[Preprint] Initial Review and Analysis of COVID-19 Host Genetics and Associated Phenotypes

Preprint posted on Preprints.org, 2020

Recommended citation: Y. Tanigawa, M. Rivas, Initial Review and Analysis of COVID-19 Host Genetics and Associated Phenotypes (2020). https://doi.org/10.20944/preprints202003.0356.v1

As a part of the COVID-19 Host Genetics Initiative, we perform the following set of analyses to better understand the genetic basis of COVID-19 susceptibility and severity.

  • Polygenic prediction of blood measurements
  • Global catalogue of HLA allelotype diversities
  • Global frequency catalogue of ABO blood types

This preprint is a brief description of our activities. We demonstrate the relevance of our genetic resources for analysis of the host genetics of COVID-19.


Q1. How can I find p-values for each variant in PRS models

A1. Our PRS is constructed via multivariate model

Unlike GWAS, our PRS model does not explicitly perform univariate testing, rather, we fit multivariate models. The genetic variants with non-zero BETAs are selected using our validation dataset. This means that each variant does not come with a p-value. Please check our preprint[1] for more details of our snpnet PRS procedure.

Another caveat is that our procedure does not contain some computation equivalent to fine-mapping.Still, one can interpret the genetic variants with non-zero BETAs (or its LD proxy) as the ones informative ones for polygenic prediction.

  • 1. J. Qian, W. Du, Y. Tanigawa, M. Aguirre, R. Tibshirani, M. A. Rivas, T. Hastie, A Fast and Flexible Algorithm for Solving the Lasso in Large-scale and Ultrahigh-dimensional Problems. bioRxiv, 630079 (2019). https://doi.org/10.1101/630079

Yosuke also wrote a brief summary of this COVID-19 related research activities in Japanese.