Advances in technology are enabling whole genome sequencing analysis from formalin-fixed paraffin-embedded (FFPE) specimens in clinical oncology. Various methods and tools, such as Hi-C sequencing and direct-seq technology, are being developed to improve the analysis of FFPE samples, allowing for simultaneous genetic and epigenetic analysis and high-throughput single cell chromatin accessibility profiling. These developments may enhance cancer research and diagnosis by providing high-resolution data from FFPE-preserved samples.