Mohammed El-Kebir Faculty Allocation

Mohammed El-Kebir, University of Illinois at Urbana-Champaign

Usage Details

Cancer is a genetic disease characterized by intratumor heterogeneity as well as the presence of multiple cellular populations with different sets of mutations. Cellular heterogeneity gives cancer the ability to resist treatment, and quantifying its extent is key to improving our understanding of tumorigenesis. In this project, we developed and employed novel phylogenetic (evolutionary tree-based) techniques to reconstruct the evolutionary histories of individual tumors from DNA sequencing data. Typically, this data is obtained from shotgun sequencing of tumor biopsies using either single-cell or bulk-sequencing technology. Highlights from our research outcomes include: (1) the creation of SPhyR, an algorithm that employs the k-Dollo evolutionary model to reconstruct phylogenetic trees from single-cell DNA sequencing data; and (2) a detailed analysis using simulated data on the nonuniqueness of solutions to the phylogeny estimation problem from bulk DNA sequencing data.