A standardized framework for robust fragmentomic feature extraction from cell-free DNA sequencing data.

Wang, H., Mennea, P.D., Chan, Y.K.E., Cheng, Z., Neofytou, M.C., Surani, A.A., Vijayaraghavan, A., Ditter, E.J., Bowers, R., Eldridge, M.D., Shcherbo, D.S., Smith, C.G., Markowetz, F., Cooper, W.N., Kaplan, T., Rosenfeld, N. and Zhao, H. 2025. A standardized framework for robust fragmentomic feature extraction from cell-free DNA sequencing data. Genome Biology. 26 141. https://doi.org/10.1186/s13059-025-03607-5

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Title	A standardized framework for robust fragmentomic feature extraction from cell-free DNA sequencing data.
Type	Journal article
Authors	Wang, H., Mennea, P.D., Chan, Y.K.E., Cheng, Z., Neofytou, M.C., Surani, A.A., Vijayaraghavan, A., Ditter, E.J., Bowers, R., Eldridge, M.D., Shcherbo, D.S., Smith, C.G., Markowetz, F., Cooper, W.N., Kaplan, T., Rosenfeld, N. and Zhao, H.
Abstract	Fragmentomics features of cell-free DNA represent promising non-invasive biomarkers for cancer diagnosis. A lack of systematic evaluation of biases in feature quantification hinders the adoption of such applications. We compare features derived from whole-genome sequencing of ten healthy donors using nine library kits and ten data-processing routes and validated in 1182 plasma samples from published studies. Our results clarify the variations from library preparation and feature quantification methods. We design the Trim Align Pipeline and cfDNAPro R package as unified interfaces for data pre-processing, feature extraction, and visualization to standardize multi-modal feature engineering and integration for machine learning.
Article number	141
Journal	Genome Biology
Journal citation	26
ISSN	1474-760X
Year	2025
Publisher	Springer Nature
Publisher's version	s13059-025-03607-5.pdf License CC BY 4.0 File Access Level Open (open metadata and files)
Digital Object Identifier (DOI)	https://doi.org/10.1186/s13059-025-03607-5
PubMed ID	40410787
Web address (URL)	https://europepmc.org/articles/PMC12100915
Published	23 May 2025

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A standardized framework for robust fragmentomic feature extraction from cell-free DNA sequencing data.

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