Aspergillus fumigatus is a potentially deadly human pathogen that primarily infects individuals with compromised immune systems. ~100,000 people die each year due to complications from A. fumigatus infections. In the United States in 2014, an estimated 15,000 people were hospitalized due to A. fumigatus related infections, resulting in healthcare costs totaling more than $1 billion. Treating and controlling A. fumigatus infections is particularly challenging because of the emergence of drug resistance and the increased frequency of immunocompromised individuals because of immunosuppressive medical treatments. The long-term goal is to improve treatment of A. fumigatus infections. The objective of this proposal is to determine the genetic variants and genes that contribute to A. fumigatus pathogenicity-associated traits. To date, A. fumigatus genomic research has lagged behind the pace at which DNA-sequencing technologies and computational biology methodologies have advanced. New approaches are required to decipher the polymorphisms and genes underlying the complex nature of A. fumigatus pathogenicity. The central hypothesis is that standing genetic variation at multiple loci accounts for differences in A. fumigatus pathogenicity between isolates. The rationale underlying this proposal is that completion of this work will identify novel targets for disrupting A. fumigatus pathogenicity and treating A. fumigatus infections. The central hypothesis will be tested by pursuing three specific aims: (1) Quantify natural phenotypic variation for a collection of A. fumigatus immune evasion and immune adaptation traits, (2) Identify genetic variants associated with A. fumigatus immune adaptation and immune adaptation strategies using genome-wide association analysis, and (3) Validate candidate genes and genetic variants associated with A. fumigatus pathogenicity using molecular genetic approaches. This research will be conducted with a collection of 286 diverse A. fumigatus isolates for which all genomes have been sequenced and genetic variants have been identified. These aims will be pursued using a combination of innovative statistical genomic (genome-wide association) and CRISPR/Cas9-based molecular genetic approaches. Importantly, the combination of these methods will greatly reduce false positives. The proposed research is significant because it will reveal novel insights into the genetic basis of A. fumigatus pathogenicity and identify new potential drug targets. The results of this research have the potential to positively affect hundreds of thousands of individuals that are burdened by A. fumigatus infections.