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Optical genome mapping identifies rare structural variations as predisposition factors associated with severe COVID-19.

ISCIENCE 2022
Sahajpal NS, et al.

Sahajpal, N.S., Jill Lai, C.-Y., Hastie, A., Mondal, A.K, Dehkordi, S.R., van der Made, C.I., Fedrigo, O., Al-Ajli, F., Jalnapurkar, S., Byrska-Bishop, M., Kanagal-Shamanna, R., Levy, B., Schieck, M., Illig, T., Bacanu, S.-A., Chou, J.S., Randolph, A.G., Rojiani, A.M., Zody, M.C, Brownstein, C.A., Beggs, A.H., Bafna, V., Jarvis, E.D., Hoischen, A., Chaubey, A., Kolhe, R., the COVID19hostgenomesv consortium.

Impressive global efforts have identified both rare and common gene variants associated with severe COVID-19 using sequencing technologies. However, these studies lack the sensitivity to
accurately detect several classes of variants, especially large structural variants (SVs), which
account for a substantial proportion of genetic diversity including clinically relevant variation. We performed optical genome mapping on 52 severely-ill COVID-19 patients to identify rare/unique SVs as decisive predisposition factors associated with COVID-19. We identified 7 SVs involving genes implicated in two key host-viral interaction pathways: innate immunity and inflammatory response, and viral replication and spread in 9 patients, of which SVs in STK26 and DPP4 genes are the most intriguing candidates. This study is the first to systematically assess the potential role of SVs in the pathogenesis of COVID-19 severity and highlights the need to evaluate SVs along with sequencing variants to comprehensively associate genomic information with inter-individual variability in COVID-19 phenotypes.

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