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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
.... (B) Annotated CpG islands are clustered based on cell-free methyl-CpG-binding domain (cfMBD) sequencing signal strength into two clusters. Average coverage profiles for short cfDNA and regular cfDNA at methylated or unmethylated CpG islands reveal the influence of methylation levels at CpG islands...
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Research: Analysis of a cell-free DNA–based cancer screening cohort links fragmentomic profiles, nuclease levels, and plasma DNA concentrations
- Yasine Malki,
- Guannan Kang,
- W.K. Jacky Lam,
- Qing Zhou,
- Suk Hang Cheng,
- Peter P.H. Cheung,
- Jinyue Bai,
- Ming Lok Chan,
- Chui Ting Lee,
- Wenlei Peng,
- Yiqiong Zhang,
- Wanxia Gai,
- Winsome W.S. Wong,
- Mary-Jane L. Ma,
- Wenshuo Li,
- Xinzhou Xu,
- Zhuoran Gao,
- Irene O.L. Tse,
- Huimin Shang,
- L.Y. Lois Choy,
- Peiyong Jiang,
- K.C. Allen Chan,
- and Y.M. Dennis Lo
Genome Res. January 2025 35: 31-42; Published in Advance November 27, 2024, doi:10.1101/gr.279667.124
...Analysis of a cell-free DNA–based cancer screening cohort links fragmentomic profiles, nuclease levels, and plasma DNA concentrations Yasine Malki1,2,3,5, Guannan Kang1,2,3,5, W.K. Jacky Lam1,2,3,4,5, Qing Zhou1,2,3, Suk Hang Cheng1,2,3, Peter P.H. Cheung2,3, Jinyue Bai1,2,3, Ming Lok Chan2,3, Chui...
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Research: Optical genome mapping enables accurate testing of large repeat expansions
- Bart van der Sanden,
- Kornelia Neveling,
- Syukri Shukor,
- Michael D. Gallagher,
- Joyce Lee,
- Stephanie L. Burke,
- Maartje Pennings,
- Ronald van Beek,
- Michiel Oorsprong,
- Ellen Kater-Baats,
- Eveline Kamping,
- Alide A. Tieleman,
- Nicol C. Voermans,
- Ingrid E. Scheffer,
- Jozef Gecz,
- Mark A. Corbett,
- Lisenka E.L.M. Vissers,
- Andy Wing Chun Pang,
- Alex Hastie,
- Erik-Jan Kamsteeg,
- and Alexander Hoischen
Genome Res. April 2025 35: 810-823; Published in Advance March 20, 2025, doi:10.1101/gr.279491.124
...; Guruju et al. 2023). In addition, OGM is independent of sequence context and in combination with the ultra-long molecules and -wide coverage, it enables the analysis of even the most complicated regions of the in contrast to DNA sequencing approaches (Neveling et al. 2021). Therefore, OGM has a great...
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Method: BINDER achieves accurate identification of hierarchical TADs by comprehensively characterizing consensus TAD boundaries
- Yangyang Liu,
- Bingqiang Liu,
- and Juntao Liu
Genome Res. May 2025 35: 1194-1208; Published in Advance March 17, 2025, doi:10.1101/gr.279647.124
...these domains, which are commonly referred to as topologically associating domains (TADs), DNA sequences exhibit significantly increased interaction compared with sequences outside of the domains in the -wide chromatin-folding map. Notably, TADs are widespread across various species, displaying high...
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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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Research: Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing
- Nora Zidane,
- Carla Rodrigues,
- Valérie Bouchez,
- Martin Rethoret-Pasty,
- Virginie Passet,
- Sylvain Brisse,
- and Chiara Crestani
Genome Res. August 2025 35: 1758-1766; Published in Advance June 2, 2025, doi:10.1101/gr.279829.124
...Corynebacterium isolate sequenced in this study (Supplemental Fig. S8). This is very likely because of species-specific DNA modifications, such as methylation motifs that are uncommon or unique to C. rouxii, not being well represented in the training data sets of the basecalling model, especially because C...
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Method: FocalSV enables target region–based structural variant assembly and refinement using single-molecule long-read sequencing data
- Can Luo,
- Zimeng Jamie Zhou,
- Yichen Henry Liu,
- and Xin Maizie Zhou
Genome Res. October 2025 35: 2252-2272; Published in Advance August 13, 2025, doi:10.1101/gr.280282.124
...with lower proportions of phasing-informative reads.FocalSV achieves superior performance in complex somatic SV detection in cancer dataTo extend the evaluation to include SV detection beyond deletions and insertions, we analyzed additional SV types involving complex DNA rearrangements...
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Method: Multicondition and multimodal temporal profile inference during mouse embryonic development
- Ran Zhang,
- Chengxiang Qiu,
- Galina N. Filippova,
- Gang Li,
- Jay Shendure,
- Jean-Philippe Vert,
- Xinxian Deng,
- William Stafford Noble,
- and Christine M. Disteche
Genome Res. October 2025 35: 2339-2351; Published in Advance August 14, 2025, doi:10.1101/gr.279997.124
...of a population of cells can profile changes in gene expression, chromatin accessibility and structure, and DNA methylation as the cells carry out essential biological functions, differentiate, traverse the cell cycle, degenerate, or undergo stages of disease progression.Although such measurements have proven...
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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
..., Cheng SH, Yu SCY, Shang H, Olivia Tse OY, Wong J, Wong VWS, Wong GLH, et al. 2022. Single-molecule sequencing enables long cell-free DNA detection and direct methylation analysis for cancer patients. Clin Chem 68: 1151–1163. doi:10.1093/clinchem/hvac086 ↵Clark SJ, Harrison J, Paul CL, Frommer M. 1994...
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