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 4 datasets.

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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
WGS data of buffy coat from CRC patients
Illumina HiSeq 4000 7

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