Integration of Cell-Free DNA End Motifs and Fragment Lengths Can Identify Active Genes in Liquid Biopsies
Abstract
:1. Introduction
2. Results
2.1. ctDNA Is Shorter Than cfDNA of Noncancer Origin
2.2. cfDNA Originating from Genes with High Expression Is Shorter Than cfDNA from Genes with Low Expression
2.3. The Active Genes Have Distinct cfDNA FEMs
2.4. Short Fragments Have Distinct FEMs and Originate from Active Genes
3. Discussion
4. Materials and Methods
4.1. Plasma Samples
4.2. Cell-Free Chromatin Immunoprecipitaiton (cfChIP) Enrichment
4.3. In Vitro Size Selection
4.4. CAPP-Seq
4.5. ctDNA Detection
4.6. Fragment Length and FEM Analyses
4.7. High/Low-Expressed Genes and cfChIP Quantiles
4.8. Nucleosomal Positioning Analysis
4.9. Validation Data
4.10. Statistical Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Maansson, C.T.; Thomsen, L.S.; Meldgaard, P.; Nielsen, A.L.; Sorensen, B.S. Integration of Cell-Free DNA End Motifs and Fragment Lengths Can Identify Active Genes in Liquid Biopsies. Int. J. Mol. Sci. 2024, 25, 1243. https://doi.org/10.3390/ijms25021243
Maansson CT, Thomsen LS, Meldgaard P, Nielsen AL, Sorensen BS. Integration of Cell-Free DNA End Motifs and Fragment Lengths Can Identify Active Genes in Liquid Biopsies. International Journal of Molecular Sciences. 2024; 25(2):1243. https://doi.org/10.3390/ijms25021243
Chicago/Turabian StyleMaansson, Christoffer Trier, Louise Skov Thomsen, Peter Meldgaard, Anders Lade Nielsen, and Boe Sandahl Sorensen. 2024. "Integration of Cell-Free DNA End Motifs and Fragment Lengths Can Identify Active Genes in Liquid Biopsies" International Journal of Molecular Sciences 25, no. 2: 1243. https://doi.org/10.3390/ijms25021243
APA StyleMaansson, C. T., Thomsen, L. S., Meldgaard, P., Nielsen, A. L., & Sorensen, B. S. (2024). Integration of Cell-Free DNA End Motifs and Fragment Lengths Can Identify Active Genes in Liquid Biopsies. International Journal of Molecular Sciences, 25(2), 1243. https://doi.org/10.3390/ijms25021243