Journal
CLINICAL BIOCHEMISTRY
Volume 50, Issue 9, Pages 496-501Publisher
PERGAMON-ELSEVIER SCIENCE LTD
DOI: 10.1016/j.clinbiochem.2017.02.017
Keywords
Urinary cell-free DNA; Liquid biopsy; Genomewide bisulfite sequencing
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Funding
- Hong Kong Research Grants Council under the Theme-based research scheme from the Government of the Hong Kong SAR [T12-403/15-N, T12-404/11]
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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 degrees C showed that urinary cfDNA concentration decreased under first order kinetics with a half-life of 2.6 to 5.1 h. This is reflected in parallel by a decrease in the proportion of long fragments and increase in amplitude of 10 bp 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. (C) 2017 The Authors. Published by Elsevier Inc. on behalf of The Canadian Society of Clinical Chemists.
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