Genome-wide cell-free DNA termini in patients with cancer
The structure, fragmentation patterns and terminal sequences of cell-free DNA (cfDNA) are altered by nucleases and biological mechanisms in the blood of cancer patients. The cfDNA fragment-end composition recovered from low coverage WGS (<1 fold coverage) using a bespoke software (FrEIA) is aberrant in the plasma from cancer patient (n = 418, 655 samples) compared to controls (n = 117). As a standalone test FrEIA allows detection down to ~0.2% tumor fraction in vitro and in silico at 95% specificity, leading to a sensitivity of ~71% for detecting lung cancer (14/22 stage I-II, 27/38 stage III, 92/127 stage IV) and ~68% for detecting esophageal adenocarcinoma (26/44 stage II, 46/62 stage III). Additional cfDNA biological patterns can be combined with FrEIA increasing the diagnostic potential of low coverage WGS at minimal cost (mean AUROC = 0.96). Integrating multiple cfDNA biological signal augments the diagnostic performance of liquid biopsy.
- Type: Other
- Archiver: European Genome-Phenome Archive (EGA)
Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data
Dataset ID | Description | Technology | Samples |
---|---|---|---|
EGAD00001008666 | Illumina NovaSeq 6000 | 95 | |
EGAD00001009780 | Illumina NovaSeq 6000 | 64 |
Publications | Citations |
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The landscape of cell-free mitochondrial DNA in liquid biopsy for cancer detection.
Genome Biol 24: 2023 229 |
11 |
Multi-modal cell-free DNA genomic and fragmentomic patterns enhance cancer survival and recurrence analysis.
Cell Rep Med 5: 2024 101349 |
5 |