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

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COVID-19 Host Genetics analysis

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

Please check out initial draft of host genetics of COVID-19, Initial review and analysis of COVID-19 host genetics and associated phenotypes.

  • HLA: HLA frequency in UK Biobank[2].
  • ABO: The ABO blood type frequency in UK Biobank.
  • snpnet: Polygenic prediction of biomarkers and blood measurements. We deposit notebooks and scripts for polygenic risk score (PRS) analysis in this directory[3,4,5].
  • PRS_PheWAS: Application of blood measurement PRSs for disease risk prediction.

Please share ABO blood type frequency in COVID-19 patients

We replicated recent findings in Zhao et al.[6] about the significant risk reduction of the blood group O across different control groups in UK Biobank. For a robust inference of risk factors, we would like to encourage a broad sharing of ABO blood type frequencies across (1) mild, (2) moderate, and (3) severe/critical COVID-19 cases at https://tinyurl.com/abo-covid19.

Publicly available resources

Note

This repo is a summary of joint effort for the community project from the Stanford Researchers and Clinicians, including (but not limited to) the following people: Yosuke Tanigawa, Kazutoyo Osoegawa, Marcelo Fernandez Vina, Euan Ashley, Carlos Bustamante, Julia Palacios, Benjamin Pinsky, Manuel A. Rivas.

Acknowledgement

We thank Dr. Kazutoyo Osoegawa for reformatting and aggregation of the 17th IHIW NGS HLA Data. We thank Stanford Research Computing Center for providing prioritized queue for COVID-19 research[7].

Update log

Reference

  1. Tanigawa, Y. & Rivas, M. Initial Review and Analysis of COVID-19 Host Genetics and Associated Phenotypes. Preprints.org (2020).
  2. McInnes, G. et al. Global Biobank Engine: enabling genotype-phenotype browsing for biobank summary statistics. Bioinformatics (2019).
  3. Qian, J. et al. A Fast and Flexible Algorithm for Solving the Lasso in Large-scale and Ultrahigh-dimensional Problems. bioRxiv 630079 (2019).
  4. Sinnott-Armstrong, N. et al. Genetics of 38 blood and urine biomarkers in the UK Biobank. bioRxiv 660506 (2019).
  5. UK Biobank : Category 100081. Blood count - Blood assays - Assay results - Biological samples.
  6. Zhao, J. et al. Relationship between the ABO Blood Group and the COVID-19 Susceptibility. medRxiv 2020.03.11.20031096 (2020).
  7. Sherlock joins the fight against COVID-19. Stanford Research Computing Center.
  8. Kaiser, J. How sick will the coronavirus make you? The answer may be in your genes. Science (News article) (2020).

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

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