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

Study ID Alternative Stable ID Type
EGAS00001004657 Other

Study Description

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.

Study Datasets 3 datasets.

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
WGS data of plasma samples from CRC patients (N=12)
Illumina HiSeq 4000 12
WGS data of plasma samples from BRCA patients (N=10)
Illumina HiSeq 4000 10
WGS data of plasma samples from healthy individuals (N=29)
Illumina HiSeq 4000 29

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