Mutation Accumulation During Passaging in Msh2-Deficient and Control Mouse Fibroblasts

Single-cell whole-genome sequencing was applied to assess the accumulation of de novo mutations including single-nucleotide variants (SNVs) and small insertions and deletions (INDELs), during long-term passaging of Msh2-deficient (-/-) and control mouse fibroblasts. Whole-genome amplification of individual cells was carried out using single-cell multiple displacement amplification (SCMDA; Dong et al., Nat Methods 2017). To exclude germline polymorphisms, whole-genome sequencing was also performed on bulk DNA. Both single-cell and bulk samples were sequenced to a depth exceeding 20x genome-wide coverage, ensuring high-confidence mutation calling.