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Tissue-specific cell-free DNA degradation quantifies circulating tumor DNA burden

Profiling of circulating tumor DNA (ctDNA) may offer a non-invasive approach to monitor disease progression. Here, we developed a quantitative method, exploiting local tissue-specific cell-free DNA (cfDNA) degradation patterns, that accurately estimates ctDNA burden independent of genomic aberrations. Nucleosome-dependent cfDNA degradation at promoters and first exon-intron junctions was strongly associated with differential transcriptional activity in tumors and blood. A quantitative model, based on just 6 regulatory regions, could accurately predict ctDNA levels in colorectal cancer patients. Strikingly, a model restricted to blood-specific regulatory regions could predict ctDNA levels across both colorectal and breast cancer patients.

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
EGAD00001006419 Illumina HiSeq 4000 12
EGAD00001006420 Illumina HiSeq 4000 10
EGAD00001006421 Illumina HiSeq 4000 29
EGAD00001008352 Illumina HiSeq 4000 7
Publications Citations
Tissue-specific cell-free DNA degradation quantifies circulating tumor DNA burden.
Nat Commun 12: 2021 2229
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