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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 are developing a new Axiom Human Genotyping SARS-CoV-2 Research Array and soliciting your input on content now.

Be a collaborator

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 Axiom arrays for coronavirus research

 

Axiom Precision Medicine Research Array

Axiom Precision Medicine Diversity Research Array

UK Biobank Axiom Array

PharmacoScan Array

Axiom myDesign Custom Genotyping Arrays

Recommendations
for human genetic
research

 

Offers a large GWAS module, eQTL/coding regions and PGx  Offers a large GWAS module with pharmacogenetics 

Array used by the UK Biobank to genotype 500,000 participants 

Offers pharmacogenomic markers for drug discovery efforts Custom array designed with emphasis on COVID-related markers

Catalog number

902981

951962 or 951961 for Axiom Plus

905430

903026  or 902908TS

000789

GWAS module

>800,000

>800,000

> 600,000

>50,000

>800,000

Expression quantitative trait loci (eQTLs)

>16,000

>3,000

>17,000

-

>16,000

Pharmacogenomics

>1,950

>5,000

>2,400

>4,000

>4,000

Markers for ACE2 gene

11

12

8

-

>9,000

Markers for TMPRRS2

>120

> 150

> 130

-

> 150

Markers on cytokine genes

> 650

> 550

> 600

-

> 600

X chromosome markers

>35,000

>60,000

> 20,000

>650

> 60,000

HLA

> 10,400

> 14,000

> 8,200

4

> 14,000

 

A minimum of one plate with 96-arrays and associated Axiom reagents and GeneTitan MC consumables A minimum of one plate with 24- or 96-arrays. Kit includes associated reagents and GeneTitan MC consumables.  A minimum of one plate with 24- or 96-arrays. Kit includes  associated reagents and GeneTitan MC consumables.   A minimum of one plate in either 24- format or 96- format. Kit includes associated reagents and GeneTitan MC consumables.  A minimum of 10 plates for 960 samples and associated reagents and GeneTitan MC consumables