Systematic Evaluation of Cell Type Deconvolution Methods for Plasma Cell-free DNA

T Sun, J Yuan, Y Zhu, S Yang, J Zhou, X Ge, S Qu, W Li… - bioRxiv, 2024 - biorxiv.org
Plasma cell-free DNA (cfDNA) is derived from cellular death in various tissues. Investigating
the origin of cfDNA through tissue/cell type deconvolution allows us to detect changes in …

Comprehensive tissue deconvolution of cell-free DNA by deep learning for disease diagnosis and monitoring

S Li, W Zeng, X Ni, Q Liu, W Li… - Proceedings of the …, 2023 - National Acad Sciences
Plasma cell-free DNA (cfDNA) is a noninvasive biomarker for cell death of all organs.
Deciphering the tissue origin of cfDNA can reveal abnormal cell death because of diseases …

[HTML][HTML] Cell type signatures in cell-free DNA fragmentation profiles reveal disease biology

KE Stanley, T Jatsenko, S Tuveri, D Sudhakaran… - Nature …, 2024 - nature.com
Circulating cell-free DNA (cfDNA) fragments have characteristics that are specific to the cell
types that release them. Current methods for cfDNA deconvolution typically use disease …

[HTML][HTML] Comprehensive cell type decomposition of circulating cell-free DNA with CelFiE

C Caggiano, B Celona, F Garton, J Mefford… - Nature …, 2021 - nature.com
Circulating cell-free DNA (cfDNA) in the bloodstream originates from dying cells and is a
promising noninvasive biomarker for cell death. Here, we propose an algorithm, CelFiE, to …

[HTML][HTML] DNA methylation analysis explores the molecular basis of plasma cell-free DNA fragmentation

Y An, X Zhao, Z Zhang, Z Xia, M Yang, L Ma… - Nature …, 2023 - nature.com
Plasma cell-free DNA (cfDNA) are small molecules generated through a non-random
fragmentation procedure. Despite commendable translational values in cancer liquid biopsy …

[PDF][PDF] Cell type deconvolution of methylated cell-free DNA at the resolution of individual reads

P Keukeleire, S Makrodimitris… - NAR Genomics and …, 2023 - academic.oup.com
Cell-free DNA (cfDNA) are DNA fragments originating from dying cells that are detectable in
bodily fluids, such as the plasma. Accelerated cell death, for example caused by disease …

Benchmarking and optimization of cell-free DNA deconvolution

T Hill, N Redekar, TE Andargie, MK Jang… - bioRxiv, 2023 - biorxiv.org
Reference methylomes, used in deconvolution algorithms to determine cell-free DNA tissue
sources, were based on driver CpGs from either microarray or sequencing platforms. Cross …

[HTML][HTML] Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease

J Moss, J Magenheim, D Neiman, H Zemmour… - Nature …, 2018 - nature.com
Methylation patterns of circulating cell-free DNA (cfDNA) contain rich information about
recent cell death events in the body. Here, we present an approach for unbiased …

FinaleDB: a browser and database of cell-free DNA fragmentation patterns

H Zheng, MS Zhu, Y Liu - Bioinformatics, 2021 - academic.oup.com
Circulating cell-free DNA (cfDNA) is a promising biomarker for the diagnosis and prognosis
of many diseases, including cancer. The genome-wide non-random fragmentation patterns …

[HTML][HTML] Multimodal analysis of cell-free DNA whole-methylome sequencing for cancer detection and localization

F Bie, Z Wang, Y Li, W Guo, Y Hong, T Han, F Lv… - Nature …, 2023 - nature.com
Multimodal epigenetic characterization of cell-free DNA (cfDNA) could improve the
performance of blood-based early cancer detection. However, integrative profiling of cfDNA …