Feb 1 2022 COVID-19 HGI Update Q&A Report

	A	B	D
1	Asker Name	Question	Answer
2	Nathaniel Pearson	Can we run recessive model analys(es)?	live answered
3	David Condon	how will study B1 specifically be affected by release 7?	live answered
4	Iris Heid	we have GWAS summary statistics computed for the consortium phenotypes and we are happy to share ASAP (tomorrow?).	live answered
5	Iris Heid	whom should I contact to provide the data? best regards, Iris, University of Regensburg	can you email: andrea.ganna@helsinki.fi? thanks!
6	Abdou Mousas	Is there still time to be included in Data Freeze 7? We have a few thousand samples in Ioannina Cohort, Greece.	thanks! please email andrea.ganna@helsinki.fi
7	Nathaniel Pearson	(Asking on recessive, as other major viral infections show classic recessive resistance hits (e.g., cell surface markers CCR5, FUT2, etc.), and we also see such a hit for ABO here ourselves.)	This is a good point. I think that some large studies are better positioned for doing this. Unfortunately, we cannot ask all studies to do that.
8	Nathaniel Pearson	(Asking on recessive, as other major viral infections show classic recessive resistance hits (e.g., cell surface markers CCR5, FUT2, etc.), and we also see such a hit for ABO here ourselves.)	Yep — perhaps we could start by proposing a simple goldilocks threshold for minimal study population sample size, for power to detect genomewide-significant effect of homozygous genotype of frequency >=x…and then see if any hits (potentially new) in those replicate among each other and in any smaller studies that then wish to jump in after?
9	JNNasir	Apologies for the ignoranr question. I'm not a statistician! I can see p-values are significant but OR very low (1.02). How do we explain the significance of this in lay terns apart from the variant having a tiny contribution overall?	some of this common variants tag rare variants that have large effect. Some others they simply have small individual effect reflecting e.g. regulatory mechanisms. Small effect does not mean that the biology insights are not relevant. In fact, it has been shown in many traits that variants even with small OR can point to fundamental biological mechanisms
10	dermot	The single cell data was only lung? These MUC genes are expressed elsewhere to? We have PBL eQTLs with a couple of these? Thanks	live answered
11	David Condon	I was curious if any new loci would appear, or how the number of patients would change	In preliminary we find the previously found loci on chr3 and chr21 plus HLA in B1
12	Josep Mercader	Is there a plan to publish a paper on freeze 7?	if meaningful additional value, I think we would most likely, as with freeze 6, plan to update the existing papers with another ‘matters arising’
13	JNNasir	Thanks Andrea. I think we can posit interesting biologocal explnations for small OR. For me, the age related effect size will be the most interestung.	good. We will share indeed age-stratified analyses. However sample sizes will be substantially smaller.
14	Anna_Planas	Are you planning correlate with autoimmune diseases? and separate by sex?	live answered
15	andrea cossarizza	any idea to corelate with BMI?	live answered
16	Carlos Alberto Aguilar	How was handled the COVID severity in the analysis?	live answered
17	Carlos Alberto Aguilar	How was handled the COVID severity in the analysis?	Thank you for very sensible comments. We think that severity-stratified analysis is a good start to address that question. We are still underpowered to do this. But we could still compare the results from hospital-based cohorts (enriched with severe cases) and population-cohorts (enriched with mild cases) to partially address that.
18	andrea cossarizza	do you plan to include also children with long covid? we are collecting a cohort.	live answered
19	andrea cossarizza	do you plan to include also children with long covid? we are collecting a cohort.	Yes, long covid in children is also very interesting. For now we have analysed all ages together (with age as covariate in the GWAS). But the mechanisms in children might be somewhat different than those in the adults (which probably are already heterogeneous also), so a separate meta-analysis would be great if we have several cohorts with data on children. The Slack channel #covid19-hg-longcovid is a good place to discuss these additional analyses.
20	Carlos Alberto Aguilar	Which comorbidities were controlled in the analyses?
21	Taranjit Singh Rai	Can you do severity classification by WHO analysis
22	Josep Mercader	I guess an added value would be the sex-specific analyses which I belive that were not reported in freeze 6 matters arising paper (in addition to increased samples size, etc)?	we will look into that, but all the largest studies do not report sex-stratified analyses and so this means we have lower power, But we can use maybe use those to look for sex-specific efect on the existing loci
23	Johnathan Cooper-Knock	nice talk maik. are the cis-pQTLs publically available?	live answered
24	Dr. Fouzia Sadiq	That’s interesting data Liz. People around me have responded considerably bad after second dose of moderna.
25	Reza	have you looked at the spike protein epitopes used in two vaccines?
26	Nathaniel Pearson	Fair to say ‘mostly specific to Pfizer’, versus ‘most strongly detectable in Pfizer’?
27	Danielle Reed	How does vaccine reactivity relate to breakthrough susceptablity?
28	Julian Willett	What is her contact information? I am finalizing a manuscript on HLA with COVID-19 severity/susceptibility
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