ecDNA Detection

The Brunk Cytogenomics Lab, is studying extrachromosomal DNA (ecDNA), which are circular DNA that is not located on chromosomes. This type of DNA is interesting and important because it is implicated in many cancers, drug resistance, and hard-to-treat tumors. Because it is not a part of the chromosomes, it may also have unique molecular properties that cancer hijacks, which aids in proliferation.

One of the most basic and important ways to study this phenomena is through molecular visualization, where we can perform experiments to image cell nuclei. We can detect how many cells have ecDNA and the heterogeneity of ecDNA across cells, in terms of types and counts. These experiments are low throughput and time consuming, mainly because counting ecDNAs can take a very long time. Just as an example, counting 150 images of cells that have 200 ecDNAs per nuclei takes our group more than a week, if 3 people are counting full time. This is not sustainable if we want to study the dynamics of ecDNA under different conditions, which requires us to take many images and to do a lot of counting.

Using Computer Vision, this project aims to automate the process of detecting and counting ecDNA present in scans.