Current Bioinformatics Seminar
Time: 11AM Tuesdays.
Venue: Davis Auditorium and Online
26 May 2026
Analytical methods for ecDNAs in Cancer
Jennifer UretaWEHI
The amplification of oncogenes is one of the most common alterations found in cancer. Through the overexpression of oncogenes and functional elements, it provides cancer cells with selective growth advantages that contribute to tumour proliferation and survival. Although oncogene amplification is known to play a significant role in cancer development, we still do not have a complete understanding of the mechanisms responsible for it. Some genome amplifications can arise from double-strand breaks caused by mechanisms such as breakage fusion-bridge cycles and chromothripsis. The production of circular extrachromosomal DNA lacking centromeres, which unevenly segregates into their daughter cells and proliferates under selective conditions, can also lead to gene amplification. Studying the circularization of linear chromosomal DNA can help us better understand the role of and mechanisms behind gene amplifications. During my PhD, I characterised ecDNA and other high level focal amplifications in cancers, including rare cancers and brain metastases. I developed computational pipelines for the detection and analysis of ecDNA using both short-read and long-read sequencing technologies. Our findings established ecDNA as a critical driver of oncogene amplification and diversity in brain metastases and gynaecological cancers, revealing its remarkable heterogeneity across different cancer types.