Microarray Solutions for Microbiome and SARS-CoV-2 Research Benefits & Workflow

The power of genotyping today

Translating biomarkers from discovery to routine research applications will be vital to precision medicine. While large population cohort studies and private sequencing initiatives have revealed single-nucleotide polymorphisms (SNPs) and structural variants implicated in nearly 2,000 human diseases and traits, many are not within genes and have no known biological function. Better understanding the variants implicated in disease requires optimizing studies for population and imputation using meticulously designed genotyping panels and a reliable, fast, and flexible genotyping platform.

 

The Axiom Genotyping Solution is a platform of choice for large-scale genotyping research studies. Our proprietary photolithographic manufacturing process helps ensure every marker requested is present on every array, every time.

Microbiome

Genotyping panels that maximize imputation accuracy and include population-specific markers of common and rare variants are vital to genotyping research studies today. Our arrays can identify these associations for better understanding of complex diseases.

 

Our genotyping products and services comprehensively analyze data from the human microbiome—that is, all the microorganisms (such as bacteria, viruses and fungi) that exist in the body or in specific parts of the body.

Axiom Microbiome Array

The Axiom Microbiome Array enables detection of all known microorganisms in a sample with species- and strain-level identification in a single, scalable assay. The proprietary photolithographic arrays help ensure fidelity and consistency across manufacturing batches.

 

The robust biochemistry of the Axiom 2.0 Assay coupled with manual and automated target preparation methods enables consistent and high-quality results. A simplified, upstream reverse transcriptase reaction enables detection of RNA virus genomes. Automated array processing is performed using the GeneTitan Multi-Channel Instrument. The complete solution includes arrays, reagent kits, and free, easy-to-use microbiome analysis software.

Microbial Detection Analysis Software

Axiom Microbial Detection Analysis Software (MiDAS) streamlines the prediction of target identities in Axiom Microbiome Array data from an unknown sample. Features include complete analysis to strain-level, direct access to external NCBI databases, lists of microbial targets most likely present in each sample, and summaries of microbial content in both table and graphical formats.

Axiom Microbiome Services

The Affymetrix Research Service Laboratory (ARSL) provides processing of genomic DNA and reverse transcribed complimentary DNA from microbial samples. Complete analysis using Axiom MiDAS is included for detailed enumeration of microbes in each sample.

 

The Axiom Microbiome Solution interrogates non-polymorphic sequences in both family-conserved and target-specific regions from NCBI database sequences. The Axiom Microbiome Array detects over 12,000 species, including archaea, bacteria, fungi, protozoa, and viruses. The array content is sample-type agnostic, suitable for applications in nutrigenomics, agrigenomics, and animal research and modeling. This design:

  • Efficiently profiles human and animal microbiomes with a single assay 
  • Detects greater diversity and higher resolution than 16s rRNA gene sequencing 
  • Allows identification to the species, strain and sequence level as well as RNA virus detection using a cDNA template 
  • Is available in 24- and 96-array plate formats 
  • Features simplified microbial detection analysis 

SARS-CoV-2 arrays

A major challenge for clinical researchers and geneticists is learning how SARS-CoV-2, the coronavirus that causes COVID-19, interacts with the human genome, and stratifies populations to understand disease susceptibility, severity, and outcomes. 

Axiom Human Genotyping SARS-CoV-2 Research Array

Axiom genotyping arrays and associated modules can be used in various aspects of COVID-19 research: 

  • A large GWAS grid of >800K markers can support disease association research, including chronic obstructive pulmonary disease (COPD), coronary artery disease traits, and high blood pressure traits
  • Expression quantitative trait loci (eQTLs) captures information about the genetic basis of infections in global and especially non-Asian Caucasian (CEU) populations
  • The large GWAS grid allows for incorporating genetics into evaluating a large number of druggable targets 
  • Pharmacogenetics research for drug-drug and drug-gene interactions can help with studies of efficacy and effects of treatments that include but are not limited to antivirals and anti-malarial drugs 
  • Any Axiom design covers markers of the viral receptor protection Angiotensin-converting enzyme 2 (ACE2), believed to be the mechanism by which the COVID-19 virus enters the body
  • Study of inflammatory cytokine genes may increase understanding of immune response initiation, controlling viral replication and hypercytokinaemia

Predictive genomics workflow

Population genotyping projects are enabling precision medicine decisions and leading to improved health care outcomes. Many national governments and large organizations are investing in scaling up genotyping infrastructure to ensure personalized research solutions.

 

The Axiom Solution consists of a technology platform that includes assay biochemistry, automated and manual target preparation options, multiple array plate formats, and array processing on the GeneTitan Multi-Channel (MC) Instrument. This solution has applications in human genetics and microbiome research.

 

The Axiom assay and workflow begins with purified genomic DNA. The first part of the assay and workflow is Target Preparation, which includes whole genome amplification on day one, followed by DNA fragmentation and overnight precipitation on day two. On day three the DNA is resuspended and prepared for hybridization on the array. Finally, washing, ligation, and staining occurs on the GeneTitan instrument followed by scanning of the plate.  Target preparation aims to prepare the genomic targets of interest so that they can be successfully attached, or “hybridized” to the synthesized probes on the microarray for accurate results. Following hybridization, array processing involves washing non-specific binding DNA and scanning the microarray plate to detect the fluorescence signal from the genomic targets of interest. Finally, genotypes are reported in Axiom Analysis Suite.

Let’s dive deeper into each step:

  • Whole genome amplification: Since starting genomic DNA is limited and/or finite and typically original crude samples from which the DNA was extracted are also finite or not available, it is important to amplify the limited amount of starting genomic DNA so that there is plenty of DNA available to hybridize to the synthesized complimentary probes on the array plate. The Axiom assay requires 200 ng of total genomic DNA for whole genome amplification. This takes about 24 hours in a 37°C oven.
  • Fragmentation: Cut the DNA into fragment sizes that are optimal for array hybridization. If the DNA is too long, it may not bind. The Axiom assay utilizes enzymes that randomly cut DNA into 25 to 125 base pair (bp) fragments. 
  • Precipitation: Purify and collect all the DNA fragments. Overnight precipitation is standard, but there is an option for a three-hour precipitation for a quicker turnaround time.
  • Hybridization: DNA fragments pair to complimentary probe sequences on the array.
  • Wash, ligate, stain: The bound target is washed under stringent conditions to remove non-specific background to minimize background noise caused by random ligation events. Each polymorphic nucleotide is queried via a multi-color ligation event carried out on the array surface. After ligation, the arrays are stained and imaged on the Gene Titan MC Instrument. 
  • Scan: Detection of fluorescent signal
  • Data Analysis: Primary and secondary analysis. Primary analysis is generation of the genotypes. Secondary analysis includes any analysis of the genotypes to understand groups of samples, genes, variants, etc.

Propel workflow

The above steps (excluding data analysis) have been optimized into a shortened two-day workflow, the Axiom Propel workflow, with completion of scanning of the arrays by the end of day 2. In addition, the Axiom Propel workflow has been optimized to include benchtop automation to increase the throughput, allowing the processing of more plates in two days than the standard manual Axiom 2.0 assay.

For Research Use Only. Not for use in diagnostic procedures.