Genotyping is a process of determining the genetic makeup of an organism by examining its DNA sequence, exploring underlining genetic variants such as SNPs. It is typically performed with microarray technology, but PCR and sequencing are also used.

The advantage of using microarrays for genotyping is that they can process hundreds to thousands of samples, which is typical for genome-wide association studies (GWAS). Although NGS has become increasingly popular and has declined in price, microarrays continue to cost substantially less, particularly for genotyping. In addition, microarrays are somewhat easier to use, requiring less sample preparation.

New microarray-based genotyping applications continue to drive market growth. Affymetrix launched in November the Axiom turkey genotyping array, which was developed in collaboration with the USDA–Agricultural Research Service, Aviagen and Hendix Genetics. The array can be used to evaluate genetic markers associated with good traits that could help breeders improve turkey populations, and enhance quality and sustainability. Affymetrix’s portfolio of agrigenomics arrays include important animal species, such as horse, cow and chicken, as well as crops such as corn, cotton and rice.

Another key growth area for microarray-based genotyping is human leukocyte antigen (HLA) typing, which is used to improve organ transplantation success. The microarray typically is comprised of tens of thousands of sequence-specific oligonucleotide probes for HLA sequences. Current tests employ PCR-based and bead-based assays. Microarray-based HLA testing is expected to enhance these methods, providing insights into early detection of graft-vs.-host disease. Affymetrix offers the Axiom HLA array.

Microarrays are also used for measuring CNVs, which are genomic alterations resulting in an abnormal number of copies of one or more genes. Comparative genomic hybridization arrays, or CGHs, are used to identify CNVs. Agilent Technologies, a leader in array-based CGH, offers the SurePrint G3 human CGH microarray that employs a dual-color system and 60 mer oligonucleotide probes.

Illumina has a significant stake in the microarray market with its genotyping kits for whole genomes, biobanks and targeted analysis. Its BeadChip microarrays are available for humans, crops, livestock and model organisms.

The market for microarray-based genotyping totaled more than $300 million in 2014. It continues to expand robustly, driven by biobanking and GWAS, and facilitated by NGS and solid demand from food and agriculture industry. The microarray genotyping market is led by Affymetrix, Illumina and Agilent, which combine to account for the vast majority of sales.

Microarray-Based Genotyping at a Glance:

Leading Suppliers

• Affymetrix

• Illumina

• Agilent Technologies

Largest Markets

• Pharma & Biotech

• Academia

• Agriculture & Food

Instrument Cost

• $100,000–$300,000

• Assay Kits: $4,000-$7,000