In the study "Genetic mechanisms of critical illness in Covid-19", (free to download) the authors share their findings on which genomes seem to be associated with an increased likelihood of hospitalization when infected with COVID 19.

See Table 1 (page 9), to see that the Risk is represented by one letter. I'm not academically trained in genetics, so my only experience when reading these papers is that usually risks are associated with a base pair. Like "C/C', or "A/G".

enter image description here

Why is only one chemical/letter given? How does one interpret this?

*I'd like to mentioned that several genetic testing companies have the markers in this study mapped, so this could be useful information for patients and their physicians.

  • 2
    $\begingroup$ I'm not sure what's unclear; the table shows a Risk base and Alternative base for a SNP (aka, a substitute of one base for another) at a given location. What are you having trouble interpreting? $\endgroup$
    – Bryan Krause
    Dec 11, 2020 at 22:24
  • 1
    $\begingroup$ I’m voting to close this question because it requires reading an external paper to understand the question. This is a question and answer site about problems in biology in which any question must be comprehensible in itself. It is not a journal discussion group. $\endgroup$
    – David
    Dec 12, 2020 at 9:43
  • 2
    $\begingroup$ This is a quite reasonable question to ask about a style of data presentation that is not limited to a single paper. $\endgroup$ Dec 14, 2020 at 1:56

1 Answer 1


The "Risk" is the single basepair sequence (A, C, G, or T) at the precise chromosome:position location in the column to the left of it. "Alt" is the basepair present in the other allele. The complementary nucleotide is still present on the other strand, but its identity is obvious and the decision of which strand's sequence to list was made when the original reference sequence was published.

The slash notation "C/C" (as in https://www.biorxiv.org/content/10.1101/2020.12.06.413971v2 ) means that the genotype for both alleles the person is carrying has been considered jointly. In this table no such breakdown is given. Judging by their subsequent interest in transcript level, it is conceivable their model was that the two alleles would have subtle additive effects on overall expression level with a subtle effect on Covid risk, so that incomplete dominance could be assumed... but to truly understand their motivation you need to understand high-definition likelihood inference (see the overview and paper link at https://medicalxpress.com/news/2020-07-high-definition-likelihood-inference-genetic-human.html ) which requires some study.


You must log in to answer this question.

Not the answer you're looking for? Browse other questions tagged .