Covid19 and 24Genetics: new developments part II

COVID-19 unites efforts in research

Since the early days of the virus spread throughout the world, research at the international level also began. Proof of this is the different consortiums created to fight the pandemic, such as COVID-19 High-Performance Computing (HPC) Consortium, COVID-19 Genomics (COG-UK) Consortium or Host Genetics Initiative (HGI). The latter, in which 24Genetics participates through a collaboration with the Health Research Institute of the La Paz University Hospital (IdIPAZ), groups together almost 200 international research projects focused on genetic factors of susceptibility to the virus.This new entry will describe the history of genetic discoveries and the development of the research that 24Genetics is currently carrying out.

24Genetics’ collaborative research contribution

Thanks to the consortium in which 24Genetics and (HGI) participate, we discovered many and varied genetic markers. As new data is available, the genetic results have become more meaningful. One of the first studies that saw the light, with the help of HGI, identified critical markers in the antiviral defence and the inflammatory processes. These included specific chromosomes and genes such as FYCO1 (Chr. 3), IGF1 (Chr. 12) or DPP9 (Chr. 19)(Figure 1).

Figure 1. Pairo-Castineira, E., et al. Genetic mechanisms of critical illness in Covid-19. medRxiv 2020.09.24.20200048; doi: https://doi.org/10.1101/2020.09.24.2020004

Results of the research with IdiPaz

No less significantly, and with a much larger number of samples, the importance of blood group as an immunoprotective factor was raised (2). The ABO gene (Chr.3), the main actor, came out showing potential protection of between 14% and 16% in particular blood groups. The research also brought to the table more inflammatory genetic factors related to respiratory failure (Figure 2).

Figure 2. The Severe Covid-19 GWAS Group. Genomewide Association Study of Severe Covid-19 with Respiratory Failure. 2020 N Engl J Med 2020; 383:1522-1534 DOI: 10.1056/NEJMoa2020283

And what does 24Genetics contribute to all this?

In October, 24Genetics takes the baton, and with the fieldwork done by IdIPAZ and the samples already sequenced by our reference laboratories, it gets to work. One of the first tasks carried out was the filtration and “healing” of the data generated. One of the processes started was the analysis of genetic data from people with IDOC disease concerning people in intensive care (Figure 3).

Figura 3. Figura proporcionada por Lasse Folkersen, BS y PhD

It was then decided to begin using artificial intelligence by analyzing the set of clinical variables reported, to know closely, which ones were more or less important (Table 1).

Table 1. Chart provided by Carlos Ortega, Data Scientist

Artificial intelligence, on this occasion, made it possible to classify the variants by significance. In the following table, you can see the different factors obtained. However, it was necessary to validate the model; for that, we used SHAP (Shapley Additive ExPlanations). In short, this model allows the algorithm to explain the weight that each factor has (Table 2).