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The effect of pre-analytical and physiological variables on cell-free DNA fragmentation

View ORCID ProfileYmke van der Pol, View ORCID ProfileNorbert Moldovan, Sandra Verkuijlen, Jip Ramaker, Dries Boers, Wendy Onstenk, Johan de Rooij, View ORCID ProfileIdris Bahce, View ORCID ProfileD. Michiel Pegtel, View ORCID ProfileFlorent Mouliere
doi: https://doi.org/10.1101/2021.09.17.460828
Ymke van der Pol
1Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, 1081 HV, Amsterdam, The Netherlands
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  • ORCID record for Ymke van der Pol
Norbert Moldovan
1Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, 1081 HV, Amsterdam, The Netherlands
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Sandra Verkuijlen
1Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, 1081 HV, Amsterdam, The Netherlands
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Jip Ramaker
1Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, 1081 HV, Amsterdam, The Netherlands
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Dries Boers
1Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, 1081 HV, Amsterdam, The Netherlands
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Wendy Onstenk
1Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, 1081 HV, Amsterdam, The Netherlands
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Johan de Rooij
3You2Youself BV, Enschede, the Netherlands
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Idris Bahce
2Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pulmonology, Cancer Center Amsterdam, 1081 HV, Amsterdam, The Netherlands
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D. Michiel Pegtel
1Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, 1081 HV, Amsterdam, The Netherlands
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  • ORCID record for D. Michiel Pegtel
Florent Mouliere
1Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, 1081 HV, Amsterdam, The Netherlands
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  • For correspondence: f.mouliere@amsterdamumc.nl
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Abstract

Assays that account for the biological properties and fragmentation of cell-free DNA (cfDNA) can improve the performance of liquid biopsy. However, pre-analytic and physiological differences between individuals on fragmentomic analysis are poorly defined.

We analyzed the impact of collection tube, plasma processing time and physiology on the size distribution of cfDNA, their genome-wide representation and sequence diversity at the cfDNA fragment-ends using shallow Whole Genome Sequencing.

We observed that using different stabilizing collection tubes, or processing times does not affect the cfDNA fragment sizes, but can impact the genome-wide fragmentation patterns and fragment-end sequences of cfDNA. In addition, beyond differences depending on the gender, the physiological conditions tested between 63 individuals (age, body mass index, use of medication and chronic conditions) minimally influenced the outcome of fragmentomic methods.

Our results highlight that fragmentomic approaches have potential for implementation in the clinic, pending clear traceability of analytical and physiological factors.

Competing Interest Statement

F.M. is co-inventor on multiple patents related to cfDNA fragment size analysis. Other co-authors have no relevant competing interests.

Footnotes

  • ↵# co-first authors

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted September 18, 2021.
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The effect of pre-analytical and physiological variables on cell-free DNA fragmentation
Ymke van der Pol, Norbert Moldovan, Sandra Verkuijlen, Jip Ramaker, Dries Boers, Wendy Onstenk, Johan de Rooij, Idris Bahce, D. Michiel Pegtel, Florent Mouliere
bioRxiv 2021.09.17.460828; doi: https://doi.org/10.1101/2021.09.17.460828
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The effect of pre-analytical and physiological variables on cell-free DNA fragmentation
Ymke van der Pol, Norbert Moldovan, Sandra Verkuijlen, Jip Ramaker, Dries Boers, Wendy Onstenk, Johan de Rooij, Idris Bahce, D. Michiel Pegtel, Florent Mouliere
bioRxiv 2021.09.17.460828; doi: https://doi.org/10.1101/2021.09.17.460828

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