Programmable Argonaute-mediated single-nucleotide variant sequencing of cell-free DNA for multi-cancer early detection #MMPMID41339622
Guo C; Zhang J; Zhang S; Moon J; Yang R; Guan X; Hou C; Pei M; Schalper KT; Schreiber D; Liu X; Perpetua L; Chang Y; Sanders M; Ristau B; Liu C
Nat Commun 2025[Dec]; ? (?): ? PMID41339622show ga
Mutation sequencing of cell-free DNA (cfDNA) in liquid biopsy is crucial for tumor precision medicine, resistance profiling, and clinical decision-making. However, cfDNA mutation profiling in blood samples remains challenging due to its low abundance and high background noise. Here, we develop an Enzymatic Cleavage-directed Single Nucleotide Variant Sequencing (EC-SNV-Seq) assay technology for multiple cfDNA mutation detections. The EC-SNV-Seq assay integrates Argonaute-mediated cleavage and stem-loop DNA-initiated cascade-PCR amplification, achieving a sensitivity of 0.01% variant allele frequency. As a proof of concept, we apply the EC-SNV-Seq assay to detect multiple cfDNA mutations in KRAS, EGFR, and PIK3CA genes with single-nucleotide resolution. We further validate that EC-SNV-Seq detects early-stage multi-cancer and identifies single-nucleotide variants in a single patient plasma sample. Lastly, we evaluate its feasibility for multi-cancer early detection in population-scale screening using pooled plasma samples. The EC-SNV-Seq assay can enable highly sensitive and specific identification of low-frequency mutations, facilitating early cancer diagnosis and personalized treatment strategies.
Nat+Commun 2025 ; ? (?): ?
