Detection of known gene fusions in cancer cell lines using whole-genome bisulfite sequencing data

Whole-genome bisulfite sequencing (WGBS) provides multiple molecular information layers including methylation, copy number variations (CNVs), single nucleotide variants (SNVs), and fragmentome patterns in cell-free DNA (cfDNA) while gene fusion detection from WGBS data has not been widely explored. We applied a custom analysis pipeline using bisulfite-aware aligners supporting split read alignment to detect known gene fusions from WGBS data and validated this approach using cancer cell lines with characterized fusion events. Using K562 cells harboring the BCR-ABL1 fusion, WGBS-derived breakpoints showed concordance with WGS-derived coordinates. Serial dilution experiments with K562 DNA in NA12878 background at average 63X coverage established a limit of detection (LoD) of 8.1% fusion-positive DNA fraction, demonstrating 100% detection rate at ≥10%. Furthermore, our method with MCF-7 cells detected 10 of 12 validated fusions with high technical reproducibility (Pearson r > 0.99), including both inter-chromosomal and intra-chromosomal events. This approach confirms that known gene fusions can be reliably detected from WGBS data, particularly well-suited for applications where methylation and fusion profiling are both required.