Journal article
Characteristics, origin, and potential for cancer diagnostics of ultrashort plasma cell-free DNA
I Hudecova, CG Smith, R Hänsel-Hertsch, CS Chilamakuri, JA Morris, A Vijayaraghavan, K Heider, D Chandrananda, WN Cooper, D Gale, J Garcia-Corbacho, S Pacey, RD Baird, N Rosenfeld, F Mouliere
Genome Research | Published : 2022
Abstract
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..
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Awarded by Universität zu Köln
Funding Acknowledgements
We thank the Genomics, Bioinformatics, and Compliance and Biobanking core facilities at CRUK Cambridge Institute, including James Hadfield, Paul Coupland, Hannah Haydon, Matthew Eldridge, and Jorgelina Trueba. We thank the Regional Computing Centre (RRZK) of the University of Cologne for support. We thank Alexander Wolf (QIAGEN) for his suggestions and advice regarding the DNA extraction procedure used. We thank Shankar Balasubramanian for feedback concerning the G4 analysis. We acknowledge support from the Cancer Research UK Cambridge Institute, the National Institute for Health Research (NIHR) Biomedical Research Centre, NIHR Cambridge Clinical Research Centre, and Experimental Cancer Medicine Centre, as well as the support from early phase and Cancer Clinical Trial Centre research teams including Duncan Jodrell, Bristi Basu, Sarah Loewenbein, Will Dott, Constanza Linossi, and Gary Doherty. For their assistance with collection of samples from healthy volunteers, we thank Joanna Baxter and Andreia Ribeiro Da Silva from the Cambridge Blood and Stem Cell Biobank, which is supported by the Cambridge NIHR Biomedical Research Centre, Wellcome Trust-Medical Research Council (MRC) Stem Cell Institute, and the Cambridge Experimental Cancer Medicine Centre, UK. For their assistance with DNA extraction from plasma samples, we thank Shubha Anand, Isart Roca, and Francesca Nice from the Cancer Molecular Diagnostics Laboratory/Blood Processing Laboratory, which is supported by Cambridge NIHR Biomedical Research Centre, Cambridge Cancer Centre, and the Mark Foundation of Cancer Research. Finally, we thank all patients and healthy volunteers for their contribution to this study. This study was supported by grants from Cancer Research UK (CRUK) Cambridge Institute (Core Grant, A29580) and by a funding from the European Research Council (ERC) under the European Union's Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement n. 337905. R.H.-H. is supported by funding from the Center for Molecular Medicine Cologne and by the Deutsche Forschungsgemeinschaft (CRC1399). F.M. is supported by a Dutch Cancer Fund (KWF-12822).