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Identification of Host Genes and Variants influencing susceptibility to COVID-19 using a Proprietary Machine Learning Knowledge Base

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Lay summary

Breakthrough Genomics has had a long-standing commitment to helping individuals better understand their genome to empower them on their personal health journey to help them live a healthy and long life. Using its proprietary technology Breakthrough Genomics is able to identify existing and new genes associated with certain illnesses and rare diseases and we can do so faster than most other laboratories. We share GEL’s vision in trying to understand genetic differences that may explain why some people are more severely affected by COVID-19 than others.  And we believe that the GEL Research Project has the best quality genetic data and that combined with Breakthrough Genomic’s technology, we can get some critical clues to the answers.  
In early 2020, the scientific team at Breakthrough Genomics used its proprietary machine learning knowledge base to identify 28 variants encompassing 14 different genes that may be involved in susceptibility to coronavirus.  This panel of variants are referred to as the Coronavirus Genetic Susceptibility Assessment Panel (CGSA), the GEL COVID Whole Genome Sequencing data would be useful in determining whether these genes and variants correlate with COVID-19.  

The GEL COVID WGS data could be run through the Breakthrough Genomic’s cloud-based clinical interpretation software, ENLITER™ while inside the COVID Research Environment and adhering to all the Airlock and governance policies set out by Genomics England. ENLITER™ contains a custom COVID filter for reporting the initial 28 variants already identified so these variants could be analysed immediately. Meta-analysis and heterogeneity testing will be used to assess the strength of association between the gene variants and COVID-19 and COVID-19 complications risks. 

We will share this information with other GEL partners, the scientific and medical communities to further understand this public health crisis.  Our goal is to be able to better manage treatment of SARS-CoV-2 positive patients to minimize severity of COVID and prevent deaths.  We also believe that at least some of the clues, may be applicable to other infectious diseases which could impact future treatment strategies for select patients.

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