019175:DNA Methylation; D005260:Female; D055106:Genome-Wide Association Study; D018380:Hematopoietic Stem Cell Transplantation; D006801:Humans; D016030:Kidney Transplantation; D008297:Male; D017422:Sequence Analysis, DNA
chemical_list: D004247:DNA
keywords: Genomewide bisulfite sequencing; Liquid biopsy; Urinary cell-free DNA