Methods: With approval from the Office for Protection of Research subjects, peripheral blood was obtained from a group of 20 ethnically diverse adults with extrapulmonary dissemination of coccidioidomycosis. DNA was extracted from peripheral blood mononuclear cells and submitted for whole exome sequence analysis by the UCLA Core Microarray Laboratory on an Illumina HiSeq 2500 instrument. We filtered the resulting data for variants in genes known or suspected to be in pathways relating to responses to fungal infections.
Results: We identified a mean of 246,708 variants from the human reference genome per sample, of which a mean of 6336 per sample passed quality controls, affected protein sequence or splicing, and had a frequency of 10% or less in an exome database of ~60,706 un-phenotyped individuals. We identified 3 African American individuals with polymorphisms in the gene (CHIT1) encoding human chitinase that are known to reduce enzymatic activity. One of these individuals also possessed a missense change in the coding sequence of Dectin-1, a C-type lectin–like receptor involved in the recognition of cell wall components by macrophages and other antigen presenting cells.
Conclusion: Exome sequencing is an excellent tool for the unbiased discovery of genetic variants and can successfully be used with archived tissue. The genetic causes of cocci seem to be complex and multifactorial. CHIT1, CLEC7A, and other genes in related pathways are intriguing candidates for further validation and investigation. Using whole exome analysis, we have identified two genetic polymorphisms that may contribute to macrophage dysfunction, enhancing the risk of dissemination of coccidioidomycosis.
A. Heidari, None
D. Aguirre, None
R. Grewal, None
R. H. Johnson, None