DAGIP: alleviating cell-free DNA sequencing biases with optimal transport
Cell-free DNA (cfDNA) is a rich source of biomarkers for various pathophysiological conditions. Preanalytical variables, such as the library preparation protocol or sequencing platform, are major confounders of cfDNA analysis. We present DAGIP, a novel data correction method that builds on optimal transport theory and deep learning, which explicitly corrects for the effect of such preanalytical variables and can infer technical biases. Our method improves cancer detection and copy number alteration analysis by alleviating the sources of variation that are not of biological origin. It also enhances fragmentomic analysis of cfDNA. DAGIP allows the integration of cohorts from different studies.
Authors
- D. Timmerman (ORCID: https://orcid.org/0000-0002-3707-6645)
- Daniele Raimondi (ORCID: https://orcid.org/0000-0003-1157-1899)
- Antoine Passemiers (ORCID: https://orcid.org/0000-0002-9492-7311)
- Sabine Tejpar (ORCID: https://orcid.org/0000-0003-3281-8643)
- Stefania Tuveri (ORCID: https://orcid.org/0000-0003-4051-4295)
- Yves Moreau (ORCID: https://orcid.org/0000-0002-4647-6560)
- Pieter Busschaert
- Tatjana Jatsenko (ORCID: https://orcid.org/0000-0002-7423-0963)
- Adriaan Vanderstichele (ORCID: https://orcid.org/0000-0002-3984-2948)
- An Coosemans (ORCID: https://orcid.org/0000-0002-7321-4339)
- Joris Robert Vermeesch (ORCID: https://orcid.org/0000-0002-3071-1191)
- Diether Lambrechts (ORCID: https://orcid.org/0000-0002-3429-302X)
- Peter Vandenberghe (ORCID: https://orcid.org/0000-0003-4719-1935)
Institutions
- Université de Montpellier (FR)
- Statistics Belgium (BE)
- VIB-KU Leuven Center for Cancer Biology (BE)
- Institut de Génétique Moléculaire de Montpellier (FR)
- KU Leuven (BE)
Publication Details
- Journal
- Genome biology
- Published
- 2025-03-07
- DOI
- https://doi.org/10.1186/s13059-025-03511-y
- Citations
- 3
- Primary Topic
- Cancer Genomics and Diagnostics
- Type
- article
- Field-Weighted Citation Impact
- 2.81
Funders
- Agentschap Innoveren en Ondernemen
- Vlaams Supercomputer Centrum
- Fonds Wetenschappelijk Onderzoek
- KU Leuven
- Kom op tegen Kanker
- Vlaamse regering