Published: Oct. 22, 2019

Kate Bubar, Biofrontiers Institute, University of Colorado Boulder Estimating the overlap between malaria parasite sequence reads Over half a million people die from malaria every year. The disease pathogenesis and subsequent fatality can be linked to PfEMP1, a protein encoded by var genes. Each parasite genome has sixty highly variable var genes. Changing the var gene that is expressed enables the infected red blood cells to avoid the immune system, and the malaria infection persists. By quantifying the number and frequency of identical var genes between malaria parasites, we hope to better understand the ways in which they evade the immune system. I will first explain common measurements of beta diversity, the diversity of species from one environment to another, and why using these measurements is a naive approach to this problem. I will then present our novel approach for estimating gene overlap from short read data and ideas for future work.