Computational Approaches to Study ecDNA in Cancer Genomics

The mysterious and ubiquitous extrachromosomal circular DNA (ecDNA) is present independently of the chromosomal DNA in genomes of eukaryotes. ecDNA, found in eukaryotes, orchestrates cellular functions and causes illnesses, including cancer. Nevertheless, there is a wealth of untapped study potential in determining its complete impact on health and illness. A precise and clear overview of the landscape of techniques, from biogenesis to functional analysis, is provided in this chapter, which is necessary for unravelling the complexity of ecDNA. A thorough review of cutting-edge methods for studying ecDNAs, including high-throughput sequencing, bioinformatics, and experimental validations, is provided here. In cancer genomics, computational methods are essential for understanding ecDNA, especially when combined with improved sequencing techniques. To better understand the function of ecDNAs in cancer progression and oncogene amplification, these techniques use genomic data to detect, characterize, and recreate ecDNA structures. Additionally, we outline the direction for future studies, including new methodological avenues and perhaps revolutionary ways to ecDNA project design.