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Review: Artificial intelligence and machine learning in cell-free-DNA-based diagnostics
- W.H. Adrian Tsui,
- Spencer C. Ding,
- Peiyong Jiang,
- and Y.M. Dennis Lo
Genome Res. January 2025 35: 1-19; doi:10.1101/gr.278413.123
...@cuhk.edu.hkAbstractThe discovery of circulating fetal and tumor cell-free DNA (cfDNA) molecules in plasma has opened up tremendous opportunities in noninvasive diagnostics such as the detection of fetal chromosomal aneuploidies and cancers and in posttransplantation monitoring. The advent of high-throughput sequencing...
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Method: A novel approach for in vivo DNA footprinting using short double-stranded cell-free DNA from plasma
- Jan Müller,
- Christina Hartwig,
- Mirko Sonntag,
- Lisa Bitzer,
- Christopher Adelmann,
- Yevhen Vainshtein,
- Karolina Glanz,
- Sebastian O. Decker,
- Thorsten Brenner,
- Georg F. Weber,
- Arndt von Haeseler,
- and Kai Sohn
Genome Res. August 2024 34: 1185-1195; Published in Advance September 13, 2024, doi:10.1101/gr.279326.124
...3 histone modifications and gene transcription. The diagnostic potential of short double-stranded cell-free DNA (cfDNA) in blood plasma has not yet been recognized. When comparing short double-stranded cfDNA from patient samples of pancreatic ductal adenocarcinoma with colorectal carcinoma or septic...
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Research: Characteristics, origin, and potential for cancer diagnostics of ultrashort plasma cell-free DNA
- Irena Hudecova,
- Christopher G. Smith,
- Robert Hänsel-Hertsch,
- Chandra S. Chilamakuri,
- James A. Morris,
- Aadhitthya Vijayaraghavan,
- Katrin Heider,
- Dineika Chandrananda,
- Wendy N. Cooper,
- Davina Gale,
- Javier Garcia-Corbacho,
- Simon Pacey,
- Richard D. Baird,
- Nitzan Rosenfeld,
- and Florent Mouliere
Genome Res. February 2022 32: 215-227; Published in Advance December 20, 2021, doi:10.1101/gr.275691.121
...are released into the blood circulation following cell death and by active secretion (Stroun et al. 2000) while maintaining genetic and epigenetic signatures of the cell of origin (Heitzer et al. 2020). The fragmentation of cell-free DNA (cfDNA) in blood plasma can reflect its tissue of origin and mechanisms...
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Research: Nuclease deficiencies alter plasma cell-free DNA methylation profiles
- Diana S.C. Han,
- Meng Ni,
- Rebecca W.Y. Chan,
- Danny K.L. Wong,
- Linda T. Hiraki,
- Stefano Volpi,
- Peiyong Jiang,
- Kathy O. Lui,
- K.C. Allen Chan,
- Rossa W.K. Chiu,
- and Y.M. Dennis Lo
Genome Res. November 2021 31: 2008-2021; Published in Advance September 1, 2021, doi:10.1101/gr.275426.121
...Genova, Italy ↵6 These authors contributed equally to this work. Corresponding author: loym@cuhk.edu.hkAbstractThe effects of DNASE1L3 or DNASE1 deficiency on cell-free DNA (cfDNA) methylation were explored in plasma of mice deficient in these nucleases and in DNASE1L3-deficient humans. Compared to wild...
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Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
- Qiuhui Li,
- Ayse G. Keskus,
- Justin Wagner,
- Michal B. Izydorczyk,
- Winston Timp,
- Fritz J. Sedlazeck,
- Alison P. Klein,
- Justin M. Zook,
- Mikhail Kolmogorov,
- and Michael C. Schatz
Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
...to traditional tissue biopsies in cancer management, offering a minimally invasive method for analyzing circulating tumor cells, cell-free DNA (cfDNA), and other biomarkers in bodily fluids (Ignatiadis et al. 2021; Zhu et al. 2023). Recent advancements in long-read sequencing technologies have further enhanced...
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