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Article

Comprehensive benchmarking of methods for mutation calling in circulating tumor DNA.

Nature communications - 18 Dec 2025

Carrié Hanaé, Sim Ngak Leng, Wong Pui Mun, Gan Anna, Lau Yi Ting, Poon Polly, Thangaraju Saranya, Tan Iain, Yap Yoon Sim, Krishnamachari Kiran, Wong Limsoon, Skanderup Anders

Abstract excerpt

Detection of somatic mutations in cell-free DNA (cfDNA) is challenging due to low variant allele frequencies and extensive DNA degradation. Here we develop a benchmarking strategy using longitudinal patient-matched cfDNA samples from individuals with colorectal and breast cancer. Samples with high and ultra-low levels of tumor-derived DNA are combined into controlled dilution series that preserve the properties...

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Identifiers

PMID: 41407694
DOI: 10.1038/s41467-025-67842-x
PMCID: PMC12852940

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