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.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

4 Datasets 1 Publication

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	WGS data of plasma samples from CRC patients (N=12)	Illumina HiSeq 4000	12
EGAD00001006420	WGS data of plasma samples from BRCA patients (N=10)	Illumina HiSeq 4000	10
EGAD00001006421	WGS data of plasma samples from healthy individuals (N=29)	Illumina HiSeq 4000	29
EGAD00001008352	WGS data of buffy coat from CRC patients	Illumina HiSeq 4000	7

Publications	Citations
Tissue-specific cell-free DNA degradation quantifies circulating tumor DNA burden. Zhu G, Guo YA, Ho D, Poon P, Poh ZW, Wong PM, Gan A, Chang MM, Kleftogiannis D, Lau YT, Tay B, Lim WJ, Chua C, Tan TJ, Koo SL, Chong DQ, Yap YS, Tan I, Ng S, Skanderup AJ. Nat Commun 12: 2021 2229	31