Deep whole genome ctDNA chronology of treatment-resistant prostate cancer

1 Dataset 1 Publication

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Dataset ID	Description	Technology	Samples
EGAD00001008460	Circulating tumor DNA (ctDNA) in blood plasma is an emerging tool for clinical cancer genotyping and longitudinal disease monitoring. We performed deep whole-genome sequencing of serial plasma and synchronous metastases in patients with aggressive prostate cancer. We comprehensively assess all classes of genomic alterations and demonstrate that ctDNA harbors multiple dominant populations whose evolutionary histories frequently indicate whole-genome doubling and shifts in mutational processes. Although tissue and ctDNA showed concordant clonally-expanded cancer driver alterations, each individual metastasis contributed only a minor share of total ctDNA. By comparing serial ctDNA before and after clinical progression on potent androgen receptor (AR) pathway inhibitors, we reveal population restructuring converging solely on AR augmentation as the dominant genomic driver of acquired treatment-resistance. Finally we leverage nucleosome footprints in ctDNA to infer mRNA abundance in synchronously biopsied metastases, including treatment-induced changes in AR pathway transcriptional activity.	unspecified	117

Publications	Citations
Image-based DNA sequencing encoding for detecting low-mosaicism somatic mobile element insertions. Tan M, Lin Z, Chen Z, Zhou H, Park J, He Z, Lee EA, Gao Z, Zhu X. Nat Commun 16: 2025 9195	0