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

ABSTRACT: 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 of authentic cell-free DNA, including each patient's germline and blood-cell mutation backgrounds. Using deep whole-genome (150x) and exome (2,000x) sequencing, we define a reference set of ~37,000 single nucleotide variants and ~58,000 indels to benchmark nine somatic variant callers across varying ctDNA levels and sequencing depths. We also explore machine learning-based tuning of

SUBMITTER: Carrie H 

PROVIDER: S-EPMC12852940 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature