Cost effective arrays for rapid epidemiological investigation of SARS-CoV-2 infection (COVID-19) susceptibility in relation to underlying health conditions

A major challenge for healthcare providers and geneticists is to learn how SARS-CoV-2, the coronavirus that causes the COVID-19 disease, interacts with the human genome and to stratify populations in order to understand disease susceptibility, severity, and outcomes.

We have launched our new Axiom Human Genotyping SARS-CoV-2 Research Array.

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Axiom genotyping arrays and associated modules for human genotyping research can be used in various aspects of SARS-CoV-2 infection research:

  • Susceptibility to COVID-19 and relevant GWAS markers: A large GWAS grid  of >800K markers can suppoort research of disease associations including chronic obstructive pulmonary disease (COPD), coronary artery disease traits, and high blood pressure traits across multiple populations to assess risk severity.
  • Expression quantitative trait loci (eQTLs): Information about the genetic basis of coronavirus infections in global populations and especially non-Asian Caucasian (CEU) populations is limited. Both ACE2 expression and function may be different in CEU populations.
  • Pharmacogenetics research for drug discovery and targets: The large GWAS grid offers the ability to use results from various association studies and thus incorporate genetics into evaluating a large number of druggable targets. Focused arrays with pharmacogenomic content offer the ability to look at a large number of genes involved in drug absorption, distribution, metabolism, and excretion, including the complex CYP genes.
  • Pharmacogenetics research for drug-drug and drug-gene interactions: Pharmacogenomics research will be important in understanding the efficacy and dosage of drugs administered as part of the various research studies. The pharmacogenomic research content can help with studies of efficacy and therapeutic effects of treatments that include but are not limited to antivirals and anti-malarial drugs.
  • Angiotensin-converting enzyme 2 (ACE2) receptors: The viral receptor protein ACE2 exists on the host cell surface. This is believed to be the mechanism by which the virus enters the body. Study of ACE2 protein requires maximizing the number of X-chromosome markers on the array. There are over 9,000 markers in the ACE2 protein. Any Axiom design can maximize the coverage of these variants.
  • Cytokine genes: Inflammatory cytokine genes may influence the function of immunopathological processes in influenza-like illnesses. Study of these genes may help understand the initiation of immune response, controlling viral replication and hypercytokinaemia.

Summary of relevant content in the new Axiom Human Genotyping SARS-CoV-2 Research Array

Category Number of Markers*
SARS-CoV-2 Susceptibility Research Variant Module >135,000
SARS-CoV-2 putative receptor variants >1,200
Signaling pathway variants >130,000
Variants on X-Chromosome >60,000
SARS-CoV-2 Severity Research Module – Underlying conditions implicated in severity of SARS-CoV-2 infections >16,000
Blood phenotypes and blood groups >1,200
Diabetes >800
Cardiovascular disease >1,300
Stroke >50
Lung function and COPD >9,000
BMI >1,000
Asthma >500
SARS-CoV-2 Immune Response and Therapeutic Treatment Research Variants Module >24,000
ADME and protein markers for druggable targets >6,000
Immunoglobulin and miRNA markers for vaccine research >12,000
HLA/KIR markers for immune response research after vaccination >9,000
Multi-ethnic Genome Wide Association Study (GWAS) Grid >725,000
ACMG 59 Variants >6,000
Functional coding-region variants including eQTL and loss-of-function variants >24,000