Plasma DNA motif analysis - EGA European Genome-Phenome Archive

Dataset ID	Description	Technology	Samples
EGAD00001005093	None	Illumina HiSeq 4000	118
EGAD50000001737	This dataset comprises fastq or bam files derived from sequencing data of dsDNA and ssDNA libraries from 138 plasma cfDNA samples.	Illumina NovaSeq 6000 Sequel II	138

Publications	Citations
Epigenetic analysis of cell-free DNA by fragmentomic profiling. Zhou Q, Kang G, Jiang P, Qiao R, Lam WKJ, Yu SCY, Ma ML, Ji L, Cheng SH, Gai W, Peng W, Shang H, Chan RWY, Chan SL, Wong GLH, Hiraki LT, Volpi S, Wong VWS, Wong J, Chiu RWK, Chan KCA, Lo YMD. Proc Natl Acad Sci U S A 119: 2022 e2209852119	80
A novel approach for the non-invasive diagnosis of pulmonary nodules using low-depth whole-genome sequencing of cell-free DNA. Zhang B, Liang H, Liu W, Zhou X, Qiao S, Li F, Tian P, Li C, Ma Y, Zhang H, Zhang Z, Nanjo S, Russo A, Puig-Butillé JA, Wu K, Wang C, Zhao X, Yue D. Transl Lung Cancer Res 11: 2022 2094-2110	3
Detecting Liver Cancer Using Cell-Free DNA Fragmentomes. Foda ZH, Annapragada AV, Boyapati K, Bruhm DC, Vulpescu NA, Medina JE, Mathios D, Cristiano S, Niknafs N, Luu HT, Goggins MG, Anders RA, Sun J, Meta SH, Thomas DL, Kirk GD, Adleff V, Phallen J, Scharpf RB, Kim AK, Velculescu VE. Cancer Discov 13: 2023 616-631	98
Fragmentation landscape of cell-free DNA revealed by deconvolutional analysis of end motifs. Zhou Z, Ma ML, Chan RWY, Lam WKJ, Peng W, Gai W, Hu X, Ding SC, Ji L, Zhou Q, Cheung PPH, Yu SCY, Teoh JYC, Szeto CC, Wong J, Wong VWS, Wong GLH, Chan SL, Hui EP, Ma BBY, Chan ATC, Chiu RWK, Chan KCA, Lo YMD, Jiang P. Proc Natl Acad Sci U S A 120: 2023 e2220982120	49
Language model enables end-to-end accurate detection of cancer from cell-free DNA. Shen H, Liu J, Chen K, Li X. Brief Bioinform 25: 2024 bbae053	2
Development of a deep learning model for cancer diagnosis by inspecting cell-free DNA end-motifs. Shen H, Yang M, Liu J, Chen K, Li X. NPJ Precis Oncol 8: 2024 160	8
Large language model produces high accurate diagnosis of cancer from end-motif profiles of cell-free DNA. Liu J, Shen H, Chen K, Li X. Brief Bioinform 25: 2024 bbae430	7
Analysis of a cell-free DNA-based cancer screening cohort links fragmentomic profiles, nuclease levels, and plasma DNA concentrations. Malki Y, Kang G, Lam WKJ, Zhou Q, Cheng SH, Cheung PPH, Bai J, Chan ML, Lee CT, Peng W, Zhang Y, Gai W, Wong WWS, Ma ML, Li W, Xu X, Gao Z, Tse IOL, Shang H, Choy LYL, Jiang P, Chan KCA, Lo YMD. Genome Res 35: 2025 31-42	3
EM-DeepSD: A Deep Neural Network Model Based on Cell-Free DNA End-Motif Signal Decomposition for Cancer Diagnosis. Zhao ZY, Huang CL, Wang TM, Zhou SH, Pei L, Jia WH, Jia WH. Diagnostics (Basel) 15: 2025 1156	0