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

The COVID19hostgenomesv Consortium, Nikhil Shri Sahajpal, Chi Yu Jill Lai, Alex Hastie, Ashis K. Mondal, Siavash Raeisi Dehkordi, Caspar I. van der Made, Olivier Fedrigo, Farooq Al-Ajli, Sawan Jalnapurkar, Marta Byrska-Bishop, Rashmi Kanagal-Shamanna, Brynn Levy, Maximilian Schieck, Thomas Illig, Silviu Alin Bacanu, Janet S. Chou, Adrienne G. Randolph, Amyn M. Rojiani, Michael C. ZodyCatherine A. Brownstein, Alan H. Beggs, Vineet Bafna, Erich D. Jarvis, Alexander Hoischen, Alka Chaubey, KOLHE RAVINDRA

Research output: Contribution to journalArticlepeer-review

12 Scopus citations


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 nine 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 interindividual variability in COVID-19 phenotypes.

Original languageEnglish (US)
Article number103760
Issue number2
StatePublished - Feb 18 2022


  • Genetic sample
  • Genomics
  • Virology

ASJC Scopus subject areas

  • General


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