Bionano Genomics, Inc. announced the first publication from the COVID-19 Host Genome Structural Variant Consortium. The study found that optical genome mapping (OGM) with Bionano’s Saphyr System identified structural variants (SVs) that affect genes in pathways that control immune and inflammatory response, viral reproduction and mucosal function. The authors believe these SVs may provide key insights into the pathogenesis of COVID-19 and outcomes in patients who become severely ill. The consortium was formed by Dr. Ravindra Kolhe from Augusta University with the goal of identifying large SVs that factor into the clinical course and outcomes of patients who contract COVID-19. Unlike other analyses of the host genome which are usually limited to genome-wide association studies or exome/genome sequencing and aim to detect single basepair changes, the consortium focuses on finding larger variants in patients’ genomes because they are believed to have a greater potential to impact genes. The consortium has selected OGM with the Saphyr System for genome analysis owing to Saphyr’s documented performance as the leading platform for detecting these large SVs. The current study received contributions from scientists at Augusta University, the University of California San Diego, Radboud University Medical Center, The Rockefeller University, University of Texas M.D. Anderson Cancer Center, Columbia University Medical Center, Virginia Commonwealth University, New York Genome Center, Harvard Medical School, and Bionano Genomics. The study reports the analysis of the genomes of 37 patients who were admitted to the ICU at Augusta University with severe COVID-19 disease. 30 patients needed mechanical ventilation with a mean intubation duration of 12 days. Of the 37 patients, 25 recovered and 12 died. The SVs revealed by Saphyr were confirmed with other technologies such as quantitative PCR. One of the most compelling findings among the SVs identified was the duplication of the STK26 gene, a key element of the Toll-Like Receptor signaling pathway which controls the cell’s response to viral infection. In the follow-on analysis of the expression of the STK26 gene in patients with the duplication, the study found significant upregulation of STK26 in all severely ill patients tested but not in asymptomatic COVID-19 patients, implying the duplication to be a potential novel, prognostic biomarker for the severe immune response seen in severely ill patients.