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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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Research: Genomic origin, fragmentomics, and transcriptional properties of long cell-free DNA molecules in human plasma
- Huiwen Che,
- Peiyong Jiang,
- L.Y. Lois Choy,
- Suk Hang Cheng,
- Wenlei Peng,
- Rebecca W.Y. Chan,
- Jing Liu,
- Qing Zhou,
- W.K. Jacky Lam,
- Stephanie C.Y. Yu,
- So Ling Lau,
- Tak Y. Leung,
- John Wong,
- Vincent Wai-Sun Wong,
- Grace L.H. Wong,
- Stephen L. Chan,
- K.C. Allen Chan,
- and Y.M. Dennis Lo
Genome Res. February 2024 34: 189-200; Published in Advance February 26, 2024, doi:10.1101/gr.278556.123
...Department of Clinical Oncology, Sir Y.K. Pao Centre for Cancer, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China Corresponding author: loym@cuhk.edu.hkAbstractRecent studies have revealed an unexplored population of long cell-free DNA (cfDNA) molecules in human...
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Method: Detection and characterization of jagged ends of double-stranded DNA in plasma
- Peiyong Jiang,
- Tingting Xie,
- Spencer C. Ding,
- Ze Zhou,
- Suk Hang Cheng,
- Rebecca W.Y. Chan,
- Wing-Shan Lee,
- Wenlei Peng,
- John Wong,
- Vincent W.S. Wong,
- Henry L.Y. Chan,
- Stephen L. Chan,
- Liona C.Y. Poon,
- Tak Y. Leung,
- K.C. Allen Chan,
- Rossa W.K. Chiu,
- and Y.M. Dennis Lo
Genome Res. August 2020 30: 1144-1153; Published in Advance August 14, 2020, doi:10.1101/gr.261396.120
...recent interest, leading to the emerging field of cell-free DNA fragmentomics. However, one aspect of plasma DNA fragmentomics as to whether double-stranded plasma molecules might carry single-stranded ends, termed a jagged end in this study, remains underexplored. We have developed two approaches...
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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
..., Victoria 3010, Australia Corresponding authors: f.mouliere@amsterdamumc.nl, nitzan.rosenfeld@cruk.cam.ac.ukAbstractCurrent evidence suggests that plasma cell-free DNA (cfDNA) is fragmented around a mode of 166 bp. Data supporting this view has been mainly acquired through the analysis of double-stranded cfDNA...
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Method: Reconstructing double-stranded DNA fragments on a single-molecule level reveals patterns of degradation in ancient samples
- Lukas Bokelmann,
- Isabelle Glocke,
- and Matthias Meyer
Genome Res. October 2020 30: 1449-1457; Published in Advance September 22, 2020, doi:10.1101/gr.263863.120
...Andrew J, Daza Riza M, Shendure J. 2016. Cell-free DNA comprises an in vivo nucleosome footprint that informs its tissues-of-origin. Cell 164: 57–68. doi:10.1016/j.cell.2015.11.050 ↵Sozzi G, Conte D, Leon M, Ciricione R, Roz L, Ratcliffe C, Roz E, Cirenei N, Bellomi M, Pelosi G, et al. 2003...

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